ValueSet Converters

Tools for converting value sets in different formats. Such as converting extensional value sets in CSV format to JSON format able to be uploaded to a FHIR server.

Set up / installation

1. You must have Python3 installed.
2. Run to clone repo: git clone https://github.com/HOT-Ecosystem/ValueSet-Converters.git
3. Change directory: cd ValueSet-Converters
4. Make & use virtual environment: virtualenv env; source env/bin/activate
5. Run to install dependencies: pip install -r requirements.txt
6. To use the "VSAC to OMOP/FHIR JSON" tool, which fetches from Google Sheets, you'll need the following:
   3.a. Access to this google sheet.
   3.b. Place credentials.json and token.json inside the env/ directory. These can be obtained from Joe (will upload them to a Google Drive folder later).
7. Create an env/.env file based on env/.env.example, replacing VSAC_API_KEY with your own VSAC API key as shown in your profile. More instructions on getting an API key can be found in "Step 1" on this page.

Tools

First, cd into the directory where this repository was cloned.

1. CSV to FHIR JSON

First, convert your CSV to have column names like the example below. Then can run these commands.

Syntax

python3 -m value_set_csv_to_fhir_json path/to/FILE.csv

Example

python3 -m value_set_csv_to_fhir_json examples/1/input/n3cLikeExtensionalValueSetExample.csv

Before:

valueSet.id,valueSet.name,valueSet.description,valueSet.status,valueSet.codeSystem,valueSet.codeSystemVersion,concept.code,concept.display
1,bear family,A family of bears.,draft,http://loinc.org,2.36,1234,mama bear
1,bear family,A family of bears.,draft,http://loinc.org,2.36,1235,papa bear
1,bear family,A family of bears.,draft,http://loinc.org,2.36,1236,baby bear

After:

{
    "resourceType": "ValueSet",
    "id": 1,
    "meta": {
        "profile": [
            "http://hl7.org/fhir/StructureDefinition/shareablevalueset"
        ]
    },
    "text": {
        "status": "generated",
        "div": "
  

   \"http://www.w3.org/1999/xhtml\">\n\t\t\t
   
A family of bears.
\n\t\t
  
"
    },
    "name": "bear family",
    "title": "bear family",
    "status": "draft",
    "description": "A family of bears.",
    "compose": {
        "include": [
            {
                "system": "http://loinc.org",
                "version": 2.36,
                "concept": [
                    {
                        "code": 1234,
                        "display": "mama bear"
                    },
                    {
                        "code": 1235,
                        "display": "papa bear"
                    },
                    {
                        "code": 1236,
                        "display": "baby bear"
                    }
                ]
            }
        ]
    }
}

2. VSAC to OMOP/FHIR JSON

This will fetch from the following google sheet: https://docs.google.com/spreadsheets/d/1jzGrVELQz5L4B_-DqPflPIcpBaTfJOUTrVJT5nS_j18/edit#gid=1335629675

Syntax

• With default options: python3 -m value_set_vsac_to_json
• Choosing an output format: python3 -m value_set_vsac_to_json -f omop

Options: