Add sce upload

src/api.v2/constants.js

@@ -1,7 +1,7 @@
 // Pipeline names
 const QC_PROCESS_NAME = 'qc';
 const GEM2S_PROCESS_NAME = 'gem2s';
-const SEURAT_PROCESS_NAME = 'seurat';
+const OBJ2S_PROCESS_NAME = 'obj2s';
 const OLD_QC_NAME_TO_BE_REMOVED = 'pipeline';
 const SUBSET_PROCESS_NAME = 'subset';
 const COPY_PROCESS_NAME = 'copy';
@@ -44,7 +44,7 @@ const ACCOUNT_ID = {
 module.exports = {
   QC_PROCESS_NAME,
   GEM2S_PROCESS_NAME,
-  SEURAT_PROCESS_NAME,
+  OBJ2S_PROCESS_NAME,
   OLD_QC_NAME_TO_BE_REMOVED,
   SUBSET_PROCESS_NAME,
   COPY_PROCESS_NAME,

src/api.v2/controllers/seuratController.js → src/api.v2/controllers/obj2sController.js

@@ -1,10 +1,10 @@
-const { runSeurat, handleSeuratResponse } = require('../helpers/pipeline/seurat');
+const { runObj2s, handleObj2sResponse } = require('../helpers/pipeline/obj2s');
 const { OK } = require('../../utils/responses');
 const getLogger = require('../../utils/getLogger');
 const parseSNSMessage = require('../../utils/parseSNSMessage');
 const snsTopics = require('../../config/snsTopics');
 
-const logger = getLogger('[SeuratController] - ');
+const logger = getLogger('[Obj2sController] - ');
 
 const handleResponse = async (req, res) => {
   let result;
@@ -22,10 +22,10 @@ const handleResponse = async (req, res) => {
   const isSnsNotification = parsedMessage !== undefined;
   if (isSnsNotification) {
     try {
-      await handleSeuratResponse(io, parsedMessage);
+      await handleObj2sResponse(io, parsedMessage);
     } catch (e) {
       logger.error(
-        'seurat pipeline response handler failed with error: ', e,
+        'obj2s pipeline response handler failed with error: ', e,
       );
 
       res.status(200).send('nok');
@@ -36,16 +36,16 @@ const handleResponse = async (req, res) => {
   res.status(200).send('ok');
 };
 
-const handleSeuratRequest = async (req, res) => {
+const handleObj2sRequest = async (req, res) => {
   const params = {
     experimentId: req.params.experimentId,
   };
 
-  await runSeurat(params, req.headers.authorization);
+  await runObj2s(params, req.headers.authorization);
   res.json(OK());
 };
 
 module.exports = {
-  handleSeuratRequest,
+  handleObj2sRequest,
   handleResponse,
 };

src/api.v2/events/validateAndSubmitWork.js

@@ -33,15 +33,15 @@ const validateAndSubmitWork = async (req) => {
     experimentId, pipelineConstants.QC_PROCESS_NAME,
   );
 
-  const { seurat: { status: seuratPipelineStatus } } = await getPipelineStatus(
-    experimentId, pipelineConstants.SEURAT_PROCESS_NAME,
+  const { obj2s: { status: obj2sPipelineStatus } } = await getPipelineStatus(
+    experimentId, pipelineConstants.OBJ2S_PROCESS_NAME,
   );
 
-  if (!checkSomeEqualTo([qcPipelineStatus, seuratPipelineStatus], pipelineConstants.SUCCEEDED)) {
-    throw new Error(`Work request can not be handled because pipeline is ${qcPipelineStatus} or seurat status is ${seuratPipelineStatus}`);
+  if (!checkSomeEqualTo([qcPipelineStatus, obj2sPipelineStatus], pipelineConstants.SUCCEEDED)) {
+    throw new Error(`Work request can not be handled because pipeline is ${qcPipelineStatus} or obj2s status is ${obj2sPipelineStatus}`);
   }
 
