Commit Graph

2215 Commits

Author SHA1 Message Date
dotasek ef6f92a21e WIP return validation fragments 2023-09-21 09:50:08 -04:00
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
Grahame Grieve 31ea68f69b Fix bug checking for implicit value sets 2023-09-21 12:42:36 +10:00
Grahame Grieve 9ef82e7e23 Fix bug checking of mixing snomed display types 2023-09-21 12:42:18 +10:00
Grahame Grieve 66b69deb37 reduce size of validatable concept map - for now 2023-09-21 12:41:55 +10:00
Grahame Grieve 6f17713ae8 Improve UCUM validation BP rule 2023-09-21 12:41:23 +10:00
Grahame Grieve a6f43420d5 publication WG checking not for example resources 2023-09-20 16:58:17 +10:00
Grahame Grieve eecc6633d3 Improved rendering of codes in include when rendering valuesets 2023-09-20 11:12:50 +10:00
Grahame Grieve 91abf50cdc Fix issue with dom-6 and contained elements 2023-09-20 11:11:05 +10:00
Grahame Grieve 46c12d1a22 Performance improvements for type handling, and rename NamedElement to ValidatedFragment 2023-09-19 09:58:36 +10:00
Grahame Grieve 4d2868f21e Add support for validating WG info in HL7 resources 2023-09-15 22:01:30 -07:00
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
Grahame Grieve 65ea3ddf95 Merge remote-tracking branch 'origin/master' 2023-09-15 13:13:40 -07:00
Grahame Grieve 1b65cb5ca2 Suppress wrong invariants on compiler magic types 2023-09-15 12:47:15 -07:00
Grahame Grieve 96ce441f9a more IG publisher efficiency work 2023-09-15 10:15:04 -07:00
Grahame Grieve c6b7a4f47d start working on cross-version extensions 2023-09-15 10:14:43 -07:00
Grahame Grieve f90308d7d3 easy CDA validation 2023-09-15 10:14:23 -07:00
Grahame Grieve a620e2aa30 fix NPE validating concept maps 2023-09-15 10:14:06 -07:00
Grahame Grieve a59a9619d9 Improve error message from validator when invariants fail 2023-09-15 10:13:02 -07:00
Grahame Grieve a6b6a9d330 Add R4B binding-definition URL to validator exception list 2023-09-12 15:48:22 -07:00
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
Grahame Grieve 6b38a730e9 SHC signature verification 2023-09-08 07:35:11 +10:00
Grahame Grieve 304fa3f493 Adjust tests for best-practice flag 2023-09-08 04:21:14 +10:00
Grahame Grieve c610e7a8b5 Make Best Practice Recommendations work properly 2023-09-07 22:01:13 +10:00
Grahame Grieve a061db8f01 Fix issue not validating bundles when there are multiple profiles on entry.resource 2023-09-07 17:07:09 +10:00
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
Grahame Grieve f1f45f91e1 fix npe 2023-09-06 11:14:56 +10:00
Grahame Grieve 87f7984f8b test concept map code validity 2023-09-06 09:12:25 +10:00
Thomas Papke f05b2f5966
Update to cqframework 2.11 and remove unused common-beanutils declaration (#1419) 2023-09-05 09:08:22 -04:00
Grahame Grieve d7d56f5cec Support for IPS-AU 2023-09-04 13:40:29 +10:00
Grahame Grieve 5cc4e3ef03 rework the way intermediary content is handled in the validator + fix impose-profile handling for IPS-AU 2023-09-04 13:38:22 +10:00
Grahame Grieve bfac7f06de Add SHLinks validation 2023-09-02 23:21:32 +07:00
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 54f36aec4c more FHIRPath fixes 2023-08-31 08:15:33 +02:00
Grahame Grieve 4bba1c2cde fix bugs in FHIRPath checking and track special time when validating resources 2023-08-31 06:30:29 +02:00
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 a22338cd54 fix up failing tests 2023-08-28 15:58:37 +02:00
Grahame Grieve 0d98d80eac more cache changes 2023-08-28 14:53:25 +02:00
Grahame Grieve 684f6bd740 fix test cases 2023-08-28 12:56:47 +02:00
Grahame Grieve 333ffc340e Accept-Language 2023-08-25 16:21:56 +02:00
Grahame Grieve 7eaa723ec9 rewrite the way language works in value sets 2023-08-25 13:09:36 +02:00
dotasek 985b66c276 Add version to agent header
