Commit Graph

2589 Commits

Author SHA1 Message Date
Grahame Grieve fae2d1336c remove "LOINC 2711-0 Oxygen saturation in Venous blood" from the list in the validator that checks whether an observation is a vital sign 2024-05-21 16:51:45 -05:00
markiantorno 1f6aaa1db3 Updating version to: 6.3.9-SNAPSHOT and incrementing test cases dependency. 2024-05-20 13:16:27 +00:00
markiantorno 5165942802 Release: v6.3.8
## Validator Changes

* Fix bug processing extension with explicit type slicing
* Fix wrong language code from java locale
* Don't accidently hit other terminology servers for code systems handled natively by tx.fhir.org
* Validate Additional Bindings (provisional - usage context is todo)
* Improved system specific checking of value set filters - particularly LOINC and SNOMED CT, and update LOINC validation to the latest understanding of LOINC filters

## WHO I18n Project

* Add importing translations to native resources
* Finish Migrating text phrases to i18n framework
* Fix bugs with loading translations (#1592)

## Security

* Move all network access to go through ManagedWebAccess
* More security documentation

## Other code changes

* Put jurisdiction in npm package.json
* Add testing ontoserver to test suite
* Fix NPE testing Ontoserver
* fix tx tester calling run ok when a filter is applied and tests fail
* Fix name of preferred when rendering AdditionalBindings
* Add AdditionalBinding version conversion in profiles
* Fix SNOWMED spelling
* Fix rendering of multiple imports in value sets
***NO_CI***
2024-05-20 12:30:29 +00:00
Grahame Grieve a86fe5a2d2 FIx up issues with calling translation on the wrong set of properties (#1592) 2024-05-20 04:38:17 -05:00
Grahame Grieve de79e47de6 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2024-05-19 06:11:17 -05:00
Grahame Grieve f15f9f394e Refactor system specific checking of value set filters 2024-05-18 07:36:30 -05:00
Grahame Grieve 5956da771e fix NPE testing Ontoserver 2024-05-18 03:25:46 -05:00
Grahame Grieve 0645c79eb6 add testing ontoserver to test suite 2024-05-18 03:25:34 -05:00
Grahame Grieve 29442c0b1d fix tx tester calling run ok when a filter is applied and tests fail 2024-05-18 03:25:23 -05:00
Grahame Grieve 6ba9a11c51 Validate Additional Bindings (provisional - usage context is todo) 2024-05-18 03:24:54 -05:00
Grahame Grieve 4911f4fef8 updates for ManagedWebAccess 2024-05-18 14:58:33 +10:00
Grahame Grieve a510a6d1aa introduce ManagedWebAccess 2024-05-16 13:34:50 +10:00
Grahame Grieve 5ae44c23d5 fix up LOINC validation for value set filters 2024-05-12 22:28:15 +10:00
markiantorno 248b8b1ac8 Updating version to: 6.3.8-SNAPSHOT and incrementing test cases dependency. 2024-05-10 05:02:38 +00:00
markiantorno d81fc5d82d Release: v6.3.7
## Validator Changes

* Fix bug where some #refs are not resolved to the root of the resource in FHIRPath slicing evaluation
* Fix bug passing wrong type to tx server when using inferSystem
* Fix bug processing version of CodeSystem.supplements incorrectly
* Don't process wrong parent when processing snapshot of element with profiled type that is not reprofiled
* Fix typo in OID message
* Fix handling value set exclude filters
* Allow code system declared properties to be self-referential

## I18n changes

* More comprehensive internationalization phrase coverage reporting on project page
* Move many rendering phrases into i18n framework

## Rendering Changes

* Fix issue with unknown element rendering fixed value for Attachment
* Fix bug calculating value set expansion size for multiple imports
* Fix bug using wrong message for value sets that are too costly to expand
* Fix extension urls not being linked in tree view
* rendering improvements and remove static use of describeSystem
* Fix NPE rendering profile comparisons
* Fix bug where slicing and grouping gets mixed up rendering profile tree

## Other code changes

* Wrap general exception for IWorkerContext (Catch missed exception from HAPI)
* Shim interfaces and classes to support clinical reasoning project updates.
* Fix duplicate txServer getters and setters
* Use extension class on Exception to force try-catch blocks on checkCodeOnServer calls (#1609)
* rework OID handling for better consistency
* handle time outs doing vsac import (starlink obstructions)
***NO_CI***
2024-05-10 04:18:38 +00:00
Grahame Grieve bf842f0181 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2024-05-10 09:50:21 +10:00
Grahame Grieve ffec50c71b
Merge pull request #1617 from hapifhir/2024-05-gg-misc2
2024 05 gg misc2
2024-05-09 23:06:24 +00:00
Grahame Grieve ee5987a301
Merge pull request #1618 from hapifhir/do-20240509-fix-clicontext-fields
Fix duplicate txServer getters and setters
2024-05-09 22:59:31 +00:00
Grahame Grieve 5a9ef0b57c move supplement version test cases to normal test cases 2024-05-10 08:58:20 +10:00
Grahame Grieve 5259bf9847 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2024-05-10 08:49:11 +10:00
Grahame Grieve 4b32505953
Merge pull request #1614 from Boereck/fix/canonical_split_base_validator
Fix/canonical split base validator
2024-05-09 22:48:30 +00:00
dotasek 33220f40eb Merge remote-tracking branch 'origin/master' into do-20240122-base-engine 2024-05-09 15:28:15 -04:00
dotasek.dev 2c2e935f0a Fix duplicate txServer getters and setters 2024-05-09 15:26:20 -04:00
Grahame Grieve ba3dc45863 Fix bug where some #refs are not resolved to the root of the resource in FHIRPath slicing evaluation 2024-05-09 19:16:33 +10:00
dotasek 178f7b0fa1
Use extension class on Exception to force try-catch blocks on checkCodeOnServer calls (#1609)
* Catch missed exception from HAPI

* Wrap general exception for IWorkerContext
2024-05-08 10:18:01 -04:00
Max Bureck be0d718ac7 Changed use of message ID string in test to use constant instead 2024-05-08 14:52:11 +02:00
Max Bureck 962aee14a3 Added test case for CodeSystem.supplements with versioned canonical 2024-05-08 11:45:56 +02:00
Max Bureck 81f02da5c2 Fix split logic of canonical into url and version in several places
Removed
- org.hl7.fhir.r4b.renderers.DataRenderer#versionFromCanonical
- org.hl7.fhir.r4b.renderers.DataRenderer#systemFromCanonical
- org.hl7.fhir.r5.renderers.DataRenderer#versionFromCanonical
- org.hl7.fhir.r5.renderers.DataRenderer#systemFromCanonical
- org.hl7.fhir.validation.BaseValidator#versionFromCanonical
- org.hl7.fhir.validation.BaseValidator#systemFromCanonical

Replaced all usages of aforementioned methods by the use of
org.hl7.fhir.utilities.CanonicalPair.

