rxome-generator 0.1.1 → 0.1.4

package/README.md

@@ -1,10 +1,11 @@
-# rxome-qrcode-generator
-Generates QR codes containing medical information for use with the RxOME database.
-**Right now, it works only with the test API**
+# FindMe2Care (RxOME) QR-code generator
+Generates QR codes containing medical information for use with the FindMe2Care database
+(formerly called RxOME).
+**Right now, it works only with the test API (-t, Coder.TESTAPI)**
 
 ## LICENSE
 
-Copyright (c) 2022 MGZ-Tech GmbH, GeneTalk GmbH
+Copyright (c) 2022 MGZ-Tech GmbH
 
 All rights reserved, unauthorized use prohibited.
 
@@ -32,14 +33,19 @@ In case the patient already has a pseudonym that will be used for the QR code,
 the known pseudonym can be specified in the MetaData section of the input JSON data. 
 Additionally, the command line tool
 offers a command line argument, `-p`, for specifying a known pseudonym.
+Note that this pseudonym must be a valid RxOME pseudonym, that is, it has to be generated by
+RxOME for a previous medical statement. Using an arbitrary pseudonym will render the 
+generated QR-Code useless, as it cannot be processed by RxOME.
 
 By default, the keywords in the JSON file are expected to be noted in camelCase. However, the tool
 can convert snake_case to camelCase (command line: -s, library: function convertToCamelCase).
 
+## Installation
+> `npm install rxome-generator`
 
 ## Basic Usage
 
-###Command Line Tool
+### Command Line Tool
 
 Generate a QR code *inputfile*.png from a JSON file *inputfile*.json containing all medical data in PhenoPacket format, meta data and credentials (using camelCase for keywords):
 
@@ -48,7 +54,7 @@ Generate a QR code *inputfile*.png from a JSON file *inputfile*.json containing
 For detailed descriptions see 
 > `rxcode g --help`
 
-###Library Functions
+### Library Functions
 Import the library with
 > `const Coder = require( 'rxome-generator' );`
 
@@ -101,7 +107,8 @@ Pleace specify *either* a file containing the API access key (keyFile, -k)
 *or* the key itself (key, -s).
 
 When a pseudonym is given (either in the meta data or with command line option `-P`), 
-the QR code will be generated using this pseudonym. Otherwise, a new one will be 
+the QR code will be generated using this pseudonym (this must be a valid/known RxOME
+pseudonym, see introduction). Otherwise, a new one will be 
 fetched from the server. In both cases, the
 pseudonym used will be part of the output for futher processing or storing.
 
@@ -110,7 +117,7 @@ pseudonym used will be part of the output for futher processing or storing.
   ...
   metaData: {
     ...
-     pseudonym: 'anonymous' 
+     pseudonym: '19T5K7042' 
   }
   credentials: {
     keyId: <lab-id/key-id, corresponding to private key>
@@ -179,20 +186,21 @@ The type of genetic test performed to obtain a variant can be specified in an ex
         "acmgPathogenicityClassification": "Pathogenic",
         "variationDescriptor": {
           "geneContext": {
-          "expressions": [
-            {
-              "syntax": "hgvs.c",
-              "value": "NM_017837.4(PIGV):c.1022C>A (p.Ala341Glu)"
-            }
-          ],
-          "allelicState": {
-            "id": "GENO_0000136"
-          },
-          "extensions": [
-            {
-              "name": "Single gene sequencing"
-            }
-          ]
+            "expressions": [
+              {
+                "syntax": "hgvs.c",
+                "value": "NM_017837.4(PIGV):c.1022C>A (p.Ala341Glu)"
+              }
+            ],
+            "allelicState": {
+              "id": "GENO_0000136"
+            },
+            "extensions": [
+              {
+                "name": "Single gene sequencing"
+              }
+            ]
+          }
         }
       }
     }
@@ -289,7 +297,7 @@ Options:
   -u, --user <user string>  API access user (default: credentials.user 
                             or metaData.submittedBy or info@rxome.net)
   -c, --created <date>      Date (default: input file, metaData.created)
-  -l, --lab <lab>           Laboratory name (default: input file, metaData.createdBy)
+  -l, --lab <lab>           Laboratory name (default: input file, metaData.createdBy or lab name stored in the user account)
   -e, --email <email>       Laboratory email (default: input file, metaData.submittedBy)
   -S, --snake               Read payload formatted in snake_case (default: camelCase)
   -t, --test                Use test API instead of production API
@@ -319,6 +327,11 @@ rxcode g -t -o qrcode.png demos/demo_data_full.json
 
