rxome-generator 0.1.4 → 1.0.1

package/README.TODO

@@ -0,0 +1,4 @@
+## 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

package/README.md

@@ -5,7 +5,7 @@ Generates QR codes containing medical information for use with the FindMe2Care d
 
 ## LICENSE
 
-Copyright (c) 2022 MGZ-Tech GmbH
+Copyright (c) 2023 RxOME GmbH
 
 All rights reserved, unauthorized use prohibited.
 
@@ -67,7 +67,8 @@ The following two async library functions generate QR codes:
 
 This function creates the QR code from the given data and writes it as PNG file specified by *filename*. 
 The credentials for accessing the RxOME API (i.e., fetching a pseudonym and the encryption key) have to be
-part of the data object (see below). Returns the pseudonym used to generate the QR code.
+part of the data object (see below). Returns the pseudonym used to generate the QR code and the unencrypted 
+content of the QR code.
 
 > `Coder.makeQR( data, api = RXAPI, apiEntry = APIENTRY )`
 
@@ -76,7 +77,9 @@ Generates a QR code object as Data URL that can be placed on a web page. As abov
 ```
 {
     qr_code: (QR code),
-    pseudonym: (pseudonym used to generate the QR code)
+    pseudonym: (pseudonym used to generate the QR code),
+    qr_data: content of the QR code (with encrypted medical data; i.e., a 1:1 image of the QR code content),
+    qr_content: content of the QR code but with unencrypted medical data for documentation purposes
 }
 ```
 
@@ -239,13 +242,12 @@ are removed. On top level, the following section will be passed over to the QR c
 ### Overview
 
 ```
-RxOME.net QR Code generation tool
+FindMe2care QR Code generation tool
 
 Usage: rxcode [options] [command]
 
 Basic usage: rxcode g <input json file>: generates QR Code with the basefilename of the inputfile.
-Before first use, please generate an API access key (rxcode -k) and deposit the public key 
-on the RxOME server.
+Before first use, please generate an API access key (rxcode -k) and deposit the public key on the FindMe2care server.
 
 
 Options:
@@ -254,20 +256,22 @@ Options:
 
 Commands:
   generate|g [options] [input file]     generate QR Code from PhenoPacket JSON
-  convert|c [options] [input file]      convert case style of keys in JSON files from snake_case 
-                                        to camelCase (and vice versa)
+  convert|c [options] [input file]      convert case style of keys in JSON files from snake_case to camelCase
+                                        (and vice versa)
   preprocess|p [options] [input file]   perform preprocessing steps
   verify|v [input file]                 verify input file against phenopacket schema
   apikeys|k [options] [file prefix]     generate key pair for API access
   ping|P [options] <id> <key>           Ping API/check API credentials
-  encode|e [options] [input file]       encrypt medical payload (just for testing)
-  decode|d [options] [input file]       decode coded message
+  encrypt|e [options] [input file]      encrypt message (just for testing)
+  decrypt|d [options] [input file]      decrypt coded message or medical data
+  data-keys|K [options] [file prefix]   generate key pair for data encryption (see -e, -d; just for testing)
   pheno2proto|E [options] [input file]  encode PhenoPacket to protobuf (just for testing)
   proto2pheno|D [options] [input file]  decode protobuf to PhenoPacket (just for testing)
+  settings|S [options]                  Print current settings
   statistics|s [input file]             print memory consuption for several stages and alternatives
-  rxome-keys [options] [file prefix]    generate key pair for qr code data encryption 
-                                        (just for testing)
   help [command]                        display help for command
+
+Author: Tom Kamphans, GeneTalk GmbH, 2022, (c) 2023 RxOME GmbH
 ```
 
 ### Generating QR codes
@@ -275,7 +279,7 @@ Commands:
 Use the 'g' command for actually generating a QR code:
 
 ```
-RxOME.net QR Code generation tool
+FindMe2care QR Code generation tool
 
 Usage: rxcode generate|g [options] [input file]
 
@@ -285,27 +289,32 @@ The command line arguments precede the data from the JSON input file.
 Output: prints the given or new pseudonym.
 
 Arguments:
-  input file                Input JSON file (default: STDIN)
+  input file                   Input JSON file (default: STDIN)
 
 Options:
-  -o, --output <filename>   Filename for the QR code (default: <inputfile>.png)
-  -p, --pseudonym           Pseudonym for patient, if known. Otherwise a new is generated
-  -i, --keyId <id>          API access ID (default: input file, credentials.keyId 
-                            or metaData.createdBy)
-  -k, --keyFile <filename>  Filename with API access key (default: use -s)
-  -s, --key <key string>    API access key (default: input file, credentials.key)
-  -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 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
-  -D, --debug               Some output for debugging
-  -h, --help                display help for command
+  -o, --output <filename>      Filename for the QR code (default: <inputfile>.png)
+  -p, --pseudonym <pseudonym>  For re-evaluations: pseudonym for patient. Otherwise a new is generated
+                               (default: "")
+  -i, --keyId <id>             API access ID (default: input file, credentials.keyId or metaData.createdBy)
+  -k, --keyFile <filename>     Filename with API access key (default: use -s)
+  -s, --key <key string>       API access key (default: input file, credentials.key)
+  -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 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
+  -L, --localhost              Connect to localhost API
+  -D, --debug                  Some output for debugging
+  -h, --help                   display help for command
+
+Author: Tom Kamphans, GeneTalk GmbH, 2022, (c) 2023 RxOME GmbH
 ```
 
-Writes the pseudonym used to generate the QR code to STDOUT.
+Writes the pseudonym used to generate the QR code to STDOUT. With -D given, this further writes the
+(unencrypted) content of the QR code to STDOUT.
 
