Commit Graph

942 Commits

Author SHA1 Message Date
Grahame Grieve f860af857d Fix conversion issue associated with ConceptMap.element.target.equivalence in versions previous to R5 (use proper extension URL, and move extension so it can be a modifier. And fix for modifierExtension handling) 2023-10-09 17:41:26 +11:00
markiantorno 9ec1c68cfc Updating version to: 6.1.13-SNAPSHOT and incrementing test cases dependency. 2023-10-05 02:20:25 +00:00
markiantorno d705905c8c Release: v6.1.12
## Validator Changes

* fix CDA parsing error for sdtc:raceCode
* fix xml output to deal with namespaces properly
* fix FHIRPath join implementation to make separator parameter optional

## Other code changes

* Improve rendering for xml_no_order extension
* add command line demo app
* rework xig into 3 steps
* add userData to JSON element
* Initial SQL On FHIR implementation
* Add getDistalNames() to FHIRPath for SQL-on-FHIR support
***NO_CI***
2023-10-05 01:50:02 +00:00
markiantorno 627e40934b Updating version to: 6.1.12-SNAPSHOT and incrementing test cases dependency. 2023-10-02 13:18:11 +00:00
markiantorno 9b5c26be25 Release: v6.1.11
## Validator Changes

* Fix FHIRPath type resolution for logical models
* Update parsers to record the element format for logical model validation
* fix profile matching for CDA logical models

## Other code changes

* Upgrade PackageVisitor for XIG
***NO_CI***
2023-09-30 18:21:42 +00:00
markiantorno f9b3dbde57 Updating version to: 6.1.11-SNAPSHOT and incrementing test cases dependency. 2023-09-29 11:11:34 +00:00
markiantorno ddd3889268 Release: v6.1.10
## Validator Changes

* Change Mapping type validation error to warning validating maps
* Add support for special case codes in v2 (NNnnn)
* Fix problem parsing logical model cda fragments
* Fix parsing logical model list attributes
* Fix issue parsing parameters in a target expression

## Other code changes

* Handle additional bindings when generating snapshots for R5 profiles
* Fix problem rendering additional bindings in R5
* Fix for new pubpack version
***NO_CI***
2023-09-29 10:45:20 +00:00
markiantorno 90d683907d Updating version to: 6.1.10-SNAPSHOT and incrementing test cases dependency. 2023-09-27 16:01:56 +00:00
markiantorno b276d8a793 Release: v6.1.9
## Validator Changes

* Fix for issue parsing SHC and not recording line/col correctly
* Fix issue validating CDA FHIR Path constraints
* Better error handling validating codes in concept maps
* Validate special resource rules on contained resources and Bundle entries
* Improved error messages of observation bp
* Fix up WG internal model for changes to workgroups
* fix misleading error message inferring system when filters in play
* Fix type handling for logical models (CDA fixes)
* Fix up parsing of logical models
* Fix bug parsing extension with no value in JSON for the validator

## Other code changes

* Major uplift of PEModel to support generated code for profiles in R4 + R5
* Add removeChild in R4/R4B/R5 model
* Fix version conversion issue between r4 and r5 charge definition issue
* Fix rendering extension and missed profile on Reference()
***NO_CI***
2023-09-27 15:35:08 +00:00
markiantorno 7d4816f628 Updating version to: 6.1.9-SNAPSHOT and incrementing test cases dependency. 2023-09-21 19:51:51 +00:00
markiantorno 8413995d8b Release: v6.1.8
## Validator Changes

* no changes

## Other code changes

* Fix typo in CodeSystem renderer fixed string
***NO_CI***
2023-09-21 19:24:42 +00:00
markiantorno 14e6f210e6 Updating version to: 6.1.8-SNAPSHOT and incrementing test cases dependency. 2023-09-21 06:36:25 +00:00
markiantorno 23a0bc3f14 Release: v6.1.7
## Validator Changes

* Significant Performance improvements parsing JSON resources
* Refactor Type handling for faster performance
* Validate the stated publisher/WG/contacts for HL7 published resources
* Better error message when diff contains bad paths
* pass dependent resources to server and make sure cache-id is filled out properly in all contexts
* Fix error in FML parser parsing parameters
* Fix issue with dom-6 and contained elements (Internal ChildMap synchro issues)
* Better handling of errors from tx.fhir.org
* Fix bug checking for implicit value sets
* Fix bug checking of mixing snomed display types
* Reduce size of validatable concept map to 500 - for now + better handling of errors on server batches
* Improve UCUM validation BP rule

