Releases | Open Source Science

What's Changed

Security updates

Remove commons-lang (CVE-2025-48924)
Update Derby to 10.16.1.1 (CVE-2022-46337)

Full Changelog: https://github.com/aehrc/pathling/compare/v8.0.0...v8.0.1

- Java
Published by johngrimes 9 months ago

pathling - v8.0.0

This release features our new SQL on FHIR view runner, a completely reworked and more performant query engine, and many other changes.

As part of this release, we took the decision to significantly change the focus and scope of Pathling with the purpose of rebuilding it around the SQL on FHIR specification.

This will mean that the server implementation will be temporarily removed. It will also mean that the scope of FHIRPath functions will be temporarily reduced to the minimal FHIRPath subset defined within the SQL on FHIR Shareable View Definition specification (with the exception of the terminology functions).

We have released this functionality as version 8, and we have spawned three work streams to build upon this new foundation:

Implementation of a new server focused upon the Bulk Data Access IG and the draft SQL on FHIR server API. This server will not include the aggregate or extract operations.
Expansion of the scope of the FHIRPath implementation to achieve full or close to full coverage of the FHIRPath spec.
Implementation of Parquet on FHIR as the new schema for lossless persistence of FHIR data for analytics.

We think that this is the best way to align Pathling to user needs, and also to make sure that the code base is sustainable going forwards.

If you are a current user of the server, aggregate or extract operations, please continue using the v7.x series. We are happy to continue maintaining and accepting contributions to this series as requested by users, but will be focusing our enhancement efforts on v8.

Major dependency updates

Spark 3.5.6
HAPI 8.2.1
Java 17

Full Changelog: https://github.com/aehrc/pathling/compare/v7.2.0...v8.0.0

- Java
Published by johngrimes 9 months ago

pathling - v7.2.0

What's Changed

New features

Implement Python and R bulk client APIs by @johngrimes in https://github.com/aehrc/pathling/pull/2162 ### Dependency updates
Upgrade Spark from 3.5.0 to 3.5.5
Upgrade HAPI from 7.0.2 to 7.6.1
Upgrade Delta Lake from 3.2.0 to 3.3.0
Upgrade Spring Boot from 3.2.0 to 3.3.5
And many more...

This release ships our new bulk client capability in the Java, Scala, Python and R APIs. This automates the task of retrieving a bulk extract from a FHIR server and querying it using Pathling.

Check out the documentation here: https://pathling.csiro.au/docs/libraries/fhirpath-query#fhir-bulk-data-api

Full Changelog: https://github.com/aehrc/pathling/compare/v7.1.0...v7.2.0

- Java
Published by github-actions[bot] about 1 year ago

pathling - v7.1.0

What's Changed

New features

Add Parquet and Delta import by @jkiddo and @johngrimes in https://github.com/aehrc/pathling/pull/2062

Full Changelog: https://github.com/aehrc/pathling/compare/v7.0.1...v7.1.0

- Java
Published by github-actions[bot] over 1 year ago

pathling - v7.0.1

What's Changed

Bug fixes

Fix issue with CORS not working when authentication is disabled by @johngrimes in https://github.com/aehrc/pathling/pull/1927

Full Changelog: https://github.com/aehrc/pathling/compare/v7.0.0...v7.0.1

- Java
Published by github-actions[bot] about 2 years ago

pathling - v7.0.0

What's Changed

New features

Full encoding and decoding support for References by @piotrszul in https://github.com/aehrc/pathling/pull/1786 (also see #1784 from @chgl)
Save mode (append, error, overwrite or ignore) can now be set when saving a data source to Parquet and NDJSON formats through the library API ### Bug fixes
Fixed a bug where year-only dates passed to the until function would always return an empty result ### Dependency updates
Upgraded from Java 11 to 17
Upgraded to Spark 3.5.1
Upgraded to Delta Lake 3.2.0
Upgraded to HAPI 7.0.2
Upgraded to Spring Boot 3.2.0 ### Changes to defaults
databricks.delta.schema.autoMerge.enabled is now set to false by default in the server (see #1785 from @chgl)

Important note: Because this release contains schema changes, you may need to re-import your data.

If you override JVM options (or JAVA_TOOL_OPTIONS in the case of the Docker image), you may need to add --add-exports=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED. This is a new requirement due to tighter controls over class access in Java 17.

