Commit Graph

3695 Commits

Author SHA1 Message Date
Grahame Grieve ce06b3f9c5 refactor UserDataNames round 2 2024-11-16 21:16:36 +11:00
Grahame Grieve 3873d56764 Support ViewDefinition as a custom resource 2024-11-16 21:15:42 +11:00
Grahame Grieve c38420a280 expose user data through ResourceWrapper 2024-11-16 21:14:57 +11:00
Grahame Grieve 356661eef0 Implementation for ViewDefinition as custom resource 2024-11-14 22:51:13 +10:30
Grahame Grieve a5c23e119c expose User data through ResourceWrapper interface 2024-11-14 22:50:40 +10:30
Grahame Grieve 4f61f6f29e refactor UserData names to use constants 2024-11-14 22:50:20 +10:30
dotasek b0b79cd779 Don't return a mutable object in getClientHeaders 2024-11-13 17:20:11 -05:00
dotasek cc75799664 Updating version to: 6.4.2-SNAPSHOT and incrementing test cases dependency. 2024-11-12 21:52:10 +00:00
dotasek d306cb0dcb 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 21:19:51 +00:00
dotasek 06fbc0c77b Roll back to fix release (again) 2024-11-12 15:42:50 -05:00
dotasek 63c77e52fa 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 18:54:04 +00:00
dotasek be330ba38a Rollback to fix release 2024-11-12 12:40:55 -05:00
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 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 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
dotasek d724a27d95 Final rename 2024-11-08 14:35:36 -05:00
dotasek fb6a22c3b1 Clean up comments and JavaDoc 2024-11-08 14:29:40 -05:00
dotasek cc00bb903c Move tests to utilities. Clarify missing functionality 2024-11-08 11:26:43 -05:00
dotasek 2bbfcb8845 Resolve all deletions enclosed in FIXME + fix headers in dstu2 postfeed 2024-11-08 11:08:06 -05:00
dotasek 822f0866b4 Fix api-key token mixup, more tests 2024-11-07 18:07:23 -05:00
dotasek e9917defb0 Rename ...AccessBuilder classes to ...Accessor 2024-11-07 17:53:14 -05:00
dotasek 4592dc1a82 Tests 1 2024-11-07 17:42:32 -05:00
dotasek 2c57f5954e Remove conflicting authorization header setting methods 2024-11-07 15:44:25 -05:00
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 6775a09adb Make sure codegen directory exists 2024-11-05 09:56:06 -05:00
Grahame Grieve 31764fc016 Fix to use derived element cardinality not element base cardinality when elementdefinition-json-name is present 2024-11-05 20:58:26 +10:30
Grahame Grieve 441f7b4e47 update code generation 2024-11-05 19:19:42 +10:30
Grahame Grieve 497b502a1c compile fix 2024-11-05 10:15:40 +10:30
Grahame Grieve 478c338e10 Fix NPE in FHIRPath engine 2024-11-05 06:06:59 +10:30
Grahame Grieve b76a71d337 compile fix 2024-11-04 17:31:29 +10:30
Grahame Grieve 6040ad950c Merge remote-tracking branch 'origin/master' 2024-11-04 17:19:42 +10:30
Grahame Grieve b493f3bb5c Fix issue not retaining extension context when checking constraint expressions in profiles 2024-11-03 07:18:04 +10:30
Grahame Grieve 479b5a7527 update r4 codegen 2024-11-03 07:12:44 +10:30
mrunibe 8d780e0784 hapifhir#1699 set index when adding children
instead of calling numberChildren() recursively whenever an element is
added.
2024-11-02 18:25:25 +01:00
mrunibe f909a0c228 hapifhir#1699 Testcase for numberChildren 2024-11-02 18:25:25 +01:00
mrunibe d90c6b3a07 Perf tuning: skip numberChildren
hapifhir#1699 defer numberChildren to end of transform
2024-11-02 18:25:25 +01:00
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
Michael Rebsamen 18b4fc1714 Perf tuning: skip numberChildren
hapifhir/org.hl7.fhir.core#1699 Workaround for performance issue with FML transform: Growing/large lists getting very slow due to numberChildren() getting called recursively for every element that is added to a list.

