From 5ecc076f411f680687ec4fdaa7d82b314eeb3805 Mon Sep 17 00:00:00 2001
From: Nayib Gloria <55710092+nayib-jose-gloria@users.noreply.github.com>
Date: Mon, 23 Sep 2024 19:45:45 -0400
Subject: [PATCH 1/5] chore: isolate dev env for schema 5.2 test migration
 (#7342)

---
 .github/workflows/build-images-and-create-deployment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-images-and-create-deployment.yml b/.github/workflows/build-images-and-create-deployment.yml
index fbe35ab94cdd7..9a3ae1a7cffc8 100644
--- a/.github/workflows/build-images-and-create-deployment.yml
+++ b/.github/workflows/build-images-and-create-deployment.yml
@@ -45,7 +45,7 @@ jobs:
         uses: avakar/create-deployment@v1
         # To stop deployment to a specific DEPLOYMENT_STAGE remove it from condition below.
         # The DEPLOYMENT_STAGE that should be present are dev, stage, prod.
-        if: env.DEPLOYMENT_STAGE == 'prod' || env.DEPLOYMENT_STAGE == 'stage' || env.DEPLOYMENT_STAGE == 'dev'
+        if: env.DEPLOYMENT_STAGE == 'prod' || env.DEPLOYMENT_STAGE == 'stage'
         with:
           auto_merge: false
           environment: ${{ env.DEPLOYMENT_STAGE }}

From 5e98d1df659eebdf35de6844b45e51c871c40893 Mon Sep 17 00:00:00 2001
From: Mim Hastie <mim@clevercanary.com>
Date: Thu, 26 Sep 2024 12:44:19 -0700
Subject: [PATCH 2/5] feat: 5.2.0 dev stage UI (#7345)

---
 .../common/Filter/common/constants.ts         | 140 ++++------
 frontend/tests/features/filter/constants.ts   | 240 ++++++++++++++++++
 .../features/filter/useCategoryFilter.test.ts |  76 ++----
 frontend/tests/features/filter/utils.test.ts  |  14 +-
 4 files changed, 306 insertions(+), 164 deletions(-)
 create mode 100644 frontend/tests/features/filter/constants.ts

