Commit Graph

2901 Commits

Author SHA1 Message Date
Grahame Grieve bb2e87c250 automatically process markdown in code system concept definitions 2023-08-18 13:47:16 +10:00
Grahame Grieve c32492a66b improve error draft error where possible 2023-08-18 13:46:56 +10:00
Grahame Grieve 87a9a58771 fix for testing IGs 2023-08-17 21:19:56 +10:00
Grahame Grieve f7c606e88b rendering fixes for IGs 2023-08-17 18:29:59 +10:00
Grahame Grieve 0d1072616e rework comparison and related rendering 2023-08-17 18:14:12 +10:00
Grahame Grieve eacffd11df Add support for external strings for tx tests 2023-08-17 11:14:34 +10:00
Grahame Grieve c71d3a107d always return x-caused-by-unknown-system when system is unknown 2023-08-16 22:38:21 +10:00
Grahame Grieve 57d1a973e4 fix return paths when validating codes 2023-08-16 22:38:01 +10:00
Grahame Grieve 3cb9c195a0 change to used-xxx parameters instead of version 2023-08-16 22:37:48 +10:00
Grahame Grieve bf5a2ba768 More work on comparison functionality 2023-08-16 22:29:11 +10:00
dotasek 976915f3bc Merge branch 'master' into do-20230815-bump-okhttp-dependencies 2023-08-15 17:41:02 -04:00
dotasek dacc73a114 Bump okhttp dependency, exclude vulnerable transitives 2023-08-15 12:52:01 -04:00
Grahame Grieve ced8a36f37 Work on comparison and rendering for showing differences properly 2023-08-15 19:33:39 +10:00
Grahame Grieve ebc755bc2a Check consistency between standards status and resource status 2023-08-14 21:11:49 +10:00
Grahame Grieve e3dd645b75 more differencing improvements 2023-08-14 15:36:08 +10:00
Grahame Grieve dd70d185df improve error message when comparing JSON arrays 2023-08-14 15:35:53 +10:00
Grahame Grieve a57afef5a4 Fix up return issue code for unkown issues 2023-08-14 15:35:36 +10:00
Grahame Grieve 0fc4398dfc Rendering improvements for showing difference analysis (WIP) 2023-08-14 15:34:54 +10:00
Grahame Grieve b45f6caf60 Improve error message for unknown properties 2023-08-14 15:33:48 +10:00
Grahame Grieve 9cde582732 Update Comparers for annotating models with version differences 2023-08-14 15:33:24 +10:00
Grahame Grieve 1d4eefa62b Rename implySystem to inferSystem per TI decision 2023-08-13 19:55:52 +10:00
Grahame Grieve 2474c198c7 fix FML parser problem 2023-08-12 23:06:27 +10:00
Grahame Grieve a5ff5b50a8 rework how extensions are handled after discussion with Michael 2023-08-11 22:27:50 +10:00
Grahame Grieve ec31868486 improve version annotation presentation 2023-08-11 14:16:50 +10:00
Grahame Grieve 9c65d7a20f Fix for NPE validating codes 2023-08-11 14:16:29 +10:00
Grahame Grieve 4a11c5ffe1 fix failing test 2023-08-11 14:16:15 +10:00
Grahame Grieve 6041660e9b Improved error messages on server failure 2023-08-11 14:16:09 +10:00
Grahame Grieve 991a2defee Start working on showing changes when rendering 2023-08-11 12:26:21 +10:00
Grahame Grieve b7fd419509 Check experimental / draft in mini terminology service 2023-08-11 12:25:37 +10:00
Grahame Grieve 1208d691b2 Fix loading issues in test mode for simplifier packages 2023-08-11 12:25:01 +10:00
Grahame Grieve 9625f9b818 remove spurious logging 2023-08-11 12:24:38 +10:00
Grahame Grieve d9df51fa63 Add test case for PE Engine based on issue #1343 2023-08-11 12:24:25 +10:00
Grahame Grieve b85b588825 restructure validators to properly validate deprecated dependencies 2023-08-11 12:24:08 +10:00
Grahame Grieve 5aefd6a268 add flat mode to tests, and add experimental functionality 2023-08-11 12:11:22 +10:00
Grahame Grieve cce9d9cdac
Merge pull request #1388 from hapifhir/ExampleScenarioPause
Added support for pause
2023-08-10 00:05:00 +10:00
Grahame Grieve 952dedd06b #1343 - addChild error in PEBuilder 2023-08-09 19:48:01 +10:00
Grahame Grieve 93868669fe Fix issue in FHIRPath .combine focus handling 2023-08-09 16:29:08 +10:00
Grahame Grieve 8d826aba44 fix rendering issue in subscription topic 2023-08-09 16:27:56 +10:00
Lloyd McKenzie d8c8f26e2b Fix bad link in response 2023-08-08 19:55:17 -06:00
Lloyd McKenzie 7155b940fd Added support for pause 2023-08-08 14:18:50 -06:00
Grahame Grieve 4b006f82ab delay loading content when loading IGs 2023-08-08 21:36:46 +10:00
Grahame Grieve 752f0e1983 fix bug in warning about No valid Display Names found 2023-08-08 19:58:51 +10:00
Grahame Grieve 4c132852c0 include ExampleScenario renderer in factory and refactor 2023-08-08 19:58:27 +10:00
Lloyd McKenzie 820a945807 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core into ExampleScenarioRendering 2023-08-07 09:27:29 -06:00
Lloyd McKenzie 6eeeb2400f Removed debug code, handle escaping of aliases 2023-08-07 09:27:05 -06:00
markiantorno 9c3a6a7f37 Updating version to: 6.0.26-SNAPSHOT and incrementing test cases dependency. 2023-08-04 17:55:11 +00:00
markiantorno bc3f348108 Release: v6.0.25
## Validator Changes