Improved CanonicalPair to avoid multiple lookup of the | character. And
added a few convenience methods to the class.

This fixes the issues of #1611 (not replacing all canonical splits in
other places of the code).
2024-05-07 16:46:14 +02:00
Grahame Grieve c24fde0bb6 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2024-05-05 18:17:33 +10:00
Grahame Grieve f79fdb44ec rendering improvements and remove static use of describeSystem 2024-05-05 18:12:57 +10:00
Grahame Grieve a28ba7ee2e allow code system declared proporties to be self-referential 2024-04-25 22:00:08 +10:00
markiantorno 9ce2c57b8b Updating version to: 6.3.7-SNAPSHOT and incrementing test cases dependency. 2024-04-23 08:51:21 +00:00
markiantorno 46bdec9054 Release: v6.3.6
## Validator Changes

* fix NPE loading resources
* Don't enforce ids on elements when processing CDA
* Send supplements to tx server
* fix bug processing code bindings when value sets are complex (multiple filters)
* fix spelling of heirarchy
* Look up CodeSystem from terminology server
* Don't use tx-registry when manual terminology server is set

## Other code changes

* More work on WHO language support ($1592)
* allow validation message to have count
* render versions in profile links when necessary
* rework OID handling for better OID -> CodeSystem resolution
* fix up vsac importer for changes to client
* don't send xhtml for tx operations
* FHIRPath: Backport the defineVariable code to the R4 and R4B fhirpath implementations
* FHIRPath: Remove the alias/aliasAs custom functions (use standard defineVariable now)
* Bump lombok (#1603)
***NO_CI***
2024-04-23 08:03:57 +00:00
Grahame Grieve 60bf358bfa Look up CodeSystem from terminology server + don't use tx-registry when manual terminology server is set 2024-04-23 08:34:25 +10:00
Grahame Grieve 46500069a4 Don't run $lookup and $translate tests on internal terminology server 2024-04-22 17:11:30 +10:00
Grahame Grieve 84d0b13b2f re-Add support for $lookup and $translate in tx tests 2024-04-20 23:37:29 +10:00
Grahame Grieve 74e5f1d493 Don't enforce ids on elements when processing CDA 2024-04-20 23:37:07 +10:00
Grahame Grieve 3fb9bc20f4 fix spelling of heirarchy 2024-04-20 23:32:52 +10:00
markiantorno ed18ec2cc6 Updating version to: 6.3.6-SNAPSHOT and incrementing test cases dependency. 2024-04-16 22:47:50 +00:00
markiantorno ccf66ece0b Release: v6.3.5
## Validator Changes

* Fix up path management in the validator for resolving references in Bundles
* Add support for defineVariable in FHIRPath
* Fix problem with CDA element having multiple types
* Fix problem with 'is' not working in FHIRPath for CDA types
* Fix issue processing CDA generic type names
* Fix for NPE processing tx server response
* Add support for code system supplements when communicating with tx server

## Other code changes

* OSGI: make sure JUnit 4 and 5 dependencies are optional (#1596) (Also removed duplicate managed versions of JUnit 4.13.2 and mockwebserver 4.11.0)
* Render CapabilityStatement.imports (and instantiates)
* Terminology Service Tests - minor improvements for running in HAPI, add $lookup & $translate support, create R4 clone
* Add support for $translate to terminology client
* More i18n work in rendering context (WHO project)
* Add isServerSide for seeing if code systems are only supported on the server
* Fix R4B loading issue that lead to wrong web paths for R4B resources
* Fix problems rendering Binary files in IGs
* Add support for rendering logical URIs
* Remove path.toFile()

## Security

* Finish moving all local file access to go through ManagedFileAccess

## WHO Internationalization work

* More work on date rendering
***NO_CI***
2024-04-16 22:01:50 +00:00
Grahame Grieve 1268145ef7 compile fix 2024-04-16 20:30:31 +10:00
Grahame Grieve f9a11d97f7 more removing Path.toFile() 2024-04-16 19:37:42 +10:00
Grahame Grieve 32296cfdb6 fix merge error 2024-04-16 17:01:19 +10:00
Grahame Grieve 0d7c837b85
Merge branch 'master' into 2024-04-gg-lookup 2024-04-16 16:15:37 +10:00
Grahame Grieve 7796c93066 update for turning tx tests off 2024-04-16 12:40:35 +10:00
Grahame Grieve 1f7f57bade Add support for $translate to terminology client 2024-04-15 22:41:45 +10:00
Grahame Grieve e78042940e Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2024-04-13 05:03:39 +10:00
Grahame Grieve d26ce8e10d fix for NPE 2024-04-13 05:03:33 +10:00
Grahame Grieve 63852b4082 Fix issue processing CDA generic type names 2024-04-12 22:14:31 +10:00
Grahame Grieve 30a532f23b create R4 clone of tx tests 2024-04-12 22:12:20 +10:00
Grahame Grieve 4ceac5012b Look up support in Tx Tests 2024-04-11 08:29:34 +10:00
Grahame Grieve df93da2735 update tests to depend on snapshot 2024-04-10 08:19:15 +10:00
Grahame Grieve 8ce99140aa More i18n work (#1592) 2024-04-10 08:18:58 +10:00
Grahame Grieve 0038e3a57b Fix up path management in the validator for resolving references in Bundles 2024-04-10 08:18:06 +10:00
dotasek 81f26a80e2 Fix destination for diff output of TerminologyServiceTests 2024-04-05 09:59:04 -04:00
dotasek.dev cc555ba419 Merge branch 'master' into do-20240319-tx-test-reuse 2024-04-04 12:50:27 -04:00
dotasek.dev 2500f26290 Fix compilation 2024-04-04 09:05:53 -04:00
markiantorno 1f3d2838d9 Updating version to: 6.3.5-SNAPSHOT and incrementing test cases dependency. 2024-04-04 01:47:30 +00:00
markiantorno 45e8d86478 Release: v6.3.4
## Validator Changes

