Commit Graph

1512 Commits

Author SHA1 Message Date
dotasek 7b3e206b1c Fix JsonObjectTests interaction with Instant 2023-02-02 13:52:01 -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 5dc19cd052 Tweak spacing. 2023-02-01 11:55:11 -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
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 08ed54fd35 Rework Package API to allow for authentication on package servers 2023-01-31 10:32:21 +11:00
Grahame Grieve 4ab03c5c93 cater for "." in XML element and attribute names 2023-01-31 07:23:52 +11:00
dotasek cca38587ce
Cleanup jetbrains annotations (#1090)
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-01-23 18:27:47 -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 f8e6371e1f
Merge branch 'master' into gg-202301-sm-errors 2023-01-20 19:44:24 +11:00
Grahame Grieve 68b36d3cb5 go-publish related changes 2023-01-20 11:23:17 +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
dotasek 885e55352f
FTPClient: upload file path creation, logging, and improved default path (#1078)
* More logging of errors.

* WIP create path for file to upload.

* WIP Tests

* More tests

* Improved logging and path fixes

* Clean up imports

* Rename test

* add testing code

Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>
2023-01-18 12:42:59 -05:00
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 4b1a3dba46 Improve URN validation 2023-01-16 22:13:53 +11:00
Grahame Grieve a61d860ddb FTP passive mode 2023-01-16 22:13:38 +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
dotasek 625ecac3c8
Bump commons-net to 3.9.0 (#1070)
Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-01-13 22:11:51 -05:00
dotasek dc9d5d0ed1 Set file transfers to binary type, ensure file contents match 2023-01-11 13:41:43 -05:00
dotasek edf6d75551
Implement FTP Client (#1064)
* Start with tests against fake FTP

* Dummy test file

* Switch to our FTPClient, make tests break

* Implement FTPClient

* Rely on end caller to set path delimiters

* User port 8021 for tests (not protected in azure pipelines)

* Let mocks use Windows filesystem

* Gentle refactor

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-01-09 20:06:21 -05:00
dotasek 0fd3c4af42 Merge branch 'master' into do-reintroduce-saxon-dependency 2023-01-06 17:00:40 -05:00
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
dotasek df100a2d34 Restore saxon dependency dropped by HAPI FHIR 2023-01-05 17:11:35 -05:00
Grahame Grieve e794eca959 Changes to support upgrades to IG publisher -go-publish process 2023-01-05 08:44:45 +11:00
Grahame Grieve 19f1171962 json date handling related changes 2023-01-05 08:43:57 +11:00
Jim Balhoff 673e36b989 Merge branch 'master' into rdf-wg-r5-merging 2023-01-04 15:04:48 -05:00
Grahame Grieve db48892b66 fix failing test 2023-01-03 14:57:08 +11:00
Grahame Grieve f3fc19a906 refactor profile generation (utils -> renderer) + add new views 2023-01-03 14:54:11 +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
Quentin Ligier 858c06f097
Fix appending text in ProfileUtilities
If the base text was null, appending a text in the derived element (using "...") would show a "null" before the text. This commit adds the method Utilities.appendDerivedTextToBase() to implement to correct behavior.
2022-12-23 18:52:47 +01:00
Grahame Grieve 37844bd395 update xver dependency 2022-12-17 08:07:43 +11:00
Grahame Grieve 6b1ae35ef3 * Add validator support for fhir_comments in R2/R2B (#1042) + Add validator checks around versions in extension URLs 2022-12-17 07:11:06 +11:00
markiantorno aaa5c9d6a4 Updating version to: 5.6.89-SNAPSHOT and incrementing test cases dependency. 2022-12-16 01:40:27 +00:00
markiantorno a3a1e79674 Release: v5.6.88
## Validator Changes

* Remove use of .fhir/package-client cache (only use the main .fhir/package now)

## Other code changes

* Hack work around for broken template input for R5 OperationOutcome
* Fix up problems with test case consistency in R5 test cases
* Add R5-snapshot3 version enum to R4 version list
***NO_CI***
2022-12-16 01:19:52 +00:00
Grahame Grieve 8b7890bea2 removing caching package client - rests on invalid assumptions 2022-12-16 08:49:30 +11:00
markiantorno ba67d790b8 Updating version to: 5.6.88-SNAPSHOT and incrementing test cases dependency. 2022-12-14 03:25:16 +00:00
markiantorno 6d8cd59f1e Release: v5.6.87
## Validator Changes

* Change Java minimum version from 8 to 11
* Fix Error message missing parameter (very minor fix)

