Commit Graph

9069 Commits

Author SHA1 Message Date
nathaniel.doef cfce82576a - version bump 2022-07-25 18:49:13 -04:00
nathaniel.doef 388f1297cb - Create HapiFhirCliRestfulClientFactory to encapsulate new HTTPS functionality. Remove modifications to the FhirContext API. 2022-07-25 18:45:19 -04:00
nathaniel.doef 327603dad0 - Code coverage 2022-07-25 18:45:19 -04:00
nathaniel.doef 41fc718062 - Ken's code review: javadoc 2022-07-25 18:45:19 -04:00
nathaniel.doef 1709b70a02 - Ken's code review: method renaming 2022-07-25 18:45:19 -04:00
nathaniel.doef 1f3b6f0cdf - Ken's code review changes 2022-07-25 18:45:19 -04:00
nathaniel.doef 7d1de3dc3f - ci 2022-07-25 18:45:19 -04:00
nathaniel.doef 893ac96882 - remove OkHttpClient HTTPS support 2022-07-25 18:45:19 -04:00
nathaniel.doef e637df72fc - changelog 2022-07-25 18:45:18 -04:00
nathaniel.doef dd2a27dbab - clean up 2022-07-25 18:45:18 -04:00
nathaniel.doef 00e008a8c1 - tests / refactor 2022-07-25 18:45:18 -04:00
nathaniel.doef 85d368afbf - tests 2022-07-25 18:45:18 -04:00
nathaniel.doef 8716365548 - tests 2022-07-25 18:45:18 -04:00
nathaniel.doef fcc3bdf0bf - ci fixes 2022-07-25 18:45:18 -04:00
nathaniel.doef a5e4d488c4 - refactor and tests 2022-07-25 18:45:18 -04:00
nathaniel.doef a85b0aece4 - ci fixes 2022-07-25 18:45:18 -04:00
nathaniel.doef eb8c4c04a5 - ci fixes 2022-07-25 18:45:18 -04:00
nathaniel.doef db73da300b - ci fixes 2022-07-25 18:45:18 -04:00
nathaniel.doef eb52629842 - ci fixes 2022-07-25 18:45:18 -04:00
nathaniel.doef 98132bb507 - to use resources and files 2022-07-25 18:45:18 -04:00
nathaniel.doef 25d8a0f5e1 - add TLS support for JaxRsClient and OkHttpClient
- add tests
2022-07-25 18:45:18 -04:00
nathaniel.doef 5388f729fb move BaseRestServerHelper to Hapi-Fhir 2022-07-25 18:45:18 -04:00
nathaniel.doef 27d5791d25 wip functional
TODO
- add tests
- look at adding TLS to other RestfulClientFactory classes (FhirwebRestfulClientFactory, JaxRsRestfulClientFactory, OkHttpRestfulClientFactory)
2022-07-25 18:45:18 -04:00
Ken Stevens 533019f051
Response Terminology Wiring (#3807)
* cleaned up response terminology wiring

* jpa is failing atm

* bump pom versions

* double build RAM

* bump hapi version to PRE-22

* license headers

* re-bump to PRE-22

* tag intermittent

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-25 18:41:01 -04:00
Ken Stevens f01e4a7ad2
Remote Terminology support refactor (#3822)
* Revert "test passes with a lot of copy/paste"

This reverts commit f2f28e22ef.

* make translateOutcomeToResults public

* double RAM

* final consolidation.  move shared code out to static utility methods

* revert azure memory
disable jacoco on jpaserver test prokect

* bump hapi version

* rebump hapi to PRE-21

* licenses

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-25 11:47:31 -04:00
Ken Stevens 611c1d9d2c
enable partition-aware subscription activation (#3844)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-25 06:59:49 +00:00
Tadgh 6d9bbbec1c
Add support for deletes to stu3/dstu2 subscriptions. (#3836)
* Add support for DSTU3 delete subscrion events, add test

* Add changelogP
2022-07-22 19:24:59 +00:00
Nathan Doef cbcf3f1942
3829 Fix Subscriptions created with package installer and partitioning enabled bug (#3830)
* - failing test + increase existing code coverage

* - fix: use RequestPartitionId.defaultPartition() to handle malformed default partitions

* - changelog

* - typo
2022-07-22 13:12:07 -04:00
Etienne Poirier d2fd0989c3
3820 Providing an exception for search request with invalid or incomplete tokenParam (#3825)
* Creating an exception to be raised when searching for _tag/_provide/_security where the associated tokenParam is not properly formatted.

* Adding changelogs.

* Adding integration test.

* Rewording ChangeLog.

* Rewording exception message.

* Addressing code review comments.

* Addressing code review comments.

* Bumping hapi-fhir version to 6.1.0-PRE20-SNAPSHOT

* Modifications to pass checkstyle.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-07-22 11:55:44 -04:00
Tadgh 0a1e782a8e
3817 enhance subscription before message delivery (#3824)
* Add changelog

* implementation and changes

* collection implementation

* tidy
2022-07-22 01:56:27 +00:00
JasonRoberts-smile f5697e13c9
3755 use batch2 job after search parameter change (#3806)
* broke some tests

* invoke batch 2 reindex

* changelog

* fix compile error after merge

* fix failing test

* hook up partition support

* fix some failing tests

* deprecate the old reindex service

* fix more failing tests

* fix broken test
2022-07-21 12:26:15 -07:00
Ken Stevens 85384feac7
separate elastic tests into their own project (#3827)
* move elastic tests out into their own project in the hopes it solves ci memory issues

* move elastic tests out into their own project in the hopes it solves ci memory issues

