Commit Graph

2670 Commits

Author SHA1 Message Date
dotasek 29cc135f6c Release: v6.4.1
## Validator Changes

* Support authentication for terminology servers (see https://confluence.hl7.org/display/FHIR/Using+fhir-settings.json)
* Fix issue where valdiator not retaining extension context when checking constraint expressions in profiles
* Validate min-length when found in extension
* Correct bug parsing json-property-key values with meant validation failed
* Fix problem validating json-property-key value pairs
* Fix special case r5 loading of terminology to fix validation error on ExampleScenario
* Improve handling of JSON format errors
* Fix bug where extension slices defined in other profiles are not found when processing slices based on extension
* Validate fhirpath expression in slice discriminators
* Fix slicing by type and profile to allow multiple options per slice
* List measure choices when a match by version can't be found
* Check server metadata when executing terminology test cases

## Other code changes

* More work on code generation for profiles
* Render min-length extension on profiles
* Clone SQL on FHIR engine to R4, and update FHIRPath engine based on R5 current code
* Update SQL on FHIR engine to allow push as well as pull
* Change R5 tx server to use http://tx.fhir.org/r5 (instead of /r4)
* Update output from tx-tester to include release ready statement
* Fix rendering of Logical Models for polymorphic elements, and rendering target profiles with versions
* Render contained resources in List resource
* #1790 - Fix versionFromCanonical returns system instead and systemFromCanonical returns version
***NO_CI***
2024-11-12 16:30:30 +00:00
Grahame Grieve 8c4440e497 fix tests and update release notes 2024-11-12 20:14:20 +10:30
Grahame Grieve 8a831a9e45 Start testing metadata in tx tests, and consequent bugs and library upgrades for that (patternMode in ComparisonUtilities) 2024-11-12 13:24:09 +10:30
dotasek 730a1781ee Remove FIXMEs reviewed as OK by Grahame 2024-11-11 15:21:17 -05:00
dotasek 5cbb45abec Allow ManagedWebAccess to fetch specific server types for auth 2024-11-11 14:35:06 -05:00
dotasek 4ee4a89a76 Fix refactor misses 2024-11-11 11:06:09 -05:00
dotasek 4c5c71411b
Merge branch 'master' into 2024-11-gg-web-mode2 2024-11-09 11:19:10 -05:00
Grahame Grieve 60acdd0b88 Add mode to web access 2024-11-09 18:39:12 +10:30
Grahame Grieve 275df1aba6
Merge branch 'master' into 2024-11-gg-slice-validation 2024-11-09 08:20:36 +10:30
Grahame Grieve 28b19212e4 Validate slice expressions where possible 2024-11-09 08:19:07 +10:30
Grahame Grieve 93a1f192f1 Fix bug where extension slices defined in other profiles are not found when processing slices based on extension 2024-11-09 08:13:58 +10:30
dotasek 59fe0c6d20
Manage FhirRequestBuilders via ManagedWebAccess (#1788)
* WIP start moving FhirRequestBuilder to ManagedWebAccess

* Update PECodeGenerator.java

* WIP keep moving FhirRequestBuilder to ManagedWebAccess + fix some tests

* WIP move logging, retry, timeout and proxy

* WIP move accept to parameter

* WIP some HTTP Header refactoring, rename FhirRequest to HTTPRequest

* WIP fix removed import

* Tidy up code

***NO_CI***

* Fix for renamed class

* Change mem settings for build

* Adjust pipeline mem again

* Apply changes to r4b

* Actually add headers from HTTPRequest to OkHttp request

* Use ManagedFhirWebAccess in r4

* Removing leftover okttp usage

* Remove unused classes and okhttp usages and add tests for r4

* Make dstu3 use ManagedFhirWebAccess

* Make sure we get response headers

* Add test coverage (some failing) for DSTU2 ClientUtils

* Add FHIRToolingClient tests

* Use ManagedFhirWebAccess for DSTU2

* WIP restore format header tests - turns out they break

* Fix format header issues

* Switch to static fhirBuilder for all FhirRequestBuilders

+ Fix null user agent issue
+ Load ManagedWebAccess from FHIR settings
+ Add terminology servers to FhirSettings

