Commit Graph

9945 Commits

Author SHA1 Message Date
Long Ma 0e8f474b51 revert 6e208f16ec 2024-07-16 12:24:19 -06:00
Tadgh 88f8a66596
Add attribution (#6103) 2024-07-16 11:08:59 -07:00
Long Ma 6e208f16ec bump to 7.5.0-snapshot 2024-07-16 10:43:14 -06:00
TipzCM 7e7aae6060
batching subscription msgs (#6084) 2024-07-16 09:22:35 -04:00
jmarchionatto 5f9b40e3f5
Allow overriding RestfulServer's contextPath (#6113)
* Move IncomingRequestAddressStrategy::determineServletContextPath into IServerAddressStrategy to permit overriding (#6038)

* add changelog

* add contributor as developer

---------

Co-authored-by: Alex Kopp <akopp@athenahealth.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-07-15 16:24:17 -07:00
Etienne Poirier e07684474f
Cleanup work following merge of 6101 (#6110)
* - reverting commented out changes
- removing personal todo

* removing changelog since the related change was reverted.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-07-15 13:47:08 -04:00
TipzCM 875b224ac6
fixing canonical search (#6105) 2024-07-15 13:29:00 -04:00
Justin McKelvy d2c12a7ac3
6083 clinical reasoning version bump v38 (#6089)
* version bump clinical reasoning

* specifying required patch type

* bumping to 7.3.11-SNAPSHOT

* fix file name

* remove default fhirPatch until bug fixed
2024-07-12 18:24:26 -07:00
Renaud Subiger b6bcb292b6
Use server name as narrative text in CapabilityStatement (#6060)
* Use server name as narrative text in CapabilityStatement

* Credit for #6060

* Fix spotless

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-07-12 16:56:28 -04:00
jdar8 ec7538c78f
Jd 20240704 fix mdm phonetic matching on humanname exception (#6078)
* failing test

* fix and changelog

* edit changelog issue number

* mvn spotless

* address code review comment

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
2024-07-12 09:54:45 -07:00
Renaud Subiger 40d42f3ba5
Rename methods to prevent duplicate bean names (#6098) 2024-07-11 18:05:38 -07:00
Etienne Poirier bd31bcb290
emergency fix - reverting changes introduced in 6092 to get pipeline running. (#6101)
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-07-11 21:26:39 +00:00
volodymyr-korzh 6c446277e3
Patient everything operation with offset query parameter throws exception (#6085)
* Patient $everything operation with _offset query parameter throws exception - tests and implementation
* Patient $everything operation with _offset query parameter throws exception - added changelog
2024-07-11 15:24:54 -06:00
Ken Stevens 7e9faf84b8 change is unit tested 2024-07-10 17:52:40 -04:00
Aditya Dave 16b002d1dd
fix changelog (#6093) 2024-07-10 18:04:31 +00:00
Etienne Poirier c235488580
6090 requestpartitionhelpersvc throws an unexpected exception when resolving partition for non partitionable resource (#6092)
* initial failing test.

* fix and test modification

* adding changelog

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-07-10 10:59:17 -04:00
VK-SMILECDR e3f64c23a2
logback test extention assert (#6087)
* initial check-in

* HAPI logback test extension cleanup

* bump version

* revert mistake change

* changes based on review
2024-07-09 20:06:06 +00:00
Aditya Dave ce0160e7f9
cds hooks allow arbitrary strings for extensions (#6026)
* changes to context booter and basecdsservicejson

* cleanup CdsHooksContextBooter

* javadocs

* change JsonNode to CdsHooksExtension

* failing test for service extensions...

* fix extension serialization

* fix extension serialization

* failing test for request extensions not getting parsed...

* try adding a custom deserializer for extension

* try adding a custom deserializer for extension

* try adding a custom deserializer for extension

* wire up CdsServiceRegistryImpl

* fix wiring object mapper

* merge master

* get hook in deserializer

* create CdsServiceRequestJsonDeserializer..

* spotless

* fix for cds service feedback for  CdsHooksControllerTest.java

* spotless

* cleanup...

* spotless...

* docs

* enable tests for CdsHooksContextBooterTest

* more cleanup...

* refactor CdsServiceRequestJsonDeserializer

* apply suggestion

* spotless....

* fix checkstyle...

* spotless

* split custom extension classes into its own package for tests

* add changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6023-fix-allowing-arbitrary-json-for-cds-hooks-extensions.yaml

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6023-fix-allowing-arbitrary-json-for-cds-hooks-extensions.yaml

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/api/json/CdsHooksExtension.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* fix comments

* rename

* fix the comment

* spotless

* version bump to 7.3.9-SNAPSHOT

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-07-09 09:45:21 -04:00
Tadgh 3ffb695b6b
increase string value storage length to accomodate larger contains searches (#6037)
* wip test writing

* add test to ES suite as well

* wip

* Changelog

* spotless

* Address review comments

* Test corrections

* Fixes for tests

* Fix changelog
2024-07-09 06:54:24 +00:00
Tadgh fee1b75242
6056 drop derby jars (#6057)
* Remove most of derby, add changelog

* Upgrade information

* Upgrade notes, bump to jdk17 version

* Fix issue#
2024-07-08 22:50:17 +00:00
Luke deGruchy ef0aa11e00
Introduce TRM_CONCEPT_DESIG.VAL_VC column to replace VAL (#6080)
* Extend TRM_CONCEPT_DESIG.VAL column from 2,000 to 4,000 characters.