diff --git a/frontend/src/components/common/Filter/common/constants.ts b/frontend/src/components/common/Filter/common/constants.ts
index 18176c3862008..147494e7b3204 100644
--- a/frontend/src/components/common/Filter/common/constants.ts
+++ b/frontend/src/components/common/Filter/common/constants.ts
@@ -26,78 +26,56 @@ export const DEVELOPMENT_STAGE_ONTOLOGY_TERM_SET: OntologyTermSet = {
         {
           label: "Embryonic human (0–56 days)",
           ontology_term_id: "HsapDv:0000002",
+        },
+        {
+          label: "Fetal (>56 days–birth)",
+          ontology_term_id: "HsapDv:0000037",
+        },
+      ],
+    },
+    {
+      label: "Postnatal human",
+      ontology_term_id: "HsapDv:0010000",
+      children: [
+        {
+          label: "Pediatric (0-15 years)",
+          ontology_term_id: "HsapDv:0000264",
           children: [
             {
-              label: "Carnegie (CS1)",
-              ontology_term_id: "HsapDv:0000003",
-            },
-            {
-              label: "Cleavage (CS2)",
-              ontology_term_id: "HsapDv:0000004",
-            },
-            {
-              label: "Blastula (CS3–5)",
-              ontology_term_id: "HsapDv:0000006",
+              label: "Newborn human (0-28 days)",
+              ontology_term_id: "HsapDv:0000262",
             },
             {
-              label: "Gastrula (CS6)",
-              ontology_term_id: "HsapDv:0000010",
+              label: "Infant (28 days-1 year)",
+              ontology_term_id: "HsapDv:0000261",
             },
             {
-              label: "Neurula (CS7–8)",
-              ontology_term_id: "HsapDv:0000012",
+              label: "Child (1-5 years)",
+              ontology_term_id: "HsapDv:0000265",
             },
             {
-              label: "Organogenesis (CS9–23)",
-              ontology_term_id: "HsapDv:0000015",
+              label: "Juvenile (5-15 years)",
+              ontology_term_id: "HsapDv:0000271",
             },
           ],
         },
-        {
-          label: "Fetal (>56 days–birth)",
-          ontology_term_id: "HsapDv:0000037",
-        },
       ],
     },
     {
-      label: "Immature (0–12 years)",
-      ontology_term_id: "HsapDv:0000080",
+      label: "Adult (15+ years)",
+      ontology_term_id: "HsapDv:0000258",
       children: [
         {
-          label: "Newborn human (0–1 month)",
-          ontology_term_id: "HsapDv:0000082",
-        },
-        {
-          label: "Infant (1–23 months)",
-          ontology_term_id: "HsapDv:0000083",
+          label: "Young adult (15-40 years)",
+          ontology_term_id: "HsapDv:0000266",
         },
         {
-          label: "Child (2–12 years)",
-          ontology_term_id: "HsapDv:0000081",
-        },
-      ],
-    },
-    {
-      label: "Mature (13+ years)",
-      ontology_term_id: "HsapDv:0000204",
-      children: [
-        {
-          label: "Adolescent (13–19 years)",
-          ontology_term_id: "HsapDv:0000086",
+          label: "Middle aged (40-60 years)",
+          ontology_term_id: "HsapDv:0000267",
         },
         {
-          label: "Human adult (19+ years)",
-          ontology_term_id: "HsapDv:0000087",
-          children: [
-            {
-              label: "Early adulthood (19–45 years)",
-              ontology_term_id: "HsapDv:0000088",
-            },
-            {
-              label: "Late adulthood (45+ years)",
-              ontology_term_id: "HsapDv:0000091",
-            },
-          ],
+          label: "Late adult (60+ years)",
+          ontology_term_id: "HsapDv:0000227",
         },
       ],
     },
@@ -110,32 +88,6 @@ export const DEVELOPMENT_STAGE_ONTOLOGY_TERM_SET: OntologyTermSet = {
         {
           label: "Embryonic mouse",
           ontology_term_id: "MmusDv:0000002",
-          children: [
-            {
-              label: "Thelier stage 1 (TS1)",
-              ontology_term_id: "MmusDv:0000003",
-            },
-            {
-              label: "Cleavage (TS2–3)",
-              ontology_term_id: "MmusDv:0000004",
-            },
-            {
-              label: "Blastula (TS4–8)",
-              ontology_term_id: "MmusDv:0000007",
-            },
-            {
-              label: "Gastrula (TS9–10)",
-              ontology_term_id: "MmusDv:0000013",
-            },
-            {
-              label: "Thelier stage 11 (TS11)",
-              ontology_term_id: "MmusDv:0000017",
-            },
-            {
-              label: "Organogenesis (TS11–22)",
-              ontology_term_id: "MmusDv:0000018",
-            },
-          ],
         },
         {
           label: "Fetal (TS23–26)",
@@ -144,34 +96,34 @@ export const DEVELOPMENT_STAGE_ONTOLOGY_TERM_SET: OntologyTermSet = {
       ],
     },
     {
-      label: "Post-partum (Birth+)",
+      label: "Postnatal mouse",
       ontology_term_id: "MmusDv:0000092",
       children: [
         {
-          label: "Immature (0–6 weeks)",
+          label: "Immature (0-6 weeks)",
           ontology_term_id: "MmusDv:0000043",
-          children: [
-            {
-              label: "Thelier stage 27 (0–3 days)",
-              ontology_term_id: "MmusDv:0000036",
-            },
-            {
-              label: "Premature (3 days–6 weeks)",
-              ontology_term_id: "MmusDv:0000112",
-            },
-          ],
         },
         {
           label: "Mature (6+ weeks)",
           ontology_term_id: "MmusDv:0000110",
           children: [
             {
-              label: "Early adulthood (6 weeks–7 months)",
-              ontology_term_id: "MmusDv:0000061",
+              label: "Prime adult (6 weeks-18 months)",
+              ontology_term_id: "MmusDv:0000136",
+              children: [
+                {
+                  label: "Young adult (6 weeks-10 months)",
+                  ontology_term_id: "MmusDv:0000153",
+                },
+                {
+                  label: "Middle aged (10-18 months)",
+                  ontology_term_id: "MmusDv:0000135",
+                },
+              ],
             },
             {
-              label: "Late adulthood (7+ months)",
-              ontology_term_id: "MmusDv:0000097",
+              label: "Late adult (18+ months)",
+              ontology_term_id: "MmusDv:0000134",
             },
           ],
         },
diff --git a/frontend/tests/features/filter/constants.ts b/frontend/tests/features/filter/constants.ts
new file mode 100644
index 0000000000000..5550d98ea15f5
--- /dev/null
+++ b/frontend/tests/features/filter/constants.ts
@@ -0,0 +1,240 @@
+import {
+  OntologyTermSet,
+  ONTOLOGY_VIEW_KEY,
+} from "src/components/common/Filter/common/entities";
+
+/**
+ * Test-specific ontology term set optimized for testing completeness; should not
+ * be updated on schema update. Ontology values do not matter here, only ontology
