Commit Graph

2280 Commits

Author SHA1 Message Date
Grahame Grieve 1b86b29d1f fix bug caused by changing DiagnosticReport.conclusion to markdown 2023-02-18 15:13:37 +11:00
Grahame Grieve 38a55d261d update table generator to suppress external links in base row and column 2023-02-18 15:13:13 +11:00
dksharma dadc3701e4 Added method comments for better understand of utility method usage 2023-02-17 15:59:54 -06:00
Jose Costa Teixeira 0e2e333fa9
remove example label when not existing 2023-02-17 21:56:51 +01:00
dksharma 3eff78bdb9 Updated code to leverage EXTENDS and not duplicate datatype definitions with usage 2023-02-16 18:57:06 -06:00
dksharma 6ebda8c6fc pom changes reverted to match master 2023-02-15 23:47:47 -06:00
dksharma e6ca865d68 ShExGenerator Tests included from working branch 2023-02-15 23:28:50 -06:00
dksharma b248d00ee7 ShExGenerator.java Changes included from working branch 2023-02-15 23:21:58 -06:00
Jim Balhoff 53710b5390 Merge branch 'rdf-wg-r5' into rdf-wg-r5-with-generated 2023-02-15 10:00:28 -05:00
markiantorno 9c768415f2 Updating version to: 5.6.99-SNAPSHOT and incrementing test cases dependency. 2023-02-15 10:37:45 +00:00
markiantorno 7ec74d0321 Release: v5.6.98
## Validator Changes

* Fix bug checking canonical URLs in bundles with dashes in them
* Fix extension messages (modifier and normal messages reversed)
* Change how error location paths are reported in bundles for easier resolution (no counting!)
* fix bugs checking whether binding is allowed in corner cases

## Other code changes

* Rendering Improvements: Additional Bindings, Search Parameters, Operation Definitions
* FHIRPath implementations for comparable(), highBoundary(), lowBoundary()
* Fix list of canonical resources from VersionUtilities
* Fix bug parsing html entities in XHTML parser
* Rename extension to http://hl7.org/fhir/StructureDefinition/structuredefinition-imposeProfile
***NO_CI***
2023-02-15 10:13:36 +00:00
Grahame Grieve 7f454098b9 search parameter rendering improvements 2023-02-15 12:14:48 +11:00
Grahame Grieve 26f7b3a803 FHIR-38789 SD_Dependencies extension needs work 2023-02-15 12:12:28 +11:00
Grahame Grieve 5c413822bd Search Parameter Rendering improvements 2023-02-15 11:55:18 +11:00
Jim Balhoff 97772ada1e Merge branch 'master' into rdf-wg-r5 2023-02-14 13:47:28 -05:00
Grahame Grieve b46160bc8b FHIR-27761 Tooling issues around multi-level Operations 2023-02-14 15:08:55 +11:00
Grahame Grieve de3ec0d27b fix npe + render OperationDefinition parameter standards status 2023-02-14 12:34:19 +11:00
Grahame Grieve d9f98902b9 fix npe 2023-02-14 11:01:59 +11:00
Grahame Grieve d5d83bea9c fix broken links in R5 builds 2023-02-14 09:53:22 +11:00
Jim Balhoff d67470a6e1 Add MeSH triples. 2023-02-13 14:24:49 -05:00
Grahame Grieve 4ae0dfe8f4 rendering fixes 2023-02-13 20:29:56 +11:00
Grahame Grieve ccb5004766 fix issues with URL regex 2023-02-13 11:07:11 +11:00
Jim Balhoff a72ccaa0ed Merge branch 'rdf-wg-r5' into rdf-wg-r5-with-generated 2023-02-10 12:43:35 -05:00
Jim Balhoff a547458274 Update loinc namespace. 2023-02-10 12:43:15 -05:00
Grahame Grieve bd424e7b60 fixes after more testing 2023-02-10 16:18:33 +11:00
Grahame Grieve 11c887edc5 FHIR-34417: implementations for comparable(), highBoundary(), lowBoundary() 2023-02-10 10:02:40 +11:00
Jim Balhoff 92cae24b1b Add generated RdfParser code. 2023-02-08 14:09:01 -05:00
markiantorno 97604fdff5 Updating version to: 5.6.98-SNAPSHOT and incrementing test cases dependency. 2023-02-07 12:55:19 +00:00
markiantorno c91376f3b9 Release: v5.6.97
## Validator Changes

