SIMSBIOHUB-379: Parse intake key-value pairs

api/package.json

@@ -78,10 +78,10 @@
     "@types/mocha": "~9.0.0",
     "@types/multer": "~1.4.7",
     "@types/node": "~14.14.31",
+    "@types/object-inspect": "~1.8.1",
     "@types/pg": "~8.6.1",
     "@types/sinon": "~10.0.4",
     "@types/sinon-chai": "~3.2.5",
-    "@types/object-inspect": "~1.8.1",
     "@types/swagger-ui-express": "~4.1.3",
     "@types/uuid": "~8.3.1",
     "@types/yamljs": "~0.2.31",

api/src/paths/submission/intake.ts

@@ -4,7 +4,9 @@ import { SOURCE_SYSTEM } from '../../constants/database';
 import { getServiceAccountDBConnection } from '../../database/db';
 import { HTTP400 } from '../../errors/http-error';
 import { defaultErrorResponses } from '../../openapi/schemas/http-responses';
+import { ISubmissionFeature } from '../../repositories/submission-repository';
 import { authorizeRequestHandler } from '../../request-handlers/security/authorization';
+import { SearchIndexService } from '../../services/search-index-service';
 import { SubmissionService } from '../../services/submission-service';
 import { ValidationService } from '../../services/validation-service';
 import { getKeycloakSource } from '../../utils/keycloak-utils';
@@ -40,26 +42,28 @@ POST.apiDoc = {
         schema: {
           title: 'BioHub Data Submission',
           type: 'object',
-          required: ['id', 'type', 'properties', 'features'],
+          required: ['id', 'name', 'description', 'features'],
           properties: {
             id: {
               title: 'Unique id of the submission',
               type: 'string'
             },
-            type: {
+            name: {
+              title: 'The name of the submission. Should not include sensitive information.',
               type: 'string',
-              enum: ['submission']
+              maxLength: 200
             },
-            properties: {
-              title: 'Dataset properties',
-              type: 'object',
-              properties: {}
+            description: {
+              title: 'A description of the submission. Should not include sensitive information.',
+              type: 'string',
+              maxLength: 3000
             },
             features: {
               type: 'array',
               items: {
                 $ref: '#/components/schemas/SubmissionFeature'
               },
+              maxItems: 1,
               additionalProperties: false
             }
           },
@@ -100,10 +104,12 @@ export function submissionIntake(): RequestHandler {
     }
 
     const submission = {
-      ...req.body,
-      properties: { ...req.body.properties, additionalInformation: req.body.properties.additionalInformation }
+      id: req.body.id,
+      name: req.body.name,
+      description: req.body.description
     };
-    const id = req.body.id;
+
+    const submissionFeatures: ISubmissionFeature[] = req.body.features;
 
     const connection = getServiceAccountDBConnection(sourceSystem);
 
@@ -112,19 +118,28 @@ export function submissionIntake(): RequestHandler {
 
       const submissionService = new SubmissionService(connection);
       const validationService = new ValidationService(connection);
+      const searchIndexService = new SearchIndexService(connection);
 
-      // validate the submission submission
-      if (!(await validationService.validateDatasetSubmission(submission))) {
-        throw new HTTP400('Invalid submission submission');
+      // validate the submission
+      if (!(await validationService.validateSubmissionFeatures(submissionFeatures))) {
+        throw new HTTP400('Invalid submission');
       }
 
       // insert the submission record
-      const response = await submissionService.insertSubmissionRecordWithPotentialConflict(id);
+      const response = await submissionService.insertSubmissionRecordWithPotentialConflict(
+        submission.id,
+        submission.name,
+        submission.description
+      );
 
       // insert each submission feature record
-      await submissionService.insertSubmissionFeatureRecords(response.submission_id, submission.features);
+      await submissionService.insertSubmissionFeatureRecords(response.submission_id, submissionFeatures);
+
+      // Index the submission feature record properties
+      await searchIndexService.indexFeaturesBySubmissionId(response.submission_id);
 
       await connection.commit();
+
       res.status(200).json(response);
     } catch (error) {
       defaultLog.error({ label: 'submissionIntake', message: 'error', error });

api/src/paths/submission/search-idx.ts

@@ -0,0 +1,85 @@
+import { RequestHandler } from 'express';
+import { Operation } from 'express-openapi';
+import { SOURCE_SYSTEM } from '../../constants/database';
+import { getAPIUserDBConnection, getDBConnection } from '../../database/db';
+import { defaultErrorResponses } from '../../openapi/schemas/http-responses';
+import { authorizeRequestHandler } from '../../request-handlers/security/authorization';
+import { SearchIndexService } from '../../services/search-index-service';
+import { getLogger } from '../../utils/logger';
+
+const defaultLog = getLogger('paths/dataset/search-index');
+
+export const POST: Operation = [
+  authorizeRequestHandler(() => {
+    return {
+      and: [
+        {
+          validServiceClientIDs: [SOURCE_SYSTEM['SIMS-SVC-4464']],
+          discriminator: 'ServiceClient'
+        }
+      ]
+    };
+  }),
+  indexSubmission()
+];
+
+POST.apiDoc = {
+  description: 'Index dataset in BioHub',
+  tags: ['dataset'],
+  security: [
+    {
+      Bearer: []
+    }
+  ],
+  parameters: [
+    {
+      description: 'Submission ID',
+      in: 'query',
+      name: 'submissionId',
+      schema: {
+        type: 'integer',
+        minimum: 1
+      },
+      required: true
+    }
+  ],
+  responses: {
+    200: {
+      description: 'TODO', // TODO
+      content: {
+        'application/json': {
+          schema: {
+            // TODO
+          }
+        }
+      }
+    },
+    ...defaultErrorResponses
+  }
+};
+
+export function indexSubmission(): RequestHandler {
+  return async (req, res) => {
+    const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection();
+
+    const submissionId = Number(req.query.submissionId);
+
+    try {
+      await connection.open();
+
+      const searchIndexService = new SearchIndexService(connection);
+
+      // Index the submission record
+      const response = await searchIndexService.indexFeaturesBySubmissionId(submissionId);
+
+      await connection.commit();
+      res.status(200).json(response);
+    } catch (error) {
+      defaultLog.error({ label: 'datasetIntake', message: 'error', error });
+      await connection.rollback();
+      throw error;
+    } finally {
+      connection.release();
+    }
+  };
+}