rxome-generator 0.1.0 → 0.1.3

package/-

@@ -0,0 +1 @@
+answer to life the universe and everything

package/README.md

@@ -1,7 +1,15 @@
-# rxome-qrcode-generator
-Generates QR codes containing medical information for use with the RxOME database.
+# 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)**
 
-**Right now, it works only with the test API**
+## LICENSE
+
+Copyright (c) 2022 MGZ-Tech GmbH
+
+All rights reserved, unauthorized use prohibited.
+
+## Purpose
 
 This package offers a JavaScript library for generating QR codes from medical data as well as
 a command line tool as front end to this library. Both expect the medical data in JSON format
@@ -25,14 +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):
 
@@ -41,7 +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' );`
 
@@ -94,7 +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.
 
@@ -103,7 +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>
@@ -172,20 +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"
+              }
+            ]
+          }
         }
       }
     }
@@ -195,7 +210,7 @@ The type of genetic test performed to obtain a variant can be specified in an ex
 
 ### Additional Remarks
 
-Additional remarks can be specified in a *comment* field in the top level:
+Additional remarks can be specified in a *comment* field on the top level:
 
 ```
 {
@@ -282,7 +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
@@ -312,6 +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.json

@@ -139,11 +139,12 @@
     "created": "2021-05-14T10:35:00Z",
     "createdBy": "mgz",
     "submittedBy": "a_clinician@mgz-muenchen.de",
-    "phenopacketSchemaVersion": "2.0"
+    "phenopacketSchemaVersion": "2.0",
+    "pseudonym": "_DEMO_PSEUDONYM_"
   },
   "credentials": {
-    "key": "QhcoRruGBVP39XCh8BujCE+q42qCRy/tu2CQ4YmRBgg=",
-    "keyId": "mgz",
+    "key": "lBSkSxe/+UBWOeF5OJdQgf9qZhiI85hYE6yJCuWjCNk=",
+    "keyId": "rxome",
     "user": "a_clinician@mgz-muenchen.de"
   }
 }

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/demos/demo_data_full_compressed.json

@@ -51,7 +51,8 @@
     "created": "2021-05-14T10:35:00Z",
     "createdBy": "mgz",
     "submittedBy": "a_clinician@mgz-muenchen.de",
-    "phenopacketSchemaVersion": "2.0"
+    "phenopacketSchemaVersion": "2.0",
+    "pseudonym": "_DEMO_PSEUDONYM_"
   },
   "compressedFeatures": {
     "includes": [
@@ -69,8 +70,8 @@
     "excludes": ["HP:0031360", "HP:0001234"]
   },
   "credentials": {
-    "key": "QhcoRruGBVP39XCh8BujCE+q42qCRy/tu2CQ4YmRBgg=",
-    "keyId": "mgz",
+    "key": "lBSkSxe/+UBWOeF5OJdQgf9qZhiI85hYE6yJCuWjCNk=",
+    "keyId": "rxome",
     "user": "a_clinician@mgz-muenchen.de"
   }
 }

package/demos/demo_decrypt.json

@@ -0,0 +1 @@
+{"key":"\n-----BEGIN PGP PRIVATE KEY BLOCK-----\n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\nMnR+TVPz/zYEEAbxEEurgfWdn1c8B0AM\n=Sgm6\n-----END PGP PRIVATE KEY BLOCK-----\n","cipher":"\n-----BEGIN PGP MESSAGE-----\n\nwV4DwTe9/0b1zzgSAQdAxe4Phva3n19MInlPhQS4OxG78y+3mTsNHVfsk5OF\nnGAwld5yaBCzLoudwGLQ17qIkABl9rhONf8VJMNoTOZOf8nPoouCKdXxktv7\ndG1wvV2s0lsBvUBUmaOzix1hEF6YeUr7mfc+MBBt/2gfoyT4Kujgrg25YoZ6\nqUgqga2eSZ6O+OhyjuFo3rZVXl1MFY6lfu+X+i4cCE2VWiAQOwVNnqFdY9FF\nuOPuzhz7UstK\n=KKxC\n-----END PGP MESSAGE-----\n"}

package/demos/demo_encrypt.json

@@ -0,0 +1 @@
+{"key":"\n-----BEGIN PGP PUBLIC KEY BLOCK-----\n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\nwdAaqwEAgLeTf9P+wI0ydH5NU/P/NgQQBvEQS6uB9Z2fVzwHQAw=\n=w+2C\n-----END PGP PUBLIC KEY BLOCK-----\n","message":"answer to life the universe and everything"}

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-demo.js → rxome-api-demo.cjs}

@@ -35,8 +35,10 @@ VBvfFVhJAPoDhf5yKxJ+oJV3ls8IyoBBAeMeAYFBrA8r89fKT0nFBA==
 `
 
 const R_ID = 'rxome';
-const R_PRIVATE_KEY = 'NamaTB+xwDFxtkQyBBkjRr5GEaXNtCw/G4qydnhQk5Y=';
-const R_PUBLIC_KEY  = 'XvbhLWKbA1wfKsx3B7FKQuDQsZTZ/dMXWiD1MehBxZg=';
+const R_PUBLIC_KEY =  '60uReCXTn7KTEIExM4KveKstBGI3TaSrQss4biaesNs=';
+const R_PRIVATE_KEY = 'lBSkSxe/+UBWOeF5OJdQgf9qZhiI85hYE6yJCuWjCNk=';
+// const R_PRIVATE_KEY = 'NamaTB+xwDFxtkQyBBkjRr5GEaXNtCw/G4qydnhQk5Y=';
