Commit Graph

9693 Commits

Author SHA1 Message Date
Chris O Riordan 4649f90a1f Add additional test cases 2023-12-18 09:25:04 -08:00
Chris O Riordan f22c7c100f Merge remote-tracking branch 'origin/master' into 4634-rule-builder 2023-12-18 09:15:11 -08:00
Emre Dincturk 77da1deeda
added retry for PessimisticLockingFailureException on transactions (#5554) 2023-12-18 08:35:36 -08:00
Chris O Riordan 50dfe90979 Remove excess from changelog and add additional tests 2023-12-15 11:52:32 -08:00
James Agnew 7863f03c68
Fix postgres / Remove use of LOB content column (#5555)
* Work on fixing postgres

* Test fix

* wip

* wip

* wip

* wip

* wip

* adding support for h2 embedded and renaming postgressIT

* Work on postgres

* Remove use of gzip content on postgres

* Cleanup

* Test fixes

* Spotless

* Restore fake db for DDL generator

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-12-15 08:07:26 -05:00
Chris O Riordan a3e7a41162 Update RuleBuilder to effectively handle Patient Type-Level Exports 2023-12-14 16:25:51 -08:00
James Agnew d187399ce5
LastUpdated search doesn't work with HFQL (#5510)
* LastUpdated search doesn't work with HFQL

* Spotless
2023-12-14 17:24:04 -05:00
Luke deGruchy c4ac940e14
Migration: Add new indexes to hfj_spidx_string and hfj_spidx_uri if collation is NOT 'C' (#5544)
* First commit for conditional logic in execute migration tasks along with logic to create new indexes on hfj_spidx_string and hfj_spidx_uri if sp_normalized_value or sp_uri, respectively, have a collation other than "C".

* More fixes.  Still TODOs to resolve.

* Add changelog.  Clean up TODOs.  New message code for precondition SQL checking.  javadoc.  Unit test enhancements.

* Spotless.  Small tweaks.  Fix conditional logic for more than one checking.

* Add details to upgrade document.

* Code review feedback.

* Spotless
2023-12-14 21:04:15 +00:00
Luke deGruchy 9f81fa334c
Fix bad doc links referring to .md instead of .html. (#5551)
* Fix bad doc links referring to .md instead of .html.

* Fix link path

* Fix link in changelog.
2023-12-14 19:13:26 +00:00
RBRi 592856c779
HtmlUnit excludes for xerxes/xml-api no longer required (#5545)
Since version 2.68 HtmlUnit does no longer uses xerces. You can cleanup the pom a bit here.
2023-12-13 13:15:52 -05:00
Tadgh 9e20659680
Add docs, upgrade guide, upgrade.md (#5543) 2023-12-12 23:08:00 +00:00
Martha Mitran 564ae46008
Fixes for validation lookupCode method and improve remote terminology tests (#5535)
* Fixes for validation lookupCode method:

(1) NullPointerException when processing designation in the remote terminology implementation
(2) Inconsistency between input and output type  vs.  for property parameter across the board
(3) Fix most of the warnings in the updated classes.
(4) Code review changes

* Fix unit test failure by reverting assertion to FOO_COLUMN.

* Revert commit.

* Update tests

* Update tests - move utility class back

* Update fix and tests

* spotless fix

* Missing branches for exception cases and add tests for the same

* Spotless fix

* fix tests

* fix test

* Address code review comments. Write the remote terminology tests in a way to make them more readable.

* Revert moving utility test class

* Small changes in tests

* Small changes

* fix checkstyle

* Minor changes in exception handling and add a missing test

* Address code review comments. Decouple other tests from lookupCode tests.

* Update declaration of constants

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
2023-12-12 10:05:21 -05:00
James Agnew b28fe3b882
Jakarta Bump Part 2 (#5533)
* Make expunge service extensible

* Work

* Licence headers

* Version bump some dependencies

* Version bumps

* Adapt to new html unit version

* Reintroduce errorprone

* Test fix

* Header

* Work on jakarta

* Test fixes

* Restore errorprone

* More pom tweaks

* Apply spotless

* Errorprone tweak

* errorprone tweak

* Version bump

* License headers

* Version bump

* Postgres bump
2023-12-11 18:24:40 -05:00
TynerGjs d8298e38d4
Resovle 5505-remove-broken-member-match-from-hapi (#5517)
* - Removed IConsentExtensionProvider, MemberMatchR4ResourceProvider and MemberMatcherR4Helper, as well as corresponding usages and tests

* - Removed IMemberMatchConsentHook.java

* spotless reformat

* added changelog

* removed constants for $member-match parameters

* removed error message for $member-match

* completely removed MemberMatchR4ResourceProvider.java

* removed operation constant for $member-match

* version bump
2023-12-07 13:16:31 -05:00
volodymyr-korzh 4d0670b0ad
Empty, id-only content Payload types are not supported for Topic based Subscriptions (#5499)
* added support of Empty, id-only content Payload types for Topic based Subscriptions
2023-12-07 09:05:51 -07:00
Luke deGruchy 78a50f92bc
Replace all nullable/nonnull imports of javax.annotation with jakarta.annotation (#5540)
* Replace all nullable/nonnull imports of javax.annotation with jakarta.annotation.

