aehrc/pathling

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Tools that make it easier to use FHIR and clinical terminology within data analytics, built on Apache Spark.

Stars: 134
Forks: 24
Open beginner issues: 0
Indexed issues: 124
Avg merge: 1d 15h
Merged PRs (30d): 8

Dominant language: Java
License: Apache-2.0
Last GitHub push: Sep 14, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

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124 open issues indexed

Forgeable delimiters in the $sql-export cache key Open

bug java

Difficulty 4/5 3-5 days Newbie friendliness 58/100

aehrc/pathling#2768 · Opened Sep 18, 2026
Parquet on FHIR M6 — Completion Open

encoders

Difficulty 5/5 Over a week Newbie friendliness 25/100

aehrc/pathling#2766 · Opened Sep 17, 2026
Parquet on FHIR M5 — The gaps Open

encoders

Difficulty 5/5 Over a week Newbie friendliness 28/100

aehrc/pathling#2765 · Opened Sep 17, 2026
Parquet on FHIR M4 — The flip Open

encoders

Difficulty 5/5 Over a week Newbie friendliness 25/100

aehrc/pathling#2764 · Opened Sep 17, 2026
Parquet on FHIR M3 — Ingest formats Open

encoders

Difficulty 5/5 Over a week Newbie friendliness 28/100

aehrc/pathling#2763 · Opened Sep 17, 2026
Parquet on FHIR M2 — The engine, layout-tolerant Open

encoders

Difficulty 5/5 Over a week Newbie friendliness 25/100

aehrc/pathling#2762 · Opened Sep 17, 2026
Parquet on FHIR M1 — The layout Open

encoders

Difficulty 5/5 Over a week Newbie friendliness 20/100

aehrc/pathling#2761 · Opened Sep 17, 2026
A subquery inside a nested SQLView body is rejected as an unauthorised data source Open

bug java

Difficulty 4/5 3-5 days Newbie friendliness 48/100

aehrc/pathling#2759 · Opened Sep 14, 2026
$sql-export matches kick-offs to existing jobs without considering the inlined context, returning stale results Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

aehrc/pathling#2757 · 1 comment · Opened Sep 14, 2026
Support external tables as dependencies of SQL on FHIR queries Open

new feature server sqlonfhir

Difficulty 5/5 Over a week Newbie friendliness 45/100

aehrc/pathling#2750 · Opened Sep 9, 2026
ViewDefinition storage drops elements not modelled in ViewDefinitionResource Open

bug server sqlonfhir

Difficulty 4/5 3-5 days Newbie friendliness 65/100

aehrc/pathling#2746 · Opened Sep 6, 2026
Verify FHIR packages against the registry-published checksum on import Open

library-api new feature security

Difficulty 4/5 3-5 days Newbie friendliness 55/100

aehrc/pathling#2744 · Opened Sep 5, 2026
Support terminology syndication feeds as an import source for the local terminology store Open

library-api new feature

Difficulty 5/5 Over a week Newbie friendliness 45/100

aehrc/pathling#2745 · Opened Sep 5, 2026
Import terminology content into the local store from a FHIR terminology server Open

cli library-api new feature

Difficulty 5/5 Over a week Newbie friendliness 35/100

aehrc/pathling#2743 · Opened Sep 2, 2026
$sql-run returns 200 with header only when evaluation fails after the header is flushed Open

bug server sqlonfhir

Difficulty 3/5 1-2 days Newbie friendliness 72/100

aehrc/pathling#2742 · Opened Sep 2, 2026
Feedback: Declarative FHIR to OMOP CDM v5.4 Pipeline with Pathling (AP-HP) Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

aehrc/pathling#2733 · 1 comment · Opened Aug 24, 2026
Support subsetOf() and supersetOf() FHIRPath functions Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

aehrc/pathling#2706 · 2 comments · Opened Aug 6, 2026
memberOf() on a CodeableConcept with no codings: should the result be empty or false? Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

aehrc/pathling#2700 · Opened Aug 5, 2026
Admin UI end-to-end test waits out the job refresh interval in real time Open

testing ui

Difficulty 2/5 1-3 hours Newbie friendliness 88/100

aehrc/pathling#2693 · Opened Jul 28, 2026
The CLI's --verbose flag surfaces no library logging Open

bug cli

Difficulty 4/5 3-5 days Newbie friendliness 45/100

aehrc/pathling#2691 · Opened Jul 27, 2026
Admin UI end-to-end suite sleeps 22 seconds waiting out the job refresh interval Open

testing ui

aehrc/pathling#2690 · 1 assignee · Opened Jul 27, 2026
Deleting a running job races the Spark work it cancels Open

bug server

aehrc/pathling#2687 · 1 assignee · Opened Jul 27, 2026
Admin UI CI does not enforce coverage thresholds or the duplication check Open

ci testing ui

aehrc/pathling#2685 · 1 assignee · Opened Jul 27, 2026
Add explicit spark_conf dict parameter to PathlingContext.create() (parity with CLI's --spark-conf) Open

cli enhancement library-api python

Difficulty 4/5 3-5 days Newbie friendliness 58/100

aehrc/pathling#2669 · Opened Jul 23, 2026
Async exports fail with Wrong FS on non-default warehouse filesystems Open