+ * structure/heirarchy.
+ */
+export const TEST_ONTOLOGY_TERM_SET: OntologyTermSet = {
+  [ONTOLOGY_VIEW_KEY.HsapDv]: [
+    {
+      label: "Prenatal (conception–birth)",
+      ontology_term_id: "HsapDv:0000045",
+      children: [
+        {
+          label: "Embryonic human (0–56 days)",
+          ontology_term_id: "HsapDv:0000002",
+          children: [
+            {
+              label: "Carnegie (CS1)",
+              ontology_term_id: "HsapDv:0000003",
+            },
+            {
+              label: "Cleavage (CS2)",
+              ontology_term_id: "HsapDv:0000004",
+            },
+            {
+              label: "Blastula (CS3–5)",
+              ontology_term_id: "HsapDv:0000006",
+            },
+            {
+              label: "Gastrula (CS6)",
+              ontology_term_id: "HsapDv:0000010",
+            },
+            {
+              label: "Neurula (CS7–8)",
+              ontology_term_id: "HsapDv:0000012",
+            },
+            {
+              label: "Organogenesis (CS9–23)",
+              ontology_term_id: "HsapDv:0000015",
+            },
+          ],
+        },
+        {
+          label: "Fetal (>56 days–birth)",
+          ontology_term_id: "HsapDv:0000037",
+        },
+      ],
+    },
+    {
+      label: "Immature (0–12 years)",
+      ontology_term_id: "HsapDv:0000080",
+      children: [
+        {
+          label: "Newborn human (0–1 month)",
+          ontology_term_id: "HsapDv:0000082",
+        },
+        {
+          label: "Infant (1–23 months)",
+          ontology_term_id: "HsapDv:0000083",
+        },
+        {
+          label: "Child (2–12 years)",
+          ontology_term_id: "HsapDv:0000081",
+        },
+      ],
+    },
+    {
+      label: "Mature (13+ years)",
+      ontology_term_id: "HsapDv:0000204",
+      children: [
+        {
+          label: "Adolescent (13–19 years)",
+          ontology_term_id: "HsapDv:0000086",
+        },
+        {
+          label: "Human adult (19+ years)",
+          ontology_term_id: "HsapDv:0000087",
+          children: [
+            {
+              label: "Early adulthood (19–45 years)",
+              ontology_term_id: "HsapDv:0000088",
+            },
+            {
+              label: "Late adulthood (45+ years)",
+              ontology_term_id: "HsapDv:0000091",
+            },
+          ],
+        },
+      ],
+    },
+  ],
+  [ONTOLOGY_VIEW_KEY.MmusDv]: [
+    {
+      label: "Prenatal",
+      ontology_term_id: "MmusDv:0000042",
+      children: [
+        {
+          label: "Embryonic mouse",
+          ontology_term_id: "MmusDv:0000002",
+          children: [
+            {
+              label: "Thelier stage 1 (TS1)",
+              ontology_term_id: "MmusDv:0000003",
+            },
+            {
+              label: "Cleavage (TS2–3)",
+              ontology_term_id: "MmusDv:0000004",
+            },
+            {
+              label: "Blastula (TS4–8)",
+              ontology_term_id: "MmusDv:0000007",
+            },
+            {
+              label: "Gastrula (TS9–10)",
+              ontology_term_id: "MmusDv:0000013",
+            },
+            {
+              label: "Thelier stage 11 (TS11)",
+              ontology_term_id: "MmusDv:0000017",
+            },
+            {
+              label: "Organogenesis (TS11–22)",
+              ontology_term_id: "MmusDv:0000018",
+            },
+          ],
+        },
+        {
+          label: "Fetal (TS23–26)",
+          ontology_term_id: "MmusDv:0000031",
+        },
+      ],
+    },
+    {
+      label: "Post-partum (Birth+)",
+      ontology_term_id: "MmusDv:0000092",
+      children: [
+        {
+          label: "Immature (0–6 weeks)",
+          ontology_term_id: "MmusDv:0000043",
+          children: [
+            {
+              label: "Thelier stage 27 (0–3 days)",
+              ontology_term_id: "MmusDv:0000036",
+            },
+            {
+              label: "Premature (3 days–6 weeks)",
+              ontology_term_id: "MmusDv:0000112",
+            },
+          ],
+        },
+        {
+          label: "Mature (6+ weeks)",
+          ontology_term_id: "MmusDv:0000110",
+          children: [
+            {
+              label: "Early adulthood (6 weeks–7 months)",
+              ontology_term_id: "MmusDv:0000061",
+            },
+            {
+              label: "Late adulthood (7+ months)",
+              ontology_term_id: "MmusDv:0000097",
+            },
+          ],
+        },
+      ],
+    },
+  ],
+  [ONTOLOGY_VIEW_KEY.UBERON]: [
+    {
+      label: "Embryo",
+      ontology_term_id: "UBERON:0000068",
+      children: [
+        {
+          label: "Zygote",
+          ontology_term_id: "UBERON:0000106",
+        },
+        {
+          label: "Cleavage",
+          ontology_term_id: "UBERON:0000107",
+        },
+        {
+          label: "Blastula",
+          ontology_term_id: "UBERON:0000108",
+        },
+        {
+          label: "Gastrula",
+          ontology_term_id: "UBERON:0000109",
+        },
+        {
+          label: "Neurula",
+          ontology_term_id: "UBERON:0000110",
+        },
+        {
+          label: "Organogenesis",
+          ontology_term_id: "UBERON:0000111",
+        },
+        {
+          label: "Late embryonic",
+          ontology_term_id: "UBERON:0007220",
+        },
+      ],
+    },
+    {
+      label: "Post embryonic",
+      ontology_term_id: "UBERON:0000092",
+      children: [
+        {
+          label: "Larval",
+          ontology_term_id: "UBERON:0000069",
+        },
+        {
+          label: "Pupal",
+          ontology_term_id: "UBERON:0000070",
+        },
+        {
+          label: "Nursing",
+          ontology_term_id: "UBERON:0018685",
+        },
+        {
+          label: "Fully formed",
+          ontology_term_id: "UBERON:0000066",
+          children: [
+            {
+              label: "Sexually immature",
+              ontology_term_id: "UBERON:0000112",
+            },
+            {
+              label: "Post-juvenile adult",
+              ontology_term_id: "UBERON:0000113",
+            },
+          ],
+        },
+      ],
+    },
+  ],
+};
diff --git a/frontend/tests/features/filter/useCategoryFilter.test.ts b/frontend/tests/features/filter/useCategoryFilter.test.ts
index 961fae27ed5d7..28cf9ff69b130 100644
--- a/frontend/tests/features/filter/useCategoryFilter.test.ts
+++ b/frontend/tests/features/filter/useCategoryFilter.test.ts
@@ -68,7 +68,6 @@ import {
 import {
   CategoryValueId,
   CATEGORY_FILTER_ID,
-  CuratedOntologyCategoryFilterConfig,
   DatasetRow,
   MultiPanelCategoryFilterUIState,
   MultiPanelOntologyCategoryView,
@@ -80,6 +79,7 @@ import {
   SelectCategoryValueView,
 } from "src/components/common/Filter/common/entities";
 import { test } from "tests/common/test";
+import { TEST_ONTOLOGY_TERM_SET } from "./constants";
 
