pathling
FHIR data analytics, terminology queries, and SQL views
All Skills in This Repository (20)
Pure Emerald Level Indicators
aehrcpathling-python
Query and transform FHIR data with the Pathling Python API in Spark.
aehrcopenspec-apply-change
Implement OpenSpec change tasks and update progress automatically.
aehrchapi-fhir-server
Implement FHIR servers with HAPI FHIR Plain Server framework.
aehrcopenspec-explore
Explores ideas and investigates codebases through adaptive dialogue and ASCII diagrams within OpenSpec systems.
aehrcopenspec-verify-change
Verify code implementations against openspec change artifacts using the openspec CLI.
aehrcopenspec-new-change
Scaffold a new change directory in the OpenSpec system.
aehrcradix-ui
Guide building accessible React UIs with Radix Themes and Radix Primitives.
aehrcsql-on-fhir
Create SQL on FHIR ViewDefinitions to flatten FHIR resources into tabular formats.
aehrcjmh-benchmarks
Write and execute Java microbenchmarks with the Java Microbenchmark Harness.
aehrcfhir-bulk-data
Implement HL7 FHIR Bulk Data Access with $export and NDJSON workflows.
aehrcfhir-api
Implement FHIR RESTful API servers and clients per HL7 FHIR specifications.
aehrcopenspec-archive-change
Archive completed changes after verifying artifact and task completion status.
Frequently Asked Questions
FAQPage SchemaHow to install Pathling?▼
Run `npx skills add aehrc/pathling --all -g -y` in your terminal to install all skills in this suite globally.
How to query FHIR data with SQL?▼
The sql-on-fhir skill helps you write ViewDefinitions that flatten FHIR resources into tabular rows and columns using FHIRPath expressions. You can then run or export these views as CSV, NDJSON, or Parquet.
How to write SNOMED CT ECL queries?▼
The snomed-ecl skill guides you through Expression Constraint Language syntax, including hierarchy navigation, attribute constraints, and filters. It also covers using ECL inside FHIR value sets and terminology server calls.
Can I use Pathling with Python?▼
Yes. The pathling-python skill covers the Pathling Python API, including reading NDJSON and Bundles, running terminology functions like member_of and translate, and building SQL on FHIR views from Spark DataFrames.
Does Pathling support bulk FHIR data export?▼
Yes. The fhir-bulk-data skill explains the $export operation, asynchronous polling workflow, NDJSON output format, and SMART Backend Services authorisation for large-scale data extraction.
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