Merge remote-tracking branch 'origin/dev' into sampling-container

api/.pipeline/templates/api.dc.yaml

@@ -121,6 +121,16 @@ parameters:
     description: S3 key optional prefix
     required: false
     value: 'sims'
+  # Request limits
+  - name: MAX_REQ_BODY_SIZE
+    description: Maximum request body size in bytes
+    value: '52428800'
+  - name: MAX_UPLOAD_NUM_FILES
+    description: Maximum number of files uploaded in a single request
+    value: '10'
+  - name: MAX_UPLOAD_FILE_SIZE
+    description: Maximum upload file size in bytes
+    value: '52428800'
   # Logging
   - name: LOG_LEVEL
     value: 'silent'
@@ -162,12 +172,12 @@ parameters:
   - name: GCNOTIFY_ONBOARDING_REQUEST_EMAIL_TEMPLATE
     description: gcnotify email template id
     value: 7779a104-b863-40ac-902f-1aa607d2071a
+  - name: GCNOTIFY_REQUEST_RESUBMIT_TEMPLATE
+    description: gcnotify email resubmit template id
+    value: c973da33-1f2b-435a-9429-d8ab4fd273c5
   - name: GCNOTIFY_ONBOARDING_REQUEST_SMS_TEMPLATE
     description: gcnotify sms template id
     value: af2f1e40-bd72-4612-9c5a-567ee5b26ca5
-  - name: GCNOTIFY_REQUEST_RESUBMIT_TEMPLATE
-    description: gcnotify request resubmit email template
-    value: c973da33-1f2b-435a-9429-d8ab4fd273c5
   - name: GCNOTIFY_EMAIL_URL
     value: https://api.notification.canada.ca/v2/notifications/email
   - name: GCNOTIFY_SMS_URL
@@ -336,6 +346,13 @@ objects:
                   value: ${KEYCLOAK_API_HOST}
                 - name: KEYCLOAK_API_ENVIRONMENT
                   value: ${KEYCLOAK_API_ENVIRONMENT}
+                # Request limits
+                - name: MAX_REQ_BODY_SIZE
+                  value: ${MAX_REQ_BODY_SIZE}
+                - name: MAX_UPLOAD_NUM_FILES
+                  value: ${MAX_UPLOAD_NUM_FILES}
+                - name: MAX_UPLOAD_FILE_SIZE
+                  value: ${MAX_UPLOAD_FILE_SIZE}
                 # Object Store (S3)
                 - name: OBJECT_STORE_URL
                   valueFrom:
@@ -357,6 +374,8 @@ objects:
                     secretKeyRef:
                       key: object_store_bucket_name
                       name: ${OBJECT_STORE_SECRETS}
+                - name: S3_KEY_PREFIX
+                  value: ${S3_KEY_PREFIX}
                 # Logging
                 - name: LOG_LEVEL
                   value: ${LOG_LEVEL}
@@ -387,6 +406,8 @@ objects:
                   value: ${GCNOTIFY_ADMIN_EMAIL}
                 - name: GCNOTIFY_ONBOARDING_REQUEST_EMAIL_TEMPLATE
                   value: ${GCNOTIFY_ONBOARDING_REQUEST_EMAIL_TEMPLATE}
+                - name: GCNOTIFY_REQUEST_RESUBMIT_TEMPLATE
+                  value: ${GCNOTIFY_REQUEST_RESUBMIT_TEMPLATE}
                 - name: GCNOTIFY_ONBOARDING_REQUEST_SMS_TEMPLATE
                   value: ${GCNOTIFY_ONBOARDING_REQUEST_SMS_TEMPLATE}
                 - name: GCNOTIFY_EMAIL_URL

api/src/app.ts

@@ -13,20 +13,24 @@ import {
 } from './middleware/critterbase-proxy';
 import { rootAPIDoc } from './openapi/root-api-doc';
 import { authenticateRequest, authenticateRequestOptional } from './request-handlers/security/authentication';
+import { loadEvironmentVariables } from './utils/env-config';
 import { scanFileForVirus } from './utils/file-utils';
 import { getLogger } from './utils/logger';
 
+// Load and validate the environment variables
+loadEvironmentVariables();
+
 const defaultLog = getLogger('app');
 
 const HOST = process.env.API_HOST;
-const PORT = Number(process.env.API_PORT);
+const PORT = process.env.API_PORT;
 
