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5869 Commits

Author SHA1 Message Date
Grahame Grieve 5a858949d4 Merge remote-tracking branch 'origin/master' 2023-07-21 21:18:42 +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 e324047735 Fix issue with type evaluation in R3 checking FHIRPath types 2023-07-21 21:16:48 +10:00
Grahame Grieve 4e8f0f0c0c
Merge pull request #1353 from hapifhir/2023-07-gg-context-fixes 
2023 07 gg context fixes
 2023-07-21 14:48:19 +10:00
Lloyd McKenzie b1e5a749ca Fixed errors with test case 2023-07-20 22:31:19 -06:00
Grahame Grieve 8cf086b203 update R4 and R4B FHIRPath implementations for changes picked up in R5 usage 2023-07-21 14:09:11 +10:00
Grahame Grieve d8e2e020af fix failing tests 2023-07-21 12:41:56 +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 93e1b3e4b3 fix missing extensions when converting value set properties 2023-07-21 05:37:16 +10:00
Grahame Grieve f52df7c0cc Fix obligation rendering message 2023-07-20 08:21:51 +10:00
Grahame Grieve fc75c0ea6b fix up bi-di warning message 2023-07-20 08:21:34 +10:00
Grahame Grieve 616cf5fdb3 Add provisional support for alternate codes 2023-07-20 08:21:19 +10:00
Grahame Grieve 274c49bde5 Workaround ClinicalImpression definition problem in core spec 2023-07-20 08:20:18 +10:00
Grahame Grieve 38052a6e75 ICFImporter for staging support of ICF 2023-07-20 08:19:59 +10:00
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
dotasek d95af6d968
Bump databind to 2.15.2 (#1354) 2023-07-18 11:47:06 -04:00
Grahame Grieve 3f67cbee9e Merge remote-tracking branch 'origin/master' 2023-07-18 11:12:10 +10:00
Grahame Grieve 4fb70ba1e8 other missed code 2023-07-18 11:08:57 +10:00
Grahame Grieve 8c0539136c suppress spurious error message 2023-07-18 11:08:09 +10:00
Grahame Grieve 55c12301ba remove shex 2023-07-18 11:06:06 +10:00
Grahame Grieve 27961d3da5 Finish off OMOP Importer 2023-07-18 11:05:21 +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 89d0f6f867
Remove weso shex (#1352) 
* Bump shex dependency

* Bump jackson to 2.15.2

* Bump thymeleaf to 3.1.1.RELEASE

* Remove es.weso shexs_2.12 and ignored tests
 2023-07-17 18:20:53 -04:00
dotasek bdb415cf8a
Bump thymeleaf to 3.1.1.RELEASE (#1349) 2023-07-17 16:35:28 -04:00
dotasek ceceb6c7d5
Bump shex dependency (#1351) 2023-07-17 16:35:00 -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
Lloyd McKenzie 57a9580db7 Added test case for ExampleScenario conversion and significantly bulked up the conversion process 2023-07-13 22:59:12 -06:00
dotasek a91749760e
Create owasp.yml 2023-07-13 15:45:31 -04:00
dotasek 8cf4a62f32
Remove unneeded resources (#1346) 2023-07-12 16:46:42 -04:00
dotasek 6598c1d28e
Add test for setVsAsUrl parameter setting (#1345) 2023-07-12 16:16:09 -04:00
Grahame Grieve eef3ebc5f1
Merge pull request #1341 from hapifhir/2023-07-gg-r5-fhirpath-type-slices 
Fix checking FHIRPath statements on inner elements of type slices
 2023-07-12 06:06:31 +10:00
dotasek ca2b26fc3b
Temporarily disable CodeQL ReDoS and overly-large-range (#1344) 
* Nudge to allow branch push

* Add codeql config

* Move codeql config around

* Move config file into init step

* Shuffle config-file index

* Change to correct query id

* Shuffle and switch to polynomial-redos

* Ignore both redos queries

* Ignore java/overly-large-range

* Add comment on exclude
 2023-07-11 13:42:54 -04:00
Lloyd McKenzie d0d90c72eb Fixed issues with ExampleScenario conversion. resourceType was getting stripped, as was operation.number. 2023-07-09 23:13:26 -06:00
Grahame Grieve 5e30c0ee92 Fix checking FHIRPath statements on inner elements of type slices 2023-07-09 08:03:35 +10:00
Grahame Grieve c2e4b2090f
Merge pull request #1340 from hapifhir/2023-07-gg-r5-ns-support 
fix scan of naming systems
 2023-07-08 23:20:02 +10:00
Grahame Grieve c174400e73 fix scan of naming systems 2023-07-08 22:08:36 +10:00
Grahame Grieve 1384b143d9
Merge pull request #1339 from hapifhir/2023-07-gg-r5-invariants 
fix issue checking invariant expressions in R5
 2023-07-08 22:07:10 +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 d6fdaeb308 set up release 2023-07-07 14:50:10 +10:00
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 99ff8b5ae1
Merge pull request #1336 from hapifhir/gg-202307-rendering 
Gg 202307 rendering
 2023-07-07 14:36:01 +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