Commit Graph

1822 Commits

Author SHA1 Message Date
dotasek 6b7ac47076
Don't access getBinaries directly in XVerExtensionManager (#864)
* Don't access getBinaries directly in XVerExtensionManager

* Remove getBinaries() add getBinaryKeysAsSet()

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-07-22 11:13:42 -04:00
markiantorno fa0597f864 Updating version to: 5.6.53-SNAPSHOT and incrementing test cases dependency. 2022-07-22 06:10:23 +00:00
markiantorno aa6094c451 Release: v5.6.52
## Validator Changes

* Fix issue with startsWith in FHIRPath engine
* Fix bugs validating references (some references not resolved)
* Fix minor issue supporting 4.3.0 (R4B)
* fix bug loading R5 extensions

## Other code changes

* Fix NPE rendering bundles
* R5 Changes to ConceptMap
* Fix bug rendering extensions
* Fix bug accessing polymorphic fields when rendering
* Fix bug around lazy loading packages when validating references
* Add ability to suppress serialising ids when serialising element models
***NO_CI***
2022-07-22 05:50:56 +00:00
Grahame Grieve a82bbeb887
Merge pull request #873 from hapifhir/gg-202207-version-annotations
fix up version annotations
2022-07-22 15:16:01 +10:00
Grahame Grieve 5284773527 fix up version annotations 2022-07-22 14:27:26 +10:00
Grahame Grieve 78c372961e
Merge pull request #872 from hapifhir/gg-202207-bug-fixes
Gg 202207 bug fixes
2022-07-22 13:19:50 +10:00
Grahame Grieve 4800d8a498 fix rendering of extensions in Profiles 2022-07-22 11:23:30 +10:00
Grahame Grieve be51677623 Add ability to suppress serialising ids 2022-07-22 07:58:51 +10:00
Grahame Grieve 49cf36cc50 fix bug rendering extensoins 2022-07-20 11:27:00 +10:00
Grahame Grieve fa54433022 fix bug loading R5 extensions 2022-07-20 11:26:49 +10:00
Grahame Grieve 0bf2ea7551 Fix bug accessing polymorphic fields 2022-07-20 11:26:20 +10:00
Grahame Grieve 2b626a9361 Changes to ConceptMap rendering as discussed with Vocab Committee 2022-07-20 11:25:10 +10:00
Grahame Grieve 421162d146 Fix NPE rendering bundles 2022-07-20 11:24:34 +10:00
Grahame Grieve e150b50f54 Fix issue with startsWith in FHIRPath engine 2022-07-20 11:24:13 +10:00
dotasek 14494d23b9
Use property to set apache poi version (#861)
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-07-18 10:43:51 -04:00
markiantorno bb13edfdc0 Updating version to: 5.6.52-SNAPSHOT and incrementing test cases dependency. 2022-07-18 10:41:30 +00:00
markiantorno 078ca1e13a Release: v5.6.51
## Validator Changes

* no changes

## Other code changes

* Update R5 for revised ConceptMap in R5 cibuild, and release new core library for R5 build process
***NO_CI***
2022-07-18 10:23:13 +00:00
Grahame Grieve 392b064433 updates for new release of R5 2022-07-18 17:56:23 +10:00
Grahame Grieve a7303995cc Merge remote-tracking branch 'origin/master' 2022-07-12 12:29:31 +10:00
dependabot[bot] 169abbed09
Bump poi from 4.0.1 to 4.1.1 in /org.hl7.fhir.r5
Bumps poi from 4.0.1 to 4.1.1.