* Validate fixed/pattern values are not changed in derived profiles
* Fix NPE validating some profiles
* FHIRPath validation: consider sub-extensions when checking extension($) use
* Fix validation of concept maps containing SCT
* Preserve message id from terminology service so editors can use it to remove hints and warnings

## Other code changes

* Fix ConceptMap.group.target conversion from R3 to R5
* Fix NPE in list renderer
* fix bug showing 'required' instead of 'current' rendering additional bindings
* Fix bad references generating narratives in bundles
* Fix bug showing extension binding twice
* Various improvements to structure map validation to support cross-version mappings
* Add rendering for UsageContext and ContactDetail
* Fix broken link in xver IG for R2
* Fix bug rendering resources in Parameters resource
* Not-pretty xhtml gets line breaks before block tags to keep line length down (work around a jekyll issue)
* Improved ConceptMap rendering for cross-version IG
* Handle xhtml:div type for old FHIR version
* FML: strip '-' from rules names when parsing
* Update FML parsers to accept R5 metadata in R4 FML format
* Break out helper classes for Terminology Service Tester

## Security

* Add start of security notes
* Start moving file access to all go through ManagedFileAccess

## WHO Internationalization work:

* Add library to parse IETF Language definitions
* Move message translations to .po files as the master source & write convertor
* Much work making rendering i18n-able
* i18n for Patient renderer
* Refactor language handling in R5 renderers
***NO_CI***
2024-04-04 00:55:36 +00:00
dotasek 7a8ac05075 Merge remote-tracking branch 'origin/master' into do-20240319-tx-test-reuse 2024-04-03 14:07:03 -04:00
dotasek e356bd7017 Merge remote-tracking branch 'origin/master' into do-20240319-tx-test-reuse 2024-04-03 10:17:10 -04:00
Grahame Grieve 69fa06adfd Fix NPE validating some profiles 2024-04-03 20:14:49 +11:00
Grahame Grieve 808d4619d6 various improvements to structure map validation 2024-04-03 20:14:27 +11:00
Grahame Grieve 0d57115ede preserve message id from terminology service so editors can use it in suppressed-messages.txt 2024-04-03 20:13:34 +11:00
Grahame Grieve 2c6f1b6a59 start moving file access to all go through ManagedFileAccess 2024-04-03 20:11:16 +11:00
Grahame Grieve 211e4efb44 validate fixed/pattern values in derived profiles 2024-03-26 08:43:35 +11:00
Grahame Grieve 3d57cec0f1 fix validation of concept maps containing SCT 2024-03-26 06:27:42 +11:00
Grahame Grieve a4055877c4 more work on multi-language rendering, and add test id to error message on comparison 2024-03-25 10:06:00 +11:00
dotasek.dev 6032e64ffc more renaming 2024-03-22 11:10:01 -04:00
Grahame Grieve 02b6e80b6d refactor language handling in R5 renderers 2024-03-22 22:49:31 +11:00
dotasek.dev 0549903ade Separate loading logic from data 2024-03-20 19:27:19 -04:00
dotasek.dev 4793e574b1 Break out helper classes 2024-03-20 18:52:20 -04:00
dotasek.dev 890776604d variable renaming 2024-03-20 18:26:10 -04:00
dotasek.dev 69491f1996 Merge remote-tracking branch 'origin/master' into do-20240319-tx-test-reuse 2024-03-20 14:27:54 -04:00
markiantorno 0cebf9af9f Updating version to: 6.3.4-SNAPSHOT and incrementing test cases dependency. 2024-03-20 13:31:17 +00:00
markiantorno ec51399045 Release: v6.3.3
## Validator Changes

* Fix grammar in validation messages
* Fix NPE in validator for SIDs
* Duplicate designations in a code system is a warning, not an error
* Fix value set validation to validate codes in example code systems

## Other code changes

* Improved multi-language support for IG development (LanguageUtils)
***NO_CI***
2024-03-20 12:38:29 +00:00
Grahame Grieve 9a66c1968e more work on language utilities 2024-03-20 22:44:13 +11:00
Grahame Grieve 1ecbf365be fix NPE in validator for SIDs 2024-03-20 21:00:16 +11:00
Grahame Grieve 95cd30d100 duplicate designations is a warning, not an error 2024-03-20 20:59:59 +11:00
Grahame Grieve 8f2f414c78 Fix value set validation to validate codes in example code systems 2024-03-20 20:59:41 +11:00
dotasek.dev 82c36de65d WIP refactor terminology service tests for reuse outside core 2024-03-19 17:53:45 -04:00
markiantorno b2e3c261e4 Updating version to: 6.3.3-SNAPSHOT and incrementing test cases dependency. 2024-03-18 15:09:50 +00:00
markiantorno 5b5a0a2cdf Release: v6.3.2
## Validator Changes

* CodeSystem property validation improvements
* More valueset validation improvements after real world testing
* Fix processing of NotSelectable filters using in | not-in
* Fix wrong collection type checking FHIRPath subsetOf parameter type

## Other code changes

* Fix rendering of contained resources in Kindling
* Put jurisdiction in NPM package file
* Rendering improvements for xver IG
* More xver support for concept maps
* Fix NPE in ContextUtilities (kindling)
* Add OID Assigner utility
***NO_CI***
2024-03-18 14:24:12 +00:00
Grahame Grieve 30545d31c1 CodeSystem property validation improvements 2024-03-18 18:09:56 +11:00
Grahame Grieve e39bbba7ef More valueset validation improvements after real world testing 2024-03-14 16:48:39 +11:00
markiantorno da3bb9e353 Updating version to: 6.3.2-SNAPSHOT and incrementing test cases dependency. 2024-03-10 21:41:17 +00:00
markiantorno 072be957d4 Release: v6.3.1
## Validator Changes