* Fix problem with evaluating extension contexts
* Fix up support for inactive codes and fix error message syntax
* Fix issue with collection status of resolve() being wrong
* Improved paths in profile error messages
* Fix problem with extension slicing being missed sometimes.
* Fix problem with code validation caching ignoring whitespace
* Produce useful error message when whitespace is wrong in display name
* Support for x-version extensions when generating snapshots

## Other code changes

* Render inactive property in expansions
* Resolve URL for x-version extensions
* Don't warn for loading a wrong version package more than once
* Do not supercede R4 terminology when loading R5 IGs
* Migrate type support when generating differentials
***NO_CI***
2023-08-04 17:27:42 +00:00
Grahame Grieve 4727bc57ff Fix up support for inactive codes and fix error message syntax 2023-08-04 18:44:40 +10:00
Grahame Grieve f1571ea2b4 Do not supercede R4 terminology when loading R5 IGs 2023-08-04 18:42:40 +10:00
Grahame Grieve e0b9a6dcc7 migrate type support when generating differentials 2023-08-04 18:42:18 +10:00
Grahame Grieve 7da1e419e9 remove unwanted debugging statements 2023-08-04 11:57:18 +10:00
Grahame Grieve c069538d2e what happened to that code? 2023-08-04 11:54:18 +10:00
Grahame Grieve ad08255740 Merge remote-tracking branch 'origin/master' 2023-08-04 11:49:19 +10:00
Grahame Grieve 45b5631e62 Fix issue with collection status of resolve() being wrong 2023-08-04 11:47:44 +10:00
Grahame Grieve 8cc698af5d Improved paths in profile error messages, and fix problem with extension slicing being missed sometimes. 2023-08-04 11:47:08 +10:00
dotasek f835c7efe4 Only trim whitespace outside of the json 2023-08-03 16:38:42 -04:00
Grahame Grieve 6d0883468b
2023 08 gg extension paths (#1380)
* fix problem with whitespace in terminology caching

* Support for x-version extensions when generating snapshots

* Fix problem with evaluating extension contexts

* Produce useful error message when whitespace is wrong in display name

* Resolve URL for x-version extensions

* render inactive property in expansions

* fix tests

* ping build

* Point to correct test-cases version

---------

Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-08-03 16:12:48 -04:00
Grahame Grieve b668f4a04a fix tests 2023-08-03 21:33:57 +10:00
Grahame Grieve dfc8a006e2 render inactive property in expansions 2023-08-03 20:29:22 +10:00
Grahame Grieve ecefe55cd5 Resolve URL for x-version extensions 2023-08-03 20:29:00 +10:00
Grahame Grieve 3a5dffa4a7 Produce useful error message when whitespace is wrong in display name 2023-08-03 20:28:42 +10:00
Grahame Grieve df4432b49d Fix problem with evaluating extension contexts 2023-08-03 20:28:04 +10:00
Grahame Grieve 09b6fda419 Support for x-version extensions when generating snapshots 2023-08-03 20:27:20 +10:00
Grahame Grieve 24d67798d6 fix problem with whitespace in terminology caching 2023-08-03 20:26:57 +10:00
markiantorno 011167a218 Updating version to: 6.0.25-SNAPSHOT and incrementing test cases dependency. 2023-08-02 23:28:12 +00:00
markiantorno 42274a7bd3 Release: v6.0.24
## Validator Changes

* Create warnings for status on terminology resources
* Don't load resources from core examples package

## Other code changes

* fix up copy directory for case differences
***NO_CI***
2023-08-02 23:02:37 +00:00
Lloyd McKenzie 9cb786bcd4 Changed to use StringBuilder as recommended 2023-08-02 10:59:05 -06:00
Grahame Grieve b23e31d44c fix narrative rendering 2023-08-02 22:53:57 +10:00
Grahame Grieve 42aef4ad40 fix for npe 2023-08-02 21:38:01 +10:00
Grahame Grieve 32f2f6acc7 warnings for status on terminology resources 2023-08-02 18:12:02 +10:00
Lloyd McKenzie 3c06f76df7 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core into FixExampleScenarioConversion 2023-08-01 09:38:11 -06:00
Lloyd McKenzie cbebc13501 Added support for ExampleScenario rendering 2023-08-01 09:37:30 -06:00
Grahame Grieve d314a927af FIx up problem resolving URLs 2023-07-31 14:38:09 +10:00
Grahame Grieve be8276bd4a Add rendering for UsageContext 2023-07-31 14:37:51 +10:00
Grahame Grieve b42c908328 More improved FHIRPath checking when validating 2023-07-31 14:37:41 +10:00
Grahame Grieve bd3d718256 Update obligation handling code for split definitions 2023-07-29 08:48:54 +10:00
markiantorno 0165495626 Updating version to: 6.0.24-SNAPSHOT and incrementing test cases dependency. 2023-07-27 14:23:16 +00:00
markiantorno db5d2b07c3 Release: v6.0.23
## Validator Changes

* Update IPS versions for -ips parameter (and get it working again)
* fix up validation of constraints in differentials (wasn't always happening)
* add warnings when collection status isn't right
* Better information messages when CodeSystem.content = not-present
* Add character check in validator for illegal XML Unicode characters
* Fix path problem in NpmPackage (some simplifier packages couldn't be processed)
* Fix NPE validating codes in value sets with improper expansions

## Other code changes

* Add support for Liquid assign
* Switch to DateTime type for Android Support
* Code clean up: remove unused imports
* Fix JSON unicode encoding handling of chars <32 code points
***NO_CI***
2023-07-27 13:56:32 +00:00
Grahame Grieve 06c865badf Fix NPE validating codes in value sets with improper expansions 2023-07-27 17:50:42 +10:00
Grahame Grieve 4eff9a3b68 fix up validation of FHIRPaths in differentials, and add warnings when collection status isn't right 2023-07-27 17:49:57 +10:00
Grahame Grieve a3c32d86a0 add support for Liquid assign + Fix JSON unicode encoding and add character check in validator for illegal XML Unicode characters 2023-07-26 12:32:51 +10:00
Grahame Grieve fefd1ad1d6 fix -ips parameter and add -check-ips-codes parameter 2023-07-26 00:59:02 +10:00
markiantorno 592fba54cc Updating version to: 6.0.23-SNAPSHOT and incrementing test cases dependency. 2023-07-22 17:06:10 +00:00
markiantorno b7fd3be910 Release: v6.0.22
## Validator Changes