## Other code changes

* Refactoring package-list.json handling
* Upgrade code to latest R5 release (Snapshot 3)
* Fix bug with version patching loading package for the first time + fix bug determining spec reference
* Add Ids to profile spreadsheets
***NO_CI***
2022-12-14 02:48:33 +00:00
Grahame Grieve 659457bb65
Merge branch 'master' into gg-202212-r5-update 2022-12-14 11:55:31 +11:00
Grahame Grieve 9aeb39671b fix to get tests passing again. If I'm lucky 2022-12-14 11:54:14 +11:00
Grahame Grieve 72eae55218 fix new bug in package manager 2022-12-14 09:59:25 +11:00
Grahame Grieve e9d8400a78 fix package loading bug 2022-12-14 09:09:53 +11:00
Grahame Grieve d1d391496e upgrade to new R5 release 2022-12-13 21:13:29 +11:00
markiantorno 0e619971c4 Updating version to: 5.6.87-SNAPSHOT and incrementing test cases dependency. 2022-12-12 20:14:04 +00:00
markiantorno bbf74e6f91 Release: v5.6.86
## Validator Changes

* Change Java minimum version from 8 to 11
* Fix Error message missing parameter (very minor fix)

## Other code changes

* Refactoring package-list.json handling
***NO_CI***
2022-12-12 19:56:58 +00:00
Grahame Grieve f5d486f171 refactoring package-list.json handling 2022-12-12 19:54:37 +11:00
markiantorno 915d5e89b7 Updating version to: 5.6.86-SNAPSHOT and incrementing test cases dependency. 2022-12-09 18:40:17 +00:00
markiantorno c01a9444a4 Release: v5.6.85
## Validator Changes

* Change rules around Document and Link Message validation (see [Jira](https://jira.hl7.org/browse/FHIR-39502) and [Zulip](https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/Entry.20isn't.20reachable.20by.20traversing.20from.20first.20Bundle.20entry) for details)
* Allow https://example in questionnaire example links

## Other code changes

* Rendering Improvements for deprecated codes Including deprecation reason
* Add Accept header fetching JSON
* Fix version comparison bug
* Fixes for producing profile summary in IGs
* Add contents to .index.json and bump to v2
* Fix stated package & version in alternate versions packages
* Refactor ProfileUtilities.generateSnapshot
* Fix bug in XHTML generation around empty tags
* Fix NPE appending slashes
* Fix rendering timing to not use a specific verb
* Fix R2 - RX ValueSet convertor for Code Systems
***NO_CI***
2022-12-09 18:23:37 +00:00
Grahame Grieve 89486c17fc
Merge pull request #1029 from hapifhir/gg-202212-json-header
Gg 202212 json header
2022-12-10 00:01:26 +11:00
Grahame Grieve 1786122763
Update org.hl7.fhir.utilities/src/main/resources/Messages.properties
Co-authored-by: Vadim Peretokin <vperetokin@hey.com>
2022-12-09 23:30:59 +11:00
Grahame Grieve ee8a58b7e1
Update org.hl7.fhir.utilities/src/main/resources/Messages.properties
Co-authored-by: Vadim Peretokin <vperetokin@hey.com>
2022-12-09 23:30:06 +11:00
Grahame Grieve 7c2c44b333 Add Accept header fetching JSON 2022-12-09 20:09:12 +11:00
Grahame Grieve 474f84c903 fix bug doing version comparison 2022-12-09 20:09:01 +11:00
Grahame Grieve 771fb0ac00 Changes related to validation of document and message links 2022-12-09 11:09:17 +11:00
Grahame Grieve 73cd123234
Merge pull request #1028 from hapifhir/gg-202212-xlsx-csv
Gg 202212 xlsx csv
2022-12-07 06:11:32 +11:00
dotasek d762740950
Bump HAPI FHIR to 6.2.1 + jacoco + byte_buddy (#1007)
* Bump HAPI FHIR to 6.2.1 + jacoco + byte_buddy

* Failing test

* GitHub complains about missing newlines.

* ACTUALLY bump HAPI, include saxon libs that disappeared

* Update maven.compiler.* properties, drop surefire-java-8 profile

* bump exec plugin

* Try running with JAVA_HOME explicitly

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-12-06 10:52:52 -05:00
Grahame Grieve 064c4ce896 Add contents to .index.json in package (per update to spec) 2022-12-06 16:21:56 +11:00
Grahame Grieve 66f46bc319 remove test that shouldn't have been committed 2022-12-05 17:56:12 +11:00
Grahame Grieve b778641cf6 fix bug in XHTML generation 2022-12-05 17:27:52 +11:00
Grahame Grieve 5d29a88552 fix npe appending slashes 2022-12-05 17:27:43 +11:00
Grahame Grieve a0c28f3326 Round trip XHTML faithfully wrt empty elements 2022-12-05 13:41:31 +11:00
Grahame Grieve cd8c970045 Add logging to package client 2022-12-01 16:56:55 +11:00
markiantorno 7966deb05c Updating version to: 5.6.85-SNAPSHOT and incrementing test cases dependency. 2022-12-01 05:52:06 +00:00
markiantorno b0d3dae149 Release: v5.6.84
## Validator Changes

* Perform canonical resolution using package dependencies even for version specific references (workaround for VSAC bad behaviour)