+ remove unused getValidationEngine methods in Common
2023-08-24 15:31:09 -04:00
Grahame Grieve 63e090a2d9
Merge pull request #1405 from hapifhir/do-20230823-swap-out-xpp3
Swap out xpp3 dependency
2023-08-24 09:18:56 +02:00
Grahame Grieve debbff6319
Merge pull request #1407 from hapifhir/2023-08-gg-fix-1404
#1404 Fix problem validating code systems with content = not-present
2023-08-24 09:17:37 +02:00
Grahame Grieve 0b18b3a3b3 #1404 Fix problem validating code systems with content = not-present 2023-08-24 06:38:15 +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
Grahame Grieve f5f35d5815 in order to get the tests passing 2023-08-22 14:46:04 +10:00
dotasek 9ae060b5d9 Bump ucum version 2023-08-21 09:32:52 -04:00
Grahame Grieve f795394fd2 Sorting ValueSet.expansion.contains in the tx tests 2023-08-21 19:35:10 +10:00
Grahame Grieve 390e25ddae more test fixes 2023-08-19 22:46:23 +10:00
Grahame Grieve e4f6ec5a7b more revisions to tests 2023-08-19 20:18:15 +10:00
Grahame Grieve 497a81a544 Track and report inactive status when reported from terminology server 2023-08-19 20:17:42 +10:00
Grahame Grieve 6f0d54a8dc terminology service bug fixes 2023-08-19 09:03:59 +10:00
Grahame Grieve 0d1072616e rework comparison and related rendering 2023-08-17 18:14:12 +10:00
Grahame Grieve eacffd11df Add support for external strings for tx tests 2023-08-17 11:14:34 +10:00
Grahame Grieve 4d7ecec87c more status checking 2023-08-16 22:39:28 +10:00
Grahame Grieve 3beb0c78e2 Merge remote-tracking branch 'origin/master' 2023-08-16 19:27:48 +10:00
Grahame Grieve e6ef3572ea revise operation issue sorter for tx testing 2023-08-16 19:27:41 +10:00
Grahame Grieve 1711abc322
Merge branch 'master' into do-20230815-bump-okhttp-dependencies 2023-08-16 09:10:47 +10:00
dotasek 976915f3bc Merge branch 'master' into do-20230815-bump-okhttp-dependencies 2023-08-15 17:41:02 -04:00
dotasek ea5270824d Merge branch 'master' into do-20230815-bump-thymeleaf 2023-08-15 17:40:46 -04:00
dotasek dacc73a114 Bump okhttp dependency, exclude vulnerable transitives 2023-08-15 12:52:01 -04:00
dotasek b438e8cd64 Move thymeleaf version to dependencyManagement 2023-08-15 11:27:50 -04:00
dotasek 7c03910a63 Bump thymeleaf 2023-08-15 10:50:29 -04:00
dotasek 2fa0587c1f Fix commonmark class not found 2023-08-15 10:34:58 -04:00
dotasek 81eba4b825 Clean imports 2023-08-15 10:34:31 -04:00
Grahame Grieve ea4e592910 CodeSystem validation around count and content 2023-08-15 19:34:24 +10:00
Grahame Grieve 2b15c545fc comparison tests to include rendering as well 2023-08-15 19:33:56 +10:00
Grahame Grieve ebc755bc2a Check consistency between standards status and resource status 2023-08-14 21:11:49 +10:00
Grahame Grieve 839deaf575 fix up return code in tx tests 2023-08-14 15:39:43 +10:00
Grahame Grieve 14162902de fix tests + fix FML parser problem 2023-08-12 23:06:16 +10:00
Grahame Grieve 369d01646e fix sorting 2023-08-11 16:29:44 +10:00
Grahame Grieve b85b588825 restructure validators to properly validate deprecated dependencies 2023-08-11 12:24:08 +10:00
Grahame Grieve 5aefd6a268 add flat mode to tests, and add experimental functionality 2023-08-11 12:11:22 +10:00
Grahame Grieve 4b006f82ab delay loading content when loading IGs 2023-08-08 21:36:46 +10:00
Grahame Grieve 1dd1c4ad90 better error when extension URL not fixed 2023-08-05 20:58:49 +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
Grahame Grieve 26b41ee080 fix server address 2023-08-04 20:48:05 +10:00
Grahame Grieve ad08255740 Merge remote-tracking branch 'origin/master' 2023-08-04 11:49:19 +10:00
Grahame Grieve 45b5631e62 Fix issue with collection status of resolve() being wrong 2023-08-04 11:47:44 +10:00
Grahame Grieve 6d0883468b
2023 08 gg extension paths (#1380)
* fix problem with whitespace in terminology caching