* Add support for private NPM registries requiring authentication
* Don't check FHIRPaths on differentials - not enough type info to test reliably
* Fix bugs in FHIRPath handling of logical models
* Fix minor bugs in type handling for Logical Models and R3 Profile validation
* Remove spurious warning message validating CDA documents
* Add value set qa checking
* Fixes to validator for new CDA package (proper handling of logical model types)
* Fix up bi-di warning message
* Add provisional support for alternate codes
* Workaround ClinicalImpression definition problem in core spec
* Fix to get context variables right when running invariants + fix for parent not always being populated + check type in derived profiles
* Fix checking FHIRPath statements on inner elements of type slices
* Fix scan of naming systems (error validating namespaces)
* Fix issue checking invariant expressions in R5

## Other code changes

* FHIRPath in HAPI mode: Strip returned IIdType of qualifier, version, and resourceType
* Update R4 and R4B FHIRPath implementations for changes picked up in R5 usage
* Fix obligation rendering message
* Fix missing extensions when converting value set properties
* Fix type of x-unknown-code-system in $validate-code response
* Fix CDA validation test case
* Much work on TxServer test case framework + Update terminology server implementation and tests for changes to test cases
* OMOP Vocabulary and ICFImporter development
* Add OWASP dependency check (#1347), upgrade many packages, remove ShEx
* Add github action to upload results
* Remove unused javalin dependency, also generate html reports
* Added test case for ExampleScenario conversion (R4/R5) and significantly bulked up the conversion process
* Remove unneeded resources (#1346) (help16.png)
* Add test for setVsAsUrl parameter setting (#1345)
***NO_CI***
2023-07-22 16:41:19 +00:00
dotasek 2654e85df3
Implement private NPM server (#1337)
* WIP start adding NPM data.

* WIP 2 Testing against verdaccio npm

* WIP private npm package servers

* WIP2 add server type config

* WIP3 parse tarball url

* Fix package date parsing, start mocking server tests

* Add dummy package, assert authorization and content

* Add more tests

* Add serverType to settings test

* Ignore tgz files for bidi check

* tighter bidi ignore

* different ignore regex

* Make packageManagement settings, allow ignoring default package servers

* New tests + token authentication

* Manage 404s when configured servers don't have package
2023-07-22 11:01:36 -04:00
dotasek b62f9afc5a
Remove resourceType, version, and qualifier from FHIRPath id results (#1357)
* Breaking test

* Strip returned IIdType of qualifier, version, and resourceType

* Add fix to r4b

* Add fix to r5
2023-07-22 11:01:13 -04:00
Grahame Grieve bb4379f5dd fix bugs in type handling 2023-07-22 21:01:08 +10:00
Grahame Grieve 363045c1c8 Fix bugs in FHIRPath handling of logical models 2023-07-22 08:18:55 +10:00
Grahame Grieve 5a858949d4 Merge remote-tracking branch 'origin/master' 2023-07-21 21:18:42 +10:00
Grahame Grieve e324047735 Fix issue with type evaluation in R3 checking FHIRPath types 2023-07-21 21:16:48 +10:00
Grahame Grieve 4e8f0f0c0c
Merge pull request #1353 from hapifhir/2023-07-gg-context-fixes
2023 07 gg context fixes
2023-07-21 14:48:19 +10:00
Grahame Grieve d8e2e020af fix failing tests 2023-07-21 12:41:56 +10:00
Grahame Grieve cf1b53bba0 Update terminology server implementation and tests for changes to test cases 2023-07-21 05:38:09 +10:00
Grahame Grieve f52df7c0cc Fix obligation rendering message 2023-07-20 08:21:51 +10:00
Grahame Grieve 616cf5fdb3 Add provisional support for alternate codes 2023-07-20 08:21:19 +10:00
Grahame Grieve 274c49bde5 Workaround ClinicalImpression definition problem in core spec 2023-07-20 08:20:18 +10:00
dotasek 2f11af9bfa
Return HumanName getText() preferentially in getNameAsSingleString (#1355)
* Failing tests

* Return getText if it exists in HumanName
2023-07-18 12:22:53 -04:00
Grahame Grieve 3f67cbee9e Merge remote-tracking branch 'origin/master' 2023-07-18 11:12:10 +10:00
Grahame Grieve 8c0539136c suppress spurious error message 2023-07-18 11:08:09 +10:00
Grahame Grieve 55c12301ba remove shex 2023-07-18 11:06:06 +10:00
dotasek 89d0f6f867
Remove weso shex (#1352)
* Bump shex dependency

* Bump jackson to 2.15.2

* Bump thymeleaf to 3.1.1.RELEASE

* Remove es.weso shexs_2.12 and ignored tests
2023-07-17 18:20:53 -04:00
dotasek ceceb6c7d5
Bump shex dependency (#1351) 2023-07-17 16:35:00 -04:00
Lloyd McKenzie 57a9580db7 Added test case for ExampleScenario conversion and significantly bulked up the conversion process 2023-07-13 22:59:12 -06:00
dotasek 6598c1d28e
Add test for setVsAsUrl parameter setting (#1345) 2023-07-12 16:16:09 -04:00
Grahame Grieve 5e30c0ee92 Fix checking FHIRPath statements on inner elements of type slices 2023-07-09 08:03:35 +10:00
Grahame Grieve c174400e73 fix scan of naming systems 2023-07-08 22:08:36 +10:00
markiantorno 6a187a9232 Updating version to: 6.0.22-SNAPSHOT and incrementing test cases dependency. 2023-07-07 12:36:19 +00:00
markiantorno 45ae02cf1d Release: v6.0.21
## Validator Changes

