fix: pr comments

bcgov · Dec 4, 2024 · 32b4c89 · 32b4c89
1 parent 7cc6f4a
commit 32b4c89
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Showing 5 changed files with 82 additions and 59 deletions.
diff --git a/api/src/services/import-services/critter/critter-header-configs.ts b/api/src/services/import-services/critter/critter-header-configs.ts
@@ -1,6 +1,11 @@
 import { z } from 'zod';
 import { CSVConfigUtils } from '../../../utils/csv-utils/csv-config-utils';
-import { CSVCellSetter, CSVCellValidator, CSVParams } from '../../../utils/csv-utils/csv-config-validation.interface';
+import {
+  CSVCellSetter,
+  CSVCellValidator,
+  CSVError,
+  CSVParams
+} from '../../../utils/csv-utils/csv-config-validation.interface';
 import { validateZodCell } from '../../../utils/csv-utils/csv-header-configs';
 import { NestedRecord } from '../../../utils/nested-record';
 import { CritterCSVStaticHeader } from './import-critters-service';
@@ -9,9 +14,10 @@ import { CritterCSVStaticHeader } from './import-critters-service';
  * Get the critter alias cell validator.
  *
  * Rules:
- *  1. The cell must be a string with a length between 1 and 50
- *  2. The cell must be unique in the survey
- *  3. The cell must be unique in the CSV
+ *  1. The cell can be a string with a length between 1 and 50
+ *  2. The cell can be a number with a min value of 0
+ *  3. The cell must be unique in the survey
+ *  4. The cell must be unique in the CSV
  *
  * @param {Set<string>} surveyAliases The survey aliases.
  * @param {CSVConfigUtils<CritterCSVStaticHeader>} configUtils The CSV config utils.
@@ -22,7 +28,7 @@ export const getCritterAliasCellValidator = (
   configUtils: CSVConfigUtils<CritterCSVStaticHeader>
 ): CSVCellValidator => {
   return (params: CSVParams) => {
-    const cellErrors = validateZodCell(params, z.string().trim().min(1).max(50));
+    const cellErrors = validateZodCell(params, z.union([z.string().trim().min(1).max(50), z.number().min(0)]));
     const isAliasUnique = configUtils.isCellUnique('ALIAS', params.cell);
 
     if (cellErrors.length) {
@@ -69,18 +75,13 @@ export const getCritterCollectionUnitCellValidator = (
       return [];
     }
 
-    // The row TSN value
-    const rowTsn = Number(configUtils.getCellValue('ITIS_TSN', params.row));
-
-    // The collection unit cell value
-    const collectionUnitCellValue = String(params.cell);
-
-    // The collection category (for clarity)
-    const collectionCategory = params.header;
+    const rowTsn = Number(configUtils.getCellValue('ITIS_TSN', params.row)); // Row TSN
+    const collectionUnitCellValue = String(params.cell); // Cell value
+    const collectionCategory = params.header; // Current header ie: collection category
 
     const rowDictionaryTsn = rowDictionary.get(rowTsn);
 
-    // Check if the row TSN has collection units
+    // Check if the row TSN has associated collection units
     if (!rowDictionaryTsn) {
       return [
         {
@@ -160,8 +161,8 @@ export const getCritterSexCellValidator = (
   configUtils: CSVConfigUtils<CritterCSVStaticHeader>
 ): CSVCellValidator => {
   return (params: CSVParams) => {
-    const rowTsn = Number(configUtils.getCellValue('ITIS_TSN', params.row));
-    const sexCellValue = String(params.cell);
+    const rowTsn = Number(configUtils.getCellValue('ITIS_TSN', params.row)); // Row TSN
+    const sexCellValue = String(params.cell); // Cell value
 
     const rowDictionaryTsn = rowDictionary.get(rowTsn);
 
