From 8d8fd222b619d3a109d4d2832f9ba0e347aa1a55 Mon Sep 17 00:00:00 2001
From: Vihang Shah <83380615+svihang8@users.noreply.github.com>
Date: Wed, 22 Jan 2025 21:59:19 -0500
Subject: [PATCH 1/3] added function to retrieve all sampleid

---
 src/pages/patientView/SampleManager.tsx | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/pages/patientView/SampleManager.tsx b/src/pages/patientView/SampleManager.tsx
index 4666bb2cb6d..72b40c02c2b 100644
--- a/src/pages/patientView/SampleManager.tsx
+++ b/src/pages/patientView/SampleManager.tsx
@@ -125,6 +125,17 @@ export function getSpecimenCollectionDayMap(
     return collectionDayMap;
 }
 
+export function sampleIdsForSamples(samples: Array<ClinicalDataBySampleId>) {
+    let output: { id: string; value: string }[] = [];
+    samples.forEach((sample, sampleIndex) => {
+        output.push({
+            id: sample.id,
+            value: sample.id,
+        });
+    });
+    return output;
+}
+
 export function clinicalAttributeListForSamples(
     samples: Array<ClinicalDataBySampleId>
 ) {

From d2267f6f7e816eb5977dfa0c29dc194e6975d70c Mon Sep 17 00:00:00 2001
From: Vihang Shah <83380615+svihang8@users.noreply.github.com>
Date: Wed, 22 Jan 2025 22:01:16 -0500
Subject: [PATCH 2/3] added selection by sampleid ui feature

---
 .../patientView/timeline/VAFChartControls.tsx | 140 +++++++++++++++++-
 .../timeline/VAFChartUtils.spec.ts            |  14 ++
 .../patientView/timeline/VAFChartUtils.ts     |  22 +++
 .../patientView/timeline/VAFChartWrapper.tsx  |   1 +
 .../timeline/VAFChartWrapperStore.tsx         |   6 +
 5 files changed, 182 insertions(+), 1 deletion(-)

diff --git a/src/pages/patientView/timeline/VAFChartControls.tsx b/src/pages/patientView/timeline/VAFChartControls.tsx
index 1caf97384b4..66eb2cacc89 100644
--- a/src/pages/patientView/timeline/VAFChartControls.tsx
+++ b/src/pages/patientView/timeline/VAFChartControls.tsx
@@ -1,11 +1,13 @@
-import React from 'react';
+import React, { useEffect, useState } from 'react';
 import { observer } from 'mobx-react';
 import ReactSelect from 'react-select';
 import SampleManager, {
     clinicalAttributeListForSamples,
+    sampleIdsForSamples,
 } from '../SampleManager';
 import LabeledCheckbox from '../../../shared/components/labeledCheckbox/LabeledCheckbox';
 import VAFChartWrapperStore from './VAFChartWrapperStore';
+import _ from 'lodash';
 
 interface IVAFChartControlsProps {
     wrapperStore: VAFChartWrapperStore;
@@ -13,9 +15,65 @@ interface IVAFChartControlsProps {
 }
 
 export const GROUP_BY_NONE = 'None';
+export const SELECT_SAMPLE_ALL = {
+    label: 'All',
+    value: 'All',
+};
+export const SELECT_SAMPLE_NONE = {
+    label: 'None',
+    value: 'None',
+};
 
 const VAFChartControls: React.FunctionComponent<IVAFChartControlsProps> = observer(
     function({ wrapperStore, sampleManager }) {
+        const [
+            isInitialSelectedSamples,
+            setisInitialSelectedSamples,
+        ] = useState(true);
+
+        const selectedSamplesOptions = [
+            SELECT_SAMPLE_ALL,
+            SELECT_SAMPLE_NONE,
+            ...sampleIdsForSamples(sampleManager.samples).map(item => ({
+                label: `${item.value}`,
+                value: `${item.id}`,
+            })),
+        ];
+
+        function selectSamplesByValue() {
+            let allSelectedSamples = selectedSamplesOptions;
+            allSelectedSamples = allSelectedSamples.filter(sample => {
+                return (
+                    sample.label != SELECT_SAMPLE_ALL.label &&
+                    sample.label != SELECT_SAMPLE_NONE.label
+                );
+            });
+            if (isInitialSelectedSamples) {
+                console.log('running initial');
+                wrapperStore.setSelectedSamplesOptions(allSelectedSamples);
+                setisInitialSelectedSamples(!isInitialSelectedSamples);
+            }
+            if (wrapperStore.selectedSamplesOptions.length === 0) {
+                return {
+                    label: 'None',
+                    value: 'None',
+                };
+            }
+            if (
+                _.isEqual(
+                    wrapperStore.selectedSamplesOptions,
+                    allSelectedSamples
+                )
+            ) {
+                return {
+                    label: 'All',
+                    value: 'All',
+                };
+            }
+
+            return wrapperStore.selectedSamplesOptions;
+        }
+
         const groupByOptions = [
             {
                 label: GROUP_BY_NONE,
@@ -34,6 +92,8 @@ const VAFChartControls: React.FunctionComponent<IVAFChartControlsProps> = observ
                 opt => opt.value == wrapperStore.groupByOption
             );
 
+            console.log(`Group By Value : ${value}`);
+
             return value
                 ? {
                       label: value.label,
@@ -42,8 +102,86 @@ const VAFChartControls: React.FunctionComponent<IVAFChartControlsProps> = observ
                 : '';
         }
 
+        const SelectedSampleChecklistComponent: React.FC<any> = props => {
+            const { data, isSelected, innerRef, innerProps } = props;
+            return (
+                <div
+                    ref={innerRef}
+                    {...innerProps}
+                    style={{
+                        display: 'flex',
+                        alignItems: 'center',
+                        padding: '5px',
+                    }}
+                >
+                    <input
+                        type="checkbox"
+                        checked={isSelected}
+                        onChange={() => {}}
+                        style={{ marginRight: '10px' }}
+                    />
+                    <label>{data.label}</label>
+                </div>
+            );
+        };
+
         return (
             <div className={'VAFChartControls'} data-test={'VAFChartControls'}>
+                <label>
+                    Select Samples:&nbsp;
+                    <ReactSelect
+                        name={'select-by-sample-select'}
+                        value={selectSamplesByValue()}
+                        options={selectedSamplesOptions}
+                        onChange={(options: Array<any>) => {
+                            if (options.indexOf(SELECT_SAMPLE_ALL) !== -1) {
+                                wrapperStore.setSelectedSamplesOptions(
+                                    sampleIdsForSamples(
+                                        sampleManager.samples
+                                    ).map(item => ({
+                                        label: `${item.value}`,
+                                        value: `${item.id}`,
+                                    }))
+                                );
+                            } else if (
+                                options.indexOf(SELECT_SAMPLE_NONE) !== -1
+                            ) {
+                                wrapperStore.setSelectedSamplesOptions([]);
+                            } else {
+                                console.log(
+                                    `options before filter : ${JSON.stringify(
+                                        options
+                                    )}`
+                                );
+                                options = options.filter(
+                                    sample =>
+                                        sample.label !=
+                                            SELECT_SAMPLE_NONE.label &&
+                                        sample.label != SELECT_SAMPLE_ALL.label
+                                );
+                                console.log(
+                                    `options after filter : ${JSON.stringify(
+                                        options
+                                    )}`
+                                );
+                                wrapperStore.setSelectedSamplesOptions(options);
+                            }
+                        }}
+                        styles={{
+                            container: (styles: any) => ({
+                                ...styles,
+                                width: 250,
+                            }),
+                        }}
+                        isMulti
+                        components={{
+                            Option: SelectedSampleChecklistComponent,
+                        }}
+                        closeMenuOnSelect={false}
+                        hideSelectedOptions={false}
+                    />
+                </label>
+
                 <label>
                     Group by:&nbsp;
                     <ReactSelect
diff --git a/src/pages/patientView/timeline/VAFChartUtils.spec.ts b/src/pages/patientView/timeline/VAFChartUtils.spec.ts
index 64941fa66d3..203f7b52c61 100644
--- a/src/pages/patientView/timeline/VAFChartUtils.spec.ts
+++ b/src/pages/patientView/timeline/VAFChartUtils.spec.ts
@@ -187,6 +187,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
+                    [],
                     {}
                 ),
                 {
@@ -228,6 +229,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
+                    [],
                     {}
                 ),
                 {
@@ -380,6 +382,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
+                    [],
                     {}
                 ),
                 {
@@ -515,6 +518,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
+                    [],
                     {}
                 ),
                 {
@@ -611,6 +615,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
+                    [],
                     {}
                 ),
                 {
@@ -736,6 +741,7 @@ describe('VAFChartUtils', () => {
                         ]
                     ),
                     GROUP_BY_NONE,
+                    [],
                     {}
                 ),
                 {
@@ -833,6 +839,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2], [3]),
                     GROUP_BY_NONE,
+                    [],
                     {}
                 ),
                 {
@@ -918,6 +925,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     'SampleType',
+                    [],
                     {
                         sample1: 'Primary',
                         sample2: 'Recurrence',
@@ -1078,6 +1086,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     'SampleCollectionSource',
+                    [],
                     {
                         sample1: 'Outside',
                         sample2: 'Inside',
@@ -1190,6 +1199,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     'SampleCollectionSource',
+                    [],
                     {
                         sample1: 'Outside',
                         sample2: 'Inside',
@@ -1276,6 +1286,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     'SampleCollectionSource',
+                    [],
                     {
                         sample1: 'Outside',
                         sample2: 'Inside',
@@ -1388,6 +1399,7 @@ describe('VAFChartUtils', () => {
                         ]
                     ),
                     'SampleCollectionSource',
+                    [],
                     {
                         sample1: 'Outside',
                         sample2: 'Inside',
@@ -1470,6 +1482,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2], [3]),
                     'SampleType',
+                    [],
                     {
                         sample1: 'Primary',
                         sample2: 'Recurrence',
@@ -1552,6 +1565,7 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3, 4], []),
                     'TumorPurity',
+                    [],
                     { sample2: '40', sample3: '30', sample4: '30' }
                 ),
                 {
diff --git a/src/pages/patientView/timeline/VAFChartUtils.ts b/src/pages/patientView/timeline/VAFChartUtils.ts
index d806286c9fb..baa120d91e2 100644
--- a/src/pages/patientView/timeline/VAFChartUtils.ts
+++ b/src/pages/patientView/timeline/VAFChartUtils.ts
@@ -53,10 +53,32 @@ export function computeRenderData(
     mutationProfileId: string,
     coverageInformation: CoverageInformation,
     groupByOption: string,
+    selectedSamplesOption: string[],
     sampleIdToClinicalValue: { [sampleId: string]: string }
 ) {
     const grayPoints: IPoint[] = []; // points that are purely interpolated for rendering, dont have data of their own
     const lineData: IPoint[][] = [];
+    console.log(`Selected Samples : ${JSON.stringify(selectedSamplesOption)}`);
+    samples = samples.filter(sample => {
+        return _.some(selectedSamplesOption, {
+            label: sample.sampleId,
+            value: sample.sampleId,
+        });
+    });
+    mutations = mutations
+        .map(mutationArr =>
+            mutationArr.filter(mutation => {
+                return _.some(selectedSamplesOption, {
+                    label: mutation.sampleId,
+                    value: mutation.sampleId,
+                });
+            })
+        )
+        .filter(mutation => mutation.length > 0);
+    console.log(`Samples : ${JSON.stringify(samples)}`);
+    console.log(`Count of Samples : ${samples.length}`);
+    console.log(`Mutations : ${JSON.stringify(mutations)}`);
+    console.log(`Count of Mutations : ${mutations.length}`);
 
     if (groupByOption && groupByOption != GROUP_BY_NONE)
         mutations = splitMutationsBySampleGroup(
diff --git a/src/pages/patientView/timeline/VAFChartWrapper.tsx b/src/pages/patientView/timeline/VAFChartWrapper.tsx
index 178c92ad578..564cf1681d3 100644
--- a/src/pages/patientView/timeline/VAFChartWrapper.tsx
+++ b/src/pages/patientView/timeline/VAFChartWrapper.tsx
@@ -183,6 +183,7 @@ export default class VAFChartWrapper extends React.Component<
             this.props.mutationProfileId,
             this.props.coverageInformation,
             this.props.wrapperStore.groupByOption!,
+            this.props.wrapperStore.selectedSamplesOptions,
             this.sampleIdToClinicalValue
         ).lineData;
     }
diff --git a/src/pages/patientView/timeline/VAFChartWrapperStore.tsx b/src/pages/patientView/timeline/VAFChartWrapperStore.tsx
index b045955019c..b4e83f5a762 100644
--- a/src/pages/patientView/timeline/VAFChartWrapperStore.tsx
+++ b/src/pages/patientView/timeline/VAFChartWrapperStore.tsx
@@ -3,6 +3,7 @@ import { getServerConfig } from 'config/config';
 
 export default class VAFChartWrapperStore {
     @observable groupByOption: string | null = null;
+    @observable selectedSamplesOptions: Array<string> = [];
 
     @observable _showSequentialMode: boolean = getServerConfig()
         .vaf_sequential_mode_default;
@@ -30,6 +31,11 @@ export default class VAFChartWrapperStore {
         this.groupByOption = value;
     }
 
+    @action
+    setSelectedSamplesOptions(value: Array<any>) {
+        this.selectedSamplesOptions = value;
+    }
+
     @action
     setShowSequentialMode(value: boolean) {
         this._showSequentialMode = value;

From 5a6185b1ca7a8889f06d2cbda0555e01c7708112 Mon Sep 17 00:00:00 2001
From: Vihang Shah <83380615+svihang8@users.noreply.github.com>
Date: Thu, 23 Jan 2025 20:24:13 -0500
Subject: [PATCH 3/3] refactored selection feature to make it more concise and
 remove all and none redudancy

---
 .../src/generated/CBioPortalAPI-docs.json     |  5323 +-------
 .../generated/CBioPortalAPIInternal-docs.json | 10487 ++++++++--------
 .../patientView/timeline/VAFChartControls.tsx |   104 +-
 .../timeline/VAFChartUtils.spec.ts            |    92 +-
 .../patientView/timeline/VAFChartUtils.ts     |     2 +-
 .../timeline/VAFChartWrapperStore.tsx         |     2 +-
 6 files changed, 5408 insertions(+), 10602 deletions(-)

diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json
index 540248d96d8..e44511c6e7c 100644
--- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json
+++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json
@@ -1,5322 +1 @@
-{
-  "swagger": "2.0",
-  "info": {
-    "contact": {
-      "email": "cbioportal@googlegroups.com",
-      "name": "cbioportal",
-      "url": "https://www.cbioportal.org"
-    },
-    "description": "A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.",
-    "license": {
-      "name": "License",
-      "url": "https://github.com/cBioPortal/cbioportal/blob/master/LICENSE"
-    },
-    "title": "cBioPortal web Public API [Alpha]",
-    "version": "1.0 (beta). Backwards compatibility will be maintained (after 1.0 release)"
-  },
-  "paths": {
-    "/api/cancer-types": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "cancerTypeId",
-              "name",
-              "dedicatedColor",
-              "shortName",
-              "parent"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/TypeOfCancer"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Cancer Types"
-        ],
-        "description": "Get all cancer types",
-        "operationId": "getAllCancerTypesUsingGET"
-      }
-    },
-    "/api/cancer-types/{cancerTypeId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Cancer Type ID e.g. acc",
-            "in": "path",
-            "name": "cancerTypeId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "type": "string"
-            }
-          }
-        },
-        "tags": [
-          "Cancer Types"
-        ],
-        "description": "Get a cancer type",
-        "operationId": "getCancerTypeUsingGET"
-      }
-    },
-    "/api/clinical-attributes": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "clinicalAttributeId",
-              "displayName",
-              "description",
-              "datatype",
-              "patientAttribute",
-              "priority",
-              "studyId"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalAttribute"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Clinical Attributes"
-        ],
-        "description": "Get all clinical attributes",
-        "operationId": "getAllClinicalAttributesUsingGET"
-      }
-    },
-    "/api/clinical-attributes/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "studyIds",
-            "required": true,
-            "schema": {
-              "description": "List of Study IDs",
-              "items": {
-                "maxLength": 10000000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalAttribute"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Clinical Attributes"
-        ],
-        "description": "Fetch clinical attributes",
-        "operationId": "fetchClinicalAttributesUsingPOST"
-      }
-    },
-    "/api/clinical-data/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SAMPLE",
-            "description": "Type of the clinical data",
-            "enum": [
-              "SAMPLE",
-              "PATIENT"
-            ],
-            "in": "query",
-            "name": "clinicalDataType",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "clinicalDataMultiStudyFilter",
-            "schema": {
-              "$ref": "#/definitions/ClinicalDataMultiStudyFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Clinical Data"
-        ],
-        "description": "Fetch clinical data by patient IDs or sample IDs (all studies)",
-        "operationId": "fetchClinicalDataUsingPOST"
-      }
-    },
-    "/api/copy-number-segments/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Chromosome",
-            "in": "query",
-            "name": "chromosome",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "sampleIdentifiers",
-            "schema": {
-              "description": "List of sample identifiers",
-              "items": {
-                "$ref": "#/definitions/SampleIdentifier"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/CopyNumberSeg"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Copy Number Segments"
-        ],
-        "description": "Fetch copy number segments by sample ID",
-        "operationId": "fetchCopyNumberSegmentsUsingPOST"
-      }
-    },
-    "/api/gene-panel-data/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "genePanelDataMultipleStudyFilter",
-            "schema": {
-              "$ref": "#/definitions/GenePanelDataMultipleStudyFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenePanelData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Gene Panel Data"
-        ],
-        "description": "Fetch gene panel data",
-        "operationId": "fetchGenePanelDataInMultipleMolecularProfilesUsingPOST"
-      }
-    },
-    "/api/gene-panels": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "genePanelId",
-              "description"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenePanel"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Gene Panels"
-        ],
-        "description": "Get all gene panels",
-        "operationId": "getAllGenePanelsUsingGET"
-      }
-    },
-    "/api/gene-panels/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "genePanelIds",
-            "required": true,
-            "schema": {
-              "description": "List of Gene Panel IDs",
-              "items": {
-                "maxLength": 10000000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenePanel"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Gene Panels"
-        ],
-        "description": "Get gene panel",
-        "operationId": "fetchGenePanelsUsingPOST"
-      }
-    },
-    "/api/gene-panels/{genePanelId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Gene Panel ID e.g. NSCLC_UNITO_2016_PANEL",
-            "in": "path",
-            "name": "genePanelId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/GenePanel"
-            }
-          }
-        },
-        "tags": [
-          "Gene Panels"
-        ],
-        "description": "Get gene panel",
-        "operationId": "getGenePanelUsingGET"
-      }
-    },
-    "/api/generic-assay-data/{molecularProfileId}/generic-assay/{genericAssayStableId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Generic Assay stable ID",
-            "in": "path",
-            "name": "genericAssayStableId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Generic Assay Data"
-        ],
-        "description": "Get generic_assay_data in a molecular profile",
-        "operationId": "getGenericAssayDataInMolecularProfileUsingGET"
-      }
-    },
-    "/api/generic-assay-meta/generic-assay/{genericAssayStableId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Generic Assay stable ID",
-            "in": "path",
-            "name": "genericAssayStableId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayMeta"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Generic Assays"
-        ],
-        "description": "Fetch meta data for generic-assay by ID",
-        "operationId": "getGenericAssayMeta_gaUsingGET"
-      }
-    },
-    "/api/generic-assay-meta/{molecularProfileId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayMeta"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Generic Assays"
-        ],
-        "description": "Fetch meta data for generic-assay by ID",
-        "operationId": "getGenericAssayMetaUsingGET"
-      }
-    },
-    "/api/generic_assay_data/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "genericAssayDataMultipleStudyFilter",
-            "schema": {
-              "$ref": "#/definitions/GenericAssayDataMultipleStudyFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Generic Assay Data"
-        ],
-        "description": "Fetch generic_assay_data",
-        "operationId": "fetchGenericAssayDataInMultipleMolecularProfilesUsingPOST"
-      }
-    },
-    "/api/generic_assay_data/{molecularProfileId}/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "genericAssayFilter",
-            "required": true,
-            "schema": {
-              "$ref": "#/definitions/GenericAssayFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Generic Assay Data"
-        ],
-        "description": "fetch generic_assay_data in a molecular profile",
-        "operationId": "fetchGenericAssayDataInMolecularProfileUsingPOST"
-      }
-    },
-    "/api/generic_assay_meta/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "genericAssayMetaFilter",
-            "required": true,
-            "schema": {
-              "$ref": "#/definitions/GenericAssayMetaFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayMeta"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Generic Assays"
-        ],
-        "description": "Fetch meta data for generic-assay by ID",
-        "operationId": "fetchGenericAssayMetaUsingPOST"
-      }
-    },
-    "/api/genes": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Search keyword that applies to hugo gene symbol of the genes",
-            "in": "query",
-            "name": "keyword",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "description": "Alias of the gene",
-            "in": "query",
-            "name": "alias",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "entrezGeneId",
-              "hugoGeneSymbol",
-              "type",
-              "cytoband",
-              "length"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Gene"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Genes"
-        ],
-        "description": "Get all genes",
-        "operationId": "getAllGenesUsingGET"
-      }
-    },
-    "/api/genes/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "ENTREZ_GENE_ID",
-            "enum": [
-              "ENTREZ_GENE_ID",
-              "HUGO_GENE_SYMBOL"
-            ],
-            "in": "query",
-            "name": "geneIdType",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "geneIds",
-            "required": true,
-            "schema": {
-              "description": "List of Gene IDs",
-              "items": {
-                "maxLength": 10000000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Gene"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Genes"
-        ],
-        "description": "Fetch genes by ID",
-        "operationId": "fetchGenesUsingPOST"
-      }
-    },
-    "/api/genes/{geneId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Entrez Gene ID or Hugo Gene Symbol e.g. 1 or A1BG",
-            "in": "path",
-            "name": "geneId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/Gene"
-            }
-          }
-        },
-        "tags": [
-          "Genes"
-        ],
-        "description": "Get a gene",
-        "operationId": "getGeneUsingGET"
-      }
-    },
-    "/api/genes/{geneId}/aliases": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Entrez Gene ID or Hugo Gene Symbol e.g. 1 or A1BG",
-            "in": "path",
-            "name": "geneId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "type": "string"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Genes"
-        ],
-        "description": "Get aliases of a gene",
-        "operationId": "getAliasesOfGeneUsingGET"
-      }
-    },
-    "/api/health": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/ServerStatusMessage"
-            }
-          }
-        },
-        "tags": [
-          "Server running status"
-        ],
-        "description": "Get the running status of the server",
-        "operationId": "getServerStatusUsingGET"
-      }
-    },
-    "/api/info": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/Info"
-            }
-          }
-        },
-        "tags": [
-          "Info"
-        ],
-        "description": "Get information about the running instance",
-        "operationId": "getInfoUsingGET"
-      }
-    },
-    "/api/molecular-data/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "molecularDataMultipleStudyFilter",
-            "schema": {
-              "$ref": "#/definitions/MolecularDataMultipleStudyFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/NumericGeneMolecularData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Molecular Data"
-        ],
-        "description": "Fetch molecular data",
-        "operationId": "fetchMolecularDataInMultipleMolecularProfilesUsingPOST"
-      }
-    },
-    "/api/molecular-profiles": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "molecularProfileId",
-              "molecularAlterationType",
-              "datatype",
-              "name",
-              "description",
-              "showProfileInAnalysisTab"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/MolecularProfile"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Molecular Profiles"
-        ],
-        "description": "Get all molecular profiles",
-        "operationId": "getAllMolecularProfilesUsingGET"
-      }
-    },
-    "/api/molecular-profiles/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "molecularProfileFilter",
-            "schema": {
-              "$ref": "#/definitions/MolecularProfileFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/MolecularProfile"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Molecular Profiles"
-        ],
-        "description": "Fetch molecular profiles",
-        "operationId": "fetchMolecularProfilesUsingPOST"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID e.g. acc_tcga_mutations",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/MolecularProfile"
-            }
-          }
-        },
-        "tags": [
-          "Molecular Profiles"
-        ],
-        "description": "Get molecular profile",
-        "operationId": "getMolecularProfileUsingGET"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}/discrete-copy-number": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID e.g. acc_tcga_gistic",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Sample List ID e.g. acc_tcga_all",
-            "in": "query",
-            "name": "sampleListId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "HOMDEL_AND_AMP",
-            "description": "Type of the copy number event",
-            "enum": [
-              "HOMDEL_AND_AMP",
-              "HOMDEL",
-              "AMP",
-              "GAIN",
-              "HETLOSS",
-              "DIPLOID",
-              "ALL"
-            ],
-            "in": "query",
-            "name": "discreteCopyNumberEventType",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/DiscreteCopyNumberData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Discrete Copy Number Alterations"
-        ],
-        "description": "Get discrete copy number alterations in a molecular profile",
-        "operationId": "getDiscreteCopyNumbersInMolecularProfileUsingGET"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}/discrete-copy-number/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID e.g. acc_tcga_gistic",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "HOMDEL_AND_AMP",
-            "description": "Type of the copy number event",
-            "enum": [
-              "HOMDEL_AND_AMP",
-              "HOMDEL",
-              "AMP",
-              "GAIN",
-              "HETLOSS",
-              "DIPLOID",
-              "ALL"
-            ],
-            "in": "query",
-            "name": "discreteCopyNumberEventType",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "discreteCopyNumberFilter",
-            "required": true,
-            "schema": {
-              "$ref": "#/definitions/DiscreteCopyNumberFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/DiscreteCopyNumberData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Discrete Copy Number Alterations"
-        ],
-        "description": "Fetch discrete copy number alterations in a molecular profile by sample ID",
-        "operationId": "fetchDiscreteCopyNumbersInMolecularProfileUsingPOST"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}/gene-panel-data/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID e.g. nsclc_unito_2016_mutations",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "genePanelDataFilter",
-            "required": true,
-            "schema": {
-              "$ref": "#/definitions/GenePanelDataFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenePanelData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Gene Panel Data"
-        ],
-        "description": "Get gene panel data",
-        "operationId": "getGenePanelDataUsingPOST"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}/molecular-data": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Sample List ID e.g. acc_tcga_all",
-            "in": "query",
-            "name": "sampleListId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Entrez Gene ID e.g. 1",
-            "format": "int32",
-            "in": "query",
-            "name": "entrezGeneId",
-            "required": true,
-            "type": "integer"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/NumericGeneMolecularData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Molecular Data"
-        ],
-        "description": "Get all molecular data in a molecular profile",
-        "operationId": "getAllMolecularDataInMolecularProfileUsingGET"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}/molecular-data/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "molecularDataFilter",
-            "required": true,
-            "schema": {
-              "$ref": "#/definitions/MolecularDataFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/NumericGeneMolecularData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Molecular Data"
-        ],
-        "description": "Fetch molecular data in a molecular profile",
-        "operationId": "fetchAllMolecularDataInMolecularProfileUsingPOST"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}/mutations": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID e.g. acc_tcga_mutations",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Sample List ID e.g. acc_tcga_all",
-            "in": "query",
-            "name": "sampleListId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Entrez Gene ID",
-            "format": "int32",
-            "in": "query",
-            "name": "entrezGeneId",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "entrezGeneId",
-              "center",
-              "mutationStatus",
-              "validationStatus",
-              "tumorAltCount",
-              "tumorRefCount",
-              "normalAltCount",
-              "normalRefCount",
-              "aminoAcidChange",
-              "startPosition",
-              "endPosition",
-              "referenceAllele",
-              "variantAllele",
-              "proteinChange",
-              "mutationType",
-              "ncbiBuild",
-              "variantType",
-              "refseqMrnaId",
-              "proteinPosStart",
-              "proteinPosEnd",
-              "keyword"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Mutation"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Mutations"
-        ],
-        "description": "Get mutations in a molecular profile by Sample List ID",
-        "operationId": "getMutationsInMolecularProfileBySampleListIdUsingGET"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}/mutations/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID e.g. acc_tcga_mutations",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "entrezGeneId",
-              "center",
-              "mutationStatus",
-              "validationStatus",
-              "tumorAltCount",
-              "tumorRefCount",
-              "normalAltCount",
-              "normalRefCount",
-              "aminoAcidChange",
-              "startPosition",
-              "endPosition",
-              "referenceAllele",
-              "variantAllele",
-              "proteinChange",
-              "mutationType",
-              "ncbiBuild",
-              "variantType",
-              "refseqMrnaId",
-              "proteinPosStart",
-              "proteinPosEnd",
-              "keyword"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "mutationFilter",
-            "required": true,
-            "schema": {
-              "$ref": "#/definitions/MutationFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Mutation"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Mutations"
-        ],
-        "description": "Fetch mutations in a molecular profile",
-        "operationId": "fetchMutationsInMolecularProfileUsingPOST"
-      }
-    },
-    "/api/mutations/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "entrezGeneId",
-              "center",
-              "mutationStatus",
-              "validationStatus",
-              "tumorAltCount",
-              "tumorRefCount",
-              "normalAltCount",
-              "normalRefCount",
-              "aminoAcidChange",
-              "startPosition",
-              "endPosition",
-              "referenceAllele",
-              "variantAllele",
-              "proteinChange",
-              "mutationType",
-              "ncbiBuild",
-              "variantType",
-              "refseqMrnaId",
-              "proteinPosStart",
-              "proteinPosEnd",
-              "keyword"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "mutationMultipleStudyFilter",
-            "schema": {
-              "$ref": "#/definitions/MutationMultipleStudyFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Mutation"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Mutations"
-        ],
-        "description": "Fetch mutations in multiple molecular profiles by sample IDs",
-        "operationId": "fetchMutationsInMultipleMolecularProfilesUsingPOST"
-      }
-    },
-    "/api/patients": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Search keyword that applies to ID of the patients",
-            "in": "query",
-            "name": "keyword",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "patientId"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Patient"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Patients"
-        ],
-        "description": "Get all patients",
-        "operationId": "getAllPatientsUsingGET"
-      }
-    },
-    "/api/patients/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "patientFilter",
-            "schema": {
-              "$ref": "#/definitions/PatientFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Patient"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Patients"
-        ],
-        "operationId": "fetchPatientsUsingPOST"
-      }
-    },
-    "/api/sample-lists": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "sampleListId",
-              "category",
-              "studyId",
-              "name",
-              "description"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/SampleList"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Sample Lists"
-        ],
-        "description": "Get all sample lists",
-        "operationId": "getAllSampleListsUsingGET"
-      }
-    },
-    "/api/sample-lists/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "sampleListIds",
-            "required": true,
-            "schema": {
-              "description": "List of sample list IDs",
-              "items": {
-                "maxLength": 10000000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/SampleList"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Sample Lists"
-        ],
-        "description": "Fetch sample lists by ID",
-        "operationId": "fetchSampleListsUsingPOST"
-      }
-    },
-    "/api/sample-lists/{sampleListId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Sample List ID e.g. acc_tcga_all",
-            "in": "path",
-            "name": "sampleListId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/SampleList"
-            }
-          }
-        },
-        "tags": [
-          "Sample Lists"
-        ],
-        "description": "Get sample list",
-        "operationId": "getSampleListUsingGET"
-      }
-    },
-    "/api/sample-lists/{sampleListId}/sample-ids": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Sample List ID e.g. acc_tcga_all",
-            "in": "path",
-            "name": "sampleListId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "type": "string"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Sample Lists"
-        ],
-        "description": "Get all sample IDs in a sample list",
-        "operationId": "getAllSampleIdsInSampleListUsingGET"
-      }
-    },
-    "/api/samples": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Search keyword that applies to the study ID",
-            "in": "query",
-            "name": "keyword",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "sampleId",
-              "sampleType"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Sample"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Samples"
-        ],
-        "description": "Get all samples matching keyword",
-        "operationId": "getSamplesByKeywordUsingGET"
-      }
-    },
-    "/api/samples/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "sampleFilter",
-            "schema": {
-              "$ref": "#/definitions/SampleFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Sample"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Samples"
-        ],
-        "description": "Fetch samples by ID",
-        "operationId": "fetchSamplesUsingPOST"
-      }
-    },
-    "/api/studies": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Search keyword that applies to name and cancer type of the studies",
-            "in": "query",
-            "name": "keyword",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "studyId",
-              "cancerTypeId",
-              "name",
-              "description",
-              "publicStudy",
-              "pmid",
-              "citation",
-              "groups",
-              "status",
-              "importDate"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/CancerStudy"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Studies"
-        ],
-        "description": "Get all studies",
-        "operationId": "getAllStudiesUsingGET"
-      }
-    },
-    "/api/studies/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "studyIds",
-            "required": true,
-            "schema": {
-              "description": "List of Study IDs",
-              "items": {
-                "maxLength": 10000000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/CancerStudy"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Studies"
-        ],
-        "description": "Fetch studies by IDs",
-        "operationId": "fetchStudiesUsingPOST"
-      }
-    },
-    "/api/studies/tags/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "studyIds",
-            "required": true,
-            "schema": {
-              "description": "List of Study IDs",
-              "items": {
-                "type": "string"
-              },
-              "type": "array"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/CancerStudyTags"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Studies"
-        ],
-        "description": "Get the study tags by IDs",
-        "operationId": "getTagsForMultipleStudiesUsingPOST"
-      }
-    },
-    "/api/studies/{studyId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/CancerStudy"
-            }
-          }
-        },
-        "tags": [
-          "Studies"
-        ],
-        "description": "Get a study",
-        "operationId": "getStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/clinical-attributes": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "clinicalAttributeId",
-              "displayName",
-              "description",
-              "datatype",
-              "patientAttribute",
-              "priority",
-              "studyId"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalAttribute"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Clinical Attributes"
-        ],
-        "description": "Get all clinical attributes in the specified study",
-        "operationId": "getAllClinicalAttributesInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/clinical-attributes/{clinicalAttributeId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Clinical Attribute ID e.g. CANCER_TYPE",
-            "in": "path",
-            "name": "clinicalAttributeId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/ClinicalAttribute"
-            }
-          }
-        },
-        "tags": [
-          "Clinical Attributes"
-        ],
-        "description": "Get specified clinical attribute",
-        "operationId": "getClinicalAttributeInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/clinical-data": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Attribute ID e.g. CANCER_TYPE",
-            "in": "query",
-            "name": "attributeId",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SAMPLE",
-            "description": "Type of the clinical data",
-            "enum": [
-              "SAMPLE",
-              "PATIENT"
-            ],
-            "in": "query",
-            "name": "clinicalDataType",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "clinicalAttributeId",
-              "value"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Clinical Data"
-        ],
-        "description": "Get all clinical data in a study",
-        "operationId": "getAllClinicalDataInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/clinical-data/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SAMPLE",
-            "description": "Type of the clinical data",
-            "enum": [
-              "SAMPLE",
-              "PATIENT"
-            ],
-            "in": "query",
-            "name": "clinicalDataType",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "clinicalDataSingleStudyFilter",
-            "required": true,
-            "schema": {
-              "$ref": "#/definitions/ClinicalDataSingleStudyFilter"
-            }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Clinical Data"
-        ],
-        "description": "Fetch clinical data by patient IDs or sample IDs (specific study)",
-        "operationId": "fetchAllClinicalDataInStudyUsingPOST"
-      }
-    },
-    "/api/studies/{studyId}/molecular-profiles": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "molecularProfileId",
-              "molecularAlterationType",
-              "datatype",
-              "name",
-              "description",
-              "showProfileInAnalysisTab"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/MolecularProfile"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Molecular Profiles"
-        ],
-        "description": "Get all molecular profiles in a study",
-        "operationId": "getAllMolecularProfilesInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/patients": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "patientId"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Patient"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Patients"
-        ],
-        "description": "Get all patients in a study",
-        "operationId": "getAllPatientsInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/patients/{patientId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Patient ID e.g. TCGA-OR-A5J2",
-            "in": "path",
-            "name": "patientId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/Patient"
-            }
-          }
-        },
-        "tags": [
-          "Patients"
-        ],
-        "description": "Get a patient in a study",
-        "operationId": "getPatientInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/patients/{patientId}/clinical-data": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Patient ID e.g. TCGA-OR-A5J2",
-            "in": "path",
-            "name": "patientId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Attribute ID e.g. AGE",
-            "in": "query",
-            "name": "attributeId",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "clinicalAttributeId",
-              "value"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Clinical Data"
-        ],
-        "description": "Get all clinical data of a patient in a study",
-        "operationId": "getAllClinicalDataOfPatientInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/patients/{patientId}/samples": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Patient ID e.g. TCGA-OR-A5J2",
-            "in": "path",
-            "name": "patientId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "sampleId",
-              "sampleType"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Sample"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Samples"
-        ],
-        "description": "Get all samples of a patient in a study",
-        "operationId": "getAllSamplesOfPatientInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/sample-lists": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "sampleListId",
-              "category",
-              "studyId",
-              "name",
-              "description"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/SampleList"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Sample Lists"
-        ],
-        "description": "Get all sample lists in a study",
-        "operationId": "getAllSampleListsInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/samples": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "sampleId",
-              "sampleType"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Sample"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Samples"
-        ],
-        "description": "Get all samples in a study",
-        "operationId": "getAllSamplesInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/samples/{sampleId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Sample ID e.g. TCGA-OR-A5J2-01",
-            "in": "path",
-            "name": "sampleId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/Sample"
-            }
-          }
-        },
-        "tags": [
-          "Samples"
-        ],
-        "description": "Get a sample in a study",
-        "operationId": "getSampleInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/samples/{sampleId}/clinical-data": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Sample ID e.g. TCGA-OR-A5J2-01",
-            "in": "path",
-            "name": "sampleId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Attribute ID e.g. CANCER_TYPE",
-            "in": "query",
-            "name": "attributeId",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "clinicalAttributeId",
-              "value"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalData"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Clinical Data"
-        ],
-        "description": "Get all clinical data of a sample in a study",
-        "operationId": "getAllClinicalDataOfSampleInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/samples/{sampleId}/copy-number-segments": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Sample ID e.g. TCGA-OR-A5J2-01",
-            "in": "path",
-            "name": "sampleId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Chromosome",
-            "in": "query",
-            "name": "chromosome",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 20000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 20000,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "chromosome",
-              "start",
-              "end",
-              "numberOfProbes",
-              "segmentMean"
-            ],
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/CopyNumberSeg"
-              },
-              "type": "array"
-            }
-          }
-        },
-        "tags": [
-          "Copy Number Segments"
-        ],
-        "description": "Get copy number segments in a sample in a study",
-        "operationId": "getCopyNumberSegmentsInSampleInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/tags": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "type": "object"
-            }
-          }
-        },
-        "tags": [
-          "Studies"
-        ],
-        "description": "Get the tags of a study",
-        "operationId": "getTagsUsingGET"
-      }
-    }
-  },
-  "definitions": {
-    "AlleleSpecificCopyNumber": {
-      "properties": {
-        "ascnIntegerCopyNumber": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "ascnMethod": {
-          "type": "string"
-        },
-        "ccfExpectedCopies": {
-          "format": "float",
-          "type": "number"
-        },
-        "ccfExpectedCopiesUpper": {
-          "format": "float",
-          "type": "number"
-        },
-        "clonal": {
-          "type": "string"
-        },
-        "expectedAltCopies": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "minorCopyNumber": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "totalCopyNumber": {
-          "format": "int32",
-          "type": "integer"
-        }
-      },
-      "type": "object"
-    },
-    "CancerStudy": {
-      "properties": {
-        "allSampleCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "cancerType": {
-          "$ref": "#/definitions/TypeOfCancer"
-        },
-        "cancerTypeId": {
-          "type": "string"
-        },
-        "citation": {
-          "type": "string"
-        },
-        "cnaSampleCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "completeSampleCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "description": {
-          "type": "string"
-        },
-        "groups": {
-          "type": "string"
-        },
-        "importDate": {
-          "format": "date-time",
-          "type": "string"
-        },
-        "massSpectrometrySampleCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "methylationHm27SampleCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "miRnaSampleCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "mrnaMicroarraySampleCount": {
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-          "type": "integer"
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-        "studyId"
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diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json
index 4b857f37010..922f708f084 100644
--- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json
+++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json
@@ -1,6583 +1,6694 @@
 {
-  "swagger": "2.0",
+  "openapi": "3.0.1",
   "info": {
+    "title": "cBioPortal web Public API [Alpha]",
+    "description": "A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.",
     "contact": {
-      "email": "cbioportal@googlegroups.com",
       "name": "cbioportal",
-      "url": "https://www.cbioportal.org"
+      "url": "https://www.cbioportal.org",
+      "email": "cbioportal@googlegroups.com"
     },
-    "description": "A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.",
     "license": {
       "name": "License",
       "url": "https://github.com/cBioPortal/cbioportal/blob/master/LICENSE"
     },
-    "title": "cBioPortal web Public API [Alpha]",
     "version": "1.0 (beta). Backwards compatibility will be maintained (after 1.0 release)"
   },
+  "externalDocs": {
+    "description": "SpringShop Wiki Documentation",
+    "url": "https://springshop.wiki.github.org/docs"
+  },
+  "servers": [
+    {
+      "url": "https://www.cbioportal.org",
+      "description": "Generated server url"
+    }
+  ],
   "paths": {
-    "/api/alteration-enrichments/fetch": {
+    "/api/treatments/sample": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Treatments"
         ],
+        "description": "Get all sample level treatments",
+        "operationId": "getAllSampleTreatmentsUsingPOST",
         "parameters": [
           {
-            "default": "SAMPLE",
-            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
-            "enum": [
-              "SAMPLE",
-              "PATIENT"
-            ],
+            "name": "tier",
             "in": "query",
-            "name": "enrichmentType",
             "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "molecularProfileCasesGroupAndAlterationTypeFilter",
             "schema": {
-              "$ref": "#/definitions/MolecularProfileCasesGroupAndAlterationTypeFilter"
+              "type": "string",
+              "default": "Agent",
+              "enum": [
+                "Agent",
+                "AgentClass",
+                "AgentTarget"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/AlterationEnrichment"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/SampleTreatmentRow"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Alteration Enrichments"
-        ],
-        "operationId": "fetchAlterationEnrichmentsUsingPOST",
-        "summary": "Fetch alteration enrichments in molecular profiles"
+        }
       }
     },
-    "/api/cache": {
-      "delete": {
-        "produces": [
-          "text/plain"
+    "/api/treatments/patient": {
+      "post": {
+        "tags": [
+          "Treatments"
         ],
+        "description": "Get all patient level treatments",
+        "operationId": "getAllPatientTreatmentsUsingPOST",
         "parameters": [
           {
-            "description": "Secret API key passed in HTTP header. The key is configured in application.properties of the portal instance.",
-            "in": "header",
-            "name": "X-API-KEY",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": true,
-            "description": "Clear Spring-managed caches",
+            "name": "tier",
             "in": "query",
-            "name": "springManagedCache",
             "required": false,
-            "type": "boolean"
+            "schema": {
+              "type": "string",
+              "default": "Agent",
+              "enum": [
+                "Agent",
+                "AgentClass",
+                "AgentTarget"
+              ]
+            }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "type": "string"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/PatientTreatmentRow"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Cache"
-        ],
-        "operationId": "clearAllCachesUsingDELETE",
-        "summary": "Clear and reinitialize caches"
+        }
       }
     },
-    "/api/clinical-attributes/counts/fetch": {
+    "/api/treatments/display-sample": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Treatments"
         ],
+        "description": "Should sample level treatments be displayed",
+        "operationId": "getContainsSampleTreatmentDataUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "clinicalAttributeCountFilter",
+            "name": "tier",
+            "in": "query",
+            "required": false,
             "schema": {
-              "$ref": "#/definitions/ClinicalAttributeCountFilter"
+              "type": "string",
+              "default": "Agent",
+              "enum": [
+                "Agent",
+                "AgentClass",
+                "AgentTarget"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 10000000,
+                "minItems": 1,
+                "uniqueItems": true,
+                "type": "array",
+                "description": "List of Study IDs",
+                "items": {
+                  "maxLength": 10000000,
+                  "minLength": 1,
+                  "type": "string"
+                }
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalAttributeCount"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "boolean"
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Clinical Attributes Count"
-        ],
-        "description": "Get counts for clinical attributes according to their data availability for selected samples/patients",
-        "operationId": "getClinicalAttributeCountsUsingPOST"
+        }
       }
     },
-    "/api/clinical-data-bin-counts/fetch": {
+    "/api/treatments/display-patient": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Treatments"
         ],
+        "description": "Should patient level treatments be displayed",
+        "operationId": "getContainsTreatmentDataUsingPOST",
         "parameters": [
           {
-            "default": "DYNAMIC",
-            "description": "Method for data binning",
-            "enum": [
-              "STATIC",
-              "DYNAMIC"
-            ],
+            "name": "tier",
             "in": "query",
-            "name": "dataBinMethod",
             "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "clinicalDataBinCountFilter",
             "schema": {
-              "$ref": "#/definitions/ClinicalDataBinCountFilter"
+              "type": "string",
+              "default": "Agent",
+              "enum": [
+                "Agent",
+                "AgentClass",
+                "AgentTarget"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 10000000,
+                "minItems": 1,
+                "uniqueItems": true,
+                "type": "array",
+                "description": "List of Study IDs",
+                "items": {
+                  "maxLength": 10000000,
+                  "minLength": 1,
+                  "type": "string"
+                }
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalDataBin"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "boolean"
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch clinical data bin counts by study view filter",
-        "operationId": "fetchClinicalDataBinCountsUsingPOST"
+        }
       }
     },
-    "/api/clinical-data-counts/fetch": {
+    "/api/survival-data/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Survival"
         ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "clinicalDataCountFilter",
-            "schema": {
-              "$ref": "#/definitions/ClinicalDataCountFilter"
+        "description": "Fetch survival data",
+        "operationId": "fetchSurvivalDataUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/SurvivalRequest"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalDataCountItem"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalData"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch clinical data counts by study view filter",
-        "operationId": "fetchClinicalDataCountsUsingPOST"
+        }
       }
     },
-    "/api/clinical-data-density-plot/fetch": {
+    "/api/structuralvariant-genes/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
-        "parameters": [
-          {
-            "description": "Clinical Attribute ID of the X axis",
-            "in": "query",
-            "name": "xAxisAttributeId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": 50,
-            "description": "Number of the bins in X axis",
-            "format": "int32",
-            "in": "query",
-            "name": "xAxisBinCount",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Starting point of the X axis, if different than smallest value",
-            "in": "query",
-            "name": "xAxisStart",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "description": "Starting point of the X axis, if different than largest value",
-            "in": "query",
-            "name": "xAxisEnd",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "description": "Clinical Attribute ID of the Y axis",
-            "in": "query",
-            "name": "yAxisAttributeId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": 50,
-            "description": "Number of the bins in Y axis",
-            "format": "int32",
-            "in": "query",
-            "name": "yAxisBinCount",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "description": "Starting point of the Y axis, if different than smallest value",
-            "in": "query",
-            "name": "yAxisStart",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "description": "Starting point of the Y axis, if different than largest value",
-            "in": "query",
-            "name": "yAxisEnd",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "default": false,
-            "description": "Use log scale for X axis",
-            "in": "query",
-            "name": "xAxisLogScale",
-            "required": false,
-            "type": "boolean"
-          },
-          {
-            "default": false,
-            "description": "Use log scale for Y axis",
-            "in": "query",
-            "name": "yAxisLogScale",
-            "required": false,
-            "type": "boolean"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+        "description": "Fetch structural variant genes by study view filter",
+        "operationId": "fetchStructuralVariantGenesUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/DensityPlotData"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/AlterationCountByGene"
+                  }
+                }
+              }
             }
           }
-        },
+        }
+      }
+    },
+    "/api/structuralvariant-counts/fetch": {
+      "post": {
         "tags": [
           "Study View"
         ],
-        "description": "Fetch clinical data density plot bins by study view filter",
-        "operationId": "fetchClinicalDataDensityPlotUsingPOST"
+        "description": "Fetch structural variant genes by study view filter",
+        "operationId": "fetchStructuralVariantCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
+            }
+          }
+        },
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/AlterationCountByStructuralVariant"
+                  }
+                }
+              }
+            }
+          }
+        }
       }
     },
-    "/api/clinical-data-enrichments/fetch": {
+    "/api/structural-variant/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Structural Variants"
         ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "groupFilter",
-            "schema": {
-              "$ref": "#/definitions/GroupFilter"
+        "description": "Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers",
+        "operationId": "fetchStructuralVariantsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StructuralVariantFilter"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalDataEnrichment"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/StructuralVariant"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Clinical Data Enrichments"
-        ],
-        "description": "Fetch clinical data enrichments for the sample groups",
-        "operationId": "fetchClinicalEnrichmentsUsingPOST"
+        }
       }
     },
-    "/api/clinical-data-table/fetch": {
+    "/api/sample-lists-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
-        "parameters": [
-          {
-            "default": 0,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 1000000,
-            "minimum": 0,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list. Zero represents the first page.",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": "",
-            "description": "Search term to filter sample rows. Samples are returned with a partial match to the search term for any sample clinical attribute.",
-            "in": "query",
-            "name": "searchTerm",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "description": "sampleId, patientId, or the ATTR_ID to sorted by",
-            "in": "query",
-            "name": "sortBy",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
-            "name": "direction",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+        "description": "Fetch case list sample counts by study view filter",
+        "operationId": "fetchCaseListCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/SampleClinicalDataCollection"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/CaseListDataCount"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch clinical data for the Clinical Tab of Study View",
-        "operationId": "fetchClinicalDataClinicalTableUsingPOST"
+        }
       }
     },
-    "/api/clinical-data-violin-plots/fetch": {
+    "/api/resource-definitions/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Resource Definitions"
         ],
+        "description": "Get all resource definitions for specified studies",
+        "operationId": "fetchResourceDefinitionsUsingPOST",
         "parameters": [
           {
-            "description": "Clinical Attribute ID of the categorical attribute",
-            "in": "query",
-            "name": "categoricalAttributeId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Clinical Attribute ID of the numerical attribute",
-            "in": "query",
-            "name": "numericalAttributeId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Starting point of the violin plot axis, if different than smallest value",
-            "in": "query",
-            "name": "axisStart",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "description": "Ending point  of the violin plot axis, if different than largest value",
-            "in": "query",
-            "name": "axisEnd",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "default": 100,
-            "description": "Number of points in the curve",
-            "in": "query",
-            "name": "numCurvePoints",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "default": false,
-            "description": "Use log scale for the numerical attribute",
-            "in": "query",
-            "name": "logScale",
-            "required": false,
-            "type": "boolean"
-          },
-          {
-            "default": 1,
-            "description": "Sigma stepsize multiplier",
+            "name": "projection",
             "in": "query",
-            "name": "sigmaMultiplier",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "number"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
             "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 10000000,
+                "minItems": 1,
+                "type": "array",
+                "description": "List of Study IDs",
+                "items": {
+                  "maxLength": 10000000,
+                  "minLength": 1,
+                  "type": "string"
+                }
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/ClinicalViolinPlotData"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ResourceDefinition"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch violin plot curves per categorical clinical data value, filtered by study view filter",
-        "operationId": "fetchClinicalDataViolinPlotsUsingPOST"
+        }
       }
     },
-    "/api/clinical-event-type-counts/fetch": {
+    "/api/reference-genome-genes/{genomeName}/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Reference Genome Genes"
         ],
+        "description": "Fetch genes of reference genome of interest",
+        "operationId": "fetchReferenceGenomeGenesUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "studyViewFilter",
+            "name": "genomeName",
+            "in": "path",
+            "description": "Name of Reference Genome hg19",
+            "required": true,
             "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+              "type": "string"
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 100000,
+                "minItems": 1,
+                "type": "array",
+                "description": "List of Gene IDs",
+                "items": {
+                  "maxLength": 100000,
+                  "minLength": 1,
+                  "type": "string"
+                }
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalEventTypeCount"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ReferenceGenomeGene"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Get Counts of Clinical Event Types by Study View Filter",
-        "operationId": "getClinicalEventTypeCountsUsingPOST"
+        }
       }
     },
-    "/api/clinical-events-meta/fetch": {
+    "/api/mutation-data-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
+        "description": "Fetch mutation data counts by GenomicDataCountFilter",
+        "operationId": "fetchMutationDataCountsUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "clinicalEventAttributeRequest",
+            "name": "projection",
+            "in": "query",
+            "description": "Level of detail of the response",
+            "required": false,
             "schema": {
-              "$ref": "#/definitions/ClinicalEventAttributeRequest"
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/GenomicDataCountFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalEvent"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenomicDataCountItem"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Clinical Events"
-        ],
-        "description": "Fetch clinical events meta",
-        "operationId": "fetchClinicalEventsMetaUsingPOST"
+        }
       }
     },
-    "/api/cna-genes/fetch": {
+    "/api/mutation-counts-by-position/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Mutations Count"
         ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+        "description": "Fetch mutation counts in all studies by gene and position",
+        "operationId": "fetchMutationCountsByPositionUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 10000000,
+                "minItems": 1,
+                "type": "array",
+                "description": "List of Mutation Position Identifiers",
+                "items": {
+                  "$ref": "#/components/schemas/MutationPositionIdentifier"
+                }
+              }
             }
-          }
-        ],
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/CopyNumberCountByGene"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/MutationCountByPosition"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch CNA genes by study view filter",
-        "operationId": "fetchCNAGenesUsingPOST"
+        }
       }
     },
-    "/api/column-store/treatments/patient-counts/fetch": {
+    "/api/mutated-genes/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
-        "parameters": [
-          {
-            "default": "Agent",
-            "enum": [
-              "Agent",
-              "AgentClass",
-              "AgentTarget"
-            ],
-            "in": "query",
-            "name": "tier",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+        "description": "Fetch mutated genes by study view filter",
+        "operationId": "fetchMutatedGenesUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/PatientTreatmentReport"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/AlterationCountByGene"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "study-view-column-store-controller"
-        ],
-        "description": "Get all patient level treatments",
-        "operationId": "fetchPatientTreatmentCountsUsingPOST"
+        }
       }
     },
-    "/api/column-store/treatments/sample-counts/fetch": {
+    "/api/molecular-profiles/{molecularProfileId}/variant-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Variant Counts"
         ],
+        "description": "Get counts of specific variants within a mutation molecular profile",
+        "operationId": "fetchVariantCountsUsingPOST",
         "parameters": [
           {
-            "default": "Agent",
-            "enum": [
-              "Agent",
-              "AgentClass",
-              "AgentTarget"
-            ],
-            "in": "query",
-            "name": "tier",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
+            "name": "molecularProfileId",
+            "in": "path",
+            "description": "Molecular Profile ID e.g. acc_tcga_mutations",
+            "required": true,
             "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+              "type": "string"
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 50000,
+                "minItems": 1,
+                "type": "array",
+                "description": "List of variant count identifiers",
+                "items": {
+                  "$ref": "#/components/schemas/VariantCountIdentifier"
+                }
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/SampleTreatmentReport"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/VariantCount"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "study-view-column-store-controller"
-        ],
-        "operationId": "fetchSampleTreatmentCountsUsingPOST"
+        }
       }
     },
-    "/api/cosmic-counts/fetch": {
+    "/api/molecular-profiles/{molecularProfileId}/mutation-spectrums/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Mutation Spectrums"
         ],
+        "description": "Fetch mutation spectrums in a molecular profile",
+        "operationId": "fetchMutationSpectrumsUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "keywords",
+            "name": "molecularProfileId",
+            "in": "path",
+            "description": "Molecular Profile ID e.g. acc_tcga_mutations",
             "required": true,
             "schema": {
-              "description": "List of keywords",
-              "items": {
-                "maxLength": 50000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 50000,
-              "minItems": 1,
-              "type": "array"
+              "type": "string"
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/MutationSpectrumFilter"
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/CosmicMutation"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/MutationSpectrum"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Cosmic Counts"
-        ],
-        "description": "Get counts within the COSMIC database by keywords",
-        "operationId": "fetchCosmicCountsUsingPOST"
+        }
       }
     },
-    "/api/custom-data-bin-counts/fetch": {
+    "/api/molecular-profiles/{molecularProfileId}/mrna-percentile/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "mRNA Percentile"
         ],
+        "description": "Get mRNA expression percentiles for list of genes for a sample",
+        "operationId": "fetchMrnaPercentileUsingPOST",
         "parameters": [
           {
-            "default": "DYNAMIC",
-            "description": "Method for data binning",
-            "enum": [
-              "STATIC",
-              "DYNAMIC"
-            ],
-            "in": "query",
-            "name": "dataBinMethod",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "clinicalDataBinCountFilter",
-            "schema": {
-              "$ref": "#/definitions/ClinicalDataBinCountFilter"
+            "name": "molecularProfileId",
+            "in": "path",
+            "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "name": "sampleId",
+            "in": "query",
+            "description": "Sample ID e.g. TCGA-OR-A5J2-01",
+            "required": true,
+            "schema": {
+              "type": "string"
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 10000000,
+                "minItems": 1,
+                "type": "array",
+                "description": "List of Entrez Gene IDs",
+                "items": {
+                  "maximum": 10000000,
+                  "minimum": 1,
+                  "type": "integer",
+                  "format": "int32"
+                }
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalDataBin"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/MrnaPercentile"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch custom data bin counts by study view filter",
-        "operationId": "fetchCustomDataBinCountsUsingPOST"
+        }
       }
     },
-    "/api/custom-data-counts/fetch": {
+    "/api/molecular-profiles/{molecularProfileId}/discrete-copy-number-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Discrete Copy Number Alteration Counts"
         ],
+        "description": "Get counts of specific genes and alterations within a CNA molecular profile",
+        "operationId": "fetchCopyNumberCountsUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "clinicalDataCountFilter",
+            "name": "molecularProfileId",
+            "in": "path",
+            "description": "Molecular Profile ID e.g. acc_tcga_gistic",
+            "required": true,
             "schema": {
-              "$ref": "#/definitions/ClinicalDataCountFilter"
+              "type": "string"
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 50000,
+                "minItems": 1,
+                "type": "array",
+                "description": "List of copy number count identifiers",
+                "items": {
+                  "$ref": "#/components/schemas/CopyNumberCountIdentifier"
+                }
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalDataCountItem"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/CopyNumberCount"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch custom data counts by study view filter",
-        "operationId": "fetchCustomDataCountsUsingPOST"
+        }
       }
     },
-    "/api/custom-driver-annotation-report/fetch": {
+    "/api/molecular-profiles/co-expressions/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Co-Expressions"
         ],
+        "description": "Calculates correlations between a genetic entity from a specific profile and another profile from the same study",
+        "operationId": "fetchCoExpressionsUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "molecularProfileIds",
+            "name": "molecularProfileIdA",
+            "in": "query",
+            "description": "Molecular Profile ID from the Genetic Entity referenced in the co-expression filter e.g. acc_tcga_rna_seq_v2_mrna",
             "required": true,
             "schema": {
-              "description": "List of Molecular Profile Ids",
-              "items": {
-                "type": "string"
-              },
-              "type": "array"
+              "type": "string"
             }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
+          },
+          {
+            "name": "molecularProfileIdB",
+            "in": "query",
+            "description": "Molecular Profile ID (can be the same as molecularProfileIdA) e.g. acc_tcga_rna_seq_v2_mrna",
+            "required": true,
             "schema": {
-              "$ref": "#/definitions/CustomDriverAnnotationReport"
+              "type": "string"
             }
-          }
-        },
-        "tags": [
-          "Custom driver annotations"
-        ],
-        "operationId": "fetchAlterationDriverAnnotationReportUsingPOST",
-        "summary": "Return availability of custom driver annotations for molecular profiles"
-      }
-    },
-    "/api/data-access-token": {
-      "get": {
-        "produces": [
-          "application/octet-stream"
-        ],
-        "parameters": [],
-        "responses": {
-          "200": {
-            "description": "OK",
+          },
+          {
+            "name": "threshold",
+            "in": "query",
+            "description": "Threshold",
+            "required": false,
             "schema": {
-              "type": "string"
+              "type": "number",
+              "format": "double",
+              "default": 0.3
             }
           }
-        },
-        "tags": [
-          "Data Access Tokens"
         ],
-        "description": "Create a new data access token",
-        "operationId": "downloadDataAccessTokenUsingGET"
-      }
-    },
-    "/api/data-access-token/oauth2": {
-      "get": {
-        "produces": [
-          "application/octet-stream"
-        ],
-        "parameters": [],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/CoExpressionFilter"
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "type": "string"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/CoExpression"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Data Access Tokens"
-        ],
-        "operationId": "downloadOAuth2DataAccessTokenUsingGET"
+        }
       }
     },
-    "/api/data-access-tokens": {
-      "delete": {
-        "parameters": [],
-        "responses": {
-          "200": {
-            "description": "OK"
-          }
-        },
+    "/api/molecular-profile-sample-counts/fetch": {
+      "post": {
         "tags": [
-          "Data Access Tokens"
-        ],
-        "description": "Delete all data access tokens",
-        "operationId": "revokeAllDataAccessTokensUsingDELETE"
-      },
-      "get": {
-        "produces": [
-          "application/octet-stream"
+          "Study View"
         ],
-        "parameters": [],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/DataAccessToken"
-              },
-              "type": "array"
+        "description": "Fetch sample counts by study view filter",
+        "operationId": "fetchMolecularProfileSampleCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
             }
           }
         },
-        "tags": [
-          "Data Access Tokens"
-        ],
-        "description": "Retrieve all data access tokens",
-        "operationId": "getAllDataAccessTokensUsingGET"
-      },
-      "post": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/DataAccessToken"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenomicDataCount"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Data Access Tokens"
-        ],
-        "description": "Get all data access tokens",
-        "operationId": "createDataAccessTokenUsingPOST"
+        }
       }
     },
-    "/api/data-access-tokens/{token}": {
-      "delete": {
-        "parameters": [
-          {
-            "description": "token",
-            "in": "path",
-            "name": "token",
-            "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK"
-          }
-        },
+    "/api/genomic-data-counts/fetch": {
+      "post": {
         "tags": [
-          "Data Access Tokens"
-        ],
-        "description": "Delete a data access token",
-        "operationId": "revokeDataAccessTokenUsingDELETE"
-      },
-      "get": {
-        "produces": [
-          "application/octet-stream"
