[BIOMAGE-1804] Implement load & save processing settings for api v2

src/api.v2/controllers/experimentController.js

@@ -82,10 +82,28 @@ const updateSamplePosition = async (req, res) => {
   res.json(OK());
 };
 
+const getProcessingConfig = async (req, res) => {
+  const { params: { experimentId } } = req;
+  logger.log('Getting processing config for experiment ', experimentId);
+
+  const result = await new Experiment().getProcessingConfig(experimentId);
+  res.json(result);
+};
+
+const updateProcessingConfig = async (req, res) => {
+  const { params: { experimentId }, body } = req;
+  logger.log('Updating processing config for experiment ', experimentId);
+
+  await new Experiment().updateProcessingConfig(experimentId, body);
+  res.json(OK());
+};
+
 module.exports = {
   getAllExperiments,
   getExperiment,
   createExperiment,
+  updateProcessingConfig,
   patchExperiment,
   updateSamplePosition,
+  getProcessingConfig,
 };

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

@@ -4,6 +4,8 @@ const stub = {
   getAllExperiments: jest.fn(),
   getExperimentData: jest.fn(),
   updateSamplePosition: jest.fn(),
+  updateProcessingConfig: jest.fn(),
+  getProcessingConfig: jest.fn(),
   addSample: jest.fn(),
   deleteSample: jest.fn(),
   ...BasicModel,

src/api.v2/model/experiment.js

@@ -0,0 +1,183 @@
+const _ = require('lodash');
+
+const BasicModel = require('./BasicModel');
+const sqlClient = require('../../sql/sqlClient');
+const { collapseKeyIntoArray } = require('../../sql/helpers');
+
+const { NotFoundError } = require('../../utils/responses');
+
+const tableNames = require('../helpers/tableNames');
+
+
+const getLogger = require('../../utils/getLogger');
+
+const logger = getLogger('[ExperimentModel] - ');
+
+
+const experimentFields = [
+  'id',
+  'name',
+  'description',
+  'samples_order',
+  'processing_config',
+  'notify_by_email',
+  'created_at',
+  'updated_at',
+];
+
+class Experiment extends BasicModel {
+  constructor(sql = sqlClient.get()) {
+    super(sql, tableNames.EXPERIMENT, experimentFields);
+  }
+
+  async getAllExperiments(userId) {
+    const fields = [
+      'id',
+      'name',
+      'description',
+      'samples_order',
+      'notify_by_email',
+      'created_at',
+      'updated_at',
+    ];
+
+    const aliasedExperimentFields = fields.map((field) => `e.${field}`);
+    function mainQuery() {
+      this.select([...aliasedExperimentFields, 'm.key'])
+        .from(tableNames.USER_ACCESS)
+        .where('user_id', userId)
+        .join(`${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);
+
+    return result;
+  }
+
+  async getExperimentData(experimentId) {
+    function mainQuery() {
+      this.select('*')
+        .from(tableNames.EXPERIMENT)
+        .leftJoin(tableNames.EXPERIMENT_EXECUTION, `${tableNames.EXPERIMENT}.id`, `${tableNames.EXPERIMENT_EXECUTION}.experiment_id`)
+        .where('id', experimentId)
+        .as('mainQuery');
+    }
+
+    const experimentExecutionFields = [
+      'params_hash', 'state_machine_arn', 'execution_arn',
+    ];
+
+    const pipelineExecutionKeys = experimentExecutionFields.reduce((acum, current) => {