 <img src="qrcode.png" width="400">
 
+## Testing
+Codes generated by the test API (i.e., with the `-t` switch or `API=Coder.TESTAPI`) can be decoded online using the following tool:
+
+Todo: URL Code-Reader Demo
+
 ## Debugging
 To check the connection to the API on RxOME server API use
 

package/demos/demo_data_full.yaml

@@ -0,0 +1,100 @@
+  "subject": {
+    "id": "proband A",
+    "dateOfBirth": "1994-01-01T00:00:00Z",
+    "sex": "FEMALE"
+  },
+  "phenotypicFeatures": 
+[HPOin]
+HP:0030084
+HP:0000555
+HP:0000486
+HP:0000541
+HP:0084369
+HP:0112358
+HP:0000145
+HP:1234567
+HP:9876543
+HP:5678912
+
+[HPOex]
+HP:0031360
+HP:0001234
+
+  "interpretations": [
+    {
+      "id": "interpretation.id",
+      "progressStatus": "SOLVED",
+      "diagnosis": {
+        "disease": {
+          "id": "OMIM:263750"
+        },
+        "genomicInterpretations": [
+          {
+            "variantInterpretation": {
+              "acmgPathogenicityClassification": "PATHOGENIC",
+              "variationDescriptor": {
+                "geneContext": {
+                  "valueId": "HGNC:9884",
+                  "symbol": "RB1"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_000321.2:c.958C>T"
+                  }
+                ],
+                "allelicState": {
+                  "id": "GENO:0000135"
+                },
+                "extensions": [
+                  {
+                    "name": "test-type",
+                    "value": "Exome, short read"
+                  }
+                ]
+              }
+            }
+          },
+          {
+            "variantInterpretation": {
+              "acmgPathogenicityClassification": "LIKELY_PATHOGENIC",
+              "variationDescriptor": {
+                "geneContext": {
+                  "valueId": "HGNC:9884",
+                  "symbol": "RB1"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_000321.2:c.1234A>G"
+                  }
+                ],
+                "allelicState": {
+                  "label": "heterozygous"
+                },
+                "extensions": [
+                  {
+                    "name": "test-type",
+                    "value": "Exome, short read"
+                  }
+                ]
+              }
+            }
+          }
+        ]
+      }
+    }
+  ],
+  "metaData": {
+    "created": "2021-05-14T10:35:00Z",
+    "createdBy": "mgz",
+    "submittedBy": "a_clinician@mgz-muenchen.de",
+    "phenopacketSchemaVersion": "2.0",
+    "pseudonym": "_DEMO_PSEUDONYM_"
+  },
+  "credentials": {
+    "key": "lBSkSxe/+UBWOeF5OJdQgf9qZhiI85hYE6yJCuWjCNk=",
+    "keyId": "rxome",
+    "user": "a_clinician@mgz-muenchen.de"
+  }
+}

package/index.js

@@ -1,3 +1,3 @@
-export * from './lib/rxome-api';
-export * from './lib/rxome-api-demo';
-export * from './lib/rxome-generator';
+export * from './lib/rxome-api.cjs';
+export * from './lib/rxome-api-demo.cjs';
+export * from './lib/rxome-generator.cjs';

package/lib/{rxome-api.js → rxome-api.cjs}

@@ -4,8 +4,8 @@ const Protobuf = require('protobufjs');
 const { stringify } = require('querystring');
 //const BASE64 = require('@protobufjs/base64')
 