+          "Study View"
         ],
-        "parameters": [
-          {
-            "description": "token",
-            "in": "path",
-            "name": "token",
-            "required": true,
-            "type": "string"
+        "description": "Fetch genomic data counts by GenomicDataCountFilter",
+        "operationId": "fetchGenomicDataCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/GenomicDataCountFilter"
+              }
+            }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/DataAccessToken"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenomicDataCountItem"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Data Access Tokens"
-        ],
-        "description": "Retrieve an existing data access token",
-        "operationId": "getDataAccessTokenUsingGET"
+        }
       }
     },
-    "/api/expression-enrichments/fetch": {
+    "/api/genomic-data-bin-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
+        "description": "Fetch genomic data bin counts by study view filter",
+        "operationId": "fetchGenomicDataBinCountsUsingPOST",
         "parameters": [
           {
-            "default": "SAMPLE",
-            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
-            "enum": [
-              "SAMPLE",
-              "PATIENT"
-            ],
+            "name": "dataBinMethod",
             "in": "query",
-            "name": "enrichmentType",
+            "description": "Method for data binning",
             "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "groupsContainingSampleAndMolecularProfileIdentifiers",
             "schema": {
-              "description": "List of groups containing sample and molecular profile identifiers",
-              "items": {
-                "$ref": "#/definitions/MolecularProfileCasesGroupFilter"
-              },
-              "type": "array"
+              "type": "string",
+              "default": "DYNAMIC",
+              "enum": [
+                "STATIC",
+                "DYNAMIC"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/GenomicDataBinCountFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenomicEnrichment"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenomicDataBin"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Enrichments"
-        ],
-        "description": "Fetch genomic enrichments in a molecular profile",
-        "operationId": "fetchGenomicEnrichmentsUsingPOST"
+        }
       }
     },
-    "/api/filtered-samples/fetch": {
+    "/api/genetic-profiles/{geneticProfileId}/geneset-genetic-data/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Gene Set Scores"
         ],
+        "description": "Fetch gene set \"genetic data\" items (gene set scores) by profile Id, gene set ids and sample ids",
+        "operationId": "fetchGeneticDataItemsUsingPOST",
         "parameters": [
           {
-            "default": false,
-            "description": "Whether to negate the study view filters",
-            "in": "query",
-            "name": "negateFilters",
-            "required": false,
-            "type": "boolean"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
+            "name": "geneticProfileId",
+            "in": "path",
+            "description": "Genetic profile ID, e.g. gbm_tcga_gsva_scores",
+            "required": true,
             "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+              "type": "string"
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/GenesetDataFilterCriteria"
+              }
+            }
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Sample"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenesetMolecularData"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch sample IDs by study view filter",
-        "operationId": "fetchFilteredSamplesUsingPOST"
+        }
       }
     },
-    "/api/generic-assay-binary-enrichments/fetch": {
+    "/api/genesets/{genesetId}/expression-correlation/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Gene Set Correlation"
         ],
+        "description": "Get the genes in a gene set that have expression correlated to the gene set scores (calculated using Spearman's correlation)",
+        "operationId": "fetchCorrelatedGenesUsingPOST",
         "parameters": [
           {
-            "default": "SAMPLE",
-            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
-            "enum": [
-              "SAMPLE",
-              "PATIENT"
-            ],
+            "name": "genesetId",
+            "in": "path",
+            "description": "Gene set ID, e.g. HINATA_NFKB_MATRIX.",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "name": "geneticProfileId",
             "in": "query",
-            "name": "enrichmentType",
+            "description": "Genetic Profile ID e.g. gbm_tcga_gsva_scores",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "name": "correlationThreshold",
+            "in": "query",
+            "description": "Correlation threshold (for absolute correlation value, Spearman correlation)",
             "required": false,
-            "type": "string"
+            "schema": {
+              "maximum": 1,
+              "minimum": 0,
+              "type": "number",
+              "format": "double",
+              "default": 0.3
+            }
           },
           {
-            "in": "body",
-            "name": "groupsContainingSampleAndMolecularProfileIdentifiers",
+            "name": "sampleListId",
+            "in": "query",
+            "description": "Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all",
+            "required": false,
             "schema": {
-              "description": "List of groups containing sample and molecular profile identifiers",
-              "items": {
-                "$ref": "#/definitions/MolecularProfileCasesGroupFilter"
-              },
-              "type": "array"
+              "type": "string"
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "array",
+                "description": "Fill this one if you want to specify a subset of samples: sampleIds: custom list of samples or patients to query, e.g. [\"TCGA-A1-A0SD-01\", \"TCGA-A1-A0SE-01\"]",
+                "items": {
+                  "type": "string"
+                }
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayBinaryEnrichment"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenesetCorrelation"
+                  }
+                }
+              }
             }
           }
-        },
+        }
+      }
+    },
+    "/api/genesets/fetch": {
+      "post": {
         "tags": [
-          "Generic Assay Enrichment Data"
+          "Gene Sets"
         ],
-        "description": "Fetch generic assay binary data enrichments in a molecular profile",
-        "operationId": "fetchGenericAssayBinaryDataEnrichmentInMultipleMolecularProfilesUsingPOST"
+        "description": "Fetch gene sets by ID",
+        "operationId": "fetchGenesetsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 10000000,
+                "minItems": 1,
+                "type": "array",
+                "description": "List of Geneset IDs",
+                "items": {
+                  "maxLength": 10000000,
+                  "minLength": 1,
+                  "type": "string"
+                }
+              }
+            }
+          },
+          "required": true
+        },
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/Geneset"
+                  }
+                }
+              }
+            }
+          }
+        }
       }
     },
-    "/api/generic-assay-categorical-enrichments/fetch": {
+    "/api/geneset-hierarchy/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Gene Set Hierarchy"
         ],
+        "description": "Get gene set hierarchical organization information. I.e. how different gene sets relate to other gene sets, in a hierarchy",
+        "operationId": "fetchGenesetHierarchyInfoUsingPOST",
         "parameters": [
           {
-            "default": "SAMPLE",
-            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
-            "enum": [
-              "SAMPLE",
-              "PATIENT"
-            ],
+            "name": "geneticProfileId",
             "in": "query",
-            "name": "enrichmentType",
+            "description": "Genetic Profile ID e.g. gbm_tcga_gsva_scores. The final hierarchy  will only include gene sets scored in the specified profile.",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "name": "percentile",
+            "in": "query",
+            "description": "Percentile (for score calculation). Which percentile to use when determining the *representative score*",
             "required": false,
-            "type": "string"
+            "schema": {
+              "maximum": 100,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 75
+            }
+          },
+          {
+            "name": "scoreThreshold",
+            "in": "query",
+            "description": "Gene set score threshold (for absolute score value). Filters out gene sets where the GSVA(like) *representative score* is under this threshold.",
+            "required": false,
+            "schema": {
+              "maximum": 1,
+              "minimum": 0,
+              "type": "number",
+              "format": "double",
+              "default": 0.4
+            }
           },
           {
-            "in": "body",
-            "name": "groupsContainingSampleAndMolecularProfileIdentifiers",
+            "name": "pvalueThreshold",
+            "in": "query",
+            "description": "p-value threshold. Filters out gene sets for which the score p-value is higher than this threshold.",
+            "required": false,
             "schema": {
-              "description": "List of groups containing sample and molecular profile identifiers",
-              "items": {
-                "$ref": "#/definitions/MolecularProfileCasesGroupFilter"
-              },
-              "type": "array"
+              "maximum": 1,
+              "minimum": 0,
+              "type": "number",
+              "format": "double",
+              "default": 0.05
+            }
+          },
+          {
+            "name": "sampleListId",
+            "in": "query",
+            "description": "Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all",
+            "required": false,
+            "schema": {
+              "type": "string"
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "array",
+                "description": "Fill this one if you want to specify a subset of samples: sampleIds: custom list of samples or patients to query, e.g. [\"TCGA-A1-A0SD-01\", \"TCGA-A1-A0SE-01\"]",
+                "items": {
+                  "type": "string"
+                }
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayCategoricalEnrichment"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenesetHierarchyInfo"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Generic Assay Enrichment Data"
-        ],
-        "description": "Fetch generic assay categorical data enrichments in a molecular profile",
-        "operationId": "fetchGenericAssayCategoricalDataEnrichmentInMultipleMolecularProfilesUsingPOST"
+        }
       }
     },
-    "/api/generic-assay-data-bin-counts/fetch": {
+    "/api/generic-assay-enrichments/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Enrichments"
         ],
+        "description": "Fetch generic assay enrichments in a molecular profile",
+        "operationId": "fetchGenericAssayEnrichmentsUsingPOST",
         "parameters": [
           {
-            "default": "DYNAMIC",
-            "description": "Method for data binning",
-            "enum": [
-              "STATIC",
-              "DYNAMIC"
-            ],
+            "name": "enrichmentType",
             "in": "query",
-            "name": "dataBinMethod",
+            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
             "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "genericAssayDataBinCountFilter",
             "schema": {
-              "$ref": "#/definitions/GenericAssayDataBinCountFilter"
+              "type": "string",
+              "default": "SAMPLE",
+              "enum": [
+                "SAMPLE",
+                "PATIENT"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "array",
+                "description": "List of groups containing sample and molecular profile identifiers",
+                "items": {
+                  "$ref": "#/components/schemas/MolecularProfileCasesGroupFilter"
+                }
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayDataBin"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenericAssayEnrichment"
+                  }
+                }
+              }
             }
           }
-        },
+        }
+      }
+    },
+    "/api/generic-assay-data-counts/fetch": {
+      "post": {
         "tags": [
           "Study View"
         ],
-        "description": "Fetch generic assay data bin counts by study view filter",
-        "operationId": "fetchGenericAssayDataBinCountsUsingPOST"
+        "description": "Fetch generic assay data counts by study view filter",
+        "operationId": "fetchGenericAssayDataCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/GenericAssayDataCountFilter"
+              }
+            }
+          }
+        },
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenericAssayDataCountItem"
+                  }
+                }
+              }
+            }
+          }
+        }
       }
     },
-    "/api/generic-assay-data-counts/fetch": {
+    "/api/generic-assay-data-bin-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
+        "description": "Fetch generic assay data bin counts by study view filter",
+        "operationId": "fetchGenericAssayDataBinCountsUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "genericAssayDataCountFilter",
+            "name": "dataBinMethod",
+            "in": "query",
+            "description": "Method for data binning",
+            "required": false,
             "schema": {
-              "$ref": "#/definitions/GenericAssayDataCountFilter"
+              "type": "string",
+              "default": "DYNAMIC",
+              "enum": [
+                "STATIC",
+                "DYNAMIC"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/GenericAssayDataBinCountFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayDataCountItem"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenericAssayDataBin"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch generic assay data counts by study view filter",
-        "operationId": "fetchGenericAssayDataCountsUsingPOST"
+        }
       }
     },
-    "/api/generic-assay-enrichments/fetch": {
+    "/api/generic-assay-categorical-enrichments/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Generic Assay Enrichment Data"
         ],
+        "description": "Fetch generic assay categorical data enrichments in a molecular profile",
+        "operationId": "fetchGenericAssayCategoricalDataEnrichmentInMultipleMolecularProfilesUsingPOST",
         "parameters": [
           {
-            "default": "SAMPLE",
-            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
-            "enum": [
-              "SAMPLE",
-              "PATIENT"
-            ],
-            "in": "query",
             "name": "enrichmentType",
+            "in": "query",
+            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
             "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "groupsContainingSampleAndMolecularProfileIdentifiers",
             "schema": {
-              "description": "List of groups containing sample and molecular profile identifiers",
-              "items": {
-                "$ref": "#/definitions/MolecularProfileCasesGroupFilter"
-              },
-              "type": "array"
+              "type": "string",
+              "default": "SAMPLE",
+              "enum": [
+                "SAMPLE",
+                "PATIENT"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "array",
+                "description": "List of groups containing sample and molecular profile identifiers",
+                "items": {
+                  "$ref": "#/components/schemas/MolecularProfileCasesGroupFilter"
+                }
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenericAssayEnrichment"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenericAssayCategoricalEnrichment"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Enrichments"
-        ],
-        "description": "Fetch generic assay enrichments in a molecular profile",
-        "operationId": "fetchGenericAssayEnrichmentsUsingPOST"
+        }
       }
     },
-    "/api/geneset-hierarchy/fetch": {
+    "/api/generic-assay-binary-enrichments/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Generic Assay Enrichment Data"
         ],
+        "description": "Fetch generic assay binary data enrichments in a molecular profile",
+        "operationId": "fetchGenericAssayBinaryDataEnrichmentInMultipleMolecularProfilesUsingPOST",
         "parameters": [
           {
-            "description": "Genetic Profile ID e.g. gbm_tcga_gsva_scores. The final hierarchy  will only include gene sets scored in the specified profile.",
-            "in": "query",
-            "name": "geneticProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": 75,
-            "description": "Percentile (for score calculation). Which percentile to use when determining the *representative score*",
-            "format": "int32",
-            "in": "query",
-            "maximum": 100,
-            "minimum": 1,
-            "name": "percentile",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0.4,
-            "description": "Gene set score threshold (for absolute score value). Filters out gene sets where the GSVA(like) *representative score* is under this threshold.",
-            "format": "double",
-            "in": "query",
-            "maximum": 1,
-            "minimum": 0,
-            "name": "scoreThreshold",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "default": 0.05,
-            "description": "p-value threshold. Filters out gene sets for which the score p-value is higher than this threshold.",
-            "format": "double",
-            "in": "query",
-            "maximum": 1,
-            "minimum": 0,
-            "name": "pvalueThreshold",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "description": "Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all",
+            "name": "enrichmentType",
             "in": "query",
-            "name": "sampleListId",
+            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
             "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "fillThisOneIfYouWantToSpecifyASubsetOfSamples:Sampleids:CustomListOfSamplesOrPatientsToQuery,EG. [\"tcgaA1A0Sd01\", \"tcgaA1A0Se01\"]",
             "schema": {
-              "description": "Fill this one if you want to specify a subset of samples: sampleIds: custom list of samples or patients to query, e.g. [\"TCGA-A1-A0SD-01\", \"TCGA-A1-A0SE-01\"]",
-              "items": {
-                "type": "string"
-              },
-              "type": "array"
+              "type": "string",
+              "default": "SAMPLE",
+              "enum": [
+                "SAMPLE",
+                "PATIENT"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "array",
+                "description": "List of groups containing sample and molecular profile identifiers",
+                "items": {
+                  "$ref": "#/components/schemas/MolecularProfileCasesGroupFilter"
+                }
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenesetHierarchyInfo"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenericAssayBinaryEnrichment"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Gene Set Hierarchy"
-        ],
-        "description": "Get gene set hierarchical organization information. I.e. how different gene sets relate to other gene sets, in a hierarchy",
-        "operationId": "fetchGenesetHierarchyInfoUsingPOST"
+        }
       }
     },
-    "/api/genesets": {
-      "get": {
-        "produces": [
-          "application/json"
+    "/api/filtered-samples/fetch": {
+      "post": {
+        "tags": [
+          "Study View"
         ],
+        "description": "Fetch sample IDs by study view filter",
+        "operationId": "fetchFilteredSamplesUsingPOST",
         "parameters": [
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 2147483647,
-            "minimum": 1,
-            "name": "pageSize",
-            "required": false,
-            "type": "integer"
-          },
-          {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
+            "name": "negateFilters",
             "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
+            "description": "Whether to negate the study view filters",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "type": "boolean",
+              "default": false
+            }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Geneset"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/Sample"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Gene Sets"
-        ],
-        "description": "Get all gene sets",
-        "operationId": "getAllGenesetsUsingGET"
+        }
       }
     },
-    "/api/genesets/fetch": {
+    "/api/expression-enrichments/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Enrichments"
         ],
+        "description": "Fetch genomic enrichments in a molecular profile",
+        "operationId": "fetchGenomicEnrichmentsUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "genesetIds",
-            "required": true,
+            "name": "enrichmentType",
+            "in": "query",
+            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
+            "required": false,
             "schema": {
-              "description": "List of Geneset IDs",
-              "items": {
-                "maxLength": 10000000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
+              "type": "string",
+              "default": "SAMPLE",
+              "enum": [
+                "SAMPLE",
+                "PATIENT"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "array",
+                "description": "List of groups containing sample and molecular profile identifiers",
+                "items": {
+                  "$ref": "#/components/schemas/MolecularProfileCasesGroupFilter"
+                }
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Geneset"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/GenomicEnrichment"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Gene Sets"
-        ],
-        "description": "Fetch gene sets by ID",
-        "operationId": "fetchGenesetsUsingPOST"
+        }
       }
     },
-    "/api/genesets/version": {
+    "/api/data-access-tokens": {
       "get": {
-        "produces": [
-          "application/json"
+        "tags": [
+          "Data Access Tokens"
         ],
-        "parameters": [],
+        "description": "Retrieve all data access tokens",
+        "operationId": "getAllDataAccessTokensUsingGET",
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "type": "string"
+            "content": {
+              "*/*": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/DataAccessToken"
+                  }
+                }
+              }
             }
           }
-        },
+        }
+      },
+      "post": {
         "tags": [
-          "Gene Sets"
-        ],
-        "description": "Get the geneset version",
-        "operationId": "getGenesetVersionUsingGET"
-      }
-    },
-    "/api/genesets/{genesetId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Gene set ID e.g. GNF2_ZAP70",
-            "in": "path",
-            "name": "genesetId",
-            "required": true,
-            "type": "string"
-          }
+          "Data Access Tokens"
         ],
+        "description": "Get all data access tokens",
+        "operationId": "createDataAccessTokenUsingPOST",
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/Geneset"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/DataAccessToken"
+                }
+              }
             }
           }
-        },
+        }
+      },
+      "delete": {
         "tags": [
-          "Gene Sets"
+          "Data Access Tokens"
         ],
-        "description": "Get a gene set",
-        "operationId": "getGenesetUsingGET"
+        "description": "Delete all data access tokens",
+        "operationId": "revokeAllDataAccessTokensUsingDELETE",
+        "responses": {
+          "200": {
+            "description": "OK"
+          }
+        }
       }
     },
-    "/api/genesets/{genesetId}/expression-correlation/fetch": {
+    "/api/custom-driver-annotation-report/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Custom driver annotations"
         ],
-        "parameters": [
-          {
-            "description": "Gene set ID, e.g. HINATA_NFKB_MATRIX.",
-            "in": "path",
-            "name": "genesetId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Genetic Profile ID e.g. gbm_tcga_gsva_scores",
-            "in": "query",
-            "name": "geneticProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": 0.3,
-            "description": "Correlation threshold (for absolute correlation value, Spearman correlation)",
-            "format": "double",
-            "in": "query",
-            "maximum": 1,
-            "minimum": 0,
-            "name": "correlationThreshold",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "description": "Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all",
-            "in": "query",
-            "name": "sampleListId",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "fillThisOneIfYouWantToSpecifyASubsetOfSamples:Sampleids:CustomListOfSamplesOrPatientsToQuery,EG. [\"tcgaA1A0Sd01\", \"tcgaA1A0Se01\"]",
-            "schema": {
-              "description": "Fill this one if you want to specify a subset of samples: sampleIds: custom list of samples or patients to query, e.g. [\"TCGA-A1-A0SD-01\", \"TCGA-A1-A0SE-01\"]",
-              "items": {
-                "type": "string"
-              },
-              "type": "array"
+        "summary": "Return availability of custom driver annotations for molecular profiles",
+        "operationId": "fetchAlterationDriverAnnotationReportUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "array",
+                "description": "List of Molecular Profile Ids",
+                "items": {
+                  "type": "string"
+                }
+              }
             }
-          }
-        ],
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenesetCorrelation"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/CustomDriverAnnotationReport"
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Gene Set Correlation"
-        ],
-        "description": "Get the genes in a gene set that have expression correlated to the gene set scores (calculated using Spearman's correlation)",
-        "operationId": "fetchCorrelatedGenesUsingPOST"
+        }
       }
     },
-    "/api/genetic-profiles/{geneticProfileId}/geneset-genetic-data/fetch": {
+    "/api/custom-data-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
-        "parameters": [
-          {
-            "description": "Genetic profile ID, e.g. gbm_tcga_gsva_scores",
-            "in": "path",
-            "name": "geneticProfileId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "genesetDataFilterCriteria",
-            "required": true,
-            "schema": {
-              "$ref": "#/definitions/GenesetDataFilterCriteria"
+        "description": "Fetch custom data counts by study view filter",
+        "operationId": "fetchCustomDataCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/ClinicalDataCountFilter"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenesetMolecularData"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalDataCountItem"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Gene Set Scores"
-        ],
-        "description": "Fetch gene set \"genetic data\" items (gene set scores) by profile Id, gene set ids and sample ids",
-        "operationId": "fetchGeneticDataItemsUsingPOST"
+        }
       }
     },
-    "/api/genomic-data-bin-counts/fetch": {
+    "/api/custom-data-bin-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
+        "description": "Fetch custom data bin counts by study view filter",
+        "operationId": "fetchCustomDataBinCountsUsingPOST",
         "parameters": [
           {
-            "default": "DYNAMIC",
-            "description": "Method for data binning",
-            "enum": [
-              "STATIC",
-              "DYNAMIC"
-            ],
-            "in": "query",
             "name": "dataBinMethod",
+            "in": "query",
+            "description": "Method for data binning",
             "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "genomicDataBinCountFilter",
             "schema": {
-              "$ref": "#/definitions/GenomicDataBinCountFilter"
+              "type": "string",
+              "default": "DYNAMIC",
+              "enum": [
+                "STATIC",
+                "DYNAMIC"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/ClinicalDataBinCountFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenomicDataBin"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalDataBin"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch genomic data bin counts by study view filter",
-        "operationId": "fetchGenomicDataBinCountsUsingPOST"
+        }
       }
     },
-    "/api/genomic-data-counts/fetch": {
+    "/api/cosmic-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Cosmic Counts"
         ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "genomicDataCountFilter",
-            "schema": {
-              "$ref": "#/definitions/GenomicDataCountFilter"
+        "description": "Get counts within the COSMIC database by keywords",
+        "operationId": "fetchCosmicCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "maxItems": 50000,
+                "minItems": 1,
+                "type": "array",
+                "description": "List of keywords",
+                "items": {
+                  "maxLength": 50000,
+                  "minLength": 1,
+                  "type": "string"
+                }
+              }
             }
-          }
-        ],
+          },
+          "required": true
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenomicDataCountItem"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/CosmicMutation"
+                  }
+                }
+              }
             }
           }
-        },
+        }
+      }
+    },
+    "/api/cna-genes/fetch": {
+      "post": {
         "tags": [
           "Study View"
         ],
-        "description": "Fetch genomic data counts by GenomicDataCountFilter",
-        "operationId": "fetchGenomicDataCountsUsingPOST"
+        "description": "Fetch CNA genes by study view filter",
+        "operationId": "fetchCNAGenesUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
+            }
+          }
+        },
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/CopyNumberCountByGene"
+                  }
+                }
+              }
+            }
+          }
+        }
       }
     },
-    "/api/molecular-profile-sample-counts/fetch": {
+    "/api/clinical-events-meta/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Clinical Events"
         ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+        "description": "Fetch clinical events meta",
+        "operationId": "fetchClinicalEventsMetaUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/ClinicalEventAttributeRequest"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/GenomicDataCount"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalEvent"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch sample counts by study view filter",
-        "operationId": "fetchMolecularProfileSampleCountsUsingPOST"
+        }
       }
     },
-    "/api/molecular-profiles/co-expressions/fetch": {
+    "/api/clinical-event-type-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
-        "parameters": [
-          {
-            "description": "Molecular Profile ID from the Genetic Entity referenced in the co-expression filter e.g. acc_tcga_rna_seq_v2_mrna",
-            "in": "query",
-            "name": "molecularProfileIdA",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Molecular Profile ID (can be the same as molecularProfileIdA) e.g. acc_tcga_rna_seq_v2_mrna",
-            "in": "query",
-            "name": "molecularProfileIdB",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "default": 0.3,
-            "description": "Threshold",
-            "format": "double",
-            "in": "query",
-            "name": "threshold",
-            "required": false,
-            "type": "number"
-          },
-          {
-            "in": "body",
-            "name": "coExpressionFilter",
-            "required": true,
-            "schema": {
-              "$ref": "#/definitions/CoExpressionFilter"
+        "description": "Get Counts of Clinical Event Types by Study View Filter",
+        "operationId": "getClinicalEventTypeCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/CoExpression"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalEventTypeCount"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Co-Expressions"
-        ],
-        "description": "Calculates correlations between a genetic entity from a specific profile and another profile from the same study",
-        "operationId": "fetchCoExpressionsUsingPOST"
+        }
       }
     },
-    "/api/molecular-profiles/{molecularProfileId}/discrete-copy-number-counts/fetch": {
+    "/api/clinical-data-violin-plots/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
+        "description": "Fetch violin plot curves per categorical clinical data value, filtered by study view filter",
+        "operationId": "fetchClinicalDataViolinPlotsUsingPOST",
         "parameters": [
           {
-            "description": "Molecular Profile ID e.g. acc_tcga_gistic",
-            "in": "path",
-            "name": "molecularProfileId",
+            "name": "categoricalAttributeId",
+            "in": "query",
+            "description": "Clinical Attribute ID of the categorical attribute",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "in": "body",
-            "name": "copyNumberCountIdentifiers",
+            "name": "numericalAttributeId",
+            "in": "query",
+            "description": "Clinical Attribute ID of the numerical attribute",
             "required": true,
             "schema": {
-              "description": "List of copy number count identifiers",
-              "items": {
-                "$ref": "#/definitions/CopyNumberCountIdentifier"
-              },
-              "maxItems": 50000,
-              "minItems": 1,
-              "type": "array"
+              "type": "string"
             }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
+          },
+          {
+            "name": "axisStart",
+            "in": "query",
+            "description": "Starting point of the violin plot axis, if different than smallest value",
+            "required": false,
             "schema": {
-              "items": {
-                "$ref": "#/definitions/CopyNumberCount"
-              },
-              "type": "array"
+              "type": "number"
             }
-          }
-        },
-        "tags": [
-          "Discrete Copy Number Alteration Counts"
-        ],
-        "description": "Get counts of specific genes and alterations within a CNA molecular profile",
-        "operationId": "fetchCopyNumberCountsUsingPOST"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}/mrna-percentile/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
+          },
           {
-            "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
+            "name": "axisEnd",
+            "in": "query",
+            "description": "Ending point  of the violin plot axis, if different than largest value",
+            "required": false,
+            "schema": {
+              "type": "number"
+            }
           },
           {
-            "description": "Sample ID e.g. TCGA-OR-A5J2-01",
+            "name": "numCurvePoints",
             "in": "query",
-            "name": "sampleId",
-            "required": true,
-            "type": "string"
+            "description": "Number of points in the curve",
+            "required": false,
+            "schema": {
+              "type": "number",
+              "default": 100
+            }
           },
           {
-            "in": "body",
-            "name": "entrezGeneIds",
-            "required": true,
+            "name": "logScale",
+            "in": "query",
+            "description": "Use log scale for the numerical attribute",
+            "required": false,
             "schema": {
-              "description": "List of Entrez Gene IDs",
-              "items": {
-                "format": "int32",
-                "maximum": 10000000,
-                "minimum": 1,
-                "type": "integer"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
+              "type": "boolean",
+              "default": false
+            }
+          },
+          {
+            "name": "sigmaMultiplier",
+            "in": "query",
+            "description": "Sigma stepsize multiplier",
+            "required": false,
+            "schema": {
+              "type": "number",
+              "default": 1
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/MrnaPercentile"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/ClinicalViolinPlotData"
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "mRNA Percentile"
-        ],
-        "description": "Get mRNA expression percentiles for list of genes for a sample",
-        "operationId": "fetchMrnaPercentileUsingPOST"
+        }
       }
     },
-    "/api/molecular-profiles/{molecularProfileId}/mutation-spectrums/fetch": {
+    "/api/clinical-data-table/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
+        "description": "Fetch clinical data for the Clinical Tab of Study View",
+        "operationId": "fetchClinicalDataClinicalTableUsingPOST",
         "parameters": [
           {
-            "description": "Molecular Profile ID e.g. acc_tcga_mutations",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
+            "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
+            "required": false,
+            "schema": {
+              "maximum": 1000000,
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "in": "body",
-            "name": "mutationSpectrumFilter",
-            "required": true,
+            "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list. Zero represents the first page.",
+            "required": false,
             "schema": {
-              "$ref": "#/definitions/MutationSpectrumFilter"
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
             }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
+          },
+          {
+            "name": "searchTerm",
+            "in": "query",
+            "description": "Search term to filter sample rows. Samples are returned with a partial match to the search term for any sample clinical attribute.",
+            "required": false,
             "schema": {
-              "items": {
-                "$ref": "#/definitions/MutationSpectrum"
-              },
-              "type": "array"
+              "type": "string",
+              "default": ""
             }
-          }
-        },
-        "tags": [
-          "Mutation Spectrums"
-        ],
-        "description": "Fetch mutation spectrums in a molecular profile",
-        "operationId": "fetchMutationSpectrumsUsingPOST"
-      }
-    },
-    "/api/molecular-profiles/{molecularProfileId}/variant-counts/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
+          },
           {
-            "description": "Molecular Profile ID e.g. acc_tcga_mutations",
-            "in": "path",
-            "name": "molecularProfileId",
-            "required": true,
-            "type": "string"
+            "name": "sortBy",
+            "in": "query",
+            "description": "sampleId, patientId, or the ATTR_ID to sorted by",
+            "required": false,
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "in": "body",
-            "name": "variantCountIdentifiers",
-            "required": true,
+            "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
+            "required": false,
             "schema": {
-              "description": "List of variant count identifiers",
-              "items": {
-                "$ref": "#/definitions/VariantCountIdentifier"
-              },
-              "maxItems": 50000,
-              "minItems": 1,
-              "type": "array"
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/VariantCount"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/SampleClinicalDataCollection"
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Variant Counts"
-        ],
-        "description": "Get counts of specific variants within a mutation molecular profile",
-        "operationId": "fetchVariantCountsUsingPOST"
+        }
       }
     },
-    "/api/mutated-genes/fetch": {
+    "/api/clinical-data-enrichments/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Clinical Data Enrichments"
         ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+        "description": "Fetch clinical data enrichments for the sample groups",
+        "operationId": "fetchClinicalEnrichmentsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/GroupFilter"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/AlterationCountByGene"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalDataEnrichment"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch mutated genes by study view filter",
-        "operationId": "fetchMutatedGenesUsingPOST"
+        }
       }
     },
-    "/api/mutation-counts-by-position/fetch": {
+    "/api/clinical-data-density-plot/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
+        "description": "Fetch clinical data density plot bins by study view filter",
+        "operationId": "fetchClinicalDataDensityPlotUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "mutationPositionIdentifiers",
+            "name": "xAxisAttributeId",
+            "in": "query",
+            "description": "Clinical Attribute ID of the X axis",
             "required": true,
             "schema": {
-              "description": "List of Mutation Position Identifiers",
-              "items": {
-                "$ref": "#/definitions/MutationPositionIdentifier"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
+              "type": "string"
             }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
+          },
+          {
+            "name": "xAxisBinCount",
+            "in": "query",
+            "description": "Number of the bins in X axis",
+            "required": false,
             "schema": {
-              "items": {
-                "$ref": "#/definitions/MutationCountByPosition"
-              },
-              "type": "array"
+              "type": "integer",
+              "format": "int32",
+              "default": 50
             }
-          }
-        },
-        "tags": [
-          "Mutations Count"
-        ],
-        "description": "Fetch mutation counts in all studies by gene and position",
-        "operationId": "fetchMutationCountsByPositionUsingPOST"
-      }
-    },
-    "/api/mutation-data-counts/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
+          },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
+            "name": "xAxisStart",
             "in": "query",
-            "name": "projection",
+            "description": "Starting point of the X axis, if different than smallest value",
             "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "genomicDataCountFilter",
             "schema": {
-              "$ref": "#/definitions/GenomicDataCountFilter"
+              "type": "number"
             }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
+          },
+          {
+            "name": "xAxisEnd",
+            "in": "query",
+            "description": "Starting point of the X axis, if different than largest value",
+            "required": false,
             "schema": {
-              "items": {
-                "$ref": "#/definitions/GenomicDataCountItem"
-              },
-              "type": "array"
+              "type": "number"
             }
-          }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch mutation data counts by GenomicDataCountFilter",
-        "operationId": "fetchMutationDataCountsUsingPOST"
-      }
-    },
-    "/api/reference-genome-genes/{genomeName}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
+          },
           {
-            "description": "Name of Reference Genome hg19",
-            "in": "path",
-            "name": "genomeName",
+            "name": "yAxisAttributeId",
+            "in": "query",
+            "description": "Clinical Attribute ID of the Y axis",
             "required": true,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
             "schema": {
-              "items": {
-                "$ref": "#/definitions/ReferenceGenomeGene"
-              },
-              "type": "array"
+              "type": "string"
             }
-          }
-        },
-        "tags": [
-          "Reference Genome Genes"
-        ],
-        "description": "Get all reference genes",
-        "operationId": "getAllReferenceGenomeGenesUsingGET"
-      }
-    },
-    "/api/reference-genome-genes/{genomeName}/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Name of Reference Genome hg19",
-            "in": "path",
-            "name": "genomeName",
-            "required": true,
-            "type": "string"
           },
           {
-            "in": "body",
-            "name": "geneIds",
-            "required": true,
+            "name": "yAxisBinCount",
+            "in": "query",
+            "description": "Number of the bins in Y axis",
+            "required": false,
             "schema": {
-              "description": "List of Gene IDs",
-              "items": {
-                "maxLength": 100000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 100000,
-              "minItems": 1,
-              "type": "array"
+              "type": "integer",
+              "format": "int32",
+              "default": 50
             }
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
+          },
+          {
+            "name": "yAxisStart",
+            "in": "query",
+            "description": "Starting point of the Y axis, if different than smallest value",
+            "required": false,
             "schema": {
-              "items": {
-                "$ref": "#/definitions/ReferenceGenomeGene"
-              },
-              "type": "array"
+              "type": "number"
             }
-          }
-        },
-        "tags": [
-          "Reference Genome Genes"
-        ],
-        "description": "Fetch genes of reference genome of interest",
-        "operationId": "fetchReferenceGenomeGenesUsingPOST"
-      }
-    },
-    "/api/reference-genome-genes/{genomeName}/{geneId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Name of Reference Genome hg19",
-            "in": "path",
-            "name": "genomeName",
-            "required": true,
-            "type": "string"
           },
           {
-            "description": "Entrez Gene ID 207",
-            "format": "int32",
-            "in": "path",
-            "name": "geneId",
-            "required": true,
-            "type": "integer"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
+            "name": "yAxisEnd",
+            "in": "query",
+            "description": "Starting point of the Y axis, if different than largest value",
+            "required": false,
             "schema": {
-              "$ref": "#/definitions/ReferenceGenomeGene"
+              "type": "number"
             }
-          }
-        },
-        "tags": [
-          "Reference Genome Genes"
-        ],
-        "description": "Get a gene of a reference genome of interest",
-        "operationId": "getReferenceGenomeGeneUsingGET"
-      }
-    },
-    "/api/resource-definitions/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
+          },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
+            "name": "xAxisLogScale",
             "in": "query",
-            "name": "projection",
+            "description": "Use log scale for X axis",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "boolean",
+              "default": false
+            }
           },
           {
-            "in": "body",
-            "name": "studyIds",
-            "required": true,
+            "name": "yAxisLogScale",
+            "in": "query",
+            "description": "Use log scale for Y axis",
+            "required": false,
             "schema": {
-              "description": "List of Study IDs",
-              "items": {
-                "maxLength": 10000000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array"
+              "type": "boolean",
+              "default": false
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/StudyViewFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ResourceDefinition"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/DensityPlotData"
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Resource Definitions"
-        ],
-        "description": "Get all resource definitions for specified studies",
-        "operationId": "fetchResourceDefinitionsUsingPOST"
+        }
       }
     },
-    "/api/sample-lists-counts/fetch": {
+    "/api/clinical-data-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+        "description": "Fetch clinical data counts by study view filter",
+        "operationId": "fetchClinicalDataCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/ClinicalDataCountFilter"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/CaseListDataCount"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalDataCountItem"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch case list sample counts by study view filter",
-        "operationId": "fetchCaseListCountsUsingPOST"
+        }
       }
     },
-    "/api/structural-variant/fetch": {
+    "/api/clinical-data-bin-counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Study View"
         ],
+        "description": "Fetch clinical data bin counts by study view filter",
+        "operationId": "fetchClinicalDataBinCountsUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "structuralVariantFilter",
+            "name": "dataBinMethod",
+            "in": "query",
+            "description": "Method for data binning",
+            "required": false,
             "schema": {
-              "$ref": "#/definitions/StructuralVariantFilter"
+              "type": "string",
+              "default": "DYNAMIC",
+              "enum": [
+                "STATIC",
+                "DYNAMIC"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/ClinicalDataBinCountFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/StructuralVariant"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalDataBin"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Structural Variants"
-        ],
-        "description": "Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers",
-        "operationId": "fetchStructuralVariantsUsingPOST"
+        }
       }
     },
-    "/api/structuralvariant-counts/fetch": {
+    "/api/clinical-attributes/counts/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Clinical Attributes Count"
         ],
-        "parameters": [
-          {
-            "in": "body",
-            "name": "studyViewFilter",
-            "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+        "description": "Get counts for clinical attributes according to their data availability for selected samples/patients",
+        "operationId": "getClinicalAttributeCountsUsingPOST",
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/ClinicalAttributeCountFilter"
+              }
             }
           }
-        ],
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/AlterationCountByStructuralVariant"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalAttributeCount"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Study View"
-        ],
-        "description": "Fetch structural variant genes by study view filter",
-        "operationId": "fetchStructuralVariantCountsUsingPOST"
+        }
       }
     },
-    "/api/structuralvariant-genes/fetch": {
+    "/api/alteration-enrichments/fetch": {
       "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+        "tags": [
+          "Alteration Enrichments"
         ],
+        "summary": "Fetch alteration enrichments in molecular profiles",
+        "operationId": "fetchAlterationEnrichmentsUsingPOST",
         "parameters": [
           {
-            "in": "body",
-            "name": "studyViewFilter",
+            "name": "enrichmentType",
+            "in": "query",
+            "description": "Type of the enrichment e.g. SAMPLE or PATIENT",
+            "required": false,
             "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+              "type": "string",
+              "default": "SAMPLE",
+              "enum": [
+                "SAMPLE",
+                "PATIENT"
+              ]
             }
           }
         ],
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "$ref": "#/components/schemas/MolecularProfileCasesGroupAndAlterationTypeFilter"
+              }
+            }
+          }
+        },
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/AlterationCountByGene"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/AlterationEnrichment"
+                  }
+                }
+              }
             }
           }
-        },
+        }
+      }
+    },
+    "/api/timestamps": {
+      "get": {
         "tags": [
-          "Study View"
+          "Timestamps"
         ],
-        "description": "Fetch structural variant genes by study view filter",
-        "operationId": "fetchStructuralVariantGenesUsingPOST"
+        "description": "Get the last time each static resource was updated",
+        "operationId": "getAllTimestampsUsingGET",
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object"
+                }
+              }
+            }
+          }
+        }
       }
     },
-    "/api/studies/{studyId}/clinical-events": {
+    "/api/studies/{studyId}/significantly-mutated-genes": {
       "get": {
-        "produces": [
-          "application/json"
-        ],
+        "tags": [
+          "Significantly Mutated Genes"
+        ],
+        "description": "Get significantly mutated genes in a study",
+        "operationId": "getSignificantlyMutatedGenesUsingGET",
         "parameters": [
           {
-            "description": "Study ID e.g. lgg_ucsf_2014",
-            "in": "path",
             "name": "studyId",
+            "in": "path",
+            "description": "Study ID e.g. acc_tcga",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
             "name": "projection",
+            "in": "query",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
             "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "maximum": 10000000,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
           },
           {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
             "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "eventType",
-              "startNumberOfDaysSinceDiagnosis",
-              "endNumberOfDaysSinceDiagnosis"
-            ],
-            "in": "query",
             "name": "sortBy",
+            "in": "query",
+            "description": "Name of the property that the result list is sorted by",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "enum": [
+                "entrezGeneId",
+                "hugoGeneSymbol",
+                "rank",
+                "numberOfMutations",
+                "pValue",
+                "qValue"
+              ]
+            }
           },
           {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
             "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
+            }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalEvent"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/MutSig"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Clinical Events"
-        ],
-        "description": "Get all clinical events in a study",
-        "operationId": "getAllClinicalEventsInStudyUsingGET"
+        }
       }
     },
-    "/api/studies/{studyId}/patients/{patientId}/clinical-events": {
+    "/api/studies/{studyId}/significant-copy-number-regions": {
       "get": {
-        "produces": [
-          "application/json"
+        "tags": [
+          "Significant Copy Number Regions"
         ],
+        "description": "Get significant copy number alteration regions in a study",
+        "operationId": "getSignificantCopyNumberRegionsUsingGET",
         "parameters": [
           {
-            "description": "Study ID e.g. lgg_ucsf_2014",
-            "in": "path",
             "name": "studyId",
-            "required": true,
-            "type": "string"
-          },
-          {
-            "description": "Patient ID e.g. P01",
             "in": "path",
-            "name": "patientId",
+            "description": "Study ID e.g. acc_tcga",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
             "name": "projection",
+            "in": "query",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
             "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "maximum": 10000000,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
           },
           {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
             "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "eventType",
-              "startNumberOfDaysSinceDiagnosis",
-              "endNumberOfDaysSinceDiagnosis"
-            ],
-            "in": "query",
             "name": "sortBy",
+            "in": "query",
+            "description": "Name of the property that the result list is sorted by",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "enum": [
+                "chromosome",
+                "cytoband",
+                "widePeakStart",
+                "widePeakEnd",
+                "qValue",
+                "amp"
+              ]
+            }
           },
           {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
             "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
+            }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalEvent"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/Gistic"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Clinical Events"
-        ],
-        "description": "Get all clinical events of a patient in a study",
-        "operationId": "getAllClinicalEventsOfPatientInStudyUsingGET"
+        }
       }
     },
-    "/api/studies/{studyId}/patients/{patientId}/resource-data": {
+    "/api/studies/{studyId}/samples/{sampleId}/resource-data": {
       "get": {
-        "produces": [
-          "application/json"
+        "tags": [
+          "Resource Data"
         ],
+        "description": "Get all resource data of a sample in a study",
+        "operationId": "getAllResourceDataOfSampleInStudyUsingGET",
         "parameters": [
           {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
             "name": "studyId",
+            "in": "path",
+            "description": "Study ID e.g. acc_tcga",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "description": "Patient ID e.g. TCGA-OR-A5J2",
+            "name": "sampleId",
             "in": "path",
-            "name": "patientId",
+            "description": "Sample ID e.g. TCGA-OR-A5J2-01",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "description": "Resource ID",
-            "in": "query",
             "name": "resourceId",
+            "in": "query",
+            "description": "Resource ID",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
             "name": "projection",
+            "in": "query",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
             "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "maximum": 10000000,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
           },
           {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
             "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "ResourceId",
-              "url"
-            ],
-            "in": "query",
             "name": "sortBy",
+            "in": "query",
+            "description": "Name of the property that the result list is sorted by",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "enum": [
+                "ResourceId",
+                "url"
+              ]
+            }
           },
           {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
             "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
+            }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ResourceData"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ResourceData"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Resource Data"
-        ],
-        "description": "Get all resource data of a patient in a study",
-        "operationId": "getAllResourceDataOfPatientInStudyUsingGET"
+        }
       }
     },
-    "/api/studies/{studyId}/resource-data": {
+    "/api/studies/{studyId}/resource-definitions": {
       "get": {
-        "produces": [
-          "application/json"
+        "tags": [
+          "Resource Definitions"
         ],
+        "description": "Get all resource definitions in the specified study",
+        "operationId": "getAllResourceDefinitionsInStudyUsingGET",
         "parameters": [
           {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
             "name": "studyId",
+            "in": "path",
+            "description": "Study ID e.g. acc_tcga",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "description": "Resource ID",
+            "name": "projection",
             "in": "query",
-            "name": "resourceId",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "default": "SUMMARY",
             "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
-            "name": "projection",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
             "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "maximum": 10000000,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
           },
           {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
             "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "ResourceId",
-              "url"
-            ],
-            "in": "query",
             "name": "sortBy",
+            "in": "query",
+            "description": "Name of the property that the result list is sorted by",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "enum": [
+                "resourceId",
+                "displayName",
+                "description",
+                "resourceType",
+                "priority",
+                "openByDefault",
+                "studyId"
+              ]
+            }
           },
           {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
             "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
+            }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ResourceData"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ResourceDefinition"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Resource Data"
-        ],
-        "description": "Get all resource data for a study",
-        "operationId": "getAllStudyResourceDataInStudyUsingGET"
+        }
       }
     },
-    "/api/studies/{studyId}/resource-data-all": {
+    "/api/studies/{studyId}/resource-definitions/{resourceId}": {
       "get": {
-        "produces": [
-          "application/json"
-        ],
+        "tags": [
+          "Resource Definitions"
+        ],
+        "description": "Get specified resource definition",
+        "operationId": "getResourceDefinitionInStudyUsingGET",
         "parameters": [
           {
+            "name": "studyId",
+            "in": "path",
             "description": "Study ID e.g. acc_tcga",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "name": "resourceId",
             "in": "path",
+            "description": "Resource ID",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/ResourceDefinition"
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    "/api/studies/{studyId}/resource-data": {
+      "get": {
+        "tags": [
+          "Resource Data"
+        ],
+        "description": "Get all resource data for a study",
+        "operationId": "getAllStudyResourceDataInStudyUsingGET",
+        "parameters": [
+          {
             "name": "studyId",
+            "in": "path",
+            "description": "Study ID e.g. acc_tcga",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "description": "Resource ID",
-            "in": "query",
             "name": "resourceId",
+            "in": "query",
+            "description": "Resource ID",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
             "name": "projection",
+            "in": "query",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
             "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "maximum": 10000000,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
           },
           {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
             "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "ResourceId",
-              "url"
-            ],
-            "in": "query",
             "name": "sortBy",
+            "in": "query",
+            "description": "Name of the property that the result list is sorted by",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "enum": [
+                "ResourceId",
+                "url"
+              ]
+            }
           },
           {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
             "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
+            }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ResourceData"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ResourceData"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Resource Data"
-        ],
-        "description": "Get all resource data for for all patients and all samples within a study",
-        "operationId": "getAllStudyResourceDataInStudyPatientSampleUsingGET"
+        }
       }
     },
-    "/api/studies/{studyId}/resource-definitions": {
+    "/api/studies/{studyId}/resource-data-all": {
       "get": {
-        "produces": [
-          "application/json"
+        "tags": [
+          "Resource Data"
         ],
+        "description": "Get all resource data for for all patients and all samples within a study",
+        "operationId": "getAllStudyResourceDataInStudyPatientSampleUsingGET",
         "parameters": [
           {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
             "name": "studyId",
+            "in": "path",
+            "description": "Study ID e.g. acc_tcga",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
+            "name": "resourceId",
             "in": "query",
-            "name": "projection",
+            "description": "Resource ID",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
+            "name": "projection",
             "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
-            "name": "pageSize",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
+            "name": "pageSize",
             "in": "query",
-            "minimum": 0,
-            "name": "pageNumber",
+            "description": "Page size of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "maximum": 10000000,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
           },
           {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "resourceId",
-              "displayName",
-              "description",
-              "resourceType",
-              "priority",
-              "openByDefault",
-              "studyId"
-            ],
+            "name": "pageNumber",
             "in": "query",
-            "name": "sortBy",
+            "description": "Page number of the result list",
             "required": false,
-            "type": "string"
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
+            "name": "sortBy",
             "in": "query",
-            "name": "direction",
+            "description": "Name of the property that the result list is sorted by",
             "required": false,
-            "type": "string"
-          }
-        ],
-        "responses": {
-          "200": {
-            "description": "OK",
             "schema": {
-              "items": {
-                "$ref": "#/definitions/ResourceDefinition"
-              },
-              "type": "array"
+              "type": "string",
+              "enum": [
+                "ResourceId",
+                "url"
+              ]
             }
-          }
-        },
-        "tags": [
-          "Resource Definitions"
-        ],
-        "description": "Get all resource definitions in the specified study",