* Fix up processing conditions in -watch mode
* Fixes for validating against logical models (for fixed up CDA core package)
* Better testing of extension context (when limited to profile)
* Fix handling of UCUM codes when no terminology server
* Report hints and warnings on some code validation that had been not reported
* Better validation of valuesets when checking derived profiles

## Other code changes

* Render reference identifier if there is one when rendering references
* Hide empty place holder column when rendering by profile
* Fix npe rendering extensions + improve base64 presentation
* OMOP terminology importer
* update SPDX code system in R4/R4B for support for not-open-source
* Fix up type handling for conversions between R4/R4B and R5 (OperationDefinition fix)
***NO_CI***
2023-07-07 12:10:05 +00:00
Grahame Grieve c6e68dc9c6 Fixes to validator for new CDA package (proper handling of logical model types) 2023-07-07 09:38:55 +10:00
Grahame Grieve 9a48340b6c render reference identifier if there is one 2023-07-07 05:01:16 +10:00
Grahame Grieve b46f968665 hide empty place holder column 2023-07-07 05:00:59 +10:00
Grahame Grieve 0004e06a5d fix npe rendering extensions + improve base64 presentation 2023-07-07 05:00:51 +10:00
Grahame Grieve 7166d55153 better validation of derived valuesets + better handling of validation failures on UCUM when no terminology server 2023-07-05 07:22:30 +10:00
Grahame Grieve 70e123e69b Fix up rendering of base64 content 2023-07-05 07:18:12 +10:00
markiantorno 6db701767a Updating version to: 6.0.21-SNAPSHOT and incrementing test cases dependency. 2023-06-30 23:19:08 +00:00
markiantorno 6a6c425562 Release: v6.0.20
## Validator Changes

* no changes

## Other code changes

 * Fix for SPDR not-open-source in code
 * fix name and title in VSAC import process
 * More work on Android support + fix issues in NPM package installation that caused
***NO_CI***
2023-06-30 22:52:51 +00:00
markiantorno 3c8e26f078 Updating version to: 6.0.20-SNAPSHOT and incrementing test cases dependency. 2023-06-30 05:37:45 +00:00
markiantorno 3b82a4d829 Release: v6.0.19
## Validator Changes

* no changes

## Other code changes

* Fix for SPDR not-open-source in code
* fix name and title in VSAC import process
* More work on Android support
***NO_CI***
2023-06-30 05:08:20 +00:00
Grahame Grieve de8a2f0f73 Re-add support for not-open-source in the R5 code base 2023-06-30 08:41:02 +10:00
markiantorno 06a1d523a3 Updating version to: 6.0.19-SNAPSHOT and incrementing test cases dependency. 2023-06-29 05:12:43 +00:00
markiantorno 76955fa3d5 Release: v6.0.18
## Validator Changes

* Fix issue loading SPDX value set + Fix missing code for 'not-open-source'
* Allow target to be treated as source when validating FML
* Fix issues validating names and urls for logical models
* Don't duplicate warnings about missing expressions on invariants in R5

## Other code changes

* Handle case where base hasn't got a snapshot generating snapshots
***NO_CI***
2023-06-29 04:47:28 +00:00
Grahame Grieve 236cf06946 Handle case where base hasn't got a snapshot generating snapshots 2023-06-29 13:17:15 +10:00
markiantorno 7ffbe7703d Updating version to: 6.0.18-SNAPSHOT and incrementing test cases dependency. 2023-06-28 07:13:43 +00:00
markiantorno 345151b132 Release: v6.0.17
## Validator Changes

* Fix check for correct type name use in logical models (for CDA)
* Fix bug loading packages (introduced working on minimal loading)
* Fir NPE processing R3 Structure Definitions
* exempt ele-1 from constraint consistency checking
* Add -watch-scan-delay and -watch-settle-time
* fix missing error validating structure maps
* Fix bug with erroneous warning in snapshot generation about profile not being found
* Update SPDX code system to latest version
* Output proper filename in validation log

## Other code changes

* Refactor version utility code
* Fix help placeholders
* Better error when handling loading resources
* fix duplicate element generation in CDA.AD type snapshot generation
* Fix message about rendering problem. Actual solution... not sure.
* Minimal Memory model changes for Npm for Android
***NO_CI***
2023-06-28 06:47:19 +00:00
Grahame Grieve 9b94e6a1ec Fix test for correct type name in logical models (CDA) 2023-06-28 15:10:20 +10:00
Grahame Grieve 284ad1c2be fix bug loading package 2023-06-28 11:06:09 +10:00
Grahame Grieve 704d498300 Fix NPE handling R3 structure definitions 2023-06-28 05:56:14 +10:00
Grahame Grieve 3bb5e8d06d better error handling loading resources 2023-06-27 22:18:35 +10:00
Grahame Grieve 1a144091c4 fix duplicate element generation in CDA.AD type snapshot generation 2023-06-27 22:18:14 +10:00
Grahame Grieve 40380ff0f3 Fix message about rendering problem. Actual solution... not sure. 2023-06-24 09:06:19 +10:00
Grahame Grieve 189c3c7b7d Fix bug with erroneous warning in IG publisher log about profile not found 2023-06-24 09:06:01 +10:00
Grahame Grieve 2f253f3457 Update SPDX implementation 2023-06-24 08:55:51 +10:00
markiantorno 67cb3006f2 Updating version to: 6.0.17-SNAPSHOT and incrementing test cases dependency. 2023-06-21 07:40:48 +00:00
markiantorno 8bd0f0b1ad Release: v6.0.16
## Validator Changes

Post DevDays Release - many significant changes!

