Add environmental variables & sampling methods to standards page

api/src/models/standards-view.ts

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+import { z } from 'zod';
+import {
+  CBQualitativeMeasurementTypeDefinition,
+  CBQuantitativeMeasurementTypeDefinition
+} from '../services/critterbase-service';
+
+const QualitativeMeasurementSchema = z.object({
+  name: z.string(),
+  description: z.string().nullable(),
+  options: z.array(
+    z.object({
+      name: z.string(),
+      description: z.string().nullable()
+    })
+  )
+});
+
+const QuantitativeMeasurementSchema = z.object({
+  name: z.string(),
+  description: z.string().nullable(),
+  unit: z.string().nullable()
+});
+
+const MethodAttributesSchema = z.object({
+  qualitative: z.array(QualitativeMeasurementSchema),
+  quantitative: z.array(QuantitativeMeasurementSchema)
+});
+
+export const EnvironmentStandardsSchema = z.object({
+  qualitative: z.array(QualitativeMeasurementSchema),
+  quantitative: z.array(QuantitativeMeasurementSchema)
+});
+
+export type EnvironmentStandards = z.infer<typeof EnvironmentStandardsSchema>;
+
+export const MethodStandardSchema = z.object({
+  method_lookup_id: z.number(),
+  name: z.string(),
+  description: z.string().nullable(),
+  attributes: MethodAttributesSchema
+});
+
+export type MethodStandard = z.infer<typeof MethodStandardSchema>;
+
+export interface ISpeciesStandards {
+  tsn: number;
+  scientificName: string;
+  measurements: {
+    quantitative: CBQuantitativeMeasurementTypeDefinition[];
+    qualitative: CBQualitativeMeasurementTypeDefinition[];
+  };
+  markingBodyLocations: { id: string; key: string; value: string }[];
+}

api/src/openapi/schemas/standards.ts

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+import { OpenAPIV3 } from 'openapi-types';
+
+export const EnvironmentStandardsSchema: OpenAPIV3.SchemaObject = {
+  type: 'object',
+  description:
+    'Environment standards response object showing supported environmental variables and associated information',
+  additionalProperties: false,
+  properties: {
+    qualitative: {
+      type: 'array',
+      description: 'Array of qualitative environmental variables',
+      items: {
+        type: 'object',
+        properties: {
+          name: {
+            type: 'string',
+            description: 'Name of the environmental variable'
+          },
+          description: {
+            type: 'string',
+            description: 'Description of the environmental variable',
+            nullable: true
+          },
+          options: {
+            type: 'array',
+            description: 'Array of options for the qualitative variable',
+            items: {
+              type: 'object',
+              properties: {
+                name: {
+                  type: 'string',
+                  description: 'Description of the environmental variable option'
+                },
+                description: {
+                  type: 'string',
+                  description: 'Description of the environmental variable option',
+                  nullable: true
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    quantitative: {
+      type: 'array',
+      description: 'Array of quantitative environmental variables',
+      items: {
+        type: 'object',
+        properties: {
+          name: {
+            type: 'string',
+            description: 'Name of the quantitative environmental variable'
+          },
+          description: {
+            type: 'string',
+            description: 'Description of the quantitative environmental variable',
+            nullable: true
+          },
+          unit: {
+            type: 'string',
+            description: 'Unit of measurement of the quantitative environmental variable',
+            nullable: true
+          }
+        }
+      }
+    }
+  }
+};
+
+export const MethodStandardSchema: OpenAPIV3.SchemaObject = {
+  type: 'array',
+  items: {
+    type: 'object',
+    additionalProperties: false,
+    properties: {
+      method_lookup_id: { type: 'number' },
+      name: { type: 'string' },
+      description: { type: 'string', nullable: true },
+      attributes: {
+        type: 'object',
+        additionalProperties: false,
+        properties: {
+          qualitative: {
+            type: 'array',
+            items: {
+              type: 'object',
+              additionalProperties: false,
+              properties: {
+                name: {
+                  type: 'string'
+                },
+                description: {
+                  type: 'string',
+                  nullable: true
+                },
+                options: {
+                  type: 'array',
+                  items: {
+                    type: 'object',
+                    additionalProperties: false,
+                    properties: {
+                      name: {
+                        type: 'string'
+                      },
+                      description: {
+                        type: 'string',
+                        nullable: true
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          },
+          quantitative: {
+            type: 'array',
+            items: {
+              type: 'object',
+              additionalProperties: false,
+              properties: {
+                name: {
+                  type: 'string'
+                },
+                description: {
+                  type: 'string',
+                  nullable: true
+                },
+                unit: { type: 'string', nullable: true }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+};

