# 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](https://github.com/bmeg/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` and `iceberg` are synonymous in this context.
## Examples
The commands:
```commandline
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:
```commandline
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](docs/CONTRIBUTING.md) for developer notes.
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"description": "# iceberg-schema-tools\nCreate and maintain central iceberg schema. Render and validate FHIR data.\n\n## Overview\n\n\n\n\n\nCode that generates the base schema from FHIR goes here. Additional tools are provided to lints, validates and visualize the schema.\n\nNote: The actual schemas are stored in [iceberg](https://github.com/bmeg/iceberg)\n\n\n## Setup\n\n```\npip install iceberg-tools\n```\n\n\n## Use\n\n```\n$ iceberg schema\nUsage: iceberg schema [OPTIONS] COMMAND [ARGS]...\n\n Manage bmeg or gen3 schemas from FHIR resources.\n\nOptions:\n --help Show this message and exit.\n\nCommands:\n generate Generate from FHIR resources.\n compile Create aggregated json file from individual yaml schemas\n\n$ iceberg data\n\nUsage: iceberg data [OPTIONS] COMMAND [ARGS]...\n\n Project data (ResearchStudy, ResearchSubjects, Patient, etc.).\n\nOptions:\n --help Show this message and exit.\n\nCommands:\n simplify Renders PFB friendly flattened records.\n validate Check FHIR data for validity and conventions.\n validate-simplified Check simplified data for validity and conventions.\n pfb Write simplified FHIR files to a PFB.\n migrate Migrate from FHIR R4B to R5.0.\n report Aggregate avro pfb files into a cytoscape tsv.\n\n```\n\n> Note: `pfb_fhir` and `iceberg` are synonymous in this context.\n\n## Examples\n\nThe commands:\n```commandline\npfb_fhir schema generate simplified\npfb_fhir data simplify --schema_path iceberg/schemas/simplified/simplified-fhir.json tests/fixtures/simplify/study/ tmp/simplified\npfb_fhir data pfb tmp/simplified/ tmp/study.pfb\ntree tmp\n\n```\n\nWill generate the following output:\n```commandline\nINFO:'Records with relationships': 59413\nINFO:'Records': 59460\ntmp\n\u251c\u2500\u2500 simplified\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 Condition.ndjson\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 DocumentReference.ndjson\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 Encounter.ndjson\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 MedicationAdministration.ndjson\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 Observation.ndjson\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 Patient.ndjson\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 ResearchStudy.ndjson\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 ResearchSubject.ndjson\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 Specimen.ndjson\n\u2502\u00a0\u00a0 \u2514\u2500\u2500 Task.ndjson\n\u2514\u2500\u2500 study.pfb\n\n```\n\n## Contributing\nSee [CONTRIBUTING.md](docs/CONTRIBUTING.md) for developer notes.\n\n\n",
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