Merge branch 'develop' into feature/DEVSU-2670-add-compatibility-matrix

Author: bnguyen-bcgsc

README.md

@@ -155,6 +155,16 @@ Once you are done with testing, delete the temporary database
 dropdb -U ipr_service -h iprdevdb.bcgsc.ca DEVSU-777-temp-ipr-sync-dev
 ```
 
+## Seeder
+
+Use seeder to load the default templates, projects and users for db.
+
+```bash
+npx sequelize-cli db:seed:all --url "postgres://$IPR_SERVICE_USER:$IPR_SERVICE_PASS@$IPR_DATABASE_SERVER/$IPR_DATABASE_NAME"
+
+npx sequelize-cli db:seed:undo --url "postgres://$IPR_SERVICE_USER:$IPR_SERVICE_PASS@$IPR_DATABASE_SERVER/$IPR_DATABASE_NAME"
+```
+
 ## Database Insert Not Through API
 
 When adding/inserting entries directly into a database table without using the API, be sure to update the primary key (id)
@@ -247,7 +257,7 @@ pm2 start current/pm2.config.js --env production
 │   │
 │   ├── middleware                      # Middleware
 │   │                                   Location for all globally required middleware definitions.
-│   │ 
+│   │
 │   ├── schemas                         # Schemas
 │   │                                   Location for all globally required schema definitions.
 │   │
@@ -299,7 +309,7 @@ pm2 start current/pm2.config.js --env production
 │
 ├── migrations                          # Migrations
 │                                       Contains files for updating db schemas and data
-│ 
+│
 └── migrationTools                      # Migration Tools
                                         Contains files with functions to help with migrations
 ```
@@ -337,7 +347,7 @@ The search feature enables users to search for report(s) that match a given set
 
 Syntax: **/reports?searchParams=[<category>|<keyword>|<threshold>]**
 
-- *[]*: indicators of a search parameter block. A query can contain one or many parameter blocks 
+- *[]*: indicators of a search parameter block. A query can contain one or many parameter blocks
 - *category*: the search category that a report belongs to. Possible values include patientId, projectName, diagnosis, keyVariant, kbVariant, structuralVariant, smallMutation, and therapeuticTarget
 - *keyword*: the search keyword that a report can match with. Could be a variant name or a therapeutic target name
 - *threshold*: the matching threshold scales from 0 to 1 and determines the cutoff of similarity between the search keyword and a match value. A threshold of 1 means the entire match value or a substring of it is identical to the search keyword.

app/middleware/__mocks__/graphkbIprLogin.js

@@ -52,6 +52,9 @@ module.exports = (sequelize, Sq) => {
     description: {
       type: Sq.TEXT,
     },
+    editable: {
+      type: Sq.BOOLEAN,
+    },
   }, {
     ...DEFAULT_OPTIONS,
     tableName: 'templates',

app/middleware/graphkbIprLogin.js

@@ -2,7 +2,7 @@ const {StatusCodes} = require('http-status-codes');
 const express = require('express');
 
 const logger = require('../../log');
-const loginMiddleware = require('../../middleware/graphkb');
+const graphkbLoginMiddleware = require('../../middleware/graphkb');
 const {
   graphkbAutocomplete,
   graphkbEvidenceLevels,
@@ -63,7 +63,7 @@ const errorMap = {
   },
 };
 
-router.use(loginMiddleware);
+router.use(graphkbLoginMiddleware);
 
 /**
  * Autocomplete endpoint for interfacing with GraphKB. This endpoint is used by the client

app/models/template/template.js

@@ -35,6 +35,10 @@ router.route('/:template([A-z0-9-]{36})')
     return res.json(req.template.view('public'));
   })
   .put(async (req, res) => {
+    if (!req.template.editable) {
+      logger.error(`The template "${req.template.name}" is not editable.`);
+      return res.status(HTTP_STATUS.BAD_REQUEST).json({error: {message: `The template "${req.template.name}" is not editable.`}});
+    }
     // Validate request against schema
     try {
       validateAgainstSchema(updateSchema, req.body, false);

app/routes/graphkb/index.js

@@ -8,12 +8,9 @@ const {isAdmin, isManager} = require('../../libs/helperFunctions');
 
 const validateAgainstSchema = require('../../libs/validateAgainstSchema');
 const {createSchema, updateSchema, notificationUpdateSchema} = require('../../schemas/user');
-const graphkbIprLoginMiddleware = require('../../middleware/graphkbIprLogin');
 
 const router = express.Router({mergeParams: true});
 