 // Max size of the body of the request (bytes)
-const MAX_REQ_BODY_SIZE = Number(process.env.MAX_REQ_BODY_SIZE) || 52428800;
+const MAX_REQ_BODY_SIZE = process.env.MAX_REQ_BODY_SIZE;
 // Max number of files in a single request
-const MAX_UPLOAD_NUM_FILES = Number(process.env.MAX_UPLOAD_NUM_FILES) || 10;
+const MAX_UPLOAD_NUM_FILES = process.env.MAX_UPLOAD_NUM_FILES;
 // Max size of a single file (bytes)
-const MAX_UPLOAD_FILE_SIZE = Number(process.env.MAX_UPLOAD_FILE_SIZE) || 52428800;
+const MAX_UPLOAD_FILE_SIZE = process.env.MAX_UPLOAD_FILE_SIZE;
 
 // Get initial express app
 const app: express.Express = express();

api/src/constants/dates.ts

@@ -0,0 +1,22 @@
+/*
+ * Date formats.
+ *
+ * See BC Gov standards: https://www2.gov.bc.ca/gov/content/governments/services-for-government/policies-procedures/web-content-development-guides/writing-for-the-web/web-style-guide/numbers
+ */
+export const DefaultDateFormat = 'YYYY-MM-DD'; // 2020-01-05
+
+export const DefaultDateFormatReverse = 'DD-MM-YYYY'; // 05-01-2020
+
+export const AltDateFormat = 'YYYY/MM/DD'; // 2020/01/05
+
+export const AltDateFormatReverse = 'DD/MM/YYYY'; // 05/01/2020
+
+/*
+ * Time formats.
+ */
+export const DefaultTimeFormat = 'HH:mm:ss'; // 23:00:00
+
+/*
+ * Datetime formats.
+ */
+export const DefaultDateTimeFormat = `${DefaultDateFormat}T${DefaultTimeFormat}`; // 2020-01-05T23:00:00

api/src/database/db.ts

@@ -18,14 +18,14 @@ import { asyncErrorWrapper, getGenericizedKeycloakUserInformation, syncErrorWrap
 const defaultLog = getLogger('database/db');
 
 const getDbHost = () => process.env.DB_HOST;
-const getDbPort = () => Number(process.env.DB_PORT);
+const getDbPort = () => process.env.DB_PORT;
 const getDbUsername = () => process.env.DB_USER_API;
 const getDbPassword = () => process.env.DB_USER_API_PASS;
 const getDbDatabase = () => process.env.DB_DATABASE;
 
-const DB_POOL_SIZE: number = Number(process.env.DB_POOL_SIZE) || 20;
-const DB_CONNECTION_TIMEOUT: number = Number(process.env.DB_CONNECTION_TIMEOUT) || 0;
-const DB_IDLE_TIMEOUT: number = Number(process.env.DB_IDLE_TIMEOUT) || 10000;
+const DB_POOL_SIZE = 20;
+const DB_CONNECTION_TIMEOUT = 0;
+const DB_IDLE_TIMEOUT = 10000;
 
 export const DB_CLIENT = 'pg';
 

api/src/models/alert-view.ts

@@ -0,0 +1,29 @@
+import { z } from 'zod';
+
+// Define the alert schema
+export const IAlert = z.object({
+  alert_id: z.number(),
+  alert_type_id: z.number().int(),
+  name: z.string(),
+  message: z.string(),
+  severity: z.enum(['info', 'success', 'error', 'warning']),
+  data: z.object({}).nullable(),
+  record_end_date: z.string().nullable(),
+  status: z.enum(['active', 'expired'])
+});
+
+// Infer types from the schema
+export type IAlert = z.infer<typeof IAlert>;
+export type IAlertCreateObject = Omit<IAlert, 'alert_id' | 'status'>;
+export type IAlertUpdateObject = Omit<IAlert, 'status'>;
+
+// Filter object for viewing alerts
+export interface IAlertFilterObject {
+  expiresBefore?: string;
+  expiresAfter?: string;
+  types?: string[];
+}
+
+// Define severity and status types
+export type IAlertSeverity = 'info' | 'success' | 'error' | 'warning';
+export type IAlertStatus = 'active' | 'expired';

api/src/models/project-survey-attachments.ts

@@ -1,4 +1,4 @@
-import { default as dayjs } from 'dayjs';
+import dayjs from 'dayjs';
 import { ATTACHMENT_TYPE } from '../constants/attachments';
 import { getLogger } from '../utils/logger';
 import { SurveySupplementaryData } from './survey-view';

