rxome-generator

v1.0.2

Published

a year ago

Generates QR codes containing medical information for use with the FindMe2Care platform.

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tomkamphans

RxOME FineMe2care genetics variants qr-codes phenopacket

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

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 according to a subset of the PhenoPacket standard (with some additions), see below. The medical data will be encrypted before generating the QR code. This encrypted data can be decrypted by the database backend only. The meta data is transmitted unencrypted.

Every QR code is tagged with a unique pseudonym that is downloaded from the RxOME server. Thus, the tools require an active internet connection. Furthermore, the user or the facility applying the QR generator has to sign up to the RxOME server. The communication to the server API is secured with a protocol that uses an asymmetric pair of keys, a private key (the API access key) is used to sign the API enquiry, a public key is uploaded to the server and used to verify the signature, see generating user credentials.

When generating a QR code and, thus, downloading a pseudonym, the user needs to specify the corresponding credentials (keyID and key) for accessing the RxOME server. The command line tool offers command line options for the API access credentials. Further, they can be specified in the input JSON file (see 'MetaData and credentials' below), where the command line options precede the data in the JSON file.

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

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):

rxcode g inputfile.json

For detailed descriptions see

rxcode g --help

Library Functions

Import the library with

const Coder = require( 'rxome-generator' );

The following two async library functions generate QR codes:

Coder.writeQR( filename, data, api = RXAPI )

filename: name for PNG file with the QR code data: object containing medical data, meta data, and credentials (format: see below) api: omit in production mode, set to Coder.TESTAPI in test mode.

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 and the unencrypted content of the QR code.

Coder.makeQR( data, api = RXAPI, apiEntry = APIENTRY )

Generates a QR code object as Data URL that can be placed on a web page. As above, the credentials are specified as part of the data object. Returns an object:

{
    qr_code: (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
}

Both writeQR and makeQR take care of the preprocessing steps (sanitizing, compessing, encoding). However, converting the keys in the data object to camelCase is not part of the preprocessing. Use the following function to convert keys from snake_case to camelCase:

Coder.convertToCamelCase( data )

Additionally, the data can be verified with

Coder.verify( data )

Note that the credential information perhaps stored in the data package is not part of the PhenoPacket standard.

Modifications to the PhenoPacket Standard

Meta Data and Credentials

For convenience, all data needed to generate a QR code can be specified in one JSON file (or, when using the library functions, one JavaScript object). In addition to the medical data, the JSON files or objects accepted by rxcode and the rxcode library may contain the credentials to access the RxOME API and - if existing - the patients pseudonym from earlier issued QR codes. Note that the information given in the credential section is mandatory when using the library functions. When using the command line, these data can be part of the input JSON or specified using command line arguments. 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 (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.

{
  ...
  metaData: {
    ...
     pseudonym: '19T5K7042' 
  }
  credentials: {
    keyId: <lab-id/key-id, corresponding to private key>
    key: <private key>
    keyFile: <name of file containing private key> // please specify key OR keyFile
    user: e.g., [email protected]
  }
 
}

Phenotypic Features

The rxome library extends the PhenoPacket schema for storing phenotypicFeatures (HPO terms). In addition the notation suggested by PhenoPackets:

"phenotypicFeatures": [
    {
      "type": {
        "id": "HP:0003155"
      }
    },
    {
      "type": {
        "id": "HP:0001249"
      }
    },
    {
      "type": {
        "id": "HP:0001250"
      }
    },    {
      "type": {
        "id": "HP: 0031360"
      },
      "excluded": true
    }
  ]

the terms can be stored in a shorter and more convenient form:

  "compressedFeatures": {
    "included": [
      "HP:0003155",
      "HP:0001249",
      "HP:0001250"
    ],
    "excluded": [
      "HP:0031360"
    ]
  }

Data Source

The type of genetic test performed to obtain a variant can be specified in an extension field to the genomic interpretation:

"genomicInterpretations": [
  [
    {
      "variantInterpretation": {
        "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"
              }
            ]
          }
        }
      }
    }
  ]
]

Additional Remarks

Additional remarks can be specified in a comment field on the top level:

{
  "id": "QR-Code ID",
  "comment": "useful remarks",
  "subject": {
...

Whitelist Filter

Before packing the data, needless sections (that is, sections that are not evaluted by RxOME) are removed. On top level, the following section will be passed over to the QR code:

id
comment
subject
phenotypicFeatures
interpretations
diagnosis
metaData
credentials (not passed to QR code, but also not removed by whitelist filtering)

Command-Line Tool

Overview

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 FindMe2care server.


Options:
  -V, --version                         output the version number
  -h, --help                            display help for command

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)
  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
  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
  help [command]                        display help for command

Author: Tom Kamphans, GeneTalk GmbH, 2022, (c) 2023 RxOME GmbH

Generating QR codes

Use the 'g' command for actually generating a QR code:

FindMe2care QR Code generation tool

Usage: rxcode generate|g [options] [input file]

Generate QR Code from PhenoPacket JSON. The credential information keyId and either key or keyFile 
are mandatory and can be specified either in the input JSON file or by command line arguments.
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)

Options:
  -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
                               [email protected])
  -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. 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

rxcode k myLabId

This yields two files: myLabId.private.apikey and myLabId.public.apikey. Store the private key safely. 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

rxcode g -t -o qrcode.png demos/demo_data_full.json

Debugging

To check the connection to the API on RxOME server API use

rxcode P -d your_id your_key

If you want to make sure that all data from your input is transmitted correctly, you can use the pheno2proto and the corresponding proto2pheno commands to encode and decode your file. Compare the output of proto2pheno with your original file:

rxcode E -b my_file.json > my_file.pbuf
rxcode D -bp my_file.pbuf > my_new_file.json
diff my_new_file.json my_file.json

Payload Example File

{
  "id": "QR-Code ID",
  "comment": "useful remarks",
  "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": "[email protected]",
    "phenopacketSchemaVersion": "2.0"
  }
}