-        "operationId": "getAllResourceDefinitionsInStudyUsingGET"
-      }
-    },
-    "/api/studies/{studyId}/resource-definitions/{resourceId}": {
-      "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [
-          {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
-            "name": "studyId",
-            "required": true,
-            "type": "string"
           },
           {
-            "description": "Resource ID",
-            "in": "path",
-            "name": "resourceId",
-            "required": true,
-            "type": "string"
+            "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
+            "required": false,
+            "schema": {
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
+            }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "$ref": "#/definitions/ResourceDefinition"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ResourceData"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Resource Definitions"
-        ],
-        "description": "Get specified resource definition",
-        "operationId": "getResourceDefinitionInStudyUsingGET"
+        }
       }
     },
-    "/api/studies/{studyId}/samples/{sampleId}/resource-data": {
+    "/api/studies/{studyId}/patients/{patientId}/resource-data": {
       "get": {
-        "produces": [
-          "application/json"
+        "tags": [
+          "Resource Data"
         ],
+        "description": "Get all resource data of a patient in a study",
+        "operationId": "getAllResourceDataOfPatientInStudyUsingGET",
         "parameters": [
           {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
             "name": "studyId",
+            "in": "path",
+            "description": "Study ID e.g. acc_tcga",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "description": "Sample ID e.g. TCGA-OR-A5J2-01",
+            "name": "patientId",
             "in": "path",
-            "name": "sampleId",
+            "description": "Patient ID e.g. TCGA-OR-A5J2",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "description": "Resource ID",
-            "in": "query",
             "name": "resourceId",
+            "in": "query",
+            "description": "Resource ID",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
             "name": "projection",
+            "in": "query",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
             "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "maximum": 10000000,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
           },
           {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
             "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "ResourceId",
-              "url"
-            ],
-            "in": "query",
             "name": "sortBy",
+            "in": "query",
+            "description": "Name of the property that the result list is sorted by",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "enum": [
+                "ResourceId",
+                "url"
+              ]
+            }
           },
           {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
             "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
+            }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ResourceData"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ResourceData"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Resource Data"
-        ],
-        "description": "Get all resource data of a sample in a study",
-        "operationId": "getAllResourceDataOfSampleInStudyUsingGET"
+        }
       }
     },
-    "/api/studies/{studyId}/significant-copy-number-regions": {
+    "/api/studies/{studyId}/patients/{patientId}/clinical-events": {
       "get": {
-        "produces": [
-          "application/json"
+        "tags": [
+          "Clinical Events"
         ],
+        "description": "Get all clinical events of a patient in a study",
+        "operationId": "getAllClinicalEventsOfPatientInStudyUsingGET",
         "parameters": [
           {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
             "name": "studyId",
+            "in": "path",
+            "description": "Study ID e.g. lgg_ucsf_2014",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "name": "patientId",
+            "in": "path",
+            "description": "Patient ID e.g. P01",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
             "name": "projection",
+            "in": "query",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
             "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "maximum": 10000000,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
           },
           {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
             "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "chromosome",
-              "cytoband",
-              "widePeakStart",
-              "widePeakEnd",
-              "qValue",
-              "amp"
-            ],
-            "in": "query",
             "name": "sortBy",
+            "in": "query",
+            "description": "Name of the property that the result list is sorted by",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "enum": [
+                "eventType",
+                "startNumberOfDaysSinceDiagnosis",
+                "endNumberOfDaysSinceDiagnosis"
+              ]
+            }
           },
           {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
             "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
+            }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/Gistic"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalEvent"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Significant Copy Number Regions"
-        ],
-        "description": "Get significant copy number alteration regions in a study",
-        "operationId": "getSignificantCopyNumberRegionsUsingGET"
+        }
       }
     },
-    "/api/studies/{studyId}/significantly-mutated-genes": {
+    "/api/studies/{studyId}/clinical-events": {
       "get": {
-        "produces": [
-          "application/json"
+        "tags": [
+          "Clinical Events"
         ],
+        "description": "Get all clinical events in a study",
+        "operationId": "getAllClinicalEventsInStudyUsingGET",
         "parameters": [
           {
-            "description": "Study ID e.g. acc_tcga",
-            "in": "path",
             "name": "studyId",
+            "in": "path",
+            "description": "Study ID e.g. lgg_ucsf_2014",
             "required": true,
-            "type": "string"
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "default": "SUMMARY",
-            "description": "Level of detail of the response",
-            "enum": [
-              "ID",
-              "SUMMARY",
-              "DETAILED",
-              "META"
-            ],
-            "in": "query",
             "name": "projection",
+            "in": "query",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "default": 10000000,
-            "description": "Page size of the result list",
-            "format": "int32",
-            "in": "query",
-            "maximum": 10000000,
-            "minimum": 1,
             "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "maximum": 10000000,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
           },
           {
-            "default": 0,
-            "description": "Page number of the result list",
-            "format": "int32",
-            "in": "query",
-            "minimum": 0,
             "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list",
             "required": false,
-            "type": "integer"
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
+            }
           },
           {
-            "description": "Name of the property that the result list is sorted by",
-            "enum": [
-              "entrezGeneId",
-              "hugoGeneSymbol",
-              "rank",
-              "numberOfMutations",
-              "pValue",
-              "qValue"
-            ],
-            "in": "query",
             "name": "sortBy",
+            "in": "query",
+            "description": "Name of the property that the result list is sorted by",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "enum": [
+                "eventType",
+                "startNumberOfDaysSinceDiagnosis",
+                "endNumberOfDaysSinceDiagnosis"
+              ]
+            }
           },
           {
-            "default": "ASC",
-            "description": "Direction of the sort",
-            "enum": [
-              "ASC",
-              "DESC"
-            ],
-            "in": "query",
             "name": "direction",
+            "in": "query",
+            "description": "Direction of the sort",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "ASC",
+              "enum": [
+                "ASC",
+                "DESC"
+              ]
+            }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/MutSig"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ClinicalEvent"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Significantly Mutated Genes"
-        ],
-        "description": "Get significantly mutated genes in a study",
-        "operationId": "getSignificantlyMutatedGenesUsingGET"
+        }
       }
     },
-    "/api/survival-data/fetch": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+    "/api/reference-genome-genes/{genomeName}": {
+      "get": {
+        "tags": [
+          "Reference Genome Genes"
         ],
+        "description": "Get all reference genes",
+        "operationId": "getAllReferenceGenomeGenesUsingGET",
         "parameters": [
           {
-            "in": "body",
-            "name": "survivalRequest",
+            "name": "genomeName",
+            "in": "path",
+            "description": "Name of Reference Genome hg19",
+            "required": true,
             "schema": {
-              "$ref": "#/definitions/SurvivalRequest"
+              "type": "string"
             }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/ClinicalData"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/ReferenceGenomeGene"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Survival"
-        ],
-        "description": "Fetch survival data",
-        "operationId": "fetchSurvivalDataUsingPOST"
+        }
       }
     },
-    "/api/timestamps": {
+    "/api/reference-genome-genes/{genomeName}/{geneId}": {
       "get": {
-        "produces": [
-          "application/json"
-        ],
-        "parameters": [],
-        "responses": {
-          "200": {
-            "description": "OK",
-            "schema": {
-              "type": "object"
-            }
-          }
-        },
         "tags": [
-          "Timestamps"
-        ],
-        "description": "Get the last time each static resource was updated",
-        "operationId": "getAllTimestampsUsingGET"
-      }
-    },
-    "/api/treatments/display-patient": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+          "Reference Genome Genes"
         ],
+        "description": "Get a gene of a reference genome of interest",
+        "operationId": "getReferenceGenomeGeneUsingGET",
         "parameters": [
           {
-            "default": "Agent",
-            "enum": [
-              "Agent",
-              "AgentClass",
-              "AgentTarget"
-            ],
-            "in": "query",
-            "name": "tier",
-            "required": false,
-            "type": "string"
+            "name": "genomeName",
+            "in": "path",
+            "description": "Name of Reference Genome hg19",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
           },
           {
-            "in": "body",
-            "name": "studyIds",
+            "name": "geneId",
+            "in": "path",
+            "description": "Entrez Gene ID 207",
             "required": true,
             "schema": {
-              "description": "List of Study IDs",
-              "items": {
-                "maxLength": 10000000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array",
-              "uniqueItems": true
+              "type": "integer",
+              "format": "int32"
             }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "type": "boolean"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/ReferenceGenomeGene"
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Treatments"
-        ],
-        "description": "Should patient level treatments be displayed",
-        "operationId": "getContainsTreatmentDataUsingPOST"
+        }
       }
     },
-    "/api/treatments/display-sample": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+    "/api/genesets": {
+      "get": {
+        "tags": [
+          "Gene Sets"
         ],
+        "description": "Get all gene sets",
+        "operationId": "getAllGenesetsUsingGET",
         "parameters": [
           {
-            "default": "Agent",
-            "enum": [
-              "Agent",
-              "AgentClass",
-              "AgentTarget"
-            ],
+            "name": "projection",
             "in": "query",
-            "name": "tier",
+            "description": "Level of detail of the response",
             "required": false,
-            "type": "string"
+            "schema": {
+              "type": "string",
+              "default": "SUMMARY",
+              "enum": [
+                "ID",
+                "SUMMARY",
+                "DETAILED",
+                "META"
+              ]
+            }
           },
           {
-            "in": "body",
-            "name": "studyIds",
-            "required": true,
+            "name": "pageSize",
+            "in": "query",
+            "description": "Page size of the result list",
+            "required": false,
             "schema": {
-              "description": "List of Study IDs",
-              "items": {
-                "maxLength": 10000000,
-                "minLength": 1,
-                "type": "string"
-              },
-              "maxItems": 10000000,
-              "minItems": 1,
-              "type": "array",
-              "uniqueItems": true
+              "maximum": 2147483647,
+              "minimum": 1,
+              "type": "integer",
+              "format": "int32",
+              "default": 10000000
+            }
+          },
+          {
+            "name": "pageNumber",
+            "in": "query",
+            "description": "Page number of the result list",
+            "required": false,
+            "schema": {
+              "minimum": 0,
+              "type": "integer",
+              "format": "int32",
+              "default": 0
             }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "type": "boolean"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/Geneset"
+                  }
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Treatments"
-        ],
-        "description": "Should sample level treatments be displayed",
-        "operationId": "getContainsSampleTreatmentDataUsingPOST"
+        }
       }
     },
-    "/api/treatments/patient": {
-      "post": {
-        "consumes": [
-          "application/json"
-        ],
-        "produces": [
-          "application/json"
+    "/api/genesets/{genesetId}": {
+      "get": {
+        "tags": [
+          "Gene Sets"
         ],
+        "description": "Get a gene set",
+        "operationId": "getGenesetUsingGET",
         "parameters": [
           {
-            "default": "Agent",
-            "enum": [
-              "Agent",
-              "AgentClass",
-              "AgentTarget"
-            ],
-            "in": "query",
-            "name": "tier",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
+            "name": "genesetId",
+            "in": "path",
+            "description": "Gene set ID e.g. GNF2_ZAP70",
+            "required": true,
             "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+              "type": "string"
             }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
-            "schema": {
-              "items": {
-                "$ref": "#/definitions/PatientTreatmentRow"
-              },
-              "type": "array"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/Geneset"
+                }
+              }
             }
           }
-        },
-        "tags": [
-          "Treatments"
-        ],
-        "description": "Get all patient level treatments",
-        "operationId": "getAllPatientTreatmentsUsingPOST"
+        }
       }
     },
-    "/api/treatments/sample": {
-      "post": {
-        "consumes": [
-          "application/json"
+    "/api/genesets/version": {
+      "get": {
+        "tags": [
+          "Gene Sets"
         ],
-        "produces": [
-          "application/json"
+        "description": "Get the geneset version",
+        "operationId": "getGenesetVersionUsingGET",
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "string"
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    "/api/data-access-tokens/{token}": {
+      "get": {
+        "tags": [
+          "Data Access Tokens"
         ],
+        "description": "Retrieve an existing data access token",
+        "operationId": "getDataAccessTokenUsingGET",
         "parameters": [
           {
-            "default": "Agent",
-            "enum": [
-              "Agent",
-              "AgentClass",
-              "AgentTarget"
-            ],
-            "in": "query",
-            "name": "tier",
-            "required": false,
-            "type": "string"
-          },
-          {
-            "in": "body",
-            "name": "studyViewFilter",
+            "name": "token",
+            "in": "path",
+            "description": "token",
+            "required": true,
             "schema": {
-              "$ref": "#/definitions/StudyViewFilter"
+              "type": "string"
             }
           }
         ],
         "responses": {
           "200": {
             "description": "OK",
+            "content": {
+              "*/*": {
+                "schema": {
+                  "$ref": "#/components/schemas/DataAccessToken"
+                }
+              }
+            }
+          }
+        }
+      },
+      "delete": {
+        "tags": [
+          "Data Access Tokens"
+        ],
+        "description": "Delete a data access token",
+        "operationId": "revokeDataAccessTokenUsingDELETE",
+        "parameters": [
+          {
+            "name": "token",
+            "in": "path",
+            "description": "token",
+            "required": true,
             "schema": {
-              "items": {
-                "$ref": "#/definitions/SampleTreatmentRow"
-              },
-              "type": "array"
+              "type": "string"
             }
           }
-        },
+        ],
+        "responses": {
+          "200": {
+            "description": "OK"
+          }
+        }
+      }
+    },
+    "/api/data-access-token": {
+      "get": {
         "tags": [
-          "Treatments"
+          "Data Access Tokens"
         ],
-        "description": "Get all sample level treatments",
-        "operationId": "getAllSampleTreatmentsUsingPOST"
+        "description": "Create a new data access token",
+        "operationId": "downloadDataAccessTokenUsingGET",
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "*/*": {
+                "schema": {
+                  "type": "string"
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    "/api/data-access-token/oauth2": {
+      "get": {
+        "tags": [
+          "Data Access Tokens"
+        ],
+        "operationId": "downloadOAuth2DataAccessTokenUsingGET",
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "*/*": {
+                "schema": {
+                  "type": "string"
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    "/api/cache": {
+      "delete": {
+        "tags": [
+          "Cache"
+        ],
+        "summary": "Clear and reinitialize caches",
+        "operationId": "clearAllCachesUsingDELETE",
+        "parameters": [
+          {
+            "name": "X-API-KEY",
+            "in": "header",
+            "description": "Secret API key passed in HTTP header. The key is configured in application.properties of the portal instance.",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "name": "springManagedCache",
+            "in": "query",
+            "description": "Clear Spring-managed caches",
+            "required": false,
+            "schema": {
+              "type": "boolean",
+              "default": true
+            }
+          }
+        ],
+        "responses": {
+          "200": {
+            "description": "OK",
+            "content": {
+              "text/plain": {
+                "schema": {
+                  "type": "string"
+                }
+              }
+            }
+          }
+        }
       }
     }
   },
-  "definitions": {
-    "AlterationCountByGene": {
-      "properties": {
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "entrezGeneIds": {
-          "items": {
-            "format": "int32",
-            "type": "integer"
-          },
-          "type": "array"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "hugoGeneSymbols": {
-          "items": {
-            "type": "string"
-          },
-          "type": "array"
-        },
-        "matchingGenePanelIds": {
-          "items": {
-            "type": "string"
+  "components": {
+    "schemas": {
+      "AlterationFilter": {
+        "type": "object",
+        "properties": {
+          "includeGermline": {
+            "type": "boolean"
           },
-          "type": "array",
-          "uniqueItems": true
-        },
-        "numberOfAlteredCases": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "numberOfProfiledCases": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "qValue": {
-          "type": "number"
-        },
-        "totalCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "uniqueEventKey": {
-          "type": "string"
-        }
-      },
-      "type": "object"
-    },
-    "AlterationCountByStructuralVariant": {
-      "properties": {
-        "entrezGeneIds": {
-          "items": {
-            "format": "int32",
-            "type": "integer"
-          },
-          "type": "array"
-        },
-        "gene1EntrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "gene1HugoGeneSymbol": {
-          "type": "string"
-        },
-        "gene2EntrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "gene2HugoGeneSymbol": {
-          "type": "string"
-        },
-        "hugoGeneSymbols": {
-          "items": {
-            "type": "string"
+          "includeSomatic": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "matchingGenePanelIds": {
-          "items": {
-            "type": "string"
+          "includeUnknownStatus": {
+            "type": "boolean"
           },
-          "type": "array",
-          "uniqueItems": true
-        },
-        "numberOfAlteredCases": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "numberOfProfiledCases": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "totalCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "uniqueEventKey": {
-          "type": "string"
-        }
-      },
-      "type": "object"
-    },
-    "AlterationEnrichment": {
-      "properties": {
-        "counts": {
-          "items": {
-            "$ref": "#/definitions/CountSummary"
+          "includeDriver": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "cytoband": {
-          "type": "string"
-        },
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "pValue": {
-          "type": "number"
-        }
-      },
-      "required": [
-        "counts",
-        "entrezGeneId",
-        "hugoGeneSymbol"
-      ],
-      "type": "object"
-    },
-    "AlterationFilter": {
-      "properties": {
-        "copyNumberAlterationEventTypes": {
-          "additionalProperties": {
+          "includeVUS": {
             "type": "boolean"
           },
-          "type": "object"
-        },
-        "includeDriver": {
-          "type": "boolean"
-        },
-        "includeGermline": {
-          "type": "boolean"
-        },
-        "includeSomatic": {
-          "type": "boolean"
-        },
-        "includeUnknownOncogenicity": {
-          "type": "boolean"
-        },
-        "includeUnknownStatus": {
-          "type": "boolean"
-        },
-        "includeUnknownTier": {
-          "type": "boolean"
-        },
-        "includeVUS": {
-          "type": "boolean"
-        },
-        "mutationEventTypes": {
-          "additionalProperties": {
+          "includeUnknownOncogenicity": {
             "type": "boolean"
           },
-          "type": "object"
-        },
-        "structuralVariants": {
-          "type": "boolean"
-        },
-        "tiersBooleanMap": {
-          "additionalProperties": {
+          "tiersBooleanMap": {
+            "type": "object",
+            "additionalProperties": {
+              "type": "boolean"
+            }
+          },
+          "includeUnknownTier": {
             "type": "boolean"
           },
-          "type": "object"
-        }
-      },
-      "type": "object"
-    },
-    "AndedPatientTreatmentFilters": {
-      "properties": {
-        "filters": {
-          "items": {
-            "$ref": "#/definitions/OredPatientTreatmentFilters"
+          "mutationEventTypes": {
+            "type": "object",
+            "additionalProperties": {
+              "type": "boolean"
+            }
           },
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
-    "AndedSampleTreatmentFilters": {
-      "properties": {
-        "filters": {
-          "items": {
-            "$ref": "#/definitions/OredSampleTreatmentFilters"
+          "copyNumberAlterationEventTypes": {
+            "type": "object",
+            "additionalProperties": {
+              "type": "boolean"
+            }
           },
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
-    "BinsGeneratorConfig": {
-      "properties": {
-        "anchorValue": {
-          "type": "number"
-        },
-        "binSize": {
-          "type": "number"
-        }
-      },
-      "type": "object"
-    },
-    "CaseListDataCount": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "label": {
-          "type": "string"
-        },
-        "value": {
-          "type": "string"
+          "structuralVariants": {
+            "type": "boolean"
+          }
         }
       },
-      "type": "object"
-    },
-    "ClinicalAttribute": {
-      "properties": {
-        "clinicalAttributeId": {
-          "type": "string"
-        },
-        "datatype": {
-          "type": "string"
-        },
-        "description": {
-          "type": "string"
-        },
-        "displayName": {
-          "type": "string"
-        },
-        "patientAttribute": {
-          "type": "boolean"
-        },
-        "priority": {
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
+      "AndedPatientTreatmentFilters": {
+        "type": "object",
+        "properties": {
+          "filters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/OredPatientTreatmentFilters"
+            }
+          }
         }
       },
-      "required": [
-        "clinicalAttributeId",
-        "displayName",
-        "patientAttribute",
-        "studyId"
-      ],
-      "type": "object"
-    },
-    "ClinicalAttributeCount": {
-      "properties": {
-        "clinicalAttributeId": {
-          "type": "string"
-        },
-        "count": {
-          "format": "int32",
-          "type": "integer"
+      "AndedSampleTreatmentFilters": {
+        "type": "object",
+        "properties": {
+          "filters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/OredSampleTreatmentFilters"
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "ClinicalAttributeCountFilter": {
-      "description": "List of SampleIdentifiers or Sample List ID",
-      "properties": {
-        "sampleIdentifiers": {
-          "items": {
-            "$ref": "#/definitions/SampleIdentifier"
-          },
-          "maxItems": 10000000,
-          "minItems": 1,
-          "type": "array"
-        },
-        "sampleListId": {
-          "type": "string"
+      "ClinicalDataFilter": {
+        "type": "object",
+        "properties": {
+          "values": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/DataFilterValue"
+            }
+          },
+          "attributeId": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "ClinicalData": {
-      "properties": {
-        "clinicalAttribute": {
-          "$ref": "#/definitions/ClinicalAttribute"
-        },
-        "clinicalAttributeId": {
-          "type": "string"
-        },
-        "patientAttribute": {
-          "type": "boolean"
-        },
-        "patientId": {
-          "type": "string"
-        },
-        "sampleId": {
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "uniquePatientKey": {
-          "type": "string"
-        },
-        "uniqueSampleKey": {
-          "type": "string"
-        },
-        "value": {
-          "type": "string"
+      "DataFilter": {
+        "type": "object",
+        "properties": {
+          "values": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/DataFilterValue"
+            }
+          }
         }
       },
-      "required": [
-        "clinicalAttributeId",
-        "patientId",
-        "studyId"
-      ],
-      "type": "object"
-    },
-    "ClinicalDataBin": {
-      "properties": {
-        "attributeId": {
-          "type": "string"
-        },
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "end": {
-          "type": "number"
-        },
-        "specialValue": {
-          "type": "string"
-        },
-        "start": {
-          "type": "number"
+      "DataFilterValue": {
+        "type": "object",
+        "properties": {
+          "start": {
+            "type": "number"
+          },
+          "end": {
+            "type": "number"
+          },
+          "value": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "ClinicalDataBinCountFilter": {
-      "description": "Clinical data bin count filter",
-      "properties": {
-        "attributes": {
-          "items": {
-            "$ref": "#/definitions/ClinicalDataBinFilter"
-          },
-          "type": "array"
-        },
-        "studyViewFilter": {
-          "$ref": "#/definitions/StudyViewFilter"
+      "GeneFilter": {
+        "type": "object",
+        "properties": {
+          "molecularProfileIds": {
+            "uniqueItems": true,
+            "type": "array",
+            "items": {
+              "type": "string"
+            }
+          },
+          "geneQueries": {
+            "type": "array",
+            "items": {
+              "type": "array",
+              "items": {
+                "$ref": "#/components/schemas/GeneFilterQuery"
+              }
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "ClinicalDataBinFilter": {
-      "properties": {
-        "attributeId": {
-          "type": "string"
-        },
-        "binMethod": {
-          "enum": [
-            "MEDIAN",
-            "QUARTILE",
-            "CUSTOM",
-            "GENERATE"
-          ],
-          "type": "string"
-        },
-        "binsGeneratorConfig": {
-          "$ref": "#/definitions/BinsGeneratorConfig"
-        },
-        "customBins": {
-          "items": {
-            "type": "number"
+      "GeneFilterQuery": {
+        "type": "object",
+        "properties": {
+          "includeGermline": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "disableLogScale": {
-          "type": "boolean"
-        },
-        "end": {
-          "type": "number"
-        },
-        "start": {
-          "type": "number"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalDataCount": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "value": {
-          "type": "string"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalDataCountFilter": {
-      "description": "Clinical data count filter",
-      "properties": {
-        "attributes": {
-          "items": {
-            "$ref": "#/definitions/ClinicalDataFilter"
-          },
-          "type": "array"
-        },
-        "studyViewFilter": {
-          "$ref": "#/definitions/StudyViewFilter"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalDataCountItem": {
-      "properties": {
-        "attributeId": {
-          "type": "string"
-        },
-        "counts": {
-          "items": {
-            "$ref": "#/definitions/ClinicalDataCount"
+          "includeSomatic": {
+            "type": "boolean"
           },
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalDataEnrichment": {
-      "properties": {
-        "clinicalAttribute": {
-          "$ref": "#/definitions/ClinicalAttribute"
-        },
-        "method": {
-          "type": "string"
-        },
-        "pValue": {
-          "type": "number"
-        },
-        "score": {
-          "type": "number"
-        }
-      },
-      "required": [
-        "clinicalAttribute",
-        "method",
-        "pValue",
-        "score"
-      ],
-      "type": "object"
-    },
-    "ClinicalDataFilter": {
-      "properties": {
-        "attributeId": {
-          "type": "string"
-        },
-        "values": {
-          "items": {
-            "$ref": "#/definitions/DataFilterValue"
+          "includeUnknownStatus": {
+            "type": "boolean"
           },
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalEvent": {
-      "properties": {
-        "attributes": {
-          "items": {
-            "$ref": "#/definitions/ClinicalEventData"
+          "includeDriver": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "endNumberOfDaysSinceDiagnosis": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "eventType": {
-          "type": "string"
-        },
-        "patientId": {
-          "type": "string"
-        },
-        "startNumberOfDaysSinceDiagnosis": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "uniquePatientKey": {
-          "type": "string"
-        },
-        "uniqueSampleKey": {
-          "type": "string"
-        }
-      },
-      "required": [
-        "eventType",
-        "patientId",
-        "studyId"
-      ],
-      "type": "object"
-    },
-    "ClinicalEventAttributeRequest": {
-      "description": "clinical events Request",
-      "properties": {
-        "clinicalEventRequests": {
-          "items": {
-            "$ref": "#/definitions/ClinicalEventRequest"
-          },
-          "type": "array",
-          "uniqueItems": true
-        },
-        "patientIdentifiers": {
-          "items": {
-            "$ref": "#/definitions/PatientIdentifier"
+          "includeVUS": {
+            "type": "boolean"
           },
-          "maxItems": 10000000,
-          "minItems": 1,
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalEventData": {
-      "properties": {
-        "key": {
-          "type": "string"
-        },
-        "value": {
-          "type": "string"
-        }
-      },
-      "required": [
-        "key",
-        "value"
-      ],
-      "type": "object"
-    },
-    "ClinicalEventRequest": {
-      "properties": {
-        "attributes": {
-          "items": {
-            "$ref": "#/definitions/ClinicalEventData"
+          "includeUnknownOncogenicity": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "eventType": {
-          "type": "string"
-        }
-      },
-      "required": [
-        "eventType"
-      ],
-      "type": "object"
-    },
-    "ClinicalEventRequestIdentifier": {
-      "properties": {
-        "clinicalEventRequests": {
-          "items": {
-            "$ref": "#/definitions/ClinicalEventRequest"
-          },
-          "maxItems": 10000000,
-          "minItems": 0,
-          "type": "array",
-          "uniqueItems": true
-        },
-        "position": {
-          "enum": [
-            "FIRST",
-            "LAST"
-          ],
-          "type": "string"
-        }
-      },
-      "required": [
-        "position"
-      ],
-      "type": "object"
-    },
-    "ClinicalEventSample": {
-      "properties": {
-        "patientId": {
-          "type": "string"
-        },
-        "sampleId": {
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "timeTaken": {
-          "format": "int32",
-          "type": "integer"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalEventTypeCount": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "eventType": {
-          "type": "string"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalViolinPlotBoxData": {
-      "properties": {
-        "median": {
-          "format": "double",
-          "type": "number"
-        },
-        "q1": {
-          "format": "double",
-          "type": "number"
-        },
-        "q3": {
-          "format": "double",
-          "type": "number"
-        },
-        "whiskerLower": {
-          "format": "double",
-          "type": "number"
-        },
-        "whiskerUpper": {
-          "format": "double",
-          "type": "number"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalViolinPlotData": {
-      "properties": {
-        "axisEnd": {
-          "format": "double",
-          "type": "number"
-        },
-        "axisStart": {
-          "format": "double",
-          "type": "number"
-        },
-        "rows": {
-          "items": {
-            "$ref": "#/definitions/ClinicalViolinPlotRowData"
+          "tiersBooleanMap": {
+            "type": "object",
+            "additionalProperties": {
+              "type": "boolean"
+            }
           },
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalViolinPlotIndividualPoint": {
-      "properties": {
-        "sampleId": {
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "value": {
-          "format": "double",
-          "type": "number"
-        }
-      },
-      "type": "object"
-    },
-    "ClinicalViolinPlotRowData": {
-      "properties": {
-        "boxData": {
-          "$ref": "#/definitions/ClinicalViolinPlotBoxData"
-        },
-        "category": {
-          "type": "string"
-        },
-        "curveData": {
-          "items": {
-            "format": "double",
-            "type": "number"
+          "includeUnknownTier": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "individualPoints": {
-          "items": {
-            "$ref": "#/definitions/ClinicalViolinPlotIndividualPoint"
+          "hugoGeneSymbol": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "numSamples": {
-          "format": "int32",
-          "type": "integer"
-        }
-      },
-      "type": "object"
-    },
-    "CoExpression": {
-      "properties": {
-        "geneticEntityId": {
-          "type": "string"
-        },
-        "geneticEntityType": {
-          "enum": [
-            "GENE",
-            "GENESET",
-            "PHOSPHOPROTEIN",
-            "GENERIC_ASSAY"
-          ],
-          "type": "string"
-        },
-        "pValue": {
-          "type": "number"
-        },
-        "spearmansCorrelation": {
-          "type": "number"
+          "entrezGeneId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "alterations": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "enum": [
+                "AMP",
+                "GAIN",
+                "DIPLOID",
+                "HETLOSS",
+                "HOMDEL"
+              ]
+            }
+          }
         }
       },
-      "required": [
-        "geneticEntityId",
-        "geneticEntityType",
-        "pValue",
-        "spearmansCorrelation"
-      ],
-      "type": "object"
-    },
-    "CoExpressionFilter": {
-      "description": "List of Sample IDs/Sample List ID and Entrez Gene ID/Gene set ID",
-      "properties": {
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "genesetId": {
-          "type": "string"
-        },
-        "sampleIds": {
-          "items": {
-            "maxLength": 10000000,
-            "minLength": 1,
+      "GenericAssayDataFilter": {
+        "type": "object",
+        "properties": {
+          "values": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/DataFilterValue"
+            }
+          },
+          "stableId": {
             "type": "string"
           },
-          "maxItems": 10000000,
-          "minItems": 1,
-          "type": "array"
-        },
-        "sampleListId": {
-          "type": "string"
+          "profileType": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "CopyNumberCount": {
-      "properties": {
-        "alteration": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "molecularProfileId": {
-          "type": "string"
-        },
-        "numberOfSamples": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "numberOfSamplesWithAlterationInGene": {
-          "format": "int32",
-          "type": "integer"
+      "GenomicDataFilter": {
+        "type": "object",
+        "properties": {
+          "values": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/DataFilterValue"
+            }
+          },
+          "hugoGeneSymbol": {
+            "type": "string"
+          },
+          "profileType": {
+            "type": "string"
+          }
         }
       },
-      "required": [
-        "alteration",
-        "entrezGeneId",
-        "molecularProfileId",
-        "numberOfSamples",
-        "numberOfSamplesWithAlterationInGene"
-      ],
-      "type": "object"
-    },
-    "CopyNumberCountByGene": {
-      "properties": {
-        "alteration": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "cytoband": {
-          "type": "string"
-        },
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "entrezGeneIds": {
-          "items": {
-            "format": "int32",
-            "type": "integer"
-          },
-          "type": "array"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "hugoGeneSymbols": {
-          "items": {
+      "MutationDataFilter": {
+        "required": [
+          "categorization"
+        ],
+        "type": "object",
+        "properties": {
+          "hugoGeneSymbol": {
             "type": "string"
           },
-          "type": "array"
-        },
-        "matchingGenePanelIds": {
-          "items": {
+          "profileType": {
             "type": "string"
           },
-          "type": "array",
-          "uniqueItems": true
-        },
-        "numberOfAlteredCases": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "numberOfProfiledCases": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "qValue": {
-          "type": "number"
-        },
-        "totalCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "uniqueEventKey": {
-          "type": "string"
+          "categorization": {
+            "type": "string",
+            "enum": [
+              "MUTATED",
+              "MUTATION_TYPE"
+            ]
+          },
+          "values": {
+            "type": "array",
+            "items": {
+              "type": "array",
+              "items": {
+                "$ref": "#/components/schemas/DataFilterValue"
+              }
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "CopyNumberCountIdentifier": {
-      "properties": {
-        "alteration": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
+      "OredPatientTreatmentFilters": {
+        "type": "object",
+        "properties": {
+          "filters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/PatientTreatmentFilter"
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "CosmicMutation": {
-      "properties": {
-        "cosmicMutationId": {
-          "type": "string"
-        },
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "keyword": {
-          "type": "string"
-        },
-        "proteinChange": {
-          "type": "string"
+      "OredSampleTreatmentFilters": {
+        "type": "object",
+        "properties": {
+          "filters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/SampleTreatmentFilter"
+            }
+          }
         }
       },
-      "required": [
-        "cosmicMutationId",
-        "count",
-        "proteinChange"
-      ],
-      "type": "object"
-    },
-    "CountSummary": {
-      "properties": {
-        "alteredCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "name": {
-          "type": "string"
-        },
-        "profiledCount": {
-          "format": "int32",
-          "type": "integer"
+      "PatientTreatmentFilter": {
+        "type": "object",
+        "properties": {
+          "treatment": {
+            "type": "string"
+          }
         }
       },
-      "required": [
-        "alteredCount",
-        "name",
-        "profiledCount"
-      ],
-      "type": "object"
-    },
-    "CustomDriverAnnotationReport": {
-      "properties": {
-        "hasBinary": {
-          "type": "boolean"
-        },
-        "tiers": {
-          "items": {
+      "SampleIdentifier": {
+        "type": "object",
+        "properties": {
+          "sampleId": {
             "type": "string"
           },
-          "type": "array",
-          "uniqueItems": true
-        }
-      },
-      "type": "object"
-    },
-    "DataAccessToken": {
-      "properties": {
-        "creation": {
-          "format": "date-time",
-          "type": "string"
-        },
-        "expiration": {
-          "format": "date-time",
-          "type": "string"
-        },
-        "token": {
-          "type": "string"
-        },
-        "username": {
-          "type": "string"
+          "studyId": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "DataFilter": {
-      "properties": {
-        "values": {
-          "items": {
-            "$ref": "#/definitions/DataFilterValue"
+      "SampleTreatmentFilter": {
+        "type": "object",
+        "properties": {
+          "treatment": {
+            "type": "string"
           },
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
-    "DataFilterValue": {
-      "properties": {
-        "end": {
-          "type": "number"
-        },
-        "start": {
-          "type": "number"
-        },
-        "value": {
-          "type": "string"
-        }
-      },
-      "type": "object"
-    },
-    "DensityPlotBin": {
-      "properties": {
-        "binX": {
-          "type": "number"
-        },
-        "binY": {
-          "type": "number"
-        },
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "maxX": {
-          "type": "number"
-        },
-        "maxY": {
-          "type": "number"
-        },
-        "minX": {
-          "type": "number"
-        },
-        "minY": {
-          "type": "number"
+          "time": {
+            "type": "string",
+            "enum": [
+              "Pre",
+              "Post"
+            ]
+          }
         }
       },
-      "type": "object"
-    },
-    "DensityPlotData": {
-      "properties": {
-        "bins": {
-          "items": {
-            "$ref": "#/definitions/DensityPlotBin"
+      "StructuralVariantFilterQuery": {
+        "type": "object",
+        "properties": {
+          "includeGermline": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "pearsonCorr": {
-          "format": "double",
-          "type": "number"
-        },
-        "spearmanCorr": {
-          "format": "double",
-          "type": "number"
-        }
-      },
-      "required": [
-        "bins"
-      ],
-      "type": "object"
-    },
-    "GeneFilter": {
-      "properties": {
-        "geneQueries": {
-          "items": {
-            "items": {
-              "$ref": "#/definitions/GeneFilterQuery"
-            },
-            "type": "array"
+          "includeSomatic": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "molecularProfileIds": {
-          "items": {
-            "type": "string"
+          "includeUnknownStatus": {
+            "type": "boolean"
           },
-          "type": "array",
-          "uniqueItems": true
-        }
-      },
-      "type": "object"
-    },
-    "GeneFilterQuery": {
-      "properties": {
-        "alterations": {
-          "items": {
-            "enum": [
-              "AMP",
-              "GAIN",
-              "DIPLOID",
-              "HETLOSS",
-              "HOMDEL"
-            ],
-            "type": "string"
+          "includeDriver": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "includeDriver": {
-          "type": "boolean"
-        },
-        "includeGermline": {
-          "type": "boolean"
-        },
-        "includeSomatic": {
-          "type": "boolean"
-        },
-        "includeUnknownOncogenicity": {
-          "type": "boolean"
-        },
-        "includeUnknownStatus": {
-          "type": "boolean"
-        },
-        "includeUnknownTier": {
-          "type": "boolean"
-        },
-        "includeVUS": {
-          "type": "boolean"
-        },
-        "tiersBooleanMap": {
-          "additionalProperties": {
+          "includeVUS": {
             "type": "boolean"
           },
-          "type": "object"
-        }
-      },
-      "type": "object"
-    },
-    "GenericAssayBinaryEnrichment": {
-      "properties": {
-        "counts": {
-          "items": {
-            "$ref": "#/definitions/GenericAssayCountSummary"
+          "includeUnknownOncogenicity": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "genericEntityMetaProperties": {
-          "additionalProperties": {
-            "type": "string"
+          "tiersBooleanMap": {
+            "type": "object",
+            "additionalProperties": {
+              "type": "boolean"
+            }
           },
-          "type": "object"
-        },
-        "groupsStatistics": {
-          "items": {
-            "$ref": "#/definitions/GroupStatistics"
+          "includeUnknownTier": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "name": {
-          "type": "string"
-        },
-        "pValue": {
-          "type": "number"
-        },
-        "qValue": {
-          "type": "number"
-        },
-        "stableId": {
-          "type": "string"
+          "gene1Query": {
+            "$ref": "#/components/schemas/StructuralVariantGeneSubQuery"
+          },
+          "gene2Query": {
+            "$ref": "#/components/schemas/StructuralVariantGeneSubQuery"
+          }
         }
       },
-      "required": [
-        "counts",
-        "genericEntityMetaProperties",
-        "groupsStatistics",
-        "name",
-        "pValue",
-        "qValue",
-        "stableId"
-      ],
-      "type": "object"
-    },
-    "GenericAssayCategoricalEnrichment": {
-      "properties": {
-        "genericEntityMetaProperties": {
-          "additionalProperties": {
+      "StructuralVariantGeneSubQuery": {
+        "type": "object",
+        "properties": {
+          "hugoSymbol": {
             "type": "string"
           },
-          "type": "object"
-        },
-        "groupsStatistics": {
-          "items": {
-            "$ref": "#/definitions/GroupStatistics"
+          "entrezId": {
+            "type": "integer",
+            "format": "int32"
           },
-          "type": "array"
-        },
-        "name": {
-          "type": "string"
-        },
-        "pValue": {
-          "type": "number"
-        },
-        "qValue": {
-          "type": "number"
-        },
-        "stableId": {
-          "type": "string"
-        }
-      },
-      "required": [
-        "genericEntityMetaProperties",
-        "groupsStatistics",
-        "name",
-        "pValue",
-        "qValue",
-        "stableId"
-      ],
-      "type": "object"
-    },
-    "GenericAssayCountSummary": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "name": {
-          "type": "string"
-        },
-        "totalCount": {
-          "format": "int32",
-          "type": "integer"
+          "specialValue": {
+            "type": "string",
+            "enum": [
+              "ANY_GENE",
+              "NO_GENE"
+            ]
+          }
         }
       },
-      "required": [
-        "count",
-        "name",
-        "totalCount"
-      ],
-      "type": "object"
-    },
-    "GenericAssayDataBin": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "end": {
-          "type": "number"
-        },
-        "profileType": {
-          "type": "string"
-        },
-        "specialValue": {
-          "type": "string"
-        },
-        "stableId": {
-          "type": "string"
-        },
-        "start": {
-          "type": "number"
-        }
-      },
-      "type": "object"
-    },
-    "GenericAssayDataBinCountFilter": {
-      "description": "Generic assay data bin count filter",
-      "properties": {
-        "genericAssayDataBinFilters": {
-          "items": {
-            "$ref": "#/definitions/GenericAssayDataBinFilter"
-          },
-          "type": "array"
+      "StudyViewFilter": {
+        "type": "object",
+        "properties": {
+          "sampleIdentifiers": {
+            "maxItems": 2147483647,
+            "minItems": 1,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/SampleIdentifier"
+            }
+          },
+          "studyIds": {
+            "maxItems": 2147483647,
+            "minItems": 1,
+            "type": "array",
+            "items": {
+              "maxLength": 2147483647,
+              "minLength": 1,
+              "type": "string"
+            }
+          },
+          "clinicalDataFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalDataFilter"
+            }
+          },
+          "geneFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GeneFilter"
+            }
+          },
+          "structuralVariantFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/StudyViewStructuralVariantFilter"
+            }
+          },
+          "sampleTreatmentFilters": {
+            "$ref": "#/components/schemas/AndedSampleTreatmentFilters"
+          },
+          "sampleTreatmentGroupFilters": {
+            "$ref": "#/components/schemas/AndedSampleTreatmentFilters"
+          },
+          "sampleTreatmentTargetFilters": {
+            "$ref": "#/components/schemas/AndedSampleTreatmentFilters"
+          },
+          "patientTreatmentFilters": {
+            "$ref": "#/components/schemas/AndedPatientTreatmentFilters"
+          },
+          "patientTreatmentGroupFilters": {
+            "$ref": "#/components/schemas/AndedPatientTreatmentFilters"
+          },
+          "patientTreatmentTargetFilters": {
+            "$ref": "#/components/schemas/AndedPatientTreatmentFilters"
+          },
+          "genomicProfiles": {
+            "type": "array",
+            "items": {
+              "type": "array",
+              "items": {
+                "type": "string"
+              }
+            }
+          },
+          "genomicDataFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GenomicDataFilter"
+            }
+          },
+          "genericAssayDataFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GenericAssayDataFilter"
+            }
+          },
+          "caseLists": {
+            "type": "array",
+            "items": {
+              "type": "array",
+              "items": {
+                "type": "string"
+              }
+            }
+          },
+          "customDataFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalDataFilter"
+            }
+          },
+          "alterationFilter": {
+            "$ref": "#/components/schemas/AlterationFilter"
+          },
+          "clinicalEventFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/DataFilter"
+            }
+          },
+          "mutationDataFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/MutationDataFilter"
+            }
+          }
         },
-        "studyViewFilter": {
-          "$ref": "#/definitions/StudyViewFilter"
+        "description": "Study view filter"
+      },
+      "StudyViewStructuralVariantFilter": {
+        "type": "object",
+        "properties": {
+          "molecularProfileIds": {
+            "uniqueItems": true,
+            "type": "array",
+            "items": {
+              "type": "string"
+            }
+          },
+          "structVarQueries": {
+            "type": "array",
+            "items": {
+              "type": "array",
+              "items": {
+                "$ref": "#/components/schemas/StructuralVariantFilterQuery"
+              }
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "GenericAssayDataBinFilter": {
-      "properties": {
-        "binMethod": {
-          "enum": [
-            "MEDIAN",
-            "QUARTILE",
-            "CUSTOM",
-            "GENERATE"
-          ],
-          "type": "string"
-        },
-        "binsGeneratorConfig": {
-          "$ref": "#/definitions/BinsGeneratorConfig"
+      "ClinicalEventSample": {
+        "type": "object",
+        "properties": {
+          "patientId": {
+            "type": "string"
+          },
+          "sampleId": {
+            "type": "string"
+          },
+          "studyId": {
+            "type": "string"
+          },
+          "timeTaken": {
+            "type": "integer",
+            "format": "int32"
+          }
+        }
+      },
+      "SampleTreatmentRow": {
+        "type": "object",
+        "properties": {
+          "time": {
+            "type": "string",
+            "enum": [
+              "Pre",
+              "Post"
+            ]
+          },
+          "treatment": {
+            "type": "string"
+          },
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "samples": {
+            "uniqueItems": true,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalEventSample"
+            }
+          }
+        }
+      },
+      "PatientTreatmentRow": {
+        "type": "object",
+        "properties": {
+          "treatment": {
+            "type": "string"
+          },
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "samples": {
+            "uniqueItems": true,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalEventSample"
+            }
+          }
+        }
+      },
+      "ClinicalEventData": {
+        "required": [
+          "key",
+          "value"
+        ],
+        "type": "object",
+        "properties": {
+          "key": {
+            "type": "string"
+          },
+          "value": {
+            "type": "string"
+          }
+        }
+      },
+      "ClinicalEventRequest": {
+        "required": [
+          "eventType"
+        ],
+        "type": "object",
+        "properties": {
+          "eventType": {
+            "type": "string"
+          },
+          "attributes": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalEventData"
+            }
+          }
+        }
+      },
+      "ClinicalEventRequestIdentifier": {
+        "required": [
+          "position"
+        ],
+        "type": "object",
+        "properties": {
+          "clinicalEventRequests": {
+            "maxItems": 10000000,
+            "minItems": 0,
+            "uniqueItems": true,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalEventRequest"
+            }
+          },
+          "position": {
+            "type": "string",
+            "enum": [
+              "FIRST",
+              "LAST"
+            ]
+          }
+        }
+      },
+      "PatientIdentifier": {
+        "type": "object",
+        "properties": {
+          "patientId": {
+            "type": "string"
+          },
+          "studyId": {
+            "type": "string"
+          }
+        }
+      },
+      "SurvivalRequest": {
+        "required": [
+          "attributeIdPrefix"
+        ],
+        "type": "object",
+        "properties": {
+          "patientIdentifiers": {
+            "maxItems": 10000000,
+            "minItems": 1,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/PatientIdentifier"
+            }
+          },
+          "attributeIdPrefix": {
+            "type": "string"
+          },
+          "startEventRequestIdentifier": {
+            "$ref": "#/components/schemas/ClinicalEventRequestIdentifier"
+          },
+          "endEventRequestIdentifier": {
+            "$ref": "#/components/schemas/ClinicalEventRequestIdentifier"
+          },
+          "censoredEventRequestIdentifier": {
+            "$ref": "#/components/schemas/ClinicalEventRequestIdentifier"
+          }
         },
-        "customBins": {
-          "items": {
+        "description": "Survival Data Request"
+      },
+      "ClinicalAttribute": {
+        "required": [
+          "clinicalAttributeId",
+          "displayName",
+          "patientAttribute",
+          "studyId"
+        ],
+        "type": "object",
+        "properties": {
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+          },
+          "description": {
+            "type": "string"
+          },
+          "datatype": {
+            "type": "string"
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+          "patientAttribute": {
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+          },
+          "priority": {
+            "type": "string"
+          },
+          "clinicalAttributeId": {
+            "type": "string"
+          },
+          "studyId": {
+            "type": "string"
+          }
+        }
+      },
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+        "required": [
+          "clinicalAttributeId",
+          "patientId",
+          "studyId"
+        ],
+        "type": "object",
+        "properties": {
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+            "type": "string"
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+          "uniquePatientKey": {
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+          },
+          "sampleId": {
+            "type": "string"
+          },
+          "patientId": {
+            "type": "string"
+          },
+          "studyId": {
+            "type": "string"
+          },
+          "clinicalAttribute": {
+            "$ref": "#/components/schemas/ClinicalAttribute"
+          },
+          "patientAttribute": {
+            "type": "boolean"
+          },
+          "clinicalAttributeId": {
+            "type": "string"
+          },
+          "value": {
+            "type": "string"
+          }
+        }
+      },
+      "AlterationCountByGene": {
+        "type": "object",
+        "properties": {
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+            "type": "integer",
+            "format": "int32"
+          },
+          "totalCount": {
+            "type": "integer",
+            "format": "int32"
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+            "format": "int32"
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+            "type": "array",
+            "items": {
+              "type": "string"
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+          },
+          "entrezGeneId": {
+            "type": "integer",
+            "format": "int32"
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+          "hugoGeneSymbol": {
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+          "uniqueEventKey": {
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             "type": "number"
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+            "format": "int32"
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           },
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-          "type": "boolean"
-        },
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-          "type": "number"
-        },
-        "profileType": {
-          "type": "string"
+          "gene1EntrezGeneId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "gene1HugoGeneSymbol": {
+            "type": "string"
+          },
+          "gene2EntrezGeneId": {
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+            "format": "int32"
+          },
+          "gene2HugoGeneSymbol": {
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+            "type": "array",
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+              "format": "int32"
+            }
+          }
+        }
+      },
+      "SampleMolecularIdentifier": {
+        "type": "object",
+        "properties": {
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+          },
+          "molecularProfileId": {
+            "type": "string"
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+            "minItems": 0,
+            "type": "array",
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+            }
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+            "minItems": 0,
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+              "minLength": 0,
+              "type": "string"
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+            "minItems": 0,
+            "type": "array",
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+            }
+          }
         },
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-          "type": "string"
+        "description": "List of entrezGeneIds, structural variant queries and molecularProfileIds or sampleMolecularIdentifiers"
+      },
+      "StructuralVariantQuery": {
+        "type": "object",
+        "properties": {
+          "gene1": {
+            "$ref": "#/components/schemas/StructuralVariantGeneSubQuery"
+          },
+          "gene2": {
+            "$ref": "#/components/schemas/StructuralVariantGeneSubQuery"
+          }
+        }
+      },
+      "StructuralVariant": {
+        "type": "object",
+        "properties": {
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+            "type": "string"
+          },
+          "uniquePatientKey": {
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+            "format": "int32"
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+          "site1HugoSymbol": {
+            "type": "string"
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+          "site1EnsemblTranscriptId": {
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+          "site1Chromosome": {
+            "type": "string"
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+            "format": "int32"
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+          "site1Contig": {
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+            "format": "int32"
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+          "site2Description": {
+            "type": "string"
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+          "site2EffectOnFrame": {
+            "type": "string"
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+          "ncbiBuild": {
+            "type": "string"
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+          "dnaSupport": {
+            "type": "string"
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+            "type": "string"
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+            "format": "int32"
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+          "tumorReadCount": {
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+            "format": "int32"
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+            "format": "int32"
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+          "tumorVariantCount": {
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+            "format": "int32"
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+          "normalPairedEndReadCount": {
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+            "format": "int32"
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+          "tumorPairedEndReadCount": {
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+            "format": "int32"
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+            "format": "int32"
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+          "tumorSplitReadCount": {
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+            "format": "int32"
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+            "type": "string"
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+            "format": "int32"
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+          "driverFilterAnn": {
+            "type": "string"
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+            "type": "string"
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+          "driverTiersFilterAnn": {
+            "type": "string"
+          },
+          "svStatus": {
+            "type": "string"
+          },
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+            "type": "object"
+          }
+        }
+      },
+      "CaseListDataCount": {
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+            "type": "string"
+          },
+          "value": {
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+            "format": "int32"
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+        }
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+          "resourceId",
+          "resourceType",
+          "studyId"
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+            "enum": [
+              "STUDY",
+              "SAMPLE",
+              "PATIENT"
+            ]
+          },
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+          "openByDefault": {
+            "type": "boolean"
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+            "type": "string"
+          }
+        }
+      },
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+          "entrezGeneId",
+          "referenceGenomeId"
+        ],
+        "type": "object",
+        "properties": {
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+            "type": "integer",
+            "format": "int32"
+          },