* no changes

## Other code changes

* Fix for Extensions moving in R5
***NO_CI***
2023-02-07 12:28:44 +00:00
Grahame Grieve ba731b0051 Fix R5 loading problem 2023-02-07 09:53:51 +10:00
markiantorno eec7c33e63 Updating version to: 5.6.97-SNAPSHOT and incrementing test cases dependency. 2023-02-05 21:04:53 +00:00
markiantorno 729e7afb33 Release: v5.6.96
## Validator Changes

* no changes

## Other code changes

* Fix bug with duplicate value in getResourceNames()
***NO_CI***
2023-02-05 20:42:24 +00:00
Grahame Grieve 1d4f1e9d90 fix bug with duplicate value in getResourceNames() 2023-02-06 05:38:02 +11:00
markiantorno b3cebe7bc6 Updating version to: 5.6.96-SNAPSHOT and incrementing test cases dependency. 2023-02-03 20:09:35 +00:00
markiantorno 1696b56b50 Release: v5.6.95
## Validator Changes

* Fixes for FHIRPath as() operator in r4 and r5

## Other code changes

* no changes
***NO_CI***
2023-02-03 19:45:12 +00:00
Grahame Grieve ea9333b322
Gg 202302 fhirpath as (#1102)
* fix type of issue source extension

* update extension extractor

* FHIRPath changes for as - case and singleton issues

* minor fixes for extension rendering

* Update test cases version

---------

Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-02-03 13:14:51 -05:00
markiantorno ea41a8b6a6 Updating version to: 5.6.95-SNAPSHOT and incrementing test cases dependency. 2023-02-02 17:07:22 +00:00
markiantorno 67329e20ad Release: v5.6.94
## Validator Changes

* no changes

## Other code changes

* Test release
***NO_CI***
2023-02-02 16:34:58 +00:00
Jim Balhoff d596a6c343 Use leading underscore for properties with objects with modifier extensions. 2023-02-01 19:49:24 -05:00
Jim Balhoff 12bf57886f For resources with a modifierExtension, use a leading underscore for the rdf:type. 2023-02-01 13:05:47 -05:00
markiantorno e922cc2a97 Updating version to: 5.6.94-SNAPSHOT and incrementing test cases dependency. 2023-02-01 07:27:59 +00:00
markiantorno 4e97bb0d5a Release: v5.6.93
## Validator Changes

* Fix for NPE rendering resources
* Consider CanonicalResource to be a CanonicalResource when validating profile references
* Work around error in R5 sdf-29 invariant

## Other code changes

* XHTML processing: Cater for "." in XML element and attribute names
* Handle R3 encoding of primitive values when validating profiles
* Improve error messaging when validating StructureDefinition
* Temporary Support for MedicationStatement in R5
* Work around for Identifier.use = ? in THO R5 package (old error)
* Rework Package API to allow for authentication on package servers
* Structure mapping now finds source Structure Definition by URI and sets ParserBase logical property appropriately.
* DOn't convert ig-r4 when converting package versions
***NO_CI***
2023-02-01 07:02:20 +00:00
Grahame Grieve 4a79e89f62 Merge remote-tracking branch 'origin/master' 2023-02-01 14:49:19 +11:00
Grahame Grieve 2cc8ff5e23 extension related validation fixes 2023-02-01 14:49:14 +11:00
Neelima Karipineni 61e63b128a
Enhancements to StructureMap transform to support logical models as source and value set lookup (#1092)
* implement resolveValueSet from AHDIS Matchbox

* get SD from map source type, set logical model

* test for getSourceResourceFromStructureMap DefinitionException

* test resolveValueSet

* test transform logical source

* fix formatting
2023-01-31 16:56:02 -05:00
Jim Balhoff 69ce2b45f2 Output lists in examples using RDF lists. Don’t output fhir:index. 2023-01-31 14:11:29 -05:00
Grahame Grieve 7ad4bd62c6 fix for NPE rendering resources 2023-01-31 07:23:12 +11:00
Grahame Grieve d859e0b4bd Temporary Support for MedicationStatement in R5 (going to be renamed again) 2023-01-31 07:22:33 +11:00
Jim Balhoff 890971d110 Output type triples for value[x] nodes. Use simple property names. 2023-01-27 17:35:36 -05:00
Jim Balhoff 00d1ab3517 Use fhir:v for literal values in examples. 2023-01-22 19:14:49 -05:00
Jim Balhoff b7576dee79 Don’t output ontology import declaration in examples. 2023-01-22 19:14:08 -05:00
markiantorno cb441456a8 Updating version to: 5.6.93-SNAPSHOT and incrementing test cases dependency. 2023-01-20 23:14:26 +00:00
markiantorno dc677cad51 Release: v5.6.92
## Validator Changes