---
updated-dependencies:
- dependency-name: org.apache.poi:poi
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
2022-06-29 17:13:11 +00:00
Grahame Grieve 023aea34fb R4B and R5 extension changes 2022-06-28 15:39:15 +03:00
markiantorno 982ce5f58f Updating version to: 5.6.51-SNAPSHOT and incrementing test cases dependency. 2022-06-24 18:48:18 +00:00
markiantorno 4a654122fb Release: v5.6.50
## Validator Changes

* Improved logging when discriminator doesn't match doing slicing
* Use correct IPS branch when validating
* Load R5 extensions when validating (draft)
* Make it possible to run tests cases directly from validator (see command line help)

## Other code changes

* Regenerate R4B code for final R4B release
* Reduce text logging when running tests
* Minor test case fixes
* Fix fetching package by canonical to use pkgcanonical instead of canonical
* Fix broken link rendering code system references
* improvements to profile validation
***NO_CI***
2022-06-24 18:32:05 +00:00
dotasek ae8b21014a Bump version to 5.6.50-SNAPSHOT 2022-06-24 11:29:30 -04:00
markiantorno 891aaf4a20 Release: v5.6.49
## Validator Changes

* Improved logging when discriminator doesn't match doing slicing
* Use correct IPS branch when validating
* Load R5 extensions when validating (draft)
* Make it possible to run tests cases directly from validator (see command line help)

## Other code changes

* Regenerate R4B code for final R4B release
* Reduce text logging when running tests
* Minor test case fixes
* Fix fetching package by canonical to use pkgcanonical instead of canonical
* Fix broken link rendering code system references
* improvements to profile validation
***NO_CI***
2022-06-24 12:41:29 +00:00
Grahame Grieve 95dee12d0e
Merge pull request #844 from hapifhir/gg-202206-amsterdam
Gg 202206 amsterdam
2022-06-24 13:53:33 +02:00
Grahame Grieve ba7b0d8bfa reduce text logging running tests 2022-06-24 13:15:55 +02:00
Grahame Grieve a81b5e2a9d Fix broken link rendering code systems 2022-06-24 11:41:54 +02:00
Grahame Grieve 38b0ed94ed fix logging bug in JsonParser 2022-06-24 11:41:33 +02:00
Grahame Grieve 2c46cfe690 Add loading R5 extensions 2022-06-24 11:41:19 +02:00
Grahame Grieve 636c651d76 Improvements to profile comparison 2022-06-24 11:40:42 +02:00
dotasek 8a3d7d3670 Catch ClassCastException and report clearer error message 2022-06-22 13:43:28 -04:00
dotasek 003be69129 More specific Exception type for test 2022-06-22 13:24:09 -04:00
dotasek 8ab27b2cb3 Failing test 2022-06-22 13:20:05 -04:00
Grahame Grieve 45efd0afaf
Merge pull request #839 from hapifhir/dotasek-fix-datetime-tozulu-day-message
Fix validation message for toCalendarZulu day validation
2022-06-21 22:18:13 +02:00
dotasek 0ecba5bf2a Fix validation message for toCalendarZulu day validation 2022-06-20 09:26:11 -04:00
dotasek af7fd15667 Rebuild caches + fix parse of JSON in FHIRRequestBuilder 2022-06-17 18:15:48 -04:00
dotasek 35fbd191ac Add tests and tix for terminologyCapabilitiesQuick 2022-06-17 15:00:58 -04:00
dotasek 6ac813addd Add tests and fix for terminologyCapabilities 2022-06-17 11:21:11 -04:00
dotasek 093904abb1 Log errors, don't throw them down a hole 2022-06-17 10:42:55 -04:00
dotasek 36f4524c7e Add method to for retrying capabilities statements 2022-06-17 10:01:56 -04:00
dotasek 2195d76807 Assert preferredResourceFormat values in test 2022-06-17 10:01:06 -04:00
dotasek 7935f8238f Start with failing test 2022-06-17 09:43:50 -04:00
dotasek 1fee28fe84
Feature - run JUnit tests from validator_cli (#835)
* WIP add initial test running code

* Importing test modules fix breaking tests 1

* Clean up pom dependencies, move execution before context load

* Re-org and document cli pom

* Set more dependencies to compile. Print entries in classpath

* Try running via internal Executors

* Clearer class names + provide clear output

* Clean up test summarys and output + update class regex to junit default

* Refactor to avoid having to extend class

* Trim down dependency additions in pom + javadoc

* Add the rest of the modules to TestExecutor

* Parse additional params for classname filter and module

* Add experimental JUnit 4 runner in case JUnit 5 hates us.

* Include JUnit4 tests via adapters. Need to refactor for better naming.

