Commit Graph

336 Commits

Author SHA1 Message Date
jmarchionatto 43ed8ca051
Issue 4052 addition of properties to the loinc terminology uploading process (#4100)
* Allow for easier override of DataSource and dialect

* Add debug logging

* Load AskAtOrderEntry and AssociatedObservations properties from loinc.cvs.
Add changelog.

* Add disabled sandbox test used to develop loinc upload modifications

* Add flags to easily select running mode

* Add validation counters and use gziped csv input to save space in repo

* Implement revision suggestions.
As test is a sandbox remove large files and add readme and test notes to locate them before running the test.

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-10-03 08:48:40 -04:00
Ken Stevens e9a855d3f6
remove spring batch (#4064)
* remove spring batch
it compiles
expect test failures

* fix test transaction manager bean name (wow that was quite the hunt the wumpus!)

* fix test and fix build

* fix test and fix build

* fix test

* remove spring batch schema initialization

* bump hapi version

* fix schema migrator

* bump to PRE-10

* merge master

* change logs

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-09-30 13:18:48 -04:00
Tadgh b472c4bb54
4083 batch permissions (#4095)
* Move threadpool factory into a bean

* Move threadpool factory into a bean

* change return type

* Add license files

* Version bump

* Fix test
2022-09-29 17:24:05 +00:00
michaelabuckley 96b92153f6
Implement composite search parameters in HibernateSearch for JPA (#3839)
Implement composite search parameters in Lucene/Elasticsearch Hibernate Search indexing

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-09-27 00:20:06 +00:00
James Agnew 3bab3544ec
Reduce SQL queries for _include (#4007)
* Rework includes processing for reuse

* Optimize include

* Test fixes

* Bump version down

* Fixed

* Update

* Test fixes

* Start to add javadoc

* Test fixes
2022-09-25 15:22:06 -04:00
michaelabuckley ee1cb4e392
Cleanup and utilities from composite work (#4066)
Utilities and cleanup from composite work #4066
2022-09-24 00:47:25 +00:00
Tadgh 5a978646c5
Add changelog, test, and implementation (#4055) 2022-09-21 21:18:12 -07:00
Tadgh c3339f38c3
Rel 6 1 2 mergeback (#4033)
* Bump for CVE (#3856)

* Bump for CVE

* Bump spring-data version

* Fix compile

* Cut over to spring bom

* Bump to RC1

* remove RC

* do not contrain reindex for common SP updates (#3876)

* only fast-track jobs with exactly one chunk (#3879)

* Fix illegalstateexception when an exception is thrown during stream response (#3882)

* Finish up changelog, minor refactor

* reset buffer only

* Hack for some replacements

* Failure handling

* wip

* Fixed the issue (#3845)

* Fixed the issue

* Changelog modification

* Changelog modification

* Implemented seventh character extended code and the corresponding dis… (#3709)

* Implemented seventh character extended code and the corresponding display

* Modifications

* Changes on previous test according to modifications made in ICD10-CM XML file

* Subscription sending delete events being skipped (#3888)

* fixed bug and added test

* refactor

* Update for CVE (#3895)

* updated pointcuts to work as intended (#3903)

* updated pointcuts to work as intended

* added changelog

* review fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)

* Add test and implementation

* Add changelog

* 3899 code in limits (#3901)

* Add implementation, changelog, test

* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

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

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

* 3884 overlapping searchparameter undetected rel 6 1 (#3909)

* Applying all changes from previous dev branch to current one pointing to rel_6_1

* Fixing merge conflict related to Msg.code value.

* Fixing Msg.code value.

* Making checkstyle happy.

* Making sure that all tests are passing.

* Passing all tests after fixing Msg.code

* Passing all tests.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)

* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete

* created unit test for skip of delete operation while processing duplicating create entries

* moved unit test to FhirSystemDaoR4Test

* 3379 mdm fixes (#3906)

* added MdmLinkCreateSvcimplTest

* fixed creating mdm-link not setting the resource type correctly

* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on

* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java

Change order of tests such that assertEquals takes expected value then actual value

Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* added changelog, also changed a setup function in test to beforeeach

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* Fix to the issue (#3855)

* Fix to the issue

* Progress

* fixed the issue

* Addressing suggestions

* add response status code to MethodOutcome

* Addressing suggestions

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)

* Respect caching in bullk export, fix bug with completed date on empty jobs

* add changelog

* Add impl

* Add breaking test

* Complete failing test

* more broken tests

* Fix more tests'

* Fix paging bug

* Fix another brittle test

* 3915 do not collapse rules with filters (#3916)

* do not attempt to merge compartment permissions with filters

* changelog

* Rename to IT for concurrency problems

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Version bump

* fix $mdm-submit output (#3917)

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Gl3407 bundle offset size (#3918)

* begin with failing test

* fixed

* change log

* rollback default count change and corresponding comments

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Offset interceptor now only works for external calls

* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.

