Merge pull request #330 from hms-dbmi-cellenics/sample-create-delete-v2

Sample create delete api v2

.eslintrc.js

@@ -19,6 +19,6 @@ module.exports = {
     "no-console": "off",
     // no-return-await disabled because of https://stackoverflow.com/a/44806230
     "no-return-await": "off",
-    "no-multiple-empty-lines": "off",
+    "no-multiple-empty-lines": "off"
   },
 };

src/api.v2/controllers/experimentController.js

@@ -1,18 +1,18 @@
-/* eslint-disable import/prefer-default-export */
 const _ = require('lodash');
 
-const experiment = require('../model/experiment');
-const userAccess = require('../model/userAccess');
+const Experiment = require('../model/Experiment');
+const UserAccess = require('../model/UserAccess');
 
 const getLogger = require('../../utils/getLogger');
 const { OK } = require('../../utils/responses');
+const sqlClient = require('../../sql/sqlClient');
 
 const logger = getLogger('[ExperimentController] - ');
 
 const getAllExperiments = async (req, res) => {
   const { user: { sub: userId } } = req;
 
-  const data = await experiment.getAllExperiments(userId);
+  const data = await new Experiment().getAllExperiments(userId);
 
   res.json(data);
 };
@@ -22,7 +22,7 @@ const getExperiment = async (req, res) => {
 
   logger.log(`Getting experiment ${experimentId}`);
 
-  const data = await experiment.getExperimentData(experimentId);
+  const data = await new Experiment().getExperimentData(experimentId);
 
   logger.log(`Finished getting experiment ${experimentId}`);
 
@@ -36,8 +36,10 @@ const createExperiment = async (req, res) => {
 
   logger.log('Creating experiment');
 
-  await experiment.create({ id: experimentId, name, description });
-  await userAccess.createNewExperimentPermissions(user.sub, experimentId);
+  await sqlClient.get().transaction(async (trx) => {
+    await new Experiment(trx).create({ id: experimentId, name, description });
+    await new UserAccess(trx).createNewExperimentPermissions(user.sub, experimentId);
+  });
 
   logger.log(`Finished creating experiment ${experimentId}`);
 
@@ -51,7 +53,7 @@ const patchExperiment = async (req, res) => {
 
   const snakeCasedKeysToPatch = _.mapKeys(body, (_value, key) => _.snakeCase(key));
 
-  await experiment.update(experimentId, snakeCasedKeysToPatch);
+  await new Experiment().update(experimentId, snakeCasedKeysToPatch);
 
   logger.log(`Finished updating experiment ${experimentId}`);
 
@@ -73,7 +75,7 @@ const updateSamplePosition = async (req, res) => {
     return;
   }
 
-  await experiment.updateSamplePosition(experimentId, oldPosition, newPosition);
+  await new Experiment().updateSamplePosition(experimentId, oldPosition, newPosition);
 
   logger.log(`Finished reordering samples in ${experimentId}`);
 

src/api.v2/controllers/sampleController.js

@@ -0,0 +1,55 @@
+const Sample = require('../model/Sample');
+const Experiment = require('../model/Experiment');
+const MetadataTrack = require('../model/MetadataTrack');
+
+const getLogger = require('../../utils/getLogger');
+const { OK } = require('../../utils/responses');
+
+const sqlClient = require('../../sql/sqlClient');
+
+const logger = getLogger('[SampleController] - ');
+
+const createSample = async (req, res) => {
+  const {
+    params: { experimentId, sampleId },
+    body: { name, sampleTechnology },
+  } = req;
+
+  logger.log('Creating sample');
+
+  await sqlClient.get().transaction(async (trx) => {
+    await new Sample(trx).create({
+      id: sampleId,
+      experiment_id: experimentId,
+      name,
+      sample_technology: sampleTechnology,
+    });
+
+    await new Experiment(trx).addSample(experimentId, sampleId);
+
+    await new MetadataTrack(trx)
+      .createNewSampleValues(experimentId, sampleId);
+  });
+
+  logger.log(`Finished creating sample ${sampleId} for experiment ${experimentId}`);
+
+  res.json(OK());
+};
+
+const deleteSample = async (req, res) => {
+  const { params: { experimentId, sampleId } } = req;
+
+  await sqlClient.get().transaction(async (trx) => {
+    await new Sample(trx).destroy(sampleId);
+    await new Experiment(trx).deleteSample(experimentId, sampleId);
+  });
+
+  logger.log(`Finished deleting sample ${sampleId} from experiment ${experimentId}`);
+
+  res.json(OK());
+};
+
+module.exports = {
+  createSample,
+  deleteSample,
+};

