SIMSBIOHUB-665: Habitat Features Database Schema

api/src/database-models/alert.ts

@@ -1,4 +1,5 @@
 import { z } from 'zod';
+import { AlertSeverity } from '../database-units/alert_severity';
 
 /**
  * Alert Model.
@@ -10,7 +11,7 @@ export const AlertModel = z.object({
   alert_type_id: z.number(),
   name: z.string(),
   message: z.string(),
-  severity: z.enum(['info', 'success', 'error', 'warning']),
+  severity: AlertSeverity,
   data: z.object({}).nullable(),
   record_end_date: z.string().nullable(),
   create_date: z.string(),

api/src/database-units/alert_severity.ts

@@ -0,0 +1,10 @@
+import { z } from 'zod';
+
+/**
+ * Alert Severity Data Type.
+ *
+ * @description Data type for `alert_severity`.
+ */
+export const AlertSeverity = z.enum(['info', 'warning', 'error', 'success']);
+
+export type AlertSeverity = z.infer<typeof AlertSeverity>;

api/src/database-units/quantitative_unit.ts

@@ -0,0 +1,31 @@
+import { z } from 'zod';
+
+/**
+ * Quantitative Unit Data Type.
+ *
+ * @description Data type for `quantitative_unit`.
+ */
+export const QuantitativeUnit = z.enum([
+  'millimeter',
+  'centimeter',
+  'meter',
+  'milligram',
+  'gram',
+  'kilogram',
+  'percent',
+  'celsius',
+  'ppt',
+  'SCF',
+  'degrees',
+  'pH',
+  'seconds',
+  'meters squared',
+  'count',
+  'GHz',
+  'Hz',
+  'amps',
+  'volts',
+  'megapixels'
+]);
+
+export type QuantitativeUnit = z.infer<typeof QuantitativeUnit>;

api/src/models/alert-view.ts

@@ -1,9 +1,12 @@
 import { z } from 'zod';
 import { AlertRecord } from '../database-models/alert';
 
+export const AlertStatus = z.enum(['active', 'expired']);
+export type AlertStatus = z.infer<typeof AlertStatus>;
+
 export const AlertRecordWithStatus = AlertRecord.extend({
   create_date: z.string(),
-  status: z.enum(['active', 'expired'])
+  status: AlertStatus
 });
 export type AlertRecordWithStatus = z.infer<typeof AlertRecordWithStatus>;
 
@@ -17,7 +20,3 @@ export interface IAlertFilterObject {
   expiresAfter?: string;
   types?: string[];
 }
-
-// Define severity and status types
-export type IAlertSeverity = 'info' | 'success' | 'error' | 'warning';
-export type IAlertStatus = 'active' | 'expired';

api/src/paths/alert/index.test.ts

@@ -6,7 +6,7 @@ import { SYSTEM_IDENTITY_SOURCE } from '../../constants/database';
 import { SYSTEM_ROLE } from '../../constants/roles';
 import * as db from '../../database/db';
 import { HTTPError } from '../../errors/http-error';
-import { IAlertSeverity, IAlertStatus } from '../../models/alert-view';
+import { AlertRecordWithStatus } from '../../models/alert-view';
 import { AlertService } from '../../services/alert-service';
 import { getMockDBConnection, getRequestHandlerMocks } from '../../__mocks__/db';
 import { createAlert, getAlerts } from '../alert';
@@ -21,14 +21,14 @@ describe('getAlerts', () => {
   describe('as a system user', () => {
     it('returns a list of system alerts', async () => {
       const mockTotal = 10;
-      const mockAlerts = [
+      const mockAlerts: AlertRecordWithStatus[] = [
         {
           alert_id: 1,
           name: 'Alert 1',
           message: 'Message 1',
           alert_type_id: 1,
-          severity: 'error' as IAlertSeverity,
-          status: 'active' as IAlertStatus,
+          severity: 'error',
+          status: 'active',
           data: null,
           record_end_date: null,
           create_date: '2020-01-01T10:10:10'
@@ -38,8 +38,8 @@ describe('getAlerts', () => {
           name: 'Alert 2',
           message: 'Message 2',
           alert_type_id: 2,
-          severity: 'error' as IAlertSeverity,
-          status: 'active' as IAlertStatus,
+          severity: 'error',
+          status: 'active',
           data: null,
           record_end_date: null,
           create_date: '2020-01-01T10:10:10'

api/src/paths/alert/{alertId}/index.test.ts

@@ -7,7 +7,7 @@ import { SYSTEM_IDENTITY_SOURCE } from '../../../constants/database';
 import { SYSTEM_ROLE } from '../../../constants/roles';
 import * as db from '../../../database/db';
 import { HTTPError } from '../../../errors/http-error';
-import { IAlertSeverity, IAlertStatus } from '../../../models/alert-view';
+import { AlertRecordWithStatus } from '../../../models/alert-view';
 import { AlertService } from '../../../services/alert-service';
 import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db';
 