* do not reindex searchparam jobs on startup

* Fix oracle non-enterprise attempting online index add (#3925)

* 3922 delete expunge large dataset (#3923)

* lower batchsize of delete requests so that we do not get sql exceptions

* blah

* fix test

* updated tests to not fail

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* add index

* Fix up colun grab

* Revert offset mode change

* Revert fix for null/system request details checks for reindex purposes

* Fix bug and add test for SP Validating Interceptor (#3930)

* wip

* Fix uptests

* Fix index online test

* Fix SP validating interceptor logic

* Updating version to: 6.1.1 post release.

* fix compile error

* Deploy to sonatype (#3934)

* adding sonatype profile to checkstyle module

* adding sonatype profile to tinder module

* adding sonatype profile to base pom

* adding final deployToSonatype profile

* wip

* Revert version enum

* Updating version to: 6.1.1 post release.

* Add test, changelog, and implementation

* Add backport info

* Create failing test

* Implemented the fix, fixed existing unit tests

* added changelog

* added test case for no filter, exclude 1 patient

* wip

* Add backport info

* Add info of new version

* Updating version to: 6.1.2 post release.

* bump info and backport for 6.1.2

* Bump for hapi

* Implement bug fixes, add new tests (#4022)

* Implement bug fixes, add new tests

* tidy

* Tidy

* refactor for cleaning

* More tidying

* Lower logging

* Split into nested tests, rename, add todos

* Typo

* Code review

* add backport info

* Tidy versionenum

* Fix import

* Remove files that were repackaged

Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
2022-09-15 22:18:32 +00:00
Tadgh cb3cc1f434
Iam opensearch auth (#4011)
* Bump HS version, add support for credential provider

* License files

* Use index settings file instead of injecting a template at boot

* Changelog

* Typo

* fix logs

* Add javadoc
2022-09-09 23:24:06 +00:00
jdar8 c647154777
Everything operation with type param code review fixes (#3926)
* check for valid resource type

* add test and refactor test class

* refactor auto get method name

* introduce parameter object to patient everything methods

* introduce parameter object to patient everything methods

* change record to class

* add hapi error code

* refactor

* refactor

* change code num

* refactor getmethodname to util method

* add docs and rename fields to conform to fhir standard

* typo

* version bump

* resolving merge conflicts.

* Bumping version

* Bumping version to 6.2.0-PRE5-SNAPSHOT

* Encapsulating parameters in a PatientEverythingParameters object.

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-09-07 06:44:36 -04:00
Kai Kewley dd5c49a9ef
Add support for ICD-10 International Version (Fixes #3734) (#3849)
* Update CLI upload examples for R4.

* Fixes #3734 Add support for ICD-10 (International)

Include all concept properties in ICD-10 loader.

Remove newlines and tabs from ICD Rubrics.

* Bump Msg code and use in Term Loader.

* Added a changelog entry for this addition.

* Update icd10-dummy-test-en.xml

* Added a default impl to the new interface method to avoid breaking upstream projects.

Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com>
Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: Kevin SmileCDR <kevinsmilecdr@Kevins-MacBook-Pro-2.local>
2022-09-06 09:11:45 -04:00
Ken Stevens 100b8f9190
batch2 rework (#3964)
* consolidated Batch2Helper
check status in assert before running maintenance
ignore illegal job instance state transition

* Fix mock tests

* rename intermittent to IT

* extra logging

* into to debug

* review feedback

* added more logging

* removed fasttracking.  replaced with support for triggering a maintenance run

* fixed tests

* fixed tests

* add asserts

* licenses

* snakeyaml cve version bump

* data migration

* merge origin/master

* merge origin/master

* fix test (support triggering jobs when scheduling is disabled)

* add counter to abort potential infinite loop after 100000 calls

* compile error

* move multipartition mdm tests out to a separate IT
update mongo job instance creation with new logic

* fix race condition

* back out infinite loop circuit breaker.  it breaks terminology tests that depend on this loop running > 100000 times.

