Add Ecological Units to Survey Focal Species (#1343)

* add ecological units to survey focal species * fix broken tests * address code smells * Fix react exhaustive deps warnings * ignore-skip * Updates/fixes/tweaks --------- Co-authored-by: Nick Phura <[email protected]>
bcgov · Sep 6, 2024 · c6e2f46 · c6e2f46
1 parent e1a31b8
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diff --git a/api/src/models/survey-create.ts b/api/src/models/survey-create.ts
@@ -1,6 +1,6 @@
 import { SurveyStratum } from '../repositories/site-selection-strategy-repository';
 import { PostSurveyBlock } from '../repositories/survey-block-repository';
-import { ITaxonomy } from '../services/platform-service';
+import { ITaxonomyWithEcologicalUnits } from '../services/platform-service';
 import { PostSurveyLocationData } from './survey-update';
 
 export class PostSurveyObject {
@@ -89,7 +89,7 @@ export class PostSurveyDetailsData {
 }
 
 export class PostSpeciesData {
-  focal_species: ITaxonomy[];
+  focal_species: ITaxonomyWithEcologicalUnits[];
 
   constructor(obj?: any) {
     this.focal_species = (obj?.focal_species?.length && obj.focal_species) || [];

diff --git a/api/src/models/survey-update.ts b/api/src/models/survey-update.ts
@@ -1,7 +1,7 @@
 import { Feature } from 'geojson';
 import { SurveyStratum, SurveyStratumRecord } from '../repositories/site-selection-strategy-repository';
 import { PostSurveyBlock } from '../repositories/survey-block-repository';
-import { ITaxonomy } from '../services/platform-service';
+import { ITaxonomyWithEcologicalUnits } from '../services/platform-service';
 
 export class PutSurveyObject {
   survey_details: PutSurveyDetailsData;
@@ -99,7 +99,7 @@ export class PutSurveyDetailsData {
 }
 
 export class PutSurveySpeciesData {
-  focal_species: ITaxonomy[];
+  focal_species: ITaxonomyWithEcologicalUnits[];
 
   constructor(obj?: any) {
     this.focal_species = (obj?.focal_species?.length && obj?.focal_species) || [];

diff --git a/api/src/models/survey-view.ts b/api/src/models/survey-view.ts
@@ -7,7 +7,7 @@ import { SurveyBlockRecord } from '../repositories/survey-block-repository';
 import { SurveyLocationRecord } from '../repositories/survey-location-repository';
 import { SurveyUser } from '../repositories/survey-participation-repository';
 import { SystemUser } from '../repositories/user-repository';
-import { ITaxonomy } from '../services/platform-service';
+import { ITaxonomyWithEcologicalUnits } from '../services/platform-service';
 
 export interface ISurveyAdvancedFilters {
   keyword?: string;
@@ -101,7 +101,7 @@ export class GetSurveyFundingSourceData {
 }
 
 export class GetFocalSpeciesData {
-  focal_species: ITaxonomy[];
+  focal_species: ITaxonomyWithEcologicalUnits[];
 
   constructor(obj?: any[]) {
     this.focal_species = [];

diff --git a/api/src/openapi/schemas/critter.ts b/api/src/openapi/schemas/critter.ts
@@ -1,5 +1,34 @@
 import { OpenAPIV3 } from 'openapi-types';
 
+export const collectionUnitsSchema: OpenAPIV3.SchemaObject = {
+  type: 'array',
+  items: {
+    type: 'object',
+    additionalProperties: false,
+    required: ['collection_category_id', 'collection_unit_id'],
+    properties: {
+      critter_collection_unit_id: {
+        type: 'string',
+        format: 'uuid'
+      },
+      collection_category_id: {
+        type: 'string',
+        format: 'uuid'
+      },
+      collection_unit_id: {
+        type: 'string',
+        format: 'uuid'
+      },
+      unit_name: {
+        type: 'string'
+      },
+      category_name: {
+        type: 'string'
+      }
+    }
+  }
+};
+
 export const critterSchema: OpenAPIV3.SchemaObject = {
   type: 'object',
   additionalProperties: false,
@@ -54,40 +83,7 @@ export const critterSchema: OpenAPIV3.SchemaObject = {
         }
       }
     },
-    collection_units: {
-      type: 'array',
-      items: {
-        type: 'object',
-        additionalProperties: false,
-        required: [
-          'critter_collection_unit_id',
-          'collection_category_id',
-          'collection_unit_id',
-          'unit_name',
-          'category_name'
-        ],
-        properties: {
-          critter_collection_unit_id: {
-            type: 'string',
-            format: 'uuid'
-          },
-          collection_category_id: {
-            type: 'string',
-            format: 'uuid'
-          },
-          collection_unit_id: {
-            type: 'string',
-            format: 'uuid'
-          },
-          unit_name: {
-            type: 'string'
-          },
-          category_name: {
-            type: 'string'
-          }
-        }
-      }
-    }
+    collection_units: collectionUnitsSchema
   }
 };
 

diff --git a/api/src/openapi/schemas/survey.ts b/api/src/openapi/schemas/survey.ts
@@ -55,6 +55,30 @@ export const surveyDetailsSchema: OpenAPIV3.SchemaObject = {
   }
 };
 