-const API = 'https://www.rxome.net';
-const TESTAPI = 'http://stage.rxome.net';
+const API = 'https://app.findme2care.de';
+const TESTAPI = 'https://stage.findme2care.de';
 const APIENTRY = 'api/v1';
 const VSTR = 'API1.0'
 const IS_DEMO = '_DEMO_PSEUDONYM_';
@@ -74,6 +74,8 @@ catch (e) {
  }
 }
 
+exports.readSigKey = readSigKey;
+
 /************************************************************************************/
 
 exports.signData = async( keyId, user, keyB64, created, debug = false ) => {

package/lib/{rxome-generator.js → rxome-generator.cjs}

@@ -10,7 +10,7 @@ const PhenoPacketDescriptor = require("./phenopackets.json");
 
 //const { constants } = require('buffer');
 
-const RxAPI= require('./rxome-api');
+const RxAPI= require('./rxome-api.cjs');
 
 const apiVer = '1.0';
 const RXAPI = RxAPI.API;
@@ -55,7 +55,7 @@ try {
     const {qrData, pseudonym} = await exports.prepareQR( data, api, apiEntry );
     //const base64Data = qr_code.replace(/^data:image\/png;base64,/, "");
     //FS.writeFile(filename, base64Data, 'base64', (err) => {console.log(err)} );
-    QRCode.toFile( filename, qrData, { type: 'png'} )
+    QRCode.toFile( filename, JSON.stringify( qrData ), { type: 'png'} )
     return pseudonym
   }
 }
@@ -291,13 +291,12 @@ exports.prepareQR = async ( data, api = RXAPI, apiEntry = APIENTRY ) => {
   const key = await this.fetchKey( credentials, metaData.pseudonym || '', api, false, apiEntry );
 
   // check:
-  const buff = RxAPI.base64ToBuffer( base64Medical );
-  const pheno = exports.decodePhenoPacket( buff );
+  //const buff = RxAPI.base64ToBuffer( base64Medical );
+  //const pheno = exports.decodePhenoPacket( buff );
   //const medicalDeciphered = JSON.parse( JSON.stringify( pheno ));
   //console.log( JSON.stringify(medicalDeciphered,' ', 2 ))
 
   const cipher = await exports.encode( key.key, base64Medical );
-  //console.log( 'Cipher:', JSON.stringify(cipher) );
 
   //delete metaData.pseudonym;
   const newMetaData = Object.fromEntries( 
@@ -305,17 +304,18 @@ exports.prepareQR = async ( data, api = RXAPI, apiEntry = APIENTRY ) => {
   )
 
   const qrData = {
+    createdBy: key.lab,
     ...newMetaData,
+    labid: key.lab_id,
     keyver: key.version,
     apiver: apiVer,
     pseudonym: key.pseudonym,
     payload: cipher.toString()
   }
-  // console.log( qrData );
-  // console.log( "QR-Data " , JSON.stringify( qrData ).length );
+  console.log( "[QR Generator lib ]", qrData, "\nLength: ", JSON.stringify( qrData ).length  );
 
   return {
-    qrData: JSON.stringify( qrData ),
+    qrData: qrData,
     pseudonym: key.pseudonym
   }
 }
@@ -324,7 +324,7 @@ exports.prepareQR = async ( data, api = RXAPI, apiEntry = APIENTRY ) => {
 exports.makeQR = async ( data, api = RXAPI, apiEntry = APIENTRY ) => {
   const {qrData, pseudonym} = await exports.prepareQR( data, api, apiEntry );
   return {
-    qr_code: await QRCode.toDataURL( qrData ),
+    qr_code: await QRCode.toDataURL( JSON.stringify( qrData )),
     pseudonym: pseudonym,
     qr_data: qrData
   }

package/package.json

@@ -1,9 +1,9 @@
 {
   "name": "rxome-generator",
-  "version": "0.1.1",
+  "version": "0.1.4",
   "description": "Generates QR codes containing medical information for use with RxOME database.",
   "main": "index.js",
-  "type": "commonjs",
+  "type": "module",
   "scripts": {
     "test": "jest --verbose",
     "testcoder": "jest --verbose -t 'Coder'",
@@ -24,7 +24,6 @@
     "phenopacket"
   ],
   "author": "Tom Kamphans",
-  "license": "MIT",
   "license" : "SEE LICENSE IN README.md",
   "bugs": {
     "url": "https://github.com/GeneTalkTK/rxome-qrcode-generator/issues"

