2453 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
dotasek
a155475feb Fix test and set up apiKey for package client servers 2024-11-11 17:59:40 -05:00
dotasek
36142f4904 Fixes for getting configured servers from fhir-settings 2024-11-11 16:50:39 -05:00
dotasek
7c796b4ba4 Simplify FhirSettings format. 2024-11-11 16:25:18 -05:00
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
cac080b5bd Fix merge issue. 2024-11-11 09:23:59 -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
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
765ba8baed Fix get bytes for -1 or chunked content 2024-11-08 15:22:50 -05:00
dotasek
d724a27d95 Final rename 2024-11-08 14:35:36 -05:00
dotasek
cc00bb903c Move tests to utilities. Clarify missing functionality 2024-11-08 11:26:43 -05:00
dotasek
ebcbf4db49 More TODO erasures. Plus found missing functionality 2024-11-08 11:18:57 -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
e45c0b2bf0 Merge remote-tracking branch 'origin/master' into do-20241021-tx-auth 2024-11-05 10:51:21 -05:00
dotasek
ac7c7332d3 Use ManagedFhirWebAccess for DSTU2 2024-11-04 17:49:31 -05:00
Grahame Grieve
ada49aee5b More json parsing improvements 2024-11-04 20:25:30 +10:30
Grahame Grieve
c6e5521f4a Merge remote-tracking branch 'origin/master' 2024-11-04 17:45:58 +10:30
Grahame Grieve
c06051838f
Merge pull request #1763 from alfy91/dev-fix_json_validation
fix parenthesis matching for JSON validation.
2024-11-04 17:45:46 +10:30
Grahame Grieve
8bf76f151d validate min-length when found in extension 2024-11-02 19:19:32 +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
dotasek
c5aaf43121 Make sure we get response headers 2024-10-30 19:08:38 -04:00
Grahame Grieve
8ceb1024c0 Update output from tx-tester to include release ready statement 2024-10-30 21:07:32 +10:30
dotasek
fe58a8a2c5 Actually add headers from HTTPRequest to OkHttp request 2024-10-29 11:09:47 -04:00
dotasek
f82f8764cf Tidy up code
***NO_CI***
2024-10-25 17:01:09 -04:00
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
89be42a649 Merge remote-tracking branch 'origin/master' 2024-10-24 07:16:05 +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
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
a94e1bc2af WIP keep moving FhirRequestBuilder to ManagedWebAccess + fix some tests 2024-10-22 17:33:50 -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