* Increase to 8,000 chars.  Add jira to changelog.

* Implement new design.   Still needs new/updated tests.

* Fix setter.

* Make both columns nullable.  Fix changelog.  Add better error message for HapiMigrator.

* Enhance test.

* Small code review suggestion.

* Cosmetic change to re-trigger build.
2024-07-08 18:19:33 +00:00
Etienne Poirier aafa445d19
Wrapping $meta-add and $meta-delete operation in transactionService execution to support partitioning (#6082)
* wrapping metaAdd/Delete operation in transactionService.execute to have the tenant acknowledged by Spring.

* spotless happiness.

* fixing broken test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-07-08 07:33:02 -04:00
Martha Mitran ecef72729f
Add support for running the reindex job across resources in multiple partitions and all partitions (#6009)
* Cleanup and fix compile warnings

* Cleanup and enhance batch2 jobs to support running them across multiple partitions.

* Add some documentation and fix build in the pipeline.

* Fix tests

* Add support for RequestPartitionId.allPartitions as input to the IJobPartitionProvider. Add tests and fix one test. Add missing changelog.

* Separate basic partition provider logic so it can be reused by Mongo. Update documentation.

* Revert change to apply certain validation only for creates.

* Remove added logs

* spotless fix

* Address code review comments
2024-07-05 22:23:07 -07:00
James Agnew 5e519810ff
Combo Parameter Permutations (#6073)
* Combo permutations

* Work on combo

* Add tests

* Add changelog

* Spotless

* Test fix

* Drop label

* Add tests

* Spotles

* Account for review comments
2024-07-05 12:05:58 -04:00
dotasek 8a41da4a18
Add warning in javadoc (#6081) 2024-07-05 09:05:20 -04:00
VK-SMILECDR 2aa11b2605
add simple LogbackTestExtensionAssert (#6076) 2024-07-04 17:34:05 +00:00
TipzCM 371aad2b08
fixing deprecated thymeleaf syntax (#6064) 2024-07-04 15:08:26 +00:00
dotasek 724339c886
Bump jetty_version from 12.0.3 to 12.0.9 (#6022)
* jetty_version from 12.0.3 to 12.0.9

* Changelog

* Try to resolve test issue

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-07-02 08:22:18 -07:00
Luke deGruchy 34da5c1b34
Ensure DropPrimaryKeyTask respects dry-run (#6062)
* Remove code to SQL query from BaseTask.  Move code to DropPrimaryKeyTask and gate it for NOT dry-run.

* Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropPrimaryKeyTask.java

Commit code review suggestion

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>

* Code review feedback.

* Code review feedback.

* Remove isTransactional().

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
2024-07-02 09:22:55 -04:00
TipzCM 2fc873d3b6
added PATCH (#6059) 2024-06-28 11:53:22 -04:00
TipzCM 315a05eeb8
schema migrator validation skips skippable tasks (#6050) 2024-06-27 13:16:47 -04:00
TipzCM 39396b136f
update release date (#6055) 2024-06-27 15:44:53 +00:00
jmarchionatto bc8d873c7f
Assertj json extension (#6039)
* Assertj json extension

* Allow chained invocations

* Rename

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-06-27 14:42:14 +00:00
TipzCM 90251b31ab
fixing issue with infinite cache refresh loop (#6045)
* fixing step 1

* spotless

* cleanup

* cleanup

* cleanup

* review fixes

* review fix

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-06-27 09:27:33 -04:00
James Agnew 7224245217
Combo SearchParameter improvements (#5885)
* Start supporting combo refs

* Work on error codes

* Add tests

* Work on tests

* Fixes

* CLeanup

* Add changelog

* Test fixes

* Test fix

* Clean up tests

* Test cleanup

* Work on tests

* Revert change

* Optimize storage

* Add tests

* Work on tests

* Update docs

* Spotless

* Test fixes

* Revert breaking change

* Merge

* Bump guava

* Address review comments

* Test fixes

* Test fix

* FIx tests

* Address review comments

* Spotless

* Test fix

* Revert change
2024-06-27 08:42:04 -04:00
Tadgh bd83bc17cd
6046 text does not work with r5 (#6051)
* Initial commit of failing test

* wip

* Hack a side-route to not use analyzed versions of the field

* spotless

* Add concept of contains for special

* Changelog, docs

* spotless

* another test

* wip

* refactor

* spotless
2024-06-26 23:20:15 +00:00
jmarchionatto 0c642b6113
Improve search param extraction flexibility (#6030)
* Allow extractor to extract values for Resource-level parameters also

* Rename flag

* spotless

* Allow setting test-specific resource provider

* Add tests

* Move common mockings to setup

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-06-26 11:36:47 -04:00
TipzCM 7b68c4d91d
fixed validation issue (#6041)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-06-25 15:10:26 -04:00
Luke deGruchy d4e3698f37
Handle conditional creates across partitions with duplicate search URLs by updating ResourceSearchUrlEntity (#5983)
* First commit.