-  // add the embedding etag if the work request, needed by trajectory analysis & download seurat object
+  // add the embedding etag if the work request, needed by trajectory analysis & download obj2s object
   workRequest = await addEmbeddingEtag(experimentId, workRequest);
 
   await validateRequest(workRequest, 'WorkRequest.v2.yaml');

src/api.v2/helpers/backendStatus/getExperimentBackendStatus.js

@@ -3,19 +3,19 @@ const getPipelineStatus = require('../pipeline/getPipelineStatus');
 const getWorkerStatus = require('../worker/getWorkerStatus');
 
 const getExperimentBackendStatus = async (experimentId) => {
-  const [{ gem2s }, { qc }, { seurat }, { worker }] = await Promise.all(
+  const [{ gem2s }, { qc }, { obj2s }, { worker }] = await Promise.all(
     [
       getPipelineStatus(experimentId, constants.GEM2S_PROCESS_NAME),
       getPipelineStatus(experimentId, constants.QC_PROCESS_NAME),
-      getPipelineStatus(experimentId, constants.SEURAT_PROCESS_NAME),
+      getPipelineStatus(experimentId, constants.OBJ2S_PROCESS_NAME),
       getWorkerStatus(experimentId),
     ],
   );
 
   const formattedResponse = {
     [constants.OLD_QC_NAME_TO_BE_REMOVED]: qc,
     gem2s,
-    seurat,
+    obj2s,
     worker,
   };
 

src/api.v2/helpers/pipeline/__mocks__/getExperimentBackendStatus.js

@@ -13,7 +13,7 @@ const response = {
     status: pipelineConstants.NOT_CREATED,
     stopDate: null,
   },
-  seurat: {
+  obj2s: {
     completedSteps: [],
     startDate: null,
     status: pipelineConstants.NOT_CREATED,

src/api.v2/helpers/pipeline/__mocks__/getPipelineStatus.js

@@ -8,7 +8,7 @@ const responseTemplates = {
     status: pipelineConstants.SUCCEEDED,
     stopDate: null,
   },
-  seurat: {
+  obj2s: {
     completedSteps: [],
     startDate: null,
     status: pipelineConstants.NOT_CREATED,

src/api.v2/helpers/pipeline/getPipelineStatus.js

@@ -34,10 +34,10 @@ const gem2sPipelineSteps = [
   'UploadToAWS',
 ];
 
-const seuratPipelineSteps = [
-  'DownloadSeurat',
-  'ProcessSeurat',
-  'UploadSeuratToAWS',
+const obj2sPipelineSteps = [
+  'DownloadObj2sFile',
+  'ProcessObj2s',
+  'UploadObj2sToAWS',
 ];
 
 // pipelineStepNames are the names of pipeline steps for which we
@@ -87,8 +87,8 @@ const buildCompletedStatus = (processName, date, shouldRerun) => {
     case pipelineConstants.GEM2S_PROCESS_NAME:
       completedSteps = gem2sPipelineSteps;
       break;
-    case pipelineConstants.SEURAT_PROCESS_NAME:
-      completedSteps = seuratPipelineSteps;
+    case pipelineConstants.OBJ2S_PROCESS_NAME:
+      completedSteps = obj2sPipelineSteps;
       break;
     case pipelineConstants.QC_PROCESS_NAME:
       completedSteps = qcPipelineSteps;
@@ -260,7 +260,7 @@ const getCompletedSteps = async (
       .map((rawStepName) => stepNameToBackendStepNames[rawStepName]);
 
     completedSteps = stepsCompletedInPreviousRuns.concat(lastRunExecutedSteps);
-  } if (processName === 'gem2s' || processName === 'seurat') {
+  } if (processName === 'gem2s' || processName === 'obj2s') {
     completedSteps = lastRunExecutedSteps;
   }
 

src/api.v2/helpers/pipeline/hooks/sendNotification.js

@@ -1,7 +1,7 @@
 const { authenticationMiddlewareSocketIO } = require('../../../middlewares/authMiddlewares');
 
 const {
-  SUCCEEDED, FAILED, QC_PROCESS_NAME, SEURAT_PROCESS_NAME,
+  SUCCEEDED, FAILED, QC_PROCESS_NAME, OBJ2S_PROCESS_NAME,
 } = require('../../../constants');
 