+// const R_PUBLIC_KEY  = 'XvbhLWKbA1wfKsx3B7FKQuDQsZTZ/dMXWiD1MehBxZg=';
 
 const J_ID = 'rxomej'
 const J_PRIVATE_KEY = 'QhcoRruGBVP39XCh8BujCE+q42qCRy/tu2CQ4YmRBgg=';

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

@@ -1,16 +1,20 @@
 const Axios = require( 'axios' );
 const ED = require( 'noble-ed25519' );
 const Protobuf = require('protobufjs');
+const { stringify } = require('querystring');
 //const BASE64 = require('@protobufjs/base64')
 
 const API = 'https://www.rxome.net';
-const TESTAPI = 'https://testapi.gene-talk.de';
+const TESTAPI = 'http://stage.rxome.net';
 const APIENTRY = 'api/v1';
 const VSTR = 'API1.0'
+const IS_DEMO = '_DEMO_PSEUDONYM_';
+
 exports.API = API;
 exports.TESTAPI = TESTAPI;
 exports.APIENTRY = APIENTRY;
 exports.VSTR = VSTR;
+exports.IS_DEMO = IS_DEMO;
 
 /************************************************************************************
  * Helper functions
@@ -70,6 +74,8 @@ catch (e) {
  }
 }
 
+exports.readSigKey = readSigKey;
+
 /************************************************************************************/
 
 exports.signData = async( keyId, user, keyB64, created, debug = false ) => {
@@ -97,13 +103,15 @@ exports.fetchData = async ( url, credentials, pseudonym = '', debug = false ) =>
   const user = credentials.user || `${keyId}@rxome.net`;
   const keyB64 = credentials.key || readSigKey( process.cwd()+'/'+credentials.keyFile );
 
-  auth = await exports.signData( keyId, user, keyB64, created, debug );
+  const auth = await exports.signData( keyId, user, keyB64, created, debug );
 
+  FS = require( 'fs' );
   return Axios({
                 url: url,
                 method: 'GET',
                 params: { 
-                  pslab: !!pseudonym.trim() 
+                  pslab: !!pseudonym.trim(),
+                  demo: pseudonym === IS_DEMO
                 },
                 headers: {		
                   Authorization: auth,

package/lib/rxome-api.test.js

@@ -4,16 +4,16 @@ const ED = require( 'noble-ed25519' );
 
 describe('API access', () => {
   test.skip('generates valid API access keys', async () => {
-    await RxAPI.generateApiKeys( 'jesttest' );
-    expect( FS.existsSync('jesttest.private.apikey') ).toBe( true );
-    expect( FS.existsSync('jesttest.public.apikey') ).toBe( true );
-    expect( FS.statSync('jesttest.private.apikey').size - 44 ).toBeLessThan( 2 );
-    expect( FS.statSync('jesttest.public.apikey').size - 44 ).toBeLessThan( 2 );
+    await RxAPI.generateApiKeys( '__TESTSUITE_jesttest' );
+    expect( FS.existsSync('__TESTSUITE_jesttest.private.apikey') ).toBe( true );
+    expect( FS.existsSync('__TESTSUITE_jesttest.public.apikey') ).toBe( true );
+    expect( FS.statSync('__TESTSUITE_jesttest.private.apikey').size - 44 ).toBeLessThan( 2 );
+    expect( FS.statSync('__TESTSUITE_jesttest.public.apikey').size - 44 ).toBeLessThan( 2 );
 
     const message='Answer to life the universe and everything';
     const messageUi8 = RxAPI.unpack(Array.from(message));
-    const privKey = RxAPI.unpack([...RxAPI.base64ToBuffer( FS.readFileSync('jesttest.private.apikey'))])
-    const pubKey = RxAPI.unpack([...RxAPI.base64ToBuffer( FS.readFileSync('jesttest.public.apikey'))])
+    const privKey = RxAPI.unpack([...RxAPI.base64ToBuffer( FS.readFileSync('__TESTSUITE_jesttest.private.apikey'))])
+    const pubKey = RxAPI.unpack([...RxAPI.base64ToBuffer( FS.readFileSync('__TESTSUITE_jesttest.public.apikey'))])
     const signature = await ED.sign(messageUi8, privKey);
     const isValid = await ED.verify(signature, messageUi8, pubKey);
     expect( isValid ).toBeTruthy;

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/lib/rxome-generator.test.js

@@ -7,7 +7,8 @@ const Axios = require( 'axios' );
 
 const RXAPI = RxAPI.API;
 const RXTESTAPI = RxAPI.TESTAPI;
-const RXLOCALAPI = 'http:localhost:3000';
+// const RXTESTAPI = 'http://localhost:3000';
+const RXLOCALAPI = 'http://localhost:3000';
 
 const CREDENTIALS = {
   id: ApiDemo.DEMO_API_ID,
@@ -28,13 +29,15 @@ const PUBLIC_KEY  = ApiDemo.CRYPT_PUBLIC_KEY;
 const DEMO_API_PRIVATE_KEY = ApiDemo.DEMO_API_PRIVATE_KEY;
