Use updated endpoint for blast form submission (#739)

src/content/app/tools/blast/components/blast-job-submit/BlastJobSubmit.test.tsx

@@ -80,7 +80,10 @@ const mockState = merge({}, initialState, {
 
 const expectedPayload = {
   species: selectedSpecies,
-  querySequences: sequences.map((seq) => toFasta(seq)),
+  sequences: sequences.map((seq, index) => ({
+    id: index + 1,
+    value: toFasta(seq)
+  })),
   parameters: {
     title: jobName,
     database,

src/content/app/tools/blast/components/blast-job-submit/BlastJobSubmit.tsx

@@ -42,7 +42,7 @@ import type { BlastSubmission } from 'src/content/app/tools/blast/state/blast-re
 
 export type PayloadParams = {
   species: Species[];
-  querySequences: string[];
+  sequences: { id: number; value: string }[];
   parameters: Partial<Record<BlastParameterName, string>> & {
     title: string;
     stype: SequenceType;
@@ -100,13 +100,16 @@ const BlastJobSubmit = () => {
 export const createBlastSubmissionData = (
   blastFormData: BlastFormState
 ): PayloadParams => {
-  const sequences = blastFormData.sequences.map((sequence) =>
-    toFasta(sequence)
-  );
+  // labelling sequences with complely artificial identifiers
+  // so that job ids in the response can be matched to individual combinations of sequences and genome ids
+  const sequences = blastFormData.sequences.map((sequence, index) => ({
+    id: index + 1,
+    value: toFasta(sequence)
+  }));
 
   return {
     species: blastFormData.selectedSpecies,
-    querySequences: sequences,
+    sequences,
     parameters: {
       title: blastFormData.settings.jobName,
       database: blastFormData.settings.parameters.database,

src/content/app/tools/blast/state/blast-api/blastApiSlice.ts

@@ -24,16 +24,25 @@ import type { BlastSubmission } from '../blast-results/blastResultsSlice';
 
 export type BlastSubmissionPayload = {
   species: Species[];
-  querySequences: string[];
+  sequences: { id: number; value: string }[];
   parameters: Record<string, string>;
 };
 
 export type BlastSubmissionResponse = {
-  submissionId: string;
-  jobs: Array<{
-    jobId?: string;
-    error?: string;
-  }>;
+  submission_id: string;
+  jobs: Array<SubmittedJob | RejectedJob>;
+};
+
+export type SubmittedJob = {
+  job_id: string;
+  sequence_id: number;
+  genome_id: string;
+};
+
+export type RejectedJob = {
+  sequence_id: number;
+  genome_id: string;
+  error: string;
 };
 
 const blastApiSlice = restApiSlice.injectEndpoints({
@@ -50,8 +59,8 @@ const blastApiSlice = restApiSlice.injectEndpoints({
     >({
       query(payload) {
         const body = {
-          genomeIds: payload.species.map(({ genome_id }) => genome_id),
-          querySequences: payload.querySequences,
+          genome_ids: payload.species.map(({ genome_id }) => genome_id),
+          query_sequences: payload.sequences,
           parameters: payload.parameters
         };
         return {
@@ -61,20 +70,25 @@ const blastApiSlice = restApiSlice.injectEndpoints({
         };
       },
       transformResponse(response: BlastSubmissionResponse, _, payload) {
-        const { submissionId, jobs } = response;
+        const { submission_id: submissionId, jobs } = response;
         // TODO: decide what to do when a submission returns error jobs
-        const results = jobs.map((job) => ({
-          jobId: job.jobId as string,
-          status: 'RUNNING',
-          seen: false,
-          data: null
-        }));
+        const results = jobs
+          .filter((job): job is SubmittedJob => 'job_id' in job)
+          .map((job) => ({
+            jobId: job.job_id,
+            genomeId: job.genome_id,
+            sequenceId: job.sequence_id,
+            status: 'RUNNING',
+            seen: false,
+            data: null
+          }));
+
         return {
           submissionId,
           submission: {
             submittedData: {
               species: payload.species,
-              sequences: payload.querySequences,
+              sequences: payload.sequences,
               parameters: payload.parameters
             },
             results,

src/content/app/tools/blast/state/blast-results/blastResultsSlice.ts

@@ -37,11 +37,13 @@ export type JobStatus =
 export type BlastSubmission = {
   submittedData: {
     species: Species[];
-    sequences: string[]; // Or perhaps parsed sequences?
+    sequences: { id: number; value: string }[]; // TODO: consider whether to have strings or parsed sequences
     parameters: Partial<Record<BlastParameterName, string>>;
   };
   results: Array<{
     jobId: string;
+    sequenceId: number;
+    genomeId: string;
     status: JobStatus;
     seen: boolean;
     data: null; // TODO: add data type

src/content/app/tools/blast/state/epics/tests/blastEpics.test.ts

@@ -142,7 +142,7 @@ describe('blast epics', () => {
           'http://tools-api-url/blast/jobs/status/:jobId',
           (req, res, ctx) => {
             const { jobId } = req.params;
-            if (jobId === firstJobInResponse.jobId) {
+            if (jobId === firstJobInResponse.job_id) {
               firstJobPollCount++;
               return firstJobPollCount >= firstJobMaxPollCount
                 ? res(ctx.json(createFinishedJobStatusResponse()))
@@ -176,14 +176,14 @@ describe('blast epics', () => {
 