* fix slicing by type and profile to allow multiple options per slice

* List measure choices when a match by version can't be found

* Validate fhirpath expression in slice discriminators

* Remove conflicting authorization header setting methods

* fix VSAC importer for changes to ManagedWebAccess

* Tests 1

* Rename ...AccessBuilder classes to ...Accessor

* Fix api-key token mixup, more tests

* Resolve all deletions enclosed in FIXME + fix headers in dstu2 postfeed

* More TODO erasures. Plus found missing functionality

* Move tests to utilities. Clarify missing functionality

* Clean up comments and JavaDoc

* Final rename

* update vsac access code

* Fix get bytes for -1 or chunked content

---------

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Grahame Grieve <grahameg@gmail.com>
Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>
2024-11-08 16:42:26 -05:00
Grahame Grieve a93ab69231 Validate fhirpath expression in slice discriminators 2024-11-07 22:16:27 +10:30
Grahame Grieve ee7dc203f6 List measure choices when a match by version can't be found 2024-11-07 22:15:54 +10:30
Grahame Grieve 0c4da028b3 fix slicing by type and profile to allow multiple options per slice 2024-11-07 22:14:49 +10:30
dotasek afd9e7a471 Merge remote-tracking branch 'origin/master' into do-20241021-tx-auth 2024-11-06 19:19:53 -05:00
dotasek b6ef81c9f3 Switch to static fhirBuilder for all FhirRequestBuilders
+ Fix null user agent issue
+ Load ManagedWebAccess from FHIR settings
+ Add terminology servers to FhirSettings
2024-11-06 09:47:27 -05:00
dotasek ac7c7332d3 Use ManagedFhirWebAccess for DSTU2 2024-11-04 17:49:31 -05:00
Grahame Grieve b493f3bb5c Fix issue not retaining extension context when checking constraint expressions in profiles 2024-11-03 07:18:04 +10:30
mrunibe b75e401090 Perf tuning FML: re-use FHIRPathEngine in new Property
hapifhir/org.hl7.fhir.core#1703 FML transform create heavyweight
FHIRPathEngine objects for every new Property. Re-use existing
ProfileUtilities/FHIRPathEngine objects from StructureMapUtilities.
2024-11-02 18:25:25 +01:00
Grahame Grieve 4112da2191 ditto 2024-11-02 19:19:37 +10:30
dotasek bdc02a5622 Merge remote-tracking branch 'origin/master' into do-20241021-tx-auth 2024-11-01 09:16:36 -04:00
Grahame Grieve 90b6583ac5 Update SQL on FHIR engine for changes as suggested by James 2024-11-01 08:06:51 +10:30
Grahame Grieve a65de7b980 Correct fix for bug parsing json-property-key values 2024-11-01 08:04:28 +10:30
dotasek 2f95e3fe9f Remove unused classes and okhttp usages and add tests for r4 2024-10-30 09:30:09 -04:00
Grahame Grieve 8ceb1024c0 Update output from tx-tester to include release ready statement 2024-10-30 21:07:32 +10:30
dotasek 03b0c163be Merge branch 'master' into do-20241021-tx-auth 2024-10-25 13:56:06 -04:00
markiantorno 54d239a38a Updating version to: 6.4.1-SNAPSHOT and incrementing test cases dependency. 2024-10-24 14:15:50 +00:00
markiantorno 26c445c8fc Release: v6.4.0
## Validator Changes

* Improve warning messages about collections in SQL ViewDefinitions
* Fix type evaluation of .item() in FHIRPath
* Revise message about unknown usage context on additional binding
* Add support for code generation
* Add check for # in CanonicalResource.version
* Fix problem parsing urls in cds-hooks formats
* Fix issues with output folder running tx tests
* Fix bug evaluating resolve() in contained resources when doing slicing