merge upstream
2024-11-02 18:25:15 +01:00
Grahame Grieve adaa3fa708 improve build() signature in generated profile code 2024-11-02 22:51:08 +10:30
Grahame Grieve f8456fb767 compile fixes 2024-11-02 19:24:52 +10:30
Grahame Grieve 8bf76f151d validate min-length when found in extension 2024-11-02 19:19:32 +10:30
Grahame Grieve a6f6bdf282 update generated code 2024-11-02 19:19:09 +10:30
Grahame Grieve 607c4fa98b Render min-length extension on profiles 2024-11-02 19:18:39 +10:30
Grahame Grieve a541971532 more work on code generation for profiles 2024-11-02 11:51:14 +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 4db933235a PECodeGenerator fixes 2024-11-01 23:11:45 +10:30
Grahame Grieve c2aa01c02a
Merge pull request #1782 from ahdis/oe_context
base workercontext adjustements
2024-11-01 16:27:24 +10:30
Grahame Grieve 4d61317196
Merge pull request #1796 from hapifhir/2024-11-gg-sweep
2024 11 gg sweep
2024-11-01 15:55:06 +10:30
Grahame Grieve 90b6583ac5 Update SQL on FHIR engine for changes as suggested by James 2024-11-01 08:06:51 +10:30
Grahame Grieve 509f8d46c1 update R5 engine for style fixes from R4 2024-11-01 08:06:14 +10:30
Grahame Grieve a65de7b980 Correct fix for bug parsing json-property-key values 2024-11-01 08:04:28 +10:30
Brian Postlethwaite 323ec42c32 Corrent the parameter order for the assert parameters 2024-10-31 10:05:40 +11:00
Brian Postlethwaite 01af08030f #1794
Update the implementation of the `toString` fhirpath function to: (pending FHIR-48737)
* not return the text 'null' when no primitive value exists (when extension only)
* throw an error if more than 1 item is to be returned (doesn't support collections)
* return an empty set when no primitive values exist (when extension only)
2024-10-31 10:04:57 +11:00
dotasek 2f95e3fe9f Remove unused classes and okhttp usages and add tests for r4 2024-10-30 09:30:09 -04:00
Grahame Grieve 6533f2bd36 Fix rendering of Logical Models for polymorphic elements, and rendering target profiles with versions 2024-10-30 21:06:58 +10:30
Grahame Grieve 8a9039f08f Fix problem validating json key value pairs 2024-10-30 21:05:57 +10:30
Grahame Grieve 1850995465 Render contained resources in List resource 2024-10-30 21:05:22 +10:30
Grahame Grieve e8973a90d8 #1790 - Fix versionFromCanonical returns system instead and systemFromCanonical returns version 2024-10-30 21:05:03 +10:30
Grahame Grieve 1100fe2855 fix special case r5 loading of terminology to fix validation error on ExampleScenario 2024-10-30 21:04:05 +10:30
dotasek 2fdfaf8602 Removing leftover okttp usage 2024-10-29 18:32:58 -04:00
dotasek a5ef974c3d Use ManagedFhirWebAccess in r4 2024-10-29 17:07:41 -04:00
dotasek 0ebf628bec
Fix expected generated code (#1793)
* Fix expected generated code

* Update PECodeGenerator.java

---------

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
2024-10-29 10:21:53 -04:00
Grahame Grieve c7f747519c test generated code 2024-10-28 07:33:05 +11:00
dotasek 03b0c163be Merge branch 'master' into do-20241021-tx-auth 2024-10-25 13:56:06 -04:00
dotasek 0b45b0b882 WIP some HTTP Header refactoring, rename FhirRequest to HTTPRequest 2024-10-25 13:55:33 -04:00
dotasek b33de12e49 WIP move accept to parameter 2024-10-24 13:57:51 -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 0bb0aac47b Capture missing snapshot generation messages 2024-10-24 16:47:58 +10:30
Grahame Grieve a632594a67 track OID status 2024-10-24 07:16:36 +10:30
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 7c075ae347 Improve warning messages about collections in SQL ViewDefinitions 2024-10-23 23:00:48 +10:30
Grahame Grieve 44b6888cb8 Improve rendering of coded values 2024-10-23 23:00:29 +10:30
Grahame Grieve 93c7c3da68 fix type evaluation of .item() in FHIRPath 2024-10-23 23:00:13 +10:30
Grahame Grieve 832906da13 update tests for changes to PE code generation 2024-10-23 22:59:54 +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
dotasek a94e1bc2af WIP keep moving FhirRequestBuilder to ManagedWebAccess + fix some tests 2024-10-22 17:33:50 -04:00
Jens Kristian Villadsen f9ce823d7c
Update PECodeGenerator.java 2024-10-22 22:37:28 +02:00
dotasek ac6ef81797 Merge remote-tracking branch 'origin/master' into do-20241021-tx-auth 2024-10-21 17:50:47 -04:00
dotasek 435dbbec9b WIP start moving FhirRequestBuilder to ManagedWebAccess 2024-10-21 17:19:53 -04:00
Grahame Grieve d6c3a9df0b Add support for NCI code rendering 2024-10-22 05:16:45 +10:30
Grahame Grieve ede7628b44 profile code generation fixes 2024-10-22 05:16:31 +10:30
Grahame Grieve 6e10d7d595 remove Encounter Renderer 2024-10-21 22:48:54 +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 63446c17c4 fix bug with profile code generation 2024-10-18 21:57:41 +08:00
Grahame Grieve 6694be1ffe Fix problem parsing urls in cds-hooks formats 2024-10-18 20:50:53 +08:00