@@ -210,3 +211,41 @@ export const getCritterSexCellSetter = (
     return rowDictionary.get(rowTsn, sexCellValue);
   };
 };
+
+/**
+ * Get the Wildlife Health ID header cell validator.
+ *
+ * Rules:
+ *  1. The Wildlife Health ID must be in the format 'XX-XXXX' or undefined
+ *  2. The Wildlife Health ID must be unique in the CSV
+ *
+ * @param {CSVConfigUtils<CritterCSVStaticHeader>} configUtils The CSV config utils.
+ * @returns {*} {CSVCellValidator} The validate cell callback
+ */
+export const getWlhIDCellValidator = (configUtils: CSVConfigUtils<CritterCSVStaticHeader>): CSVCellValidator => {
+  return (params: CSVParams) => {
+    const cellErrors: CSVError[] = [];
+
+    if (params.cell === undefined) {
+      return [];
+    }
+
+    const isWlhIdUnique = configUtils.isCellUnique('ALIAS', params.cell);
+
+    if (!/^\d{2}-.+/.exec(String(params.cell))) {
+      cellErrors.push({
+        error: `Invalid Wildlife Health ID format`,
+        solution: `Update the Wildlife Health ID to match the expected format 'XX-XXXX'`
+      });
+    }
+
+    if (!isWlhIdUnique) {
+      cellErrors.push({
+        error: `Wildlife Health ID already exists in the CSV`,
+        solution: `Update the Wildlife Health ID to be unique`
+      });
+    }
+
+    return cellErrors;
+  };
+};
diff --git a/api/src/services/import-services/critter/import-critters-service.ts b/api/src/services/import-services/critter/import-critters-service.ts
@@ -11,11 +11,7 @@ import {
   CSVHeaderConfig,
   CSVRowValidated
 } from '../../../utils/csv-utils/csv-config-validation.interface';
-import {
-  getDescriptionCellValidator,
-  getTsnCellValidator,
-  getWlhIDCellValidator
-} from '../../../utils/csv-utils/csv-header-configs';
+import { getDescriptionCellValidator, getTsnCellValidator } from '../../../utils/csv-utils/csv-header-configs';
 import { getLogger } from '../../../utils/logger';
 import { NestedRecord } from '../../../utils/nested-record';
 import { CritterbaseService, IBulkCreate } from '../../critterbase-service';
@@ -27,7 +23,8 @@ import {
   getCritterCollectionUnitCellSetter,
   getCritterCollectionUnitCellValidator,
   getCritterSexCellSetter,
-  getCritterSexCellValidator
+  getCritterSexCellValidator,
+  getWlhIDCellValidator
 } from './critter-header-configs';
 
 const defaultLog = getLogger('services/import/import-critters-service');
@@ -69,8 +66,8 @@ export class ImportCrittersService extends DBService {
         ITIS_TSN: { aliases: ['TAXON', 'SPECIES', 'TSN'] },
         ALIAS: { aliases: ['NICKNAME', 'NAME', 'ANIMAL_ID'] },
         SEX: { aliases: ['TEST'] },
-        WLH_ID: { aliases: ['WILDLIFE_HEALTH_ID'], validateCell: getWlhIDCellValidator() },
-        DESCRIPTION: { aliases: ['COMMENTS', 'COMMENT', 'NOTES'], validateCell: getDescriptionCellValidator() }
+        WLH_ID: { aliases: ['WILDLIFE_HEALTH_ID', 'WILD LIFE HEALTH ID', 'WLHID'] },
+        DESCRIPTION: { aliases: ['COMMENTS', 'COMMENT', 'NOTES'] }
       },
       ignoreDynamicHeaders: false
     };
@@ -96,7 +93,7 @@ export class ImportCrittersService extends DBService {
    * @returns {*} {Promise<CSVError[]>} List of inserted survey critter ids
    */
   async importCSVWorksheet(): Promise<CSVError[]> {
-    const config = await this._getCSVConfig();
+    const config = await this.getCSVConfig();
 
     const { errors, rows } = validateCSVWorksheet(this.worksheet, config);
 
@@ -132,7 +129,7 @@ export class ImportCrittersService extends DBService {
    *
    * @returns {*} {Promise<CSVConfig<CritterCSVStaticHeader>>} The Critter CSV config
    */
-  async _getCSVConfig(): Promise<CSVConfig<CritterCSVStaticHeader>> {
+  async getCSVConfig(): Promise<CSVConfig<CritterCSVStaticHeader>> {
     const [tsnHeaderConfig, aliasHeaderConfig, sexHeaderConfig, dynamicHeadersConfig] = await Promise.all([
       this._getTsnHeaderConfig(),
       this._getAliasHeaderConfig(),
@@ -144,10 +141,12 @@ export class ImportCrittersService extends DBService {
       staticHeadersConfig: {
         ITIS_TSN: tsnHeaderConfig,
         ALIAS: aliasHeaderConfig,
-        SEX: sexHeaderConfig
+        SEX: sexHeaderConfig,
+        WLH_ID: getWlhIDCellValidator(this.configUtils),
+        DESCRIPTION: getDescriptionCellValidator()
       },
       dynamicHeadersConfig: dynamicHeadersConfig,
-      ignoreDynamicHeaders: dynamicHeadersConfig ? false : true
+      ignoreDynamicHeaders: !dynamicHeadersConfig
     });
   }
 
