Pathling

<!-- Release notes generated using configuration in .github/release.yml at 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

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](https://pathling.csiro.au/docs/encoders) page within the documentation.

<!-- Release notes generated using configuration in .github/release.yml at v5.1.0 -->

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

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

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

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](https://delta.io/) 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](https://pathling.csiro.au/docs/configuration.html).

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