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+            "type": "integer",
+            "format": "int32"
+          },
+          "hugoGeneSymbol": {
+            "type": "string"
+          },
+          "chromosome": {
+            "type": "string"
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+          "cytoband": {
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+            "format": "int64"
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+            "type": "integer",
+            "format": "int64"
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+        }
+      },
+      "GenomicDataCountFilter": {
+        "type": "object",
+        "properties": {
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+            "items": {
+              "$ref": "#/components/schemas/GenomicDataFilter"
+            }
+          },
+          "studyViewFilter": {
+            "$ref": "#/components/schemas/StudyViewFilter"
+          }
         },
-        "start": {
-          "type": "number"
+        "description": "Genomic data count filter"
+      },
+      "GenomicDataCount": {
+        "type": "object",
+        "properties": {
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+            "type": "string"
+          },
+          "value": {
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+            "format": "int32"
+          }
         }
       },
-      "type": "object"
-    },
-    "GenericAssayDataCount": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
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+        "type": "object",
+        "properties": {
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+            "type": "string"
+          },
+          "profileType": {
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+            "items": {
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+            }
+          }
+        }
+      },
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+        "type": "object",
+        "properties": {
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+            "format": "int32"
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+          "proteinPosStart": {
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+            "format": "int32"
+          },
+          "proteinPosEnd": {
+            "type": "integer",
+            "format": "int32"
+          }
+        }
+      },
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+          "count",
+          "entrezGeneId",
+          "proteinPosEnd",
+          "proteinPosStart"
+        ],
+        "type": "object",
+        "properties": {
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+            "format": "int32"
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+        }
+      },
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+            "type": "integer",
+            "format": "int32"
+          },
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+          }
+        }
+      },
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+          "molecularProfileId",
+          "numberOfSamples",
+          "numberOfSamplesWithKeyword",
+          "numberOfSamplesWithMutationInGene"
+        ],
+        "type": "object",
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+          "keyword": {
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+          "numberOfSamplesWithMutationInGene": {
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+            "format": "int32"
+          },
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+            "format": "int32"
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+          }
         },
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-          "type": "string"
+        "description": "List of Sample IDs/Sample List ID"
+      },
+      "MutationSpectrum": {
+        "required": [
+          "CtoA",
+          "CtoG",
+          "CtoT",
+          "TtoA",
+          "TtoC",
+          "TtoG",
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+          "sampleId",
+          "studyId"
+        ],
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         }
       },
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-          },
-          "type": "array"
-        },
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-          "$ref": "#/definitions/StudyViewFilter"
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+          "patientId",
+          "percentile",
+          "sampleId",
+          "studyId",
+          "zScore"
+        ],
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+          "zScore": {
+            "type": "number"
+          }
         }
       },
-      "type": "object"
-    },
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-        "counts": {
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+            "format": "int32"
           },
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-        },
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+          }
         }
       },
-      "type": "object"
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-        },
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-        },
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-            "$ref": "#/definitions/DataFilterValue"
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+          "entrezGeneId",
+          "molecularProfileId",
+          "numberOfSamples",
+          "numberOfSamplesWithAlterationInGene"
+        ],
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           },
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+          }
         }
       },
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-    },
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             "type": "string"
           },
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-            "$ref": "#/definitions/GroupStatistics"
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+            "format": "int32"
           },
-          "type": "array"
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-        },
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-          "type": "number"
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         },
-        "stableId": {
-          "type": "string"
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+      },
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+          "geneticEntityId",
+          "geneticEntityType",
+          "pValue",
+          "spearmansCorrelation"
+        ],
+        "type": "object",
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+            "type": "string"
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+          "geneticEntityType": {
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+            "enum": [
+              "GENE",
+              "GENESET",
+              "PHOSPHOPROTEIN",
+              "GENERIC_ASSAY"
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+          },
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         }
       },
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-    "Geneset": {
-      "properties": {
-        "description": {
-          "type": "string"
-        },
-        "genesetId": {
-          "type": "string"
-        },
-        "name": {
-          "type": "string"
-        },
-        "refLink": {
-          "type": "string"
-        },
-        "representativePvalue": {
-          "format": "double",
-          "type": "number"
-        },
-        "representativeScore": {
-          "format": "double",
-          "type": "number"
+      "BinsGeneratorConfig": {
+        "type": "object",
+        "properties": {
+          "binSize": {
+            "type": "number"
+          },
+          "anchorValue": {
+            "type": "number"
+          }
         }
       },
-      "type": "object"
-    },
-    "GenesetCorrelation": {
-      "properties": {
-        "correlationValue": {
-          "format": "double",
-          "type": "number"
-        },
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "expressionGeneticProfileId": {
-          "type": "string"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
+      "GenomicDataBinCountFilter": {
+        "type": "object",
+        "properties": {
+          "studyViewFilter": {
+            "$ref": "#/components/schemas/StudyViewFilter"
+          },
+          "genomicDataBinFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GenomicDataBinFilter"
+            }
+          }
         },
-        "zScoreGeneticProfileId": {
-          "type": "string"
-        }
+        "description": "Genomic data bin count filter"
       },
-      "type": "object"
-    },
-    "GenesetDataFilterCriteria": {
-      "description": "Search criteria to return the values for a given set of samples and gene set items. genesetIds: The list of identifiers for the gene sets of interest, e.g. HINATA_NFKB_MATRIX. Use one of these if you want to specify a subset of samples:(1) sampleListId: Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all or (2) sampleIds: custom list of samples or patients to query, e.g. TCGA-BH-A1EO-01, TCGA-AR-A1AR-01",
-      "properties": {
-        "genesetIds": {
-          "items": {
-            "type": "string"
+      "GenomicDataBinFilter": {
+        "type": "object",
+        "properties": {
+          "disableLogScale": {
+            "type": "boolean"
           },
-          "type": "array"
-        },
-        "sampleIds": {
-          "items": {
+          "customBins": {
+            "type": "array",
+            "items": {
+              "type": "number"
+            }
+          },
+          "binMethod": {
+            "type": "string",
+            "enum": [
+              "MEDIAN",
+              "QUARTILE",
+              "CUSTOM",
+              "GENERATE"
+            ]
+          },
+          "binsGeneratorConfig": {
+            "$ref": "#/components/schemas/BinsGeneratorConfig"
+          },
+          "start": {
+            "type": "number"
+          },
+          "end": {
+            "type": "number"
+          },
+          "hugoGeneSymbol": {
             "type": "string"
           },
-          "type": "array"
-        },
-        "sampleListId": {
-          "type": "string"
+          "profileType": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "GenesetHierarchyInfo": {
-      "properties": {
-        "genesets": {
-          "items": {
-            "$ref": "#/definitions/Geneset"
+      "GenomicDataBin": {
+        "type": "object",
+        "properties": {
+          "specialValue": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "nodeId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "nodeName": {
-          "type": "string"
-        },
-        "parentId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "parentNodeName": {
-          "type": "string"
-        }
-      },
-      "type": "object"
-    },
-    "GenesetMolecularData": {
-      "properties": {
-        "geneset": {
-          "$ref": "#/definitions/Geneset"
-        },
-        "genesetId": {
-          "type": "string"
-        },
-        "geneticProfileId": {
-          "type": "string"
-        },
-        "patientId": {
-          "type": "string"
-        },
-        "sampleId": {
-          "type": "string"
-        },
-        "stableId": {
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "uniquePatientKey": {
-          "type": "string"
-        },
-        "uniqueSampleKey": {
-          "type": "string"
-        },
-        "value": {
-          "type": "string"
+          "start": {
+            "type": "number"
+          },
+          "end": {
+            "type": "number"
+          },
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "hugoGeneSymbol": {
+            "type": "string"
+          },
+          "profileType": {
+            "type": "string"
+          }
         }
       },
-      "required": [
-        "geneticProfileId",
-        "patientId",
-        "sampleId",
-        "studyId",
-        "value"
-      ],
-      "type": "object"
-    },
-    "GenomicDataBin": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "end": {
-          "type": "number"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "profileType": {
-          "type": "string"
-        },
-        "specialValue": {
-          "type": "string"
+      "GenesetDataFilterCriteria": {
+        "type": "object",
+        "properties": {
+          "genesetIds": {
+            "type": "array",
+            "items": {
+              "type": "string"
+            }
+          },
+          "sampleListId": {
+            "type": "string"
+          },
+          "sampleIds": {
+            "type": "array",
+            "items": {
+              "type": "string"
+            }
+          }
         },
-        "start": {
-          "type": "number"
-        }
+        "description": "Search criteria to return the values for a given set of samples and gene set items. genesetIds: The list of identifiers for the gene sets of interest, e.g. HINATA_NFKB_MATRIX. Use one of these if you want to specify a subset of samples:(1) sampleListId: Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all or (2) sampleIds: custom list of samples or patients to query, e.g. TCGA-BH-A1EO-01, TCGA-AR-A1AR-01"
       },
-      "type": "object"
-    },
-    "GenomicDataBinCountFilter": {
-      "description": "Genomic data bin count filter",
-      "properties": {
-        "genomicDataBinFilters": {
-          "items": {
-            "$ref": "#/definitions/GenomicDataBinFilter"
-          },
-          "type": "array"
-        },
-        "studyViewFilter": {
-          "$ref": "#/definitions/StudyViewFilter"
+      "Geneset": {
+        "type": "object",
+        "properties": {
+          "genesetId": {
+            "type": "string"
+          },
+          "name": {
+            "type": "string"
+          },
+          "description": {
+            "type": "string"
+          },
+          "refLink": {
+            "type": "string"
+          },
+          "representativeScore": {
+            "type": "number",
+            "format": "double"
+          },
+          "representativePvalue": {
+            "type": "number",
+            "format": "double"
+          }
         }
       },
-      "type": "object"
-    },
-    "GenomicDataBinFilter": {
-      "properties": {
-        "binMethod": {
-          "enum": [
-            "MEDIAN",
-            "QUARTILE",
-            "CUSTOM",
-            "GENERATE"
-          ],
-          "type": "string"
-        },
-        "binsGeneratorConfig": {
-          "$ref": "#/definitions/BinsGeneratorConfig"
-        },
-        "customBins": {
-          "items": {
-            "type": "number"
+      "GenesetMolecularData": {
+        "required": [
+          "geneticProfileId",
+          "patientId",
+          "sampleId",
+          "studyId",
+          "value"
+        ],
+        "type": "object",
+        "properties": {
+          "uniqueSampleKey": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "disableLogScale": {
-          "type": "boolean"
-        },
-        "end": {
-          "type": "number"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "profileType": {
-          "type": "string"
-        },
-        "start": {
-          "type": "number"
+          "uniquePatientKey": {
+            "type": "string"
+          },
+          "sampleId": {
+            "type": "string"
+          },
+          "patientId": {
+            "type": "string"
+          },
+          "studyId": {
+            "type": "string"
+          },
+          "value": {
+            "type": "string"
+          },
+          "genesetId": {
+            "type": "string"
+          },
+          "geneset": {
+            "$ref": "#/components/schemas/Geneset"
+          },
+          "stableId": {
+            "type": "string"
+          },
+          "geneticProfileId": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "GenomicDataCount": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "label": {
-          "type": "string"
-        },
-        "uniqueCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "value": {
-          "type": "string"
+      "GenesetCorrelation": {
+        "type": "object",
+        "properties": {
+          "entrezGeneId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "hugoGeneSymbol": {
+            "type": "string"
+          },
+          "correlationValue": {
+            "type": "number",
+            "format": "double"
+          },
+          "expressionGeneticProfileId": {
+            "type": "string"
+          },
+          "zScoreGeneticProfileId": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "GenomicDataCountFilter": {
-      "description": "Genomic data count filter",
-      "properties": {
-        "genomicDataFilters": {
-          "items": {
-            "$ref": "#/definitions/GenomicDataFilter"
-          },
-          "type": "array"
-        },
-        "studyViewFilter": {
-          "$ref": "#/definitions/StudyViewFilter"
+      "GenesetHierarchyInfo": {
+        "type": "object",
+        "properties": {
+          "nodeId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "nodeName": {
+            "type": "string"
+          },
+          "parentId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "parentNodeName": {
+            "type": "string"
+          },
+          "genesets": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/Geneset"
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "GenomicDataCountItem": {
-      "properties": {
-        "counts": {
-          "items": {
-            "$ref": "#/definitions/GenomicDataCount"
+      "MolecularProfileCaseIdentifier": {
+        "required": [
+          "caseId",
+          "molecularProfileId"
+        ],
+        "type": "object",
+        "properties": {
+          "molecularProfileId": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "profileType": {
-          "type": "string"
+          "caseId": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "GenomicDataFilter": {
-      "properties": {
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "profileType": {
-          "type": "string"
-        },
-        "values": {
-          "items": {
-            "$ref": "#/definitions/DataFilterValue"
+      "MolecularProfileCasesGroupFilter": {
+        "type": "object",
+        "properties": {
+          "name": {
+            "type": "string"
           },
-          "type": "array"
+          "molecularProfileCaseIdentifiers": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/MolecularProfileCaseIdentifier"
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "GenomicEnrichment": {
-      "properties": {
-        "cytoband": {
-          "type": "string"
-        },
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "groupsStatistics": {
-          "items": {
-            "$ref": "#/definitions/GroupStatistics"
+      "GenericAssayEnrichment": {
+        "required": [
+          "genericEntityMetaProperties",
+          "groupsStatistics",
+          "name",
+          "pValue",
+          "qValue",
+          "stableId"
+        ],
+        "type": "object",
+        "properties": {
+          "groupsStatistics": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GroupStatistics"
+            }
           },
-          "type": "array"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "pValue": {
-          "type": "number"
+          "stableId": {
+            "type": "string"
+          },
+          "name": {
+            "type": "string"
+          },
+          "genericEntityMetaProperties": {
+            "type": "object",
+            "additionalProperties": {
+              "type": "string"
+            }
+          },
+          "pValue": {
+            "type": "number"
+          },
+          "qValue": {
+            "type": "number"
+          }
         }
       },
-      "required": [
-        "entrezGeneId",
-        "groupsStatistics",
-        "hugoGeneSymbol",
-        "pValue"
-      ],
-      "type": "object"
-    },
-    "Gistic": {
-      "properties": {
-        "amp": {
-          "type": "boolean"
-        },
-        "chromosome": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "cytoband": {
-          "type": "string"
-        },
-        "genes": {
-          "items": {
-            "$ref": "#/definitions/GisticToGene"
+      "GroupStatistics": {
+        "required": [
+          "meanExpression",
+          "name",
+          "standardDeviation"
+        ],
+        "type": "object",
+        "properties": {
+          "name": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "qValue": {
-          "type": "number"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "widePeakEnd": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "widePeakStart": {
-          "format": "int32",
-          "type": "integer"
+          "meanExpression": {
+            "type": "number"
+          },
+          "standardDeviation": {
+            "type": "number"
+          }
         }
       },
-      "required": [
-        "amp",
-        "chromosome",
-        "cytoband",
-        "qValue",
-        "studyId",
-        "widePeakEnd",
-        "widePeakStart"
-      ],
-      "type": "object"
-    },
-    "GisticToGene": {
-      "properties": {
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
+      "GenericAssayDataCountFilter": {
+        "type": "object",
+        "properties": {
+          "genericAssayDataFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GenericAssayDataFilter"
+            }
+          },
+          "studyViewFilter": {
+            "$ref": "#/components/schemas/StudyViewFilter"
+          }
         },
-        "hugoGeneSymbol": {
-          "type": "string"
-        }
+        "description": "Generic assay data count filter"
       },
-      "required": [
-        "entrezGeneId",
-        "hugoGeneSymbol"
-      ],
-      "type": "object"
-    },
-    "Group": {
-      "properties": {
-        "name": {
-          "type": "string"
-        },
-        "sampleIdentifiers": {
-          "items": {
-            "$ref": "#/definitions/SampleIdentifier"
+      "GenericAssayDataCount": {
+        "type": "object",
+        "properties": {
+          "value": {
+            "type": "string"
           },
-          "maxItems": 10000000,
-          "minItems": 1,
-          "type": "array"
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          }
         }
       },
-      "type": "object"
-    },
-    "GroupFilter": {
-      "description": "List of altered and unaltered Sample/Patient IDs",
-      "properties": {
-        "groups": {
-          "items": {
-            "$ref": "#/definitions/Group"
+      "GenericAssayDataCountItem": {
+        "type": "object",
+        "properties": {
+          "stableId": {
+            "type": "string"
           },
-          "maxItems": 2147483647,
-          "minItems": 2,
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
-    "GroupStatistics": {
-      "properties": {
-        "meanExpression": {
-          "type": "number"
-        },
-        "name": {
-          "type": "string"
-        },
-        "standardDeviation": {
-          "type": "number"
+          "counts": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GenericAssayDataCount"
+            }
+          }
         }
       },
-      "required": [
-        "meanExpression",
-        "name",
-        "standardDeviation"
-      ],
-      "type": "object"
-    },
-    "MolecularProfileCaseIdentifier": {
-      "properties": {
-        "caseId": {
-          "type": "string"
+      "GenericAssayDataBinCountFilter": {
+        "type": "object",
+        "properties": {
+          "studyViewFilter": {
+            "$ref": "#/components/schemas/StudyViewFilter"
+          },
+          "genericAssayDataBinFilters": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GenericAssayDataBinFilter"
+            }
+          }
         },
-        "molecularProfileId": {
-          "type": "string"
+        "description": "Generic assay data bin count filter"
+      },
+      "GenericAssayDataBinFilter": {
+        "type": "object",
+        "properties": {
+          "disableLogScale": {
+            "type": "boolean"
+          },
+          "customBins": {
+            "type": "array",
+            "items": {
+              "type": "number"
+            }
+          },
+          "binMethod": {
+            "type": "string",
+            "enum": [
+              "MEDIAN",
+              "QUARTILE",
+              "CUSTOM",
+              "GENERATE"
+            ]
+          },
+          "binsGeneratorConfig": {
+            "$ref": "#/components/schemas/BinsGeneratorConfig"
+          },
+          "start": {
+            "type": "number"
+          },
+          "end": {
+            "type": "number"
+          },
+          "stableId": {
+            "type": "string"
+          },
+          "profileType": {
+            "type": "string"
+          }
         }
       },
-      "required": [
-        "caseId",
-        "molecularProfileId"
-      ],
-      "type": "object"
-    },
-    "MolecularProfileCasesGroupAndAlterationTypeFilter": {
-      "description": "List of groups containing sample identifiers and list of Alteration Types",
-      "properties": {
-        "alterationEventTypes": {
-          "$ref": "#/definitions/AlterationFilter"
-        },
-        "molecularProfileCasesGroupFilter": {
-          "items": {
-            "$ref": "#/definitions/MolecularProfileCasesGroupFilter"
+      "GenericAssayDataBin": {
+        "type": "object",
+        "properties": {
+          "specialValue": {
+            "type": "string"
+          },
+          "start": {
+            "type": "number"
+          },
+          "end": {
+            "type": "number"
+          },
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "stableId": {
+            "type": "string"
           },
-          "maxItems": 10000000,
-          "minItems": 1,
-          "type": "array"
+          "profileType": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "MolecularProfileCasesGroupFilter": {
-      "properties": {
-        "molecularProfileCaseIdentifiers": {
-          "items": {
-            "$ref": "#/definitions/MolecularProfileCaseIdentifier"
+      "GenericAssayCategoricalEnrichment": {
+        "required": [
+          "genericEntityMetaProperties",
+          "groupsStatistics",
+          "name",
+          "pValue",
+          "qValue",
+          "stableId"
+        ],
+        "type": "object",
+        "properties": {
+          "groupsStatistics": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GroupStatistics"
+            }
           },
-          "type": "array"
-        },
-        "name": {
-          "type": "string"
+          "stableId": {
+            "type": "string"
+          },
+          "name": {
+            "type": "string"
+          },
+          "genericEntityMetaProperties": {
+            "type": "object",
+            "additionalProperties": {
+              "type": "string"
+            }
+          },
+          "pValue": {
+            "type": "number"
+          },
+          "qValue": {
+            "type": "number"
+          }
         }
       },
-      "type": "object"
-    },
-    "MrnaPercentile": {
-      "properties": {
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "molecularProfileId": {
-          "type": "string"
-        },
-        "patientId": {
-          "type": "string"
-        },
-        "percentile": {
-          "type": "number"
-        },
-        "sampleId": {
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "uniquePatientKey": {
-          "type": "string"
-        },
-        "uniqueSampleKey": {
-          "type": "string"
-        },
-        "zScore": {
-          "type": "number"
+      "GenericAssayBinaryEnrichment": {
+        "required": [
+          "counts",
+          "genericEntityMetaProperties",
+          "groupsStatistics",
+          "name",
+          "pValue",
+          "qValue",
+          "stableId"
+        ],
+        "type": "object",
+        "properties": {
+          "groupsStatistics": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GroupStatistics"
+            }
+          },
+          "stableId": {
+            "type": "string"
+          },
+          "name": {
+            "type": "string"
+          },
+          "genericEntityMetaProperties": {
+            "type": "object",
+            "additionalProperties": {
+              "type": "string"
+            }
+          },
+          "counts": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/GenericAssayCountSummary"
+            }
+          },
+          "pValue": {
+            "type": "number"
+          },
+          "qValue": {
+            "type": "number"
+          }
         }
       },
-      "required": [
-        "entrezGeneId",
-        "molecularProfileId",
-        "patientId",
-        "percentile",
-        "sampleId",
-        "studyId",
-        "zScore"
-      ],
-      "type": "object"
-    },
-    "MutSig": {
-      "properties": {
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "numberOfMutations": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "pValue": {
-          "type": "number"
-        },
-        "qValue": {
-          "type": "number"
-        },
-        "rank": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "studyId": {
-          "type": "string"
+      "GenericAssayCountSummary": {
+        "required": [
+          "count",
+          "name",
+          "totalCount"
+        ],
+        "type": "object",
+        "properties": {
+          "name": {
+            "type": "string"
+          },
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "totalCount": {
+            "type": "integer",
+            "format": "int32"
+          }
         }
       },
-      "required": [
-        "entrezGeneId",
-        "hugoGeneSymbol",
-        "numberOfMutations",
-        "pValue",
-        "qValue",
-        "rank",
-        "studyId"
-      ],
-      "type": "object"
-    },
-    "MutationCountByPosition": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "proteinPosEnd": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "proteinPosStart": {
-          "format": "int32",
-          "type": "integer"
+      "Sample": {
+        "required": [
+          "patientId",
+          "sampleId",
+          "studyId"
+        ],
+        "type": "object",
+        "properties": {
+          "uniqueSampleKey": {
+            "type": "string"
+          },
+          "uniquePatientKey": {
+            "type": "string"
+          },
+          "sampleType": {
+            "type": "string",
+            "enum": [
+              "Primary Solid Tumor",
+              "Recurrent Solid Tumor",
+              "Primary Blood Tumor",
+              "Recurrent Blood Tumor",
+              "Metastatic",
+              "Blood Derived Normal",
+              "Solid Tissues Normal"
+            ]
+          },
+          "sequenced": {
+            "type": "boolean"
+          },
+          "copyNumberSegmentPresent": {
+            "type": "boolean"
+          },
+          "sampleId": {
+            "type": "string"
+          },
+          "patientId": {
+            "type": "string"
+          },
+          "studyId": {
+            "type": "string"
+          }
         }
       },
-      "required": [
-        "count",
-        "entrezGeneId",
-        "proteinPosEnd",
-        "proteinPosStart"
-      ],
-      "type": "object"
-    },
-    "MutationDataFilter": {
-      "properties": {
-        "categorization": {
-          "enum": [
-            "MUTATED",
-            "MUTATION_TYPE"
-          ],
-          "type": "string"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "profileType": {
-          "type": "string"
-        },
-        "values": {
-          "items": {
+      "GenomicEnrichment": {
+        "required": [
+          "entrezGeneId",
+          "groupsStatistics",
+          "hugoGeneSymbol",
+          "pValue"
+        ],
+        "type": "object",
+        "properties": {
+          "groupsStatistics": {
+            "type": "array",
             "items": {
-              "$ref": "#/definitions/DataFilterValue"
-            },
-            "type": "array"
+              "$ref": "#/components/schemas/GroupStatistics"
+            }
+          },
+          "entrezGeneId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "hugoGeneSymbol": {
+            "type": "string"
+          },
+          "cytoband": {
+            "type": "string"
           },
-          "type": "array"
+          "pValue": {
+            "type": "number"
+          }
         }
       },
-      "required": [
-        "categorization"
-      ],
-      "type": "object"
-    },
-    "MutationPositionIdentifier": {
-      "properties": {
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "proteinPosEnd": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "proteinPosStart": {
-          "format": "int32",
-          "type": "integer"
+      "DataAccessToken": {
+        "type": "object",
+        "properties": {
+          "token": {
+            "type": "string"
+          },
+          "username": {
+            "type": "string"
+          },
+          "expiration": {
+            "type": "string",
+            "format": "date-time"
+          },
+          "creation": {
+            "type": "string",
+            "format": "date-time"
+          }
         }
       },
-      "type": "object"
-    },
-    "MutationSpectrum": {
-      "properties": {
-        "CtoA": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "CtoG": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "CtoT": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "TtoA": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "TtoC": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "TtoG": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "molecularProfileId": {
-          "type": "string"
-        },
-        "patientId": {
-          "type": "string"
-        },
-        "sampleId": {
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "uniquePatientKey": {
-          "type": "string"
-        },
-        "uniqueSampleKey": {
-          "type": "string"
+      "CustomDriverAnnotationReport": {
+        "type": "object",
+        "properties": {
+          "hasBinary": {
+            "type": "boolean"
+          },
+          "tiers": {
+            "uniqueItems": true,
+            "type": "array",
+            "items": {
+              "type": "string"
+            }
+          }
         }
       },
-      "required": [
-        "CtoA",
-        "CtoG",
-        "CtoT",
-        "TtoA",
-        "TtoC",
-        "TtoG",
-        "molecularProfileId",
-        "patientId",
-        "sampleId",
-        "studyId"
-      ],
-      "type": "object"
-    },
-    "MutationSpectrumFilter": {
-      "description": "List of Sample IDs/Sample List ID",
-      "properties": {
-        "sampleIds": {
-          "items": {
-            "maxLength": 10000000,
-            "minLength": 1,
-            "type": "string"
-          },
-          "maxItems": 10000000,
-          "minItems": 1,
-          "type": "array"
+      "ClinicalDataCountFilter": {
+        "type": "object",
+        "properties": {
+          "attributes": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalDataFilter"
+            }
+          },
+          "studyViewFilter": {
+            "$ref": "#/components/schemas/StudyViewFilter"
+          }
         },
-        "sampleListId": {
-          "type": "string"
-        }
+        "description": "Clinical data count filter"
       },
-      "type": "object"
-    },
-    "OredPatientTreatmentFilters": {
-      "properties": {
-        "filters": {
-          "items": {
-            "$ref": "#/definitions/PatientTreatmentFilter"
+      "ClinicalDataCount": {
+        "type": "object",
+        "properties": {
+          "value": {
+            "type": "string"
           },
-          "type": "array"
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          }
         }
       },
-      "type": "object"
-    },
-    "OredSampleTreatmentFilters": {
-      "properties": {
-        "filters": {
-          "items": {
-            "$ref": "#/definitions/SampleTreatmentFilter"
+      "ClinicalDataCountItem": {
+        "type": "object",
+        "properties": {
+          "attributeId": {
+            "type": "string"
           },
-          "type": "array"
+          "counts": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalDataCount"
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "PatientIdentifier": {
-      "properties": {
-        "patientId": {
-          "type": "string"
+      "ClinicalDataBinCountFilter": {
+        "type": "object",
+        "properties": {
+          "studyViewFilter": {
+            "$ref": "#/components/schemas/StudyViewFilter"
+          },
+          "attributes": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalDataBinFilter"
+            }
+          }
         },
-        "studyId": {
-          "type": "string"
-        }
+        "description": "Clinical data bin count filter"
       },
-      "type": "object"
-    },
-    "PatientTreatment": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "treatment": {
-          "type": "string"
+      "ClinicalDataBinFilter": {
+        "type": "object",
+        "properties": {
+          "disableLogScale": {
+            "type": "boolean"
+          },
+          "customBins": {
+            "type": "array",
+            "items": {
+              "type": "number"
+            }
+          },
+          "binMethod": {
+            "type": "string",
+            "enum": [
+              "MEDIAN",
+              "QUARTILE",
+              "CUSTOM",
+              "GENERATE"
+            ]
+          },
+          "binsGeneratorConfig": {
+            "$ref": "#/components/schemas/BinsGeneratorConfig"
+          },
+          "start": {
+            "type": "number"
+          },
+          "end": {
+            "type": "number"
+          },
+          "attributeId": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "PatientTreatmentFilter": {
-      "properties": {
-        "treatment": {
-          "type": "string"
+      "ClinicalDataBin": {
+        "type": "object",
+        "properties": {
+          "specialValue": {
+            "type": "string"
+          },
+          "start": {
+            "type": "number"
+          },
+          "end": {
+            "type": "number"
+          },
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "attributeId": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "PatientTreatmentReport": {
-      "properties": {
-        "patientTreatments": {
-          "items": {
-            "$ref": "#/definitions/PatientTreatment"
+      "CosmicMutation": {
+        "required": [
+          "cosmicMutationId",
+          "count",
+          "proteinChange"
+        ],
+        "type": "object",
+        "properties": {
+          "cosmicMutationId": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "totalPatients": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "totalSamples": {
-          "format": "int32",
-          "type": "integer"
+          "proteinChange": {
+            "type": "string"
+          },
+          "keyword": {
+            "type": "string"
+          },
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          }
         }
       },
-      "type": "object"
-    },
-    "PatientTreatmentRow": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "samples": {
-          "items": {
-            "$ref": "#/definitions/ClinicalEventSample"
+      "CopyNumberCountByGene": {
+        "type": "object",
+        "properties": {
+          "numberOfAlteredCases": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "totalCount": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "numberOfProfiledCases": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "matchingGenePanelIds": {
+            "uniqueItems": true,
+            "type": "array",
+            "items": {
+              "type": "string"
+            }
           },
-          "type": "array",
-          "uniqueItems": true
-        },
-        "treatment": {
-          "type": "string"
+          "entrezGeneId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "hugoGeneSymbol": {
+            "type": "string"
+          },
+          "alteration": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "cytoband": {
+            "type": "string"
+          },
+          "uniqueEventKey": {
+            "type": "string"
+          },
+          "hugoGeneSymbols": {
+            "type": "array",
+            "items": {
+              "type": "string"
+            }
+          },
+          "entrezGeneIds": {
+            "type": "array",
+            "items": {
+              "type": "integer",
+              "format": "int32"
+            }
+          },
+          "qValue": {
+            "type": "number"
+          }
         }
       },
-      "type": "object"
-    },
-    "ReferenceGenomeGene": {
-      "properties": {
-        "chromosome": {
-          "type": "string"
-        },
-        "cytoband": {
-          "type": "string"
-        },
-        "end": {
-          "format": "int64",
-          "type": "integer"
-        },
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "hugoGeneSymbol": {
-          "type": "string"
-        },
-        "referenceGenomeId": {
-          "format": "int32",
-          "type": "integer"
+      "ClinicalEventAttributeRequest": {
+        "type": "object",
+        "properties": {
+          "patientIdentifiers": {
+            "maxItems": 10000000,
+            "minItems": 1,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/PatientIdentifier"
+            }
+          },
+          "clinicalEventRequests": {
+            "uniqueItems": true,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalEventRequest"
+            }
+          }
         },
-        "start": {
-          "format": "int64",
-          "type": "integer"
-        }
+        "description": "clinical events Request"
       },
-      "required": [
-        "entrezGeneId",
-        "referenceGenomeId"
-      ],
-      "type": "object"
-    },
-    "ResourceData": {
-      "properties": {
-        "patientId": {
-          "type": "string"
-        },
-        "resourceDefinition": {
-          "$ref": "#/definitions/ResourceDefinition"
-        },
-        "resourceId": {
-          "type": "string"
-        },
-        "sampleId": {
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "uniquePatientKey": {
-          "type": "string"
-        },
-        "uniqueSampleKey": {
-          "type": "string"
-        },
-        "url": {
-          "type": "string"
+      "ClinicalEvent": {
+        "required": [
+          "eventType",
+          "patientId",
+          "studyId"
+        ],
+        "type": "object",
+        "properties": {
+          "uniqueSampleKey": {
+            "type": "string"
+          },
+          "uniquePatientKey": {
+            "type": "string"
+          },
+          "studyId": {
+            "type": "string"
+          },
+          "patientId": {
+            "type": "string"
+          },
+          "eventType": {
+            "type": "string"
+          },
+          "attributes": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalEventData"
+            }
+          },
+          "startNumberOfDaysSinceDiagnosis": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "endNumberOfDaysSinceDiagnosis": {
+            "type": "integer",
+            "format": "int32"
+          }
         }
       },
-      "required": [
-        "resourceId",
-        "studyId",
-        "url"
-      ],
-      "type": "object"
-    },
-    "ResourceDefinition": {
-      "properties": {
-        "description": {
-          "type": "string"
-        },
-        "displayName": {
-          "type": "string"
-        },
-        "openByDefault": {
-          "type": "boolean"
-        },
-        "priority": {
-          "type": "string"
-        },
-        "resourceId": {
-          "type": "string"
-        },
-        "resourceType": {
-          "enum": [
-            "STUDY",
-            "SAMPLE",
-            "PATIENT"
-          ],
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
+      "ClinicalEventTypeCount": {
+        "type": "object",
+        "properties": {
+          "eventType": {
+            "type": "string"
+          },
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          }
         }
       },
-      "required": [
-        "displayName",
-        "resourceId",
-        "resourceType",
-        "studyId"
-      ],
-      "type": "object"
-    },
-    "Sample": {
-      "properties": {
-        "copyNumberSegmentPresent": {
-          "type": "boolean"
-        },
-        "patientId": {
-          "type": "string"
-        },
-        "sampleId": {
-          "type": "string"
-        },
-        "sampleType": {
-          "enum": [
-            "Primary Solid Tumor",
-            "Recurrent Solid Tumor",
-            "Primary Blood Tumor",
-            "Recurrent Blood Tumor",
-            "Metastatic",
-            "Blood Derived Normal",
-            "Solid Tissues Normal"
-          ],
-          "type": "string"
-        },
-        "sequenced": {
-          "type": "boolean"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "uniquePatientKey": {
-          "type": "string"
-        },
-        "uniqueSampleKey": {
-          "type": "string"
+      "ClinicalViolinPlotBoxData": {
+        "type": "object",
+        "properties": {
+          "whiskerLower": {
+            "type": "number",
+            "format": "double"
+          },
+          "whiskerUpper": {
+            "type": "number",
+            "format": "double"
+          },
+          "median": {
+            "type": "number",
+            "format": "double"
+          },
+          "q1": {
+            "type": "number",
+            "format": "double"
+          },
+          "q3": {
+            "type": "number",
+            "format": "double"
+          }
         }
       },
-      "required": [
-        "patientId",
-        "sampleId",
-        "studyId"
-      ],
-      "type": "object"
-    },
-    "SampleClinicalDataCollection": {
-      "properties": {
-        "byUniqueSampleKey": {
-          "additionalProperties": {
+      "ClinicalViolinPlotData": {
+        "type": "object",
+        "properties": {
+          "rows": {
+            "type": "array",
             "items": {
-              "$ref": "#/definitions/ClinicalData"
-            },
-            "type": "array"
+              "$ref": "#/components/schemas/ClinicalViolinPlotRowData"
+            }
           },
-          "type": "object"
+          "axisStart": {
+            "type": "number",
+            "format": "double"
+          },
+          "axisEnd": {
+            "type": "number",
+            "format": "double"
+          }
         }
       },
-      "type": "object"
-    },
-    "SampleIdentifier": {
-      "properties": {
-        "sampleId": {
-          "type": "string"
-        },
-        "studyId": {
-          "type": "string"
+      "ClinicalViolinPlotIndividualPoint": {
+        "type": "object",
+        "properties": {
+          "sampleId": {
+            "type": "string"
+          },
+          "studyId": {
+            "type": "string"
+          },
+          "value": {
+            "type": "number",
+            "format": "double"
+          }
         }
       },
-      "type": "object"
-    },
-    "SampleMolecularIdentifier": {
-      "properties": {
-        "molecularProfileId": {
-          "type": "string"
-        },
-        "sampleId": {
-          "type": "string"
+      "ClinicalViolinPlotRowData": {
+        "type": "object",
+        "properties": {
+          "category": {
+            "type": "string"
+          },
+          "numSamples": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "curveData": {
+            "type": "array",
+            "items": {
+              "type": "number",
+              "format": "double"
+            }
+          },
+          "boxData": {
+            "$ref": "#/components/schemas/ClinicalViolinPlotBoxData"
+          },
+          "individualPoints": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/ClinicalViolinPlotIndividualPoint"
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "SampleTreatmentFilter": {
-      "properties": {
-        "time": {
-          "enum": [
-            "Pre",
-            "Post"
-          ],
-          "type": "string"
-        },
-        "treatment": {
-          "type": "string"
+      "SampleClinicalDataCollection": {
+        "type": "object",
+        "properties": {
+          "byUniqueSampleKey": {
+            "type": "object",
+            "additionalProperties": {
+              "type": "array",
+              "items": {
+                "$ref": "#/components/schemas/ClinicalData"
+              }
+            }
+          }
         }
       },
-      "type": "object"
-    },
-    "SampleTreatmentReport": {
-      "properties": {
-        "totalSamples": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "treatments": {
-          "items": {
-            "$ref": "#/definitions/SampleTreatmentRow"
+      "Group": {
+        "type": "object",
+        "properties": {
+          "sampleIdentifiers": {
+            "maxItems": 10000000,
+            "minItems": 1,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/SampleIdentifier"
+            }
           },
-          "type": "array"
+          "name": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "SampleTreatmentRow": {
-      "properties": {
-        "count": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "samples": {
-          "items": {
-            "$ref": "#/definitions/ClinicalEventSample"
-          },
-          "type": "array",
-          "uniqueItems": true
-        },
-        "time": {
-          "enum": [
-            "Pre",
-            "Post"
-          ],
-          "type": "string"
+      "GroupFilter": {
+        "type": "object",
+        "properties": {
+          "groups": {
+            "maxItems": 2147483647,
+            "minItems": 2,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/Group"
+            }
+          }
         },
-        "treatment": {
-          "type": "string"
-        }
+        "description": "List of altered and unaltered Sample/Patient IDs"
       },
-      "type": "object"
-    },
-    "StructuralVariant": {
-      "properties": {
-        "annotation": {
-          "type": "string"
-        },
-        "breakpointType": {
-          "type": "string"
-        },
-        "comments": {
-          "type": "string"
-        },
-        "connectionType": {
-          "type": "string"
-        },
-        "dnaSupport": {
-          "type": "string"
-        },
-        "driverFilter": {
-          "type": "string"
-        },
-        "driverFilterAnn": {
-          "type": "string"
-        },
-        "driverTiersFilter": {
-          "type": "string"
-        },
-        "driverTiersFilterAnn": {
-          "type": "string"
-        },
-        "eventInfo": {
-          "type": "string"
-        },
-        "length": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "molecularProfileId": {
-          "type": "string"
-        },
-        "namespaceColumns": {
-          "type": "object"
-        },
-        "ncbiBuild": {
-          "type": "string"
-        },
-        "normalPairedEndReadCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "normalReadCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "normalSplitReadCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "normalVariantCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "patientId": {
-          "type": "string"
-        },
-        "rnaSupport": {
-          "type": "string"
-        },
-        "sampleId": {
-          "type": "string"
-        },
-        "site1Chromosome": {
-          "type": "string"
-        },
-        "site1Contig": {
-          "type": "string"
-        },
-        "site1Description": {
-          "type": "string"
-        },
-        "site1EnsemblTranscriptId": {
-          "type": "string"
-        },
-        "site1EntrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "site1HugoSymbol": {
-          "type": "string"
-        },
-        "site1Position": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "site1Region": {
-          "type": "string"
-        },
-        "site1RegionNumber": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "site2Chromosome": {
-          "type": "string"
-        },
-        "site2Contig": {
-          "type": "string"
-        },
-        "site2Description": {
-          "type": "string"
-        },
-        "site2EffectOnFrame": {
-          "type": "string"
-        },
-        "site2EnsemblTranscriptId": {
-          "type": "string"
-        },
-        "site2EntrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "site2HugoSymbol": {
-          "type": "string"
-        },
-        "site2Position": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "site2Region": {
-          "type": "string"
-        },
-        "site2RegionNumber": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "studyId": {
-          "type": "string"
-        },
-        "svStatus": {
-          "type": "string"
-        },
-        "tumorPairedEndReadCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "tumorReadCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "tumorSplitReadCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "tumorVariantCount": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "uniquePatientKey": {
-          "type": "string"
-        },
-        "uniqueSampleKey": {
-          "type": "string"
-        },
-        "variantClass": {
-          "type": "string"
+      "ClinicalDataEnrichment": {
+        "required": [
+          "clinicalAttribute",
+          "method",
+          "pValue",
+          "score"
+        ],
+        "type": "object",
+        "properties": {
+          "clinicalAttribute": {
+            "$ref": "#/components/schemas/ClinicalAttribute"
+          },
+          "score": {
+            "type": "number"
+          },
+          "method": {
+            "type": "string"
+          },
+          "pValue": {
+            "type": "number"
+          }
         }
       },
-      "type": "object"
-    },
-    "StructuralVariantFilter": {
-      "description": "List of entrezGeneIds, structural variant queries and molecularProfileIds or sampleMolecularIdentifiers",
-      "properties": {
-        "entrezGeneIds": {
-          "items": {
-            "format": "int32",
-            "maximum": 10000000,
-            "minimum": 0,
-            "type": "integer"
-          },
-          "maxItems": 10000000,
-          "minItems": 0,
-          "type": "array"
-        },
-        "molecularProfileIds": {
-          "items": {
-            "maxLength": 10000000,
-            "minLength": 0,
-            "type": "string"
+      "DensityPlotBin": {
+        "type": "object",
+        "properties": {
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "binX": {
+            "type": "number"
           },
-          "maxItems": 10000000,
-          "minItems": 0,
-          "type": "array"
-        },
-        "sampleMolecularIdentifiers": {
-          "items": {
-            "$ref": "#/definitions/SampleMolecularIdentifier"
+          "binY": {
+            "type": "number"
           },
-          "maxItems": 10000000,
-          "minItems": 0,
-          "type": "array"
-        },
-        "structuralVariantQueries": {
-          "items": {
-            "$ref": "#/definitions/StructuralVariantQuery"
+          "minX": {
+            "type": "number"
+          },
+          "maxX": {
+            "type": "number"
           },
-          "maxItems": 10000000,
-          "minItems": 0,
-          "type": "array"
+          "minY": {
+            "type": "number"
+          },
+          "maxY": {
+            "type": "number"
+          }
         }
       },
-      "type": "object"
-    },
-    "StructuralVariantFilterQuery": {
-      "properties": {
-        "gene1Query": {
-          "$ref": "#/definitions/StructuralVariantGeneSubQuery"
-        },
-        "gene2Query": {
-          "$ref": "#/definitions/StructuralVariantGeneSubQuery"
-        },
-        "includeDriver": {
-          "type": "boolean"
-        },
-        "includeGermline": {
-          "type": "boolean"
-        },
-        "includeSomatic": {
-          "type": "boolean"
-        },
-        "includeUnknownOncogenicity": {
-          "type": "boolean"
-        },
-        "includeUnknownStatus": {
-          "type": "boolean"
-        },
-        "includeUnknownTier": {
-          "type": "boolean"
-        },
-        "includeVUS": {
-          "type": "boolean"
-        },
-        "tiersBooleanMap": {
-          "additionalProperties": {
-            "type": "boolean"
+      "DensityPlotData": {
+        "required": [
+          "bins"
+        ],
+        "type": "object",
+        "properties": {
+          "bins": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/DensityPlotBin"
+            }
+          },
+          "pearsonCorr": {
+            "type": "number",
+            "format": "double"
           },
-          "type": "object"
+          "spearmanCorr": {
+            "type": "number",
+            "format": "double"
+          }
         }
       },
-      "type": "object"
-    },
-    "StructuralVariantGeneSubQuery": {
-      "properties": {
-        "entrezId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "hugoSymbol": {
-          "type": "string"
+      "ClinicalAttributeCountFilter": {
+        "type": "object",
+        "properties": {
+          "sampleIdentifiers": {
+            "maxItems": 10000000,
+            "minItems": 1,
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/SampleIdentifier"
+            }
+          },
+          "sampleListId": {
+            "type": "string"
+          }
         },
-        "specialValue": {
-          "enum": [
-            "ANY_GENE",
-            "NO_GENE"
-          ],
-          "type": "string"
-        }
+        "description": "List of SampleIdentifiers or Sample List ID"
       },
-      "type": "object"
-    },
-    "StructuralVariantQuery": {
-      "properties": {
-        "gene1": {
-          "$ref": "#/definitions/StructuralVariantGeneSubQuery"
-        },
-        "gene2": {
-          "$ref": "#/definitions/StructuralVariantGeneSubQuery"
+      "ClinicalAttributeCount": {
+        "type": "object",
+        "properties": {
+          "count": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "clinicalAttributeId": {
+            "type": "string"
+          }
         }
       },
-      "type": "object"
-    },
-    "StudyViewFilter": {
-      "description": "Study view filter",
-      "properties": {
-        "alterationFilter": {
-          "$ref": "#/definitions/AlterationFilter"
-        },
-        "caseLists": {
-          "items": {
+      "MolecularProfileCasesGroupAndAlterationTypeFilter": {
+        "type": "object",
+        "properties": {
+          "alterationEventTypes": {
+            "$ref": "#/components/schemas/AlterationFilter"
+          },
+          "molecularProfileCasesGroupFilter": {
+            "maxItems": 10000000,
+            "minItems": 1,
+            "type": "array",
             "items": {
-              "type": "string"
-            },
-            "type": "array"
-          },
-          "type": "array"
-        },
-        "clinicalDataFilters": {
-          "items": {
-            "$ref": "#/definitions/ClinicalDataFilter"
-          },
-          "type": "array"
+              "$ref": "#/components/schemas/MolecularProfileCasesGroupFilter"
+            }
+          }
         },
-        "clinicalEventFilters": {
-          "items": {
-            "$ref": "#/definitions/DataFilter"
+        "description": "List of groups containing sample identifiers and list of Alteration Types"
+      },
+      "AlterationEnrichment": {
+        "required": [
+          "counts",
+          "entrezGeneId",
+          "hugoGeneSymbol"
+        ],
+        "type": "object",
+        "properties": {
+          "entrezGeneId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "hugoGeneSymbol": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "customDataFilters": {
-          "items": {
-            "$ref": "#/definitions/ClinicalDataFilter"
+          "cytoband": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "geneFilters": {
-          "items": {
-            "$ref": "#/definitions/GeneFilter"
+          "counts": {
+            "type": "array",
+            "items": {
+              "$ref": "#/components/schemas/CountSummary"
+            }
           },
-          "type": "array"
-        },
-        "genericAssayDataFilters": {
-          "items": {
-            "$ref": "#/definitions/GenericAssayDataFilter"
+          "pValue": {
+            "type": "number"
+          }
+        }
+      },
+      "CountSummary": {
+        "required": [
+          "alteredCount",
+          "name",
+          "profiledCount"
+        ],
+        "type": "object",
+        "properties": {
+          "name": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "genomicDataFilters": {
-          "items": {
-            "$ref": "#/definitions/GenomicDataFilter"
+          "alteredCount": {
+            "type": "integer",
+            "format": "int32"
           },
-          "type": "array"
-        },
-        "genomicProfiles": {
-          "items": {
-            "items": {
-              "type": "string"
-            },
-            "type": "array"
+          "profiledCount": {
+            "type": "integer",
+            "format": "int32"
+          }
+        }
+      },
+      "MutSig": {
+        "required": [
+          "entrezGeneId",
+          "hugoGeneSymbol",
+          "numberOfMutations",
+          "pValue",
+          "qValue",
+          "rank",
+          "studyId"
+        ],
+        "type": "object",
+        "properties": {
+          "entrezGeneId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "hugoGeneSymbol": {
+            "type": "string"
           },
-          "type": "array"
-        },
-        "mutationDataFilters": {
-          "items": {
-            "$ref": "#/definitions/MutationDataFilter"
+          "rank": {
+            "type": "integer",
+            "format": "int32"
           },
-          "type": "array"
-        },
-        "patientTreatmentFilters": {
-          "$ref": "#/definitions/AndedPatientTreatmentFilters"
-        },
-        "patientTreatmentGroupFilters": {
-          "$ref": "#/definitions/AndedPatientTreatmentFilters"
-        },
-        "patientTreatmentTargetFilters": {
-          "$ref": "#/definitions/AndedPatientTreatmentFilters"
-        },
-        "sampleIdentifiers": {
-          "items": {
-            "$ref": "#/definitions/SampleIdentifier"
+          "studyId": {
+            "type": "string"
           },
-          "maxItems": 2147483647,
-          "minItems": 1,
-          "type": "array"
-        },
-        "sampleTreatmentFilters": {
-          "$ref": "#/definitions/AndedSampleTreatmentFilters"
-        },
-        "sampleTreatmentGroupFilters": {
-          "$ref": "#/definitions/AndedSampleTreatmentFilters"
-        },
-        "sampleTreatmentTargetFilters": {
-          "$ref": "#/definitions/AndedSampleTreatmentFilters"
-        },
-        "structuralVariantFilters": {
-          "items": {
-            "$ref": "#/definitions/StudyViewStructuralVariantFilter"
+          "numberOfMutations": {
+            "type": "integer",
+            "format": "int32"
           },
-          "type": "array"
-        },
-        "studyIds": {
-          "items": {
-            "maxLength": 2147483647,
-            "minLength": 1,
-            "type": "string"
+          "pValue": {
+            "type": "number"
           },
-          "maxItems": 2147483647,
-          "minItems": 1,
-          "type": "array"
+          "qValue": {
+            "type": "number"
+          }
         }
       },
-      "type": "object"
-    },
-    "StudyViewStructuralVariantFilter": {
-      "properties": {
-        "molecularProfileIds": {
-          "items": {
+      "Gistic": {
+        "required": [
+          "amp",
+          "chromosome",
+          "cytoband",
+          "qValue",
+          "studyId",
+          "widePeakEnd",
+          "widePeakStart"
+        ],
+        "type": "object",
+        "properties": {
+          "chromosome": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "cytoband": {
             "type": "string"
           },
-          "type": "array",
-          "uniqueItems": true
-        },
-        "structVarQueries": {
-          "items": {
+          "widePeakStart": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "widePeakEnd": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "amp": {
+            "type": "boolean"
+          },
+          "genes": {
+            "type": "array",
             "items": {
-              "$ref": "#/definitions/StructuralVariantFilterQuery"
-            },
-            "type": "array"
+              "$ref": "#/components/schemas/GisticToGene"
+            }
           },
-          "type": "array"
-        }
-      },
-      "type": "object"
-    },
-    "SurvivalRequest": {
-      "description": "Survival Data Request",
-      "properties": {
-        "attributeIdPrefix": {
-          "type": "string"
-        },
-        "censoredEventRequestIdentifier": {
-          "$ref": "#/definitions/ClinicalEventRequestIdentifier"
-        },
-        "endEventRequestIdentifier": {
-          "$ref": "#/definitions/ClinicalEventRequestIdentifier"
-        },
-        "patientIdentifiers": {
-          "items": {
-            "$ref": "#/definitions/PatientIdentifier"
+          "studyId": {
+            "type": "string"
           },
-          "maxItems": 10000000,
-          "minItems": 1,
-          "type": "array"
-        },
-        "startEventRequestIdentifier": {
-          "$ref": "#/definitions/ClinicalEventRequestIdentifier"
+          "qValue": {
+            "type": "number"
+          }
         }
       },
-      "required": [
-        "attributeIdPrefix"
-      ],
-      "type": "object"
-    },
-    "VariantCount": {
-      "properties": {
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "keyword": {
-          "type": "string"
-        },
-        "molecularProfileId": {
-          "type": "string"
-        },
-        "numberOfSamples": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "numberOfSamplesWithKeyword": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "numberOfSamplesWithMutationInGene": {
-          "format": "int32",
-          "type": "integer"
+      "GisticToGene": {
+        "required": [
+          "entrezGeneId",
+          "hugoGeneSymbol"
+        ],
+        "type": "object",
+        "properties": {
+          "entrezGeneId": {
+            "type": "integer",
+            "format": "int32"
+          },
+          "hugoGeneSymbol": {
+            "type": "string"
+          }
         }
       },
-      "required": [
-        "entrezGeneId",
-        "molecularProfileId",
-        "numberOfSamples",
-        "numberOfSamplesWithKeyword",
-        "numberOfSamplesWithMutationInGene"
-      ],
-      "type": "object"
-    },
-    "VariantCountIdentifier": {
-      "properties": {
-        "entrezGeneId": {
-          "format": "int32",
-          "type": "integer"
-        },
-        "keyword": {
-          "type": "string"
+      "ResourceData": {
+        "required": [
+          "resourceId",
+          "studyId",
+          "url"
+        ],
+        "type": "object",
+        "properties": {
+          "uniqueSampleKey": {
+            "type": "string"
+          },
+          "uniquePatientKey": {
+            "type": "string"
+          },
+          "sampleId": {
+            "type": "string"
+          },
+          "patientId": {
+            "type": "string"
+          },
+          "studyId": {
+            "type": "string"
+          },
+          "resourceId": {
+            "type": "string"
+          },
+          "url": {
+            "type": "string"
+          },
+          "resourceDefinition": {
+            "$ref": "#/components/schemas/ResourceDefinition"
+          }
         }
-      },
-      "type": "object"
+      }
     }
-  },
-  "externalDocs": {
-    "description": "SpringShop Wiki Documentation",
-    "url": "https://springshop.wiki.github.org/docs"
-  },
-  "x-components": {}
-}
\ No newline at end of file
+  }
+}
diff --git a/src/pages/patientView/timeline/VAFChartControls.tsx b/src/pages/patientView/timeline/VAFChartControls.tsx
index 66eb2cacc89..a6999ed61d2 100644
--- a/src/pages/patientView/timeline/VAFChartControls.tsx
+++ b/src/pages/patientView/timeline/VAFChartControls.tsx
@@ -8,7 +8,7 @@ import SampleManager, {
 import LabeledCheckbox from '../../../shared/components/labeledCheckbox/LabeledCheckbox';
 import VAFChartWrapperStore from './VAFChartWrapperStore';
 import _ from 'lodash';
-
+import { CheckedSelect } from 'cbioportal-frontend-commons';
 interface IVAFChartControlsProps {
     wrapperStore: VAFChartWrapperStore;
     sampleManager: SampleManager;
@@ -23,6 +23,7 @@ export const SELECT_SAMPLE_NONE = {
     label: 'None',
     value: 'None',
 };
+export const SELECTED_SAMPLE_PLACEHOLDER = 'Selected Samples';
 
