add submission context and review page

api/src/openapi/root-api-doc.ts

@@ -168,6 +168,28 @@ export const rootAPIDoc = {
           }
         },
         additionalProperties: false
+      },
+      feature: {
+        type: 'object',
+        required: ['submission_feature_id', 'submission_id', 'feature_type', 'data', 'parent_submission_feature_id'],
+        properties: {
+          submission_feature_id: {
+            type: 'number'
+          },
+          submission_id: {
+            type: 'number'
+          },
+          feature_type: {
+            type: 'string'
+          },
+          data: {
+            type: 'object'
+          },
+          parent_submission_feature_id: {
+            type: 'number',
+            nullable: true
+          }
+        }
       }
     }
   }

api/src/paths/dataset/intake.ts → api/src/paths/submission/intake.ts

@@ -10,7 +10,11 @@ import { ValidationService } from '../../services/validation-service';
 import { getKeycloakSource } from '../../utils/keycloak-utils';
 import { getLogger } from '../../utils/logger';
 
-const defaultLog = getLogger('paths/dataset/intake');
+const defaultLog = getLogger('paths/submission/intake');
+
+/*
+TODO: UPDATED PATH TO SUBMISSION/INTAKE NEED TO UPDATE SIMS TO USE THIS PATH
+*/
 
 export const POST: Operation = [
   authorizeRequestHandler(() => {
@@ -23,12 +27,12 @@ export const POST: Operation = [
       ]
     };
   }),
-  datasetIntake()
+  submissionIntake()
 ];
 
 POST.apiDoc = {
-  description: 'Submit dataset to BioHub',
-  tags: ['dataset'],
+  description: 'Submit submission to BioHub',
+  tags: ['submission'],
   security: [
     {
       Bearer: []
@@ -48,7 +52,7 @@ POST.apiDoc = {
             },
             type: {
               type: 'string',
-              enum: ['dataset']
+              enum: ['submission']
             },
             properties: {
               title: 'Dataset properties',
@@ -89,7 +93,7 @@ POST.apiDoc = {
   }
 };
 
-export function datasetIntake(): RequestHandler {
+export function submissionIntake(): RequestHandler {
   return async (req, res) => {
     const sourceSystem = getKeycloakSource(req['keycloak_token']);
 
@@ -99,7 +103,7 @@ export function datasetIntake(): RequestHandler {
       ]);
     }
 
-    const dataset = {
+    const submission = {
       ...req.body,
       properties: { ...req.body.properties, additionalInformation: req.body.properties.additionalInformation }
     };
@@ -113,21 +117,21 @@ export function datasetIntake(): RequestHandler {
       const submissionService = new SubmissionService(connection);
       const validationService = new ValidationService(connection);
 
-      // validate the dataset submission
-      if (!(await validationService.validateDatasetSubmission(dataset))) {
-        throw new HTTP400('Invalid dataset submission');
+      // validate the submission submission
+      if (!(await validationService.validateDatasetSubmission(submission))) {
+        throw new HTTP400('Invalid submission submission');
       }
 
       // insert the submission record
       const response = await submissionService.insertSubmissionRecordWithPotentialConflict(id);
 
       // insert each submission feature record
-      await submissionService.insertSubmissionFeatureRecords(response.submission_id, dataset.features);
+      await submissionService.insertSubmissionFeatureRecords(response.submission_id, submission.features);
 
       await connection.commit();
       res.status(200).json(response);
     } catch (error) {
-      defaultLog.error({ label: 'datasetIntake', message: 'error', error });
+      defaultLog.error({ label: 'submissionIntake', message: 'error', error });
       await connection.rollback();
       throw error;
     } finally {

api/src/paths/submission/{submissionUUID}/index.ts

@@ -0,0 +1,126 @@
+import { RequestHandler } from 'express';
+import { Operation } from 'express-openapi';
+import { getAPIUserDBConnection, getDBConnection } from '../../../database/db';
+import { defaultErrorResponses } from '../../../openapi/schemas/http-responses';
+import { SubmissionService } from '../../../services/submission-service';
+import { getLogger } from '../../../utils/logger';
+
+const defaultLog = getLogger('paths/submission/{submissionUUID}}');
+
+export const GET: Operation = [getSubmissionInformation()];
+
+GET.apiDoc = {
+  description: 'retrieves submission data from the submission table',
+  tags: ['eml'],
+  security: [
+    {
+      OptionalBearer: []
+    }
+  ],
+  parameters: [
+    {
+      description: 'submission uuid',
+      in: 'path',
+      name: 'submissionUUID',
+      schema: {
+        type: 'string',
+        format: 'uuid'
+      },
+      required: true
+    }
+  ],
+  responses: {
+    200: {
+      description: 'Dataset metadata response object.',
+      content: {
+        'application/json': {
+          schema: {
+            type: 'object',
+            required: ['submission', 'features'],
+            properties: {
+              submission: {
+                type: 'object',
+                required: ['submission_id', 'uuid', 'security_review_timestamp'],
+                properties: {
+                  submission_id: {
+                    type: 'number'
+                  },
+                  uuid: {
+                    type: 'string',
+                    format: 'uuid'
+                  },
+                  security_review_timestamp: {
+                    type: 'string',
+                    format: 'date-time',
+                    nullable: true
+                  }
+                }
+              },
+              features: {
+                required: ['dataset', 'sampleSites', 'animals', 'observations'],
+                properties: {
+                  dataset: {
+                    type: 'array',
+                    items: {
+                      $ref: '#/components/schemas/feature'
+                    }
+                  },
+                  sampleSites: {
+                    type: 'array',
+                    items: {
+                      $ref: '#/components/schemas/feature'
+                    }
+                  },
+                  animals: {
+                    type: 'array',
+                    items: {
+                      $ref: '#/components/schemas/feature'
+                    }
+                  },
+                  observations: {
+                    type: 'array',
+                    items: {
+                      $ref: '#/components/schemas/feature'
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    ...defaultErrorResponses
+  }
+};
+
+/**
+ * Retrieves submission data from the submission table.
+ *
+ * @returns {RequestHandler}
+ */
+export function getSubmissionInformation(): RequestHandler {
+  return async (req, res) => {
+    const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection();
+
+    const submissionUUID = String(req.params.submissionUUID);
+
+    try {
+      await connection.open();
+
+      const submissionService = new SubmissionService(connection);
+
+      const result = await submissionService.getSubmissionAndFeaturesBySubmissionUUID(submissionUUID);
+
+      await connection.commit();
+
+      res.status(200).json(result);
+    } catch (error) {
+      defaultLog.error({ label: 'getSubmissionInformation', message: 'error', error });
+      await connection.rollback();
+      throw error;
+    } finally {
+      connection.release();
+    }
+  };
+}