+      acum.push(`'${current}'`);
+      acum.push(current);
+
+      return acum;
+    }, []);
+
+    const replaceNullsWithObject = (object, nullableKey) => (
+      `COALESCE(
+      ${object}
+      FILTER(
+        WHERE ${nullableKey} IS NOT NULL
+      ),
+      '{}'::jsonb
+    )`
+    );
+
+    const result = await this.sql
+      .select([
+        ...experimentFields,
+        this.sql.raw(
+          `${replaceNullsWithObject(
+            `jsonb_object_agg(pipeline_type, jsonb_build_object(${pipelineExecutionKeys.join(', ')}))`,
+            'pipeline_type',
+          )} as pipelines`,
+        ),
+      ])
+      .from(mainQuery)
+      .groupBy(experimentFields)
+      .first();
+
+    if (_.isEmpty(result)) {
+      throw new NotFoundError('Experiment not found');
+    }
+
+    return result;
+  }
+
+  // Sets samples_order as an array that has the sample in oldPosition moved to newPosition
+  async updateSamplePosition(
+    experimentId, oldPosition, newPosition,
+  ) {
+    const trx = await this.sql.transaction();
+
+    try {
+      const result = await trx(tableNames.EXPERIMENT)
+        .update({
+          samples_order: trx.raw(`(
+        SELECT jsonb_insert(samples_order - ${oldPosition}, '{${newPosition}}', samples_order -> ${oldPosition}, false)
+          FROM (
+            SELECT (samples_order)
+            FROM experiment e
+            WHERE e.id = '${experimentId}'
+          ) samples_order
+        )`),
+        }).where('id', experimentId)
+        .returning(['samples_order']);
+
+      const { samplesOrder = null } = result[0] || {};
+
+      if (_.isNil(samplesOrder)
+        || !_.inRange(oldPosition, 0, samplesOrder.length)
+        || !_.inRange(newPosition, 0, samplesOrder.length)
+      ) {
+        logger.log('Invalid positions or samples_order was broken, rolling back transaction');
+        throw new Error('Invalid update parameters');
+      }
+
+      trx.commit();
+    } catch (e) {
+      trx.rollback();
+      throw e;
+    }
+  }
+
+  async getProcessingConfig(experimentId) {
+    const result = await this.find({ id: experimentId });
+    if (_.isEmpty(result)) {
+      throw new NotFoundError('Experiment not found');
+    }
+    console.log('RESULT IS ', result[0].processingConfig);
+
+    return result[0].processingConfig;
+  }
+
+  async updateProcessingConfig(experimentId, body) {
+    const { name: stepName, body: change } = body[0];
+
+    const { processingConfig } = await this.getProcessingConfig(experimentId);
+    processingConfig[stepName] = change;
+
+    await this.update(experimentId, { processingConfig });
+  }
+
+  async addSample(experimentId, sampleId) {
+    await this.sql(tableNames.EXPERIMENT)
+      .update({
+        samples_order: this.sql.raw(`samples_order || '["${sampleId}"]'::jsonb`),
+      })
+      .where('id', experimentId);
+  }
+
+  async deleteSample(experimentId, sampleId) {
+    await this.sql(tableNames.EXPERIMENT)
+      .update({
+        samples_order: this.sql.raw(`samples_order - '${sampleId}'`),
+      })
+      .where('id', experimentId);
+  }
+}
+
+module.exports = Experiment;

