iceberg-tools 0.0.2rc3

FHIR schemas tools for bioinformatics.

iceberg-schema-tools

Create and maintain central iceberg schema. Render and validate FHIR data.

Overview

Code that generates the base schema from FHIR goes here. Additional tools are provided to lints, validates and visualize the schema.

Note: The actual schemas are stored in iceberg

Setup

pip install iceberg-tools

Use

$ iceberg schema
Usage: iceberg schema [OPTIONS] COMMAND [ARGS]...

  Manage bmeg or gen3 schemas from FHIR resources.

Options:
  --help  Show this message and exit.

Commands:
  generate  Generate from FHIR resources.
  compile   Create aggregated json file from individual yaml schemas
  publish   Copy dictionary to s3 (note:aws cli dependency)

$ iceberg data

Usage: iceberg data [OPTIONS] COMMAND [ARGS]...

  Project data (ResearchStudy, ResearchSubjects, Patient, etc.).

Options:
  --help  Show this message and exit.

Commands:
  simplify       Renders Gen3 friendly flattened records.
  validate       Check FHIR data for validity and ACED conventions.
  validate-gen3  Check Gen3 data for validity and ACED conventions.
  pfb            Write simplified FHIR files to a PFB.
  migrate        Migrate from FHIR R4B to R5.0.

Note: pfb_fhir and iceberg are synonymous in this context.

Examples

The commands:

pfb_fhir data simplify  tests/fixtures/simplify/study/ tmp/simplified
pfb_fhir data pfb tmp/simplified/ tmp/study.pfb
tree tmp

Will generate the following output:

INFO:'Records with relationships': 59413
INFO:'Records': 59460
tmp
├── simplified
│   ├── Condition.ndjson
│   ├── DocumentReference.ndjson
│   ├── Encounter.ndjson
│   ├── MedicationAdministration.ndjson
│   ├── Observation.ndjson
│   ├── Patient.ndjson
│   ├── ResearchStudy.ndjson
│   ├── ResearchSubject.ndjson
│   ├── Specimen.ndjson
│   └── Task.ndjson
└── study.pfb

Contributing

See CONTRIBUTING.md for developer notes.