1635 Add example experiments creation

src/api.v2/controllers/experimentController.js

@@ -8,33 +8,42 @@ const { OK, NotFoundError } = require('../../utils/responses');
 const sqlClient = require('../../sql/sqlClient');
 
 const getExperimentBackendStatus = require('../helpers/backendStatus/getExperimentBackendStatus');
+const Sample = require('../model/Sample');
 
 const logger = getLogger('[ExperimentController] - ');
 
 const getAllExperiments = async (req, res) => {
   const { user: { sub: userId } } = req;
+  logger.log(`Getting all experiments for user: ${userId}`);
 
   const data = await new Experiment().getAllExperiments(userId);
 
+  logger.log(`Finished getting all experiments for user: ${userId}, length: ${data.length}`);
+  res.json(data);
+};
+
+const getAllExampleExperiments = async (req, res) => {
+  logger.log('Getting example experiments');
+
+  const data = await new Experiment().getAllExampleExperiments();
+
+  logger.log(`Finished getting example experiments, length: ${data.length}`);
   res.json(data);
 };
 
 const getExperiment = async (req, res) => {
   const { params: { experimentId } } = req;
-
   logger.log(`Getting experiment ${experimentId}`);
 
   const data = await new Experiment().getExperimentData(experimentId);
 
   logger.log(`Finished getting experiment ${experimentId}`);
-
   res.json(data);
 };
 
 const createExperiment = async (req, res) => {
   const { params: { experimentId }, user, body } = req;
   const { name, description } = body;
-
   logger.log('Creating experiment');
 
   await sqlClient.get().transaction(async (trx) => {
@@ -68,7 +77,6 @@ const deleteExperiment = async (req, res) => {
     throw new NotFoundError(`Experiment ${experimentId} not found`);
   }
 
-
   logger.log(`Finished deleting experiment ${experimentId}`);
   res.json(OK());
 };
@@ -129,11 +137,51 @@ const downloadData = async (req, res) => {
   logger.log(`Providing download link for download ${downloadType} for experiment ${experimentId}`);
 
   const downloadLink = await new Experiment().getDownloadLink(experimentId, downloadType);
+
+  logger.log(`Finished providing download link for download ${downloadType} for experiment ${experimentId}`);
   res.json(downloadLink);
 };
 
+
+const cloneExperiment = async (req, res) => {
+  const getAllSampleIds = async (experimentId) => {
+    const { samplesOrder } = await new Experiment().findById(experimentId).first();
+    return samplesOrder;
+  };
+
+  const {
+    params: { experimentId: fromExperimentId },
+    body: { samplesSubsetIds = await getAllSampleIds(fromExperimentId) },
+    user: { sub: userId },
+  } = req;
+
+  logger.log(`Creating experiment to clone ${fromExperimentId} to`);
+
+  let toExperimentId;
+
+  await sqlClient.get().transaction(async (trx) => {
+    toExperimentId = await new Experiment(trx).createCopy(fromExperimentId);
+    await new UserAccess(trx).createNewExperimentPermissions(userId, toExperimentId);
+  });
+
+  logger.log(`Cloning experiment ${fromExperimentId} into ${toExperimentId}`);
+
+  const clonedSamplesOrder = await new Sample()
+    .copyTo(fromExperimentId, toExperimentId, samplesSubsetIds);
+
+  await new Experiment().updateById(
+    toExperimentId,
+    { samples_order: JSON.stringify(clonedSamplesOrder) },
+  );
+
+  logger.log(`Finished cloning experiment ${fromExperimentId}, new expeirment's id is ${toExperimentId}`);
+
+  res.json(toExperimentId);
+};
+
 module.exports = {
   getAllExperiments,
+  getAllExampleExperiments,
   getExperiment,
   createExperiment,
   updateProcessingConfig,
@@ -143,4 +191,5 @@ module.exports = {
   getProcessingConfig,
   getBackendStatus,
   downloadData,
+  cloneExperiment,
 };

src/api.v2/helpers/roles.js

@@ -18,8 +18,11 @@ const allowedResources = {
     'socket',
     '/experiments/(?<experimentId>.*)/plots-tables/(?<plotUuid>.*)',
     '/experiments/(?<experimentId>.*)/cellSets',
+    '/experiments/(?<experimentId>.*)/clone',
+  ],
+  [VIEWER]: [
+    '/experiments/(?<experimentId>.*)/clone',
   ],
-  [VIEWER]: [],
 };
 const isRoleAuthorized = (role, resource, method) => {
   // if no valid role is provided, return not authorized

src/api.v2/helpers/worker/getWorkResults.js

@@ -52,7 +52,6 @@ const getWorkResults = async (experimentId, ETag) => {
   const formattedExperimentId = formatExperimentId(experimentId);
 