* SQLs in test class work for Postgres.

* Refine DropPrimaryKeyTask.  Add migration code to do all operations except drop and add primary key.   Comment out stub test code to do all non drop and add primary key operations.  Add verification code to test to verify schema and record counts.

* Oracle drop primary key working.

* Oracle drop primary key working in test code.  Proper drop primary and add primary key tasks working in H2.

* Migration tests work on all 4 databases.

* Spotless.

* Fix compile error.

* Add hapi error codes for new Exceptions.

* Add another hapi error code.

* Cleanup TODOs.  Fix error codes.  Spotless.

* Add new partition conditional create test.  Fix bug from merging tasks class.  Add new unit Add changelog without hapi-fhir issue.

* Add test for conditional create with partitions.

* Fix TODOs.  Reverse unneeded changes.  Rename changelog.  Refinements.  Javadoc.

* Tweak changelog.

* Rename config key internally.  Spotless.

* Fix a newly introduced bug.  Cleanup.  Tweak changelog.

* Small fix.  Spotless.

* Fix compile error.

* Spotless.

* Address code review comments.

* Address more code review comments.

* Fix test.

* Fix test.
2024-06-25 12:11:47 -04:00
jdar8 11d61a5f72
Jd 20240614 6010 bundle entry search score missing (#6011)
* 6010 test

* 6010 add bundle entry search score

* 6010 support other fhir versions for search score

* 6010 changelog

* 6116 mvn spotless

* 6010 address code review comments

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
2024-06-24 08:56:00 -07:00
Tadgh bce0313458
6034 poor index generation on sql server (#6035)
* Changelog

* Remove uniqueness

* spotless

* Add migrations

* spotless

* make some space

* Handle fancier upgrade

* spotless

* Fix up where clause generation to be a bit more readable

* spotless
2024-06-22 00:36:00 +00:00
Jens Kristian Villadsen f767058239
Subscription fhirpath criteria (#5975)
* Added fhirpath-criteria evaluation

* Added test for valid fhirpath that does not evaluate to boolean

* Added resolving the variables %current and %previous

* Added test using only FP criteria

* Added test cases for valid FhirPath expressions that return non-booleans

* Added use of central cache

* Added more elaborate tests for non-sunshine scenarios

* Added changelog

* CheckStyle'd errorcode added.

* Added spotless formatting and converted FhirPathR5 expression to be Android compatible

* Applied more spotless
2024-06-21 16:46:39 -07:00
volodymyr-korzh 0397b9ddc8
Reduce storage required for indexing - stop writing sp_name, res_type, and sp_updated to hfj_spidx_* tables (#5941)
* Reduce storage required for indexing - implementation
2024-06-20 14:10:40 -06:00
TipzCM 5799c6b42b
hibernate search cannot be used for count query if non-active parameters are present (#6027)
fixing count query with fulltextsearch bug
2024-06-19 22:21:20 +00:00
TipzCM 60f456c655
mdm multidelete golden resource final resource pair throws (#6001)
* fixed a bug with mdm and multidelete
2024-06-19 21:00:37 +00:00
Martha Mitran 472984ac65
Document pointcut to use to modify request parameters (#6019)
* Document pointcut to use to modify request parameters. Add a test to exemplify.

* Add another alternate pointcut to use
2024-06-18 21:57:04 +00:00
Tadgh 61b5103535
Final hamcrest conversions (#6015)
* wip

* wip

* revert'

* Delete existing things

* docs

* removing last of hamcrest

* removing last of hamcrest

* manual fix

* remove matchers used in awaitility

* remove matchers used in awaitility

* Final checkstyle removals

* Disable suppression rule for mdm checkstyle

* Fix some awaitility, remove dead matchers

* manual fixes

* manual fixes

* filter all hamcrest mentions

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-06-18 20:46:09 +00:00
James Agnew 47d6e357b6
Fix JPA nullable primitive columns (#5926)
* Fix JPA nullable primitive columns

* Add changelog

* Spotless

* License headers

* Migration fix

* Spotless

* Cleanup

* Cleanup

* Add task skipping

* Update docs

* CLeanup

* Spotless

* Address review comments

* Test fix

* HAPI FHIR version bump
2024-06-18 13:05:29 -04:00
James Agnew ec0021cd40
Add error checker for duplicate codesystem codes (#6014)
* Add error checker

* Add changelog

* Address review comment
2024-06-18 14:25:07 +00:00
James Agnew 8947706af3
Handle Versioned Canonical Refs (#6003)
* Work on versioned canonidal refs

* Merge

* Tests working

* Working without version support

* CLean refactor

* Targets

* Remove redundant parameter

* Fix up tests

* Remove fixme

* Add changelog

* Improve changelog

* Update version

* Test fixes
2024-06-17 08:14:24 -04:00