* Add validation for CodeSystem Properties and ValueSet filters
* More validation for Code Systems: contained code systems, supplement cross checks
* Add more validation around ValueSet.compose.include.system - must be a proper URL, and not a direct reference to a supplement
* HL7: Don't require HL7 publishing status on contained resources
* Don't walk into nested bundles when validating links in bundles
* fix up implementation of notSelectable in value set filters
* Add check for multiple version matches for a versionless canonical reference

## Other code changes

* Fix narrative generator generating duplicate anchors (prefix 'hc')
* exclude .DS_Store from generated zip files
* Add cross-version support extension
* Add ConceptMap utilities in support of cross-version module
***NO_CI***
2024-03-10 20:52:29 +00:00
Grahame Grieve 9e8a010c13 ValueSetValidation improvements 2024-03-11 00:19:16 +11:00
Grahame Grieve 33a1814d4e CodeSystem validation - properties and designations 2024-03-08 22:32:55 +11:00
Grahame Grieve a51c3f96ad don't walk into nested bundles when validating links in bundles 2024-03-08 22:32:13 +11:00
Grahame Grieve a94b41add8 fix up implementation of notSelectable in value set filters 2024-03-08 22:31:53 +11:00
Grahame Grieve 13dcebb3e4 add check for multiple version matches for a versionless canonical reference 2024-03-08 22:29:51 +11:00
Grahame Grieve 1bab5bcb5b missed code 2024-03-07 13:48:21 +11:00
Grahame Grieve 19bd64f81a more validation for Code Systems (contained code systems, supplement cross check, HL7 publishing status) 2024-03-07 13:48:13 +11:00
Grahame Grieve 499d682286 rebuild txcache - except LOINC 2024-03-06 13:29:51 +11:00
Grahame Grieve 0f08bb4e49 Add more validation around ValueSet.compose.include.system - must be a proper URL, and not a reference to a supplement 2024-03-06 13:29:35 +11:00
markiantorno 48023c0ba4 Updating version to: 6.3.1-SNAPSHOT and incrementing test cases dependency. 2024-02-28 05:56:31 +00:00
markiantorno b44c34c7e2 Release: v6.3.0
## Validator Changes

* Fix significant bug where validator gets internal child lists incorrect and doesn't do complete validation when switching between validating profiles and resources directly
* Performance improvement for validator parsing - thanks Brian Postlethwaite
* Fix Crash on slicing a sliced element #862
* Fix ig loading from direct URL (#1559)
* Fix bug copying constraints into Bundle.entry.resource profiles
* Fix bug loading R5 extensions with imported value sets
* Replace dom-3 with custom java code, and check xhtml references to contained content
* Improve concept map code validation
* Update observation validator for committee decision not to enforce Blood Pressure profile for Mean Blood Pressure
* Validate value set internal codeSystem references
* Split value set validation into 10k batches for very large extensional value sets
* Hack fix for opd-3
* Fix bug where using ontoserver when not appropriate
* Fix issues with inferSystem
* Don't require HL7 committee for contained resources in HL7 namespace
* Fix where validator was ignoring minimum cardinality for XML attributes (especially in CDA)
* Improved ConceptMap validation
* Updated IG versions used for -cda and -ccda CLI validation options.
* Change validator so that it marks value properties in primitive data types as illegal

## Other code changes

* Fix code system rendering for uri properties
* Fix broken links Bundle and Profile rendering
* Take copy of code when doing local validation
* WIP: major refactor of cross version analysis
* Add support for subsumes in tx client
* Don't generate snapshots when scanning structure definitions for resource names
* Work on ConceptMap infrastructure for cross-version analysis
* Fix bug where not rendering ConceptMap relationships
* Fix wrong URLs rendering Profiles and Questionnaires
* Fix bug using wrong version constant for R3
* Updates for R5 StructureMap syntax
* Support for case sensitive Code system tests
* Add TurtleGeneratorTests for R5
* Introduce new validator cliContext option disableDefaultResourceFetcher (#1526)
* Render contained resources when rendering Patient resources
* Fix bug in FML Parser
***NO_CI***
2024-02-28 05:04:13 +00:00
Grahame Grieve db5605a5ab fix compile problem 2024-02-28 15:30:12 +11:00
Grahame Grieve da56e4296b Change validator so that it marks value properties in primitive data types as illegal 2024-02-28 12:22:33 +11:00
Grahame Grieve f22316d55f fix up structure mapping tests 2024-02-28 12:21:15 +11:00
dotasek 6b55cc8eb0 Merge branch 'master' into do-20240131-cda-ccda-cli-versions 2024-02-27 09:40:50 -05:00
Grahame Grieve 2bcc3fb7ae
Merge pull request #1568 from hapifhir/2024-02-gg-monster
2024 02 gg monster
2024-02-25 23:42:32 +11:00
Grahame Grieve 982d5521da Improved ConceptMap validation 2024-02-25 19:26:07 +11:00
Grahame Grieve 0139723822 Improved ConceptMap validation 2024-02-25 19:25:43 +11:00
Grahame Grieve 1eb8067d6b Fix where validator was ignoring minimum cardinality for XML attributes (especially in CDA) 2024-02-25 19:25:17 +11:00
Grahame Grieve 1d4898eee6 Support for case sensitive Code system tests 2024-02-25 19:22:25 +11:00
Grahame Grieve c05ad6cb2c fix bug using wrong version constant for R3 2024-02-25 19:21:58 +11:00
Dylan Hall f1096a8ebd
Introduce new validator cliContext option disableDefaultResourceFetcher (#1526)
* introduce new cliContext option doNotFetchUnknownProfiles

