Pathling

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

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.

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.

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.

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.