* Update LoadIgTests to JUnit 5

* Gentle refactor, print execution time

* Remove unnecessary interface, organize packages

* Remove cached resources (need to fix this)

* Allow setting of txCache globally for tests + fix r5 tests

* Mild refactor of TestExecutor + Reorder test execution

* Add fhirTestCasesDirectory to testConfig + get r4 tests working

* Add dstu2016may and dstu3 tests

* Add dstu2 tests

* Add convertors tests

* Refactor resourceNameForFile + don't copy existing files

* Get all txCache directories centrally and allow all to live in same dir

* Start extracting txCache resources

* Finish extracting txCache resources

* Fix failing GraphQLEngineTest

* Try an mvn install for the pull pipeline

* Clean and refactor

* Test coverage

* Fix GraphQLEngineTests for local jar run

* More refactoring, more tests

* Add bare test for TxCacheResourceExtractor

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-06-14 17:04:00 -04:00
markiantorno 3484b891d5 Updating version to: 5.6.49-SNAPSHOT and incrementing test cases dependency. 2022-06-08 07:01:23 +00:00
markiantorno 17ce4678d4 Release: v5.6.48
## Validator Changes

* Clean up the -extension parameter - make implementation conistent with documentation
* Stop auto-converting parameters to strings for string functions e.g. .length() in the FHIRPath engine
* Add parameter -implicit-fhirpath-string-conversions for old FHIRPath string conversion functionality

## Other code changes

* Fix NPE counting descendents when validating
* Fix bug processing invalid HTTP response
***NO_CI***
2022-06-08 06:41:48 +00:00
Grahame Grieve b0dfc9f281 fix bug counting children + fix issue with automatic string conversion in FHIRPath + fix bug in HTTP client + fix bug rendering profile comparison 2022-06-08 08:56:46 +10:00
markiantorno 2c8db93787 Updating version to: 5.6.48-SNAPSHOT and incrementing test cases dependency. 2022-05-27 17:24:16 +00:00
markiantorno 567a9b2ce7 Release: v5.6.47
## Validator Changes

* Significant improvement in performance of validation (10-100 fold for simple resources)
* Add output tracker to trask progress of validation (Validate %R against %P..........20..........40..........60..........80.........|)
* Alter per-1 to handle different precision on start/end
* Add support for a -jurisdiction parameter, preparing for jurisdictionally specific constraints in profiles
* Fix bug in snapshot generation where type slices on a mandatory element were all marked as mandatory
* Add warnings when potential matches are found when performing reference resolution in bundles

## Other code changes

* extend FHIRPath to support lowBoundary(), highBoundary() and precision()
* Fix for inefficiency in StructureMap engine
* Update version of PubPack used by the IGPublisher
* Handle scope on TestScript R4 <-> r5 conversion
* Fix bug converting extension context = Resource (R4 <-> R5 conversion)
* Update VSAC importer for changes to VSAC FHIR authorization
* Fix broken links in profile comparison due to cross version issues
***NO_CI***
2022-05-27 16:52:13 +00:00
Grahame Grieve 4cc0a8dfba Add support for 4.3.0 2022-05-27 22:17:32 +10:00
Grahame Grieve 655fc8b6ca Fix bug in snapshot generation where type slices on a mandatory element were all marked as mandatory 2022-05-27 13:40:38 +10:00
Grahame Grieve 8324123f73 Fix broken links in profile comparison due to cross version issues 2022-05-27 13:39:25 +10:00
Grahame Grieve ce48c435fd
Merge pull request #817 from hapifhir/gg-202205-performance
Performance work in the validator
2022-05-25 06:35:33 +10:00
Grahame Grieve 47e205883c Performance work in the validator 2022-05-23 12:23:23 +10:00
Grahame Grieve f3bed096c7
Merge pull request #813 from hapifhir/gg-202205-ts-conv
Gg 202205 ts conv
2022-05-20 08:17:04 +10:00
Grahame Grieve 51185f74ff
Merge pull request #811 from hapifhir/dotasek-structuremapping-evaluate-2
Use MAP_EXPRESSION instead of MAP_WHERE_EXPRESSION
2022-05-19 17:33:41 +10:00
Grahame Grieve d39ed690f8 Add jurisdiction parameter to Validator 2022-05-18 08:23:05 +10:00
Grahame Grieve 919d6e6d8b extend FHIRPath to support lowBoundary(), highBoundary() and precision() 2022-05-14 00:19:08 +10:00
dotasek d099c7f0f1 Use MAP_EXPRESSION instead of MAP_WHERE_EXPRESSION 2022-05-12 18:05:59 -04:00
markiantorno 3ab828c381 Updating version to: 5.6.47-SNAPSHOT and incrementing test cases dependency. 2022-05-12 10:35:09 +00:00
markiantorno eca2fa5a5c Release: v5.6.46
## Validator Changes