* rename parameter to disable-default-resource-fetcher

* missed renaming a couple items

* review feedback
2024-02-20 17:06:55 -05:00
Grahame Grieve 5783481a26 fix ig loading from direct URL (#1559) 2024-02-13 13:02:23 +11:00
Grahame Grieve d128c2d3fc rebuild tx cache 2024-02-12 16:21:36 +11:00
Grahame Grieve 9e60fdb7ad Hack fix for opd-3 2024-02-10 23:12:12 +11:00
Grahame Grieve 3e642e8bd8 validate value set internal codeSystem references 2024-02-10 23:04:56 +11:00
Grahame Grieve 368376d36d update observation validator for committee decision not to enforce Blood Pressure profile for Mean Blood Pressure 2024-02-10 23:04:06 +11:00
Grahame Grieve 1a121adc43 Improve concept map code validation 2024-02-10 23:02:29 +11:00
Grahame Grieve 3a1cc2e75a Replace dom-3 with custom java code, and check xhtml references to contained content 2024-02-10 23:01:52 +11:00
Grahame Grieve 20bf70ed68 fix bug loading R5 extensions with imported value sets 2024-02-10 22:51:32 +11:00
dotasek cb2d6c491e Set locale and language for baseEngine use 2024-01-31 16:24:37 -05:00
dotasek.dev 77f8cdb9df Fix lang and locale settings for baseEngine use 2024-01-31 15:21:32 -05:00
dotasek.dev 7855a40d4e Fix CDA and CCDA IG versions in CLI options 2024-01-31 10:49:24 -05:00
dotasek.dev 464af9de90 Only do version determination when ValidationEngine must be created 2024-01-31 09:28:08 -05:00
dotasek.dev b1973d6eb2 Fix incomplete test 2024-01-30 11:53:56 -05:00
dotasek.dev 14f2837b2b Merge commit '3a1946e37d99d43c0f49bd8b75c48209cce44546' into do-20240122-base-engine 2024-01-30 10:40:47 -05:00
markiantorno 3a1946e37d Updating version to: 6.2.16-SNAPSHOT and incrementing test cases dependency. 2024-01-30 11:13:01 +00:00
markiantorno 0bb2010409 Release: v6.2.15
## Validator Changes

* Fix bug in deciding whether a ValueSet is supported by the server
* Rework server decision making when multiple code systems being used
* Fix file type inference in ValidationService for unknown file types

## Other code changes

* Kindling related fixes for terminology stability
* Fix parameter type for system-version
* Fix mini-terminology server bugs around unknown systems
* Improvements to Identifier rendering
***NO_CI***
2024-01-30 10:29:12 +00:00
Grahame Grieve e09e0adbbe fix parameter type for system-version 2024-01-30 20:06:10 +11:00
Grahame Grieve dd3770d093 fix bug in deciding whether a value is supported by the server 2024-01-30 19:06:06 +11:00
Grahame Grieve ebfd70477c fix mini-terminology server bugs around unknown systems 2024-01-30 19:05:49 +11:00
Grahame Grieve 975f4fd28b rework server decision making when multiple code systems being used 2024-01-30 19:05:20 +11:00
dotasek 2c61dd150b Add tests for base engine use 2024-01-29 17:54:03 -05:00
dotasek.dev b0a68a788e Fix base engine println 2024-01-29 12:11:45 -05:00
Grahame Grieve c34f439da5
Merge pull request #1550 from hapifhir/do-20230119-fix-filetype-detect-in-service
Fix file type inference in ValidationService
2024-01-28 23:12:08 +11:00
Grahame Grieve 42bddb9fdb
Merge pull request #1554 from hapifhir/2024-01-gg-fix-expand-params
2024 01 gg fix expand params
2024-01-28 23:05:18 +11:00
dotasek.dev 56d3da1722 Bump version 2024-01-26 11:12:00 -05:00
dotasek 1ff9bd5915 WIP: selector widget 2024-01-25 18:17:50 -05:00
dotasek b6894435d3 Merge remote-tracking branch 'origin/master' into do-20240122-base-engine 2024-01-25 16:54:41 -05:00
dotasek fa88082c14 Merge remote-tracking branch 'origin/master' into do-20230119-fix-filetype-detect-in-service 2024-01-25 16:38:49 -05:00
Grahame Grieve 81569a3984 remove duplicate way of handling parameters on expand value set 2024-01-26 06:27:24 +11:00
markiantorno f492c2114a Updating version to: 6.2.15-SNAPSHOT and incrementing test cases dependency. 2024-01-25 17:19:04 +00:00
markiantorno 485bb2a9a7 Release: v6.2.14
## Validator Changes

* no changes

## Other code changes

* Fix text creation on wrong xhtml node type
***NO_CI***
2024-01-25 16:34:27 +00:00
Grahame Grieve 07d81e3a5b
Fix additional bindings html generation issue (#1551)
* Fix additional bindings html generation issue

* Use new test cases snapshot

---------

Co-authored-by: dotasek <dotasek.dev@gmail.com>
2024-01-24 14:47:49 -05:00
dotasek 92d46093b3 WIP add base engines to ValidationService 2024-01-23 11:45:18 -05:00
dotasek 05e3c76426 If file type is inferred to be null, return error instead of just throwing exception and never returning. 2024-01-19 09:58:22 -05:00
markiantorno 4ffe900fb3 Updating version to: 6.2.14-SNAPSHOT and incrementing test cases dependency. 2024-01-19 12:52:04 +00:00
markiantorno bebd1f31c1 Release: v6.2.13
## Validator Changes

* no changes

## Other code changes

* Fix for handling large expansions correctly
***NO_CI***
2024-01-19 12:17:24 +00:00
Grahame Grieve 41c5f8fee5
Merge pull request #1549 from hapifhir/2024-01-gg-expansion-rework
Fix the way overly large value set expansions are handled
2024-01-19 21:54:51 +11:00
Grahame Grieve a3d4c0645d Fix the way overly large value set expansions are handled 2024-01-19 20:09:57 +11:00
markiantorno a85b5e74cd Updating version to: 6.2.13-SNAPSHOT and incrementing test cases dependency. 2024-01-19 03:37:05 +00:00
markiantorno 8ff31256fe Release: v6.2.12
## Validator Changes

