Commit Graph

1779 Commits

Author SHA1 Message Date
Grahame Grieve 4a7abab5e8 Fix for parsing Bundle.issues 2023-03-16 14:05:54 +11:00
Grahame Grieve 19cb639d37 refactor how types are handled loading packages 2023-03-16 13:26:34 +11:00
markiantorno 2e36c8147a Updating version to: 5.6.111-SNAPSHOT and incrementing test cases dependency. 2023-03-14 12:43:23 +00:00
markiantorno e2967d923c Release: v5.6.110
## Validator Changes

* no changes

## Other code changes

* Fix NPE in string handling
***NO_CI***
2023-03-14 12:18:03 +00:00
Grahame Grieve 824f51f82e fixing broken links, and r4/r5 map testing 2023-03-14 13:24:00 +11:00
markiantorno b5bbe5108b Updating version to: 5.6.110-SNAPSHOT and incrementing test cases dependency. 2023-03-13 05:16:16 +00:00
markiantorno f48d413690 Release: v5.6.109
## Validator Changes

* Add format codes ```md``` and ```url``` to FHIRPath escape() and unescape()
* Add second parameter ```s_last``` to FHIRPath join() to use a different separator for the last time (e.g. ```.join(', ', 'and')```)

## Other code changes

* Parse status when parsing FML metadata
* Fix NPE in FHIRPath resolve() for contained resources ([discussion](https://chat.fhir.org/#narrow/stream/179167-hapi/topic/fix.20to.20FHIRPathEngine))
***NO_CI***
2023-03-13 04:45:19 +00:00
Grahame Grieve cf57262fe4 start working on R4/R5 conversion code 2023-03-13 13:53:53 +11:00
Grahame Grieve 07a3962ac2
Merge pull request #1167 from hapifhir/gg-202303-misc3
Gg 202303 misc3
2023-03-13 06:36:00 +11:00
Grahame Grieve 96f265653e fix run time test 2023-03-12 23:02:46 +11:00
markiantorno 209fcc8c0b Updating version to: 5.6.109-SNAPSHOT and incrementing test cases dependency. 2023-03-11 12:16:50 +00:00
markiantorno 35fb1b20c1 Release: v5.6.108
## Validator Changes

* no changes

## Other code changes

* Tdy up extensions for R5 release
* Hack R5 observation for fix after QA
* Improve StructureMap rendering again
* Clarify Error messages converting between versions
***NO_CI***
2023-03-11 11:49:55 +00:00
markiantorno a3a9017bdb Updating version to: 5.6.108-SNAPSHOT and incrementing test cases dependency. 2023-03-10 13:09:53 +00:00
markiantorno 1e43fe43f0 Release: v5.6.107
## Validator Changes

* Add support for new ColorRGB code system (special case)

## Other code changes

* Add support for special case code systems internally
***NO_CI***
2023-03-10 12:44:48 +00:00
Grahame Grieve 1212b85b5e Change from Error to FHIRException when wrong value type is wrong on polymorphic element 2023-03-10 16:12:59 +11:00
markiantorno a3473354fd Updating version to: 5.6.107-SNAPSHOT and incrementing test cases dependency. 2023-03-09 21:19:20 +00:00
markiantorno d666d0aa80 Release: v5.6.106
## Validator Changes

* no changes

## Other code changes

* Additional checks in path construction for zip slip vulnerability
***NO_CI***
2023-03-09 20:50:18 +00:00
dotasek 909f7e64fe
Additional zip-slip tests (#1162)
* Additional zip-slip tests

* Fix windows path test
2023-03-09 14:30:53 -05:00
markiantorno f49eee623b Updating version to: 5.6.106-SNAPSHOT and incrementing test cases dependency. 2023-03-09 13:06:01 +00:00
markiantorno 0b8e2c3984 Release: v5.6.105
## Validator Changes

* More validation of StructureMaps

## Other code changes

* Add new R5 version to R4 version enumeration
* Fix for NPE generating profile comparison
* Add FML renderer for StructureMaps + various parsing fixes
***NO_CI***
2023-03-09 12:38:13 +00:00
Grahame Grieve cf080d940c reduce spurious output 2023-03-09 22:20:23 +11:00
Grahame Grieve 187d3e98c7 More fixes for structure map validation 2023-03-09 09:11:31 +11:00
markiantorno 8bd83810ea Updating version to: 5.6.105-SNAPSHOT and incrementing test cases dependency. 2023-03-08 08:23:43 +00:00
markiantorno 2a2fc497c7 Release: v5.6.104
## Validator Changes

* Fix up issues validating whitespace
* Multiple fixes to StructureMap and ConceptMap validation