@@ -20,13 +20,13 @@ describe('getAlerts', () => {
 
   describe('as a system user', () => {
     it('returns a single system alert', async () => {
-      const mockAlert = {
+      const mockAlert: AlertRecordWithStatus = {
         alert_id: 1,
         name: 'Alert 1',
         message: 'Message 1',
         alert_type_id: 1,
-        severity: 'error' as IAlertSeverity,
-        status: 'active' as IAlertStatus,
+        severity: 'error',
+        status: 'active',
         data: null,
         record_end_date: null,
         create_date: '2020-01-01T10:10:10'

api/src/repositories/alert-repository.test.ts

@@ -2,7 +2,7 @@ import chai, { expect } from 'chai';
 import { QueryResult } from 'pg';
 import sinon from 'sinon';
 import sinonChai from 'sinon-chai';
-import { IAlertSeverity } from '../models/alert-view';
+import { AlertRecordWithStatus, IAlertCreateObject, IAlertUpdateObject } from '../models/alert-view';
 import { getMockDBConnection } from '../__mocks__/db';
 import { AlertRepository } from './alert-repository';
 
@@ -18,16 +18,17 @@ describe('AlertRepository', () => {
 
   describe('getAlerts', () => {
     it('should return an array of alerts with empty filters', async () => {
-      const mockRows = [
+      const mockRows: AlertRecordWithStatus[] = [
         {
           alert_id: 1,
           name: 'Alert 1',
           message: 'This is an alert.',
           alert_type_id: 1,
           data: {},
-          severity: 'error' as IAlertSeverity,
+          severity: 'error',
+          status: 'active',
           record_end_date: null,
-          status: 'active'
+          create_date: '2020-01-01'
         }
       ];
       const mockQueryResponse = { rows: mockRows, rowCount: 1 } as unknown as QueryResult<any>;
@@ -109,13 +110,13 @@ describe('AlertRepository', () => {
       });
 
       const alertRepository = new AlertRepository(mockDBConnection);
-      const alert = {
+      const alert: IAlertUpdateObject = {
         alert_id: 1,
         name: 'Updated Alert',
         message: 'Updated message',
         alert_type_id: 1,
         data: {},
-        severity: 'error' as IAlertSeverity,
+        severity: 'error',
         record_end_date: null
       };
 
@@ -135,12 +136,12 @@ describe('AlertRepository', () => {
       });
 
       const alertRepository = new AlertRepository(mockDBConnection);
-      const alert = {
+      const alert: IAlertCreateObject = {
         name: 'New Alert',
         message: 'New alert message',
         alert_type_id: 1,
         data: {},
-        severity: 'error' as IAlertSeverity,
+        severity: 'error',
         record_end_date: null
       };
 

api/src/repositories/observation-subcount-environment-repository.ts

@@ -1,26 +1,9 @@
 import SQL from 'sql-template-strings';
 import { z } from 'zod';
+import { QuantitativeUnit } from '../database-units/quantitative_unit';
 import { getKnex } from '../database/db';
 import { BaseRepository } from './base-repository';
 
-// Environment unit type definition.
-export const EnvironmentUnit = z.enum([
-  // Should be kept in sync with the database table `environment_unit`
-  'millimeter',
-  'centimeter',
-  'meter',
-  'milligram',
-  'gram',
-  'kilogram',
-  'percent',
-  'celsius',
-  'ppt',
-  'SCF',
-  'degrees',
-  'pH'
-]);
-export type EnvironmentUnit = z.infer<typeof EnvironmentUnit>;
-
 // Qualitative environment option type definition.
 const QualitativeEnvironmentOption = z.object({
   environment_qualitative_option_id: z.string().uuid(),
@@ -46,7 +29,7 @@ const QuantitativeEnvironmentTypeDefinition = z.object({
   description: z.string().nullable(),
   min: z.number().nullable(),
   max: z.number().nullable(),
-  unit: EnvironmentUnit.nullable()
+  unit: QuantitativeUnit.nullable()
 });
 export type QuantitativeEnvironmentTypeDefinition = z.infer<typeof QuantitativeEnvironmentTypeDefinition>;
 