 const getPipelineStatus = require('../getPipelineStatus');
@@ -42,7 +42,7 @@ const sendNotification = async (message) => {
   }
 
   if (experiment.notifyByEmail
-    && (([QC_PROCESS_NAME, SEURAT_PROCESS_NAME].includes(processName) && status === SUCCEEDED)
+    && (([QC_PROCESS_NAME, OBJ2S_PROCESS_NAME].includes(processName) && status === SUCCEEDED)
     || status === FAILED)) {
     try {
       const emailParams = buildPipelineStatusEmailBody(message.experimentId, status, user);

src/api.v2/helpers/pipeline/seurat.js → src/api.v2/helpers/pipeline/obj2s.js

@@ -1,7 +1,7 @@
 const _ = require('lodash');
 
 const getPipelineStatus = require('./getPipelineStatus');
-const { createSeuratPipeline } = require('./pipelineConstruct');
+const { createObj2sPipeline } = require('./pipelineConstruct');
 
 const Sample = require('../../model/Sample');
 const Experiment = require('../../model/Experiment');
@@ -15,9 +15,9 @@ const getLogger = require('../../../utils/getLogger');
 
 const { getGem2sParams, formatSamples } = require('./shouldPipelineRerun');
 
-const logger = getLogger('[SeuratService] - ');
+const logger = getLogger('[Obj2sService] - ');
 
-const { SEURAT_PROCESS_NAME } = require('../../constants');
+const { OBJ2S_PROCESS_NAME } = require('../../constants');
 
 const hookRunner = new HookRunner();
 
@@ -29,7 +29,7 @@ const updateProcessingConfig = async (payload) => {
 
   await new Experiment().updateById(experimentId, { processing_config: item.processingConfig });
 
-  logger.log(`Experiment: ${experimentId}. Saved processing config received from seurat`);
+  logger.log(`Experiment: ${experimentId}. Saved processing config received from obj2s`);
 };
 
 /**
@@ -69,35 +69,35 @@ const setupSubsetSamples = async (payload) => {
 };
 
 hookRunner.register('subsetSeurat', [setupSubsetSamples]);
-hookRunner.register('uploadSeuratToAWS', [
+hookRunner.register('uploadObj2sToAWS', [
   updateProcessingConfig,
 ]);
 
 
 hookRunner.registerAll([sendNotification]);
 
 const sendUpdateToSubscribed = async (experimentId, message, io) => {
-  const statusRes = await getPipelineStatus(experimentId, SEURAT_PROCESS_NAME);
+  const statusRes = await getPipelineStatus(experimentId, OBJ2S_PROCESS_NAME);
 
   // Concatenate into a proper response.
   const response = {
     ...message,
     status: statusRes,
-    type: SEURAT_PROCESS_NAME,
+    type: OBJ2S_PROCESS_NAME,
   };
 
   const { error = null } = message.response || {};
   if (error) {
-    logger.log(`Error in ${SEURAT_PROCESS_NAME} received`);
+    logger.log(`Error in ${OBJ2S_PROCESS_NAME} received`);
   }
 
   logger.log('Sending to all clients subscribed to experiment', experimentId);
 
   io.sockets.emit(`ExperimentUpdates-${experimentId}`, response);
 };
 
-const generateSeuratTaskParams = async (experimentId, rawSamples, authJWT) => {
-  logger.log('Generating seurat params');
+const generateObj2sTaskParams = async (experimentId, rawSamples, authJWT) => {
+  logger.log('Generating obj2s params');
   const experiment = await new Experiment().findById(experimentId).first();
   const {
     sampleTechnology,
@@ -133,42 +133,42 @@ const generateSeuratTaskParams = async (experimentId, rawSamples, authJWT) => {
   };
 };
 
-const startSeuratPipeline = async (params, authJWT) => {
-  logger.log('Creating SEURAT params...');
+const startObj2sPipeline = async (params, authJWT) => {
+  logger.log('Creating OBJ2S params...');
   const { experimentId } = params;
   const samples = await new Sample().getSamples(experimentId);
 