api/src/models/sampling-locations-view.ts

@@ -0,0 +1,19 @@
+export interface ISiteAdvancedFilters {
+  survey_id?: number;
+  keyword?: string;
+  system_user_id?: number;
+}
+
+export interface IMethodAdvancedFilters {
+  survey_id?: number;
+  sample_site_id?: number;
+  keyword?: string;
+  system_user_id?: number;
+}
+
+export interface IPeriodAdvancedFilters {
+  survey_id?: number;
+  sample_site_id?: number;
+  sample_method_id?: number;
+  system_user_id?: number;
+}

api/src/openapi/schemas/alert.ts

@@ -0,0 +1,83 @@
+import { OpenAPIV3 } from 'openapi-types';
+
+/**
+ * Base schema for system alerts
+ */
+const baseSystemAlertSchema: OpenAPIV3.SchemaObject = {
+  type: 'object',
+  description: 'Schema defining alerts created by system administrators.',
+  additionalProperties: false,
+  properties: {
+    name: {
+      description: 'Name to display as the title of the alert',
+      type: 'string'
+    },
+    message: {
+      description: 'Message to display on the alert',
+      type: 'string'
+    },
+    alert_type_id: {
+      description: 'Type of the alert, controlling how it is displayed.',
+      type: 'number'
+    },
+    severity: {
+      description: 'Severity level of the alert',
+      type: 'string',
+      enum: ['info', 'success', 'warning', 'error']
+    },
+    data: {
+      description: 'Data associated with the alert',
+      type: 'object',
+      nullable: true
+    },
+    record_end_date: {
+      description: 'End date of the alert',
+      type: 'string',
+      nullable: true
+    }
+  }
+};
+
+/**
+ * Schema for updating system alerts
+ */
+export const systemAlertPutSchema: OpenAPIV3.SchemaObject = {
+  ...baseSystemAlertSchema,
+  required: ['alert_id', 'name', 'message', 'data', 'alert_type_id', 'record_end_date', 'severity'],
+  additionalProperties: false,
+  properties: {
+    ...baseSystemAlertSchema.properties,
+    alert_id: {
+      type: 'integer',
+      minimum: 1,
+      description: 'Primary key of the alert'
+    }
+  }
+};
+
+/**
+ * Schema for getting system alerts
+ */
+export const systemAlertGetSchema: OpenAPIV3.SchemaObject = {
+  ...baseSystemAlertSchema,
+  required: ['alert_id', 'name', 'message', 'data', 'alert_type_id', 'record_end_date', 'severity', 'status'],
+  additionalProperties: false,
+  properties: {
+    ...systemAlertPutSchema.properties,
+    status: {
+      type: 'string',
+      enum: ['active', 'expired'],
+      description:
+        'Status of the alert based on comparing the current date to record_end_date, calculated in the get query.'
+    }
+  }
+};
+
+/**
+ * Schema for creating system alerts
+ */
+export const systemAlertCreateSchema: OpenAPIV3.SchemaObject = {
+  ...baseSystemAlertSchema,
+  additionalProperties: false,
+  required: ['name', 'message', 'data', 'alert_type_id', 'record_end_date', 'severity']
+};

api/src/openapi/schemas/observation.ts

@@ -1,5 +1,6 @@
 import { OpenAPIV3 } from 'openapi-types';
 import { paginationResponseSchema } from './pagination';
+import { SampleLocationSchema } from './sample-site';
 
 export const observervationsWithSubcountDataSchema: OpenAPIV3.SchemaObject = {
   type: 'object',
@@ -60,19 +61,27 @@ export const observervationsWithSubcountDataSchema: OpenAPIV3.SchemaObject = {
             nullable: true
           },
           latitude: {
-            type: 'number'
+            type: 'number',
+            nullable: true,
+            minimum: -90,
+            maximum: 90
           },
           longitude: {
-            type: 'number'
+            type: 'number',
+            nullable: true,
+            minimum: -180,
+            maximum: 180
           },
           count: {
             type: 'integer'
           },
           observation_date: {
-            type: 'string'
+            type: 'string',
+            nullable: true
           },
           observation_time: {
-            type: 'string'
+            type: 'string',
+            nullable: true
           },
           survey_sample_site_name: {
             type: 'string',
@@ -217,7 +226,8 @@ export const observervationsWithSubcountDataSchema: OpenAPIV3.SchemaObject = {
         'qualitative_measurements',
         'quantitative_measurements',
         'qualitative_environments',
-        'quantitative_environments'
+        'quantitative_environments',
+        'sample_sites'
       ],
       properties: {
         observationCount: {
@@ -404,7 +414,8 @@ export const observervationsWithSubcountDataSchema: OpenAPIV3.SchemaObject = {
               }
             }
           }
-        }
+        },
+        sample_sites: SampleLocationSchema
       }
     },
     pagination: { ...paginationResponseSchema }