* Support for x-version extensions when generating snapshots

* Fix problem with evaluating extension contexts

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

* Resolve URL for x-version extensions

* render inactive property in expansions

* fix tests

* ping build

* Point to correct test-cases version

---------

Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-08-03 16:12:48 -04:00
Grahame Grieve b668f4a04a fix tests 2023-08-03 21:33:57 +10:00
Grahame Grieve df4432b49d Fix problem with evaluating extension contexts 2023-08-03 20:28:04 +10:00
markiantorno 011167a218 Updating version to: 6.0.25-SNAPSHOT and incrementing test cases dependency. 2023-08-02 23:28:12 +00:00
markiantorno 42274a7bd3 Release: v6.0.24
## Validator Changes

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

## Other code changes

* fix up copy directory for case differences
***NO_CI***
2023-08-02 23:02:37 +00:00
Grahame Grieve db0413c735 Don't load resources from core examples package 2023-08-02 22:11:43 +10:00
Grahame Grieve 32f2f6acc7 warnings for status on terminology resources 2023-08-02 18:12:02 +10:00
Grahame Grieve 96b5b6c520
Merge pull request #1370 from hapifhir/2023-07-gg-extension-context-fixes
2023 07 gg extension context fixes
2023-08-02 06:05:10 +10:00
dotasek fd1eea71e6
Fix error creating new manifest file (#1372) 2023-08-01 14:03:24 -04:00
Grahame Grieve 0eb96f1f0a fixes for extensions IG testing 2023-07-31 20:46:30 +10:00
Grahame Grieve d314a927af FIx up problem resolving URLs 2023-07-31 14:38:09 +10:00
Grahame Grieve b42c908328 More improved FHIRPath checking when validating 2023-07-31 14:37:41 +10:00
Grahame Grieve c58703c63f Improved invariant checking 2023-07-29 08:49:27 +10:00
markiantorno 0165495626 Updating version to: 6.0.24-SNAPSHOT and incrementing test cases dependency. 2023-07-27 14:23:16 +00:00
markiantorno db5d2b07c3 Release: v6.0.23
## Validator Changes

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

## Other code changes

* Add support for Liquid assign
* Switch to DateTime type for Android Support
* Code clean up: remove unused imports
* Fix JSON unicode encoding handling of chars <32 code points
***NO_CI***
2023-07-27 13:56:32 +00:00
Grahame Grieve 06c865badf Fix NPE validating codes in value sets with improper expansions 2023-07-27 17:50:42 +10:00
Grahame Grieve 6afb151dff Better information when CodeSystem.content = not-present 2023-07-27 17:49:03 +10:00
Grahame Grieve a3c32d86a0 add support for Liquid assign + Fix JSON unicode encoding and add character check in validator for illegal XML Unicode characters 2023-07-26 12:32:51 +10:00
Grahame Grieve 3eef08dab8 remove unused imports 2023-07-26 08:31:21 +10:00
Grahame Grieve fefd1ad1d6 fix -ips parameter and add -check-ips-codes parameter 2023-07-26 00:59:02 +10:00
Grahame Grieve 31a76447bd Merge remote-tracking branch 'origin/master' 2023-07-25 05:55:04 +10:00
Grahame Grieve 659da6367d update IPS versions 2023-07-25 05:54:27 +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
Grahame Grieve 363045c1c8 Fix bugs in FHIRPath handling of logical models 2023-07-22 08:18:55 +10:00
Grahame Grieve 6350d9743e Don't check FHIRPaths on differentials - not enough type info to test reliably 2023-07-21 21:18:38 +10:00
Grahame Grieve ce44ab27fe fix type of x-unknown-code-system 2023-07-21 21:18:10 +10:00
Grahame Grieve 672ebf0348 Fix CDA validation test case 2023-07-21 21:17:51 +10:00
Grahame Grieve 8980df2364 add value set qa checking 2023-07-21 21:17:12 +10:00
Grahame Grieve cf1b53bba0 Update terminology server implementation and tests for changes to test cases 2023-07-21 05:38:09 +10:00
Grahame Grieve 616cf5fdb3 Add provisional support for alternate codes 2023-07-20 08:21:19 +10:00
Grahame Grieve 3f67cbee9e Merge remote-tracking branch 'origin/master' 2023-07-18 11:12:10 +10:00
Grahame Grieve ced714305d Fix to get context variables right when running invariants + fix for parent not always being populated + check type in derived profiles 2023-07-18 11:05:06 +10:00
dotasek bdb415cf8a
Bump thymeleaf to 3.1.1.RELEASE (#1349) 2023-07-17 16:35:28 -04:00
dotasek 6c2c1b21f9
Remove javalin dependency (#1348) 2023-07-14 16:51:06 -04:00
dotasek c2cb2aaa21
Add OWASP dependency check (#1347)
* Add owasp dependency scan

