Merge pull request #10 from papaemmelab/add-file-endpoint

🗂️ Add endpoint for file annotation

.github/workflows/deploy.yml

@@ -0,0 +1,34 @@
+name: Deploy to AWS Lambda using Serverless
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Node.js
+      uses: actions/setup-node@v2
+      with:
+        node-version: 18
+
+    - name: Install dependencies
+      run: npm ci
+
+    - name: Build and Compile
+      run: npm build
+
+    - name: Run Tests
+      run: npm test
+
+    - name: Deploy
+      run: npx serverless deploy
+      env:
+        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}

.gitignore

@@ -9,4 +9,7 @@ test/data/*-out.*
 test.csv
 
 # Serverless artifacts
-.serverless
+.serverless
+
+# API uploads
+uploads

README.md

@@ -21,7 +21,7 @@ API and CLI of the Molecular International Prognostic Scoring System (IPSS-M) fo
 
 - [📖 IPSS-M Publication](#page_with_curl-ipss-m-publication)
 - [🚀 API Usage](#rocket-api-usage)
-- [👾 CLI Usage](#alien-cli-usage)
+- [🤖 CLI Usage](#robot-cli-usage)
   - [🔥 Using it as a node/javascript package](#fire-using-it-as-a-nodejavascript-package)
     - [💥 IPSS-M](#boom-ipss-m)
     - [⚡️ IPSS-R and IPSS-R (Age adjusted)](#zap-ipss-r-and-ipss-r-age-adjusted)
@@ -139,7 +139,7 @@ $ curl \
 }
 ```
 
-## :alien: CLI Usage
+## :robot: CLI Usage
 
 You can use the command line interface to annotate a file with patients, where each row is a patient and each column is a variable.
 

openapi.yml

@@ -47,6 +47,31 @@ paths:
                 $ref: '#/components/schemas/IpssrResponse'
         '500':
           description: An error occurred while calculating IPSS-R risk score
+  /annotateFile:
+    post:
+      summary: Annotate a file with patients, with IPSS-M and IPSS-R risk scores.
+      requestBody:
+        required: true
+        content:
+          multipart/form-data:
+            schema:
+              type: object
+              properties:
+                file:
+                  type: string
+                  format: binary
+                  description: csv/tsv or excel file to be annotated. One patient per row.
+      responses:
+        '200':
+          description: Successful operation. Stream the annotated file as CSV.
+          content:
+            text/plain:
+              schema:
+                type: string
+        '400':
+          description: Bad request
+        '500':
+          description: An error occurred while annotating the file.
 components:
   schemas:
     Clinical:

package.json

@@ -43,10 +43,12 @@
     "vitest": "^0.34.4"
   },
   "dependencies": {
+    "@types/multer": "^1.4.11",
     "exceljs": "^4.3.0",
     "express": "^4.18.2",
     "ipssm": "^1.0.4",
     "joi": "^17.11.0",
+    "multer": "^1.4.5-lts.1",
     "papaparse": "^5.4.1",
     "serverless-http": "^3.2.0",
     "yargs": "^17.7.2"