* Handle terminology server errors better

## Other code changes

* Fix expansion related bugs and adjust tests accordingly
* Update test framework for changes to expansion functionality
* Update presentation of fixed and pattern values in profile views
* Handle toString for XhtmlNode when nodeType == null
***NO_CI***
2024-01-19 02:47:02 +00:00
Grahame Grieve bf57789467 Fix expansion related bugs and adjust tests accordingly 2024-01-19 10:39:29 +11:00
markiantorno 2156a44395 Updating version to: 6.2.12-SNAPSHOT and incrementing test cases dependency. 2024-01-18 03:15:19 +00:00
markiantorno 4ca3400a86 Release: v6.2.11
## Validator Changes

* Remove debugging code hiding error from server

## Other code changes

* fix broken links rendering questionnaires
* render target profiles on operation definition parameters
* fix up cvx importer
***NO_CI***
2024-01-18 02:26:19 +00:00
Grahame Grieve 42e3b9a948 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2024-01-18 11:46:49 +11:00
Grahame Grieve b581e36cb5 add error message for tx.fhir.org 2024-01-18 11:42:27 +11:00
markiantorno 0c431880f7 Updating version to: 6.2.11-SNAPSHOT and incrementing test cases dependency. 2024-01-17 16:48:24 +00:00
markiantorno 9c15aff0f3 Release: v6.2.10
## Validator Changes

* Fix issues with multiple terminology servers (should be live soon)
* Rework terminology system & cache to support new terminology server ecosystem
* Handle value set with exclusion filters when expanding
* Fix to consistent error messages when value sets can't be resolved

## Other code changes

* Fix bug processing empty structure maps
* Performance improvements to common IO routines, with test cases - see https://blog.qligier.ch/posts/2024-improving-perf-ig-publisher-io/ (thanks to Quentin Ligier)
***NO_CI***
2024-01-17 15:53:34 +00:00
Grahame Grieve 61b2b5e481 clarify wrong display message 2024-01-18 00:15:22 +11:00
Grahame Grieve 0a41d467b9 fix bug in external valueset processing 2024-01-17 23:39:02 +11:00
Grahame Grieve 8f5afdbcd1 fix bug with processing external valuesets 2024-01-17 23:31:54 +11:00
Grahame Grieve 686f0afaca add debugging code 2024-01-17 23:17:53 +11:00
Grahame Grieve fddd55f4be fix invalid file names in cache 2024-01-17 22:21:14 +11:00
Grahame Grieve ae944151aa fix bug processing empty structure maps 2024-01-17 20:47:10 +11:00
Grahame Grieve 14697210e5 tidy code up 2024-01-17 20:44:49 +11:00
Grahame Grieve 8613cd3944 rework terminology cache to manage multiple terminology servers 2024-01-17 20:44:37 +11:00
Grahame Grieve 510e3886d6 update tx cache for changes to cache 2024-01-17 20:36:27 +11:00
dotasek 602a113363 Fix version bump 2024-01-16 16:26:25 -05:00
Grahame Grieve fed806e40b updates for new tx ecosystem functionality 2024-01-16 22:11:50 +11:00
Grahame Grieve de0024ceec Add support for fetching unknown value sets from tx.fhir.org/ecosystem 2024-01-16 11:45:13 +11:00
Grahame Grieve 56fc442db4 revise BOM handling for stringToX routines 2024-01-15 17:29:42 +11:00
Grahame Grieve 449821a4b4 update tests to handle missing value sets properly 2024-01-15 15:04:47 +11:00
Grahame Grieve 5b0f154620 tidy up fixmes 2024-01-12 10:10:18 +11:00
Grahame Grieve 362e7e2600 more work on multiple terminology servers 2024-01-12 09:16:16 +11:00
markiantorno e2ba911f4e Updating version to: 6.2.9-SNAPSHOT and incrementing test cases dependency. 2024-01-10 21:29:35 +00:00
markiantorno a5e0b5a1dd Release: v6.2.8
## Validator Changes

* Major rework of tx and validation test cases associated with reworking terminology / validator interface and ongoing testing + reconciliation with Ontoserver
major upgrade to validation - use terminology server to perform more logic, and standardise interface based on agreements with Vocab & Ontoserver
* Improve slicing error message
* Add warning to user when referencing an extension that doesn't exist in FHIRPath
* Fix bugs in FHIRPath implementation of split() and join()
* Fix bug handling null objects in JSON (R5)
* Fix for missing search parameter definition in R4
* fix bug handling XML name extension
* Fix FHIRPath validation errors around use of %resource and %rootResource
* Correct validator enforcement of minValue for decimal and integer (#1538)