 const { describe } = test;
 
@@ -2926,6 +2926,8 @@ describe("useCategoryFilter", () => {
     //   Newborn human - HsapDv:0000082
     //   Infant - HsapDv:0000083
     //   Child - HsapDv:0000081
+    //
+    // Note, this tree matches the test ontology term test and not the current pinned ontology.
     const CATEGORY_VALUE_KEYS = new Set([
       ONTOLOGY_ID_HUMAN_PRENATAL,
       ONTOLOGY_ID_HUMAN_EMBRYONIC_HUMAN,
@@ -2960,11 +2962,7 @@ describe("useCategoryFilter", () => {
           idToDeselect,
           filters,
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(0);
       });
@@ -2993,11 +2991,7 @@ describe("useCategoryFilter", () => {
           idToDeselect,
           filters,
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(1);
         expect(
@@ -3031,11 +3025,7 @@ describe("useCategoryFilter", () => {
           idToDeselect,
           filters,
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(0);
       });
@@ -3068,11 +3058,7 @@ describe("useCategoryFilter", () => {
           idToDeselect,
           filters,
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(1);
         expect(nextFilters.includes(ONTOLOGY_ID_HUMAN_FETAL)).toBeTruthy();
@@ -3092,11 +3078,7 @@ describe("useCategoryFilter", () => {
           idToSelect,
           [], // No filters selected
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(1);
         expect(nextFilters[0]).toEqual(idToSelect);
@@ -3122,11 +3104,7 @@ describe("useCategoryFilter", () => {
             },
           ],
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(2);
         expect(nextFilters.includes(ONTOLOGY_ID_HUMAN_NEWBORN)).toBeTruthy();
@@ -3153,11 +3131,7 @@ describe("useCategoryFilter", () => {
             },
           ],
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(4);
         expect(nextFilters.includes(ONTOLOGY_ID_HUMAN_NEWBORN)).toBeTruthy();
@@ -3186,11 +3160,7 @@ describe("useCategoryFilter", () => {
             },
           ],
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(5);
         expect(nextFilters.includes(ONTOLOGY_ID_HUMAN_PRENATAL)).toBeTruthy();
@@ -3221,11 +3191,7 @@ describe("useCategoryFilter", () => {
           ONTOLOGY_ID_HUMAN_EMBRYONIC_HUMAN,
           [], // No filters
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(3);
         expect(
@@ -3259,11 +3225,7 @@ describe("useCategoryFilter", () => {
             },
           ],
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(3);
         expect(
@@ -3299,11 +3261,7 @@ describe("useCategoryFilter", () => {
             },
           ],
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(5);
         expect(nextFilters.includes(ONTOLOGY_ID_HUMAN_PRENATAL)).toBeTruthy();
@@ -3345,11 +3303,7 @@ describe("useCategoryFilter", () => {
             },
           ],
           CATEGORY_VALUE_KEYS,
-          (
-            CATEGORY_FILTER_CONFIGS_BY_ID[
-              CATEGORY_FILTER_ID.DEVELOPMENT_STAGE
-            ] as CuratedOntologyCategoryFilterConfig
-          ).source
+          TEST_ONTOLOGY_TERM_SET
         );
         expect(nextFilters.length).toEqual(2);
         expect(
diff --git a/frontend/tests/features/filter/utils.test.ts b/frontend/tests/features/filter/utils.test.ts
index c9ae0f4fd07ad..d3b330f42b6e2 100644
--- a/frontend/tests/features/filter/utils.test.ts
+++ b/frontend/tests/features/filter/utils.test.ts
@@ -3,7 +3,6 @@
  */
 
 import test, { expect } from "@playwright/test";
-import { DEVELOPMENT_STAGE_ONTOLOGY_TERM_SET } from "src/components/common/Filter/common/constants";
 import {
   findOntologyNodeById,
   findOntologyParentNode,
@@ -12,6 +11,7 @@ import {
   SYMBOL_MILLION,
   SYMBOL_THOUSAND,
 } from "src/components/common/Filter/common/utils";
+import { TEST_ONTOLOGY_TERM_SET } from "./constants";
 
 const { describe } = test;
 
@@ -156,8 +156,7 @@ describe("filter", () => {
       ].forEach((ontologyId) => {
         test(`finds ontology node with ID ${ontologyId}`, () => {
           const ontologyKey = getOntologySpeciesKey(ontologyId);
-          const ontologyRootNodes =
-            DEVELOPMENT_STAGE_ONTOLOGY_TERM_SET[ontologyKey];
+          const ontologyRootNodes = TEST_ONTOLOGY_TERM_SET[ontologyKey];
           expect(ontologyRootNodes).toBeTruthy();
           const ontologyNode = findOntologyNodeById(
             // eslint-disable-next-line @typescript-eslint/no-non-null-assertion -- truthy check above
@@ -174,8 +173,7 @@ describe("filter", () => {
       test(`finds parent of ${ONTOLOGY_ID_HUMAN_EMBRYONIC_HUMAN}`, () => {
         const ontologyId = ONTOLOGY_ID_HUMAN_EMBRYONIC_HUMAN;
         const ontologyKey = getOntologySpeciesKey(ontologyId);
-        const ontologyRootNodes =
-          DEVELOPMENT_STAGE_ONTOLOGY_TERM_SET[ontologyKey];
+        const ontologyRootNodes = TEST_ONTOLOGY_TERM_SET[ontologyKey];
         expect(ontologyRootNodes).toBeTruthy();
         const ontologyNode = findOntologyNodeById(
           // eslint-disable-next-line @typescript-eslint/no-non-null-assertion -- truthy check above
@@ -195,8 +193,7 @@ describe("filter", () => {
       test(`finds parent of ${ONTOLOGY_ID_HUMAN_CARNEGIE_CS1}`, () => {
         const ontologyId = ONTOLOGY_ID_HUMAN_CARNEGIE_CS1;
         const ontologyKey = getOntologySpeciesKey(ontologyId);
-        const ontologyRootNodes =
-          DEVELOPMENT_STAGE_ONTOLOGY_TERM_SET[ontologyKey];
+        const ontologyRootNodes = TEST_ONTOLOGY_TERM_SET[ontologyKey];
         expect(ontologyRootNodes).toBeTruthy();
         const ontologyNode = findOntologyNodeById(
           // eslint-disable-next-line @typescript-eslint/no-non-null-assertion -- truthy check above
@@ -218,8 +215,7 @@ describe("filter", () => {
       test(`doesn't find parent of ${ONTOLOGY_ID_HUMAN_PRENATAL}`, () => {
         const ontologyId = ONTOLOGY_ID_HUMAN_PRENATAL;
         const ontologyKey = getOntologySpeciesKey(ontologyId);
-        const ontologyRootNodes =
-          DEVELOPMENT_STAGE_ONTOLOGY_TERM_SET[ontologyKey];
+        const ontologyRootNodes = TEST_ONTOLOGY_TERM_SET[ontologyKey];
         expect(ontologyRootNodes).toBeTruthy();
         const ontologyNode = findOntologyNodeById(
           // eslint-disable-next-line @typescript-eslint/no-non-null-assertion -- truthy check above

From a12556f997d9caa1cfbd52453446c5c4af460df3 Mon Sep 17 00:00:00 2001
From: Trent Smith <1429913+Bento007@users.noreply.github.com>
Date: Fri, 27 Sep 2024 11:38:43 -0700
Subject: [PATCH 3/5] chore: resolve deprecation warning and update
 requirements (#7275)

## Reason for Change

- resolving deprecation errors.
- keeping requirements up to date.