@@ -212,7 +211,8 @@ export class ImportCrittersService extends DBService {
     const allowedTsns = new Set(taxonomy.map((taxon) => taxon.tsn));
 
     return {
-      validateCell: getTsnCellValidator(allowedTsns)
+      validateCell: getTsnCellValidator(allowedTsns),
+      setCellValue: (params) => Number(params.cell)
     };
   }
 
@@ -230,7 +230,8 @@ export class ImportCrittersService extends DBService {
     const surveyAliases = await this.surveyCritterService.getUniqueSurveyCritterAliases(this.surveyId);
 
     return {
-      validateCell: getCritterAliasCellValidator(surveyAliases, this.configUtils)
+      validateCell: getCritterAliasCellValidator(surveyAliases, this.configUtils),
+      setCellValue: (params) => String(params.cell)
     };
   }
 
@@ -249,14 +250,14 @@ export class ImportCrittersService extends DBService {
     const rowTsns = this.configUtils.getUniqueCellValues('ITIS_TSN');
     const measurements = await Promise.all(rowTsns.map((tsn) => this.critterbaseService.getTaxonMeasurements(tsn)));
 
-    measurements.forEach((measurement) => {
+    measurements.forEach((measurement, index) => {
       const sexMeasurement = measurement.qualitative.find(
         (measurement) => measurement.measurement_name.toLowerCase() === 'sex'
       );
 
       if (sexMeasurement) {
         sexMeasurement.options.forEach((option) => {
-          const tsn = Number(sexMeasurement.itis_tsn);
+          const tsn = Number(rowTsns[index]);
           const sexLabel = option.option_label;
 
           rowDictionary.set({ path: [tsn, sexLabel], value: option.qualitative_option_id });

diff --git a/api/src/utils/csv-utils/csv-config-validation.interface.ts b/api/src/utils/csv-utils/csv-config-validation.interface.ts
@@ -106,7 +106,7 @@ export interface CSVParams {
    *
    * @type {string | undefined}
    */
-  staticHeader?: string | undefined;
+  staticHeader?: string;
 }
 
 /**
@@ -140,19 +140,19 @@ export interface CSVError {
    *
    * @type {(string[] | number[]) | undefined}
    */
-  values?: string[] | number[] | undefined;
+  values?: string[] | number[];
   /**
    * The cell value.
    *
    * @type {unknown | undefined}
    */
-  cell?: unknown | undefined;
+  cell?: unknown;
   /**
    * The header name.
    *
    * @type {string | undefined}
    */
-  header?: string | undefined;
+  header?: string;
   /**
    * The row index the error occurred.
    *

diff --git a/api/src/utils/csv-utils/csv-header-configs.ts b/api/src/utils/csv-utils/csv-header-configs.ts
@@ -64,26 +64,3 @@ export const getDescriptionCellValidator = (): CSVCellValidator => {
     return validateZodCell(params, z.string().trim().min(1).max(250).optional());
   };
 };
-
-/**
- * Get the Wildlife Health ID header cell validator.
- *
- * Rules:
- *  1. The Wildlife Health ID must be in the format 'XX-XXXX' or undefined
- *
- * @returns {*} {CSVCellValidator} The validate cell callback
- */
-export const getWlhIDCellValidator = (): CSVCellValidator => {
-  return (params: CSVParams) => {
-    if (params.cell === undefined || String(params.cell).match(/^\d{2}-.+/)) {
-      return [];
-    }
-
-    return [
-      {
-        error: `Invalid Wildlife Health ID format`,
-        solution: `Update the Wildlife Health ID to match the expected format 'XX-XXXX'`
-      }
-    ];
-  };
-};
diff --git a/api/src/utils/nested-record.ts b/api/src/utils/nested-record.ts
@@ -13,6 +13,12 @@ interface INestedRecord<TValue> {
 /**
  * NestedRecord - A class to handle nested records with case-insensitive keys
  *
+ * @example
+ *  const record = new NestedRecord({ a: { b: 'c' } });
+ *  record.get('A', 'B'); // 'c'
+ *  record.has('A', 'B'); // true
+ *  record.set({ path: ['A', 'B'], value: 'd' });
+ *
  * @class
  * @exports
  * @template TValue - The final value type