## Other code changes

* Properly populate property definitions in expansions
* Add CVX Importer
* R6 release support
* IPS tool development
* Improved errors publishing IGs
* Refactor Context to support multiple terminology services
* change type of error when value set circularity found
* Track generated side files when rendering resources
* Support for extended Unicode characters in XHTML / XML / JSON / Turtle
***NO_CI***
2024-01-10 21:03:47 +00:00
Grahame Grieve 109ed9db2c
Merge pull request #1537 from hapifhir/2024-01-gg-mimetype-header-version
update headers on client to add ;fhirVersion=X
2024-01-10 22:15:41 +11:00
Grahame Grieve 69f13d2754 fix null flavor and rebuild cache 2024-01-10 21:26:35 +11:00
Jelmer ter Wal a50ee725f8
fix: correct usage of min decimal and integer 2024-01-10 10:45:03 +01:00
Grahame Grieve 9b9aa51e36 update headers on client to add ;fhirVersion=X 2024-01-10 15:48:47 +11:00
Grahame Grieve fe41fc9cfe Fix issue with search parameter expression validation not knowing %resource 2024-01-10 07:03:59 +11:00
Grahame Grieve b23c099fd2 WIP on validation advisor 2024-01-10 06:16:08 +11:00
Grahame Grieve 2663bea72b update test cases for new facility to compare array sizes 2024-01-09 13:22:15 +11:00
Grahame Grieve 4160d02bd1 change type of error when value set circularity found 2024-01-09 12:00:00 +11:00
Grahame Grieve d74b0e2b4a Refactor Context to support multiple terminology services 2024-01-08 21:07:08 +11:00
Grahame Grieve 85435f38a2 Improve slicing error message 2024-01-05 13:20:25 +11:00
Grahame Grieve c0f61b585f Revert "Improve message when slice is missing"
This reverts commit cadc326d26.
2024-01-05 12:41:35 +11:00
Grahame Grieve cadc326d26 Improve message when slice is missing 2024-01-05 12:39:53 +11:00
Grahame Grieve cf72798e9f Properly populate property definitions in expansions 2024-01-05 12:39:32 +11:00
Grahame Grieve 2f8c2ea5eb ping build 2024-01-04 23:46:35 +11:00
Grahame Grieve c4865e95c5 more fixing tests 2024-01-04 20:28:52 +11:00
Grahame Grieve a17550dc87 one more set of changes for tx validation 2024-01-04 17:46:09 +11:00
Grahame Grieve 2b978b4d4d more terminology qa updates 2024-01-04 14:29:19 +11:00
Grahame Grieve 92fca7a947 more tx validation improvements 2024-01-03 22:19:05 +11:00
Grahame Grieve 108c6f0847 Fix for FHIRPath split() issue 2024-01-02 22:36:00 +11:00
Grahame Grieve 8abdcc6f83 tracking source of server (fix source) 2023-12-31 08:35:18 +11:00
Grahame Grieve f392abd708 clean up code 2023-12-31 08:35:02 +11:00
Grahame Grieve 159e189520 Add support for tracking source server of issue 2023-12-31 08:34:55 +11:00
Grahame Grieve d429f48760 major upgrade to validation - use terminology server to perform more logic, and standardise interface based on agreements with Vocab & Ontoserver 2023-12-30 23:02:19 +11:00
Grahame Grieve 2dc3a5bc77
Merge pull request #1525 from hapifhir/2023-12-gg-tx-word
2023 12 gg tx work
2023-12-26 08:01:42 +11:00
Grahame Grieve 683408c3c5 Adjust validation for changes to validation behaviour 2023-12-26 07:08:39 +11:00
Grahame Grieve cf28e3b440 update terminology cache after changes to tx validation behaviour 2023-12-26 07:08:07 +11:00
Grahame Grieve 3ed816209d update terminology server for test reconciliation with tx.fhir.org 2023-12-25 00:28:39 +11:00
Grahame Grieve 0fdb8e767a Fix for missing search parameter definition in R4 2023-12-22 21:20:46 +11:00
Grahame Grieve 073311bbb6 Various fixes to terminology service after reconciliation with Michael Lawley 2023-12-22 21:20:10 +11:00
rpassas f9e7f98b4f
configurable sessions expiration (#1501)
* unit test + interface

* Renaming and moving expiry related methods to implementation

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-12-18 09:54:20 -05:00
markiantorno d4d7600635 Updating version to: 6.2.8-SNAPSHOT and incrementing test cases dependency. 2023-12-15 13:00:23 +00:00
markiantorno 6c78cc3e48 Release: v6.2.7
## Validator Changes

* Fix up validation of fragment and example value sets
* Improve handling of terminology messages + handling of example and fragment code systems
* Add support for logical_container extension (for CDA constraint validation)
* Clean up handling of xml_name
* Check for xver extension canonical urls when validating uri elements
* Upgrade xver to latest R5 definitions

## Other code changes

* Fix string index error in xver manager
* Fix rendering of type for previous versions
***NO_CI***
2023-12-15 10:50:47 +00:00
Grahame Grieve d59080b45f Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2023-12-15 02:48:27 -05:00
Grahame Grieve ea4ccdf527 Add support for logical_container extension 2023-12-15 02:44:37 -05:00
Grahame Grieve 6caef21869 fix up validation of fragment value sets 2023-12-14 20:40:50 -05:00
Grahame Grieve 8bc062e19d check for xver extension canonical urls when validating uri elements 2023-12-14 07:21:16 -05:00
markiantorno ceaa131d81 Updating version to: 6.2.7-SNAPSHOT and incrementing test cases dependency. 2023-12-13 19:07:52 +00:00
markiantorno b5902aac98 Release: v6.2.6
## Validator Changes

* Fix bug where validator doesn't actually validate web sourced input
* Fix narrative link validation and add id/idref validation
* Remove fhir-test-cases from Validator CLI JAR (#1497) (reduce size)
* Fix to CDA xsi:type validation per SD decision
* Apply regex pattern to literal format if defined
* Improvements to vital signs related messages
* Fix R4 con-3 FHIRPath expression
* Fix bug loading packages with partially specified version that doesn't exist
* Fix for occasional missing warnings around bundle link validation
* Fix using wrong resource type when validating constraints in data type definitions during R6 build
* Fix NPE in validator processing CCDA examples
* Fix problem with version dependencies when loading npm packages directly as files
* Fix for SearchParameter validation using custom resource types

## Other code changes

* Bump commonmark version
* fix Utilities display of time periods (fixed width hour:min)
* Fix stated path for error when code not in value set
* Fix rendering of trigger definition using tables inside paragraphs
* Update VSAC importer to fix timeout issues
* Refactor FHIRPath java package
* Fix problem with profiled resources being called examples in IG publisher
* Remove dependencies for unused UI experiment (#1465)
* Remove AU connectathon
* Include hamcrest dependency
* Fix breaking ValidationEngineTests
* Give kinder error message for missing param
* Fix commonmark group and bump version (#1500)
* Remove dep used for local testing
* Bump jackson & logback versions
* Fix StringType element properties not being copied in various Address, HumanName convertors
* Handle all initial value types when rendering Questionnaires
* Ensure Address.line[] element data is copied over
* Write locking on FilesystemPackageCacheManager
* Fix problems setting owning committee consistently
* Utility classes for fule system package cache pre-loading
***NO_CI***
2023-12-13 18:41:20 +00:00
dotasek 0afea8dc1d
CLI Task to preload package cache (#1508)
* WIP start building preload task