* Add github action to upload results

* Remove unused javalin dependency, also generate html reports

* formats instead of format

* Restore javalin dependency (make revert easier later if necessary)

* Set OWASP to run on PR plus better names for sarif upload
2023-07-14 10:56:40 -04:00
dotasek 8cf4a62f32
Remove unneeded resources (#1346) 2023-07-12 16:46:42 -04:00
Grahame Grieve 5e30c0ee92 Fix checking FHIRPath statements on inner elements of type slices 2023-07-09 08:03:35 +10:00
Grahame Grieve 1f6912d3a6 fix issue checking invariant expressions in R5 2023-07-08 16:44:50 +10:00
markiantorno 6a187a9232 Updating version to: 6.0.22-SNAPSHOT and incrementing test cases dependency. 2023-07-07 12:36:19 +00:00
markiantorno 45ae02cf1d Release: v6.0.21
## Validator Changes

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

## Other code changes

* Render reference identifier if there is one when rendering references
* Hide empty place holder column when rendering by profile
* Fix npe rendering extensions + improve base64 presentation
* OMOP terminology importer
* update SPDX code system in R4/R4B for support for not-open-source
* Fix up type handling for conversions between R4/R4B and R5 (OperationDefinition fix)
***NO_CI***
2023-07-07 12:10:05 +00:00
Grahame Grieve 9acd16e35a clarify code 2023-07-07 14:43:16 +10:00
Grahame Grieve cacf6696cd
Merge pull request #1333 from DarthGizka/stability-fixes-20230630
Fix typo in ValidatorUtils::readInteger(), fix accident-prone file list loop & exempt missing files from processing
2023-07-07 14:41:59 +10:00
Grahame Grieve 83fc639242 more fixing processing logical models 2023-07-07 10:17:48 +10:00
Grahame Grieve c6e68dc9c6 Fixes to validator for new CDA package (proper handling of logical model types) 2023-07-07 09:38:55 +10:00
Grahame Grieve f77392199d Add test for UCUM with no terminology server 2023-07-05 07:23:10 +10:00
Grahame Grieve 4a85513acb pick up missing hints and warnings on terminology fields 2023-07-05 07:22:46 +10:00
markiantorno 6db701767a Updating version to: 6.0.21-SNAPSHOT and incrementing test cases dependency. 2023-06-30 23:19:08 +00:00
markiantorno 6a6c425562 Release: v6.0.20
## Validator Changes

* no changes

## Other code changes

 * Fix for SPDR not-open-source in code
 * fix name and title in VSAC import process
 * More work on Android support + fix issues in NPM package installation that caused
***NO_CI***
2023-06-30 22:52:51 +00:00
Stefan Otto 213cd931f9
Update ValidationEngine.java 2023-06-30 17:20:37 +02:00
Stefan Otto a05b69288f
Update ValidatorUtils.java 2023-06-30 17:19:21 +02:00
Stefan Otto 49bc184877
fix typo in Params::readInteger() 2023-06-30 17:12:21 +02:00
markiantorno 3c8e26f078 Updating version to: 6.0.20-SNAPSHOT and incrementing test cases dependency. 2023-06-30 05:37:45 +00:00
markiantorno 3b82a4d829 Release: v6.0.19
## Validator Changes

* no changes

## Other code changes

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

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

## Other code changes

* Handle case where base hasn't got a snapshot generating snapshots
***NO_CI***
2023-06-29 04:47:28 +00:00
Grahame Grieve 37e2600186 Don't duplicate warnings about missing expressions on invariants in R5 2023-06-29 13:19:02 +10:00
Grahame Grieve efafc9fb9b Fix issues validating names and urls for logical models 2023-06-29 13:18:37 +10:00
Grahame Grieve bb66eccf45 Allow target to be treated as source when validating FML 2023-06-29 13:18:01 +10:00
markiantorno 7ffbe7703d Updating version to: 6.0.18-SNAPSHOT and incrementing test cases dependency. 2023-06-28 07:13:43 +00:00
markiantorno 345151b132 Release: v6.0.17
## Validator Changes