## Other code changes

* Fix NPE processing markdown
* Capture missing snapshot generation messages
* Track OID status
* Improve rendering of coded values
* update tests for changes to PE code generation
* Tx Tests: Add support for special header on specific tests
* Tx Tests: Fix framework to handle diagnostics correctly
* Tx Tests: check http code in tx test cases
* Add support for NCI code rendering
* Adding missing lombok annotation (cannot build without it from scratch) (#1785)
* Remove Encounter Renderer
* Profile code generation fixes
* Add r4 code gen classes
* Draft work for tx server authentication (not landed yet)
* Move XXE safe SAXParserFactory and XMLReader instantiation to XMLUtil
* Bump commons-compress version
***NO_CI***
2024-10-24 13:30:23 +00:00
Grahame Grieve 89be42a649 Merge remote-tracking branch 'origin/master' 2024-10-24 07:16:05 +10:30
Grahame Grieve e6c720450b
Merge pull request #1774 from hapifhir/do-20241009-documentbuilderfactory-refactor
Move new DocumentBuilderFactory calls to XMLUtils
2024-10-24 07:14:28 +10:30
dotasek ddb0a661dd Merge branch '2024-10-gg-tx-server-auth-1' into do-20241021-tx-auth 2024-10-23 11:55:58 -04:00
dotasek fdbf0da576 WIP move logging, retry, timeout and proxy 2024-10-23 11:55:27 -04:00
Grahame Grieve 5a4f794add Merge remote-tracking branch 'origin/master' 2024-10-23 23:34:39 +10:30
Grahame Grieve 77580465c7 revise message about unknown usage context on additional binding 2024-10-23 22:59:32 +10:30
Grahame Grieve d652aa2f30 Fix NPE processing markdown 2024-10-23 22:19:08 +10:30
dotasek fa19dc44b1 Merge remote-tracking branch 'origin/2024-10-gg-tx-server-auth' into do-20241021-tx-auth 2024-10-22 17:34:08 -04:00
Grahame Grieve 5ad6f684fe Add support for special header on specific tests 2024-10-22 18:08:18 +10:30
Grahame Grieve 533142cefd Fix test tx frmework to handle diagnostics correctly 2024-10-22 17:31:36 +10:30
Grahame Grieve c9c04aec3b check mode in tx test cases 2024-10-22 17:16:27 +10:30
dotasek ac6ef81797 Merge remote-tracking branch 'origin/master' into do-20241021-tx-auth 2024-10-21 17:50:47 -04:00
Grahame Grieve 9dc08c213c Code generation 2024-10-22 05:16:54 +10:30
Grahame Grieve e521b9f750 More work on tx tests, including testing HTTP status code 2024-10-21 22:48:43 +10:30
Grahame Grieve d613a0cb6c Add check for # in CanonicalResource.version 2024-10-18 21:58:02 +08:00
Grahame Grieve cb0759cc00 fix npe in server auth functionality 2024-10-18 20:50:26 +08:00
Grahame Grieve 6996fdf31a Ignore diagnostics in tx tests, and fix issues with output folder 2024-10-18 20:49:57 +08:00
Grahame Grieve 000d4c7cbb Add code generation functionality to the validator, and various updates to the generated code 2024-10-18 20:49:34 +08:00
dotasek d0bbc93c32
Add commons-lang3 to support commons-compress bump (#1784) 2024-10-18 00:38:24 -04:00
dotasek 2d80a09deb Merge remote-tracking branch 'origin/master' into do-20241009-documentbuilderfactory-refactor 2024-10-16 11:59:24 -04:00
Grahame Grieve ef800e372f Fix bug evaluating resolve() in contained resources when doing slicing 2024-10-15 07:51:23 +08:00
markiantorno cabee9a341 Updating version to: 6.3.33-SNAPSHOT and incrementing test cases dependency. 2024-10-14 06:03:42 +00:00
markiantorno 54bf319161 Release: v6.3.32
## Validator Changes

* Fix validation issue with open-choice questions in R4 questionnaires
* Add command line parameter ```-tx-routing```
* Add command line parameter ```-clear-tx-cache```
* Add command line parameter ```-advisor-file```

## Other code changes

* Render extensions on some data types
* Fix rendering of complex data types when doing profile rendering
***NO_CI***
2024-10-14 05:18:21 +00:00
Grahame Grieve f19f8f4ed2 rework rules based advisor 2024-10-14 12:31:51 +08:00
Grahame Grieve 3b8b2a94c3 Fix validation issue with open-choice questions in R4 questionnaires 2024-10-14 09:02:52 +08:00
Grahame Grieve 56965820ea Add support for -advisor-file, and -clear-tx-cache 2024-10-13 22:40:17 +08:00
markiantorno a7e216e2c3 Updating version to: 6.3.32-SNAPSHOT and incrementing test cases dependency. 2024-10-10 14:35:11 +00:00
markiantorno 0388bd0835 Release: v6.3.31
## Validator Changes

* Don't send expansion to tx server if there's a compose when sending value sets
* Better handling of error messages from terminology servers
* Stop hitting VSAC server directly

## Other code changes

* Add support for $id$ in terminology tests
* Move new documentbuilderfactory calls to XMLUtils (Security)
***NO_CI***
2024-10-10 13:54:40 +00:00
dotasek 7ede053a5f Move new documentbuilderfactory calls to XMLUtils 2024-10-09 09:26:41 -04:00
markiantorno c030740d9e Updating version to: 6.3.31-SNAPSHOT and incrementing test cases dependency. 2024-10-08 15:52:36 +00:00
markiantorno ad0af19fb3 Release: v6.3.30
## Validator Changes