   await validateTagMatching(formattedExperimentId, params);
-  console.log('GETTING WORK RESULTS IWTH PARAMS ', params);
   logger.log(`Found worker results for experiment: ${experimentId}, Etag: ${ETag}`);
 
   const signedUrl = getSignedUrl('getObject', params);

src/api.v2/model/Experiment.js

@@ -1,4 +1,5 @@
 const _ = require('lodash');
+const { v4: uuidv4 } = require('uuid');
 
 const BasicModel = require('./BasicModel');
 const sqlClient = require('../../sql/sqlClient');
@@ -12,6 +13,7 @@ const config = require('../../config');
 const getLogger = require('../../utils/getLogger');
 const bucketNames = require('../helpers/s3/bucketNames');
 const { getSignedUrl } = require('../../utils/aws/s3');
+const constants = require('../../utils/constants');
 
 const logger = getLogger('[ExperimentModel] - ');
 
@@ -43,20 +45,26 @@ class Experiment extends BasicModel {
     ];
 
     const aliasedExperimentFields = fields.map((field) => `e.${field}`);
-    function mainQuery() {
-      this.select([...aliasedExperimentFields, 'm.key'])
+
+    const result = await collapseKeyIntoArray(
+      this.sql.select([...aliasedExperimentFields, 'm.key'])
         .from(tableNames.USER_ACCESS)
         .where('user_id', userId)
         .join(`${tableNames.EXPERIMENT} as e`, 'e.id', `${tableNames.USER_ACCESS}.experiment_id`)
         .leftJoin(`${tableNames.METADATA_TRACK} as m`, 'e.id', 'm.experiment_id')
-        .as('mainQuery');
-    }
-
-    const result = await collapseKeyIntoArray(mainQuery, [...fields], 'key', 'metadataKeys', this.sql);
+        .as('mainQuery'), [...fields],
+      'key',
+      'metadataKeys',
+      this.sql,
+    );
 
     return result;
   }
 
+  async getAllExampleExperiments() {
+    return this.getAllExperiments(constants.PUBLIC_ACCESS_ID);
+  }
+
   async getExperimentData(experimentId) {
     function mainQuery() {
       this.select('*')
@@ -98,6 +106,26 @@ class Experiment extends BasicModel {
     return result;
   }
 
+  async createCopy(fromExperimentId) {
+    const toExperimentId = uuidv4().replace(/-/g, '');
+
+    const { sql } = this;
+
+    await sql
+      .insert(
+        sql(tableNames.EXPERIMENT)
+          .select(
+            sql.raw('? as id', [toExperimentId]),
+            'name',
+            'description',
+          )
+          .where({ id: fromExperimentId }),
+      )
+      .into(sql.raw(`${tableNames.EXPERIMENT} (id, name, description)`));
+
+    return toExperimentId;
+  }
+
   // Sets samples_order as an array that has the sample in oldPosition moved to newPosition
   async updateSamplePosition(
     experimentId, oldPosition, newPosition,

src/api.v2/model/Sample.js

@@ -1,3 +1,7 @@
+const _ = require('lodash');
+
+const { v4: uuidv4 } = require('uuid');
+
 const BasicModel = require('./BasicModel');
 const sqlClient = require('../../sql/sqlClient');
 
@@ -38,6 +42,11 @@ class Sample extends BasicModel {
     const sampleFileFields = ['sample_file_type', 'size', 'upload_status', 's3_path'];
     const sampleFileFieldsWithAlias = sampleFileFields.map((field) => `sf.${field}`);
     const fileObjectFormatted = sampleFileFields.map((field) => [`'${field}'`, field]);
+
+    // Add sample file id (needs to go separate to avoid conflict with sample id)
+    sampleFileFieldsWithAlias.push('sf.id as sf_id');
+    fileObjectFormatted.push(['\'id\'', 'sf_id']);
+
     const sampleFileObject = `jsonb_object_agg(sample_file_type,json_build_object(${fileObjectFormatted})) as files`;
     const fileNamesQuery = sql.select(['id', sql.raw(sampleFileObject)])
       .from(sql.select([...sampleFileFieldsWithAlias, 's.id'])
@@ -81,6 +90,71 @@ class Sample extends BasicModel {
       );
     });
   }
+
+  /**
+   * Creates copy samples from one experiment to another one
+   *
+   * @param {*} fromExperimentId
+   * @param {*} toExperimentId
+   */
+  async copyTo(fromExperimentId, toExperimentId, samplesOrder) {
+    const result = await this.getSamples(fromExperimentId);
+
+    const newSampleIds = [];
+
+    const metadataTrackKeys = Object.keys(result[0].metadata);
+
+    const sampleRows = [];
+    const sampleFileMapRows = [];
+    const metadataValueMapRows = [];
+
+    await this.sql.transaction(async (trx) => {
+      let metadataTracks = [];
+      if (metadataTrackKeys.length > 0) {
+        metadataTracks = await trx(tableNames.METADATA_TRACK)
+          .insert(metadataTrackKeys.map((key) => ({ experiment_id: toExperimentId, key })))
+          .returning(['id', 'key']);
+      }
+
+      // Copy each sample in order so
+      // the new samples we create follow the same order
+      samplesOrder.forEach((fromSampleId) => {
+        const sample = result.find(({ id }) => id === fromSampleId);
+
+        const toSampleId = uuidv4();
+
+        newSampleIds.push(toSampleId);
+
+        sampleRows.push({
+          id: toSampleId,
+          experiment_id: toExperimentId,
+          name: sample.name,
+          sample_technology: sample.sampleTechnology,
+        });
+
+        Object.entries(sample.files).forEach(([, file]) => {
+          sampleFileMapRows.push({
+            sample_id: toSampleId,
+            sample_file_id: file.id,
+          });
+        });
+
+        Object.entries(sample.metadata).forEach(([key, value]) => {
+          const { id } = _.find(metadataTracks, ({ key: currentKey }) => currentKey === key);
+          metadataValueMapRows.push({ metadata_track_id: id, sample_id: toSampleId, value });
+        });
+      });
+
+      await trx(tableNames.SAMPLE).insert(sampleRows);
+      await trx(tableNames.SAMPLE_TO_SAMPLE_FILE_MAP).insert(sampleFileMapRows);
+
+      if (metadataValueMapRows.length > 0) {
+        await trx(tableNames.SAMPLE_IN_METADATA_TRACK_MAP).insert(metadataValueMapRows);
+      }
+    });
+
+    return newSampleIds;
+  }
 }
 