* fix test (triggered job key was missing group)

* revert saveAllDeferred

* Almost finished getting JpaPersistenceR4IT to pass

* testBulkExportDeleteForOnGoingJob still not passing

* testBulkExportDeleteForOnGoingJob still not passing

* Removed method `fetchInstanceAndMarkInProgress`.  It was clobbering other state transitions like CANCELLED.

* undo rename of cancelled to cancelRequested.  Thymeleaf depends on the old name

* ExpandResourcesStep requires a synchronous search

* Tests are passing but man testBulkExportDeleteForOnGoingJob is a flakey test

* fix test

* fix test

* change log

* allow ERRORED -> FAILED state transition

* add a timeout to saveAllDeferred()

* improve error message on timeout message

* fix tests

* added more logging

* added more logging

* fix semaphore issue

* Msg.code

* fix test

* javadoc

* switch all batch loggers to batch troubleshooting log

* add unit test, improve logging

* move TimeoutManager to its own class.  Add tests.

* fix tests

* comment cleanup

* test race condition

* review feedback

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-09-05 00:04:54 -04:00
Ken Stevens 68c343902a
jpa test split (#3959)
* create fhir-version specific hapi-fhir-jpaserver-test projects

* moved dstu2 tests out to dstu2 test project.

* moved dstu2 tests out to dstu2 test project.

* finished moving dstu2 tests out to dstu2 test project.

* finished moving dstu2 tests out to dstu2 test project.

* dstu3 test project compiles

* start moving dstu3 resources

* letting azure pileine know about the new modules

* finished moving dstu3 resources.  this might pass

* OK this one should pass for sure

* OK this one should pass for sure

* change test poms to test scope

* move the rest of R4 test classes

* move the rest of R4 test classes

* moar r4 moves

* moar r4 moves

* moar r4 moves

* finished with r4

* finished with r4

* started r5

* started r5

* Cache busting based on source branch name

* Fix other cache key

* cache pegged to SHa1

* test cleanup

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-09-01 02:46:17 +00:00
Ken Stevens 26ca950bce
Checkstyle Abstract Class Name (#3966)
* init rev

* checkstyle enforce abstract classes start with "Base" (and vice versa)

* checkstyle enforce abstract classes start with "Base" (and vice versa)

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-08-30 22:15:32 -04:00
StevenXLi 65d4fe81ad
3947 support http delete for operation $export poll status (#3961)
* Added failing test, and the methods that are necessary to not break the build

* Implemented solution to cancel jobs via delete request for poll status

* change log added

* change log name change to pass test

* Changed implementation to work with existing infrastructure

* code review changes

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-08-30 11:30:03 -04:00
Tadgh b9caec1c42
Rel 6 0 mb 3 (#3933)
* adding version.yaml, updating version in pom.xml

* It is possible to write to a resource in a partition the user is not authorized to. (#3397)

* fixed

* remove sout

* add msg.code

* fix failed tests

* fix equal sign

* update msg code

* extract method

* Fix up code numbers

* Clean changelog

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Revert final artifact version

* add graphql test (#3585)

* added graphql birthdate test

* fix variable name

* typo

* 3506 mdm log enhancement (#3543)

* Providing Fixme's to be reworked at a later time.

* Adding // FIXME Anna to assist our Austrian friend.

* Adding logging test as a first step in addressing issue #2822.

* hapifhir#3506 part 2: enhance logging for (un)successful MDM matching

hapifhir#3506 part 2: enhance logging for (un)successful MDM matching

* Update MdmMatchLinkSvc.java

#3506 move "narrowed down" log to different place

* #3506 added scores and tests

#3506 added scores and tests

* #3506 formatting

#3506 formatting

* #3506 create changelog file

#3506 create changelog file

* #3506 fix typo

#3506 fix typo

* #3506 fix part 3, minor formatting

#3506 fix part 3, minor formatting

* #3506 fix tests

#3506 fix tests

Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>

* mdm matching (#3579)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

* begin with failing test

* fixed

* changelog

* add jira tag

* Update to 6 1 (#3582)

* added changelog folder, upped version

* version enum

* add a few more unit tests to assert proper NO_MATCH exclusion

* revert merge master doh! bad reflexes

* revert merge origin master

* unrevert revert.  ugh what a pain

* merge recovery.  fix poms.