* Trim unknown resource types when pre-adopting cross version extensions with type=Reference

## Other code changes

* Package Client: Get Packages by Dependency
* Snapshot Generator (R4b/R5): Fix generation of complex extension snapshot + improve rendering
* New tests for StructureMap execution
***NO_CI***
2022-05-12 10:18:11 +00:00
dotasek 8a8bbb7308
Add tests for evaluate transforms using json StructureMap (#807)
* Add tests for evaluate transforms using json StructureMap

Fixes issues/802

* Reduce test chatter, fix missing ',' in EVALUATE render

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-05-11 12:52:47 -04:00
dotasek cd7142faa1
Repair output of GraphQL response to include only idPart (#808)
* Repair output of GraphQL response to include only idPart

* Fix for breaking test.

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-05-11 12:01:23 -04:00
Grahame Grieve be631a5130 Trim unknown resource types when pre-adopting extensions of type Reference from future versions 2022-05-11 02:14:08 +10:00
Grahame Grieve 0999c8d460 fix issue with complex extension snapshot goes into 3rd level when it doesn't need to 2022-05-11 02:13:35 +10:00
markiantorno a4fd92633d Updating version to: 5.6.46-SNAPSHOT and incrementing test cases dependency. 2022-05-06 01:02:54 +00:00
markiantorno f2134e9643 Release: v5.6.45
## Validator Changes

* Support IGs #current where main instead of master

## Other code changes

* Add id to Profile CSVs
***NO_CI***
2022-05-06 00:29:32 +00:00
Grahame Grieve 3a696b0231 Merge remote-tracking branch 'origin/master' 2022-05-06 10:02:10 +10:00
Grahame Grieve 30daa9dd26 Add ID to profile csv 2022-05-06 09:59:51 +10:00
dotasek cc6ee9216c Fix 0 case terminology cache test (intermittent test failure) 2022-05-05 14:40:32 -04:00
Grahame Grieve 7a7e3240b4 ElementDefinition adornments 2022-05-05 23:09:55 +10:00
markiantorno 264e79bc24 Updating version to: 5.6.45-SNAPSHOT and incrementing test cases dependency. 2022-05-05 01:29:36 +00:00
markiantorno 5801daeb08 Release: v5.6.44
## Validator Changes

* Handle invalid HTTP responses better when accessing packages

## Other code changes

* Fix various rendering NPEs
***NO_CI***
2022-05-05 01:09:45 +00:00
Grahame Grieve df71644ba5 Fix NPEs 2022-05-05 05:47:54 +10:00
markiantorno 6df50d482b Updating version to: 5.6.44-SNAPSHOT and incrementing test cases dependency. 2022-04-28 02:39:13 +00:00
markiantorno 3fffad10e3 Release: v5.6.43
## Validator Changes

* fix problem with non-new data types on xver extensions
* enable -extension parameter for validator

## Other code changes

* Fix bug when converting resolved clinical status for allergy intolerance
***NO_CI***
2022-04-28 02:20:19 +00:00
Grahame Grieve 3712804353 fix problem with non-new data types on xver extensions 2022-04-28 09:47:06 +10:00
Grahame Grieve 0a58140163 enable -extension parameter for validator 2022-04-27 08:28:29 +10:00
markiantorno 5fc2e9d6ec Updating version to: 5.6.43-SNAPSHOT and incrementing test cases dependency. 2022-04-23 14:25:48 +00:00
markiantorno 4f5aa8754c Release: v5.6.42
## Validator Changes