* Show message ids in validator (-show-message--ids)
* Fix bug where message id not showing for slicing messages
* Add advisor documentation (not yet functional)
* Fix issue checking package currency for #current packages
* Add warning when code system is marked complete but has no content
* Fix bug processing adding discriminators in derived profiles
* Break valueset concept validation into multiple smaller batches for performance reasons

## Other code changes

* More work on translations in IGs
* Override inheritance of HAPI's old maven-compiler-plugin
* do not use loadPackageFromCacheOnly from outside cache manager
* Fix issues with rendering example scenario
* refactor sql view validation to fix NPE
* Fix misc warnings flagged by builds (#1772) + TRIVY typo
* Bump codeql actions to v3
* Bump checkout action to v4
* Bump commons.io to 2.14.0 (#1771)
* Workaround for ghcr rate limiting of trivy db downloads (#1770)
* Add VSACfinder (template for package analysis)
* Fix github urls
* Spelling fixes
***NO_CI***
2024-10-08 15:04:29 +00:00
Grahame Grieve c15968c0ad add missing release notes 2024-10-08 17:46:11 +08:00
Grahame Grieve bfe4fdd572 release notes 2024-10-08 17:39:33 +08:00
Grahame Grieve eb149f5abd fix missed file 2024-10-08 05:53:31 +08:00
dotasek 6439a2a732
Fix misc warnings flagged by builds (#1772) 2024-10-07 17:16:21 -04:00
Grahame Grieve 4a1aa461a9 fix text 2024-10-05 11:55:21 +08:00
Grahame Grieve cbb645b9e0 show message ids in validator + advisor documentation 2024-10-05 11:52:07 +08:00
Grahame Grieve 4241fc9d7f fix bug where message id not showing for slicing messages 2024-10-05 11:51:11 +08:00
Grahame Grieve 837aa319c0 do not use loadPackageFromCacheOnly from outside cache manager 2024-10-05 06:41:33 +08:00
Grahame Grieve 43b85c8108 Add warning when code system is marked complete but has no content 2024-10-05 06:40:05 +08:00
Grahame Grieve 6888355c84 compile fixes 2024-09-30 17:23:56 +08:00
Grahame Grieve 6890349be2 spelling fixes 2024-09-30 08:33:02 +10:00
Grahame Grieve ef6a398ebe Break valueset concept validation into multiple smaller batches for performance reasons 2024-09-30 08:32:49 +10:00
markiantorno e8a0bba072 Updating version to: 6.3.30-SNAPSHOT and incrementing test cases dependency. 2024-09-26 12:30:18 +00:00
markiantorno 53ec745184 Release: v6.3.29
## Validator Changes

* remove spurious logging statement

## Other code changes

* no changes
***NO_CI***
2024-09-26 11:44:41 +00:00
markiantorno 8358354d2f Updating version to: 6.3.29-SNAPSHOT and incrementing test cases dependency. 2024-09-25 21:46:09 +00:00
markiantorno 569fe4b697 Release: v6.3.28
## Validator Changes

* Validator supports R6 from now on (using last stable release)
* Set default language to tag not display
* Handle tx server issues better
* Do not use server piecemeal when validating complex value sets
* Add support for -txCache parameter

## Other code changes

* Add support for R6 to R4 version enumeration
* Fix SCT link to include version and point to the right place
* Add response time to tx log
* Allow for code to turn off use of cache-id on tx interface (for debugging)
* Support n/a for tx cache folder
* Update tx cache for tests
* Add more logging for too costly validation
* Fix xml annotation suppression
***NO_CI***
2024-09-25 21:01:00 +00:00
Grahame Grieve 6289638833 fix npe in test cases 2024-09-25 05:16:02 -04:00
Grahame Grieve 004d367340 fix tests 2024-09-24 22:27:50 -04:00
Grahame Grieve ea04d9a96b update tx cache for tests 2024-09-24 20:43:14 -04:00
Grahame Grieve f4096319a3 Add support for -txCache parameter 2024-09-24 20:42:48 -04:00
Grahame Grieve b37073592b set default language to tag not display 2024-09-23 09:12:17 -04:00
markiantorno be8944ab94 Updating version to: 6.3.28-SNAPSHOT and incrementing test cases dependency. 2024-09-22 18:36:30 +00:00
markiantorno 102e755283 Release: v6.3.27
## Validator Changes

* Work around problem with language value set being marked experimental
* Fix validation id/idref to resolve in document if in a document
* Fix various issues rendering and validating additional bindings with usage contexts
* Upgrade lock management in Package Cache