 ### Generating API Access Keys
 To communicate with the server API you need access credentials, that is, an id for your lab (the keyId) and a pair of corresponding keys. First, generate a pair of keys with
@@ -316,7 +325,7 @@ rxcode k myLabId
 
 This yields two files: `myLabId.private.apikey` and `myLabId.public.apikey`. Store the 
 private key safely. 
-Create a lab account on `www.rxome.net/lab` and upload the public key to your profile.
+Create a lab account on `app.findme2care.de/generate` and upload the public key to your profile.
 Afterwards, you should be able to access the API (see 'debugging' below).
 
 ## Demo
@@ -327,11 +336,6 @@ 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_without_key.json

@@ -0,0 +1,145 @@
+{
+  "id": "QR-Code ID",
+  "comment": "useful remarks De do do do de da da da",
+  "subject": {
+    "id": "proband A",
+    "dateOfBirth": "1994-01-01T00:00:00Z",
+    "sex": "FEMALE"
+  },
+  "phenotypicFeatures": [
+    {
+      "type": {
+        "id": "HP:0030084"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000555"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000486"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000541"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0084369"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0112358"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000145"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:1234567"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:9876543"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:5678912"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0031360"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001234"
+      },
+      "excluded": true
+    }
+  ],
+  "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_"
+  }
+}

package/lib/rxome-generator.cjs

@@ -52,11 +52,14 @@ try {
   }
  
   exports.writeQR = async ( filename, data, api = RXAPI, apiEntry = APIENTRY ) => {
-    const {qrData, pseudonym} = await exports.prepareQR( data, api, apiEntry );
+    const {qrData, pseudonym, content} = 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, JSON.stringify( qrData ), { type: 'png'} )
-    return pseudonym
+    return {
+      pseudonym: pseudonym,
+      qr_content: content
+    }
   }
 }
 
@@ -291,10 +294,10 @@ 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 medicalDeciphered = JSON.parse( JSON.stringify( pheno ));
-  //console.log( JSON.stringify(medicalDeciphered,' ', 2 ))
+  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 );
 
@@ -309,24 +312,32 @@ exports.prepareQR = async ( data, api = RXAPI, apiEntry = APIENTRY ) => {
     labid: key.lab_id,
     keyver: key.version,
     apiver: apiVer,
-    pseudonym: key.pseudonym,
+    pseudonym: key.pseudonym,    
     payload: cipher.toString()
   }
-  console.log( "[QR Generator lib ]", qrData, "\nLength: ", JSON.stringify( qrData ).length  );
+
+  const qrContent = {
+    ...qrData,
+    payload: medicalDeciphered
+  }
+  // console.log( "[QR Generator lib ]", qrData, "\nLength: ", JSON.stringify( qrData ).length  );
+  // console.log( "[QR Generator lib ]", JSON.stringify(qrContent, 0, 2));
 
   return {
     qrData: qrData,
-    pseudonym: key.pseudonym
+    pseudonym: key.pseudonym,
+    content: qrContent
   }
 }
 
 
 exports.makeQR = async ( data, api = RXAPI, apiEntry = APIENTRY ) => {
-  const {qrData, pseudonym} = await exports.prepareQR( data, api, apiEntry );
+  const {qrData, pseudonym, content} = await exports.prepareQR( data, api, apiEntry );
   return {
     qr_code: await QRCode.toDataURL( JSON.stringify( qrData )),
     pseudonym: pseudonym,
-    qr_data: qrData
+    qr_data: qrData,
+    qr_content: content
   }
 }
 

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "rxome-generator",
-  "version": "0.1.4",
-  "description": "Generates QR codes containing medical information for use with RxOME database.",
+  "version": "1.0.1",
+  "description": "Generates QR codes containing medical information for use with the FindMe2Care platform.",
   "main": "index.js",
   "type": "module",
   "scripts": {
@@ -18,6 +18,7 @@
   },
   "keywords": [
     "RxOME",
+    "FineMe2care",
     "genetics",
     "variants",
     "qr-codes",
@@ -45,6 +46,6 @@
     "json-loader": "^0.5.7"
   },
   "bin": {
-    "rxcode": "./rxcode"
+    "rxcode": "./rxcode.js"
   }
 }

package/rxcode.js

@@ -25,16 +25,17 @@ const DEMO_CREDENTIALS = ApiDemo.DEMO_CREDENTIALS
 const DEMO_PRIVATE_KEY = ApiDemo.CRYPT_PRIVATE_KEY
 const DEMO_PUBLIC_KEY = ApiDemo.CRYPT_PUBLIC_KEY
 
+const VERSION = '1.0.1'
 
 program
   .name('rxcode')
   .description(
 `Basic usage: rxcode g <input json file>: generates QR Code with the basefilename of the inputfile.
-Before first use, please generate an API access key (rxcode -k) and deposit the public key on the RxOME server.
+Before first use, please generate an API access key (rxcode -k) and deposit the public key on the FindMe2care server.
 `)
-  .version('1.0.0')
-  .addHelpText('beforeAll', 'RxOME.net QR Code generation tool\n')
-  .addHelpText('afterAll', '\nAuthor: Tom Kamphans, GeneTalk GmbH, 2022');
+  .version( VERSION )
+  .addHelpText('beforeAll', 'FindMe2care QR Code generation tool\n')
+  .addHelpText('afterAll', '\nAuthor: Tom Kamphans, GeneTalk GmbH, 2022, (c) 2023 RxOME GmbH');
 
 
 program.command('generate')
@@ -47,7 +48,7 @@ The command line arguments precede the data from the JSON input file.
 Output: prints the given or new pseudonym.`)
   .argument('[input file]', 'Input JSON file (default: STDIN)')
   .option('-o, --output <filename>', 'Filename for the QR code (default: <inputfile>.png)')
-  .option('-p, --pseudonym', 'vPseudonym for patient, if known. Otherwise a new is generated', '')
+  .option('-p, --pseudonym <pseudonym>', 'For re-evaluations: pseudonym for patient. Otherwise a new is generated', '')
   .option('-i, --keyId <id>', 'API access ID (default: input file, credentials.keyId or metaData.createdBy)')
   .option('-k, --keyFile <filename>', 'Filename with API access key (default: use -s)')
   .option('-s, --key <key string>', 'API access key (default: input file, credentials.key)')
@@ -93,11 +94,12 @@ Output: prints the given or new pseudonym.`)
       return 1;
     }
 
-    options.debug && console.log( "Data ", qrData );
+    // options.debug && console.log( "Data ", qrData );
   
     const outputfile = options.output || `${Path.basename((inputfile || 'qrcode.json'), '.json')}.png`
-    const psLab = await Coder.writeQR( outputfile, qrData, qrApi );
-    console.log( psLab );
+    const data = await Coder.writeQR( outputfile, qrData, qrApi );
+    console.log( data.pseudonym );
+    options.debug && console.log( JSON.stringify( data.qr_content, 0, 2) );
   });
   
 
@@ -160,7 +162,7 @@ program.command('verify')
 program.command('apikeys')
   .summary('generate key pair for API access')
   .alias('k')
-  .description('Generate key pair. A pair of these keys is necessary to communicate with the rxome API. Keep the private key and deposit the public key on the RxOme server.')
+  .description('Generate key pair. A pair of these keys is necessary to communicate with the FindMe2care API. Keep the private key and deposit the public key on the FindMe2care server.')
   .argument('[file prefix]', 'Prefix for file names (default: rxome)')
   .option('-d, --directory <dir>', 'output directory', '.')
   .action( (prefix, options) => {
@@ -330,6 +332,18 @@ program.command('proto2pheno')
   });
 
 
+program.command('settings')
+  .alias('S')
+  .description('Print current settings')
+  .option('-t, --test', 'Connect to test API')
+  .action( (options) => {
+
+    console.log('This RxOME/FindMe2care QR generator V', VERSION );
+    console.log('Connecting to', options.test ? RxAPI.TESTAPI : RxAPI.API );
+    console.log('API', options.test ? RxAPI.APIENTRY : RxAPI.APIENTRY );
+
+});
+
 program.command('statistics')
 .alias('s')
 .argument('[input file]', 'Input JSON file (default: ./demos/demo_data_full.json)')
@@ -392,7 +406,7 @@ program.command('statistics')
   //   payload: cipherBin.toString()
   // }
   // console.log( "QR-Data: ", JSON.stringify( qrData ).length )
-  //const ps_lab = await Coder.writeQR( "stat.png", qrData, RxAPI.TESTAPI );
+  //const { pseudonym, qr_content } = await Coder.writeQR( "stat.png", qrData, RxAPI.TESTAPI );
   
 
   console.log("===================================================================");
@@ -410,7 +424,7 @@ program.command('statistics')
 //   // const fileName = options.input || './demos/demo_data_full.json';
 //   // //file = inputfile || '/dev/stdin'
 //   // const data = JSON.parse( FS.readFileSync( fileName ));
-//   // // const ps_lab = await Coder.writeQR( "ZZZtest.png", data, RxAPI.TESTAPI );
+//   // // const { pseudonym, qr_content } = await Coder.writeQR( "ZZZtest.png", data, RxAPI.TESTAPI );
 //   // console.log( data );
 //   // console.log( Coder.whiteListPhenoPacket( data ) );
 //   // console.log( {