Full Changelog: https://github.com/aehrc/pathling/compare/v6.4.2...v7.0.0

- Java
Published by github-actions[bot] about 2 years ago

pathling - v6.4.2

What's Changed

Bug fixes

#1774 Fixed: pathlinginstallspark() does not work by @johngrimes

Full Changelog: https://github.com/aehrc/pathling/compare/v6.4.1...v6.4.2

- Java
Published by github-actions[bot] over 2 years ago

pathling - v6.4.1

Changes to the R library relating to CRAN submission.

Pathling is now available via CRAN! 👉 https://cran.r-project.org/package=pathling

- Java
Published by github-actions[bot] over 2 years ago

pathling - v6.4.0

What's Changed

New features

Added R API by @piotrszul in https://github.com/aehrc/pathling/pull/1611
Added Spring Boot Actuator and metrics endpoints by @chgl in https://github.com/aehrc/pathling/pull/1673
Implement reusing of async jobs for equivalent requests by @piotrszul in https://github.com/aehrc/pathling/pull/1414
Added Helm chart for deploying on Kubernetes by @johngrimes

New Contributors

@jkiddo made their first contribution in https://github.com/aehrc/pathling/pull/1772
@chgl made their first contribution in https://github.com/aehrc/pathling/pull/1673

R package

The full set of Pathling functionality is now available as an R package!

Check out the libraries documentation for information on how to install the package, along with examples of how to use it.

We're currently working on getting the package uploaded to CRAN for a simpler installation experience.

Full Changelog: https://github.com/aehrc/pathling/compare/v6.3.1...v6.4.0

- Java
Published by github-actions[bot] over 2 years ago

pathling - v6.3.1

Bug fixes

Logging broken by upgrade to SLF4J 2 #1556

Full Changelog: https://github.com/aehrc/pathling/compare/v6.3.0...v6.3.1

- Java
Published by github-actions[bot] over 2 years ago

pathling - v6.3.0

This release adds a new feature - terminology client language configuration. This allows you to control the preferred language that is requested from the terminology server for operations such as display and property.

Check out the documentation here: Multi-language support

What's Changed

New features

Preferred language configuration parameter by @Markopolo141 in https://github.com/aehrc/pathling/pull/1256

Full Changelog: https://github.com/aehrc/pathling/compare/v6.2.3...v6.3.0

- Java
Published by github-actions[bot] almost 3 years ago

pathling - v6.2.3

What's Changed

Bug fixes

Fix problems with resolution of git.properties by giving it a unique name by @johngrimes in https://github.com/aehrc/pathling/pull/1505
Implemented aliasing of the literal value columns. by @piotrszul in https://github.com/aehrc/pathling/pull/1499
Create library runtime jar by @piotrszul in https://github.com/aehrc/pathling/pull/1510

Important note

The recommended Maven artifact to use when installing Pathling as a Spark Package has changed from library-api to library-runtime. This new artifact is a shaded JAR, built to help address problems caused by classpath conflicts between cluster and Pathling dependencies.

Please review the instructions for installing Pathling to Databricks or your own cluster.

Full Changelog: https://github.com/aehrc/pathling/compare/v6.2.2...v6.2.3

- Java
Published by github-actions[bot] almost 3 years ago

pathling - v6.2.2

What's Changed

Bug fixes

Adding cleaning up of the resources owned by the terminology service by @piotrszul in https://github.com/aehrc/pathling/pull/1391

Full Changelog: https://github.com/aehrc/pathling/compare/v6.2.1...v6.2.2

- Java
Published by github-actions[bot] almost 3 years ago

pathling - v6.2.1

- Java
Published by github-actions[bot] about 3 years ago

pathling - v6.2.0

Check out the documentation for the new FHIRPath query functionality! 🔥

What's Changed

New features

Implement aggregate query in library API by @piotrszul in https://github.com/aehrc/pathling/pull/1309
Implement extract query in library API by @piotrszul in https://github.com/aehrc/pathling/pull/1264 ### Bug fixes
Implemented URN reference rewriting for Bundles by @piotrszul in https://github.com/aehrc/pathling/pull/1436

Full Changelog: https://github.com/aehrc/pathling/compare/v6.1.4...v6.2.0

- Java
Published by github-actions[bot] about 3 years ago

pathling - v6.1.4

What's Changed

Bug fixes

Switching to Cast() constructor common between spark-catalyst 3.3 and 3.4 by @piotrszul in https://github.com/aehrc/pathling/pull/1222