 const VAFChartControls: React.FunctionComponent<IVAFChartControlsProps> = observer(
     function({ wrapperStore, sampleManager }) {
@@ -32,8 +33,6 @@ const VAFChartControls: React.FunctionComponent<IVAFChartControlsProps> = observ
         ] = useState(true);
 
         const selectedSamplesOptions = [
-            SELECT_SAMPLE_ALL,
-            SELECT_SAMPLE_NONE,
             ...sampleIdsForSamples(sampleManager.samples).map(item => ({
                 label: `${item.value}`,
                 value: `${item.id}`,
@@ -42,36 +41,19 @@ const VAFChartControls: React.FunctionComponent<IVAFChartControlsProps> = observ
 
         function selectSamplesByValue() {
             let allSelectedSamples = selectedSamplesOptions;
-            allSelectedSamples = allSelectedSamples.filter(sample => {
-                return (
-                    sample.label != SELECT_SAMPLE_ALL.label &&
-                    sample.label != SELECT_SAMPLE_NONE.label
-                );
-            });
             if (isInitialSelectedSamples) {
                 console.log('running initial');
                 wrapperStore.setSelectedSamplesOptions(allSelectedSamples);
                 setisInitialSelectedSamples(!isInitialSelectedSamples);
             }
-            if (wrapperStore.selectedSamplesOptions.length === 0) {
-                return {
-                    label: 'None',
-                    value: 'None',
-                };
-            }
-            if (
-                _.isEqual(
-                    wrapperStore.selectedSamplesOptions,
-                    allSelectedSamples
-                )
-            ) {
-                return {
-                    label: 'All',
-                    value: 'All',
-                };
-            }
-
-            return wrapperStore.selectedSamplesOptions;
+            console.log(
+                `wrapper store : ${JSON.stringify(
+                    wrapperStore.selectedSamplesOptions
+                )}`
+            );
+            return wrapperStore.selectedSamplesOptions.map(sample => ({
+                value: sample.value,
+            }));
         }
 
