Commit Graph

1933 Commits

Author SHA1 Message Date
Grahame Grieve 99895e7a97 Performance improvements for validation, including -watch engine 2023-06-17 09:40:34 +10:00
dotasek 1afcd224f7 Merge branch 'master' into do-20230602-refactor-cli-params 2023-06-14 10:55:48 -04:00
Grahame Grieve 60fe0fd0f8 fix tx test on tight 2023-06-14 10:54:59 +01:00
dotasek 1a14bf3ef8 Lookahead based regex 2023-06-13 17:30:33 -04:00
dotasek 3c7abb5eff Test coverage 2023-06-13 17:29:16 -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 05134dc99d
Do 20230607 commons beanutils bump (#1297)
* Move property to module

* Document dependency exclusions, RELEASE_NOTES
2023-06-08 15:40:08 -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
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
dotasek b4a34e0bc0 Fix broken test 2023-06-05 18:19:50 -04:00
dotasek a8051d6c45 Rename to ValidationEngineTask 2023-06-05 17:06:10 -04:00
dotasek 19d557788c Add help text for each visible task 2023-06-05 16:39:45 -04:00
dotasek 88883fc5d8 Start implementing help options 2023-06-05 14:30:54 -04:00
dotasek 8eb8787053 Fix missing convert task 2023-06-05 13:51:41 -04:00
dotasek 7922a9947e Add Tests, TxTests, and Compare Tasks 2023-06-05 13:19:51 -04:00
dotasek 949a27f4e6 Tests + start refactor 2023-06-02 18:00:26 -04:00
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
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
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 cba782fcb3 Properly handle case where terminology server is not available 2023-05-29 01:13:30 +03:00
Grahame Grieve 783a8cf28b Support for Obligation Profiles 2023-05-29 01:12:46 +03:00
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 6ded6410b6 just produce the output every time 2023-05-23 20:47:49 +10:00
Grahame Grieve c48fd2b818 All to strip all paragraphs from generated html (post-markdown) 2023-05-23 17:41:03 +10:00
Grahame Grieve 10a0cc7220 Allow meaningWhenMissing on extension definitions 2023-05-23 17:40:13 +10:00
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 035841f13e #692 - error when meaning-when-missing found in profiles 2023-05-22 21:07:17 +10:00
Grahame Grieve 753ca69545 Merge remote-tracking branch 'origin/master' 2023-05-22 17:19:42 +10:00
Grahame Grieve 914615dd57 Clean up error messages on invalid dates etc 2023-05-22 17:18:37 +10:00
Grahame Grieve 96d9581669 increase checking on snapshot generation when validating profiles 2023-05-22 17:18:13 +10:00
Grahame Grieve 4dc9580c90 update tx cache 2023-05-22 17:17:35 +10:00
Grahame Grieve 7da282b5d7 update test cases for various issues encountered and fixed 2023-05-22 17:17:17 +10:00
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 8a3fce9824
Merge pull request #1249 from hapifhir/do-20230503-add-r5-conversion-to-cli
Add r5 + r4b conversion support in CLI
2023-05-17 13:31:38 +10:00
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 52db200d8b change constraints on Reference targets for logical models 2023-05-17 10:32:43 +10:00
Grahame Grieve 6d2e3ee388 Fixes for display warnings 2023-05-13 21:47:25 -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
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 de0af46394 fix npe and improve error message about uri values 2023-05-09 18:51:03 -05:00
Grahame Grieve ce46eee731 return codeableConcept from validate-code 2023-05-08 13:30:04 -05:00
Grahame Grieve 6232c54f15 Fix core 2023-05-07 12:02:00 -05:00
Grahame Grieve ae13abfc2a performance related changes 2023-05-07 11:04:04 -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
dotasek 0d30ccc72f Merge branch 'master' into do-20230503-add-r5-conversion-to-cli 2023-05-04 14:32:27 -04:00
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 3eeec47815 support for value set version 2023-05-04 13:25:43 +10:00
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
dotasek 8a0d0f768d Add r5 conversion support in cli 2023-05-03 15:24:47 -04:00
Grahame Grieve 410f08e6d6 terminology fixes - add expParams to cache key, fix up parameter types, report version 2023-05-02 16:58:54 +10:00
markiantorno 8ba62413ff Updating version to: 6.0.4-SNAPSHOT and incrementing test cases dependency. 2023-05-01 15:33:38 +00:00
markiantorno 9ed0b9ccee Release: v6.0.3
## Validator Changes