* update FHIRPath implementation for corrections to 'as' (R5 only in validator)
* Critical Security fix: enforce correct paths when unpacking archives (SecurityAdvisory-1082, CVE TBA)

## Other code changes

* Update to latest FHIRPath for older versions
* Add new ElementModel based parser for StructureMaps
* go-publish related changes
* FTP Client upload and logging improvements
* Refactor base64 handling for Android compatibility

## Security Note

The validator unzips archive files to the local file system when
it is scanning zip files it has been asked to validate, and when it is
installing packages. These processes are now resistant to the zip-slip
vulnerability.
***NO_CI***
2023-01-20 22:57:29 +00:00
dotasek b50aec5912
Advisory fix 1 (#1089)
* Update cache and comparison downloads to use https

* Zip Slip tests and fix

* Zip Slip tests 2 and fix

* Add missing tempDir child in ScannerTest

* Add win format zip test

* Add tests to r4b

* Add tests and fixes for slips in tgz processing

* Update fhir-test-cases version
2023-01-20 16:56:57 -05:00
Grahame Grieve 2c93585bb6 better error message 2023-01-21 07:36:09 +11:00
Grahame Grieve f8e6371e1f
Merge branch 'master' into gg-202301-sm-errors 2023-01-20 19:44:24 +11:00
Grahame Grieve b16fc37b02 clean up error handling when parsing structure maps 2023-01-20 04:24:42 +11:00
dotasek f58b7acfb5
Swaps isBase64 with internal implementation for Android compatibility (#1079)
* Adding animal sniffer to display all issues related to android compatibility.

* Duplicate isBase64 internally

Co-authored-by: Vitor Pamplona <vitor@vitorpamplona.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-01-18 18:40:24 -05:00
Grahame Grieve 7cc01ef7db update new FHIRPath for older versions 2023-01-19 07:57:05 +11:00
Grahame Grieve 26027fa3d6 update FHIRPath implementation for discussion at 84a07a6a92 2023-01-19 06:59:45 +11:00
Grahame Grieve d7071312ba
Merge pull request #1080 from hapifhir/gg-202301-sm-em-parser
Add ElementModel based StructureMap parser
2023-01-18 20:07:52 +11:00
Grahame Grieve 4f2fd817a3 Merge remote-tracking branch 'origin/master' 2023-01-18 12:33:59 +11:00
Grahame Grieve c9833f94d3 Add ElementModel based StructureMap parser 2023-01-18 12:32:06 +11:00
markiantorno 4367813a2c Updating version to: 5.6.92-SNAPSHOT and incrementing test cases dependency. 2023-01-17 21:59:38 +00:00
markiantorno 7b22d0355b Release: v5.6.91
## Validator Changes

* Fixed validation of URNs
* Check profiles don't have slicing on roof

## Other code changes

* Fix significant performance issue with profile xls generation
* Fix issue with setProperty dropping extensions in R3 - R5
* Debug logging improvements generating snapshots
* Fix issues with types missing in CDA IGs
* Fix problem converting ActivityDefinition R4(B)/R5
* More work on FTP Client
***NO_CI***
2023-01-17 21:40:28 +00:00
Grahame Grieve 7b99037199 fix BOM in java files 2023-01-17 12:49:14 +11:00
Grahame Grieve daf5638f3e Fix significant performance issue generating xlsx for multiple profiles 2023-01-17 11:23:39 +11:00
Grahame Grieve 8cb7e40815 Improved Error message if profile root has slicing 2023-01-17 11:23:14 +11:00
Grahame Grieve 01c131b29d see PR 1075 - fix issue with setProperty() ignoring extensions 2023-01-17 11:22:42 +11:00
Grahame Grieve 41abbb21a0 fix debug logging for snapshot generation 2023-01-17 05:36:44 +11:00
Grahame Grieve abf2e99ab6 Merge remote-tracking branch 'origin/master' 2023-01-16 10:53:57 +11:00
Grahame Grieve 1df68c95a4 Fix rendering when binding strength missing 2023-01-16 10:13:11 +11:00
Grahame Grieve 6c2a488402 fix type convertors to handle null 2023-01-16 10:12:59 +11:00
markiantorno c52777c462 Updating version to: 5.6.91-SNAPSHOT and incrementing test cases dependency. 2023-01-14 06:35:33 +00:00
markiantorno ac16aae300 Release: v5.6.90
## Validator Changes