Full Changelog: https://github.com/aehrc/pathling/compare/v6.1.3...v6.1.4

- Java
Published by github-actions[bot] over 3 years ago

pathling - v6.1.3

What's Changed

Bug fixes

Removing JSR-380 validation dependency on EL implementation. by @piotrszul in https://github.com/aehrc/pathling/pull/1195
Add IdleConnectionEvictor to guard against terminology server closing connections by @johngrimes in https://github.com/aehrc/pathling/pull/1204

Full Changelog: https://github.com/aehrc/pathling/compare/v6.1.1...v6.1.3

- Java
Published by github-actions[bot] over 3 years ago

pathling - v6.1.1

What's Changed

Bug fixes

Remove logging_level parameter and improve documentation by @johngrimes in https://github.com/aehrc/pathling/pull/1186
Ensure that Pathling git.properties takes precedence over Spark environment by @johngrimes in https://github.com/aehrc/pathling/pull/1189

Full Changelog: https://github.com/aehrc/pathling/compare/v6.1.0...v6.1.1

- Java
Published by github-actions[bot] over 3 years ago

pathling - v6.1.0

Check out the documentation for the new property and designation functionality:

And also the new configuration options for terminology caching:

What's Changed

New features

Implement 'property' FHIRPath function and UDF by @piotrszul in https://github.com/aehrc/pathling/pull/1123
Implement 'designation' FHIRPath function and UDF by @piotrszul in https://github.com/aehrc/pathling/pull/1132
Client-side terminology caching and optimisation by @johngrimes in https://github.com/aehrc/pathling/pull/1126
Implement target parameter on translate function by @johngrimes in https://github.com/aehrc/pathling/pull/1041 ### Bug fixes
Handle resolution of polymorphic Reference-typed extensions by @johngrimes in https://github.com/aehrc/pathling/pull/1143

Full Changelog: https://github.com/aehrc/pathling/compare/v6.0.4...v6.1.0

- Java
Published by github-actions[bot] over 3 years ago

pathling - v6.0.4

What's Changed

Bug fixes

Apply the same exception reporting rules for async requests as the synchronous ones. by @piotrszul in https://github.com/aehrc/pathling/pull/1049

Full Changelog: https://github.com/aehrc/pathling/compare/v6.0.3...v6.0.4

- Java
Published by github-actions[bot] over 3 years ago

pathling - v6.0.3

What's Changed

Bug fixes

Fix comparison and arithmetic operations for instants by @johngrimes in https://github.com/aehrc/pathling/pull/1029

Full Changelog: https://github.com/aehrc/pathling/compare/v6.0.2...v6.0.3

- Java
Published by github-actions[bot] over 3 years ago

pathling - v6.0.2

What's Changed

Bug fixes

Create a release version of the modified UCUM library, and use it by @johngrimes in https://github.com/aehrc/pathling/pull/1004

Full Changelog: https://github.com/aehrc/pathling/compare/v6.0.1...v6.0.2

- Java
Published by github-actions[bot] over 3 years ago

pathling - v6.0.1

Minor update to the Library API and documentation.

Full Changelog: https://github.com/aehrc/pathling/compare/v6.0.0...v6.0.1

- Java
Published by github-actions[bot] over 3 years ago

pathling - v6.0.0

What's Changed

New features

Quantities and date arithmetic by @johngrimes and @piotrszul in https://github.com/aehrc/pathling/pull/509
Implement exists function by @johngrimes in https://github.com/aehrc/pathling/pull/987
Add new Python helper function: toeclvalue_set by @johngrimes in https://github.com/aehrc/pathling/pull/979
Allow greater control over S3 configuration by @johngrimes in https://github.com/aehrc/pathling/pull/950
Added Sentry logging to async requests (with request context) by @piotrszul in https://github.com/aehrc/pathling/pull/830