package/{rxcode → rxcode.js}

@@ -1,13 +1,24 @@
 #!/usr/bin/env node
 
-const Coder = require( './lib/rxome-generator' );
-const ApiDemo = require( './lib/rxome-api-demo' );
-const RxAPI = require( './lib/rxome-api' );
-const { program } = require('commander');
-
-const FS = require( 'fs' );
-const Path = require('path');
-const { cp } = require('fs/promises');
+import * as FS from 'fs';
+// const Coder = require( './lib/rxome-generator' );
+import * as Coder from './lib/rxome-generator.cjs';
+import * as ApiDemo from './lib/rxome-api-demo.cjs' ;
+import * as RxAPI from './lib/rxome-api.cjs';
+
+import { program } from 'commander';
+import * as Path from 'path';
+// import { cp } from 'fs/promises';
+
+// const FS = require( 'fs' );
+// const Coder = require( './lib/rxome-generator' );
+// const ApiDemo = require( './lib/rxome-api-demo' );
+// const RxAPI = require( './lib/rxome-api' );
+// const { program } = require('commander');
+
+// const Path = require('path');
+// const { cp } = require('fs/promises');
+
 //const TXT = require( './assets/scripts/modules/texte.js')
 
 const DEMO_CREDENTIALS = ApiDemo.DEMO_CREDENTIALS
@@ -42,7 +53,7 @@ Output: prints the given or new pseudonym.`)
   .option('-s, --key <key string>', 'API access key (default: input file, credentials.key)')
   .option('-u, --user <user string>', 'API access user (default: credentials.user or metaData.submittedBy or info@rxome.net)')
   .option('-c, --created <date>', 'Date (default: input file, metaData.created)')
-  .option('-l, --lab <lab>', 'Laboratory name (default: input file, metaData.createdBy)')
+  .option('-l, --lab <lab>', 'Laboratory name (default: input file, metaData.createdBy or lab name stored in the user account)')
   .option('-e, --email <email>', 'Laboratory email (default: input file, metaData.submittedBy)')
   .option('-S, --snake', 'Read payload formatted in snake_case (default: camelCase)')
   .option('-t, --test', 'Use test API instead of production API')
@@ -119,7 +130,7 @@ program.command('preprocess')
   .option('-o, --output <output file>', 'Output JSON file (default: stdout)')
   .option('-C, --case', 'Apply case style converter from snake_case to camelCase')
   .option('-w, --whitelist', 'Apply whitelist filtering (remove unnecessary sections)')
-  .option('-s, --sanitize', 'A        pply sanitizing step (remove common mistakes)')
+  .option('-s, --sanitize', 'Apply sanitizing step (remove common mistakes)')
   .option('-c, --compress', 'Compact HPO term list')
   .action( async (inputfile, options) => {
     let data = JSON.parse(FS.readFileSync( inputfile || '/dev/stdin' ));
@@ -160,7 +171,7 @@ program.command('apikeys')
 program.command('ping')
   .summary('Ping API/check API credentials')
   .alias('P')
-  .argument('[id]', 'API access key ID (default: rxome)')
+  .argument('id', 'API access key ID')
   .argument('key', 'API access key')
   .option('-t, --test', 'Connect to test API')
   .option('-L, --localhost', 'Connect to localhost API')

package/rxcode.test.js

@@ -42,7 +42,9 @@ async function execCmd( cmd ) {
 
 describe('CmdLine generate', () => {
   test('generates a qr code from demo data', () => {
-    FS.rmSync( '__TESTSUITE_IMG.png' );
+    if ( FS.existsSync( '__TESTSUITE_IMG.png' )) {
+      FS.rmSync( '__TESTSUITE_IMG.png' );
+    }
     execCmd( 'rxcode g -t -o __TESTSUITE_IMG.png demos/demo_data_full.json' )
     // execCmd( 'rxcode g -L -o __TESTSUITE_IMG.png demos/demo_data_full.json' )
     .then( res => {
@@ -189,4 +191,4 @@ rxcode d -j rxome.decrypt.json
 rxcode d -j rxome.decrypt.json
 rxcode d -j < rxome.decrypt
 