* Slightly refactor exceptions

* sleep between each query

* WIP - FilesystemPackageCacheManager refactor

* Finish refactor

* Customize PackageVisitor

* Remove unused code

* Remove unused code 2

* Add debug logging for failing test

* Point withCacheFolder if to correct param

* Remove console chatter

* Rename to FilesystemPackageCacheManager.Builder

* Move logic to PackageCacheDownloader for re-use in other projects

* Fix spacing
2023-12-13 11:27:15 -05:00
Grahame Grieve 34416b8708 Fix NPE in validator processing CCDA examples 2023-12-13 09:08:06 -05:00
Grahame Grieve ff81c16aeb Fix using wrong resource type when validating constraints in data type definitions (R6) 2023-12-13 09:07:48 -05:00
Grahame Grieve 78669add28 Fix for missing warnings around bundle link validation 2023-12-13 09:07:17 -05:00
Grahame Grieve 166cb445f8 More fixes for SearchParameter validation 2023-12-12 21:00:31 +13:00
Grahame Grieve 289a74301d work around R6 validation issue validating search parameters 2023-12-12 20:32:19 +13:00
Grahame Grieve f9e11e22c1 fix problem with version dependencies when loading npm packages directly in validator 2023-12-12 15:56:23 +13:00
Grahame Grieve de7dc3023d fix validation issues on HL7 publisher 2023-12-11 16:56:27 +11:00
Grahame Grieve 4b1488438e missed files 2023-12-11 14:10:26 +11:00
Grahame Grieve e73404fe8a fix to CDA xsi:type validation per SD decision + apply regex pattern to literal format if defined + improvements to vital signs related messages 2023-12-11 14:09:57 +11:00
Grahame Grieve 2cfc7f3df7 Fix R5 con-3 FHIRPath expression 2023-12-11 14:08:48 +11:00
Grahame Grieve e697ec1c4c check extensions with fhirpath context 2023-12-05 16:56:44 +11:00
Grahame Grieve 49cd2a7bbd actually validate web source in validator 2023-12-01 16:56:45 +11:00
Grahame Grieve 0ae15f7d4d Fix narrative link validation and add id/idref validation 2023-12-01 16:56:11 +11:00
Grahame Grieve 18c4419b9e refactor FHIRPath package 2023-12-01 15:13:33 +11:00
dotasek 09e010b486
Remove dependencies for unused UI experiment (#1465) 2023-11-29 17:33:16 -05:00
dotasek 698849b9f2
Remove fhir-test-cases from Validator CLI JAR (#1497)
* WIP drop fhir-test-cases from CLI jar

* Fix missing JUnit4 tests, update to JUnit5 where possible

* Fix unused import

* Include hamcrest dependency

* Fix breaking ValidationEngineTests

* Give kinder error message for missing param
2023-11-29 14:48:18 -05:00
dotasek 37a8373b94
Fix commonmark group and bump version (#1500)
* Fix commonmark group bump version

* Remove dep used for local testing
2023-11-29 14:47:51 -05:00
dotasek 2ea6d44330 Revert "Fix commonmark group bump version"
This reverts commit 5cf89d8202.
2023-11-27 13:14:18 -05:00
dotasek 5cf89d8202 Fix commonmark group bump version 2023-11-27 11:13:31 -05:00
dotasek a04475ea9c Revert "Fix commonmark group bump version"
This reverts commit 6b45c63638.
2023-11-27 11:10:02 -05:00
dotasek 6b45c63638 Fix commonmark group bump version 2023-11-27 11:06:48 -05:00
markiantorno bf426e2d28 Updating version to: 6.2.6-SNAPSHOT and incrementing test cases dependency. 2023-11-24 19:35:02 +00:00
markiantorno 70d3c801d3 Release: v6.2.5
## Validator Changes

* Fix validator not allowing canonical resource extensions in canonical resources in bundles
* Fix bundle validation error on intneral link checking
* Check parameter type for FHIRPath where() and all()
* Validate that composite search parameters have components

## Other code changes

* Refactor timeout control on client
* Support IPS in validation tests
* Remove orphan R4B test
* Improve expansion error messages
* Fix expansion language - don't set for displayName parameter
* Adjust value set rendering for fragment code systems
* Fix NPE rendering some resources
* Fix rendering of TriggerDefinition
* Support parsing ad-hoc json data type fragments
* More memory work for IG Publisher
* Move ILoggingService & VersionUtil
* Fix timeout issue in vsac
* Introduce ips builder + Infrastructure changes for IPS builder
* Move json and xml extensions from extensions pack to tooling ig
* Add support for rendering union and intersections of profiles in profile comparison
* FHIRPath iif() test case fixes
* Add support for IPS validation in test cases
* Fix for broken markdown re-processing
* Improve identifier rendering
* Fix committee URLs
***NO_CI***
2023-11-24 19:08:02 +00:00
Grahame Grieve 3af3deab3f
Merge pull request #1493 from hapifhir/do-20231120-include-time-stamp
Include time tracking for ValidationResponse
2023-11-25 04:23:23 +11:00
Grahame Grieve d78efdad8f missed code 2023-11-24 08:53:42 +11:00
Grahame Grieve 0e69f6ad89 Support IPS in validation tests 2023-11-24 08:53:32 +11:00
Grahame Grieve c913190d7a validate that composite search parameters have components 2023-11-24 08:53:09 +11:00
Grahame Grieve 3252fb12b0 fix bundle validation error on intneral link checking 2023-11-24 08:52:36 +11:00
Grahame Grieve 3b3ddd28b2 Fix validator not allowing canonical resource extensions in bundles 2023-11-24 08:52:18 +11:00
Grahame Grieve 51ae6a596b More memory work in IGpublisher 2023-11-24 08:48:54 +11:00
Grahame Grieve bd98afaa09 refactor versionutil 2023-11-24 06:10:38 +11:00
dotasek 153c517ea2 Code cleanup, some renaming, adding correct instances of map 2023-11-22 16:05:47 -05:00
dotasek 6916854071 Include Validation time in ValidationResponse 2023-11-20 13:40:03 -05:00
Grahame Grieve f2f10bf27b update test cases 2023-11-17 07:11:24 +11:00
Grahame Grieve a4fa21a868 Add support for IPS validation in test cases 2023-11-17 07:11:13 +11:00
Grahame Grieve e009734d85 fix committee URLs 2023-11-17 07:10:02 +11:00
markiantorno 8fe88a320e Updating version to: 6.2.5-SNAPSHOT and incrementing test cases dependency. 2023-11-15 18:56:03 +00:00