## Other code changes

* Fix conversion between R3 andR4/R5 for Immunization.notGiven
* Fix parameter handling for tx server responses
* Add cast support for more types in FML implementation
* Fixes to GQL Schema generation
***NO_CI***
2022-12-01 05:35:31 +00:00
Grahame Grieve d24cc6c5ee Merge remote-tracking branch 'origin/master' 2022-12-01 08:22:19 +11:00
Grahame Grieve fedfa88ffb refactor resource reference resolution to use package dependencies whereever possible 2022-12-01 08:16:00 +11:00
dotasek d53aabe2e5
Do not delete previously undefined xmlns attributes when processing Xhtml nodes (#985)
* Add tests

* Add back unseen namespace attributes

* Gentle refactor, document setOriginalNamespacePrefix

* Update validator_test_case_version

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-11-30 16:01:28 -05:00
markiantorno 19e957ef53 Updating version to: 5.6.84-SNAPSHOT and incrementing test cases dependency. 2022-11-29 23:46:32 +00:00
markiantorno b939b33040 Release: v5.6.83
## Validator Changes

* no changes

## Other code changes

* Update FHIR test cases to released version
***NO_CI***
2022-11-29 23:29:15 +00:00
markiantorno ab00f53ee7 Updating version to: 5.6.83-SNAPSHOT and incrementing test cases dependency. 2022-11-29 18:22:35 +00:00
markiantorno b11bf21f9b Release: v5.6.82
## Validator Changes

* no changes

## Other code changes

* Fix Turtle generation
***NO_CI***
2022-11-29 18:05:15 +00:00
markiantorno 63f905d184 Updating version to: 5.6.82-SNAPSHOT and incrementing test cases dependency. 2022-11-28 18:44:16 +00:00
markiantorno 2715d811dc Release: v5.6.81
## Validator Changes

* Avoid repeated R5 Extension loading in ValidatorService
* Fix problems validating logical models
* Fix `-locale` parameter functionality
* Add Spanish internationalization phrases

## Other code changes

* ProfileUtilities: Provide Standards Status in tree view
* JSONParser: numerous r4b/r5 speed improvements and fixes
* FHIRPathEngine: Catch exceptions resolving references in r5
* Handle null source and target in ConceptMap conversions
* Provide consistent rendering of comments in examples in IGs
* Preparations for changes to IG Publisher narrative generation
* Fix for Identifier.use conversion in dstu3
***NO_CI***
2022-11-28 18:23:09 +00:00
Grahame Grieve 49f798de48 Consistency around rendering comments in examples in IGs 2022-11-26 22:24:17 -03:00
Grahame Grieve 53fb08ab19 update JSON parser used by validator to JSON5 parser 2022-11-26 18:24:29 -03:00
Grahame Grieve 363a95bb8a more replacing json library 2022-11-25 22:37:43 -03:00
Grahame Grieve 450fa1d02c minor improvements to json library 2022-11-25 22:37:18 -03:00
Grahame Grieve 61d998963a fix debugging 2022-11-24 19:56:07 -03:00
Grahame Grieve 618f98e323 Add spanish messages 2022-11-24 18:02:02 -03:00
Grahame Grieve 1617315ed8 minor improvements to validator message 2022-11-24 17:58:15 -03:00
Grahame Grieve 80f275ff18 upgrade to new JSON parser 2022-11-24 17:57:46 -03:00
Grahame Grieve b2e2c68f7e minor typo fixes in validation messages 2022-11-22 12:45:33 -03:00
markiantorno 01d212afac Updating version to: 5.6.81-SNAPSHOT and incrementing test cases dependency. 2022-11-22 14:28:51 +00:00
markiantorno 3ab720a6af Release: v5.6.80
## Validator Changes

* Improved Loading speed (20% reduction)
* Fix issue handling path on content references on deeply nested content

## Other code changes

* Fix rendering issue when reference.reference missing
* Add rule date to validation messages so new rules can be highlighted
***NO_CI***
2022-11-22 14:05:59 +00:00
Grahame Grieve 24331956f1 Add rule date to validation messages so new rules can be highlighted 2022-11-22 05:58:02 -03:00
Grahame Grieve 8136b00c86 work on loading speed for validator 2022-11-21 18:46:47 -03:00
markiantorno cc842bc114 Updating version to: 5.6.80-SNAPSHOT and incrementing test cases dependency. 2022-11-20 19:32:31 +00:00
markiantorno ee7ba71b29 Release: v5.6.79
## Validator Changes

* no changes

## Other code changes

* fix references to LOINC codes in generated narrative
***NO_CI***
2022-11-20 18:59:55 +00:00
Grahame Grieve bce3f5464f Merge remote-tracking branch 'origin/master' 2022-11-20 12:57:48 -03:00
Grahame Grieve 8e3833f58a Fix broken LOINC link 2022-11-19 03:39:35 -03:00
markiantorno d7d93b486b Updating version to: 5.6.79-SNAPSHOT and incrementing test cases dependency. 2022-11-17 21:34:46 +00:00
markiantorno 14a8c388fd Release: v5.6.78
## Validator Changes

* Validate HTML entities in XHTML in resources

## Other code changes

* Stop producing XHTML entities in resources when rendering
***NO_CI***
2022-11-17 21:15:59 +00:00