FHIR schemas tools for bioinformatics.
Project description
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
$ iceberg data
Usage: iceberg data [OPTIONS] COMMAND [ARGS]...
Project data (ResearchStudy, ResearchSubjects, Patient, etc.).
Options:
--help Show this message and exit.
Commands:
simplify Renders PFB friendly flattened records.
validate Check FHIR data for validity and conventions.
validate-simplified Check simplified data for validity and conventions.
pfb Write simplified FHIR files to a PFB.
migrate Migrate from FHIR R4B to R5.0.
report Aggregate avro pfb files into a cytoscape tsv.
Note:
pfb_fhir
andiceberg
are synonymous in this context.
Examples
The commands:
pfb_fhir schema generate simplified
pfb_fhir data simplify --schema_path iceberg/schemas/simplified/simplified-fhir.json 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.
Project details
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