Merge pull request #442 from icgc-argo/develop

fix the treatment interval validation script to accept 0 (#441)
icgc-argo · Oct 22, 2024 · 413af55 · 413af55
2 parents 235f94f + 60ba8a2
commit 413af55
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Showing 3 changed files with 534 additions and 510 deletions.
diff --git a/package.json b/package.json
@@ -1,37 +1,39 @@
 {
-  "name": "dictionary",
-  "version": "1.0.0",
-  "description": "Working space for the ARGO Data Dictionary collaboration",
-  "main": "index.js",
-  "scripts": {
-    "compile": "jest && node compile.js && npm run references",
-    "test": "jest",
-    "references": "node populateReferences.js"
-  },
-  "repository": {
-    "type": "git",
-    "url": "git+https://github.com/icgc-argo/argo-dictionary.git"
-  },
-  "author": "",
-  "license": "ISC",
-  "bugs": {
-    "url": "https://github.com/icgc-argo/argo-dictionary/issues"
-  },
-  "homepage": "https://github.com/icgc-argo/argo-dictionary#readme",
-  "dependencies": {},
-  "devDependencies": {
-    "auto-load": "^3.0.4",
-    "chalk": "^3.0.0",
-    "inquirer": "^7.0.1",
-    "jest": "^25.2.3",
-    "json-beautify": "^1.1.1",
-    "prettier": "^1.19.1",
-    "querystring": "^0.2.0",
-    "yargs": "^15.0.2"
-  },
-  "prettier": {
-    "printWidth": 100,
-    "trailingComma": "all",
-    "singleQuote": true
-  }
+	"name": "dictionary",
+	"version": "1.0.0",
+	"description": "Working space for the ARGO Data Dictionary collaboration",
+	"main": "index.js",
+	"scripts": {
+		"compile": "jest && node compile.js && npm run references",
+		"test": "jest",
+		"references": "node populateReferences.js"
+	},
+	"repository": {
+		"type": "git",
+		"url": "git+https://github.com/icgc-argo/argo-dictionary.git"
+	},
+	"author": "",
+	"license": "ISC",
+	"bugs": {
+		"url": "https://github.com/icgc-argo/argo-dictionary/issues"
+	},
+	"homepage": "https://github.com/icgc-argo/argo-dictionary#readme",
+	"devDependencies": {
+		"auto-load": "^3.0.4",
+		"chalk": "^3.0.0",
+		"inquirer": "^7.0.1",
+		"jest": "^25.2.3",
+		"json-beautify": "^1.1.1",
+		"prettier": "^1.19.1",
+		"querystring": "^0.2.0",
+		"yargs": "^15.0.2"
+	},
+	"prettier": {
+		"printWidth": 120,
+		"trailingComma": "all",
+		"semi": true,
+		"singleQuote": true,
+		"tabWidth": 4,
+		"useTabs": true
+	}
 }
diff --git a/references/validationFunctions/treatment/checkWhenNoTreatment.js b/references/validationFunctions/treatment/checkWhenNoTreatment.js
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2020 The Ontario Institute for Cancer Research. All rights reserved
+ * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved
  *
  * This program and the accompanying materials are made available under the terms of the GNU Affero General Public License v3.0.
  * You should have received a copy of the GNU Affero General Public License along with
@@ -23,63 +23,66 @@
  */
 
 const validation = () =>
-    (function validate(inputs) {
-        const { $row, $name, $field } = inputs;
-        const result = { valid: true, message: 'Ok' };
+	function validate(inputs) {
+		const { $row, $name, $field } = inputs;
+		const result = { valid: true, message: 'Ok' };
 
-        const arrayItemsInSecondArray = (arr1, arr2) => {
-            return arr2.some(arr2Item => {
-                return arr1.includes(arr2Item);
-            });
-        };
+		const arrayItemsInSecondArray = (arr1, arr2) => {
+			return arr2.some(arr2Item => {
+				return arr1.includes(arr2Item);
+			});
+		};
 
-        const coreFields = [
-            'treatment_start_interval',
-            'treatment_duration',
-            'is_primary_treatment',
-            'treatment_intent',
-            'treatment_setting',
-            'response_to_treatment_criteria_method',
-            'response_to_treatment',
-        ];
+		const coreFields = [
+			'treatment_start_interval',
+			'treatment_duration',
+			'is_primary_treatment',
+			'treatment_intent',
+			'treatment_setting',
+			'response_to_treatment_criteria_method',
+			'response_to_treatment',
+		];
 
-        const treatmentExceptionTypes = ['no treatment', 'unknown'];
+		const treatmentExceptionTypes = ['no treatment', 'unknown'];
 
-        // checks for a string just consisting of whitespace
-        const checkforEmpty = entry => {
-            return /^\s+$/g.test(decodeURI(entry).replace(/^"(.*)"$/, '$1'));
-        };
-        const treatmentTypes = $row.treatment_type.map(value => value.toLowerCase());
+		const checkforInvalid = entry => {
+			// note: negative numbers are allowed as per
+			// https://github.com/icgc-argo/argo-dictionary/issues/432 */
 
-        const recordHasTreatments = !arrayItemsInSecondArray(
-            treatmentExceptionTypes,
-            treatmentTypes,
-        );
+			return (
+				// regular falsy values
+				[null, undefined, ''].includes($field) ||
+				// whitespace-filled strings
+				/^\s+$/g.test(decodeURI(entry).replace(/^"(.*)"$/, '$1'))
+			);
+		};
 
-        if (recordHasTreatments) {
-            if (
-                coreFields.includes($name) &&
-                (!$field || $field === null || checkforEmpty($field))
-            ) {
-                return {
-                    valid: false,
-                    message: `The '${$name}' field must be submitted when the 'treatment_type' field is '${treatmentTypes}'`,
-                };
-            }
+		const treatmentTypes = $row.treatment_type.map(value => value.toLowerCase());
 
-        } else if ($field && $field != null && !checkforEmpty($field)) {
-            if (
-                coreFields.includes($name) ||
-                (typeof $field === 'string' && $field.trim().toLowerCase() != 'not applicable') ||
-                typeof $field === 'number'
-            ) {
-                return {
-                    valid: false,
-                    message: `The '${$name}' field cannot be submitted if the 'treatment_type' field is '${treatmentTypes}'`,
-                };
-            }
-        }
-        return result;
-    });
+		const recordHasTreatments = !arrayItemsInSecondArray(treatmentExceptionTypes, treatmentTypes);
+
+		if (recordHasTreatments) {
+			if (coreFields.includes($name) && checkforInvalid($field)) {
+				return {
+					valid: false,
+					message: `The '${$name}' field must be submitted when the 'treatment_type' field is '${treatmentTypes}'`,
+				};
+			}
+		} // otherwise, is there a valid value without a treatment defined
+		else if (!checkforInvalid($field)) {
+			if (
+				coreFields.includes($name) ||
+				(typeof $field === 'string' && $field.trim().toLowerCase() != 'not applicable') ||
+				!isNaN(parseFloat($field))
+			) {
+				return {
+					valid: false,
+					message: `The '${$name}' field cannot be submitted if the 'treatment_type' field is '${treatmentTypes}'`,
+				};
+			}
+		}
+
+		return result;
+	};
 
 module.exports = validation;