 const DEMO_API_PUBLIC_KEY  = ApiDemo.API_PUBLIC_KEY; 
 
+process.env.NODE_TLS_REJECT_UNAUTHORIZED = '0';
+
 describe('API access', () => {
 
   test('is able to connect to API', async () => {
-    await expect( Coder.fetchKey(CREDENTIALS, '', RXTESTAPI) ).resolves.not.toThrowError();
+    await expect( Coder.fetchKey(CREDENTIALS, RxAPI.IS_DEMO, RXTESTAPI) ).resolves.not.toThrowError();
   });
 
-  // test('should fetch key and pseudonyms', async () => {
+  // test.skip('should fetch key and pseudonyms', async () => {
   //   Coder.fetchKey(CREDENTIALS, '', RXTESTAPI)
   //   .then( result => {
   //     //console.log( PUBLIC_KEY )
@@ -46,7 +49,7 @@ describe('API access', () => {
   // });
 
   test('should fetch key and pseudonyms', () => {
-    Coder.fetchKey(CREDENTIALS, '', RXTESTAPI)
+    Coder.fetchKey(CREDENTIALS, RxAPI.IS_DEMO, RXTESTAPI)
     .then(result => {
       expect(result.pseudonym).toBe(DEMO_PSEUDONYM);
       expect(result.key.trim()).toBe(PUBLIC_KEY.trim());
@@ -63,7 +66,7 @@ describe('API access', () => {
 
   // error handling:
   test('should raise an error when url is wrong', () => {
-    Coder.fetchKey(CREDENTIALS, '', 'https://testapi.gene-talk.de/api/v1/schnitzel/', false, 'fehler')
+    Coder.fetchKey(CREDENTIALS, '', RXTESTAPI, false, '/api/v1/errortest')
       .then(data => { })
       .catch(err => {
         expect(err.message).toMatch('404');
@@ -106,7 +109,8 @@ describe('fetchDemoKey', () => {
     Coder.fetchDemoPrivateKey(CREDENTIALS, RXTESTAPI )
     .then(result => {
       expect(result.private_key.trim()).toBe(PRIVATE_KEY.trim())
-    });
+    })
+    .catch( err => { process.stderr.write( JSON.stringify( err ))});
   });
 });
 
@@ -115,7 +119,7 @@ describe('Phenopackets preprocessor', () => {
   test('converts camelCase to snake_case', () => {
     const snake = Coder.convert_to_snake_case(DEMO_DATA);
     const camel = Coder.convertToCamelCase(snake);
-    expect(JSON.stringify(snake).match(/_/g).length).toBe( 30 );
+    expect(JSON.stringify(snake).match(/_/g).length).toBe( 33 );
     expect(camel).toEqual(DEMO_DATA);
   });
 
@@ -263,7 +267,7 @@ describe('Coder', () => {
 
   test('should encode and decode with key from server', async () => {
     const message = 'A-well-a bird bird bird, bird is the word';
-    const keypkg = await Coder.fetchKey(CREDENTIALS, '', RXTESTAPI);
+    const keypkg = await Coder.fetchKey(CREDENTIALS, RxAPI.IS_DEMO, RXTESTAPI);
     expect(keypkg.pseudonym).toBe(DEMO_PSEUDONYM);
     const cipher = await Coder.encode(keypkg.key, message);
     const clear = await Coder.decode(PRIVATE_KEY, cipher);
@@ -283,20 +287,18 @@ describe('Coder', () => {
 
 
 describe('Rails', () => {
-  test.skip('should be able to decode cipher', async() => {
+  test('should be able to decode cipher', async() => {
     const message = 'A-well-a bird bird bird, bird is the word';
     const cipher = await Coder.encode(PUBLIC_KEY, message);
 
     const res = await Axios({
-      method: 'GET',
-      url: 'http://localhost:3000/api/v1/decryptTest',
+      method$: 'GET',
+      url: `${RXTESTAPI}/api/v1/decryptTest`,
       data: {
         cipher: cipher
       }
     })
-    // @TODO: do not send to localhorst
     expect( res.data?.clearText ).toEqual( message ) 
-
   });
 });
 
@@ -312,8 +314,10 @@ describe('Serial version of coder', () => {
 
   test('should encode and decode with key from server', async () => {
     const message = 'A-well-a bird bird bird, bird is the word';
-    const keypkg = await Coder.fetchKey(CREDENTIALS, '', RXTESTAPI, false);
-    const { private_key } = await Coder.fetchDemoPrivateKey(CREDENTIALS);
+    const keypkg = await Coder.fetchKey(CREDENTIALS, RxAPI.IS_DEMO, RXTESTAPI, false);
+    const { private_key } = await Coder.fetchDemoPrivateKey(CREDENTIALS, RXTESTAPI)
+    //.then( data => {console.log( data )})
+    //.catch( err => { process.stderr.write( JSON.stringify( err ))})
     expect(keypkg.pseudonym).toBe(DEMO_PSEUDONYM);
     const cipher = await Coder.encode(keypkg.key, message);
     const clear = await Coder.decode(private_key, cipher);