       // check that the job status gets updated in indexedDB
       expect(blastStorageService.updateSavedBlastJob).toHaveBeenCalledWith({
-        submissionId: successfulSubmission.submissionId,
-        jobId: firstJobInResponse.jobId,
+        submissionId: successfulSubmission.submission_id,
+        jobId: firstJobInResponse.job_id,
         fragment: { status: 'FINISHED' }
       });
 
       expect(blastStorageService.updateSavedBlastJob).toHaveBeenCalledWith({
-        submissionId: successfulSubmission.submissionId,
-        jobId: secondJobInResponse.jobId,
+        submissionId: successfulSubmission.submission_id,
+        jobId: secondJobInResponse.job_id,
         fragment: { status: 'FAILURE' }
       });
     });
@@ -199,7 +199,7 @@ describe('blast epics', () => {
             const jobId = req.params.jobId as string;
             if (!jobMap[jobId]) {
               jobMap[jobId] = true;
-              if (jobId === firstJobInResponse.jobId) {
+              if (jobId === firstJobInResponse.job_id) {
                 return res(ctx.status(404));
               } else {
                 return res.networkError('Failed to connect');
@@ -236,7 +236,7 @@ describe('blast epics', () => {
     jest
       .spyOn(blastStorageService, 'getAllBlastSubmissions')
       .mockImplementation(async () => ({
-        [successfulSubmission.submissionId]: storedBlastSubmission
+        [successfulSubmission.submission_id]: storedBlastSubmission
       }));
 
     it('polls status of unfinished jobs', async () => {
@@ -273,7 +273,7 @@ describe('blast epics', () => {
 
       // check that the job status gets updated in indexedDB
       expect(blastStorageService.updateSavedBlastJob).toHaveBeenCalledWith({
-        submissionId: successfulSubmission.submissionId,
+        submissionId: successfulSubmission.submission_id,
         jobId: unfinishedJob.jobId,
         fragment: { status: 'FINISHED' }
       });

src/content/app/tools/blast/state/epics/tests/fixtures/blastSubmissionFixtures.ts

@@ -19,7 +19,8 @@ import times from 'lodash/times';
 
 import type {
   BlastSubmissionPayload,
-  BlastSubmissionResponse
+  BlastSubmissionResponse,
+  SubmittedJob
 } from 'src/content/app/tools/blast/state/blast-api/blastApiSlice';
 import type {
   BlastSubmission,
@@ -38,7 +39,7 @@ export const createBlastSubmission = (
 
   const submission = {
     species: [human],
-    querySequences: ['ACGT'],
+    sequences: [{ id: 1, value: 'ACGT' }],
     parameters: {}
   };
 
@@ -52,7 +53,7 @@ export const createBlastSubmissionResponse = (
   fragment: Partial<BlastSubmissionResponse> = {}
 ): BlastSubmissionResponse => {
   const submission = {
-    submissionId: faker.datatype.uuid(),
+    submission_id: faker.datatype.uuid(),
     jobs: times(3, createSuccessfulBlastJobInSubmissionResponse)
   };
 
@@ -62,11 +63,14 @@ export const createBlastSubmissionResponse = (
   };
 };
 
-export const createSuccessfulBlastJobInSubmissionResponse = () => {
-  return {
-    jobId: faker.datatype.uuid()
+export const createSuccessfulBlastJobInSubmissionResponse =
+  (): SubmittedJob => {
+    return {
+      genome_id: 'human-genome-id',
+      sequence_id: 1,
+      job_id: faker.datatype.uuid()
+    };
   };
-};
 
 export const createRunningJobStatusResponse = (): { status: JobStatus } => ({
   status: 'RUNNING'
@@ -93,7 +97,7 @@ export const createStoredBlastSubmission = (
   const submission = {
     submittedData: {
       species: [human],
-      sequences: ['ACGT'],
+      sequences: [{ id: 1, value: 'ACGT' }],
       parameters: {}
     },
     results: [createStoredBlastJobResult()],
@@ -111,6 +115,8 @@ export const createStoredBlastJobResult = (
 ) => {
   return {
     jobId: faker.datatype.uuid(),
+    sequenceId: 1,
+    genomeId: 'human-genome-id',
     status: 'RUNNING' as JobStatus,
     seen: false,
     data: null,