Merge pull request #7 from papaemmelab/add-typescript

🛠  Add typescript

.github/workflows/cli-test.yml

@@ -0,0 +1,37 @@
+name: Can be run as CLI
+
+on: [push]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Use Node.js
+      uses: actions/setup-node@v2
+      with:
+        node-version: '18.x'
+
+    - name: Install dependencies
+      run: npm ci
+
+    - name: Build
+      run: npm run build
+
+    - name: Install CLI globally
+      run: npm install -g .
+
+    - name: Test CLI
+      run: |
+        # Run the CLI with the example file
+        OUTPUT=$(ipssm test/data/IPSSMexample.csv test.csv)
+        echo "$OUTPUT"
+        
+        # Check the stout for the expected output
+        if ! echo "$OUTPUT" | grep -q "File annotated successfully."; then
+            echo "CLI execution didn't work"
+            exit 1
+        fi

.github/workflows/risk-scores-test.yml

@@ -1,18 +1,14 @@
 name: Compute IPSS-M and IPSS-M Risks on IWG-PM Cohort (Bernard et al, 2022 NJEM Evid)
 
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
+on: [push]
 
 jobs:
   build:
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        node-version: [ 14.x ]
+        node-version: [ 18.x ]
 
     steps:
     - uses: actions/checkout@v2

.gitignore

@@ -1,3 +1,9 @@
 # Node modules
 node_modules
-test/data/*-out.*
+
+# Compiled JS files
+dist
+
+# Data test files
+test/data/*-out.*
+test.csv

package.json

@@ -3,15 +3,16 @@
   "version": "1.0.4",
   "description": "Javascript Package for the Molecular International Prognostic Scoring System (IPSS-M) for Myelodysplastic Syndromes.",
   "main": "index.js",
-  "type": "module",
+  "type": "commonjs",
   "bin": {
-    "ipssm": "./bin/cli.js"
+    "ipssm": "./dist/cli.js"
   },
   "directories": {
     "test": "test"
   },
   "scripts": {
-    "test": "vitest"
+    "test": "vitest",
+    "build": "tsc"
   },
   "repository": {
     "type": "git",
@@ -30,10 +31,15 @@
   },
   "homepage": "https://github.com/papaemmelab/ipssm-js#readme",
   "devDependencies": {
+    "@types/node": "^20.10.4",
+    "@types/papaparse": "^5.3.14",
+    "@types/yargs": "^17.0.32",
+    "typescript": "^5.3.3",
     "vitest": "^0.34.4"
   },
   "dependencies": {
     "exceljs": "^4.3.0",
+    "ipssm": "^1.0.4",
     "papaparse": "^5.4.1",
     "yargs": "^17.7.2"
   }

bin/cli.js → src/cli.ts

@@ -2,13 +2,13 @@
 
 import yargs from 'yargs'
 import { hideBin } from 'yargs/helpers'
-import { annotateFile } from '../index.js'
+import { annotateFile } from './index'
 
 const argv = yargs(hideBin(process.argv))
   .usage('Annotate file with IPSS-M and IPSS-R.\n\nUsage: $0 <inputFile> <outputFile>')
   .command(
     '$0 <inputFile> <outputFile>', 
-    '',
+    'Annotate with IPSS-M and IPSS-R a file with patients.',
     (yargs) => {
       yargs
         .positional('inputFile', {
@@ -27,13 +27,14 @@ const argv = yargs(hideBin(process.argv))
   .example('$0 in.csv out.csv', 'annotate a csv file.')
   .help('h')
   .alias('h', 'help')
-  .argv
+  .argv;
 
 (async () => {
   try {
+    // @ts-ignore
     await annotateFile(argv.inputFile, argv.outputFile)
     console.log('File annotated successfully.')
   } catch (error) {
-    console.error('Error annotating file:', error.message)
+    console.error('Error annotating file:', (error as Error).message)
   }
 })()

index.js → src/index.ts

@@ -1,21 +1,22 @@
-import { processInputs } from './utils/preprocess.js'
-import { computeIpssm, computeIpssr as ipssr } from './utils/risk.js'
-import { parseCsv, parseXlsx, writeCsv, writeXlsx } from './utils/parseFile.js'
+import { PatientInput, PatientOutput, IpssmScores, PatientForIpssr, CsvData } from './types'
+import { processInputs } from './utils/preprocess'
+import { computeIpssm, computeIpssr as ipssr } from './utils/risk'
+import { parseCsv, parseXlsx, writeCsv, writeXlsx } from './utils/parseFile'
 
 // IPSS-M risk score method
-const ipssm = (patientInput) => {
+const ipssm = (patientInput: PatientInput): IpssmScores => {
   const processed = processInputs(patientInput)
   return computeIpssm(processed)
 }
 
 // IPSS-M, IPSS-R, and IPSS-RA risks score from a csv/xlsx file method
-const annotateFile = async (inputFile, outputFile, skipIpssr=false) => {
+const annotateFile = async (inputFile: string, outputFile: string, skipIpssr: boolean = false): Promise<void> => {
 
   if (!inputFile || !outputFile) {
     throw new Error('Input and output files are required')
   }
 
-  let patients = []
+  let patients: PatientInput[] = []
   if (inputFile.endsWith('.csv') || inputFile.endsWith('.tsv')) {
     patients = await parseCsv(inputFile)
   } else if (inputFile.endsWith('.xlsx')) {
@@ -24,10 +25,11 @@ const annotateFile = async (inputFile, outputFile, skipIpssr=false) => {
     throw new Error('File type not supported')
   }
 
-  const annotatedPatients = patients.map((patient) => {
+  const annotatedPatients: PatientOutput[] = patients.map((patient) => {
+    // Calculate IPSS-M and add to patient object
     const ipssmResult = ipssm(patient)
-    // Add IPSS-M results to patient object
-    patient = {
+
+    let annotatedPatient: PatientOutput = {
       ...patient,
       IPSSM_SCORE: ipssmResult.means.riskScore,
       IPSSM_CAT: ipssmResult.means.riskCat,
@@ -37,27 +39,29 @@ const annotateFile = async (inputFile, outputFile, skipIpssr=false) => {
       IPSSM_CAT_WORST: ipssmResult.worst.riskCat,
     }
 
-    if (!skipIpssr) {
-      const ipssrResult = ipssr({
+    if (!skipIpssr && patient.ANC !== undefined && patient.ANC !== null) {
+      // Calculate IPSS-R and add to patient object
+      const data: PatientForIpssr = {
+        bmblast: patient.BM_BLAST,
         hb: patient.HB,
-        anc: patient.ANC,
         plt: patient.PLT,
-        bmblast: patient.BM_BLAST,
+        anc: patient.ANC,
         cytoIpssr: patient.CYTO_IPSSR,
         age: patient.AGE,
-      })
+      }
+
+      const ipssrResult = ipssr(data)
 
-      // Add IPSS-R results to patient object
-      patient = {
-        ...patient,
+      annotatedPatient = {
+        ...annotatedPatient,
         IPSSR_SCORE: ipssrResult.IPSSR_SCORE,
-        IPSSR_CAT: ipssrResult.IPSSR,
+        IPSSR_CAT: ipssrResult.IPSSR_CAT,
         IPSSRA_SCORE: ipssrResult.IPSSRA_SCORE,
-        IPSSRA_CAT: ipssrResult.IPSSRA,
+        IPSSRA_CAT: ipssrResult.IPSSRA_CAT,
       }
     }
 
-    return patient
+    return annotatedPatient
   })
 
   // Create new csv file with annotated patients