+/**
+ * Schema for creating, updating and retrieving ecological units for focal species in a SIMS survey.
+ * Prefixed with critterbase_* to match database field names in SIMS.
+ *
+ */
+export const SurveyEcologicalUnitsSchema: OpenAPIV3.SchemaObject = {
+  type: 'array',
+  items: {
+    type: 'object',
+    additionalProperties: false,
+    required: ['critterbase_collection_category_id', 'critterbase_collection_unit_id'],
+    properties: {
+      critterbase_collection_category_id: {
+        type: 'string',
+        format: 'uuid'
+      },
+      critterbase_collection_unit_id: {
+        type: 'string',
+        format: 'uuid'
+      }
+    }
+  }
+};
+
 export const surveyFundingSourceSchema: OpenAPIV3.SchemaObject = {
   title: 'survey funding source response object',
   type: 'object',
@@ -112,7 +136,7 @@ export const focalSpeciesSchema: OpenAPIV3.SchemaObject = {
   title: 'focal species response object',
   type: 'object',
   additionalProperties: false,
-  required: ['tsn', 'commonNames', 'scientificName'],
+  required: ['tsn', 'commonNames', 'scientificName', 'ecological_units'],
   properties: {
     tsn: {
       description: 'Taxonomy tsn',
@@ -137,7 +161,8 @@ export const focalSpeciesSchema: OpenAPIV3.SchemaObject = {
     kingdom: {
       description: 'Taxonomy kingdom name',
       type: 'string'
-    }
+    },
+    ecological_units: SurveyEcologicalUnitsSchema
   }
 };
 

diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.test.ts
@@ -26,9 +26,9 @@ describe('getSurveyObservedSpecies', () => {
     const mockTsns = [1, 2, 3];
     const mockSpecies = mockTsns.map((tsn) => ({ itis_tsn: tsn }));
     const mockItisResponse = [
-      { tsn: '1', commonNames: ['common name 1'], scientificName: 'scientific name 1' },
-      { tsn: '2', commonNames: ['common name 2'], scientificName: 'scientific name 2' },
-      { tsn: '3', commonNames: ['common name 3'], scientificName: 'scientific name 3' }
+      { tsn: 1, commonNames: ['common name 1'], scientificName: 'scientific name 1' },
+      { tsn: 2, commonNames: ['common name 2'], scientificName: 'scientific name 2' },
+      { tsn: 3, commonNames: ['common name 3'], scientificName: 'scientific name 3' }
     ];
     const mockFormattedItisResponse = mockItisResponse.map((species) => ({ ...species, tsn: Number(species.tsn) }));
 

diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.ts
@@ -126,7 +126,7 @@ export function getSurveyObservedSpecies(): RequestHandler {
 
       const species = await platformService.getTaxonomyByTsns(observedSpecies.flatMap((species) => species.itis_tsn));
 
-      const formattedResponse = species.map((taxon) => ({ ...taxon, tsn: Number(taxon.tsn) }));
+      const formattedResponse = species.map((taxon) => ({ ...taxon, tsn: taxon.tsn }));
 
       return res.status(200).json(formattedResponse);
     } catch (error) {

diff --git a/api/src/repositories/survey-repository.test.ts b/api/src/repositories/survey-repository.test.ts
@@ -9,7 +9,12 @@ import { PostProprietorData, PostSurveyObject } from '../models/survey-create';
 import { PutSurveyObject } from '../models/survey-update';
 import { GetAttachmentsData, GetSurveyProprietorData, GetSurveyPurposeAndMethodologyData } from '../models/survey-view';
 import { getMockDBConnection } from '../__mocks__/db';
-import { SurveyRecord, SurveyRepository, SurveyTypeRecord } from './survey-repository';
+import {
+  SurveyRecord,
+  SurveyRepository,
+  SurveyTaxonomyWithEcologicalUnits,
+  SurveyTypeRecord
+} from './survey-repository';
 
 chai.use(sinonChai);
 
@@ -140,26 +145,46 @@ describe('SurveyRepository', () => {
 
   describe('getSpeciesData', () => {
     it('should return result', async () => {
-      const mockResponse = { rows: [{ id: 1 }], rowCount: 1 } as any as Promise<QueryResult<any>>;
+      const mockRows: SurveyTaxonomyWithEcologicalUnits[] = [
+        {
+          itis_tsn: 123456,
+          ecological_units: [
+            {
+              critterbase_collection_category_id: '123-456-789',
+              critterbase_collection_unit_id: '987-654-321'
+            }
+          ]
+        },
+        {
+          itis_tsn: 654321,
+          ecological_units: []
+        }
+      ];
+      const mockResponse = { rows: mockRows, rowCount: 1 } as any as Promise<QueryResult<any>>;
       const dbConnection = getMockDBConnection({ sql: () => mockResponse });
 
       const repository = new SurveyRepository(dbConnection);
 
-      const response = await repository.getSpeciesData(1);
+      const surveyId = 1;
 
-      expect(response).to.eql([{ id: 1 }]);
+      const response = await repository.getSpeciesData(surveyId);
+
+      expect(response).to.eql(mockRows);
     });
 
     it('should return empty rows', async () => {
-      const mockResponse = { rows: [], rowCount: 1 } as any as Promise<QueryResult<any>>;
+      const mockRows: SurveyTaxonomyWithEcologicalUnits[] = [];
+      const mockResponse = { rows: mockRows, rowCount: 1 } as any as Promise<QueryResult<any>>;
       const dbConnection = getMockDBConnection({ sql: () => mockResponse });
 
       const repository = new SurveyRepository(dbConnection);
 
-      const response = await repository.getSpeciesData(1);
+      const surveyId = 1;
+
+      const response = await repository.getSpeciesData(surveyId);
 
       expect(response).to.not.be.null;
-      expect(response).to.eql([]);
+      expect(response).to.eql(mockRows);
     });
   });