Difficulty 3/5 1-2 days Newbie friendliness 74/100

aehrc/pathling#2666 · Opened Jul 23, 2026
Prototype implementation of the SQL on FHIR $materialize operation Open

new feature sqlonfhir

aehrc/pathling#2662 · 1 comment · 1 assignee · Opened Jul 20, 2026
Parquet output of SQL on FHIR results with unresolved (VOID) columns fails with an opaque 500 Open

server

aehrc/pathling#2657 · 1 assignee · Opened Jul 10, 2026
$sqlquery-run SqlValidator rejects DESCRIBE / SHOW COLUMNS — no way to introspect view schema (prefer allowing DESCRIBE) Open

new feature server

Difficulty 3/5 1-2 days Newbie friendliness 68/100

aehrc/pathling#2651 · Opened Jul 9, 2026
$sqlquery-run SqlValidator rejects window frame boundary (CurrentRow$) Open

new feature server

aehrc/pathling#2650 · 1 assignee · Opened Jul 9, 2026
Pre-import Pathling functions into the run and console namespace Open

cli

aehrc/pathling#2648 · 1 assignee · Opened Jul 8, 2026
No delimiter option for CSV in the CLI Open

cli

aehrc/pathling#2647 · 1 assignee · Opened Jul 8, 2026
Support local terminology evaluation without a terminology server Open

fhirpath library-api new feature python R

aehrc/pathling#2644 · 1 assignee · Opened Jul 7, 2026
Support SQLView resources and view composition in SQL on FHIR operations Open

server

aehrc/pathling#2638 · 1 assignee · Opened Jun 26, 2026
Remove the dbplyr pin once sparklyr supports dbplyr 2.6.0 Open

dependencies

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

aehrc/pathling#2631 · Opened Jun 18, 2026
Fix forEach schema boundary handling for recursive paths that exit the encoded schema Open

bug java sqlonfhir

Difficulty 4/5 3-5 days Newbie friendliness 68/100

aehrc/pathling#2625 · Opened May 22, 2026
Investigate custom Catalyst expression for `let` to improve performance Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 38/100

aehrc/pathling#2623 · Opened May 20, 2026
test: $import-pnp and $bulk-submit integration tests have stale-state and config gaps Open

java testing

Difficulty 3/5 1-2 days Newbie friendliness 25/100

aehrc/pathling#2621 · 1 comment · Opened May 19, 2026
fix: $import-pnp rejects its own staged files on local filesystem Open

bug java server

Difficulty 1/5 Under an hour Newbie friendliness 25/100

aehrc/pathling#2620 · 1 comment · Opened May 19, 2026
Ensure repeat directive implementation passes expanded test coverage Open

sqlonfhir testing

aehrc/pathling#2619 · 1 comment · 1 assignee · Opened May 19, 2026
Add support for extended benchmark Open

testing

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

aehrc/pathling#2611 · Opened May 12, 2026
Document `trace()` incompatibility with SQL aggregate functions Open

documentation

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

aehrc/pathling#2607 · Opened May 8, 2026
trace() entries are duplicated by non-deterministic expression re-evaluation Open

bug fhirpath java

aehrc/pathling#2594 · 1 comment · 1 assignee · Opened Apr 24, 2026
fhirpath-lab-api: sanitiseRow does not recurse into arrays of structs Open

bug fhirpath java

aehrc/pathling#2592 · 1 assignee · Opened Apr 20, 2026
Consider pinning this with a SHA ... Open

Difficulty 1/5 1-3 hours Newbie friendliness 72/100

aehrc/pathling#2577 · Opened Mar 24, 2026
Constants not working in python dataset view Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

aehrc/pathling#2574 · 1 comment · Opened Mar 18, 2026
Test bulk export against Inferno Bulk Data test kit Open

testing

Difficulty 5/5 Over a week Newbie friendliness 28/100

aehrc/pathling#2558 · Opened Feb 23, 2026
Make save mode configurable per allowed submitter for Bulk Submit Open

new feature server

Difficulty 4/5 3-5 days Newbie friendliness 45/100

aehrc/pathling#2557 · Opened Feb 23, 2026
Implement Bulk Submit data provider (submitter) functionality Open

new feature server

Difficulty 5/5 Over a week Newbie friendliness 35/100

aehrc/pathling#2556 · Opened Feb 23, 2026
Investigate impact of CVE-2025-67721 (Snappy compression) Open

security

Difficulty 4/5 3-5 days Newbie friendliness 25/100

aehrc/pathling#2540 · 1 comment · Opened Feb 5, 2026
responses use constant ETag and cache across job IDs (stale/wrong results) Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

aehrc/pathling#2529 · Opened Dec 18, 2025

aehrc/pathling

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