@@ -326,14 +330,17 @@ describe('QR Code generator', () => {
   test('should make QR code', async () => {
     const newData = { ...DEMO_DATA, metaData: { ...DEMO_DATA.metaData } };
     delete newData.metaData.pseudonym;
-    const { qr_code, pseudonym } = await Coder.makeQR(
+    //const { qr_code, pseudonym } = await 
+    Coder.makeQR(
       newData,
       RXTESTAPI
-    );
-    //console.log( qr_code.length );
-    //expect( qr_code.length ).toBe( 25750 );
-    expect(qr_code.startsWith('    data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAiQAAAIkCAYAAAAu8zBwAAA2qElEQVR4AezBQQ4by5LAQFLw/a/MectcF')).toBeTruthy;
-    expect(pseudonym).toBe(DEMO_PSEUDONYM);
+    )
+    .then( data => {
+      expect( data.qr_code.startsWith('    data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAiQAAAIkCAYAAAAu8zBwAAA2qElEQVR4AezBQQ4by5LAQFLw/a/MectcF')).toBeTruthy;
+      expect( data.pseudonym ).toBe(DEMO_PSEUDONYM);
+      expect( data.qr_data ).toBe( newData );
+    })
+    .catch( err => { process.stderr.write( JSON.stringify( err ))})
   })
 
   test('should make QR code when given lab ps', async () => {
@@ -350,8 +357,6 @@ describe('QR Code generator', () => {
       newData,
       RXTESTAPI
     );
-
-    //expect( qr_code.length ).toBe( 25750 );
     expect(qr_code.startsWith('    data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAiQAAAIkCAYAAAAu8zBwAAA2qElEQVR4AezBQQ4by5LAQFLw/a/MectcF')).toBeTruthy;
     //console.log(qr_code.length);
     expect(pseudonym).toBe( lab_ps );

package/package.json

@@ -1,9 +1,9 @@
 {
   "name": "rxome-generator",
-  "version": "0.1.0",
+  "version": "0.1.3",
   "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 +24,7 @@
     "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
@@ -42,10 +53,11 @@ 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')
+  .option('-L, --localhost', 'Connect to localhost API')
   .option('-D, --debug', 'Some output for debugging')
   .action( async (inputfile, options) => {
     const rawdata = FS.readFileSync( inputfile || '/dev/stdin' );
@@ -57,7 +69,9 @@ Output: prints the given or new pseudonym.`)
     options.created   && (qrData.metaData.created      = options.created);
     options.email     && (qrData.metaData.submittedBy  = options.email);
     options.pseudonym && (qrData.metaData.pseudonym    = options.pseudonym);
-    const qrApi = options.test ? RxAPI.TESTAPI : RxAPI.API;
+    let qrApi = RxAPI.API;
+    options.test && (qrApi = RxAPI.TESTAPI);
+    options.localhost && (qrApi = 'http://localhost:3000/');
   
     ('credentials' in qrData) || (qrData.credentials = {});
     if ( options.key ) {
@@ -91,7 +105,7 @@ program.command('convert')
   .alias('c')
   .description('convert case style of keys in JSON files from snake_case to camelCase (and vice versa)')
   .argument('[input file]', 'Input JSON file (default: STDIN)')
-  .option('-o, --output <output file>', 'Output JSON file (default: stdout)', '/dev/stdout')
+  .option('-o, --output <output file>', 'Output JSON file (default: stdout)')
   .option('-s, --snake', 'Convert to snake_case (default: convert to camelCase')
   .action( async (inputfile, options) => {
     const data = JSON.parse(FS.readFileSync( inputfile || '/dev/stdin' ));
@@ -101,7 +115,11 @@ program.command('convert')
     } else {
       newData = Coder.convertToCamelCase( data );
     }
-    FS.writeFileSync( options.output, JSON.stringify( newData ))
+    if ( options.output ) {
+      const stream = FS.createWriteStream( options.output );
+      process.stdout.write = stream.write.bind( stream );
+    }
+    process.stdout.write( JSON.stringify( newData ) );
   });
 
 
@@ -109,10 +127,10 @@ program.command('preprocess')
   .alias('p')
   .description('perform preprocessing steps')
   .argument('[input file]', 'Input JSON file (default: STDIN)')
-  .option('-o, --output <output file>', 'Output JSON file (default: stdout)', '/dev/stdout')
+  .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' ));
@@ -120,7 +138,11 @@ program.command('preprocess')
     options.whitelist && (data = Coder.whiteListPhenoPacket( data ));