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

## Other code changes

* Refactor version utility code
* Fix help placeholders
* Better error when handling loading resources
* fix duplicate element generation in CDA.AD type snapshot generation
* Fix message about rendering problem. Actual solution... not sure.
* Minimal Memory model changes for Npm for Android
***NO_CI***
2023-06-28 06:47:19 +00:00
Grahame Grieve a0c776e61d
Merge pull request #1327 from hapifhir/do-20230627-fix-help-placeholders
Fix CLI '-help' text placeholders
2023-06-28 15:51:29 +10:00
Grahame Grieve 29c2f46726 Merge remote-tracking branch 'origin/master' 2023-06-28 13:27:19 +10:00
Grahame Grieve 704d498300 Fix NPE handling R3 structure definitions 2023-06-28 05:56:14 +10:00
dotasek a114d751db Refactor version utility code 2023-06-27 11:29:24 -04:00
dotasek 50e8d990a8 Fix help placeholders 2023-06-27 10:49:55 -04:00
Grahame Grieve ec8e999162 exempt ele-1 from constraint consistency checking 2023-06-27 22:19:44 +10:00
Grahame Grieve 4b07f4f7dc fix missing error validation structure maps 2023-06-27 22:18:56 +10:00
Grahame Grieve 5a55f74a91 fix failing mock test 2023-06-27 06:22:24 +10:00
Grahame Grieve ba27fc9da7 fix testing bugs 2023-06-24 09:36:45 +10:00
Grahame Grieve d35eba6b23 Add -watch-scan-delay and -watch-settle-time 2023-06-24 09:07:07 +10:00
Stefan Otto 26eb05219a
ValidationEngine::validate(): print source file getRef() instead of Object::toString()
`ValidationUtils.SourceFile` does not override Java's default implementation of `toString()`, which is why `validate()'  currently prints "Validate org.hl7.fhir.validation.ValidatorUtils$SourceFile@5382184b" or something like that.
2023-06-22 13:00:33 +02:00
markiantorno 67cb3006f2 Updating version to: 6.0.17-SNAPSHOT and incrementing test cases dependency. 2023-06-21 07:40:48 +00:00
markiantorno 8bd0f0b1ad Release: v6.0.16
## Validator Changes

Post DevDays Release - many significant changes!

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

## Other code changes

* Add CodeQL to the build process
* Various NPE fixes
* Add getValueAsString(TemporalPrecisionEnum) method to date/time types
* Fix rendering for unresolvable ValueSets
* Remove r4b eclipse project files
* Upgrade multiple dependency libraries (per CodeQL)
* Only record sorting errors when generating snapshots when debug mode is on
* Tighten up SSL certificate checking
* Partial refactor of CLI parameter handling
* Fix path regex (per CodeQL)
* Remove erroneous logging from conversion tests
* Rendering improvements for various profile related extensions
* More work on TxTests operation (lenient wrt extensions)
* Fix handling of summary extension (delete duplicate tools summary extension, and don't inherit it)
* Reprocess URLs in Markdown extensions on both StructureDefinition and ElementDefinition
* Improve URL detection in markdown when reprocessing URLs
***NO_CI***
2023-06-21 07:09:07 +00:00
Grahame Grieve 661a0a6919 fix validation tests 2023-06-21 09:23:28 +10:00
Grahame Grieve 59320a56fc fix erroneous R5 FHIRpath constraint (" -> ') 2023-06-21 09:23:08 +10:00
Grahame Grieve 098b8d5520 fix extension context checking 2023-06-21 09:22:47 +10:00
Grahame Grieve 551892c095 Merge remote-tracking branch 'origin/master' 2023-06-20 09:11:51 +10:00
Grahame Grieve 9cf8e0368c fix up extension context checking 2023-06-20 08:36:22 +10:00
Grahame Grieve be01ae2c21 Fix for NPE 2023-06-20 07:02:36 +10:00
dotasek 829882773a
More use of dependencyManagement, bump guava (#1313) 2023-06-19 12:26:21 -04:00
Grahame Grieve 2b8e61e2cb add watch mode to validator 2023-06-19 22:43:54 +10:00
Grahame Grieve 19d3952b11 Validate FHIRPath constraints in IGs and profiles 2023-06-19 22:42:02 +10:00
Grahame Grieve b7425d64b9
Merge pull request #1291 from hapifhir/do-20230602-refactor-cli-params
Refactor Validator CLI params
2023-06-19 02:29:32 +10:00
Grahame Grieve 8fe47659e2
Merge pull request #1308 from hapifhir/do-20230613-regex-fix
Attempt to fix regex
2023-06-19 02:27:09 +10:00
Grahame Grieve dfb4404ce6 Add support for mustHaveValue and valueAlternatives + render imposesProfile + compliesWithProfile 2023-06-18 13:00:58 +10:00
Grahame Grieve 64f84274af Validation Derived Questionnaires 2023-06-17 09:41:06 +10:00
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