* Better tracking and reporting of snapshot generation issues
* Update FHIRPath implementation to R4 with all corrections and extensions from R5 implemnetation

## Other code changes

* Inclusion of SAXON dependency for processing XSLT
* Error message spacing correction
* Basic FTPClient implementation
* test NPE in markdown processing
* go-publish support
* Start implementing loading structure maps with validation
***NO_CI***
2023-01-14 06:17:06 +00:00
Grahame Grieve 615ed8d63f
Update R4 FHIRPath implementation from R5, and get all tests passing (#1063)
* Update R4 FHIRPath implementation from R5, and get all tests passing

* test NPE in markdown processing

* go-publish support

* Start implementing loading structure maps with validation

* release notes

* more work on FTP

* Fix breaking test.

* Add fhir-test-cases to r4 pom to fix breaking test

Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-01-13 23:08:40 -05:00
Grahame Grieve a06803d936 Start implementing loading structure maps with validation 2023-01-14 08:45:13 +11:00
Grahame Grieve 90f7214195 test NPE in markdown processing 2023-01-10 11:34:41 +11:00
Grahame Grieve 8902898428 better tracking and reporting of snapshot generation issues 2023-01-09 08:03:24 +11:00
markiantorno b6cec730b5 Updating version to: 5.6.90-SNAPSHOT and incrementing test cases dependency. 2023-01-06 02:08:34 +00:00
markiantorno a6745a9016 Release: v5.6.89
## Validator Changes

* Add support for fhir_comments in R2/R2B
* Add validator checking around versions in extension URLs
* Fix bug generating cross-version extensions

## Other code changes

* Fix minor NPEs running IG publisher
* Add new PE module (PEDefinition/PEInstance)
* Add support for liquid filters (resolve FHIRPath conflict)
* Fix up round-tripping of XPath constraints R4/R5
* Refactor R5 ProfileUtilities (and move rendering to rendering package)
* Fix appending text when generating snapshots
***NO_CI***
2023-01-06 01:51:20 +00:00
Grahame Grieve c828ce9eb7 fix URL TO URI 2023-01-06 10:41:21 +11:00
Grahame Grieve 45cf907204 kindling compile fixes 2023-01-05 08:43:30 +11:00
Jim Balhoff 673e36b989 Merge branch 'master' into rdf-wg-r5-merging 2023-01-04 15:04:48 -05:00
Grahame Grieve f3fc19a906 refactor profile generation (utils -> renderer) + add new views 2023-01-03 14:54:11 +11:00
Grahame Grieve b014401dd4 refactor profile rendering (more to StructureDefinitionRenderer) 2023-01-01 11:12:44 +11:00
Grahame Grieve aacefd6581 Merge remote-tracking branch 'origin/master' 2022-12-31 11:06:47 +11:00
Grahame Grieve b894cc6da7
Merge pull request #1048 from qligier/pr-fix-text-appending
Fix appending text in ProfileUtilities
2022-12-31 09:10:24 +11:00
Grahame Grieve c1262d50c5 fix up cardinality issues 2022-12-30 07:20:06 +13:00
dotasek 1380c5e52d Fix test breakage caused by capitalization 2022-12-29 13:17:47 -05:00
Grahame Grieve be9c36e037 more PE work 2022-12-29 21:37:44 +13:00
Grahame Grieve 5e67c5a57e more work 2022-12-29 17:16:40 +13:00
Grahame Grieve 44ecfbf53d more PE work 2022-12-29 10:18:47 +13:00
Grahame Grieve d532af808b more work on PE definitions 2022-12-28 16:11:45 +13:00
Grahame Grieve 50bc157ab9 more work on PE 2022-12-28 08:38:27 +13:00
Grahame Grieve 44b25be2a5 warning 2022-12-26 13:51:54 +13:00
Grahame Grieve abf8dca07b more doco 2022-12-26 13:51:16 +13:00
Grahame Grieve 9959183017 more work on PEDefinition 2022-12-26 13:28:22 +13:00
Grahame Grieve 900f471dda upgrade test case dependency 2022-12-24 08:42:02 +13:00
Grahame Grieve f87394b46e start implementing ProfiledElement 2022-12-24 07:30:09 +13:00