## Other code changes

* rename ig-r4.json to ig-r4.jsonx in IGs
* move R5 package to test cases
***NO_CI***
2023-03-08 07:53:54 +00:00
Grahame Grieve 09648b7ea0 More bug fixes validating FML 2023-03-08 11:49:23 +11:00
Grahame Grieve 6870c7a32c
Merge pull request #1157 from hapifhir/gg-202303-qa-sm-validation-5
Gg 202303 qa sm validation 5
2023-03-08 10:10:55 +11:00
Grahame Grieve 53e67bc1cb handle re-use of mapping groups when validating maps 2023-03-08 09:11:24 +11:00
markiantorno d4d160eb29 Updating version to: 5.6.104-SNAPSHOT and incrementing test cases dependency. 2023-03-07 16:31:22 +00:00
markiantorno b18181ab7e Release: v5.6.103
## Validator Changes

* Fix structure map validation issues around type
* Revise whitespace handling for unicode conformance in validator
* Improved error message for output directory requirements
* Improve compact version sorting in renderer
* Add timestamp to compact format

## Other code changes

* Fix JSON escaping utility function
* Bug fixes in XHTML processing.
* Convertors: Bug Fixes in spec evaluation
* Convertors: patchUrls now patches fhir-type extension values
* R5: Fix FML parsing missing locations
* R5: Fix location bugs in FML parsing
***NO_CI***
2023-03-07 16:03:02 +00:00
Grahame Grieve 80665f142b Merge remote-tracking branch 'origin/master' 2023-03-07 23:33:46 +11:00
Grahame Grieve 26eb1311a4 release notes 2023-03-07 23:33:35 +11:00
Grahame Grieve d6febda3f6
Merge pull request #1154 from vadi2/patch-1
Clarify output directory has to exist already
2023-03-07 23:31:05 +11:00
Grahame Grieve 77e9e3a317 add timestamp to compact format 2023-03-07 21:47:58 +11:00
Grahame Grieve e5a4d84a6f improve compact version sorting 2023-03-07 20:59:02 +11:00
Grahame Grieve 6bf26255ab fix structure map validation issues around type 2023-03-07 20:58:51 +11:00
Grahame Grieve 453f073411 rename ig-r4.json to ig-r4.jsonx 2023-03-07 20:57:27 +11:00
Vadim Peretokin 9943625df7
Clarify output directory has to exist already 2023-03-07 07:58:30 +01:00
Grahame Grieve 0c26f09721 revise whitespace handling for unicode conformance in validator 2023-03-07 06:25:45 +11:00
markiantorno 8a546d37eb Updating version to: 5.6.103-SNAPSHOT and incrementing test cases dependency. 2023-03-06 12:05:52 +00:00
markiantorno a7507e9887 Release: v5.6.102
## Validator Changes

* Add ConceptMap validation
* Add StructureMap validation
* Validate using type regex (had been omitted to now, mostly affects decimal validation)
* Add new -output-style values compact and compact-split
* Fix bug validating CDA choice elements without [x] in their names

## Other code changes

* Various fixes and utilities to support StructureMap & ConceptMap validation
* Fix Observation.value conversion between R5 and other versions
* Recognise R4B and R5 core packages
* Improvements to specification diffference engine for R5 publication
* More efficient XHTML AST model
***NO_CI***
2023-03-06 11:39:27 +00:00
Grahame Grieve e449bf9cfe Add compact rendering 2023-03-06 20:45:21 +11:00
Grahame Grieve 6559c4b245 improve SM validation message 2023-03-06 20:45:05 +11:00
Grahame Grieve cbb75520c9
Merge pull request #1107 from ahdis/oe_choice_without_x
CDA Logical model validation: if choice is only value don't add type
2023-03-06 06:11:21 +11:00
Grahame Grieve 58ad99cfd3
Merge pull request #1149 from hapifhir/gg-202303-cm-sm-validation
Gg 202303 cm sm validation
2023-03-06 06:08:59 +11:00
Grahame Grieve 356e500ab6 finish ConceptMap validation 2023-03-05 23:25:12 +11:00
Grahame Grieve ec72b1fcdd fix parsing and validating of concept maps in structure maps + validate terminology part of structure maps 2023-03-05 18:29:11 +11:00
Grahame Grieve 52c97f3c70 test primitive regexes if other tests pass 2023-03-05 06:14:07 +11:00
markiantorno ebd93f570f Updating version to: 5.6.102-SNAPSHOT and incrementing test cases dependency. 2023-03-03 04:08:44 +00:00
markiantorno f317bb15f6 Release: v5.6.101
## Validator Changes

* Fix NPE in Structure Map validation

## Other code changes

* Add back code missed when regenerating R5
* Update conversions for discovered issues for R5
***NO_CI***
2023-03-03 03:21:09 +00:00
Grahame Grieve b18e541b5f
Gg 202303 r5 fixes (#1148)
* update test package dependency

