Merge pull request #96 from Ferlab-Ste-Justine/feat/clin-3507

feat: CLIN-3507 manage add and update note and list variants with notes
Ferlab-Ste-Justine · Nov 19, 2024 · 81dd514 · 81dd514
2 parents 8d23e0c + 9c793c0
commit 81dd514
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Showing 5 changed files with 102 additions and 39 deletions.
diff --git a/.github/workflows/scan.yaml b/.github/workflows/scan.yaml
@@ -1,7 +1,7 @@
 name: build
 on:
   pull_request:
-    
+
 jobs:
   build:
     name: Build

diff --git a/.trivyignore b/.trivyignore
@@ -0,0 +1,2 @@
+# node-pkg, not fixed as of 2024-11-19
+CVE-2024-21538
diff --git a/src/db/dal/variant.ts b/src/db/dal/variant.ts
@@ -1,35 +1,55 @@
 import { Op } from 'sequelize';
+
 import VariantModel from '../models/Variant';
 
-export const addNewEntry = async function (uniqueId: string, organizationId: string, authorId: string, properties: any) {
+export const addNewEntry = async function (
+    uniqueId: string,
+    organizationId: string,
+    authorId: string,
+    properties: any,
+) {
+    const variantFound = await VariantModel.findOne({
+        order: [['timestamp', 'DESC']],
+        where: {
+            unique_id: {
+                [Op.eq]: uniqueId,
+            },
+            author_id: {
+                [Op.eq]: authorId,
+            },
+        },
+    });
+
+    const combinedProperties = { ...(variantFound?.properties || {}), ...properties };
+
     return await VariantModel.create({
         unique_id: uniqueId,
         organization_id: organizationId,
         author_id: authorId,
-        properties,
-        timestamp: new Date()
+        properties: combinedProperties,
+        timestamp: new Date(),
     });
-}
+};
 
 export const getEntriesByUniqueIdsAndOrganizations = async function (uniqueIds: string[], organizationIds: string[]) {
     return await VariantModel.findAll({
         order: [['timestamp', 'DESC']],
         where: {
             unique_id: {
-                [Op.in]: uniqueIds
+                [Op.in]: uniqueIds,
             },
             organization_id: {
-                [Op.in]: organizationIds
-            }
-        }
-    });
-}
-
-export const getEntriesByPropertiesFlags = async function (flags: string[], organizationIds: string[], uniqueIdParam: string) {
-    const flagsWhere = flags.map(f => {
-        return `properties @> '{"flags": ["${f}"]}'`;
+                [Op.in]: organizationIds,
+            },
+        },
     });
+};
 
+const getEntriesByProperties = async function (
+    whereClause: string,
+    organizationIds: string[],
+    uniqueIdParam: string
+) {
     const uniqueIdWhere = uniqueIdParam.length > 0 ? ` AND unique_id LIKE '%${uniqueIdParam}%'` : '';
 
     const result = await VariantModel.sequelize.query(`
@@ -43,7 +63,27 @@ export const getEntriesByPropertiesFlags = async function (flags: string[], orga
           FROM variants
           WHERE organization_id IN ('${organizationIds.join("', '")}') ${uniqueIdWhere}
         ) s
-        WHERE rnk = 1 AND (${flagsWhere.join(' OR ')});`);
+        WHERE rnk = 1 AND (${whereClause});`);
 
     return result;
-}
+}
+
+export const getEntriesByPropertiesFlags = async function (
+    flags: string[],
+    organizationIds: string[],
+    uniqueIdParam: string
+) {
+    const flagsWhere = flags.map((f) => `properties @> '{"flags": ["${f}"]}'`);
+
+    return await getEntriesByProperties(flagsWhere.join(' OR '), organizationIds, uniqueIdParam);
+};
+
+export const getEntriesByPropertiesNote = async function (
+    hasNote: boolean,
+    organizationIds: string[],
+    uniqueIdParam: string
+) {
+    const notesWhere = `properties ->> 'note' IS ${hasNote ? 'NOT NULL' : 'NULL'}`;
+
+    return await getEntriesByProperties(notesWhere, organizationIds, uniqueIdParam);
+}
diff --git a/src/db/models/Variant.ts b/src/db/models/Variant.ts
@@ -1,4 +1,5 @@
-import { CreationOptional, DataTypes,  Model, Optional } from 'sequelize';
+import { CreationOptional, DataTypes, Model, Optional } from 'sequelize';
+
 import sequelizeConnection from '../config';
 
 interface IVariantAttributes {
@@ -7,7 +8,7 @@ interface IVariantAttributes {
     author_id: string;
     organization_id: string;
     timestamp: Date;
-    properties: Object;
+    properties: object;
 }
 
 type VariantCreationAttributes = Optional<IVariantAttributes, 'id'>;
@@ -50,19 +51,19 @@ VariantModel.init(
             defaultValue: new Date(),
             validate: {
                 isDate: true,
-            }
+            },
         },
         properties: {
             type: DataTypes.JSONB,
             allowNull: false,
             defaultValue: {},
-        }
+        },
     },
     {
         sequelize: sequelizeConnection,
         tableName: 'variants',
-        timestamps: false
-    }
+        timestamps: false,
+    },
 );
 
