Ignixa.SqlOnFhir.Cli

Ignixa SQL on FHIR CLI

Command-line tool for processing FHIR resources using SQL on FHIR ViewDefinitions.

Installation

dotnet tool install -g Ignixa.SqlOnFhir.Cli

Usage

All commands require specifying the FHIR version first (stu3, r4, r4b, r5, or r6), followed by the operation.

Convert FHIR Resources to Parquet

Convert FHIR resources from NDJSON to Parquet format using a ViewDefinition. The output format is automatically detected from the file extension (.parquet or .csv):

ignixa-sqlonfhir r4 convert --viewdefinition myview.json --input mypatients.ndjson --out myparquetfile.parquet

Convert FHIR Resources to CSV

Convert FHIR resources from NDJSON to CSV format using a ViewDefinition:

ignixa-sqlonfhir r4 convert --viewdefinition myview.json --input mypatients.ndjson --out mycsvfile.csv

Preview Schema and Sample Data

Extract schema from a ViewDefinition and show a preview of converted rows:

ignixa-sqlonfhir r4 preview --viewdefinition myview.json --input mypatients.ndjson

This displays:

• The extracted schema (column names and types)
• A few sample rows formatted for console display

Validate ViewDefinition

Validate a ViewDefinition file for correctness:

ignixa-sqlonfhir r4 validate --viewdefinition myview.json

Examples

Sample ViewDefinition

Create a file patient-view.json:

{
  "resourceType": "ViewDefinition",
  "resource": "Patient",
  "select": [
    {
      "column": [
        {
          "name": "id",
          "path": "id",
          "type": "string"
        },
        {
          "name": "family_name",
          "path": "name.where(use='official').first().family",
          "type": "string"
        },
        {
          "name": "given_name",
          "path": "name.where(use='official').first().given.first()",
          "type": "string"
        },
        {
          "name": "birth_date",
          "path": "birthDate",
          "type": "date"
        }
      ]
    }
  ]
}

Convert to Parquet

ignixa-sqlonfhir r4 convert \
  --viewdefinition patient-view.json \
  --input patients.ndjson \
  --out patients.parquet

Convert to CSV

ignixa-sqlonfhir r4 convert \
  --viewdefinition patient-view.json \
  --input patients.ndjson \
  --out patients.csv

Preview Results

ignixa-sqlonfhir r4 preview \
  --viewdefinition patient-view.json \
  --input patients.ndjson

FHIR Version Support

The tool supports multiple FHIR versions through explicit version selection:

• stu3 - FHIR STU3 specification
• r4 - FHIR R4 specification (most common)
• r4b - FHIR R4B specification
• r5 - FHIR R5 specification
• r6 - FHIR R6 specification

Specify the version as the first argument to any command.

Output Format Detection

The convert command automatically detects the output format based on the file extension:

• .parquet - Parquet format (columnar, compressed)
• .csv - CSV format (comma-separated values)

Invalid extensions will be rejected with an error message.