 module.exports = Sample;

src/api.v2/model/UserAccess.js

@@ -19,6 +19,7 @@ const selectableProps = [
 ];
 
 const getLogger = require('../../utils/getLogger');
+const constants = require('../../utils/constants');
 
 const logger = getLogger('[UserAccessModel] - ');
 
@@ -91,11 +92,15 @@ class UserAccess extends BasicModel {
     await this.grantAccess(userId, experimentId, AccessRole.OWNER);
   }
 
+
   async canAccessExperiment(userId, experimentId, url, method) {
     const result = await this.sql(tableNames.USER_ACCESS)
-      .first()
+      // Check if user has access
       .where({ experiment_id: experimentId, user_id: userId })
-      .from(tableNames.USER_ACCESS);
+      // Or if it is a public access experiment
+      .orWhere({ experiment_id: experimentId, user_id: constants.PUBLIC_ACCESS_ID })
+      .from(tableNames.USER_ACCESS)
+      .first();
 
     // If there is no entry for this user and role, then user definitely doesn't have access
     if (_.isNil(result)) {

src/api.v2/model/__mocks__/Experiment.js

@@ -6,9 +6,11 @@ const stub = {
   updateSamplePosition: jest.fn(),
   updateProcessingConfig: jest.fn(),
   getProcessingConfig: jest.fn(),
+  createCopy: jest.fn(),
   addSample: jest.fn(),
   deleteSample: jest.fn(),
   getDownloadLink: jest.fn(),
+  getAllExampleExperiments: jest.fn(),
   ...BasicModel,
 };
 

src/api.v2/model/__mocks__/Sample.js

@@ -3,6 +3,7 @@ const BasicModel = require('./BasicModel')();
 const stub = {
   getSamples: jest.fn(),
   setNewFile: jest.fn(),
+  copyTo: jest.fn(),
   ...BasicModel,
 };
 

src/api.v2/routes/experiment.js

@@ -1,7 +1,8 @@
 const {
-  createExperiment, getExperiment, patchExperiment, deleteExperiment,
-  updateSamplePosition, getAllExperiments,
+  getAllExperiments, getAllExampleExperiments,
+  createExperiment, getExperiment, patchExperiment, deleteExperiment, cloneExperiment,
   getProcessingConfig, updateProcessingConfig,
+  updateSamplePosition,
   getBackendStatus, downloadData,
 } = require('../controllers/experimentController');
 
@@ -12,6 +13,10 @@ module.exports = {
     expressAuthenticationOnlyMiddleware,
     (req, res, next) => getAllExperiments(req, res).catch(next),
   ],
+  'experiment#getAllExampleExperiments': [
+    expressAuthenticationOnlyMiddleware,
+    (req, res, next) => getAllExampleExperiments(req, res).catch(next),
+  ],
   'experiment#getExperiment': [
     expressAuthorizationMiddleware,
     (req, res, next) => getExperiment(req, res).catch(next),
@@ -48,4 +53,8 @@ module.exports = {
     expressAuthorizationMiddleware,
     (req, res, next) => downloadData(req, res).catch(next),
   ],
+  'experiment#clone': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => cloneExperiment(req, res).catch(next),
+  ],
 };