* merge recovery.  more reverting

* merge recovery.  more reverting

* merge recovery.  more reverting

* Revert "merge recovery.  fix poms."

This reverts commit ae6e0ddb06.

* more revert revert reversions

* more revert revert reversions

* pre-review cleanup

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>

* Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586)

* When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller.

* License

* Ks 20220508 log colour (#3592)

* don't use colours when output is redirected to a file

* change log

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

* 3584 case sensitive string elasticsearch (#3596)

* Fix for case-sensitive search with newer elasticsearch

* Test and fix ascii normalization too

* more test cases

* comments

* Docs update empi usecase (#3598)

* Update diagram for use case 5

* Add new page for database support

* Licnese

* Mb norm fix (#3604)

* Normalize query since wildcard searches aren't normalized in elastic

* Handle batch2 job cancellation (#3603)

* Handle batch2 job cancellation

* Add CANCELLED status

* Remove unuseful test

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Add batch2 interfaces to obtain recent instances (#3601)

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* changelog folder

* Documentation change, added warning log and change log for ticket (#3609)

Co-authored-by: Steven Li <steven@smilecdr.com>

* fix ne for lastUpdated search param (#3589)

* init/wip

* add implementation, add tests

* add checks and some refactoring

* refactor and simplify tests

* refactor

* get rid of some of the warnings

* add changelog

* remove my todos

* redo ne logic to account for less precise dates

* add tests

* refactoring

* rename to follow convention

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>

* Version bump

* Add skip of checkstyle to upload

* Typo

* upping version enum, upping version number, 6.0.1

* Group Bulk Export rules exiting too early.  (#3643)

* Implementation, test, changelog

* Add jira link

* adding backport in yaml for 3642

* adding folder for 6.0.1 release

* pom changes to publish checkstyle to sonatype

* bad version in pom file

* Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider

* AUtomcplete error code

* updating comment indicating final erorr code

* Bump error code

* fixing version enum so release docs generate correctly, adding additional changelog for 3650

* 3684 subscription for delivering delete events formatted wrong (#3685)

* Fixed issue with delivering delete events Subscriptions

* Extracted deliverer class name to a constant, now shared across tests and interceptor class

* Added change log and doc changes

* moved the constant to a more appropriate place

Co-authored-by: Steven Li <steven@smilecdr.com>

* Version bump

* Add version enum

* Version enum and folder

* adding release pipeline yml file fo azure

* Adding autoclose for sonatype publishing (#3797)

* Add impl test and changelog (#3713)

* fix up changelog, new version

* Version bump

* Updating version to: 6.0.4 post release.

* reverting 6.0.4 commit

* Updating version to: 6.0.4 post release.

* removing double entry from preious release

* Add support for DSTU3 delete subscrion events, add test

* Add changelogP

* Add version enum

* Remove notnull

* Add test for DSTU2

* Updating version to: 6.0.5 post release.

* Fix up

* wip

* Adding solution and changeLog file.

* Adding failing test.

* fix up

* Version bump

Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
2022-08-30 02:29:02 +00:00
James Agnew 5509bd053d
Move partition interceptor (#3907)
* Add license headers

* Move partition interceptor

* More cleanup

* One more tweak

* Headers

* Add changelog

* Test logging enhancement

* Test fix

* Test fixes

* Add test method
2022-08-29 13:42:10 +00:00
Mark Iantorno caf370da31
Azure Pipelines Overhaul (#3948)
This PR changes the way HAPI is built by Azure pipelines. Instead of a FIFO queue for all tests in the project, the entire project is quickly built and cached without testing, then the individual modules are built and tested in separate jobs which can be run in parallel from each other. Each of these jobs then uploads the test coverage for that module as a build artifact. Finally, a last stage downloads all the archived tests results and aggregates them using jacoco so they can be uploaded to codecov.

This has two key benefits:

    If there is a failing test because of an intermittent, the individual failing module can be re-run instead of having to re-run the whole project build.
    The build time is decreased substantially (90min -> 45min).

This is the first run at this, I will be iterating to further reduce build times going forward.
2022-08-24 12:55:00 -04:00
Etienne Poirier b5f5cd3e75
3937 searching for resources with a target resource parameter in include fail (#3938)
* Adding failing test.