api/src/paths/standards/environment/index.test.ts

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+import chai, { expect } from 'chai';
+import { afterEach, describe, it } from 'mocha';
+import sinon from 'sinon';
+import sinonChai from 'sinon-chai';
+import * as db from '../../../database/db';
+import { HTTPError } from '../../../errors/http-error';
+import { StandardsService } from '../../../services/standards-service';
+import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db';
+import { getEnvironmentStandards } from './index'; // Adjust the import path based on your file structure
+
+chai.use(sinonChai);
+
+describe('standards/environment', () => {
+  describe('getEnvironmentStandards', () => {
+    afterEach(() => {
+      sinon.restore();
+    });
+
+    it('should retrieve environment standards successfully', async () => {
+      const mockResponse = {
+        quantitative: [
+          { name: 'Quantitative Standard 1', description: 'Description 1', unit: 'Unit' },
+          { name: 'Quantitative Standard 2', description: 'Description 2', unit: 'Unit' }
+        ],
+        qualitative: [
+          {
+            name: 'Qualitative Standard 1',
+            description: 'Description 1',
+            options: [
+              { name: 'Option 1', description: 'Option 1 Description' },
+              { name: 'Option 2', description: 'Option 2 Description' }
+            ]
+          },
+          {
+            name: 'Qualitative Standard 2',
+            description: 'Description 2',
+            options: [
+              { name: 'Option 3', description: 'Option 3 Description' },
+              { name: 'Option 4', description: 'Option 4 Description' }
+            ]
+          }
+        ]
+      };
+
+      const mockDBConnection = getMockDBConnection();
+
+      sinon.stub(db, 'getAPIUserDBConnection').returns(mockDBConnection);
+
+      sinon.stub(StandardsService.prototype, 'getEnvironmentStandards').resolves(mockResponse);
+
+      const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
+
+      const requestHandler = getEnvironmentStandards();
+
+      await requestHandler(mockReq, mockRes, mockNext);
+
+      expect(mockRes.status).to.have.been.calledWith(200);
+      expect(mockRes.json).to.have.been.calledWith(mockResponse);
+    });
+
+    it('catches and re-throws error', async () => {
+      const mockDBConnection = getMockDBConnection({
+        open: sinon.stub(),
+        commit: sinon.stub(),
+        rollback: sinon.stub(),
+        release: sinon.stub()
+      });
+
+      sinon.stub(db, 'getAPIUserDBConnection').returns(mockDBConnection);
+
+      sinon
+        .stub(StandardsService.prototype, 'getEnvironmentStandards')
+        .rejects(new Error('Failed to retrieve environment standards'));
+
+      const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
+
+      try {
+        const requestHandler = getEnvironmentStandards();
+        await requestHandler(mockReq, mockRes, mockNext);
+        expect.fail();
+      } catch (actualError) {
+        expect(mockDBConnection.open).to.have.been.calledOnce;
+        expect(mockDBConnection.rollback).to.have.been.calledOnce;
+        expect(mockDBConnection.release).to.have.been.calledOnce;
+        expect((actualError as HTTPError).message).to.equal('Failed to retrieve environment standards');
+      }
+    });
+  });
+});

api/src/paths/standards/environment/index.ts

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+import { RequestHandler } from 'express';
+import { Operation } from 'express-openapi';
+import { getAPIUserDBConnection } from '../../../database/db';
+import { EnvironmentStandardsSchema } from '../../../openapi/schemas/standards';
+import { StandardsService } from '../../../services/standards-service';
+import { getLogger } from '../../../utils/logger';
+
+const defaultLog = getLogger('paths/projects');
+
+export const GET: Operation = [getEnvironmentStandards()];
+
+GET.apiDoc = {
+  description: 'Gets lookup values for environment variables',
+  tags: ['standards'],
+  parameters: [
+    {
+      in: 'query',
+      name: 'keyword',
+      required: false,
+      schema: {
+        type: 'string',
+        nullable: true
+      }
+    }
+  ],
+  security: [],
+  responses: {
+    200: {
+      description: 'Environment data standards response object.',
+      content: {
+        'application/json': {
+          schema: EnvironmentStandardsSchema
+        }
+      }
+    },
+    400: {
+      $ref: '#/components/responses/400'
+    },
+    401: {
+      $ref: '#/components/responses/401'
+    },
+    403: {
+      $ref: '#/components/responses/403'
+    },
+    500: {
+      $ref: '#/components/responses/500'
+    },
+    default: {
+      $ref: '#/components/responses/default'
+    }
+  }
+};
+
+/**
+ * Get species data standards
+ *
+ * @returns {RequestHandler}
+ */
+export function getEnvironmentStandards(): RequestHandler {
+  return async (req, res) => {
+    const connection = getAPIUserDBConnection();
+
+    try {
+      await connection.open();
+
+      const standardsService = new StandardsService(connection);
+
+      const keyword = (req.query.keyword as string) ?? '';
+
+      const response = await standardsService.getEnvironmentStandards(keyword);
+
+      await connection.commit();
+
+      return res.status(200).json(response);
+    } catch (error) {
+      defaultLog.error({ label: 'getEnvironmentStandards', message: 'error', error });
+      connection.rollback();
+      throw error;
+    } finally {
+      connection.release();
+    }
+  };
+}