Dependency updates

Bump pytest-cov from 3.0.0 to 4.0.0 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/915
Bump joda-time from 2.10.14 to 2.12.0 by @dependabot in https://github.com/aehrc/pathling/pull/945
Bump sphinx from 5.0.2 to 5.3.0 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/957
Bump pathling.hapiFhirVersion from 6.0.3 to 6.1.3 by @dependabot in https://github.com/aehrc/pathling/pull/967
Bump java-jwt from 4.0.0 to 4.2.0 by @dependabot in https://github.com/aehrc/pathling/pull/971
Bump spring-boot-starter-parent from 2.7.2 to 2.7.5 by @dependabot in https://github.com/aehrc/pathling/pull/972
Bump pathling.sparkVersion from 3.3.0 to 3.3.1 by @dependabot in https://github.com/aehrc/pathling/pull/975
Bump gson from 2.9.0 to 2.10 by @dependabot in https://github.com/aehrc/pathling/pull/980
Bump woodstox-core from 6.3.0 to 6.4.0 by @dependabot in https://github.com/aehrc/pathling/pull/981
Bump sentry from 6.3.0 to 6.6.0 by @dependabot in https://github.com/aehrc/pathling/pull/983
Bump pytest from 7.1.2 to 7.2.0 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/985
Bump pyspark from 3.3.0 to 3.3.1 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/986
Bump pathling.hadoopVersion from 3.3.3 to 3.3.4 by @dependabot in https://github.com/aehrc/pathling/pull/775
Bump jib-maven-plugin from 3.2.1 to 3.3.0 by @dependabot in https://github.com/aehrc/pathling/pull/825
Bump delta-core_2.12 from 1.2.1 to 2.1.0 by @dependabot in https://github.com/aehrc/pathling/pull/826
Bump jackson-core from 2.13.3 to 2.13.4 by @dependabot in https://github.com/aehrc/pathling/pull/844
Bump ipython from 8.4.0 to 8.5.0 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/852
Bump maven-shade-plugin from 3.3.0 to 3.4.0 by @dependabot in https://github.com/aehrc/pathling/pull/875
Bump scala-library from 2.12.16 to 2.12.17 by @dependabot in https://github.com/aehrc/pathling/pull/876
Bump wiremock-jre8 from 2.33.2 to 2.34.0 by @dependabot in https://github.com/aehrc/pathling/pull/879
Bump jwks-rsa from 0.21.1 to 0.21.2 by @dependabot in https://github.com/aehrc/pathling/pull/883
Bump json from 20220320 to 20220924 by @dependabot in https://github.com/aehrc/pathling/pull/890
Bump scala-maven-plugin from 4.7.0 to 4.7.2 by @dependabot in https://github.com/aehrc/pathling/pull/910

Migration notes

You will need to re-import your data upon upgrading to this new major release. This is to accommodate changes to the encoders, necessitated by the new functionality relating to quantities.

There have also been changes made to the way that S3 authentication is configured. The old pathling.storage.aws.* variables have been removed in favour of a default authentication provider chain that will automatically pick up authentication within the environment. In addition to this, you can now send configuration values directly through to the underlying Hadoop AWS library.

Full Changelog: https://github.com/aehrc/pathling/compare/v5.4.0...v6.0.0

- Java
Published by github-actions[bot] over 3 years ago

pathling - v5.4.0

What's Changed

New features

Implement terminology client authentication by @johngrimes in https://github.com/aehrc/pathling/pull/654 ### Bug fixes
Fix gaps in translation of results into literals within drill-down by @johngrimes in https://github.com/aehrc/pathling/pull/739
Fix error relating to use of URN in fullUrl in batch by @johngrimes in https://github.com/aehrc/pathling/pull/741 ### Dependency updates
Bump exec-maven-plugin from 3.0.0 to 3.1.0 by @dependabot in https://github.com/aehrc/pathling/pull/711
Bump pathling.hapiFhirVersion from 6.0.2 to 6.0.3 by @dependabot in https://github.com/aehrc/pathling/pull/729
Bump sentry from 6.1.4 to 6.3.0 by @dependabot in https://github.com/aehrc/pathling/pull/731
Bump terser from 5.14.1 to 5.14.2 in /site by @dependabot in https://github.com/aehrc/pathling/pull/732
Bump spring-boot-starter-parent from 2.7.1 to 2.7.2 by @dependabot in https://github.com/aehrc/pathling/pull/735
Bump scala-maven-plugin from 4.6.3 to 4.7.0 by @dependabot in https://github.com/aehrc/pathling/pull/721
Bump delta-core_2.12 from 1.2.1 to 2.0.0 by @dependabot in https://github.com/aehrc/pathling/pull/733 ### Other changes
Replace WebSecurityConfigurerAdapter with SecurityFilterChain bean by @johngrimes in https://github.com/aehrc/pathling/pull/740

