Merge pull request #343 from hms-dbmi-cellenics/1836-metadata-tracks-…

…endpoints

[BIOMAGE-1836] Implement metadata tracks-specific endpoints

src/api.v2/controllers/metadataTrackController.js

@@ -0,0 +1,80 @@
+const MetadataTrack = require('../model/MetadataTrack');
+
+const getLogger = require('../../utils/getLogger');
+const { OK, NotFoundError } = require('../../utils/responses');
+
+const logger = getLogger('[MetadataTrackController] - ');
+
+const createMetadataTrack = async (req, res) => {
+  const {
+    params: { experimentId, metadataTrackKey },
+  } = req;
+
+  logger.log(`Creating metadata track ${metadataTrackKey} in experiment ${experimentId}`);
+
+  await new MetadataTrack().createNewMetadataTrack(experimentId, metadataTrackKey);
+
+  logger.log(`Finished creating metadata track ${metadataTrackKey} in experiment ${experimentId}`);
+
+  res.json(OK());
+};
+
+const patchMetadataTrack = async (req, res) => {
+  const {
+    params: { experimentId, metadataTrackKey: oldKey },
+    body: { key },
+  } = req;
+
+  logger.log(`Patching metadata track ${oldKey} in experiment ${experimentId}`);
+
+  const result = await new MetadataTrack()
+    .update({ experiment_id: experimentId, key: oldKey }, { key });
+
+  if (result.length === 0) {
+    throw new NotFoundError(`Metadata track ${oldKey} not found`);
+  }
+
+  logger.log(`Finished patching metadata track ${oldKey} in experiment ${experimentId}, changed to ${key}`);
+  res.json(OK());
+};
+
+const deleteMetadataTrack = async (req, res) => {
+  const {
+    params: { experimentId, metadataTrackKey },
+  } = req;
+
+  logger.log(`Creating metadata track ${metadataTrackKey} in experiment ${experimentId}`);
+
+  const result = await new MetadataTrack().delete(
+    { experiment_id: experimentId, key: metadataTrackKey },
+  );
+
+  if (result.length === 0) {
+    throw new NotFoundError(`Metadata track ${metadataTrackKey} not found`);
+  }
+
+  logger.log(`Finished creating metadata track ${metadataTrackKey} in experiment ${experimentId}`);
+
+  res.json(OK());
+};
+
+const patchValueForSample = async (req, res) => {
+  const {
+    params: { experimentId, sampleId, metadataTrackKey },
+    body: { value },
+  } = req;
+
+  logger.log(`Patching value of metadata track ${metadataTrackKey} in sample ${sampleId} in experiment ${experimentId}`);
+
+  await new MetadataTrack().patchValueForSample(experimentId, sampleId, metadataTrackKey, value);
+
+  logger.log(`Finished patching value of metadata track ${metadataTrackKey} in sample ${sampleId} in experiment ${experimentId}, changed to ${value}`);
+  res.json(OK());
+};
+
+module.exports = {
+  createMetadataTrack,
+  patchMetadataTrack,
+  deleteMetadataTrack,
+  patchValueForSample,
+};

src/api.v2/controllers/sampleController.js

@@ -52,7 +52,7 @@ const deleteSample = async (req, res) => {
   logger.log(`Deleting sample ${sampleId} from experiment ${experimentId}`);
 
   await sqlClient.get().transaction(async (trx) => {
-    await new Sample(trx).destroy(sampleId);
+    await new Sample(trx).deleteById(sampleId);
     await new Experiment(trx).deleteSample(experimentId, sampleId);
   });
 

src/api.v2/model/BasicModel.js

@@ -68,10 +68,19 @@ class BasicModel {
       .timeout(this.timeout);
   }
 
-  destroy(id) {
+  deleteById(id) {
     return this.sql.del()
       .from(this.tableName)
       .where({ id })
+      .returning(this.selectableProps)
+      .timeout(this.timeout);
+  }
+
+  delete(filters) {
+    return this.sql.del()
+      .from(this.tableName)
+      .where(filters)
+      .returning(this.selectableProps)
       .timeout(this.timeout);
   }
 }

src/api.v2/model/MetadataTrack.js

@@ -3,21 +3,48 @@ const BasicModel = require('./BasicModel');
 const sqlClient = require('../../sql/sqlClient');
 
 const tableNames = require('./tableNames');
+const { NotFoundError } = require('../../utils/responses');
 
 const sampleFields = [
   'id',
   'experiment_id',
-  'name',
-  'sample_technology',
-  'created_at',
-  'updated_at',
+  'key',
 ];
 
 class MetadataTrack extends BasicModel {
   constructor(sql = sqlClient.get()) {
     super(sql, tableNames.METADATA_TRACK, sampleFields);
   }
 