         const groupByOptions = [
@@ -127,60 +109,30 @@ const VAFChartControls: React.FunctionComponent<IVAFChartControlsProps> = observ
 
         return (
             <div className={'VAFChartControls'} data-test={'VAFChartControls'}>
-                <label>
-                    Select Samples:&nbsp;
-                    <ReactSelect
+                <div style={{ width: '100%', maxWidth: '300px' }}>
+                    <CheckedSelect
                         name={'select-by-sample-select'}
                         value={selectSamplesByValue()}
                         options={selectedSamplesOptions}
+                        placeholder={SELECTED_SAMPLE_PLACEHOLDER}
                         onChange={(options: Array<any>) => {
-                            if (options.indexOf(SELECT_SAMPLE_ALL) !== -1) {
-                                wrapperStore.setSelectedSamplesOptions(
-                                    sampleIdsForSamples(
-                                        sampleManager.samples
-                                    ).map(item => ({
-                                        label: `${item.value}`,
-                                        value: `${item.id}`,
-                                    }))
-                                );
-                            } else if (
-                                options.indexOf(SELECT_SAMPLE_NONE) !== -1
-                            ) {
-                                wrapperStore.setSelectedSamplesOptions([]);
-                            } else {
-                                console.log(
-                                    `options before filter : ${JSON.stringify(
-                                        options
-                                    )}`
-                                );
-                                options = options.filter(
-                                    sample =>
-                                        sample.label !=
-                                            SELECT_SAMPLE_NONE.label &&
-                                        sample.label != SELECT_SAMPLE_ALL.label
-                                );
-                                console.log(
-                                    `options after filter : ${JSON.stringify(
-                                        options
-                                    )}`
-                                );
-                                wrapperStore.setSelectedSamplesOptions(options);
-                            }
+                            console.log(`Options : ${JSON.stringify(options)}`);
+                            options = options.map(option => {
+                                return {
+                                    value: option.value,
+                                    label: option.value,
+                                };
+                            });
+                            wrapperStore.setSelectedSamplesOptions(options);
                         }}
-                        styles={{
-                            container: (styles: any) => ({
-                                ...styles,
-                                width: 250,
-                            }),
-                        }}
-                        isMulti
-                        components={{
-                            Option: SelectedSampleChecklistComponent,
-                        }}
-                        closeMenuOnSelect={false}
-                        hideSelectedOptions={false}
+                        // isMulti
+                        // components={{
+                        //     Option: SelectedSampleChecklistComponent,
+                        // }}
+                        // closeMenuOnSelect={false}
+                        // hideSelectedOptions={false}
                     />
-                </label>
+                </div>
 