src/api.v2/helpers/tableNames.js

@@ -0,0 +1,11 @@
+const tableNames = {
+  EXPERIMENT: 'experiment',
+  EXPERIMENT_EXECUTION: 'experiment_execution',
+  SAMPLE: 'sample',
+  USER_ACCESS: 'user_access',
+  INVITE_ACCESS: 'invite_access',
+  METADATA_TRACK: 'metadata_track',
+  SAMPLE_IN_METADATA_TRACK_MAP: 'sample_in_metadata_track_map',
+};
+
+module.exports = tableNames;

src/api.v2/middlewares/authMiddlewares.js

@@ -2,7 +2,7 @@
 // for how JWT verification works with Cognito.
 const { UnauthorizedError, UnauthenticatedError } = require('../../utils/responses');
 
-const userAccess = require('../model/userAccess');
+const UserAccess = require('../model/UserAccess');
 
 /**
  * General authorization middleware. Resolves with nothing on
@@ -20,7 +20,7 @@ const userAccess = require('../model/userAccess');
 const authorize = async (userId, resource, method, experimentId) => {
   // authResource is always experimentId in V2 because there is no project
 
-  const granted = await userAccess.canAccessExperiment(
+  const granted = await new UserAccess().canAccessExperiment(
     userId,
     experimentId,
     resource,

src/api.v2/model/BasicModel.js

@@ -0,0 +1,71 @@
+// The basic functions of a model that uses Knexjs to store and retrieve data from a
+// database using the provided `knex` instance. Custom functionality can be
+// composed on top of this set of common functions.
+//
+// The idea is that these are the most-used types of functions that most/all
+// "models" will want to have.
+
+class BasicModel {
+  constructor(sql, tableName, selectableProps = [], timeout = 4000) {
+    this.sql = sql;
+    this.tableName = tableName;
+    this.selectableProps = selectableProps;
+    this.timeout = timeout;
+  }
+
+  create(props) {
+    return this.sql.insert(props)
+      .returning(this.selectableProps)
+      .into(this.tableName)
+      .timeout(this.timeout);
+  }
+
+  findAll() {
+    return this.sql
+      .select(this.selectableProps)
+      .from(this.tableName)
+      .timeout(this.timeout);
+  }
+
+  find(filters) {
+    return this.sql.select(this.selectableProps)
+      .from(this.tableName)
+      .where(filters)
+      .timeout(this.timeout);
+  }
+
+  // Same as `find` but only returns the first match if >1 are found.
+  findOne(filters) {
+    return this.find(filters)
+      // @ts-ignore
+      .then((results) => {
+        if (!Array.isArray(results)) return results;
+
+        return results[0];
+      });
+  }
+
+  findById(id) {
+    return this.sql.select(this.selectableProps)
+      .from(this.tableName)
+      .where({ id })
+      .timeout(this.timeout);
+  }
+
+  update(id, props) {
+    return this.sql.update(props)
+      .from(this.tableName)
+      .where({ id })
+      .returning(this.selectableProps)
+      .timeout(this.timeout);
+  }
+
+  destroy(id) {
+    return this.sql.del()
+      .from(this.tableName)
+      .where({ id })
+      .timeout(this.timeout);
+  }
+}
+
+module.exports = BasicModel;