     options.sanitize && (data = Coder.sanitizePhenoPacket( data ));
     options.compress && (data = Coder.compressPhenoPacket( data ));
-    FS.writeFileSync( options.output, JSON.stringify( data ))
+    if ( options.output ) {
+      const stream = FS.createWriteStream( options.output );
+      process.stdout.write = stream.write.bind( stream );
+    }
+    process.stdout.write( JSON.stringify( data ) );
   })
   
   
@@ -149,10 +171,10 @@ 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')
+  .option('-L, --localhost', 'Connect to localhost API')
   .option('-D, --debug', 'Some output for debugging')
   .action( async (id, key, options) => {
     let qrApi = RxAPI.API;
@@ -163,15 +185,14 @@ program.command('ping')
       key: key,
       user: 'info@rxome.net'
     }
-
     options.debug && console.log( "Sending " , credentials , " to ", qrApi );
 
     Coder.fetchKey( credentials, 'HANSMOTKAMP', qrApi, options.debug )
-    .then( result => {console.log( (result?.key && result?.pseudonym === '') ? 'OK' : 'An error occured')} )
+    .then( result => { console.log('[RESULT] ', result);console.log( (result?.key && result?.pseudonym === 'HANSMOTKAMP') ? 'OK' : 'An error occured')} )
     .catch( error => {
-      console.log( error.code );
+      console.log( '[Error] ', error.code );
       if (error.response) {  // status !== 2xx
-        options.debug && console.log('\nResp. Data:\n', error.response.data);
+        // options.debug && console.log('\nResp. Data:\n', error.response.data);
         options.debug && console.log('\nResp. Headers:\n', error.response.headers);
         console.log('\nError ', error.response.status);
       } else if (error.request) { // request send, but no response
@@ -183,11 +204,11 @@ program.command('ping')
   });
 
 
-program.command('encode')
+program.command('encrypt')
   .alias('e')
   .description('encrypt message (just for testing)')
   .argument('[input file]', 'Input text file (default: STDIN)')
-  .option('-o, --output <output file>', 'Output file (default: stdout)', '/dev/stdout')
+  .option('-o, --output <output file>', 'Output file (default: stdout)')
   .option('-k, --keyfile <keyfile>', 'name of public data encryption key file (not to be confused with the API access key!)', 'rxome.public.key')
   .option('-j, --json', 'treat inputfile as json {key: ..., message: ...}', false)
   .action( async (inputfile, options) => {
@@ -203,15 +224,19 @@ program.command('encode')
       message = data.toString();
     }
     const cipher = await Coder.encode( key, message );
-    FS.writeFileSync( options.output, cipher );
+    if ( options.output ) {
+      const stream = FS.createWriteStream( options.output );
+      process.stdout.write = stream.write.bind( stream );
+    }
+    process.stdout.write( cipher );
   });
 
 
-program.command('decode')
+program.command('decrypt')
   .alias('d')
-  .description('decode coded message or medical data')
+  .description('decrypt coded message or medical data')
   .argument('[input file]', 'Input cipher file (default: STDIN)')
-  .option('-o, --output <output file>', 'Output file (default: stdout)', '/dev/stdout')
+  .option('-o, --output <output file>', 'Output file (default: stdout)')
   .option('-k, --keyfile <keyfile>', 'name of private data encryption key file', 'rxome.private.key')
   .option('-j, --json', 'treat inputfile as json {key: ..., cipher: ...}', false)
   .option('-c, --complete', 'also unpack PhenoPacket', false )
@@ -242,12 +267,16 @@ program.command('decode')
     } else {
       result = data;
     }
-    FS.writeFileSync( options.output, result );
-
+    if ( options.output ) {
+      const stream = FS.createWriteStream( options.output );
+      process.stdout.write = stream.write.bind( stream );
+    }
+    process.stdout.write( result );
   });
 
 
-program.command('rxome-keys')
+program.command('data-keys')
+  .alias('K')
   .description('generate key pair for data encryption (see -e, -d; just for testing)')
   .argument('[file prefix]', 'Prefix for file names (default: rxome)')
   .option('-d, --directory <dir>', 'output directory', '.')