* Fix checkstyle.  Update checkstyle version.
2023-12-07 09:16:48 -05:00
Chris0296 e9f15c61a8
Update Documentation Step for Batch Job being Cancelled. (#5518)
* Update Documentation Step for Batch Job being Cancelled.

* Fix changelog type
2023-12-06 17:02:54 -05:00
kateryna-mironova da9be29047
Fixed search for resources for $everything operation with partitions and MDM (#5504)
* Fixed search for resources for $everything operation with partitions and client id mode = ANY

* fixed formatting

* changelog file renamed for tests

* code review fixes: moved generics mocks to class fields, changed size > 0 to empty check

* removed unused fields

* moved fields back to methods, changed generic anys

* changed imports from javax to jakarta

* code review fixes
2023-12-06 16:26:52 -05:00
James Agnew 9027138962
Fix postgres startup failure (#5539)
* Fix postgres startup failure

* Spotless
2023-12-06 12:33:34 -05:00
Luke deGruchy 5fa20438b6
SQL Migration: Support lowercase for SQL columns and overridden column type/driver type SQL type string rules (#5534)
* 1. Allow callers to choose uppercase or lowercase column names.  Default uppercase.
2. Allow callers to pass custom sorting rules:  Default no special sorting.

* Spotless.

* Msg.code.

* Get rid of factory method and fix constructor.

* Maintain old constructor for backward compatibility.

* Fix JDK 11 compile error, spotless, and class header.

* Introduce a mechanism to override default SQL column mappings by column type and driver type.

* Add error message code.  Tweak column type algorithm.

* Replace javax.annotation with jakarta.annotation.

* Spotless.

* Fix unit test by restoring FOO_COLUMN assertion.

* Add changelog.

* Code review feedback.

* spotless

* Fix Msg.code().

* Add unit test.
2023-12-06 09:05:36 -05:00
Luke deGruchy f5cb674345
Update pre-commit from 0.3.3 to 0..3.4. (#5537)
* test branch.

* Upgrade pre-commit to 0.3.4.

* Reverse cosmetic change.
2023-12-06 00:52:53 +00:00
Tadgh 293cd3ef3c
Fix case sensitivity on package name lookup (#5524)
* 90% working test

* wip

* Modify test, changelog, add implementation

* Revert "90% working test"

This reverts commit 64a8f1d806.

* fix typo

* spotless
2023-12-05 17:43:00 +00:00
Luke deGruchy 4070b40fb1 Revert commit 2023-12-05 11:38:42 -05:00
Luke deGruchy a9db6c11a9 Test master commit hook 2023-12-05 11:37:26 -05:00
Luke deGruchy 80ca324e82 Revert commit. 2023-12-05 11:33:46 -05:00
Luke deGruchy 96fc596109 Fix unit test failure by reverting assertion to FOO_COLUMN. 2023-12-05 11:29:14 -05:00
Luke deGruchy 65f133186e Reverse commit. 2023-12-04 12:15:00 -05:00
Luke deGruchy 941ba21de3 See if I can push to master 2023-12-04 12:09:43 -05:00
Etienne Poirier fdeaf8384f
Request for exposing client id and username in batch job status api (#5526)
* initial tests and implementation of the feature persistence layer.

* initial tests and implementation pointcut to modify JobInstance before persistence.

* spotless happy.

* Addressing comments from first code review.

* happy spotless

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-12-04 11:44:48 -05:00
Luke deGruchy adb84da651 Reverse commit to master. 2023-12-04 09:11:42 -05:00
James Agnew 6d58df0f44
Jakarta/Javax Servlet Migration (#5429)
* Servlet migrsation changes

* Apply spotless

* Work on migration

* Start working on JPA migration

* Test fixes

* Test fixes

* Test fixes

* Work

* Work on servlet migration

* Work on migration

* Work on fixes

* Imports fix

* Work on tests

* Test fix

* All tests passing

* Work on migration

* Schema generator

* Refactor ID strategy

* Some test fixes

* Test fixes

* API additions

* Work on websockets

* Test fixe

* Version bump

* Work on migration

* All tests have passed!

* Work on test fixes

* Fixes

* Work on fixes

* CDR fix

* Work on migration

* Fixes

* Spotless

* Disable onetoone ban

* Adjust migratyions

* Transaction service fix

* Add tinyint to migrator

* Work

* Migration

* Compile fix

* Add license

* Test fix

* Test fix

* Cleanup

* Cleanup attempt

* Test fix

* Reslve fixmes

* Remove legacy lastn implementation

* Test cleanup

* Cleanup

* Remove dead import

* Bad import setups

* Review comments

* Review fixes

* Build fix

* Test fix

* Spotless

* Account for CR changes

* Compile fixes

* Rollback one change

* Test tweak

* License header

* Test fix

* Test fix part 2:

* Clean up tx isolation

* Spotless

* Spotless apply

* Drop min SQL Server level

* Attempted test fix

* Test fix

* Test fix

* Test fix

* Bump hibernate

* Test fix

* Test fixes

* Test fixes

* Test fixes

* Test cleanup

* One more test fix

* Test fix

* Try to fix test

* Clean up expunge

* Test fix

* Remove unneeded task

* Spotless

* Bump compiler plugin

* Spotless

* Compile fix

* Add license headers

* License header

* Test fixes

* Bump animal sniffer

* Spotless

* Bump Jetty version

* Test fix and version bump

* Cleanup

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
Luke deGruchy 113cf4002d First commit with very rough partial solution and test. 2023-12-01 17:00:05 -05:00
James Agnew d597cf2763
Allow chained searches in Bundles where the fullUrl is fully qualified (#5529)
* Allow chained searches in Bundles where the fullUrl is fully qualified

* Add changelog

* Spotless
2023-12-01 20:19:51 +00:00
Luke deGruchy ec5402abd4
Restore changes for 5502. (#5525)
* Restore changes for 5502.

* Spotless.
2023-12-01 15:16:56 +00:00
Luke deGruchy 59936ee70c
Revert 5502. (#5521) 2023-12-01 09:02:54 +00:00
Luke deGruchy 0c8258f93c Revert the revert 2023-11-30 18:54:49 -05:00
Luke deGruchy 8237c0795d test change 2023-11-30 18:23:13 -05:00
Luke deGruchy ee4ecacbdb Revert changes for 5502. 2023-11-30 18:10:05 -05:00
Michael Buckley fab00ca3a0
Expose the desired Propagation in a tx template (#5516) 2023-11-30 21:43:10 +00:00
Luke deGruchy 8fbbaef079
Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient. (#5488)
* Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient.

* Add FhirContext to ClientResponseContext.

* Introduce a ModifiedStringApacheHttpResponse.  Run spotless.

* Remove TDOOs, add and update javadoc.

* Spotless and copyright header.

* Add changelog.

* Unique error message code.

* Only trigger the interceptor if the expected return type is a Bundle.

* Fix spotless.

* Code review feedback.

* Spotless.

* Bump to 6.11.3-SNAPSHOT
2023-11-30 14:56:46 -05:00
Ken Stevens e15d0430d0
Oracle create index migration recovery (#5511) 2023-11-29 18:15:28 -05:00
James Agnew 469873aff7
Add migrator to uhnfhirtest (#5508)
* Add migrator to uhnfhirtest

* Fix spotless

* Test fix
2023-11-29 09:16:41 -05:00
TipzCM 6e683405a1
5237 fixing empty last page if even results (#5506)
paging will not return empty pages if no results left
2023-11-28 21:28:17 +00:00
Martha Mitran ee414b73d9
Pass properties through to Remote Terminology Service on CodeSystem lookup (#5477)
* Pass properties through to Remote Terminology Service on CodeSystem  operation

* Propagate list of property names throughout. Introduce a parameter object for the lookupCode method. Mark other lookupCode methods as deprecated. Add unit tests.

* Update remote terminology service tests

* Address code review comments

* Fix unit tests

* Address latest code review comments to update default methods

* Address latest code review comments to update default methods - update fallback condition

* Address latest code review comments to update default methods - update fallback condition
2023-11-28 16:12:05 -05:00
Taha 63eed3936b
(#5442) fetch should also resolve canonical URL references (#5443)
* (#5442) fetch should also resolve canonical URL references

* (#5442) - added test

* (#5442) - cleanup?

* (#5442) - changelog and reorganize test

* (#5442) PR feedback

* (#5442) PR feedback

* (#5442) cleared ValidatorResourceFetcher linter warnings

* (#5442) - new error code

* (#5442) caught additional error

* (#5442) spotless apply

* (#5442) spotless apply

---------

Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com>
2023-11-27 23:12:35 -05:00
Michael Buckley 83bfa817ae
Batch - ensure we target the default partition for non-gated jobs (#5496)
* Target the default partition for batch2 storage.
2023-11-27 17:32:58 -05:00
Etienne Poirier 4cc4682245
CLI tool command migrate-database executing in dry-run mode insert entries into table FLY_HFJ_MIGRATION (#5487)
* initial test

* Solution with changelog.

* making spotless hapi

* addressing comments from code reviews

* making the test better.

* addressing code review comment and adding test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-11-24 20:55:03 +00:00
dotasek f39dbb5751
Bump setup-java action to v3 (#5491) 2023-11-24 14:06:18 -05:00
TynerGjs d546ce34e5
Resolve 5483-update-consent-storage-to-latest-spec (#5484)
* removed the adding of memberIdentifier to the consent

* - fixed corresponding test
- added changelog
2023-11-24 13:40:13 -05:00
TynerGjs 9f827a75c7
Resolve 5480 Update member-match signature to match the spec (#5481)
* - Changed member-match function param names, and return value
- modified existing tests to accomodate for the change

* removed tests unsuitable for new return value

* resolve code review comments

* version bump
2023-11-24 09:49:33 -05:00