## Other code changes

* Fix up handling of includes in liquid templates
* Fix up rendering of profile names for abstract profile instantiations
* Improved rendering of codes in include when rendering valuesets
* Start generating .index.db as well as .index.json in packages for faster package reading
* Fix problem caching look up of implied value sets
* Add okio dependency for running vsac
***NO_CI***
2023-09-21 06:06:01 +00:00
markiantorno a68ba66d1a Updating version to: 6.1.7-SNAPSHOT and incrementing test cases dependency. 2023-09-15 22:58:19 +00:00
markiantorno 43e73b1281 Release: v6.1.6
## Validator Changes

* Add R4B binding-definition URL to validator exception list
* Correct validation when CodeSystem.content = example and server doesn't know code system
* Fix bug processing CDA snapshots
* Fix issue evaluating FHIRPath correctness on CDA.Observation
* Improve error message from validator when invariants fail
* Fix NPE validating concept maps
* Add parameter for easy CDA validation
* Suppress wrong invariants on compiler magic types
* fix NPE checking codes

## Other code changes

* Improve CodeSystem rendering - make parent property a link
* Add file tracking when npm package performing file unpacking
* Remove env variables from path builder
* Fix bug in version comparison
* fix for NPE in HAPI
* Performance improvements for IG Publisher
* Start working on cross-version extensions
* Improve rendering of message about logical target
***NO_CI***
2023-09-15 22:32:55 +00:00
markiantorno a8967b378f Updating version to: 6.1.6-SNAPSHOT and incrementing test cases dependency. 2023-09-11 01:26:15 +00:00
markiantorno a09216c6e8 Release: v6.1.5
## Validator Changes

* no changes

## Other code changes

* Add baseUrl and version methods to r5 CanonicalType
***NO_CI***
2023-09-11 01:00:01 +00:00
markiantorno 30ed1bf615 Updating version to: 6.1.5-SNAPSHOT and incrementing test cases dependency. 2023-09-10 01:22:26 +00:00
markiantorno 1c24341056 Release: v6.1.4
## Validator Changes

* Fix bug preventing Best Practice invariants being reported on, and add -best-practice parameter
* Fix issue not validating bundles when there are multiple profiles on entry.resource
* Add Japanese translations

## Other code changes

* Fixes for minor bugs discovered testing the XIG
* fix package program data path
***NO_CI***
2023-09-10 00:51:54 +00:00
dotasek 430833616a Merge branch 'master' into do-20230905-fix-system-cache-directory 2023-09-06 09:26:05 -04:00
markiantorno 980f04557c Updating version to: 6.1.4-SNAPSHOT and incrementing test cases dependency. 2023-09-06 08:22:50 +00:00
markiantorno 6d37127e63 Release: v6.1.3
## Validator Changes

* Test concept map code validity
* Rework type checking on target profiles to support imposesProfile
* Fix imposesProfile extension being missed on primary profile
* Add support for IPS-AU
* Fix warning/error message about experimental property on CodeSystems and ValueSets
* Fix unknown code message to include code system version
* Add provisional SHLinks validation

## Other code changes

* Render Requirements.reference
* Convert Requirements.reference between versions
* Fix test that breaks on local machines + Fix system path for FileSystemPackageCacheManager
* Update to cqframework 2.11 and remove unused common-beanutils declaration (#1419)
* Better xhtml logging for debugging
* Fix DF markdown engine to escape < properly
* Support for sub-packages in packagelist.json
* NPE proofing property handling for Code Systems
* rework the way intermediary content is handled in the validator
* Restore CodeQL regex queries (#1422) + Whitelist BSD 3-clause license
***NO_CI***
2023-09-06 06:12:07 +00:00
dotasek 82813a88d2 Fix system path for FileSystemPackageCacheManager 2023-09-05 15:35:21 -04:00
markiantorno bca705a3c6 Updating version to: 6.1.3-SNAPSHOT and incrementing test cases dependency. 2023-08-31 13:58:37 +00:00
markiantorno f5e218c279 Release: v6.1.2
## Validator Changes