@@ -260,7 +289,7 @@ program.command('pheno2proto')
   .alias('E')
   .description('encode PhenoPacket to protobuf (just for testing)')
   .argument('[input file]', 'Input text file (default: STDIN)')
-  .option('-o, --output <output file>', 'Output file (default: stdout)', '/dev/stdout')
+  .option('-o, --output <output file>', 'Output file (default: stdout)')
   .option('-b, --base64', 'Write output base64 encoded')
   .option('-W, --whitelist', 'Preprocess: whitelist', false )
   .option('-S, --sanitize', 'Preprocess: sanitize', false )
@@ -273,7 +302,11 @@ program.command('pheno2proto')
     const compressedMedical = options.compress ? Coder.compressPhenoPacket( sanitizedMedical ) : sanitizedMedical;
     const protobufMedical = Coder.encodePhenoPacket( compressedMedical );
     const outData = (options.base64 ? RxAPI.bufferToBase64( protobufMedical ) : protobufMedical );
-    FS.writeFileSync( options.output, outData );
+    if ( options.output ) {
+      const stream = FS.createWriteStream( options.output );
+      process.stdout.write = stream.write.bind( stream );
+    }
+    process.stdout.write( outData );
   });
 
 
@@ -281,7 +314,7 @@ program.command('proto2pheno')
   .alias('D')
   .description('decode protobuf to PhenoPacket (just for testing)')
   .argument('[input file]', 'Input cipher file (default: STDIN)')
-  .option('-o, --output <output file>', 'Output file (default: stdout)', '/dev/stdout')
+  .option('-o, --output <output file>', 'Output file (default: stdout)')
   .option('-b, --base64', 'Read input base64 encoded')
   .option('-p, --pretty', 'Pretty print output}')
 
@@ -289,7 +322,11 @@ program.command('proto2pheno')
     const input = FS.readFileSync( inputfile || '/dev/stdin' );
     const data = ( options.base64 ? Uint8Array.from([...atob(input) ].map( c => c.charCodeAt(0))): input)
     const pheno = Coder.decodePhenoPacket(data);
-    FS.writeFileSync( options.output, JSON.stringify(pheno, ' ', options.pretty ? 2 : 0) );
+    if ( options.output ) {
+      const stream = FS.createWriteStream( options.output );
+      process.stdout.write = stream.write.bind( stream );
+    }
+    process.stdout.write( JSON.stringify(pheno, ' ', options.pretty ? 2 : 0) );
   });
 
 
@@ -391,8 +428,8 @@ program.command('statistics')
 //     return Coder.decode(privateKey, cipher)
 //   })
 //   .then(clear => {console.log( JSON.parse(clear) )})
-
-//  console.log( JSON.stringify( Coder.fetchKey( DEMO_CREDENTIALS, '', RxAPI.TESTAPI )));
+// .action( async() => {
+//   console.log( JSON.stringify( await Coder.fetchDemoPrivateKey( DEMO_CREDENTIALS, '', RxAPI.TESTAPI, true )));
 
 // });
 

package/rxcode.test.js

@@ -3,22 +3,27 @@ const FS = require( 'fs' );
 //const { default: test } = require("node:test");
 const Coder = require( './lib/rxome-generator' );
 
+DEMO_TEXT = 'answer to life the universe and everything'
+
 DEMO_CIPHER = `
 -----BEGIN PGP MESSAGE-----
 
-wV4Dhx/ATfJT0nQSAQdAQB3UcIAE5hMbtWJLiaDIrIiuNBRYzYPPGe4Ry40A
-oCkw9Tf0OlDdDEqrCfGWseuYgdbgpqUSYJMTgmnmj8S2KxqU30eW10fu+lzt
-0a8vvetS0loB8ktDgqeRfFeusC8L5vBVD6r5PixaZYWjhcaL1ZrcEl211ArW
-Qvk3mk17r9xwp26rVXk5NX/feTNXr19907RdPM1oT7zWetTpwx8ow6KZZrGB
-ZcabBZ5ti/o=
-=6tRv
+wV4DwTe9/0b1zzgSAQdAxe4Phva3n19MInlPhQS4OxG78y+3mTsNHVfsk5OF
+nGAwld5yaBCzLoudwGLQ17qIkABl9rhONf8VJMNoTOZOf8nPoouCKdXxktv7
+dG1wvV2s0lsBvUBUmaOzix1hEF6YeUr7mfc+MBBt/2gfoyT4Kujgrg25YoZ6
+qUgqga2eSZ6O+OhyjuFo3rZVXl1MFY6lfu+X+i4cCE2VWiAQOwVNnqFdY9FF
+uOPuzhz7UstK
+=KKxC
 -----END PGP MESSAGE-----
 `
 
 const PRIVATE_KEY = Coder.DEMO_PRIVATE_KEY;
 const PUBLIC_KEY = Coder.DEMO_PUBLIC_KEY;
 
+jest.setTimeout(70000)
+
 async function execCmd( cmd ) {
+  // process.stderr.write( `Executing ${cmd}` )
   const exec = require('child_process').exec;
   return new Promise((resolve, reject) => {
     exec(cmd, (error, stdout, stderr) => {
@@ -36,41 +41,132 @@ async function execCmd( cmd ) {
 }
 
 describe('CmdLine generate', () => {
-  it.skip('generates a qr code from demo data', () => {
-    FS.rm( 'zzz.png' );
-    execCmd( 'rxcode g -t -o zzz.png demos/demo_data_full.json' )
-    .then( result => {