+  async createNewMetadataTrack(experimentId, key) {
+    const sampleIds = await this.sql.select(['id'])
+      .from(tableNames.SAMPLE)
+      .where({ experiment_id: experimentId });
+
+    await this.sql.transaction(async (trx) => {
+      const response = await trx
+        .insert({
+          experiment_id: experimentId,
+          key,
+        })
+        .returning(['id'])
+        .into(this.tableName);
+
+      if (sampleIds.length === 0) {
+        return;
+      }
+
+      const [{ id: metadataTrackId }] = response;
+
+      const valuesToInsert = sampleIds.map(({ id: sampleId }) => ({
+        metadata_track_id: metadataTrackId,
+        sample_id: sampleId,
+      }));
+
+      await trx(tableNames.SAMPLE_IN_METADATA_TRACK_MAP).insert(valuesToInsert);
+    });
+  }
+
   async createNewSampleValues(experimentId, sampleId) {
     const tracks = await this.sql.select(['id'])
       .from(tableNames.METADATA_TRACK)
@@ -30,11 +57,22 @@ class MetadataTrack extends BasicModel {
     const valuesToInsert = tracks.map(({ id }) => ({
       metadata_track_id: id,
       sample_id: sampleId,
-      value: 'N.A.',
     }));
 
-    await this.sql(tableNames.SAMPLE_IN_METADATA_TRACK_MAP)
-      .insert(valuesToInsert);
+    await this.sql(tableNames.SAMPLE_IN_METADATA_TRACK_MAP).insert(valuesToInsert);
+  }
+
+  async patchValueForSample(experimentId, sampleId, key, value) {
+    const [{ id }] = await this.find({ experiment_id: experimentId, key });
+
+    const result = await this.sql(tableNames.SAMPLE_IN_METADATA_TRACK_MAP)
+      .update({ value })
+      .where({ metadata_track_id: id, sample_id: sampleId })
+      .returning(['metadata_track_id']);
+
+    if (result.length === 0) {
+      throw new NotFoundError(`Metadata track ${key} or sample ${sampleId} don't exist`);
+    }
   }
 }
 

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

@@ -6,7 +6,8 @@ const stub = {
   findById: jest.fn(),
   update: jest.fn(),
   updateById: jest.fn(),
-  destroy: jest.fn(),
+  delete: jest.fn(),
+  deleteById: jest.fn(),
 };
 
 const BasicModel = jest.fn().mockImplementation(() => stub);

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

@@ -1,7 +1,9 @@
 const BasicModel = require('./BasicModel')();
 
 const stub = {
+  createNewMetadataTrack: jest.fn(),
   createNewSampleValues: jest.fn(),
+  patchValueForSample: jest.fn(),
   ...BasicModel,
 };
 

src/api.v2/routes/metadataTrack.js

@@ -0,0 +1,27 @@
+const {
+  createMetadataTrack,
+  patchMetadataTrack,
+  patchValueForSample,
+  deleteMetadataTrack,
+} = require('../controllers/metadataTrackController');
+
+const { expressAuthorizationMiddleware } = require('../middlewares/authMiddlewares');
+
+module.exports = {
+  'metadataTrack#createMetadataTrack': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => createMetadataTrack(req, res).catch(next),
+  ],
+  'metadataTrack#patchMetadataTrack': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => patchMetadataTrack(req, res).catch(next),
+  ],
+  'metadataTrack#patchSampleInMetadataTrackValue': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => patchValueForSample(req, res).catch(next),
+  ],
+  'metadataTrack#deleteMetadataTrack': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => deleteMetadataTrack(req, res).catch(next),
+  ],
+};