src/api.v2/routes/experiment.js

@@ -1,5 +1,6 @@
 const {
-  createExperiment, getExperiment, patchExperiment, updateSamplePosition, getAllExperiments,
+  createExperiment, getExperiment, patchExperiment, updateSamplePosition,
+  getAllExperiments, getProcessingConfig, updateProcessingConfig,
 } = require('../controllers/experimentController');
 
 const { expressAuthenticationOnlyMiddleware, expressAuthorizationMiddleware } = require('../middlewares/authMiddlewares');
@@ -25,4 +26,12 @@ module.exports = {
     expressAuthorizationMiddleware,
     (req, res, next) => updateSamplePosition(req, res).catch(next),
   ],
+  'experiment#getProcessingConfig': [
+    // expressAuthorizationMiddleware,
+    (req, res, next) => getProcessingConfig(req, res).catch(next),
+  ],
+  'experiment#updateProcessingConfig': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => updateProcessingConfig(req, res).catch(next),
+  ],
 };

src/specs/api.v2.yaml

@@ -58,6 +58,69 @@ paths:
                   - env
                   - clusterEnv
       description: Returns a status on the health of the API.
+  '/experiments/{experimentId}/processingConfig':
+    get:
+      summary: Get processing configuration for an experiment
+      description: Get processing configuration for an experiment
+      operationId: getProcessingConfig
+      x-eov-operation-id: experiment#getProcessingConfig
+      x-eov-operation-handler: routes/experiment
+      responses:
+        '200':
+          description: get processing configuration for an experiment
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ProcessingConfig'
+        '404':
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '400':
+          description: Bad Request
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '401':
+          description: The request lacks authentication credentials.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+    put:
+      summary: Update processing configuration for an experiment
+      description: Update processing configuration for an experiment
+      operationId: updateProcessingConfig
+      x-eov-operation-id: experiment#updateProcessingConfig
+      x-eov-operation-handler: routes/experiment
+      responses:
+        '200':
+          description: Processing configuration for an experiment
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPSuccess'
+        '404':
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '400':
+          description: Bad Request
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '401':
+          description: The request lacks authentication credentials.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
   '/experiments':
     get:
       summary: Get all experiments
@@ -330,6 +393,7 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/HTTPError'
+
 components:
   schemas:
     CreateExperiment:
@@ -338,6 +402,8 @@ components:
       $ref: './models/experiment-bodies/ExperimentInfo.v2.yaml'
     ExperimentPatch:
       $ref: './models/experiment-bodies/ExperimentPatch.v2.yaml'
+    ProcessingConfig:
+      $ref: './models/experiment-bodies/ProcessingConfig.v2.yaml'
     GetAllExperiments:
       $ref: './models/experiment-bodies/GetAllExperiments.v2.yaml'
     CreateSample:

src/specs/models/api-body-schemas/ProcessingConfig.v1.yaml

@@ -2,28 +2,28 @@ title: Processing Config schema
 description: Processing Config schema
 type: object
 properties:
-  cellSizeDistribution:
-    $ref: '../processing-config-bodies/ProcessingConfigCellSizeDistribution.v1.yaml'
-  mitochondrialContent:
-    $ref: '../processing-config-bodies/ProcessingConfigMitochondrialContent.v1.yaml'
-  readAlignment:
-    $ref: '../processing-config-bodies/ProcessingConfigReadAlignment.v1.yaml'
-  classifier:
-    $ref: '../processing-config-bodies/ProcessingConfigClassifier.v1.yaml'
-  numGenesVsNumUmis:
-    $ref: '../processing-config-bodies/ProcessingConfigNumGenesVsNumUMIs.v1.yaml'
-  doubletScores:
-    $ref: '../processing-config-bodies/ProcessingConfigDoubletScores.v1.yaml'
-  dataIntegration:
-    $ref: '../processing-config-bodies/ProcessingConfigDataIntegration.v1.yaml'
-  configureEmbedding:
-    $ref: '../processing-config-bodies/ProcessingConfigConfigureEmbedding.v1.yaml'
+  processingConfig:
+    type: object
+    properties:
+      cellSizeDistribution:
+        $ref: '../processing-config-bodies/ProcessingConfigCellSizeDistribution.v1.yaml'
+      mitochondrialContent:
+        $ref: '../processing-config-bodies/ProcessingConfigMitochondrialContent.v1.yaml'
+      readAlignment:
+        $ref: '../processing-config-bodies/ProcessingConfigReadAlignment.v1.yaml'
+      classifier:
+        $ref: '../processing-config-bodies/ProcessingConfigClassifier.v1.yaml'
+      numGenesVsNumUmis:
+        $ref: '../processing-config-bodies/ProcessingConfigNumGenesVsNumUMIs.v1.yaml'
+      doubletScores:
+        $ref: '../processing-config-bodies/ProcessingConfigDoubletScores.v1.yaml'
+      dataIntegration:
+        $ref: '../processing-config-bodies/ProcessingConfigDataIntegration.v1.yaml'
+      configureEmbedding:
+        $ref: '../processing-config-bodies/ProcessingConfigConfigureEmbedding.v1.yaml'
+
 required:
-  - cellSizeDistribution
-  - mitochondrialContent
-  - readAlignment
-  - classifier
-  - numGenesVsNumUmis
-  - doubletScores
-  - dataIntegration
-  - configureEmbedding
+  - processingConfig: [
+    'cellSizeDistribution', 'mitochondrialContent', 'readAlignment', 
+    'classifier', 'numGenesVsNumUmis', 'doubletScores', 'dataIntegration', 'configureEmbedding']
+additionalProperties: false

src/specs/models/experiment-bodies/ProcessingConfig.v2.yaml

@@ -25,4 +25,4 @@ required:
   - numGenesVsNumUmis
   - doubletScores
   - dataIntegration
-  - configureEmbedding
+  - configureEmbedding