* Add ```-watch-mode``` parameter (See [doco](https://confluence.hl7.org/display/FHIR/Using+the+FHIR+Validator#UsingtheFHIRValidator-Watchmode))
* Start checking constraint expressions defined in profiles and logical models, and update FHIRPath for logical models
* Start checking ElementDefinition.mustHaveValue and ElementDefinition.valueAlternatives
* Start validating derived questionnaires
* Tighten up checking on FHIRPath - enforce use of ```'```, and don't accept ```"``` for string delimiters
* Add ```-allow-double-quotes-in-fhirpath``` parameter ([doco](https://confluence.hl7.org/display/FHIR/Using+the+FHIR+Validator#UsingtheFHIRValidator-LegacyFHIRPathSetting))
* Fix error when validating profiles that mix canonical() and Reference() types
* Fix extension context checking
* Fix erroneous FHIRPath expression eld-11 when loading
* Fix incomplete support for ```-display-issues-are-warnings``` parameter
* Fix broken NullFlavor binding in R4
* Fix various NPE errors doing value set validation (+ logging tx operations)
* Minor performance improvements to start up time
* Auto-update implied slicing elements when min < slice min

## Other code changes

* Add CodeQL to the build process
* Various NPE fixes
* Add getValueAsString(TemporalPrecisionEnum) method to date/time types
* Fix rendering for unresolvable ValueSets
* Remove r4b eclipse project files
* Upgrade multiple dependency libraries (per CodeQL)
* Only record sorting errors when generating snapshots when debug mode is on
* Tighten up SSL certificate checking
* Partial refactor of CLI parameter handling
* Fix path regex (per CodeQL)
* Remove erroneous logging from conversion tests
* Rendering improvements for various profile related extensions
* More work on TxTests operation (lenient wrt extensions)
* Fix handling of summary extension (delete duplicate tools summary extension, and don't inherit it)
* Reprocess URLs in Markdown extensions on both StructureDefinition and ElementDefinition
* Improve URL detection in markdown when reprocessing URLs
***NO_CI***
2023-06-21 07:09:07 +00:00
Grahame Grieve 6effe6ebe9 update FHIRPath for logical models and nested type checking and fix repeat() checking 2023-06-21 09:22:18 +10:00
Grahame Grieve 04f7805be4 Auto-update extension min- slicing + fix handling of summary extension + update markdown element url handling + update url detection in markdown 2023-06-21 09:21:05 +10:00
Grahame Grieve 52abef6f2c Auto-update extension min- slicing + fix handling of summary extension + update markdown element url handling + update url detection in markdown 2023-06-21 09:20:35 +10:00
Grahame Grieve 4e5c501b1f
Merge pull request #1315 from hapifhir/do-20230619-datetimetype-string-precision
New getValueAsString(TemporalPrecisionEnum) method for DateTimeType
2023-06-20 09:56:40 +10:00
Grahame Grieve 2607d028a7 fix compile problem 2023-06-20 09:15:36 +10:00
Grahame Grieve 551892c095 Merge remote-tracking branch 'origin/master' 2023-06-20 09:11:51 +10:00
Grahame Grieve 9cf8e0368c fix up extension context checking 2023-06-20 08:36:22 +10:00
Grahame Grieve ec7b79bc1e Fix rendering for unresolvable value sets 2023-06-20 07:02:26 +10:00
dotasek ae59d97ba5 Document new method, add to all FHIR versions 2023-06-19 15:41:04 -04:00
dotasek 92fb21de1e Test and new getValueAsString(TemporalPrecisionEnum) method 2023-06-19 14:47:39 -04:00
dotasek 829882773a
More use of dependencyManagement, bump guava (#1313) 2023-06-19 12:26:21 -04:00
dotasek 195dcc0898
Fix unimplemented method in test (#1312) 2023-06-19 10:51:10 -04:00
Grahame Grieve 394077c8ec fix NPE doing valueset validation 2023-06-19 22:43:43 +10:00
Grahame Grieve 19d3952b11 Validate FHIRPath constraints in IGs and profiles 2023-06-19 22:42:02 +10:00
Grahame Grieve d1a785e5ad only record sorting errors if debugging snapshot generation 2023-06-19 22:40:08 +10:00
Grahame Grieve 38b5295f8d fix error logging headers 2023-06-19 22:39:42 +10:00
Grahame Grieve 96cadbed47
Merge pull request #1259 from hapifhir/Type-validation-fixes
Fix problem when profiling a base type that supports both Reference a…
2023-06-19 02:36:33 +10:00
Grahame Grieve 8bd4fc3ee6
Merge pull request #1309 from hapifhir/do-20230615-tx-request-lenient-display
Add lenient-display-validation param
2023-06-19 02:33:17 +10:00
Grahame Grieve 297313b30a Fix issue with broken NullFlavor binding in R4 2023-06-18 13:02:21 +10:00
Grahame Grieve dfb4404ce6 Add support for mustHaveValue and valueAlternatives + render imposesProfile + compliesWithProfile 2023-06-18 13:00:58 +10:00
Grahame Grieve 11eb2cef53 fix index error 2023-06-17 09:41:15 +10:00
Grahame Grieve 99895e7a97 Performance improvements for validation, including -watch engine 2023-06-17 09:40:34 +10:00
Grahame Grieve 2d0dcbb803 rendering improvements for profile extensions 2023-06-17 09:38:27 +10:00
dotasek f4b6ff2f6e Refactor and introduce test 2023-06-15 10:38:03 -04:00
dotasek 10c50a14f0 Add lenient-display-validation param 2023-06-15 08:31:30 -04:00
Grahame Grieve 481698cf24 Fix up terminology tests to ignore irrelevant extensions 2023-06-12 17:17:30 +01:00
dotasek ff7997d7d2
Fix older jetbrains annotations transitive dependency (#1299) 2023-06-09 14:43:49 -04:00
markiantorno 8237fb862b Updating version to: 6.0.16-SNAPSHOT and incrementing test cases dependency. 2023-06-08 21:23:36 +00:00
markiantorno cc14a4142f Release: v6.0.15
## Validator Changes