* FHIRPath fixes checking types discovered testing R6 build

## Other code changes

* Fix rendering of impose-profile extension
* Improvements to performance tracking code
* get FHIRFormat from SHC code
***NO_CI***
2023-08-31 13:29:31 +00:00
Grahame Grieve 2deb88cdc9 Merge remote-tracking branch 'origin/master' 2023-08-30 09:38:45 +02:00
Grahame Grieve ac33590b96 #1412 - fix out of memory issues 2023-08-29 17:34:03 +02:00
markiantorno 9048983155 Updating version to: 6.1.2-SNAPSHOT and incrementing test cases dependency. 2023-08-29 08:56:09 +00:00
markiantorno 2f6c61af78 Release: v6.1.1
## Validator Changes

* Fix problem validating code systems with content = not-present
* Further development of multi-language support on the tx server, and:
* Change the validator so that the default language is '*' (all languages) not 'en'

## Other code changes

* Improve license scanning and readme documentation
* Change xpp3 dependency
* Add client version to tx user-agent requests
* Suppress spurious xml parsing messages to System.err
***NO_CI***
2023-08-29 08:27:41 +00:00
Grahame Grieve d0815682b8
Merge branch 'master' into language-rework 2023-08-28 20:13:42 +02:00
Grahame Grieve 333ffc340e Accept-Language 2023-08-25 16:21:56 +02:00
dotasek 490e57fa7c Swap out xpp3 dependency 2023-08-23 15:51:44 -04:00
markiantorno fb64a720c8 Updating version to: 6.1.1-SNAPSHOT and incrementing test cases dependency. 2023-08-22 17:26:57 +00:00
markiantorno e90863a271 Release: v6.1.0
## Validator Changes

* Performance fix: Delay loading content when loading IGs
* CodeSystem validation around count and content
* Add checking around internal status consistency and across dependencies (draft/experimental/retired/deprecated)
* Improved error messages on server failure
* Fix bug in warning about No valid Display Names found
* Use Supplements when validating display names
* Fix issue in FHIRPath .combine focus handling
* Check Extension fixed values for URLs - enforce consistency
* Fix R4 FML parser problem
* Track and report inactive status when reported from terminology server
* Add defense against large terminology operations causing obscure java errors
* Fix bug with client sending too much data to tx.fhir.org (big performance hit in some cases)
* Fix obscure bug with designations in a more specific language the the code system they are in

## Other code changes

* Significant upgrade of version comparison for profiles/extensions, value sets, and code systems, and integration into rendering framework
* Many minor changes to terminology functionality (reconciliation with differences with OntoServer) including service protection
  * Rename implySystem parameter to inferSystem per TI decision
  * rework how definitions are handled after discussion with Michael
  * add flat mode to tests for Ontoserver, and add experimental functionality
* fix rendering issue in subscription topic
* Add a renderer for ExampleScenario
* Automatically render markdown in code system concept definitions
* Fix loading issues in test mode for simplifier packages
* Remove spurious logging in FHIRPath engine
* Fix addChild error in PEBuilder (#1343) + Add test case
* CPT Importer
* Dependencies fixed/updated: okhttp, thymeleaf, commonmark & UCUM
* Xhtml fluent improvements + related XHtmlNode improvements
* Release new pubpack for new icons
* Json Object comparison: fix bug in arrays with multiple optional elements + improved error messages + support for external strings
* fix cross-version extensions web references where possible
* Don't suppress exceptions in terminology clients
* Add first cut of Profile Generation code
* Stop putting invalid codes in expansions if they are not in the code system
***NO_CI***
2023-08-22 17:01:34 +00:00
dotasek 1b33d2a537 Bump minor version 2023-08-22 11:56:22 -04:00
dotasek 9ae060b5d9 Bump ucum version 2023-08-21 09:32:52 -04:00
dotasek dacc73a114 Bump okhttp dependency, exclude vulnerable transitives 2023-08-15 12:52:01 -04:00
Grahame Grieve 6041660e9b Improved error messages on server failure 2023-08-11 14:16:09 +10:00
Grahame Grieve 952dedd06b #1343 - addChild error in PEBuilder 2023-08-09 19:48:01 +10:00
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
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
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 3eef08dab8 remove unused imports 2023-07-26 08:31:21 +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 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
markiantorno 6a187a9232 Updating version to: 6.0.22-SNAPSHOT and incrementing test cases dependency. 2023-07-07 12:36:19 +00:00