clean up request flow

bcgov · Feb 1, 2024 · 5c40dd8 · 5c40dd8
1 parent 79293e4
commit 5c40dd8
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Showing 5 changed files with 25 additions and 44 deletions.
diff --git a/api/src/paths/taxonomy/taxon/index.ts b/api/src/paths/taxonomy/taxon/index.ts
@@ -44,7 +44,7 @@ GET.apiDoc = {
                   required: ['tsn', 'label'],
                   properties: {
                     tsn: {
-                      type: 'string'
+                      type: 'number'
                     },
                     label: {
                       type: 'string'
@@ -85,13 +85,11 @@ export function findTaxonBySearchTerms(): RequestHandler {
     defaultLog.debug({ label: 'findTaxonBySearchTerms', message: 'query params', query: req.query });
 
     const searchTerms = req.query.terms as string[];
-    console.log('searchTerms', searchTerms);
 
     try {
       const itisService = new ItisService();
 
       const response = await itisService.searchItisByTerm(searchTerms);
-      console.log('response', response);
 
       // Overwrite default cache-control header, allow caching up to 7 days
       res.setHeader('Cache-Control', 'max-age=604800');

diff --git a/api/src/paths/taxonomy/taxon/tsn/index.ts b/api/src/paths/taxonomy/taxon/tsn/index.ts
@@ -51,7 +51,7 @@ GET.apiDoc = {
                   required: ['tsn', 'label'],
                   properties: {
                     tsn: {
-                      type: 'string'
+                      type: 'number'
                     },
                     label: {
                       type: 'string'
@@ -101,7 +101,7 @@ export function getTaxonByTSN(): RequestHandler {
 
     const connection = getServiceAccountDBConnection(serviceClientSystemUser);
 
-    const tsnIds: number[] = (req.query.tsn as string[]).map(Number);
+    const tsnIds: number[] = (req.query.tsn as (string | number)[]).map(Number);
 
     try {
       await connection.open();

diff --git a/api/src/repositories/taxonomy-repository.ts b/api/src/repositories/taxonomy-repository.ts
@@ -59,7 +59,6 @@ export class TaxonomyRepository extends BaseRepository {
    */
   async addItisTaxonRecord(
     itisTsn: number,
-    bcTaxonCode: string | null = null,
     itisScientificName: string,
     commonName: string,
     itisData: Record<any, any>,
@@ -70,15 +69,13 @@ export class TaxonomyRepository extends BaseRepository {
         taxon
       (
         itis_tsn,
-        bc_taxon_code,
         itis_scientific_name,
         common_name,
         itis_data,
         itis_update_date
       )
       VALUES (
         ${itisTsn},
-        ${bcTaxonCode},
         ${itisScientificName},
         ${commonName},
         ${itisData},

diff --git a/api/src/services/itis-service.ts b/api/src/services/itis-service.ts
@@ -30,7 +30,7 @@ export interface IItisSearchResponse {
 }
 
 export interface IItisSearchResult {
-  tsn: string;
+  tsn: number;
   label: string;
   scientificName: string;
 }
@@ -57,7 +57,6 @@ export class ItisService {
     defaultLog.debug({ label: 'searchItisByTerm', message: 'url', url });
 
     const response = await axios.get(url);
-    console.log('response', response);
 
     if (!response.data || !response.data.response || !response.data.response.docs) {
       return [];
@@ -98,7 +97,7 @@ export class ItisService {
       const commonName = (item.commonNames && item.commonNames[0].split('$')[1]) || item.scientificName;
 
       return {
-        tsn: item.tsn,
+        tsn: Number(item.tsn),
         label: commonName,
         scientificName: item.scientificName
       };

diff --git a/api/src/services/taxonomy-service.ts b/api/src/services/taxonomy-service.ts
@@ -30,7 +30,7 @@ export interface IItisSearchResponse {
 }
 
 export interface IItisSearchResult {
-  tsn: string;
+  tsn: number;
   label: string;
   scientificName: string;
 }
@@ -58,67 +58,54 @@ export class TaxonomyService extends ESService {
    * @memberof TaxonomyService
    */
   async getTaxonByTsnIds(tsnIds: number[]): Promise<IItisSearchResult[]> {
+    // Search for taxon records in the database
     const taxon = await this.taxonRepository.getTaxonByTsnIds(tsnIds);
 
+    // If taxon records are found, return them
     if (taxon.length > 0) {
-      return this._sanitizeItisData(taxon);
+      return this._sanitizeTaxonRecordsData(taxon);
     }
 
+    // If no taxon records are found, search ITIS for the taxon records
     const itisService = new ItisService();
     const itisResponse = await itisService.searchItisByTSN(tsnIds);
 
     const taxonRecords: ItisTaxonRecord[] = [];
     for (const itisRecord of itisResponse) {
-      const taxonRecord = await this.addItisTaxonRecord(itisRecord, itisRecord.tsn);
+      // Add the taxon record to the database
+      const taxonRecord = await this.addItisTaxonRecord(itisRecord);
       taxonRecords.push(taxonRecord);
     }
 
-    return this._sanitizeItisData(taxonRecords);
+    // Return the taxon records
+    return this._sanitizeTaxonRecordsData(taxonRecords);
   }
 
-  _sanitizeItisData(itisData: ItisTaxonRecord[]): IItisSearchResult[] {
-    const sanitizedData: IItisSearchResult[] = [];
-
-    for (const itisRecord of itisData) {
-      const label = itisRecord.common_name || itisRecord.itis_scientific_name;
-      const scientificName = itisRecord.itis_scientific_name;
-      const tsn = itisRecord.itis_tsn.toString();
-
-      sanitizedData.push({ tsn, label, scientificName });
-    }
-
-    return sanitizedData;
+  _sanitizeTaxonRecordsData(itisData: ItisTaxonRecord[]): IItisSearchResult[] {
+    return itisData.map((item: ItisTaxonRecord) => {
+      return {
+        tsn: item.itis_tsn,
+        label: item.common_name || item.itis_scientific_name,
+        scientificName: item.itis_scientific_name
+      } as IItisSearchResult;
+    });
   }
 
   /**
    * Adds a new taxon record.
    *
    * @param {IItisSearchResponse} itisResponse
-   * @param {(string | null)} [bcTaxonCode=null]
    * @return {*}  {Promise<ItisTaxonRecord>}
    * @memberof TaxonomyService
    */
-  async addItisTaxonRecord(itisResponse: IItisSearchResponse, bcTaxonCode: string): Promise<ItisTaxonRecord> {
-    // TODO include optional param for aliases
-
-    let commonName = '';
+  async addItisTaxonRecord(itisResponse: IItisSearchResponse): Promise<ItisTaxonRecord> {
+    let commonName = itisResponse.scientificName;
     if (itisResponse.commonNames) {
-      switch (itisResponse.commonNames.length) {
-        case 0:
-          commonName = itisResponse.scientificName;
-          break;
-        case 1:
-          commonName = itisResponse.commonNames[0];
-          break;
-        default:
-          commonName = itisResponse.commonNames.join(', ');
-          break;
-      }
+      commonName = itisResponse.commonNames && itisResponse.commonNames[0].split('$')[1];
     }
 
     return this.taxonRepository.addItisTaxonRecord(
       Number(itisResponse.tsn),
-      bcTaxonCode,
       itisResponse.scientificName,
       commonName,
       itisResponse,