Full Changelog: https://github.com/aehrc/pathling/compare/v5.3.2...v5.4.0

- Java
Published by github-actions[bot] almost 4 years ago

pathling - v5.3.2

What's Changed

New features

Bug fixes

Fix issue with multiple non-singular columns with different types by @johngrimes in https://github.com/aehrc/pathling/pull/697
Return correct error when accessing unsupported Reference children by @johngrimes in https://github.com/aehrc/pathling/pull/698 ### Dependency updates
Bump @sentry/node from 7.5.1 to 7.6.0 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/691
Bump pathling.awsSdkVersion from 1.12.256 to 1.12.257 by @dependabot in https://github.com/aehrc/pathling/pull/692 ### Other changes
Include TypeScript sources in NPM libraries by @johngrimes in https://github.com/aehrc/pathling/pull/695
Upload benchmarks to S3 by @johngrimes in https://github.com/aehrc/pathling/pull/694

Full Changelog: https://github.com/aehrc/pathling/compare/v5.3.1...v5.3.2

- Java
Published by johngrimes almost 4 years ago

pathling - v5.3.1

What's Changed

Changes to Python library

Implement member_of, translate and subsumes functions by @johngrimes in https://github.com/aehrc/pathling/pull/653

Dependency updates

Bump scala-maven-plugin from 4.6.2 to 4.6.3 by @dependabot in https://github.com/aehrc/pathling/pull/629
Bump pathling.hapiFhirVersion from 6.0.1 to 6.0.2 by @dependabot in https://github.com/aehrc/pathling/pull/636
Bump spring-boot-starter-parent from 2.7.0 to 2.7.1 by @dependabot in https://github.com/aehrc/pathling/pull/650
Bump java-jwt from 3.19.2 to 4.0.0 by @dependabot in https://github.com/aehrc/pathling/pull/655
Bump sentry from 6.1.0 to 6.1.4 by @dependabot in https://github.com/aehrc/pathling/pull/659
Bump woodstox-core from 6.2.8 to 6.3.0 by @dependabot in https://github.com/aehrc/pathling/pull/660
Bump jsonassert from 1.5.0 to 1.5.1 by @dependabot in https://github.com/aehrc/pathling/pull/677
Bump pathling.awsSdkVersion from 1.12.240 to 1.12.256 by @dependabot in https://github.com/aehrc/pathling/pull/689
Bump sphinx from 5.0.1 to 5.0.2 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/631
Bump prettier from 2.7.0 to 2.7.1 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/625
Bump typescript from 4.7.3 to 4.7.4 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/640
Bump typescript from 4.7.3 to 4.7.4 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/642
Bump @types/jest from 28.1.1 to 28.1.3 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/647
Bump @babel/preset-env from 7.18.2 to 7.18.6 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/662
Bump @babel/preset-typescript from 7.17.12 to 7.18.6 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/664
Bump @aws-sdk/client-s3 from 3.110.0 to 3.121.0 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/671
Bump @types/node from 16.11.40 to 16.11.43 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/684
Bump @types/node from 16.11.40 to 16.11.43 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/686
Bump prettier from 2.7.0 to 2.7.1 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/626
Bump @types/aws-lambda from 8.10.100 to 8.10.101 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/639
Bump ts-node from 10.8.1 to 10.8.2 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/675
Bump @sentry/node from 7.1.1 to 7.5.1 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/685

Full Changelog: https://github.com/aehrc/pathling/compare/v5.2.0...v5.3.1

- Java
Published by github-actions[bot] almost 4 years ago

pathling - v5.2.0

What's Changed

Changes to Python library

Update Python dependencies and improve API for standalone scenario by @johngrimes in https://github.com/aehrc/pathling/pull/613

Dependency updates

Bump prettier from 2.6.2 to 2.7.0 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/607
Bump pathling.sparkVersion from 3.2.1 to 3.3.0 by @dependabot in https://github.com/aehrc/pathling/pull/614
Bump sentry from 5.7.4 to 6.1.0 by @dependabot in https://github.com/aehrc/pathling/pull/615
Bump @types/node from 16.11.36 to 16.11.40 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/617
Bump @types/node from 16.11.38 to 16.11.40 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/618
Bump @aws-sdk/client-s3 from 3.105.0 to 3.110.0 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/619
Bump pyspark from 3.2.1 to 3.3.0 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/620
Bump scala-library from 2.12.15 to 2.12.16 by @dependabot in https://github.com/aehrc/pathling/pull/588
Bump @sentry/node from 7.0.0 to 7.1.1 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/593
Bump @types/aws-lambda from 8.10.98 to 8.10.100 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/600
Bump prettier from 2.6.2 to 2.7.0 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/608
Bump pathling.awsSdkVersion from 1.12.234 to 1.12.240 by @dependabot in https://github.com/aehrc/pathling/pull/616