api/src/services/alert-service.test.ts

@@ -2,7 +2,7 @@ import chai, { expect } from 'chai';
 import { afterEach, describe, it } from 'mocha';
 import sinon from 'sinon';
 import sinonChai from 'sinon-chai';
-import { AlertRecordWithStatus, IAlertCreateObject, IAlertFilterObject, IAlertSeverity } from '../models/alert-view';
+import { AlertRecordWithStatus, IAlertCreateObject, IAlertFilterObject } from '../models/alert-view';
 import { AlertRepository } from '../repositories/alert-repository';
 import { getMockDBConnection } from '../__mocks__/db';
 import { AlertService } from './alert-service';
@@ -26,7 +26,7 @@ describe('AlertService', () => {
           message: 'Message 1',
           alert_type_id: 1,
           data: {},
-          severity: 'error' as IAlertSeverity,
+          severity: 'error',
           status: 'active',
           record_end_date: null,
           create_date: '2020-01-01T10:10:10'
@@ -73,7 +73,7 @@ describe('AlertService', () => {
         message: 'Message 1',
         alert_type_id: 1,
         data: {},
-        severity: 'error' as IAlertSeverity,
+        severity: 'error',
         status: 'active',
         record_end_date: null,
         create_date: '2020-01-01T10:10:10'
@@ -99,7 +99,7 @@ describe('AlertService', () => {
         message: 'New alert message',
         alert_type_id: 1,
         data: {},
-        severity: 'error' as IAlertSeverity,
+        severity: 'error',
         record_end_date: null
       };
 
@@ -124,7 +124,7 @@ describe('AlertService', () => {
         message: 'Updated message',
         alert_type_id: 1,
         data: {},
-        severity: 'error' as IAlertSeverity,
+        severity: 'error',
         status: 'active',
         record_end_date: null,
         create_date: '2020-01-01T10:10:10'

app/src/interfaces/useReferenceApi.interface.ts

@@ -1,7 +1,27 @@
 /**
- * A qualitative environment unit.
+ * A quantitative unit.
  */
-export type EnvironmentUnit = 'millimeter' | 'centimeter' | 'meter' | 'milligram' | 'gram' | 'kilogram';
+export type QuantitativeUnit =
+  | 'millimeter'
+  | 'centimeter'
+  | 'meter'
+  | 'milligram'
+  | 'gram'
+  | 'kilogram'
+  | 'percent'
+  | 'celsius'
+  | 'ppt'
+  | 'SCF'
+  | 'degrees'
+  | 'pH'
+  | 'seconds'
+  | 'meters squared'
+  | 'count'
+  | 'GHz'
+  | 'Hz'
+  | 'amps'
+  | 'volts'
+  | 'megapixels';
 
 /**
  * A quantitative environment type definition.
@@ -12,7 +32,7 @@ export type EnvironmentQuantitativeTypeDefinition = {
   description: string | null;
   min: number | null;
   max: number | null;
-  unit: EnvironmentUnit | null;
+  unit: QuantitativeUnit | null;
 };
 
 /**

database/src/migrations/20250206000001_rename_environment_unit_enum.ts

@@ -0,0 +1,27 @@
+import { Knex } from 'knex';
+
+/**
+ * Rename the `environment_unit` enum to `quantitative_unit`.
+ *
+ * Originally created in migration `20240417000000_obsevation_environment_tables.ts` when only the environment tables
+ * used it. But, it really contains generic units that can be used in other tables as well.
+ *
+ * @export
+ * @param {Knex} knex
+ * @return {*}  {Promise<void>}
+ */
+export async function up(knex: Knex): Promise<void> {
+  await knex.raw(`
+    ----------------------------------------------------------------------------------------
+    -- Rename the environment_unit enum to quantitative_unit
+    ----------------------------------------------------------------------------------------
+
+    SET SEARCH_PATH=biohub;
+
+    ALTER TYPE environment_unit RENAME TO quantitative_unit;
+  `);
+}
+
+export async function down(knex: Knex): Promise<void> {
+  await knex.raw(``);
+}

database/src/migrations/20250206000002_update_environments.ts

@@ -0,0 +1,42 @@
+import { Knex } from 'knex';
+
+/**
+ * Updates to environment tables:
+ * - Add missing foreign key constraint for environment_qualitative_option table.
+ * - Add indexes on 'name' column in environment_qualitative and environment_quantitative tables to improve search
+ * performance.
+ *
+ * @export
+ * @param {Knex} knex
+ * @return {*}  {Promise<void>}
+ */
+export async function up(knex: Knex): Promise<void> {
+  await knex.raw(`--sql
+    ----------------------------------------------------------------------------------------
+    -- Add missing foreign key
+    ----------------------------------------------------------------------------------------
+
+    SET SEARCH_PATH=biohub, public;
+
+    -- Add foreign key constraint
+    ALTER TABLE environment_qualitative_option
+      ADD CONSTRAINT environment_qualitative_option_fk1
+      FOREIGN KEY (environment_qualitative_id)
+      REFERENCES environment_qualitative(environment_qualitative_id);
+
+    -- Add indexes for foreign keys
+    CREATE INDEX environment_qualitative_option_idx1 ON environment_qualitative_option(environment_qualitative_id);
+
+    ----------------------------------------------------------------------------------------
+    -- Add indexes to improve search performance
+    ----------------------------------------------------------------------------------------
+
+    CREATE INDEX environment_qualitative_idx1 ON environment_qualitative(name);
+
+    CREATE INDEX environment_quantitative_idx1 ON environment_quantitative(name);
+  `);
+}
+
+export async function down(knex: Knex): Promise<void> {
+  await knex.raw(``);
+}