-*/
+*/

package/demos/demo.private.key

@@ -1,17 +0,0 @@
------BEGIN PGP PRIVATE KEY BLOCK-----
-
-xYYEY8BGEhYJKwYBBAHaRw8BAQdAegfXQCYheo+FJXoIY0qPYAeP+67inq0u
-0AZE8yrEOJ3+CQMIQ3S9CuD3PUTgKF/q8xafzIvLlEuLTCAInll8oSg9zb+2
-MTFp3EEOZifKIA9YY1ujro17MzR3p/Bfdt2ayo+Pcxq0g9JNgrHfzUeIuTxG
-xM0VZGVtbyA8aW5mb0ByeG9tZS5uZXQ+wowEEBYKAB0FAmPARhIECwkHCAMV
-CAoEFgACAQIZAQIbAwIeAQAhCRABSM3I8Z0TohYhBGfCy2DdehZ+Frs2fgFI
-zcjxnROi9ukA/RmZoF4VKDJouTjxPxCEzIqbM+9ZfHFyLmkr9EtMR0D+AP9o
-5Rauo9ium/t88qxfeCpcPTULZ4qu5GBkBHg9XCYrAceLBGPARhISCisGAQQB
-l1UBBQEBB0A82B97nnZ60gGWR2v8mn319Yb8AdKGD85ier7hwSe/OgMBCAf+
-CQMIUzDpTTSoyZrg8AVwyRZVmrXQbE9mzRtcy2sM3fbNyZCW44Rz0rgxwC+z
-1EfRC442wQSDs6pat0eeBX1Eh6vqENIRsCQNK426BD8XWWLor8J4BBgWCAAJ
-BQJjwEYSAhsMACEJEAFIzcjxnROiFiEEZ8LLYN16Fn4WuzZ+AUjNyPGdE6In
-sAD9GNlDrmnRIz+IP0XGheue6IhMLgzss2TsvRv2K8HQGqsBAIC3k3/T/sCN
-MnR+TVPz/zYEEAbxEEurgfWdn1c8B0AM
-=Sgm6
------END PGP PRIVATE KEY BLOCK-----

package/demos/demo.public.key

@@ -1,13 +0,0 @@
------BEGIN PGP PUBLIC KEY BLOCK-----
-
-xjMEY8BGEhYJKwYBBAHaRw8BAQdAegfXQCYheo+FJXoIY0qPYAeP+67inq0u
-0AZE8yrEOJ3NFWRlbW8gPGluZm9AcnhvbWUubmV0PsKMBBAWCgAdBQJjwEYS
-BAsJBwgDFQgKBBYAAgECGQECGwMCHgEAIQkQAUjNyPGdE6IWIQRnwstg3XoW
-fha7Nn4BSM3I8Z0TovbpAP0ZmaBeFSgyaLk48T8QhMyKmzPvWXxxci5pK/RL
-TEdA/gD/aOUWrqPYrpv7fPKsX3gqXD01C2eKruRgZAR4PVwmKwHOOARjwEYS
-EgorBgEEAZdVAQUBAQdAPNgfe552etIBlkdr/Jp99fWG/AHShg/OYnq+4cEn
-vzoDAQgHwngEGBYIAAkFAmPARhICGwwAIQkQAUjNyPGdE6IWIQRnwstg3XoW
-fha7Nn4BSM3I8Z0ToiewAP0Y2UOuadEjP4g/RcaF657oiEwuDOyzZOy9G/Yr
-wdAaqwEAgLeTf9P+wI0ydH5NU/P/NgQQBvEQS6uB9Z2fVzwHQAw=
-=w+2C
------END PGP PUBLIC KEY BLOCK-----