* Adding solution and changeLog file.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-08-22 08:23:35 -04:00
Tadgh e7a4c49aac
Rel 6 1 mergeback (#3927)
* Bump for CVE (#3856)

* Bump for CVE

* Bump spring-data version

* Fix compile

* Cut over to spring bom

* Bump to RC1

* remove RC

* do not contrain reindex for common SP updates (#3876)

* only fast-track jobs with exactly one chunk (#3879)

* Fix illegalstateexception when an exception is thrown during stream response (#3882)

* Finish up changelog, minor refactor

* reset buffer only

* Hack for some replacements

* Failure handling

* wip

* Fixed the issue (#3845)

* Fixed the issue

* Changelog modification

* Changelog modification

* Implemented seventh character extended code and the corresponding dis… (#3709)

* Implemented seventh character extended code and the corresponding display

* Modifications

* Changes on previous test according to modifications made in ICD10-CM XML file

* Subscription sending delete events being skipped (#3888)

* fixed bug and added test

* refactor

* Update for CVE (#3895)

* updated pointcuts to work as intended (#3903)

* updated pointcuts to work as intended

* added changelog

* review fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)

* Add test and implementation

* Add changelog

* 3899 code in limits (#3901)

* Add implementation, changelog, test

* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

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

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

* 3884 overlapping searchparameter undetected rel 6 1 (#3909)

* Applying all changes from previous dev branch to current one pointing to rel_6_1

* Fixing merge conflict related to Msg.code value.

* Fixing Msg.code value.

* Making checkstyle happy.

* Making sure that all tests are passing.

* Passing all tests after fixing Msg.code

* Passing all tests.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)

* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete

* created unit test for skip of delete operation while processing duplicating create entries

* moved unit test to FhirSystemDaoR4Test

* 3379 mdm fixes (#3906)

* added MdmLinkCreateSvcimplTest

* fixed creating mdm-link not setting the resource type correctly

* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on

* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java

Change order of tests such that assertEquals takes expected value then actual value

Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* added changelog, also changed a setup function in test to beforeeach

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* Fix to the issue (#3855)

* Fix to the issue

* Progress

* fixed the issue

* Addressing suggestions

* add response status code to MethodOutcome

* Addressing suggestions

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)

* Respect caching in bullk export, fix bug with completed date on empty jobs

* add changelog

* Add impl

* Add breaking test

* Complete failing test

* more broken tests

* Fix more tests'

* Fix paging bug

* Fix another brittle test

* 3915 do not collapse rules with filters (#3916)

* do not attempt to merge compartment permissions with filters

* changelog

* Rename to IT for concurrency problems

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Version bump

* fix $mdm-submit output (#3917)

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Gl3407 bundle offset size (#3918)

* begin with failing test

* fixed

* change log

* rollback default count change and corresponding comments

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Offset interceptor now only works for external calls

* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.

* do not reindex searchparam jobs on startup

* Fix oracle non-enterprise attempting online index add (#3925)

* 3922 delete expunge large dataset (#3923)

* lower batchsize of delete requests so that we do not get sql exceptions

* blah

* fix test

* updated tests to not fail

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* add index

* Fix up colun grab

* Bump Version for non-breaking purposes

* Fix broken test

* bump error code

* revert internal logic

* Revert offset mode change

* wip

* Revert fix for null/system request details checks for reindex purposes

* Fix bug and add test for SP Validating Interceptor (#3930)

* wip

* Fix uptests

* Fix index online test

* Fix SP validating interceptor logic

Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-08-18 17:21:27 -07:00
MykolaMedynskyiSCDR 64e1f4d381
Fixing response message when deleting non-existing or deleted resource. (#3898)
* Fixing response message when deleting non-existing or deleted resource.

* Changed names of properties.

* The full ID shown in message, not just IdPart
2022-08-11 16:37:12 -07:00
michaelabuckley 60a879c842
Renable elasticsearch tests (#3850)
* Renable elasticsearch tests

Limit elasticsearch container to 512MB instead of the default 4GB.
2022-08-07 07:09:12 +00:00
jmarchionatto a5c4b0756b
Fallback direct resource HSearch to JPA when resources are not found … (#3823)
* Fallback direct resource HSearch to JPA when resources are not found in index

* Use specific exception instead of identifying it by the message

* Add Message code to exception

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-08-05 16:39:00 +00:00
jmarchionatto ebac65cb31
Add simple local implementation of UCUM temperature canonicalization … (#3872)
* Add simple local implementation of UCUM temperature canonicalization for Celsius and Fahrenheit