* disable elastic tests temporarily

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-21 17:12:19 +00:00
jmarchionatto e5cc727013
Document the need to reindex when enabling full resource storage with indexed resources. (#3815)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-07-20 13:24:49 -04:00
Ken Stevens 599f51333f fix checkstyle 2022-07-20 10:40:37 -04:00
Ken Stevens f2f28e22ef test passes with a lot of copy/paste 2022-07-19 21:02:16 -04:00
jmarchionatto 67e67bbf44
Issue 3804 application fails to start 610 pre14 snapshot with beandefinitionoverrideexception invalid bean definition with name loadidsstep (#3805)
* shared steps

* Add changelog

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-07-19 10:00:28 -04:00
Qingyixia 592190701c
Implement patch in mongo db (#3781)
* Not the final version

* Support PATCH operation

* minor modifications

* minor modifications

* Final version

* Final version

* Version Bump

* bump version again

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-17 21:26:34 -04:00
TipzCM 8ed0a18ef4
3531 implement bulk processors (#3566)
* base batch2 bulk export steps - unimplemented

* added the basic steps

* adding tests

* we have added the tests

* added tests for bulk export stages

* implementing jpa

* 3531 adding the jpabukexportprocessorimplementation

* 3531 first step for mongo bulk export

* jpa stuff updated

* 3531 hapi fhir stuff

* trying to fix up tests

* fixing test

* fixed most tests in batch export

* deprecate

* need some more guidance here

* fixing some tests

* some steps taken

* blah

* stashing

* test

* fixing tests round 1

* many a changes

* updating version

* small updates

* merging in mster again

* fixing up serialization

* added the permission checkers

* cleanup and sonarkube crap

* some more tests

* updating adding tests

* crimes

* blah

* updatingmsg number again

* removal of commented code

* cleanup

* merge confflicts

* fixing msg

* review fixes round 1

* more review fixes

* merging in master

* fixing poms

* review points

* test fix

* test fix

* fix test race condition

* truncate error

* add stack trace to error

* rename to IT

* fix race condition in test

* finally fixed race condition in test.  this time I'm optimistic hapi ci will finally pass

* fix mock test.  not a fan of mock tests like this.

* any job definition with a reducer step must be gated.

* fixed common batch bean wiring

* fix test

* lazy init ResponseTerminologyTranslationSvc

* change the way we lazy init ResponseTerminologyTranslationSvc

* change the way we lazy init ResponseTerminologyTranslationSvc (for the third time.  this is super tricky!)

* disabling testGoldenResourceWithCircularReferenceCanBeCleared for now

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-17 17:49:03 -04:00
jmarchionatto 398ed99f86
Hsearch no scroll queries (#3799)
* Avoid scrolling result for not-asynchronous searches

* Adjust deprecated properties

* Add changelog

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-07-15 18:04:12 +00:00
TipzCM 0c644271ce
3770 fix batch2 failure loop (#3779)
* 3770 fixing error handling

* some updates to error handling

* changelog

* blah

* bumping version

* fix test failures

* code review points

* review points

* add retry test

* assert counts in the test

* test fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-15 12:42:46 -04:00
Tadgh ab4d9578e7
Make patch `add` actually add instead of replace. (#3800)
* Fix some patch problems

* Changelog
2022-07-15 16:29:16 +00:00
Mark Iantorno e0169fa6c7
Adding autoclosing for sonatype publishing (#3798) 2022-07-15 11:10:26 -04:00
jmarchionatto 98cce2a042
3664 fast elastic load (#3769)
* Start direct HSearch path

* Support no HSearch

* Spike out the direct resource query

* Implement hsearch fast load

* Fix last master merge in issues

* Implement revision requests

* Test direct resources (no IDs query) sorting

* Use mock to count freetext searches to avoid implementing interface in test

* Remove fixme

* Make listener optional as it is used only for tests

* Provide new dependency

* Widen fast path test scope and fix previously untested configurations

* Make method transactional as it can be called from outside a TX (at least testObservationLastNAllParamsPopulated does)

* Update test validation

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-07-14 15:21:43 -04:00
jdar8 5575e722d4
3788 FHIR patch on soft deleted resource undeletes resource (#3789)
* failing test

* fix

* refactor

* refactor

* changelog

* changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3788-fix-fhir-patch-on-soft-deleted-resources.yaml

Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
2022-07-14 18:41:36 +00:00
Tadgh 05ebf0286d
3790 remove legacy search builder (#3791)
* Remove legacy SB

* Add changelog

* Fix more messages

* Fix missed hapi message

* Fix up more messages
2022-07-14 16:01:44 +00:00
michaelabuckley 94a1cda512
Fix sort in hsearch - use full millis (#3787)
Fix sort in hsearch - use full millis
2022-07-13 13:32:40 -04:00
michaelabuckley 1785c07283
Mb implement token :not inmemory (#3784)
Implement token :not and fix :not-in in InMemoryMatcher

Both `:not` and `:not-in` require that NONE of the values in an OR-list match, so we need some machinery to do a none-match instead of any-match.
2022-07-13 15:51:24 +00:00
jamesagnew 6ba84e1c51 Changelog 2022-07-12 16:01:18 -04:00
dependabot[bot] 31034dd173
Bump jetty-http from 9.4.44.v20210927 to 9.4.48.v20220622 (#3766)
Bumps [jetty-http](https://github.com/eclipse/jetty.project) from 9.4.44.v20210927 to 9.4.48.v20220622.
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.44.v20210927...jetty-9.4.48.v20220622)

---
updated-dependencies:
- dependency-name: org.eclipse.jetty:jetty-http
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-07-12 15:59:00 -04:00
jamesagnew b7c316fb21 Credit for #3619 2022-07-12 15:57:26 -04:00