Ignixa.SqlOnFhir.Cli

Ignixa SQL on FHIR CLI

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

Installation

dotnet tool install -g Ignixa.SqlOnFhir.Cli

Usage

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

ignixa-sqlonfhir <version> run --views <file|dir> --input <file|dir> --out <file|dir>
ignixa-sqlonfhir <version> preview --views <file|dir> [--input <file|dir>]
ignixa-sqlonfhir <version> validate --views <file|dir>

Commands

Run ViewDefinitions

Use run to convert NDJSON resources to Parquet, CSV, or NDJSON. Single-file mode detects the format from --out; batch mode uses --format.

ignixa-sqlonfhir r4 run \
  --views patient-view.json \
  --input patients.ndjson \
  --out patients.parquet

ignixa-sqlonfhir r4 run \
  --views patient-view.json \
  --input patients.ndjson \
  --out patients.csv

ignixa-sqlonfhir r4 run \
  --views patient-view.json \
  --input patients.ndjson \
  --out patients.ndjson

Batch mode discovers ViewDefinitions in a directory and matches NDJSON inputs by resource type:

ignixa-sqlonfhir r4 run \
  --views views \
  --input fhir-ndjson \
  --out output \
  --format parquet \
  --pattern "**/*.json" \
  --input-pattern "*{resource}*.ndjson" \
  --stats-out output/stats.json

Preview Schema and Sample Data

Use preview to display the extracted schema. Add --input to show sample rows.

ignixa-sqlonfhir r4 preview --views patient-view.json

ignixa-sqlonfhir r4 preview \
  --views patient-view.json \
  --input patients.ndjson \
  --rows 10

Directory preview accepts the same --views directory and --pattern used by batch run.

Validate ViewDefinitions

Validate one ViewDefinition or every matching file in a directory:

ignixa-sqlonfhir r4 validate --views patient-view.json

ignixa-sqlonfhir r4 validate \
  --views views \
  --pattern "**/*.json"

FHIRPath Variables

run and preview accept repeatable runtime variables for ViewDefinitions that reference declared constants:

ignixa-sqlonfhir r4 run \
  --views patient-view.json \
  --input patients.ndjson \
  --out patients.csv \
  --var cohortId=research-2026 \
  --var effectiveDate=2026-01-01

Caller-provided variables override ViewDefinition constants with the same name.

Options

FHIR Version Support

• stu3 - FHIR STU3 specification
• r4 - FHIR R4 specification
• r4b - FHIR R4B specification
• r5 - FHIR R5 specification
• r6 - FHIR R6 specification

Specify the version as the first argument to any command.

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" }
      ]
    }
  ]
}