-      console.log( result.stdout )
-      console.log( result.stderr )
-    });
+  test('generates a qr code from demo data', () => {
+    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 => {
+      expect( res.error ).toBeNull();
+      expect( res.stdout ).toBe('HANSMOTKAMP\n');
+      expect( res.stderr ).toBe('');
+      expect( FS.existsSync( '__TESTSUITE_IMG.png' )).toBeTruthy();
+      const fileStats = FS.statSync( '__TESTSUITE_IMG.png' );
+      expect( Math.floor( fileStats.size / 100 )-215).toBeLessThan( 4 );
+    })
+    .catch( err => { process.stderr.write( JSON.stringify( err ))})
   });
 });
 
 
-// describe('generate keys', () => {
-//   test.skip('creates two files', async () => {
-//     const dir = '.';
-//     const ex = await execCmd( 'node rxcode.js generate testsuite foo@bar.baz ' );
-//     const publicKeyFile = `${dir}/testsuite.public.key`;
-//     const privateKeyFile = `${dir}/testsuite.private.key`;
-//     expect( ex.error ).toBeNull();
-//     expect( ex.stdout ).toBe('');
-//     expect( ex.stderr ).toBe('');
-//     expect( FS.existsSync( publicKeyFile )).toBeTruthy();
-//     expect( FS.existsSync( privateKeyFile )).toBeTruthy();
-//     const privStats = FS.statSync( privateKeyFile );
-//     expect( privStats.size ).toBe( 850 );
-//     const pubStats = FS.statSync( publicKeyFile );
-//     expect( pubStats.size ).toBe( 624 );
-//     const privateKey = FS.readFileSync( privateKeyFile, { encoding: 'utf8' }, err => { console.log(err) } );
-//     expect( privateKey ).toContain( 'BEGIN PGP PRIVATE KEY BLOCK' );
-//     const publicKey = FS.readFileSync( publicKeyFile, { encoding: 'utf8' }, err => { console.log(err) } );
-//     expect( publicKey ).toContain( 'BEGIN PGP PUBLIC KEY BLOCK' );
-//   })
+describe('generate keys', () => {
+  test('creates two files', async () => {
+    const dir = '.';
+    const ex = await execCmd( 'rxcode K __TESTSUITE' );
+    const publicKeyFile = `${dir}/__TESTSUITE.public.key`;
+    const privateKeyFile = `${dir}/__TESTSUITE.private.key`;
+    expect( ex.error ).toBeNull();
+    expect( ex.stdout ).toBe('');
+    expect( ex.stderr ).toBe('');
+    expect( FS.existsSync( publicKeyFile )).toBeTruthy();
+    expect( FS.existsSync( privateKeyFile )).toBeTruthy();
+    const privStats = FS.statSync( privateKeyFile );
+    expect( Math.floor( privStats.size / 100 )).toBe( 8 );
+    const pubStats = FS.statSync( publicKeyFile );
+    expect( Math.floor( pubStats.size / 10 )).toBe( 62 );
+    const privateKey = FS.readFileSync( privateKeyFile, { encoding: 'utf8' }, err => { console.log(err) } );
+    expect( privateKey ).toContain( 'BEGIN PGP PRIVATE KEY BLOCK' );
+    const publicKey = FS.readFileSync( publicKeyFile, { encoding: 'utf8' }, err => { console.log(err) } );
+    expect( publicKey ).toContain( 'BEGIN PGP PUBLIC KEY BLOCK' );
+  })
 
-// });
+});
 
-// //describe('encode', () => {
+describe('Cmdline encode', () => {
+  test('encodes json input', async() => {
+    execCmd( './rxcode e -j ./demos/demo_encrypt.json > __TESTSUITE_FILE_1' )
+    .then( res => {
+      expect( res.error ).toBeNull();
+      expect( res.stdout ).toBe('');
+      expect( res.stderr ).toBe('');
+      expect( FS.existsSync( '__TESTSUITE_FILE_1' )).toBeTruthy();
+      const fileStats = FS.statSync( '__TESTSUITE_FILE_1' );
+      expect( Math.floor( fileStats.size / 100 )).toBe( 3 );
+      const fileContent = FS.readFileSync( '__TESTSUITE_FILE_1', { encoding: 'utf8' }, err => { process.stderr.write(err) } );
+      expect( fileContent ).toContain( '-----BEGIN PGP MESSAGE-----' );
+      //FS.rmSync( '__TESTSUITE_FILE_1')
+    })
+    .catch( err => { process.stderr.write( JSON.stringify( err ))})  
+  })
+
+  test('decodes json input', async() => {
+    execCmd( './rxcode d -j ./demos/demo_decrypt.json > __TESTSUITE_FILE_2' )
+    .then( res => {
+      expect( res.error ).toBeNull();
+      expect( res.stdout ).toBe('');
+      expect( res.stderr ).toBe('');
+      expect( FS.existsSync( '__TESTSUITE_FILE_2' )).toBeTruthy();
+      const fileStats = FS.statSync( '__TESTSUITE_FILE_2' );
