Commit Graph

2510 Commits

Author SHA1 Message Date
dotasek b25c940146 Merge remote-tracking branch 'origin/master' into do-20240122-base-engine 2024-07-04 11:19:21 -04:00
dotasek 6c89f0230f WIP add cleanUp method. 2024-07-04 11:19:09 -04:00
markiantorno 59d0334e0e Updating version to: 6.3.15-SNAPSHOT and incrementing test cases dependency. 2024-07-04 03:22:56 +00:00
markiantorno 50ce6bb6ac Release: v6.3.14
## Validator Changes

* Add support for ND-JSON. Note that the validator is not expected to perform well on large ND-JSON files (or any other file type)
* Significant change: the validator was not checking for the end of the input when parsing a JSON resource finished. It will now start giving errors when JSON continues once the object is complete
* Add support for the create object syntax in FML when validating FML
* Improved error message when supplement url used instead of code system URL

## WHO Translation Project

* Add complete dutch translations (Thanks Alexander Henket)

## Other code changes

* Fix various rendering problems leading to non-unique html anchors
* Fix for unrendered data types
***NO_CI***
2024-07-04 02:33:38 +00:00
dotasek 91f8e27d87 Clean up unused cache work 2024-07-03 17:02:32 -04:00
Grahame Grieve e36c619a58 release notes 2024-07-04 04:04:36 +08:00
dotasek 6c3a987a16 Cleanup 2024-07-03 14:17:26 -04:00
dotasek 2ceb6644aa Merge remote-tracking branch 'origin/master' into do-20240122-base-engine 2024-07-03 10:05:03 -04:00
Grahame Grieve 62bf3e1bc0 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2024-07-02 06:44:39 +09:30
Grahame Grieve 9367ae6bc7 compile fixes 2024-07-01 06:51:08 +09:30
Grahame Grieve d76ed25172 missed files 2024-07-01 06:29:57 +09:30
Grahame Grieve 36c3745c76 support create object syntax in FML when valdiating FML 2024-07-01 06:29:41 +09:30
markiantorno 70ed025741 Updating version to: 6.3.14-SNAPSHOT and incrementing test cases dependency. 2024-06-28 01:14:27 +00:00
markiantorno b3628c7ccd Release: v6.3.13
## Validator Changes

* no changes

## Other code changes

* Rendering fixes
***NO_CI***
2024-06-28 00:27:59 +00:00
markiantorno 0736de9c2d Updating version to: 6.3.13-SNAPSHOT and incrementing test cases dependency. 2024-06-27 00:47:09 +00:00
markiantorno f14f2a42ad Release: v6.3.12
## Validator Changes

* Change how count is calculated when expanding value sets
* Fix value set expansion bugs
* Fix for fhirpath issue on command line (#1650)
* Add IG dependency validator
* work around bad r4 extension definitions
* don't reload different sub-version of extensions pack

## Other code changes

* Rework rendering library from ground up
  * Merge Fix: Fix split logic of canonical into url and version in several places (#1663)
  * Suppress spurious message when code system is unknown
  * don't raise needless and wrong exceptions about extension definitions when rendering
  * fix duplicate link creation
  * Stop recursive rendering crash
  * Obligation rendering improvements
* Handle extra profiles on resources in an IG when converting between versions
* Fixed issue with actor title not rendering in obligations
* Test and adaption for dateOp #1655
* Use assertj instead of hamcrest (#1662)
* More transifex work
* Add support for local packages during testing
***NO_CI***
2024-06-27 00:00:09 +00:00
dotasek 85654a53f5 Merge remote-tracking branch 'origin/master' into do-20240122-base-engine 2024-06-26 17:53:56 -04:00
Pieter Edelman cb330b4029
Issue #1658: recognize that mimetype subtypes can contain dashes (#1664)
* Issue #1658: recognize that mimetype subtypes can contain dashes

* Simple refactor + test case

* Allow plus sign in mimetype subtype, expand tests

* Break out base64 test and url test methods to util classes

* Add additional negative tests for data: URLs

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2024-06-26 09:09:46 -04:00
dotasek 848419952e Merge branch 'master' into do-20240122-base-engine 2024-06-26 09:05:48 -04:00
Grahame Grieve 1439c97c91 fix US core test for validator update 2024-06-26 08:32:19 +10:00
dotasek 917ff364a0 Try removing oldest sessions instead of maintaining max size 2 2024-06-25 13:33:59 -04:00
dotasek 053d29df46 Try removing oldest sessions instead of maintaining max size 2024-06-25 13:33:15 -04:00
Grahame Grieve 852f2e139d
Merge pull request #1654 from ahdis/oe_valcli_fhirpath_1650
cli fhirpath #1650
2024-06-25 23:14:38 +10:00
Grahame Grieve 9208f4848f
Merge pull request #1657 from hapifhir/2024-06-gg-vs-fixes
2024 06 gg vs fixes
2024-06-25 23:13:44 +10:00
Grahame Grieve 88e900110f Merge remote-tracking branch 'origin/master' into 2024-06-gg-rewrite-rendering 2024-06-25 19:53:04 +10:00
Grahame Grieve df82203b3d rework rendering library from ground up 2024-06-25 19:40:57 +10:00
dotasek 9b437438ca
Use assertj instead of hamcrest (#1662)
* Use assertj instead of hamcrest