## Changes

- renamed `assertEquals` to `assertEqual` to resolve deprecated assertEquals
- rename `method_whitelist` to `allowed_methods` to resolve DeprecationWarning: Using 'method_whitelist' with Retry is deprecated and will be removed in v2.0. Use 'allowed_methods' instead
- use backend/server/requirements in backend portal container. This means we can remove the duplicate requirements in backend/requirements.txt
- Update requirements for the backend portal api.
- migrate to authlib 1.x.x
---
 Dockerfile.backend                              |  2 +-
 backend/api_server/index.html                   |  4 ++--
 backend/common/auth0_manager.py                 |  2 +-
 backend/common/census_cube/utils.py             |  8 ++++----
 backend/common/server/config.py                 |  6 ++++--
 backend/portal/api/app/v1/authentication.py     |  3 +--
 .../backend/common/server/requirements.txt      |  6 +++---
 python_dependencies/backend/requirements.txt    | 17 ++++-------------
 .../unit/backend/layers/api/test_portal_api.py  |  2 +-
 tests/unit/backend/wmg/test_query.py            |  4 ++--
 10 files changed, 23 insertions(+), 31 deletions(-)

diff --git a/Dockerfile.backend b/Dockerfile.backend
index 1563bf75e66c8..22596d9642eef 100644
--- a/Dockerfile.backend
+++ b/Dockerfile.backend
@@ -22,7 +22,7 @@ RUN python3 -m pip install --upgrade pip setuptools
 # TODO: Determine if cmake is really needed for ddtrace
 # see ticket: https://github.com/chanzuckerberg/single-cell-data-portal/issues/5821
 RUN python3 -m pip install cmake
-RUN python3 -m pip install -r requirements.txt
+RUN python3 -m pip install -r requirements.txt -r ./common/server/requirements.txt
 RUN if [ "$INSTALL_DEV" = "true" ]; then python3 -m pip install -r requirements-dev.txt; fi
 # Install awscli to download wmg snapshot to the local disk
 RUN python3 -m pip install awscli
diff --git a/backend/api_server/index.html b/backend/api_server/index.html
index 148b2d3d43c72..b9a9a13eb505b 100644
--- a/backend/api_server/index.html
+++ b/backend/api_server/index.html
@@ -9,8 +9,8 @@
     />
     <link
       rel="stylesheet"
-      href="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/3.0.13/swagger-ui.css"
-      integrity="sha256-Z7Z2kffooC4H3U4Myviypq5dO2IIGkmu7VRtd1YqNn8="
+      href="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/5.17.14/swagger-ui.css"
+      integrity="sha512-MvYROlKG3cDBPskMQgPmkNgZh85LIf68y7SZ34TIppaIHQz1M/3S/yYqzIfufdKDJjzB9Qu1BV63SZjimJkPvw=="
       crossorigin="anonymous"
     />
     <style>
diff --git a/backend/common/auth0_manager.py b/backend/common/auth0_manager.py
index cf85e59954879..1814b71dcc997 100644
--- a/backend/common/auth0_manager.py
+++ b/backend/common/auth0_manager.py
@@ -30,7 +30,7 @@ def session(self):
                 total=3,
                 backoff_factor=1,
                 status_forcelist=self.config.retry_status_forcelist,
-                method_whitelist=["POST", "HEAD", "GET", "PUT", "DELETE", "OPTIONS"],
+                allowed_methods=["POST", "HEAD", "GET", "PUT", "DELETE", "OPTIONS"],
             )
             session.mount("https://", HTTPAdapter(max_retries=retry_config))
 
diff --git a/backend/common/census_cube/utils.py b/backend/common/census_cube/utils.py
index 2c85da6a72b4e..759b1bbea1d9a 100644
--- a/backend/common/census_cube/utils.py
+++ b/backend/common/census_cube/utils.py
@@ -96,17 +96,17 @@ def depluralize(x):
     return x[:-1] if x[-1] == "s" else x
 
 
-def setup_retry_session(retries=3, backoff_factor=2, status_forcelist=(500, 502, 503, 504), method_whitelist=None):
+def setup_retry_session(retries=3, backoff_factor=2, status_forcelist=(500, 502, 503, 504), allowed_methods=None):
     session = requests.Session()
 
-    if method_whitelist is None:
-        method_whitelist = {"GET"}
+    if allowed_methods is None:
+        allowed_methods = {"GET"}
 
     retry = Retry(
         total=retries,
         backoff_factor=backoff_factor,
         status_forcelist=status_forcelist,
-        allowed_methods=method_whitelist,
+        allowed_methods=allowed_methods,
     )
 
     adapter = HTTPAdapter(max_retries=retry)
diff --git a/backend/common/server/config.py b/backend/common/server/config.py
index 0306c658eb9e9..a494c34f66d23 100644
--- a/backend/common/server/config.py
+++ b/backend/common/server/config.py
@@ -51,9 +51,10 @@ def configure_flask_app(flask_app):
         SESSION_COOKIE_SECURE=require_secure_cookies,
         SESSION_COOKIE_HTTPONLY=True,
         SESSION_COOKIE_SAMESITE="Lax",
-        JSON_SORT_KEYS=True,
     )
     flask_app.json_encoder = CustomJSONEncoder
+    flask_app.json.sort_keys = True
+
     return flask_app
 
 
@@ -141,7 +142,8 @@ def create_api_app(api_paths_and_spec_files, **server_args):
     based on the deployment stage.
 
     Args:
-        api_paths_and_spec_files (list of tuples): A list where each tuple contains a base path and a specification file.
+        api_paths_and_spec_files (list of tuples): A list where each tuple contains a base path and a specification
+        file.
         **server_args: Additional arguments to be passed to the FlaskApp.
 