## Other code changes

* Fix case typo on Consent.provision in R4
* Fix R3 Quantity.copyValues()
* Remove debugging code
* Add more debugging to validation failure
* Add support for active only to VSAC importer
* Add r4b support to Package Version Generation
* Fix argument confusion in format in time validation
* Added support for tracking whether elements are ellipsed and for rendering accordingly
***NO_CI***
2024-09-22 17:51:33 +00:00
Grahame Grieve 7bafd6e3c8 remove debugging code 2024-09-22 06:40:27 -04:00
Grahame Grieve 3cec189333 Fix id/idref to resolve in document if in a document 2024-09-22 06:40:15 -04:00
Grahame Grieve 8cfcbf389e Fix various issues rendering and validating additional bindings with usage contexts 2024-09-21 00:35:01 -04:00
markiantorno f3bd5b9be8 Updating version to: 6.3.27-SNAPSHOT and incrementing test cases dependency. 2024-09-17 22:00:24 +00:00
markiantorno 46affee48f Release: v6.3.26
## Validator Changes

* Validate of experimental property on bindings
* Add -no-experimental-content flag
* Allow JSON named extensions to be structure types other than logical
* Process relative URLs properly in base when generating snapshots

## Other code changes

* Fix rendering path for value set references for kindling
* refactor error handling in ProfileUtilities
* Fix for NPE processing packages
***NO_CI***
2024-09-17 21:09:53 +00:00
Grahame Grieve fbfd81532d Merge remote-tracking branch 'origin/master' 2024-09-17 16:18:15 +08:00
Grahame Grieve 11efed6635 Validation of experimental property 2024-09-17 16:16:09 +08:00
Grahame Grieve 76c6bb6c44
Merge pull request #1741 from hapifhir/do-20240910-remove-cqframework-dependency
Remove cqlframework dependencies
2024-09-12 07:12:04 +08:00
markiantorno 4af3deff26 Updating version to: 6.3.26-SNAPSHOT and incrementing test cases dependency. 2024-09-11 18:28:22 +00:00
markiantorno f09bc48f7d Release: v6.3.25
## Validator Changes

* no changes

## Other code changes

* Fix logic for cache clearing on package cache initialization
***NO_CI***
2024-09-11 17:40:08 +00:00
dotasek 44464de807 Remove cqlframework dependencies 2024-09-10 09:38:33 -04:00
markiantorno 2c8122a42e Updating version to: 6.3.25-SNAPSHOT and incrementing test cases dependency. 2024-09-09 19:09:24 +00:00
markiantorno 813f8200a2 Release: v6.3.24
## Validator Changes

* Fix expression for con-3 properly (fix validation problem on some condition resources)
* Fix FHIRPath bug using wrong type on simple elements when checking FHIRPath types
* FHIRPath: Allow _ in constant names (per FHIRPath spec)
* Fix value set rendering creating wrong references
* Fix bug processing value set includes / excludes that are just value sets (no system value)
* Alter processing of unknown code systems per discussion at ,https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/Don't.20error.20when.20you.20can't.20find.20code.20system and implement unknown-codesystems-cause-errors
* Improve message for when elements are out of order in profile differentials

## Other code changes

* fix problem where profile rendering had spurious 'slices for' nodes everywhere
* Update SQL-On-FHIR implementation for latest cases, and clone test cases to general test care repository
* Fix problem generating value set spreadsheets
* fix concurrent modification error processing language translations
* Check for null fetcher processing ConceptMaps (#1728)
***NO_CI***
2024-09-09 18:23:37 +00:00
Grahame Grieve ffe0ab6414
2024 09 gg vs sql (#1738)
* Fix bug processing value set includes / excludes that are just value sets (no system value)

* fix value set rendering creating wrong references

* Update SQL-On-FHIR implementation for latest cases, and clone test cases to general test care repository

* Fix expression for con-3 properly (fix validation problem on some condition resources)

* FHIRPath: Allow _ in constant names (per FHIRPath spec)

* Fix FHIRPath bug using wrong type on simple elements when checking FHIRPath types

* release notes

* fix sql-on-fhir tests

---------

Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>
2024-09-09 12:27:08 -04:00
Grahame Grieve 7fc34e509a alter processing of unknown code systems per discussion at ,https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/Don't.20error.20when.20you.20can't.20find.20code.20system and implement unknown-codesystems-cause-errors 2024-09-06 22:18:01 +08:00
dotasek c260bece21
Check for null fetcher (#1728) 2024-08-30 09:44:33 -04:00
markiantorno 19c8b17575 Updating version to: 6.3.24-SNAPSHOT and incrementing test cases dependency. 2024-08-28 18:45:30 +00:00