* Trim README
2024-06-20 10:20:45 -04:00
dotasek 15e9ba30f0 Change to explicitly 'expiring' the oldest session. 2024-06-18 17:30:12 -04:00
dotasek 3a7507c832 Fix test on MaxSize 2024-06-18 16:05:50 -04:00
dotasek 4fa581d242 WIP add a decorator to limit cache size 2024-06-18 15:24:58 -04:00
Grahame Grieve a9213273b1 Suppress spurious message when code system is unknown 2024-06-18 19:45:09 +10:00
dotasek 563d6fe27a Gentle refactor + track session number 2024-06-17 11:26:25 -04:00
dotasek fbf2d01069 Merge remote-tracking branch 'origin/master' into do-20240122-base-engine 2024-06-17 11:25:12 -04:00
Grahame Grieve e91d8152b2 All compiles for the first time 2024-06-17 22:53:29 +10:00
Grahame Grieve b1a3141214 more WIP on rendering refactor 2024-06-17 22:40:52 +10:00
oliveregger 74a2018670 cli fhirpath #1650 2024-06-15 08:25:56 +02:00
Grahame Grieve e731c0c059 Add IG dependency validator 2024-06-13 12:14:03 +10:00
Grahame Grieve 6a29b4feb8 Add support for local packages during testing 2024-06-13 07:37:08 +10:00
Grahame Grieve dfa6a197e0 set up testing with local packages 2024-06-13 07:36:53 +10:00
dotasek b24fb10f54 Merge remote-tracking branch 'origin/master' into do-20240122-base-engine 2024-06-07 16:00:17 -04:00
markiantorno 03ea625a7c Updating version to: 6.3.12-SNAPSHOT and incrementing test cases dependency. 2024-06-07 03:25:47 +00:00
markiantorno 6ba8b38fc5 Release: v6.3.11
## Validator Changes

* Find value sets on tx server if not tx.fhir.org
* Do not send Content-Type header with GET requests for tx servers
* Fix npe validating code system
* Support discriminator by position
* Don't check type characteristics for unknown types

## WHO I18n Project

* Fix typos in phrases, and fix up handling of apostrophes in messages without parameters
* Test and fix for single quote escapes in I18n
* Create and test transifex configuration

## Rendering Changes

* Fix contact rendering to work properly
* Fix issue resolving contained resource rendering DiagnosticReports etc
* Handle case where Contact.value has extensions instead of a string value
* Render Parameterised types
* Fix bug with LOINC Code row showing wrongly in Profile Details view
* Partial implementation of type parameters
* Fixed rendering of actor-specific obligations, added elementIds to obligation narrative rendering
* Corrected ObligationsRenderer to handle multiple actors and multiple codes.  Also got obligations with elements to render properly (which means knowing whether you're on a table page or definitions page, what tab you're on, and whether the element for the obligation is in-scope for that tab (so you know whether to hyperlink or not).  Had to make links on the tables point to definitions because table anchors are not unique.

## Other code changes

* split out Base.canHavePrimitiveValue() from Base.hasPrimitiveValue()
* Refactor how observation profiles are registered in order to generalise management of extra profiles
  * Use validation policy to implement Observation profile rules
  * Rework validation policy management in standalone validator
* Try deploying javadoc with SNAPSHOT
* Add utility to unpack the spec.internals file
* v2 in FHIR tests
* Fix bug loading language pack NPMs
***NO_CI***
2024-06-07 02:33:16 +00:00
dotasek 93037baa9b Go back to SNAPSHOT
***NO_CI***
2024-06-06 21:58:57 -04:00
markiantorno d36d030076 Release: v6.3.11
## Validator Changes

* Find value sets on tx server if not tx.fhir.org
* Do not send Content-Type header with GET requests for tx servers
* Fix npe validating code system
* Support discriminator by position
* Don't check type characteristics for unknown types

## WHO I18n Project

* Fix typos in phrases, and fix up handling of apostrophes in messages without parameters
* Test and fix for single quote escapes in I18n
* Create and test transifex configuration

## Rendering Changes

* Fix contact rendering to work properly
* Fix issue resolving contained resource rendering DiagnosticReports etc
* Handle case where Contact.value has extensions instead of a string value
* Render Parameterised types
* Fix bug with LOINC Code row showing wrongly in Profile Details view
* Partial implementation of type parameters
* Fixed rendering of actor-specific obligations, added elementIds to obligation narrative rendering
* Corrected ObligationsRenderer to handle multiple actors and multiple codes.  Also got obligations with elements to render properly (which means knowing whether you're on a table page or definitions page, what tab you're on, and whether the element for the obligation is in-scope for that tab (so you know whether to hyperlink or not).  Had to make links on the tables point to definitions because table anchors are not unique.