Other changes

Split test suite into tranches by @johngrimes in https://github.com/aehrc/pathling/pull/596
Baseline JMH benchmark for aggregate operation. by @piotrszul in https://github.com/aehrc/pathling/pull/606

Full Changelog: https://github.com/aehrc/pathling/compare/v5.1.1...v5.2.0

- Java
Published by github-actions[bot] almost 4 years ago

pathling - v5.1.1

What's Changed

Dependency updates

Bump typescript from 4.7.2 to 4.7.3 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/572
Bump @aws-sdk/client-s3 from 3.100.0 to 3.105.0 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/583
Bump @types/node from 16.11.36 to 16.11.38 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/585
Bump jest and @types/jest in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/586
Bump @sentry/node from 6.19.7 to 7.0.0 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/555
Bump scala-maven-plugin from 4.6.1 to 4.6.2 by @dependabot in https://github.com/aehrc/pathling/pull/561
Bump maven-shade-plugin from 3.2.4 to 3.3.0 by @dependabot in https://github.com/aehrc/pathling/pull/565
Bump joda-time from 2.8.1 to 2.10.14 by @dependabot in https://github.com/aehrc/pathling/pull/566
Bump gson from 2.8.9 to 2.9.0 by @dependabot in https://github.com/aehrc/pathling/pull/567
Bump ts-node from 10.8.0 to 10.8.1 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/569
Bump @types/fhir from 0.0.34 to 0.0.35 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/570
Bump @types/aws-lambda from 8.10.97 to 8.10.98 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/571
Bump typescript from 4.7.2 to 4.7.3 in /lib/import by @dependabot in https://github.com/aehrc/pathling/pull/573
Bump @types/fhir from 0.0.34 to 0.0.35 in /lib/js by @dependabot in https://github.com/aehrc/pathling/pull/574
Bump pytest from 6.2.2 to 7.1.2 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/577
Bump build from 0.7.0 to 0.8.0 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/578
Bump twine from 4.0.0 to 4.0.1 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/579
Bump pathling.awsSdkVersion from 1.12.230 to 1.12.234 by @dependabot in https://github.com/aehrc/pathling/pull/580
Bump ipython from 8.2.0 to 8.4.0 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/581
Bump sphinx from 4.5.0 to 5.0.1 in /lib/python by @dependabot in https://github.com/aehrc/pathling/pull/582

Full Changelog: https://github.com/aehrc/pathling/compare/v5.1.0...v5.1.1

- Java
Published by github-actions[bot] almost 4 years ago

pathling - v5.1.0

This release includes a new Python API for the encoders, available through PyPI!

The encoders package is also now available via Maven Central, for Java and Scala users.

For more information, check out the Encoders page within the documentation.

What's Changed

New features

Python API for encoders by @piotrszul in https://github.com/aehrc/pathling/pull/494

Dependency updates

Update JS library dependencies by @johngrimes in https://github.com/aehrc/pathling/pull/549
Bump java-jwt from 3.19.1 to 3.19.2 by @dependabot in https://github.com/aehrc/pathling/pull/523
Bump sentry from 5.7.3 to 5.7.4 by @dependabot in https://github.com/aehrc/pathling/pull/533
Bump jackson-core from 2.13.2 to 2.13.3 by @dependabot in https://github.com/aehrc/pathling/pull/534
Bump pathling.hapiFhirVersion from 5.7.2 to 6.0.1 by @dependabot in https://github.com/aehrc/pathling/pull/548
Bump spring-boot-starter-parent from 2.6.7 to 2.7.0 by @dependabot in https://github.com/aehrc/pathling/pull/541

New Contributors

@kapsner made their first contribution in https://github.com/aehrc/pathling/pull/516

Full Changelog: https://github.com/aehrc/pathling/compare/v5.0.2...v5.1.0

- Java
Published by github-actions[bot] almost 4 years ago

pathling - v5.0.2

Bug fixes

Fixing the value column creation for NullLiteralPaths by @piotrszul in https://github.com/aehrc/pathling/pull/518

Dependency updates

Bump aws-java-sdk-bom from 1.12.209 to 1.12.211 by @dependabot in #517
Bump wiremock-jre8 from 2.33.1 to 2.33.2 by @dependabot in https://github.com/aehrc/pathling/pull/513