* Fix invalid FHIR version bug when loading IGs with explicit FHIR version

## Other code changes

* Fix reverse references in GraphQL searches
* Regenerate R4B code for candidate final release (not quite final yet)
* Various minor fixes for bugs found doing R4B finalization (wildcard types, version difference comparisons)
***NO_CI***
2022-04-23 14:06:50 +00:00
Grahame Grieve b47b0653c4 moving FHIRPublication 2022-04-23 23:18:23 +10:00
dotasek 1645982389
Fix for issues/766 - reverse references with _history in GraphQL (#790)
* Create and use getIdPart

* Add tests and changes for dstu3, r4, r4b, and r5

* Update get/set Id javadoc

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-04-22 18:06:24 -04:00
Grahame Grieve fa92f85f3c Merge remote-tracking branch 'origin/master' 2022-04-22 07:36:53 +10:00
Grahame Grieve 10f2325e19 R4B quality fixes 2022-04-22 07:36:28 +10:00
Grahame Grieve 5fef79c08d Update Validator -version handling, and improve tx server error handling 2022-04-20 11:17:40 +10:00
dotasek a7354f999e
Dotasek oe r4r5structuremapconversion (#775)
* Fix exception R5 to R4 of StructureMap #771

* Fix typo

* Enhance conversion from r5 to r4 + add failing test for r4 to r5

* WIP Convert R4 variable to R5 parameter and try to get correct dataType

* Clean up rough-work test

* Move static methods to FHIRPathConstant class

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-04-13 18:22:58 -04:00
Grahame Grieve 9928efa0d1 align additional bindings with extension definition 2022-04-13 18:07:57 +10:00
markiantorno 6328230f9f Updating version to: 5.6.42-SNAPSHOT and incrementing test cases dependency. 2022-04-12 04:03:54 +00:00
markiantorno 8785babf24 Release: v5.6.41
## Validator Changes

* Handle reslicing within the same profile
* Fix up wrong handling of context on exists() in FHIRPath
* Add hints to profiles around behavior of pattern on repeating elements
* Ignore all tooling extensions when validating
* support specifying an alternative version when loading source using -ig parameter
* Don't validate Bundle.entry.fullUrl as a reference to some other content

## Other code changes

* Improved output for unit test comparisons
* Fix conversion issues around Base64Binary
* Fix for R4/R5 DataRequirements conversion for DeviceUsage
* Add AdditionalBindings Rendering (draft)
* Display all designations when rendering ValueSets
* Fix bug where expansions have empty objects some times
* Fix R4B Snapshot generation
* Enable Linking to fragment CodeSystems
***NO_CI***
2022-04-12 03:31:27 +00:00
Grahame Grieve 6f3fe23f49 refactor additional bindings 2022-04-12 13:11:42 +10:00
Grahame Grieve b9902833c5 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir 2022-04-12 09:12:35 +10:00
Grahame Grieve d73881df55 Add Get canonical URL names 2022-04-12 09:11:39 +10:00
Grahame Grieve c3281340a0 Add Additional Bindings rendering 2022-04-12 09:11:18 +10:00
Grahame Grieve 9385557e04
Merge pull request #783 from gabriel0316/allowOtherDesignations
Allow other designations
2022-04-12 09:08:52 +10:00
Grahame Grieve fcbc13cb9c
Merge pull request #784 from gabriel0316/displayDesignations
Display all designations
2022-04-12 09:08:16 +10:00
dotasek a8da416ee3 Fix xml test + add unit tests 2022-04-11 14:57:10 -04:00
dotasek 2181cb14d5 Change tests to xml + fix breaking test 2022-04-11 14:10:53 -04:00
Gabriel 2fb5c67e32 Display all designations
With this commit all designations (incl. languages) will be displayed
in the Logical Definition and the Expansion of a ValueSet.
2022-04-08 13:39:09 +02:00
Grahame Grieve cdef76bc6d Fix bug where expansions have empty onbjects 2022-04-07 00:20:11 +10:00
Gabriel 51cd908f20 Allow other designations
With returning the url it is possible to allow other
designation.use than only the two specified
SNOMED codes.
2022-04-06 16:09:09 +02:00