* no changes

## Other code changes

* Update commons-beanutils and apache.poi dependencies
***NO_CI***
2023-06-08 20:56:04 +00:00
dotasek 7b05c7514e
Bump poi version, remove unused old dependencies (#1296) 2023-06-08 10:47:37 -04:00
markiantorno 10f466487b Updating version to: 6.0.15-SNAPSHOT and incrementing test cases dependency. 2023-06-08 05:03:27 +00:00
markiantorno 3969ac75c4 Release: v6.0.14
## Validator Changes

* no changes

## Other code changes

* Fix bugs in language handling
* Implement Trivy vulnerability scanning and update POI and okhttp libraries
***NO_CI***
2023-06-08 04:33:30 +00:00
markiantorno 619703dbf8 Updating version to: 6.0.14-SNAPSHOT and incrementing test cases dependency. 2023-06-07 13:14:17 +00:00
markiantorno b704ea50fc Release: v6.0.13
## Validator Changes

* no changes

## Other code changes

* add clear() to JsonObject
***NO_CI***
2023-06-07 12:48:04 +00:00
Grahame Grieve bfdb28b96e add JsonObject.clear() 2023-06-07 13:57:56 +02:00
markiantorno a605d944bc Updating version to: 6.0.13-SNAPSHOT and incrementing test cases dependency. 2023-06-06 21:27:18 +00:00
markiantorno 8edd61a197 Release: v6.0.12
## Validator Changes

* Improve message when there's multiple display options

## Other code changes

* Fix loading issue with r5 extensions
* NPM package compression improvements
* Update language file handling to handle context
* Remove logical models in minifier, and other improvements
* Auto update minimum slicing cardinality when slicer is assumed (extensions)
***NO_CI***
2023-06-06 20:55:08 +00:00
Grahame Grieve a4f54f519f
Merge pull request #1290 from hapifhir/gg-202206-cardinality-fixes
Gg 202206 cardinality fixes
2023-06-05 23:26:13 +02:00
Grahame Grieve 01b4219259 update language file handling to handle context properly 2023-06-05 21:16:51 +02:00
Grahame Grieve fe7cd1f39a Clean up extension loading issue 2023-06-05 21:16:28 +02:00
Grahame Grieve fd346cc67b Auto update minimum slicing cardinality when slicer is assumed (extensions) 2023-06-05 21:16:14 +02:00
Grahame Grieve 1c4ef1fa00 Improve message when there's multiple display options 2023-06-05 21:15:31 +02:00
Grahame Grieve bf19a2d2fa Remove logical models in minifier, and other improvements 2023-06-05 21:14:56 +02:00
markiantorno 72eee9cab7 Updating version to: 6.0.12-SNAPSHOT and incrementing test cases dependency. 2023-06-02 14:24:34 +00:00
markiantorno 44db954743 Release: v6.0.11
## Validator Changes

* no changes

## Other code changes

* Increment CQFramework dependency
***NO_CI***
2023-06-02 13:58:04 +00:00
Grahame Grieve c31836e734 better error reporting when parsing fails outright 2023-06-01 06:58:46 +03:00
Grahame Grieve d4d5b42aa1 add Resource Dependency walker + Resource Minifier functionality 2023-05-31 06:32:55 +03:00
markiantorno f238d1af14 Updating version to: 6.0.11-SNAPSHOT and incrementing test cases dependency. 2023-05-29 22:43:58 +00:00
markiantorno edd06865c7 Release: v6.0.10
## Validator Changes

* no changes

## Other code changes

* Delete unused package import that breaks downstream JavaDoc
***NO_CI***
2023-05-29 22:14:49 +00:00
dotasek 6626fe1952
Remove unused dependency (#1283) 2023-05-29 16:57:20 -04:00
markiantorno 253357e5aa Updating version to: 6.0.10-SNAPSHOT and incrementing test cases dependency. 2023-05-29 13:44:41 +00:00
markiantorno 4014698c7d Release: v6.0.9
## Validator Changes

* Add support for "Obligation Profiles" (see https://chat.fhir.org/#narrow/stream/179177-conformance/topic/Proposed.20new.20Profile.20features)
* Adjust slice min/max checking to ignore type slices (rules are different in this case)
* Properly handle validating mime/type when terminology server is not available

## Other code changes

* Rework Pipelines - more stability and quicker
* Fix bug where elementmodel.Element.copy() didn't clone children. Users of the Element Model (not the normal model) should check all uses of copy. (Only known users are Validator + IG publisher)
* Add nimbus & ZXing to core library dependencies for forthcoming improved SHC/SHL support
***NO_CI***
2023-05-29 13:18:12 +00:00
Grahame Grieve 8c7a5bf724 fix bug checking slice min/max 2023-05-29 03:38:48 +03:00
Grahame Grieve fe474b1ad2 properly handle... 2023-05-29 01:13:45 +03:00
Grahame Grieve 783a8cf28b Support for Obligation Profiles 2023-05-29 01:12:46 +03:00
Grahame Grieve ece4a44ff2 Merge remote-tracking branch 'origin/master' 2023-05-28 15:50:39 +03:00
Gregor Lichtner aaa7490a22 copying element children 2023-05-26 15:42:57 +02:00
Grahame Grieve d60b9009b2 get control over caching for terminology testing 2023-05-25 16:41:52 +10:00
dotasek 55ac916133
Refactor Pull Request Pipeline (#1273)
* Try multiple module target directories

* Try different format

* Try displaying cache task name + multiple caches

* Name the maven artifact cache step + add all modules

* Start consuming cached builds + targets

* Fix job list

* Fix other bad params

* Fix bad indent

* Try test task

* Try different value syntax

* Add all modules

* See if cacheing works from linux to windows

* Refactor as testUnits

* Trim tested modules

* missing colon

* It's not an image anymore, it's a unit

* Test exec

* Test exec for real

* Fix parameters format

* Fix r5 url for package fetch (#1260)

* Fix r5 url for package fetch

* Revert previous commit

* Make r6 the only packages fetched from build.fhir.org

* Update RELEASE_NOTES.md

* Update RELEASE_NOTES.md

* Release: v6.0.6
## Validator Changes

* no changes

## Other code changes

* Update R6 package tgz fetching
***NO_CI***

* Updating version to: 6.0.7-SNAPSHOT and incrementing test cases dependency.