+      expect( fileStats.size ).toBe( 42 );
+      const fileContent = FS.readFileSync( '__TESTSUITE_FILE_2', { encoding: 'utf8' }, err => { process.stderr.write(err) } );
+      expect( fileContent ).toContain( DEMO_TEXT );
+      //FS.rmSync( '__TESTSUITE_FILE_1')
+    })
+    .catch( err => { process.stderr.write( JSON.stringify( err ))})   
+  })
+
+  test('encodes and decodes a text file', async() => {
+    FS.writeFileSync( '__TESTSUITE_FILE_3', DEMO_TEXT );
+    execCmd( './rxcode e -k ./demos/demo.public.key -o __TESTSUITE_FILE_4 __TESTSUITE_FILE_3' )
+    .then( res => {
+      expect( res.error ).toBeNull();
+      expect( res.stdout ).toBe('');
+      expect( res.stderr ).toBe('');
+      expect( FS.existsSync( '__TESTSUITE_FILE_4' )).toBeTruthy();
+
+      execCmd( './rxcode d -k ./demos/demo.private.key -o __TESTSUITE_FILE_5 __TESTSUITE_FILE_4' )
+      .then( res => {
+        expect( res.error ).toBeNull();
+        expect( res.stdout ).toBe('');
+        expect( res.stderr ).toBe('');
+        expect( FS.existsSync( '__TESTSUITE_FILE_5' )).toBeTruthy();
+        const fileStats = FS.statSync( '__TESTSUITE_FILE_5' );
+        expect( fileStats.size ).toBe( 42 );
+        const fileContent = FS.readFileSync( '__TESTSUITE_FILE_5', { encoding: 'utf8' } );
+        expect( fileContent ).toContain( DEMO_TEXT );
+        //FS.rmSync( '__TESTSUITE_FILE_1')
+      })
+      //.catch( err => { process.stderr.write( JSON.stringify( err ))})
+    })
+    //.catch( err => { process.stderr.write( JSON.stringify( err ))})
+  }, 100000)
+
+  test('encodes and decodes from stdin to stdout file', async() => {
+    FS.writeFileSync( '__TESTSUITE_FILE_6', DEMO_TEXT );
+    execCmd( './rxcode e -k ./demos/demo.public.key < __TESTSUITE_FILE_6 > __TESTSUITE_FILE_7' )
+    .then( res => {
+      expect( res.error ).toBeNull();
+      expect( res.stdout ).toBe('');
+      expect( res.stderr ).toBe('');
+      expect( FS.existsSync( '__TESTSUITE_FILE_7' )).toBeTruthy();
+
+      execCmd( './rxcode d -k ./demos/demo.private.key < __TESTSUITE_FILE_7 > __TESTSUITE_FILE_8' )
+      .then( res => {
+        expect( res.error ).toBeNull();
+        expect( res.stdout ).toBe('');
+        expect( res.stderr ).toBe('');
+        expect( FS.existsSync( '__TESTSUITE_FILE_8' )).toBeTruthy();
+        const fileStats = FS.statSync( '__TESTSUITE_FILE_8' );
+        expect( fileStats.size ).toBe( 42 );
+        const fileContent = FS.readFileSync( '__TESTSUITE_FILE_8', { encoding: 'utf8' } );
+        expect( fileContent ).toContain( DEMO_TEXT );
+        //FS.rmSync( '__TESTSUITE_FILE_1')
+      })
+      //.catch( err => { process.stderr.write( JSON.stringify( err ))}) 
+    });    
+  })
+});
 
 // //});
 // describe('CmdLine help', async () => {
@@ -95,10 +191,4 @@ rxcode d -j rxome.decrypt.json
 rxcode d -j rxome.decrypt.json
 rxcode d -j < rxome.decrypt
 
-rxcode P test Cs67c7aXYhZQbjU2W/4q6sBu/oIQ8zONSBURUH8g2wQ=
-OK
-rxcode P mgz QhcoRruGBVP39XCh8BujCE+q42qCRy/tu2CQ4YmRBgg=
-OK
-rxcode P rxome NamaTB+xwDFxtkQyBBkjRr5GEaXNtCw/G4qydnhQk5Y=
-OK
-*/
+*/

package/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2022 Tom Kamphans, GeneTalk GmbH
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

package/demos/rxome.decrypt.json

@@ -1 +0,0 @@
-{"key":"\n-----BEGIN PGP PRIVATE KEY BLOCK-----\n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\nyOcQrcylWRQ4NvdK9SqsEomwxTwHkQQ=\n=YCih\n-----END PGP PRIVATE KEY BLOCK-----\n","cipher":"\n-----BEGIN PGP MESSAGE-----\n\nwV4Dhx/ATfJT0nQSAQdAkPgYRHClE5eUyl58gXBQrmZoiTtkvrOZLjnaLvFq\ncicw/28IAdW/0wuYtbd0CQf6gFMMLVmF+4Qx6OeQHehI8t+5mi7Keve1eaJp\nj2WL1TiN0lsBBbYvVdInUt3VbiywTxa+sMvfT+0crmTtsfJ6FrbD7nR22L/v\n9RgUEaY6cDrNu+PzcKGVYQj/WCqhlFflcAn+/cfcu0mRkllmbghN2uYbymff\n4M44RC1yZ0j1\n=x+N1\n-----END PGP MESSAGE-----\n"}

package/demos/rxome.encrypt.json

@@ -1 +0,0 @@
-{"key":"\n-----BEGIN PGP PRIVATE KEY BLOCK-----\n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\nyOcQrcylWRQ4NvdK9SqsEomwxTwHkQQ=\n=YCih\n-----END PGP PRIVATE KEY BLOCK-----\n","message":"answer to life the universe and everything"}