* Structure map validation improvements

## Other code changes

* Fix wrong name for systemVersion Parameter
* Language improvements for Lang Packs
* Fix up StructureMap R4/R5 conversion
***NO_CI***
2023-05-01 15:05:34 +00:00
Grahame Grieve 87ca445207 more structure map validation improvements 2023-05-01 18:10:57 +10:00
Grahame Grieve e0286a5326 fix wrong name for systemVersion Parameter 2023-05-01 18:10:33 +10:00
Grahame Grieve 43ef45813b Improvements to StructureMap validation use with profiles (+ fix various bugs) 2023-05-01 18:10:05 +10:00
markiantorno 03a1271508 Updating version to: 6.0.3-SNAPSHOT and incrementing test cases dependency. 2023-04-28 23:47:43 +00:00
markiantorno ccdaf9fe1d Release: v6.0.2
## Validator Changes

* Add support for JSON in tx client batch handling

## Other code changes

* no changes
***NO_CI***
2023-04-28 23:18:04 +00:00
markiantorno 718cd5e369 Updating version to: 6.0.2-SNAPSHOT and incrementing test cases dependency. 2023-04-28 14:29:47 +00:00
markiantorno d43d9bbdd8 Release: v6.0.1
## Validator Changes

* Improved Error messages when code is not in value set + various typo fixes
* Updated Dutch translations for error messages
* More informative failures when questionnaire value set validation fails
* Warnings when extension context is 'Element'
* Fix missing source id for tx server messages in validation output

## Other code changes

* Move HTTP logging to a sub-directory of temp
* Default to text log not HTML log for terminology logging, and don't spuriously escape the text log
* Use JSON not XML by default when using R4 terminology service
* Add support for R6 final version
* Bump HAPI to 6.4.1
***NO_CI***
2023-04-28 14:00:19 +00:00
Grahame Grieve 069dc03c90 Validate Extension Context + fix questionnaire value set validation 2023-04-28 17:28:28 +10:00
dotasek e01aa876c8
Bump HAPI to 6.4.1 (#1237)
* Bump HAPI to 6.4.1

* Fix broken checkstyle configs

* Fix checkstyle in convertors
2023-04-27 18:11:25 -04:00
markiantorno 46259c47e0 Updating version to: 6.0.1-SNAPSHOT and incrementing test cases dependency. 2023-04-26 23:45:01 +00:00
markiantorno 5a4049e0e2 Release: v6.0.0
## Validator Changes

Note: This validator release is accompanied by a new release of tx.fhir.org, and earlier versions
of the validator will not perform validation correctly for some valuesets and languages. This is
in effect a mandatory upgrade

* Major **Breaking** change: test multi-lanugage support on the terminology service API, and make many fixes.
** This release also includes full support for supplements providing designations and properties
* Add support for -install operation to install packages and generate snapshots while at it (support simplifier packages in sushi)
* Add support for ```lang-transform extract``` and ```-lang-transform inject``` to the validator (start of multi-lingual implementation support)
* Add support for -tx-tests to validator
* Change settings file to fhir-settings.json in .fhir, instead of fhir-tools-setting.ini (see [here](https://confluence.hl7.org/display/FHIR/Using+fhir-settings.json) for documentation)
* Add provisional support for running without a network: -no-network. Beware: this is not fully tested at this point
* Warning not error when the code system isn't known validating questionnaires
* Fix up loading of IG bundles
* Work around issue with R5 path in extensions pack
* Fix issue with SearchParameter validation throwing an exception if no expressions are valid