* Try using parameters

* Try another way

* Try third way

* Try fourth way

* Try fifth way

* Try 6

* Try 7

* Apply refactor

* Try iterating over images

* Try iterating over images 2

* Test all images

* Conditionally test multiplatform modules

* Test JDKs too

* Fix and()

* Add JDK image to job names + test JDKs for exec

* Better job name for setup

* Fix names

* more granular test configs

* fix repeated jobs

* name for exec jobs

* fix missing s

* Add placeholder Codecov job

* Fix complaint about job name

* Try moving codecov to test template

* Add explicit module for test

* Try setting up job name

* Try setting up job name

* Change job names to use underscore and alphanum

* Move codecov job back to master-branch

* Fix condition to match ubuntu_java_11

* Publish test reports

* Publish test reports

* use value for artifact name

* Use variable for skipJaCoCo conditions

* Skip validation temporarily

* Change artifact names.

* add jacoco:report-aggregate task

* remove leftover cut and paste line

* Improve test job display name

* Add jacoco results + codecov upload

* Fix accidental inclusions in module loop

* Remove JaCoCo coverage condition

* Bump down JaCoCo plugin

* Rearrange JaCoCo plugin

* Fix surefire and jacoco output

* Add jacoco to pipeline

* Try skipping maven cache step

* Add codecov token

* Add missing MAVEN_CACHE_FOLDER

* Change variable syntax

* Move setup to own template

* Change setup template

* rearrange pipeline yml, re-enable validation test module

* Update core version bumps

* Temporarily disable tests

* Move to PR pipeline + Fix unused pool declaration

* Disable some more.

* Restore disabled and ignored tests

* Fix task name + clean up old prototype

---------

Co-authored-by: markiantorno <markiantorno@gmail.com>
2023-05-24 13:09:13 -04:00
markiantorno 8f52ad8fe8 Updating version to: 6.0.9-SNAPSHOT and incrementing test cases dependency. 2023-05-24 14:51:20 +00:00
markiantorno 4f90606776 Release: v6.0.8
## Validator Changes

* Snapshot Generation Changes:
** Check for slicenames without any slicing
** Check that slice names are unique
** Check for additional slicing rules in a set of slices
** Check that the minimum cardinality of a set of slices is correct
* Clean up duplicate errors when dates/dateTimes/instants have invalid formats
* Handle unknown code systems consistently when validating coded elements
* Handle sub-slicing case where slice matches both the slice definition and the sub-slice definition

## Other code changes

* Add support for R4B to loader
* Change type if cache-id parameter
* Change snapshot generation to not update documentation from profile for elements with profiled types that are not extensions
* Add support for TestPlan and SubscriptionTopic in R4 IGs
***NO_CI***
2023-05-24 14:23:30 +00:00
Grahame Grieve 442d9286b5 more checking slice min and max 2023-05-24 22:28:53 +10:00
Grahame Grieve 7eea5158c5 fix npe 2023-05-24 19:06:34 +10:00
Grahame Grieve df26951336 fix npe 2023-05-24 16:57:22 +10:00
Grahame Grieve 0ec2dfab78 Add support for SubscriptionTopic in R4 IGs 2023-05-24 16:57:09 +10:00
Grahame Grieve e724c9d58b
Merge pull request #1274 from hapifhir/ja_20230523_1262_fix_asstringvalue
Fix asStringValue on IdType
2023-05-24 10:37:28 +10:00
Grahame Grieve 426fe1083a
Merge pull request #1265 from rettema/testplan_40_50
#1264 add R5 TestPlan conversion classes to R3, R4 and R4B
2023-05-24 10:37:07 +10:00
James Agnew 0eca8d14ba Fix asStringValue on IdType 2023-05-23 17:02:23 -04:00
Grahame Grieve 87d8323c91
Merge branch 'master' into gg-202304-more-snapshot 2023-05-24 06:52:50 +10:00
Grahame Grieve a7026ca51d
Merge pull request #1272 from pnewhook/getLink-enum-bug
Bundle.getLink(String) comparing string to enum
2023-05-24 06:15:58 +10:00
Richard Ettema 39d221736c
Merge branch 'hapifhir:master' into testplan_40_50 2023-05-23 16:05:09 -04:00
Peter Newhook 671ab4b964 Compare the string value of a LinkRelationTypes enum in Bundle.getLink(String)
Fixes #1266
2023-05-23 11:41:12 -04:00
Grahame Grieve a2e2ef714e Handle sub-slicing case where slice matches both the slice definition and the sub-slice definition 2023-05-23 17:39:08 +10:00
Grahame Grieve 8a5c9c7ca6 Adjust handling of slicing min issues 2023-05-23 17:37:11 +10:00
Richard Ettema 1ee320a462 revert changes to RequirementsRenderer 2023-05-22 17:54:58 -04:00
Grahame Grieve ba45c863db Merge remote-tracking branch 'origin/master' 2023-05-23 07:05:43 +10:00
Grahame Grieve 49571de18a #1266 fix Bundle.getLink() for enumeration 2023-05-23 06:13:05 +10:00
Grahame Grieve 5979d4abea
Merge pull request #1267 from antvaset/patch-1
Fix typo in ConceptMapRenderer.java
2023-05-23 05:54:51 +10:00
Grahame Grieve 753ca69545 Merge remote-tracking branch 'origin/master' 2023-05-22 17:19:42 +10:00
Grahame Grieve 7da282b5d7 update test cases for various issues encountered and fixed 2023-05-22 17:17:17 +10:00
Grahame Grieve 073e89d98d Handle unknown code systems properly 2023-05-22 17:16:08 +10:00
Grahame Grieve 7339d0ae1d Fix for NPEs 2023-05-22 17:15:44 +10:00
Grahame Grieve 30290b9567 Handle unknown code systems properly 2023-05-22 17:15:29 +10:00
Grahame Grieve 95d8399992 Handle unknown code systems properly 2023-05-22 17:15:16 +10:00
Grahame Grieve c2dfdfea0b Check for erroneous attempts to reslice 2023-05-22 17:14:49 +10:00
Grahame Grieve 6e3171d85f Check for erroneous attempts to slice or re-slice + add checking for getting slicing minimum cardinality right 2023-05-22 17:14:16 +10:00
Anton Vasetenkov b7e802ee79
Fix typo in ConceptMapRenderer.java 2023-05-19 21:16:06 +02:00
Richard Ettema e9c2a5f622 #1264 add R5 TestPlan conversion classes to R3, R4 and R4B 2023-05-18 17:36:21 -04:00
markiantorno ff8943061c Updating version to: 6.0.8-SNAPSHOT and incrementing test cases dependency. 2023-05-17 04:54:30 +00:00
markiantorno 9221395f06 Release: v6.0.7
## Validator Changes