                 <label>
                     Group by:&nbsp;
diff --git a/src/pages/patientView/timeline/VAFChartUtils.spec.ts b/src/pages/patientView/timeline/VAFChartUtils.spec.ts
index 203f7b52c61..139574cb568 100644
--- a/src/pages/patientView/timeline/VAFChartUtils.spec.ts
+++ b/src/pages/patientView/timeline/VAFChartUtils.spec.ts
@@ -88,6 +88,13 @@ describe('VAFChartUtils', () => {
             } as Sample;
         }
 
+        function makeSelectedSample(i: number) {
+            return {
+                label: `sample${i}`,
+                value: `sample${i}`,
+            };
+        }
+
         function makeMutation(
             sampleI: number,
             hugoGeneSymbol: string,
@@ -187,7 +194,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {}
                 ),
                 {
@@ -229,7 +240,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {}
                 ),
                 {
@@ -382,7 +397,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {}
                 ),
                 {
@@ -518,7 +537,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {}
                 ),
                 {
@@ -615,7 +638,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     GROUP_BY_NONE,
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {}
                 ),
                 {
@@ -741,7 +768,11 @@ describe('VAFChartUtils', () => {
                         ]
                     ),
                     GROUP_BY_NONE,
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {}
                 ),
                 {
@@ -839,7 +870,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2], [3]),
                     GROUP_BY_NONE,
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {}
                 ),
                 {
@@ -925,7 +960,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     'SampleType',
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {
                         sample1: 'Primary',
                         sample2: 'Recurrence',
@@ -1086,7 +1125,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     'SampleCollectionSource',
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {
                         sample1: 'Outside',
                         sample2: 'Inside',
@@ -1199,7 +1242,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     'SampleCollectionSource',
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {
                         sample1: 'Outside',
                         sample2: 'Inside',
@@ -1286,7 +1333,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3], []),
                     'SampleCollectionSource',
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {
                         sample1: 'Outside',
                         sample2: 'Inside',
@@ -1399,7 +1450,11 @@ describe('VAFChartUtils', () => {
                         ]
                     ),
                     'SampleCollectionSource',
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {
                         sample1: 'Outside',
                         sample2: 'Inside',
@@ -1482,7 +1537,11 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2], [3]),
                     'SampleType',
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                    ],
                     {
                         sample1: 'Primary',
                         sample2: 'Recurrence',
@@ -1565,7 +1624,12 @@ describe('VAFChartUtils', () => {
                     'mutations',
                     makeCoverageInfo([1, 2, 3, 4], []),
                     'TumorPurity',
-                    [],
+                    [
+                        makeSelectedSample(1),
+                        makeSelectedSample(2),
+                        makeSelectedSample(3),
+                        makeSelectedSample(4),
+                    ],
                     { sample2: '40', sample3: '30', sample4: '30' }
                 ),
                 {
diff --git a/src/pages/patientView/timeline/VAFChartUtils.ts b/src/pages/patientView/timeline/VAFChartUtils.ts
index baa120d91e2..3507fe898ca 100644
--- a/src/pages/patientView/timeline/VAFChartUtils.ts
+++ b/src/pages/patientView/timeline/VAFChartUtils.ts
@@ -53,7 +53,7 @@ export function computeRenderData(
     mutationProfileId: string,
     coverageInformation: CoverageInformation,
     groupByOption: string,
-    selectedSamplesOption: string[],
+    selectedSamplesOption: any[],
     sampleIdToClinicalValue: { [sampleId: string]: string }
 ) {
     const grayPoints: IPoint[] = []; // points that are purely interpolated for rendering, dont have data of their own
diff --git a/src/pages/patientView/timeline/VAFChartWrapperStore.tsx b/src/pages/patientView/timeline/VAFChartWrapperStore.tsx
index b4e83f5a762..8f4619b6fdd 100644
--- a/src/pages/patientView/timeline/VAFChartWrapperStore.tsx
+++ b/src/pages/patientView/timeline/VAFChartWrapperStore.tsx
@@ -3,7 +3,7 @@ import { getServerConfig } from 'config/config';
 
 export default class VAFChartWrapperStore {
     @observable groupByOption: string | null = null;
-    @observable selectedSamplesOptions: Array<string> = [];
+    @observable selectedSamplesOptions: Array<any> = [];
 
     @observable _showSequentialMode: boolean = getServerConfig()
         .vaf_sequential_mode_default;