-router.use(graphkbIprLoginMiddleware);
-
 // Middleware for getting/updating a user by ident
 router.param('userByIdent', async (req, res, next, ident) => {
   let result;

app/routes/template/template.js

@@ -1,4 +1,3 @@
 // Apply mocking to all tests
 jest.mock('../../app/queue.js');
 jest.mock('../../app/libs/getUser.js');
-jest.mock('../../app/middleware/graphkbIprLogin.js');

app/routes/user/user.js

@@ -0,0 +1,12 @@
+module.exports = {
+  async up(queryInterface, Sq) {
+    await queryInterface.addColumn('templates', 'editable', {
+      type: Sq.BOOLEAN,
+      defaultValue: false,
+    });
+  },
+
+  async down(queryInterface) {
+    await queryInterface.removeColumn('templates', 'editable');
+  },
+};

config/jest/jestSetup.js

@@ -0,0 +1,62 @@
+const {v4: uuidv4} = require('uuid');
+const images = require('./constants/images.json');
+const templates = require('./constants/templates.json');
+const projects = require('./constants/projects.json');
+const users = require('./constants/users.json');
+const userGroups = require('./constants/user_groups.json');
+
+const addBaseColumns = (records) => {
+  return records.map((record) => {
+    return {
+      ...record,
+      ident: uuidv4(),
+      created_at: new Date(),
+      updated_at: new Date(),
+    };
+  });
+};
+
+module.exports = {
+  async up(queryInterface, Sequelize) {
+    const templatesData = templates.map((template) => {
+      template.sections = JSON.stringify(template.sections);
+      return template;
+    });
+    await queryInterface.bulkInsert('images', addBaseColumns(images), {});
+    await queryInterface.bulkInsert('templates', addBaseColumns(templatesData), {});
+    await queryInterface.bulkInsert('projects', addBaseColumns(projects), {});
+    await queryInterface.bulkInsert('users', addBaseColumns(users), {});
+    await queryInterface.bulkInsert('user_groups', addBaseColumns(userGroups), {});
+
+    // give admin permission to user pori_admin
+    const usersData = await queryInterface.sequelize.query(
+      'SELECT id, username FROM users;',
+      {type: Sequelize.QueryTypes.SELECT},
+    );
+    const poriAdmin = usersData.find((u) => {return u.username === 'pori_admin';});
+    const groupsData = await queryInterface.sequelize.query(
+      'SELECT id, name FROM user_groups;',
+      {type: Sequelize.QueryTypes.SELECT},
+    );
+    const adminGroup = groupsData.find((g) => {return g.name === 'admin';});
+    const userGroupData = [{
+      user_id: poriAdmin.id,
+      group_id: adminGroup.id,
+      created_at: new Date(),
+      updated_at: new Date(),
+    }];
+
+    await queryInterface.bulkInsert('user_group_members', userGroupData);
+    await queryInterface.bulkInsert('user_metadata', addBaseColumns([{user_id: poriAdmin.id}]));
+  },
+
+  async down(queryInterface) {
+    await queryInterface.bulkDelete('user_metadata', null, {});
+    await queryInterface.bulkDelete('user_group_members', null, {});
+    await queryInterface.bulkDelete('templates', null, {});
+    await queryInterface.bulkDelete('images', null, {});
+    await queryInterface.bulkDelete('projects', null, {});
+    await queryInterface.bulkDelete('users', null, {});
+    await queryInterface.bulkDelete('user_groups', null, {});
+  },
+};