* Adjust conversion to not increase precision, as it matter when finding ranges

* Simplify test variables

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-08-05 14:48:37 +00:00
jmarchionatto 2e1f4c25f5
Make sure that direct resource load path is only executed for synchro… (#3833)
* Make sure that direct resource load path is only executed for synchronous searches

* Remove unneeded mockito extension

* Only allow for resource loading from fulltext index when advanced search (indexed parameters) is also enabled

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-08-04 22:19:06 +00:00
Patrick Werner b026ac10e5
Bump fhir.core to latest version (#3593)
* adding version.yaml, updating version in pom.xml

* It is possible to write to a resource in a partition the user is not authorized to. (#3397)

* fixed

* remove sout

* add msg.code

* fix failed tests

* fix equal sign

* update msg code

* extract method

* Fix up code numbers

* Clean changelog

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Revert final artifact version

* add graphql test (#3585)

* added graphql birthdate test

* fix variable name

* typo

* 3506 mdm log enhancement (#3543)

* Providing Fixme's to be reworked at a later time.

* Adding // FIXME Anna to assist our Austrian friend.

* Adding logging test as a first step in addressing issue #2822.

* hapifhir#3506 part 2: enhance logging for (un)successful MDM matching

hapifhir#3506 part 2: enhance logging for (un)successful MDM matching

* Update MdmMatchLinkSvc.java

#3506 move "narrowed down" log to different place

* #3506 added scores and tests

#3506 added scores and tests

* #3506 formatting

#3506 formatting

* #3506 create changelog file

#3506 create changelog file

* #3506 fix typo

#3506 fix typo

* #3506 fix part 3, minor formatting

#3506 fix part 3, minor formatting

* #3506 fix tests

#3506 fix tests

Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>

* mdm matching (#3579)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

* begin with failing test

* fixed

* changelog

* add jira tag

* Update to 6 1 (#3582)

* added changelog folder, upped version

* version enum

* add a few more unit tests to assert proper NO_MATCH exclusion

* revert merge master doh! bad reflexes

* revert merge origin master

* unrevert revert.  ugh what a pain

* merge recovery.  fix poms.

* merge recovery.  more reverting

* merge recovery.  more reverting

* merge recovery.  more reverting

* Revert "merge recovery.  fix poms."

This reverts commit ae6e0ddb06.

* more revert revert reversions

* more revert revert reversions

* pre-review cleanup

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>

* Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586)

* When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller.

* License

* added support for OO.issue.details from Java RI Validator

* remove duplicated Msg.code

* Ks 20220508 log colour (#3592)

* don't use colours when output is redirected to a file

* change log

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

* 3584 case sensitive string elasticsearch (#3596)

* Fix for case-sensitive search with newer elasticsearch

* Test and fix ascii normalization too

* more test cases

* comments

* Docs update empi usecase (#3598)

* Update diagram for use case 5

* Add new page for database support

* Licnese

* Mb norm fix (#3604)

* Normalize query since wildcard searches aren't normalized in elastic

* removed duplicated dependency with wrong version

* fixed test file(added a Base64 string)

* fixed tests

* fixed test:
history?_since is an instant

* removing time from date-strings in examples

* fixed more instant strings

* changed filtering of messages to messageId

* fixed messageId filter on missing profiles

* changed messageID system string to Grahames preferred String

* updated MsgIds of unsupported methods

* removed fixed commons-codec version as fhir.core uses commons-codec:1.15
This will introduce issues with the android built.

* fixed GraphQL Test

* fixing test issue caused by different message string, switch to details code assertion

* fixing test issue caused by different message string, switch to details code assertion

* updated Msg.codes

* updated Msg.codes

* fixed duplicated Msg.codes

* setErrorOnInvalidValue set to false in test

* reverted date precision test changes

* updated r5 resources to latest build version

* updated to latest snapshot, https://github.com/hapifhir/org.hl7.fhir.core/issues/884 causes test failures.

* Try to fix message codes

* Test fixes

* Checkstyle fix

* Test fix

* Try to avoid CME

Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-08-03 16:12:59 -04:00
TipzCM eae1c0ffb8
3846 migrate bulk import pull to batch2 (#3853)
* still fixing tests

* migrated a bulk import pull job t obatch 2

* changelog

* cleanup

* review fixes

* minor tweaks

* cleaningup

* tra la la

* blah

* blah

* updating msg

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-08-03 10:50:51 -04:00
Tadgh dcfaf42e73 add new version enum, bump version, new folder 2022-08-02 21:46:20 -07:00
jdar8 5f1c50a6b8
everything operation with type param (#3842)
* wip+test

* wip, rough implementation

* clean up

* clean up

* clean up unused methods

* Completing implementation.