-  const currentSeuratParams = await getGem2sParams(experimentId, samples);
-  const taskParams = await generateSeuratTaskParams(experimentId, samples, authJWT);
+  const currentObj2sParams = await getGem2sParams(experimentId, samples);
+  const taskParams = await generateObj2sTaskParams(experimentId, samples, authJWT);
 
   const {
     stateMachineArn,
     executionArn,
-  } = await createSeuratPipeline(experimentId, taskParams, authJWT);
+  } = await createObj2sPipeline(experimentId, taskParams, authJWT);
 
-  logger.log('SEURAT params created.');
+  logger.log('OBJ2S params created.');
 
   const newExecution = {
-    last_pipeline_params: currentSeuratParams,
+    last_pipeline_params: currentObj2sParams,
     state_machine_arn: stateMachineArn,
     execution_arn: executionArn,
   };
 
   // Save execution params
   await new ExperimentExecution().updateExecution(
     experimentId,
-    SEURAT_PROCESS_NAME,
+    OBJ2S_PROCESS_NAME,
     newExecution,
     params,
   );
-  logger.log('SEURAT params saved.');
+  logger.log('OBJ2S params saved.');
 
   return newExecution;
 };
 
-const handleSeuratResponse = async (io, message) => {
+const handleObj2sResponse = async (io, message) => {
   // Fail hard if there was an error.
-  await validateRequest(message, 'SeuratResponse.v2.yaml');
+  await validateRequest(message, 'OBJ2SResponse.v2.yaml');
 
   await hookRunner.run(message);
 
@@ -183,28 +183,28 @@ const handleSeuratResponse = async (io, message) => {
   await sendUpdateToSubscribed(experimentId, messageForClient, io);
 };
 
-const runSeurat = async (params, authorization) => {
+const runObj2s = async (params, authorization) => {
   const { experimentId } = params;
 
-  logger.log(`Starting seurat for experiment ${experimentId}`);
+  logger.log(`Starting obj2s for experiment ${experimentId}`);
 
   const { parentExperimentId = null } = await new ExperimentParent()
     .find({ experiment_id: experimentId })
     .first();
 
   if (parentExperimentId) {
-    throw new MethodNotAllowedError(`Experiment ${experimentId} can't run seurat`);
+    throw new MethodNotAllowedError(`Experiment ${experimentId} can't run obj2s`);
   }
 
-  const newExecution = await startSeuratPipeline(params, authorization);
+  const newExecution = await startObj2sPipeline(params, authorization);
 
-  logger.log(`Started seurat for experiment ${experimentId} successfully, `);
+  logger.log(`Started obj2s for experiment ${experimentId} successfully, `);
   logger.log('New executions data:');
   logger.log(JSON.stringify(newExecution));
 };
 
 module.exports = {
-  runSeurat,
-  startSeuratPipeline,
-  handleSeuratResponse,
+  runObj2s,
+  startObj2sPipeline,
+  handleObj2sResponse,
 };

src/api.v2/helpers/pipeline/pipelineConstruct/constructors/createNewStep.js

@@ -1,5 +1,5 @@
 const {
-  QC_PROCESS_NAME, GEM2S_PROCESS_NAME, SUBSET_PROCESS_NAME, SEURAT_PROCESS_NAME, COPY_PROCESS_NAME,
+  QC_PROCESS_NAME, GEM2S_PROCESS_NAME, SUBSET_PROCESS_NAME, OBJ2S_PROCESS_NAME, COPY_PROCESS_NAME,
 } = require('../../../../constants');
 const getGeneralParams = require('./paramsGetters/getGeneralParams');
 const getQCParams = require('./paramsGetters/getQCParams');
@@ -9,7 +9,7 @@ const buildParams = (context, stepArgs) => {
 
   if (context.processName === QC_PROCESS_NAME) {
     stepParams = getQCParams(context, stepArgs);
-  } else if ([GEM2S_PROCESS_NAME, SEURAT_PROCESS_NAME].includes(context.processName)) {
+  } else if ([GEM2S_PROCESS_NAME, OBJ2S_PROCESS_NAME].includes(context.processName)) {
     stepParams = context.taskParams;
   } else if ([SUBSET_PROCESS_NAME, COPY_PROCESS_NAME].includes(context.processName)) {
     stepParams = context.taskParams[stepArgs.taskName];