     Returns:
diff --git a/backend/portal/api/app/v1/authentication.py b/backend/portal/api/app/v1/authentication.py
index 8bae005871878..3beb65c48d844 100644
--- a/backend/portal/api/app/v1/authentication.py
+++ b/backend/portal/api/app/v1/authentication.py
@@ -8,7 +8,6 @@
 
 import requests
 from authlib.integrations.flask_client import OAuth
-from authlib.integrations.flask_client.remote_app import FlaskRemoteApp
 from flask import Response, after_this_request, current_app, g, jsonify, make_response, redirect, request, session
 
 from backend.common.authorizer import assert_authorized_token, get_userinfo_from_auth0
@@ -20,7 +19,7 @@
 oauth_client = None
 
 
-def get_oauth_client(config: CorporaAuthConfig) -> FlaskRemoteApp:
+def get_oauth_client(config: CorporaAuthConfig) -> OAuth:
     """Create an oauth client on the first invocation, then return oauth client for subsequent calls.
 
     :param config:  An object containing the auth configuration.
diff --git a/python_dependencies/backend/common/server/requirements.txt b/python_dependencies/backend/common/server/requirements.txt
index b5465d1f437b7..f3e2362d1f09e 100644
--- a/python_dependencies/backend/common/server/requirements.txt
+++ b/python_dependencies/backend/common/server/requirements.txt
@@ -1,8 +1,8 @@
 connexion[swagger-ui]~=2.14.2
 gunicorn[gevent]~=22.0.0
 furl~=2.1.2
-Flask-Cors~=3.0.6
+Flask-Cors~=4.0.1
 flask-server-timing~=0.1.2
-ddtrace~=2.8.5
+ddtrace~=2.9.2
 python-json-logger
-boto3~=1.34.114
\ No newline at end of file
+boto3~=1.34.114
diff --git a/python_dependencies/backend/requirements.txt b/python_dependencies/backend/requirements.txt
index ca313b3780a24..26bd21aaacfae 100644
--- a/python_dependencies/backend/requirements.txt
+++ b/python_dependencies/backend/requirements.txt
@@ -1,24 +1,16 @@
 alembic==1.*
-Authlib==0.14.3
-boto3>=1.11.17
+Authlib==1.3.1
 botocore>=1.14.17
-connexion[swagger-ui]==2.14.2
-dataclasses-json==0.6.6
+dataclasses-json==0.6.7
 cellxgene-ontology-guide<2
 # TODO: Check if this is really essential for APM tracing
 # see ticket: https://github.com/chanzuckerberg/single-cell-data-portal/issues/5821
 datadog==0.49.1
-ddtrace>=2.1.4, <3
-Flask>=2.2.3, <3
-Flask-Cors>=3.0.6
-flask-server-timing>=0.1.2
-gunicorn[gevent]==22.0.0
-matplotlib>=3.6.3, <3.7 # 3.7.0 isn't compatible with scanpy: https://github.com/scverse/scanpy/issues/2411
-psutil>=5.9.5, <6
+Flask # verison determined by connexion
+psutil>=6, <7
 psycopg2-binary==2.*
 pydantic>=1.10.7, <2
 python-jose[cryptography]>=3.1.0
-python-json-logger
 requests>=2.22.0
 rsa>=4.7 # not directly required, pinned by Snyk to avoid a vulnerability
 setproctitle>1.3,<2 # for gunicorn integration with datadog
@@ -26,4 +18,3 @@ SQLAlchemy-Utils
 SQLAlchemy==2.*
 tenacity
 tiledb
-Werkzeug==2.2.3
diff --git a/tests/unit/backend/layers/api/test_portal_api.py b/tests/unit/backend/layers/api/test_portal_api.py
index 698df9c2ff23d..e3dd9969327d7 100644
--- a/tests/unit/backend/layers/api/test_portal_api.py
+++ b/tests/unit/backend/layers/api/test_portal_api.py
@@ -462,7 +462,7 @@ def test__post_collection_normalizes_doi(self):
         # TODO: this endpoint should also return `version_id`
         collection = self.business_logic.get_collection_version_from_canonical(CollectionId(collection_id))
         doi = next(link.uri for link in collection.metadata.links if link.type == "DOI")  # TODO: careful
-        self.assertEquals(doi, "https://doi.org/10.1016/foo")
+        self.assertEqual(doi, "https://doi.org/10.1016/foo")
 
     # ✅
     def test__post_collection_rejects_two_dois(self):
diff --git a/tests/unit/backend/wmg/test_query.py b/tests/unit/backend/wmg/test_query.py
index d0a135c8cf335..4d8b17340b2e9 100644
--- a/tests/unit/backend/wmg/test_query.py
+++ b/tests/unit/backend/wmg/test_query.py
@@ -158,7 +158,7 @@ def test__single_dimension__returns_all_dimension_and_terms(self):
         with create_temp_wmg_snapshot(dim_size=dim_size) as snapshot:
             q = CensusCubeQuery(snapshot, self.cube_query_params)
             result = q.list_primary_filter_dimension_term_ids("tissue_ontology_term_id")
-            self.assertEquals(
+            self.assertEqual(
                 ["tissue_ontology_term_id_0", "tissue_ontology_term_id_1", "tissue_ontology_term_id_2"], result
             )
 
@@ -177,7 +177,7 @@ def exclude_one_tissue_per_organism(logical_coord: NamedTuple) -> bool:
             result = q.list_grouped_primary_filter_dimensions_term_ids(
                 "tissue_ontology_term_id", "organism_ontology_term_id"
             )
-            self.assertEquals(
+            self.assertEqual(
                 {
                     "organism_ontology_term_id_0": ["tissue_ontology_term_id_1", "tissue_ontology_term_id_2"],
                     "organism_ontology_term_id_1": ["tissue_ontology_term_id_0", "tissue_ontology_term_id_2"],

From d3eb0a4e605b6af323babac811c6abcabbebbde8 Mon Sep 17 00:00:00 2001
From: Nayib Gloria <55710092+nayib-jose-gloria@users.noreply.github.com>
Date: Thu, 3 Oct 2024 11:26:37 -0400
Subject: [PATCH 4/5] fix: Revert "chore: resolve deprecation warning and
 update requirements (#7275)" (#7350)