Full Changelog: https://github.com/aehrc/pathling/compare/v5.0.1...v5.0.2

- Java
Published by johngrimes about 4 years ago

pathling - v5.0.1

Bug fixes

Multiple trivial aggregations against resource causes hang #457
Where clauses are not applied independently to columns in extract #483
Error when executing drill-down expression: left operand not comparable to right operand #484

Dependency updates

Bump sentry from 5.7.0 to 5.7.3 #489
Bump jib-maven-plugin from 3.2.0 to 3.2.1 #468
Bump wiremock-jre8 from 2.32.0 to 2.33.1 #481
Bump pathling.hapiFhirVersion from 5.7.1 to 5.7.2 #473
Bump jacoco-maven-plugin from 0.8.7 to 0.8.8 #476
Bump aws-java-sdk-bom from 1.12.188 to 1.12.209 #507
Bump delta-core_2.12 from 1.1.0 to 1.2.1 #503
Bump lombok from 1.18.22 to 1.18.24 #492
Bump spring-boot-starter-parent from 2.6.5 to 2.6.7 #498

- Java
Published by johngrimes about 4 years ago

pathling - v5.0.0

New features

Extract operation #4
Incremental update #162
Extension content #163
Allow for nested elements at arbitrary depth #322
Asynchronous requests with progress #144
Allow use of IAM assumed roles for S3 authentication #330

Bug fixes

Extract result contains "trailing nulls" #434
AnalysisException: cannot resolve 'xhnoc2' given input columns: [1bhal4, _5kx4eg, _5tf7wt, _cboqor, _fhn6fb, _hxc7... #432
Attempt to return a Decimal value with greater than supported scale #421
Handle missing resource ID #399
AnalysisException: cannot resolve given input columns #385
RuntimeException: Problem building a LiteralPath class #381
Error should be 404: search on "List" resource #342

Migration notes

You will need to re-import your data upon upgrading to this new major release. This is to accommodate changes to the encoders, and a move to Delta Lake as the new persistence scheme. The move to Delta Lake enables our new incremental update feature, as well as future features relating to resource history.

There have also been a number of changes to configuration:

Configuration of Java VM options now uses JAVA_TOOL_OPTIONS
pathling.verboseRequestLogging has been moved to pathling.terminology.verboseLogging
The default terminology server has been changed to https://tx.ontoserver.csiro.au/fhir

Read the full configuration documentation.

- Java
Published by johngrimes about 4 years ago

pathling - v4.0.1

Dependency updates

Bump pathling.hapiFhirVersion from 5.3.3 to 5.5.0 #367
Bump pathling.sparkVersion from 3.1.1 to 3.1.2 #352
Bump scala-maven-plugin from 4.5.3 to 4.5.4 #371
Bump jackson-core from 2.12.4 to 2.12.5 #370
Bump spring-boot-starter-parent from 2.5.3 to 2.5.4 #363
Bump sentry from 4.3.0 to 5.1.2 #368
Bump wiremock-jre8 from 2.27.2 to 2.30.1 #358
Bump pathling.dockerJavaVersion from 3.2.8 to 3.2.11 #356
Bump java-jwt from 3.15.0 to 3.18.1 #355
Bump jacoco-maven-plugin from 0.8.6 to 0.8.7 #351

- Java
Published by johngrimes almost 5 years ago

pathling - v4.0.0

New features

Add operation and resource level authorisation #282
Sum function and combine operator #317
FHIRPath functions: anyTrue, anyFalse, allTrue, allFalse #325

Bug fixes

Technical version information lost on deserialisation #222
Make Coding equality semantics conformant and consistent #299
Aggregate returns invalid drill down expression #295
Error importing FHIR resources from NDJSON file containing empty lines #298
Unknown primitive type: org.hl7.fhir.r4.model.DecimalType #318
Drill-down does not preserve bracketing #319
Parallel import operations should not be allowed #321
Null aggregation following aggregation with reverseResolve #347

Dependency updates

Bump pathling.antlrVersion from 4.9.1 to 4.9.2 #288
Bump lombok from 1.18.18 to 1.18.20 #289
Bump pathling.dockerJavaVersion from 3.2.7 to 3.2.8 #290
Bump jackson-core from 2.12.1 to 2.12.4 #327
Bump woodstox-core from 6.2.5 to 6.2.6 #297
Bump pathling.hapiFhirVersion from 5.3.0 to 5.3.3 #302
Upgrade to GitHub-native Dependabot #303
Bump spring-boot-starter-parent from 2.4.4 to 2.5.3 #344
Bump scala-maven-plugin from 4.4.1 to 4.5.3 #314
Bump jwks-rsa from 0.17.0 to 0.19.0 #324

Important note: As part of this release, changes have been made to the format of the Parquet files. Any data that was imported using a Pathling version prior to 4 will need to be re-imported.