* Update terminology for changes to tx validation policy: Wrong displays change from a warning to an error
* Add parameter ```-display-issues-are-warnings``` for restoring original behaviour that display issues are warnings
* Relax constraints on Reference targets for logical models
* Update dutch and german validation error messages + minor improvements to error messages
* Fix r5 url for package fetch (#1260)  …

## Other code changes

* Fix up all terminology cache tests
* Switch to System.err for now + report missing constants
* Add I18n tests for coverage and plural validity + fix missing messages
* Partial fix for R4/R5 conversion issues
***NO_CI***
2023-05-17 04:23:04 +00:00
Grahame Grieve 0278518c26 update terminology for changes to tx validation policy 2023-05-17 11:33:45 +10:00
Grahame Grieve ef92f38d9e Fix up all terminology cache tests 2023-05-17 10:33:22 +10:00
Grahame Grieve 6d2e3ee388 Fixes for display warnings 2023-05-13 21:47:25 -07:00
Grahame Grieve 37bf22f8e9 Add path to error message 2023-05-13 21:46:58 -07:00
markiantorno 110f695e9c Updating version to: 6.0.7-SNAPSHOT and incrementing test cases dependency. 2023-05-12 23:49:33 +00:00
markiantorno 171a87c777 Release: v6.0.6
## Validator Changes

* no changes

## Other code changes

* Update R6 package tgz fetching
***NO_CI***
2023-05-12 23:22:47 +00:00
Lloyd McKenzie 8c494278f4 Fix problem when profiling a base type that supports both Reference and canonical 2023-05-11 21:54:48 -05:00
markiantorno 44c1b43516 Updating version to: 6.0.6-SNAPSHOT and incrementing test cases dependency. 2023-05-10 15:28:58 +00:00
markiantorno 91de165e2c Release: v6.0.5
## Validator Changes

* Fix NPE validating StructureMap
* Improve error message about uri values
* Fix for wrong display when server returns error
* Slight improvement in performance
* Fix FHIRPath split function (parameter is not regex)
* Stop warning that Markdown autolinks need to be escaped
* Allow NPM package versions to have the form {id}#{url} for direct access to packages

## Other code changes

* Support for NamingSystem conversion of url, version, and title (for THO)
* Update Conversion package docs (#1257)  …
* Return codeableConcept from validate-code
* Refactor: Resource Root Elements Conversion
* Minor fixes for R5 redirector
* Fix bug handling filter, and refactor terminology code
* Fix for dstu2016may Resource equals methods (#1251)  + Tests a
***NO_CI***
2023-05-10 14:58:38 +00:00
Grahame Grieve ecc2a5f634 Remove spurious logging 2023-05-10 05:46:58 -05:00
Grahame Grieve 13254f39a2 support for NamingSystem conversion of url, version, and title (for THO) 2023-05-09 18:46:39 -05:00
Grahame Grieve ce46eee731 return codeableConcept from validate-code 2023-05-08 13:30:04 -05:00
Grahame Grieve 491b5ccb4a Fix for wrong display when server returns error 2023-05-08 07:09:32 -05:00
Grahame Grieve 6232c54f15 Fix core 2023-05-07 12:02:00 -05:00
Grahame Grieve bcb0656ff5 Merge remote-tracking branch 'origin/master' 2023-05-07 11:04:07 -05:00
Grahame Grieve ae13abfc2a performance related changes 2023-05-07 11:04:04 -05:00
Sean McIlvenna fa1e0c5a71 Changes based on performance profiling validation of a large Bundle of 32 patients
Reduced execution time from >2 minutes to 36 seconds
2023-05-07 10:03:12 -05:00
Grahame Grieve d35b881cf1 Fix FHIRPath split function 2023-05-06 09:55:36 -05:00
Grahame Grieve 24b0cc2ee4 Fixes for kindling 2023-05-06 00:55:50 -05:00
Grahame Grieve f734f98c05 update for failing tests 2023-05-05 22:21:05 -05:00
Grahame Grieve b402fd1c45 Fix bug handling filter, and refactor terminology code 2023-05-05 13:55:23 -05:00
markiantorno 551fe6d7c0 Updating version to: 6.0.5-SNAPSHOT and incrementing test cases dependency. 2023-05-04 13:17:39 +00:00
markiantorno 83a45f95f9 Release: v6.0.4
## Validator Changes

* Fix bug accessing canonical resources on servers

## Other code changes

* Various changes to support terminology service testing
***NO_CI***
2023-05-04 07:22:08 +00:00
Grahame Grieve e8de25c197 fix tests 2023-05-04 10:35:03 +10:00
Grahame Grieve 806c065fcb fix version return + profile support in testing 2023-05-04 10:01:35 +10:00
Grahame Grieve 94fd0ae795 more tests fixes 2023-05-03 17:16:16 +10:00