---
 Dockerfile.backend                              |  2 +-
 backend/api_server/index.html                   |  4 ++--
 backend/common/auth0_manager.py                 |  2 +-
 backend/common/census_cube/utils.py             |  8 ++++----
 backend/common/server/config.py                 |  6 ++----
 backend/portal/api/app/v1/authentication.py     |  3 ++-
 .../backend/common/server/requirements.txt      |  6 +++---
 python_dependencies/backend/requirements.txt    | 17 +++++++++++++----
 8 files changed, 28 insertions(+), 20 deletions(-)

diff --git a/Dockerfile.backend b/Dockerfile.backend
index 22596d9642eef..1563bf75e66c8 100644
--- a/Dockerfile.backend
+++ b/Dockerfile.backend
@@ -22,7 +22,7 @@ RUN python3 -m pip install --upgrade pip setuptools
 # TODO: Determine if cmake is really needed for ddtrace
 # see ticket: https://github.com/chanzuckerberg/single-cell-data-portal/issues/5821
 RUN python3 -m pip install cmake
-RUN python3 -m pip install -r requirements.txt -r ./common/server/requirements.txt
+RUN python3 -m pip install -r requirements.txt
 RUN if [ "$INSTALL_DEV" = "true" ]; then python3 -m pip install -r requirements-dev.txt; fi
 # Install awscli to download wmg snapshot to the local disk
 RUN python3 -m pip install awscli
diff --git a/backend/api_server/index.html b/backend/api_server/index.html
index b9a9a13eb505b..148b2d3d43c72 100644
--- a/backend/api_server/index.html
+++ b/backend/api_server/index.html
@@ -9,8 +9,8 @@
     />
     <link
       rel="stylesheet"
-      href="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/5.17.14/swagger-ui.css"
-      integrity="sha512-MvYROlKG3cDBPskMQgPmkNgZh85LIf68y7SZ34TIppaIHQz1M/3S/yYqzIfufdKDJjzB9Qu1BV63SZjimJkPvw=="
+      href="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/3.0.13/swagger-ui.css"
+      integrity="sha256-Z7Z2kffooC4H3U4Myviypq5dO2IIGkmu7VRtd1YqNn8="
       crossorigin="anonymous"
     />
     <style>
diff --git a/backend/common/auth0_manager.py b/backend/common/auth0_manager.py
index 1814b71dcc997..cf85e59954879 100644
--- a/backend/common/auth0_manager.py
+++ b/backend/common/auth0_manager.py
@@ -30,7 +30,7 @@ def session(self):
                 total=3,
                 backoff_factor=1,
                 status_forcelist=self.config.retry_status_forcelist,
-                allowed_methods=["POST", "HEAD", "GET", "PUT", "DELETE", "OPTIONS"],
+                method_whitelist=["POST", "HEAD", "GET", "PUT", "DELETE", "OPTIONS"],
             )
             session.mount("https://", HTTPAdapter(max_retries=retry_config))
 
diff --git a/backend/common/census_cube/utils.py b/backend/common/census_cube/utils.py
index 759b1bbea1d9a..2c85da6a72b4e 100644
--- a/backend/common/census_cube/utils.py
+++ b/backend/common/census_cube/utils.py
@@ -96,17 +96,17 @@ def depluralize(x):
     return x[:-1] if x[-1] == "s" else x
 
 
-def setup_retry_session(retries=3, backoff_factor=2, status_forcelist=(500, 502, 503, 504), allowed_methods=None):
+def setup_retry_session(retries=3, backoff_factor=2, status_forcelist=(500, 502, 503, 504), method_whitelist=None):
     session = requests.Session()
 
-    if allowed_methods is None:
-        allowed_methods = {"GET"}
+    if method_whitelist is None:
+        method_whitelist = {"GET"}
 
     retry = Retry(
         total=retries,
         backoff_factor=backoff_factor,
         status_forcelist=status_forcelist,
-        allowed_methods=allowed_methods,
+        allowed_methods=method_whitelist,
     )
 
     adapter = HTTPAdapter(max_retries=retry)
diff --git a/backend/common/server/config.py b/backend/common/server/config.py
index a494c34f66d23..0306c658eb9e9 100644
--- a/backend/common/server/config.py
+++ b/backend/common/server/config.py
@@ -51,10 +51,9 @@ def configure_flask_app(flask_app):
         SESSION_COOKIE_SECURE=require_secure_cookies,
         SESSION_COOKIE_HTTPONLY=True,
         SESSION_COOKIE_SAMESITE="Lax",
+        JSON_SORT_KEYS=True,
     )
     flask_app.json_encoder = CustomJSONEncoder
-    flask_app.json.sort_keys = True
-
     return flask_app
 
 
@@ -142,8 +141,7 @@ def create_api_app(api_paths_and_spec_files, **server_args):
     based on the deployment stage.
 
     Args:
-        api_paths_and_spec_files (list of tuples): A list where each tuple contains a base path and a specification
-        file.
+        api_paths_and_spec_files (list of tuples): A list where each tuple contains a base path and a specification file.
         **server_args: Additional arguments to be passed to the FlaskApp.
 
     Returns:
diff --git a/backend/portal/api/app/v1/authentication.py b/backend/portal/api/app/v1/authentication.py
index 3beb65c48d844..8bae005871878 100644
--- a/backend/portal/api/app/v1/authentication.py
+++ b/backend/portal/api/app/v1/authentication.py
@@ -8,6 +8,7 @@
 
 import requests
 from authlib.integrations.flask_client import OAuth
+from authlib.integrations.flask_client.remote_app import FlaskRemoteApp
 from flask import Response, after_this_request, current_app, g, jsonify, make_response, redirect, request, session
 
 from backend.common.authorizer import assert_authorized_token, get_userinfo_from_auth0
@@ -19,7 +20,7 @@
 oauth_client = None
 
 
-def get_oauth_client(config: CorporaAuthConfig) -> OAuth:
+def get_oauth_client(config: CorporaAuthConfig) -> FlaskRemoteApp:
     """Create an oauth client on the first invocation, then return oauth client for subsequent calls.
 