- Java
Published by johngrimes almost 5 years ago

pathling - v3.2.0

New features

#74 - translate function
#280 - Line and position now included in error messages

Bug fixes

#265 - OperationDefinition shows incorrect operations in CapabilityStatement

Refactoring

#153 - Terminology service abstraction

Dependency updates

#285 - Bump woodstox-core from 6.2.3 to 6.2.5
#283 - Bump lombok-maven-plugin from 1.18.16.0 to 1.18.20.0
#266 - Bump pathling.hapiFhirVersion from 5.2.1 to 5.3.0
#269 - Bump jwks-rsa from 0.15.0 to 0.17.0
#270 - Bump pathling.sparkVersion from 3.0.1 to 3.1.1
#271 - Bump scala-maven-plugin from 4.4.0 to 4.4.1
#284 - Bump java-jwt from 3.12.1 to 3.15.0
#273 - Bump sentry from 4.1.0 to 4.3.0
#276 - Bump spring-boot-starter-parent from 2.4.2 to 2.4.4

Resolves #74, #280, #265, #153, #266, #269, #270, #271, #273, #276, #283, #284, #285.

- Java
Published by johngrimes about 5 years ago

pathling - v3.1.0

New features

#224 - FHIRPath function: not
#195 - FHIRPath function: iif

Dependency updates

#258 Bump sentry from 3.2.1 to 4.1.0
#254 Bump lombok from 1.18.16 to 1.18.18

Resolves #224, #195.

- Java
Published by johngrimes over 5 years ago

pathling - v3.0.1

Changes:

#242 Path traversal from %resource causes error within where argument
#239 Throw an error on unsuccessful access of the warehouse database location
#243 Sentry reporting not working
#238 Bump jackson-core from 2.12.0 to 2.12.1
#246 Bump commons-compiler from 3.0.9 to 3.1.3
#235 Bump pathling.antlrVersion from 4.9 to 4.9.1
#241 Bump spring-boot-starter-parent from 2.4.1 to 2.4.2
#244 Bump sentry from 3.2.0 to 3.2.1
#245 Bump pathling.hapiFhirVersion from 5.2.0 to 5.2.1
#248 Bump java-jwt from 3.12.0 to 3.12.1

Resolves #242, #239, #243, #238, #246, #235, #241, #244, #245, #248.

- Java
Published by johngrimes over 5 years ago

pathling -

This new release incorporates a number of changes:

Move to the Spring Boot framework
Upgrade to Spark 3
Refactored FHIRPath class model
Request caching
Improved error handling and reporting
Improved configuration
Support for invoking the aggregate operation with a GET request
Bug fixes and performance improvements

Breaking changes

Changes have been made to the encoding of the Parquet files from FHIR - any pre-existing Parquet data will need to be re-created from the FHIR sources before use with Pathling 3.
The format of the request to the aggregate operation has been simplified, removing the labels and flattening the structure of the parameters.
Configuration has been completely reworked - see the Configuration page for the new variable names.
Pathling now uses Spark 3 - this change will need to be reflected in any Spark cluster installations used to host Pathling.
The semantics of the subsumes function have changed, and may yield different results in Pathling 3. See subsumes for the new specification.
Source URLs used with the import operation now need to be whitelisted, for security purposes. A list of valid prefixes can be configured, by default you can import from file:///usr/share/staging.
For servers with a configured S3 warehouse source that uses authentication - you will now need to specify pathling.storage.aws.anonymousAccess=false in addition to the variables containing the authentication details, see Configuration - Storage.

Resolves #2, #6, #70, #76, #88, #157, #167, #175, #179, #181, #182, #184, #185, #186, #196, #202, #212, #213, #218, #220, #229, #233.

- Java
Published by johngrimes over 5 years ago

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pathling - v6.0.4

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pathling - v6.0.3

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pathling - v6.0.1

pathling - v6.0.0

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New features

Dependency updates

Migration notes

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pathling - v5.3.2

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Bug fixes

pathling - v5.3.1

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