## Other code changes

* Code to support translation functionality
* Partial fix for problem parsing maps from previous versions
* Fix Code System rendering for supplements, and when there's 1..2 display translations
* Remove spurious header from ConceptMap rendering
* Return ID part correctly when FhirPath expression result is converted to string
* fix problem with leaf rendering in profile driven renderer
* Fix R4B tests to be based on R4B
* fix index error validating HierarchicalTable
* fix NPE in requirements renderer
* Fix NPE in code generator
* Rework package cache manager - add testing mode
* Add link to questionnaire rendering questionnaireResponse + Fix access violation rendering questionnaire
* Fix bugs generating narratives
* Defining the existence of R6
* i18n framework for HTML generation in renderers - step #1
* Re-org validation testing to be more memory efficient
* Better error handling loading resources
* Restore broken R4 loading
* Add new R5 fields to R4/R5 conversion for ValueSet
* minor changes two HumanName.getNameAsSingleString (missed family name)
***NO_CI***
2023-04-26 23:16:02 +00:00
Grahame Grieve 085ddde843 bump major version 2023-04-27 08:00:56 +10:00
Grahame Grieve 1f76c6e944
Merge pull request #1230 from hapifhir/MapValidationStuff
Fix IG Loader problems where map conversion no longer works with a 'n…
2023-04-26 22:24:51 +10:00
Grahame Grieve 3ed7813973 language translations support in validator 2023-04-25 21:51:31 +10:00
Grahame Grieve b6b4fbcd0c more tx test fixes 2023-04-24 23:08:29 +10:00
Lloyd McKenzie 5e8f97f57c Fix IG Loader problems where map conversion no longer works with a 'null' context 2023-04-23 14:20:45 -06:00
Grahame Grieve fbaff6cdb0 add -install for packages 2023-04-21 18:53:20 +08:00
Grahame Grieve fe86ab1d7c reorg server settings 2023-04-21 18:52:36 +08:00
Grahame Grieve 45005b9ff7 fix server 2023-04-21 14:17:15 +08:00
Grahame Grieve 5a4d7f4831 remove id from terminology service tests 2023-04-21 12:26:28 +08:00
dotasek 9b4b1ae2cc
Add -fhir-settings param to Validator CLI (#1203)
* Start work

* Tests for new Param

* More tests, add param, refactor

* Rename + JsonProperty annotations

* Logging for API keys

* WIP rename search parameter + add settings object for serialization

* Switch to JSON based settings file.

* Rename FHIRSettings and remove ToolGlobalSettings

* Update default path for settings file + expand test

* Only allow single instantiation with explicitFilePath

* Move and expand tests

* Fix failing test

* Add test for FhirSettings param precedence

* Refactor to only call getInstance() internally in FhirSettings
2023-04-19 17:18:29 -04:00
dotasek 237a9c99f0
Bump jackson (#1222) 2023-04-18 09:49:53 -04:00
Grahame Grieve 3a2b5b1be4
Merge pull request #1224 from hapifhir/gg-202304-rework-tx3
Gg 202304 rework tx3
2023-04-18 11:50:50 +08:00
Grahame Grieve 5ebd695e79 don't build new manifest 2023-04-18 10:31:24 +08:00
Grahame Grieve f60f377a66 update tx cache for vlaidation 2023-04-18 09:42:08 +08:00
Grahame Grieve cc8c7be307 fix which servers tests are based on 2023-04-18 09:41:15 +08:00
Grahame Grieve 02bd1d8ce7 more fixing for language handling issues 2023-04-18 09:40:49 +08:00
dotasek 946b241e65
Bump logback (#1218)
* Fix  SimpleWorkerContextTests, ignore ExternalTerminologyServiceTests

* Bump logback

* Try explicit logback-test.xml for validation

* Try forkNode implementation
2023-04-17 10:44:30 -04:00