-export default VariantModel;
+export default VariantModel;
diff --git a/src/routes/variant.ts b/src/routes/variant.ts
@@ -1,18 +1,18 @@
 import { Request, Router } from 'express';
 import { StatusCodes } from 'http-status-codes';
 
-import Realm from '../config/realm';
 import { keycloakRealm } from '../config/env';
-import { addNewEntry, getEntriesByUniqueIdsAndOrganizations, getEntriesByPropertiesFlags } from '../db/dal/variant';
+import Realm from '../config/realm';
+import { addNewEntry, getEntriesByPropertiesFlags, getEntriesByPropertiesNote, getEntriesByUniqueIdsAndOrganizations } from '../db/dal/variant';
 
 const CLIN_GENETICIAN_ROLE = 'clin_genetician';
 
-const EMPTY_PROPERTIES = { };
+const EMPTY_PROPERTIES = {};
 
 interface UserInfo {
-    authorId: string,
-    userRoles: string[],
-    userOrganizations: string[]
+    authorId: string;
+    userRoles: string[];
+    userOrganizations: string[];
 }
 
 function getUserInfo(request: Request): UserInfo {
@@ -23,7 +23,10 @@ function getUserInfo(request: Request): UserInfo {
 }
 
 function validateCreate(userInfo: UserInfo, organization_id: string) {
-    return userInfo.userRoles.indexOf(CLIN_GENETICIAN_ROLE) > -1 && userInfo.userOrganizations.indexOf(organization_id) > -1;
+    return (
+        userInfo.userRoles.indexOf(CLIN_GENETICIAN_ROLE) > -1 &&
+        userInfo.userOrganizations.indexOf(organization_id) > -1
+    );
 }
 
 function validateGet(userInfo: UserInfo) {
@@ -42,7 +45,12 @@ variantRouter.post('/:unique_id/:organization_id', async (req, res, next) => {
         const canCreate = validateCreate(userInfo, req?.params?.organization_id);
 
         if (canCreate) {
-            const dbResponse = await addNewEntry(req?.params?.unique_id, req?.params?.organization_id, userInfo.authorId, req?.body || EMPTY_PROPERTIES);
+            const dbResponse = await addNewEntry(
+                req?.params?.unique_id,
+                req?.params?.organization_id,
+                userInfo.authorId,
+                req?.body || EMPTY_PROPERTIES,
+            );
             return res.status(StatusCodes.CREATED).send(dbResponse);
         } else {
             return res.sendStatus(StatusCodes.FORBIDDEN);
@@ -62,7 +70,7 @@ variantRouter.get('/', async (req, res, next) => {
         const canGet = validateGet(userInfo);
 
         let dbResponse = [];
-        let uniqueIds = [];
+        const uniqueIds = [];
 
         if (Array.isArray(req.query?.unique_id)) {
             uniqueIds.push(...req.query.unique_id);
@@ -78,7 +86,6 @@ variantRouter.get('/', async (req, res, next) => {
         } else {
             return res.sendStatus(StatusCodes.BAD_REQUEST);
         }
-
     } catch (e) {
         next(e);
     }
@@ -94,7 +101,8 @@ variantRouter.get('/filter', async (req, res, next) => {
         const canGet = validateGet(userInfo);
 
         let dbResponse = [];
-        let flags = [];
+        const flags = [];
+        let hasNote = null;
 
         const flagsParam = req.query?.flag;
         if (Array.isArray(flagsParam)) {
@@ -103,11 +111,23 @@ variantRouter.get('/filter', async (req, res, next) => {
             flags.push(flagsParam);
         }
 
-        let uniqueIdFilterParam = (req.query?.unique_id || '').toString().trim();
+        const noteParams = req.query?.note;
+        if (typeof noteParams === 'string') {
+            if (noteParams === 'true') {
+                hasNote = true;
+            } else if (noteParams === 'false') {
+                hasNote = false;
+            }
+        }
+
+        const uniqueIdFilterParam = (req.query?.unique_id || '').toString().trim();
 
-        if (canGet && flags.length > 0) {
+        if (canGet && hasNote !== null) {
+            dbResponse = await getEntriesByPropertiesNote(hasNote, userInfo.userOrganizations, uniqueIdFilterParam);
+            return res.status(StatusCodes.OK).send(dbResponse[0].map((r) => r.unique_id));
+        } else if (canGet && flags.length > 0) {
             dbResponse = await getEntriesByPropertiesFlags(flags, userInfo.userOrganizations, uniqueIdFilterParam);
-            return res.status(StatusCodes.OK).send(dbResponse[0].map(r => r.unique_id));
+            return res.status(StatusCodes.OK).send(dbResponse[0].map((r) => r.unique_id));
         } else if (!canGet) {
             return res.sendStatus(StatusCodes.FORBIDDEN);
         } else {
@@ -118,4 +138,4 @@ variantRouter.get('/filter', async (req, res, next) => {
     }
 });
 
-export default variantRouter;
+export default variantRouter;
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		# node-pkg, not fixed as of 2024-11-19
		CVE-2024-21538