## Other code changes

* split out Base.canHavePrimitiveValue() from Base.hasPrimitiveValue()
* Refactor how observation profiles are registered in order to generalise management of extra profiles
  * Use validation policy to implement Observation profile rules
  * Rework validation policy management in standalone validator
* Try deploying javadoc with SNAPSHOT
* Add utility to unpack the spec.internals file
* v2 in FHIR tests
* Fix bug loading language pack NPMs
***NO_CI***
2024-06-06 22:46:44 +00:00
Grahame Grieve 3265d10280 fix test cases 2024-06-06 20:35:31 +10:00
Grahame Grieve 0250f3ce34 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2024-06-06 19:40:33 +10:00
Grahame Grieve d556db6dad
Merge pull request #1632 from hapifhir/Fix_hintAboutNonMustSupport
Fix handling of hintAboutNonMustSupport to actually be useful.  Speci…
2024-06-06 09:38:16 +10:00
Grahame Grieve 34c4b9600a
Merge pull request #1642 from hapifhir/do-20240530-log-validation-session-counts
Log validation session counts
2024-06-06 09:11:04 +10:00
Grahame Grieve 537f758d82 rework validation policy management in standalone validator 2024-06-06 08:28:34 +10:00
dotasek c2d0207733 Merge remote-tracking branch 'origin/master' into do-20240122-base-engine 2024-06-05 15:29:06 -04:00
dotasek ff4e237bd5 Catch null 2024-06-05 15:29:00 -04:00
Grahame Grieve 2f38cb544c Refactor how observation profiles are registered in order to generalise management of extra profiles 2024-06-01 22:54:17 +10:00
Grahame Grieve 04e95f4e05 Partial implementation of type parameters 2024-06-01 22:51:55 +10:00
Grahame Grieve df711c0762 try again 2024-05-31 09:59:00 +10:00
dotasek a2cf7897f0 Log session cache size 2024-05-30 14:48:03 -04:00
dotasek 6d696d456a WIP on do-20240122-base-engine 2024-05-30 14:47:06 -04:00
dotasek 22ccbbfdfb Merge remote-tracking branch 'origin/master' into do-20240122-base-engine 2024-05-30 13:37:04 -04:00
dotasek 40cccaad5b Make baseEngines concurrent, just in case 2024-05-30 13:36:59 -04:00
dotasek 2e7694a91a Remove FIXME 2024-05-28 16:21:05 -04:00
dotasek b534ded480 Merge branch 'master' into do-20240122-base-engine 2024-05-27 15:30:14 -04:00
Grahame Grieve ae250c4053 fix npe validating code system 2024-05-27 23:55:58 +10:00
Grahame Grieve d279468008 Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core 2024-05-27 23:00:42 +10:00
Grahame Grieve b766cffdb1 v2 tests, support discriminator by position, and don't check type characteristics for unknown types 2024-05-26 07:56:16 -05:00
markiantorno a32e28e4e3 Updating version to: 6.3.11-SNAPSHOT and incrementing test cases dependency. 2024-05-25 23:37:56 +00:00
markiantorno d8781b8b76 Release: v6.3.10
## Validator Changes

* Fix issue validating codes with + in them
* Fix (well, hack) R4 vital signs issue with component units

## WHO I18n Project

* QA on i18n constants - remove spurious entries, add anything missing
* Remove test case for i18n coverage
* Generate properties translation files without blank entries
* Add transifex configuration
* Fix up .po file generation so that POEdit is supported, and remove duplicate constants (#1592)
* Most strings translated to Dutch, unchecked.
* Add utility to infer locale from region code

## Other code changes

* Remove Accept-Charset header
* Fix typos around CODESYSTEM_CONTENT_COMPLETE
***NO_CI***
2024-05-25 22:53:24 +00:00
Grahame Grieve a8ba174383 update cache 2024-05-25 15:12:18 -05:00
Grahame Grieve 853b4fd9ca stable baseline 2024-05-25 04:25:47 -05:00
Grahame Grieve 34c8c262bc more i18n development 2024-05-25 03:57:56 -05:00
Lloyd McKenzie addc88bd20 Fix handling of hintAboutNonMustSupport to actually be useful. Specifically:
- don't yell about missing mustSupport if differential element is setting max to 0, is just declaring slicing, or has a fixed or pattern value
- make clear *what* element doesn't have a mustSupport element in a profile that should
2024-05-22 11:34:43 -05:00
markiantorno 0d0687f1f1 Updating version to: 6.3.10-SNAPSHOT and incrementing test cases dependency. 2024-05-22 05:52:30 +00:00
markiantorno c47f248fa4 Release: v6.3.9
## Validator Changes

* remove "LOINC 2711-0 Oxygen saturation in Venous blood" from the list in the validator that checks whether an observation is a vital sign

## WHO I18n Project

* fix value set summary line display
* update the source of truth translation files

## Other code changes

* Handle more than one expectation extensions in CapabilityStatement
* Fix NPEs in Liquid renderer
***NO_CI***
2024-05-22 05:02:20 +00:00
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