✏️ Feat/ #22 Application Update methods

apps/api/README.md

@@ -25,3 +25,7 @@ This app uses features from Node ^20.9, in combination with TSX for TypeScript s
 ### Database
 
 - This application implements a Postgres database based on the following [data model](../../docs/model/README.md) and managed by [Drizzle ORM](https://orm.drizzle.team/docs/overview)
+
+- Drizzle is configured to read the schema from the build directory (`/dist`) due to a known Drizzle Kit issue with ESM imports. Any Drizzle Kit operations (including migrations) require first building the application with `pnpm run build`.
+
+- A schema dbml (database markup language) file can be generated using the script `pnpm run dbml`. This file is found at `./src/db/schema.dbml`.

apps/api/drizzle.config.ts

@@ -29,7 +29,7 @@ export const connectionString = `postgres://${PG_USER}:${PG_PASSWORD}@${PG_HOST}
 
 export default defineConfig({
 	out: './drizzle',
-	schema: './src/db/schemas/*',
+	schema: './dist/src/db/schemas/*',
 	dialect: 'postgresql',
 	dbCredentials: {
 		url: connectionString!,

apps/api/package.json

@@ -6,7 +6,8 @@
 	"scripts": {
 		"build": "rimraf ./dist && tsc",
 		"dev": "tsx watch --env-file=.env ./src/main.ts",
-		"test": "npx tsx --test --test-reporter=spec --experimental-test-coverage ./src/tests/**/*",
+		"dbml": "tsx ./src/db/dbml.ts",
+		"test": "tsx --test --test-reporter=spec --experimental-test-coverage ./tests/**/*.test.ts",
 		"start:prod": "node ./dist/src/main.js"
 	},
 	"devDependencies": {
@@ -24,6 +25,8 @@
 	},
 	"dependencies": {
 		"@pcgl-daco/data-model": "workspace:^",
+		"@types/body-parser": "^1.19.5",
+		"body-parser": "^1.20.3",
 		"cors": "^2.8.5",
 		"drizzle-orm": "^0.35.3",
 		"express": "^4.21.0",

apps/api/src/api/application-api.ts

@@ -0,0 +1,59 @@
+/*
+ * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved
+ *
+ * This program and the accompanying materials are made available under the terms of
+ * the GNU Affero General Public License v3.0. You should have received a copy of the
+ * GNU Affero General Public License along with this program.
+ *  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+ * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+import { ApplicationStates } from '@pcgl-daco/data-model/src/types.js';
+import { getDbInstance } from '../db/index.js';
+import applicationService from '../service/application-service.js';
+import { type ApplicationContentUpdates, type ApplicationService } from '../service/types.js';
+import { failure } from '../utils/results.js';
+
+/**
+ * Validates if a given Application state allows edits, then updates the record
+ * Updated records are returned in state 'DRAFT'
+ * @param id - Application ID
+ * @param update - Application Contents details to update
+ * @returns Success with Application data / Failure with Error
+ */
+export const editApplication = async ({ id, update }: { id: number; update: ApplicationContentUpdates }) => {
+	const database = getDbInstance();
+	const service: ApplicationService = applicationService(database);
+
+	const result = await service.getApplicationById({ id });
+
+	if (!result.success) {
+		return result;
+	}
+
+	const { state } = result.data;
+
+	// TODO: Replace w/ state machine https://github.com/Pan-Canadian-Genome-Library/daco/issues/58
+	const isEditState =
+		state === ApplicationStates.DRAFT ||
+		state === ApplicationStates.INSTITUTIONAL_REP_REVIEW ||
+		state === ApplicationStates.DAC_REVIEW;
+
+	if (isEditState) {
+		const result = await service.editApplication({ id, update });
+		return result;
+	} else {
+		const message = `Cannot update application with state ${state}`;
+		console.error(message);
+		return failure(message);
+	}
+};

apps/api/src/db/dbml.ts

@@ -18,7 +18,7 @@
  */
 
 import { pgGenerate } from 'drizzle-dbml-generator'; // Using Postgres for this example
-import * as schema from '../../drizzle/schema.js';
+import * as schema from './schemas/index.js';
 
 const out = './src/db/schema.dbml';
 const relational = true;

apps/api/src/db/index.ts

@@ -22,9 +22,17 @@ import { setStatus, Status } from '../app-health.js';
 
 export type PostgresDb = ReturnType<typeof drizzle>;
 
+let pgDatabase: PostgresDb;
+
+export const getDbInstance = (): PostgresDb => {
+	if (!pgDatabase) throw new Error('Not connected to Postgres database');
+	return pgDatabase;
+};
+
 export const connectToDb = (connectionString: string): PostgresDb => {
 	try {
 		const db = drizzle(connectionString);
+		pgDatabase = db;
 
 		setStatus('db', { status: Status.OK });
 		return db;

apps/api/src/db/schema.dbml

@@ -107,9 +107,9 @@ table applications {
   state application_states [not null]
   created_at timestamp [not null, default: `now()`]
   approved_at timestamp
+  updated_at timestamp
   expires_at timestamp
   contents bigint
-  updated_at timestamp
 }
 
 table collaborators {
@@ -132,6 +132,7 @@ table files {
   type file_types [not null]
   submitter_user_id varchar(100) [not null]
   submitted_at timestamp [not null]
+  content bytea [not null]
   filename varchar(255)
 }
 
@@ -150,4 +151,20 @@ table revision_requests {
   project_notes text
   requested_studies_approved boolean [not null]
   requested_studies_notes text
-}
+}
+
+ref: actions.application_id - applications.id
+
+ref: actions.revisions_request_id > revision_requests.id
+
+ref: agreements.application_id > application_contents.application_id
+
+ref: applications.contents - application_contents.id
+
+ref: application_contents.signed_pdf - files.id
+
+ref: collaborators.application_id > application_contents.application_id
+
+ref: files.application_id - applications.id
+
+ref: revision_requests.application_id > application_contents.id