* Add back code missed when regenerating R5

* fix NPE

* update conversions for discovered issues for R5

---------

Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>
2023-03-02 18:35:33 -05:00
Grahame Grieve f38da36b33 fix NPE 2023-03-03 06:30:17 +11:00
markiantorno da62438802 Updating version to: 5.6.101-SNAPSHOT and incrementing test cases dependency. 2023-03-02 03:50:02 +00:00
markiantorno 578b964cf9 Release: v5.6.100
## Major change:

* New R5 release - rebuild R5 implementation, update a lot of related code

## Validator Changes

* Load separate R5 extensions package
* Load FML directly, and validate mapping as much as possible

## Other code changes

* Fix bugs in Java R5 code generator
* Add more control at the code level over how to handle unknown profiles when generating snapshots
* Rework ConceptMap for major R5 changes
* Fix bug in CommaGeneratedStringBuilder (calling toString() multiple times duplicated content)
* handle case [reference].where(resolve() is X) when analysing types+elements in FHIRPath statements
***NO_CI***
2023-03-02 03:21:29 +00:00
Grahame Grieve 7cf15f248d update version conversions for new version of R5 2023-03-01 21:50:02 +11:00
Grahame Grieve c5d6e0f5f4 Merge remote-tracking branch 'origin/master' 2023-02-28 05:58:54 +11:00
Grahame Grieve 4c30621491 structuremap validation and invariant fixes for forthcoming R5 release 2023-02-27 18:32:38 +11:00
Grahame Grieve a62c8683f2
Merge pull request #1139 from hapifhir/gg-202302-map-validation-2
Work on StructureMap validation
2023-02-27 09:14:13 +11:00
Grahame Grieve 2bd73c650e Work on StructureMap validation 2023-02-27 07:30:04 +11:00
Grahame Grieve edf5ecf275
Merge pull request #1138 from hapifhir/gg-202302-map-validation
FML validation
2023-02-25 16:41:26 +11:00
Grahame Grieve d3a407e369 FML validation 2023-02-25 14:05:03 +11:00
dotasek 76c01a98aa
Add basic checkstyle plugin config (#1122)
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-02-24 15:05:49 -05:00
markiantorno e9607783da Updating version to: 5.6.100-SNAPSHOT and incrementing test cases dependency. 2023-02-23 18:15:08 +00:00
markiantorno e2185d7d5c Release: v5.6.99
## Validator Changes

* Fix validation for query references with empty parameter values
* Fix validation for conditional references

## Other code changes

* Fix resource rendering for conditional references
* Fix bug caused by changing DiagnosticReport.conclusion to markdown
* Track target types on references in FHIRPath
* Minor type checking fixes for FHIRPath
* Fix bugs in FHIRPath type checking discovered during R5 preparation
* Add standardsStatus support to core model
* Update okhttp library
* Allow HTTPS for terminology server URL
* Update table generator to suppress external links in base row and column
***NO_CI***
2023-02-23 17:50:57 +00:00
dotasek 5d6636ba8c
Bump okhttp version (#1131)
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-02-23 11:14:50 -05:00
Grahame Grieve bae27ef706 fix validation for query references with empty parameter values 2023-02-21 16:46:27 +11:00
Grahame Grieve 76a3129b30 fix validation of conditional references 2023-02-20 23:48:16 +11:00
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 26f7b3a803 FHIR-38789 SD_Dependencies extension needs work 2023-02-15 12:12:28 +11:00
Grahame Grieve d5d83bea9c fix broken links in R5 builds 2023-02-14 09:53:22 +11:00
Grahame Grieve 3a427385c5 FHIR QA driven changes 2023-02-12 17:53:41 +11:00
oliveregger 8b5e93dc8d if choice is only value don't add type 2023-02-07 17:36:56 +01:00
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 237670fa24 release 2023-02-07 14:18:12 +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
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
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
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
Grahame Grieve 08ed54fd35 Rework Package API to allow for authentication on package servers 2023-01-31 10:32:21 +11:00
Grahame Grieve bda3a74b40 handle R3 encoding of primitive values when validating profiles 2023-01-31 07:23:33 +11:00
dotasek f5f03442aa Better error description 2023-01-27 11:22:37 -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 7cc01ef7db update new FHIRPath for older versions 2023-01-19 07:57:05 +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 829cea8d33 Add check for slicing at the root of a profile 2023-01-17 11:41:42 +11:00
Grahame Grieve 41abbb21a0 fix debug logging for snapshot generation 2023-01-17 05:36:44 +11:00
Grahame Grieve 4b1a3dba46 Improve URN validation 2023-01-16 22:13:53 +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