     :param config:  An object containing the auth configuration.
diff --git a/python_dependencies/backend/common/server/requirements.txt b/python_dependencies/backend/common/server/requirements.txt
index f3e2362d1f09e..b5465d1f437b7 100644
--- a/python_dependencies/backend/common/server/requirements.txt
+++ b/python_dependencies/backend/common/server/requirements.txt
@@ -1,8 +1,8 @@
 connexion[swagger-ui]~=2.14.2
 gunicorn[gevent]~=22.0.0
 furl~=2.1.2
-Flask-Cors~=4.0.1
+Flask-Cors~=3.0.6
 flask-server-timing~=0.1.2
-ddtrace~=2.9.2
+ddtrace~=2.8.5
 python-json-logger
-boto3~=1.34.114
+boto3~=1.34.114
\ No newline at end of file
diff --git a/python_dependencies/backend/requirements.txt b/python_dependencies/backend/requirements.txt
index 26bd21aaacfae..ca313b3780a24 100644
--- a/python_dependencies/backend/requirements.txt
+++ b/python_dependencies/backend/requirements.txt
@@ -1,16 +1,24 @@
 alembic==1.*
-Authlib==1.3.1
+Authlib==0.14.3
+boto3>=1.11.17
 botocore>=1.14.17
-dataclasses-json==0.6.7
+connexion[swagger-ui]==2.14.2
+dataclasses-json==0.6.6
 cellxgene-ontology-guide<2
 # TODO: Check if this is really essential for APM tracing
 # see ticket: https://github.com/chanzuckerberg/single-cell-data-portal/issues/5821
 datadog==0.49.1
-Flask # verison determined by connexion
-psutil>=6, <7
+ddtrace>=2.1.4, <3
+Flask>=2.2.3, <3
+Flask-Cors>=3.0.6
+flask-server-timing>=0.1.2
+gunicorn[gevent]==22.0.0
+matplotlib>=3.6.3, <3.7 # 3.7.0 isn't compatible with scanpy: https://github.com/scverse/scanpy/issues/2411
+psutil>=5.9.5, <6
 psycopg2-binary==2.*
 pydantic>=1.10.7, <2
 python-jose[cryptography]>=3.1.0
+python-json-logger
 requests>=2.22.0
 rsa>=4.7 # not directly required, pinned by Snyk to avoid a vulnerability
 setproctitle>1.3,<2 # for gunicorn integration with datadog
@@ -18,3 +26,4 @@ SQLAlchemy-Utils
 SQLAlchemy==2.*
 tenacity
 tiledb
+Werkzeug==2.2.3

From f02db4d7e3a61f4b1378d81118c8e670fc5e44d6 Mon Sep 17 00:00:00 2001
From: Nayib Gloria <55710092+nayib-jose-gloria@users.noreply.github.com>
Date: Thu, 3 Oct 2024 11:30:07 -0400
Subject: [PATCH 5/5] fix: anndata 0.10 matrix slicing bug (#7351)

---
 backend/layers/processing/process_validate.py |  2 +-
 backend/layers/processing/schema_migration.py | 23 +++++++++++++++++++
 2 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/backend/layers/processing/process_validate.py b/backend/layers/processing/process_validate.py
index bdd9921b0b407..dd3987470e156 100644
--- a/backend/layers/processing/process_validate.py
+++ b/backend/layers/processing/process_validate.py
@@ -147,7 +147,7 @@ def extract_metadata(self, filename) -> DatasetMetadata:
             range(stride, layer_for_mean_genes_per_cell.shape[0] + stride, stride),
             strict=False,
         ):
-            chunk = layer_for_mean_genes_per_cell[bounds[0] : bounds[1], filter_gene_vars]
+            chunk = layer_for_mean_genes_per_cell[bounds[0] : bounds[1], :][:, filter_gene_vars]
             numerator += chunk.nnz if hasattr(chunk, "nnz") else numpy.count_nonzero(chunk)
             denominator += chunk.shape[0]
 
diff --git a/backend/layers/processing/schema_migration.py b/backend/layers/processing/schema_migration.py
index 2ac25b0c1f17e..8742b5382efa3 100644
--- a/backend/layers/processing/schema_migration.py
+++ b/backend/layers/processing/schema_migration.py
@@ -15,7 +15,11 @@
     CollectionVersion,
     CollectionVersionId,
     DatasetArtifactType,
+    DatasetConversionStatus,
     DatasetProcessingStatus,
+    DatasetStatusKey,
+    DatasetUploadStatus,
+    DatasetValidationStatus,
     DatasetVersionId,
 )
 from backend.layers.processing import logger
@@ -228,6 +232,25 @@ def log_errors_and_cleanup(self, collection_version_id: str) -> list:
             key_prefix = self.get_key_prefix(previous_dataset_version_id)
             object_keys_to_delete.append(f"{key_prefix}/migrated.h5ad")
             if dataset.status.processing_status != DatasetProcessingStatus.SUCCESS:
+                # If only rds failure, set rds status to skipped + processing status to successful and do not rollback
+                if (
+                    dataset.status.rds_status == DatasetConversionStatus.FAILED
+                    and dataset.status.upload_status == DatasetUploadStatus.UPLOADED
+                    and dataset.status.validation_status == DatasetValidationStatus.VALID
+                    and dataset.status.cxg_status == DatasetConversionStatus.UPLOADED
+                    and dataset.status.h5ad_status == DatasetConversionStatus.UPLOADED
+                ):
+                    self.business_logic.update_dataset_version_status(
+                        dataset.version_id,
+                        DatasetStatusKey.RDS,
+                        DatasetConversionStatus.SKIPPED,
+                    )
+                    self.business_logic.update_dataset_version_status(
+                        dataset.version_id,
+                        DatasetStatusKey.PROCESSING,
+                        DatasetProcessingStatus.SUCCESS,
+                    )
+                    continue
                 error = {
                     "message": dataset.status.validation_message,
                     "dataset_status": dataset.status.to_dict(),