* Removing TODO.

* Replacing toList() with Collectors.toList()

* support other fhir versions and everything instance

* tests wip

* tests for instance

* Adding default methods in interface

* add testsss

* Removing @Deprecated.

* fix spacing

* changelog

* reword changelog

* Removing default methods from interface.

* Bumping version to 6.1.0-PRE28-SNAPSHOT

* Adding parameter to method call following interface modification.

* Fixing documentation and parameter order for consistency.

* Bumping version to PRE30.

* Providing backward compatibility.

* fix pom

* licences

* Fixing pom dependencies.

* Fixing more pom dependencies.

* Fixing dependencies for test-utilities.

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-08-02 20:51:37 -07:00
Nathan Doef e2bed96d74
3776 add https support for hapi fhir cli using tls (#3777)
* wip functional
TODO
- add tests
- look at adding TLS to other RestfulClientFactory classes (FhirwebRestfulClientFactory, JaxRsRestfulClientFactory, OkHttpRestfulClientFactory)

* move BaseRestServerHelper to Hapi-Fhir

* - add TLS support for JaxRsClient and OkHttpClient
- add tests

* -  to use resources and files

* -  ci fixes

* -  ci fixes

* -  ci fixes

* -  ci fixes

* - refactor and tests

* - ci fixes

* - tests

* - tests

* - tests / refactor

* - clean up

* - changelog

* - remove OkHttpClient HTTPS support

* - ci

* - Ken's code review changes

* - Ken's code review: method renaming

* - Ken's code review: javadoc

* - Code coverage

* - Create HapiFhirCliRestfulClientFactory to encapsulate new HTTPS functionality. Remove modifications to the FhirContext API.

* - version bump

* - fix unable to bind port errors by using Jetty functionality to assign random ports

* Revert "- version bump"

This reverts commit cfce82576a.

* - version bump

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-08-02 09:27:02 -04:00
David 8740c10ed9
Fix 3840 broken test (#3862)
* added a paging api to ijobcoordinator

* adding changelog

* moved location

* added a comment

* Added Sort parameter to JobInstanceFetchRequest

* Bump HAPI-FHIR version

* Updated JPA api to include sort

* Add changelog

* Fix test

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: David Chen <david.chen@smilecdr.com>
2022-07-29 11:05:55 -06:00
David be0b6f1a0b
3840 add sort parameter to fetching jobs (#3861)
* added a paging api to ijobcoordinator

* adding changelog

* moved location

* added a comment

* Added Sort parameter to JobInstanceFetchRequest

* Bump HAPI-FHIR version

* Updated JPA api to include sort

* Add changelog

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: David Chen <david.chen@smilecdr.com>
2022-07-29 09:12:53 -06:00
longma1 f933ff3d9c
2878 mdm mongo support (#3748)
* small refactor

* refactored MDM module to use iterface IMDMLink, refactored MDMLink to use ResourcePersistenceId wrapper rather than pid as long

* removing IJpaIdHelperService and refactor IIdHelperService

* fixed bugs for GoldenResourceMergerSvcImpl and FindCandidateByExampleSvc

* changes to IIdHelperService

* move MdmSearchParamSvc and MdmSubmitSvcImpl out of jpaserver-mdm

* moved JpaResourceLoader to hapi-fhir-storage, renamed to ResourceLoaderImpl

* added error Msg code, removed Fixme

* fixed error code, update last used code in Msg.java to 2083

* fixed accidentally throwing unprocessableentityException

* added MdmLinkExpandSvc interface

* build adding license to files

* MdmLinkdao refactor

* fix build

* mdm config refactoring

* MdmStorageInterceptor and IExpungeEverythingService changes

* fix bug where a pid is converted to ResourcePersistenceId twice

* minor refactor to IMdmLink, change id from long to ResourcePersistenceId

* changed PageImpl to Page interface

* refactor MdmSearchExpandingInterceptor to use interface

* fixed missed refactor where the resourcePersistenceId is still assumed to be long

* resolve test failures resulting from merging master

* changed conflicting exception code

* fixed issue with bulk export wrapping resourcePid inside resourcePersistenceId

* added IMdmLinkImpl to MdmSettings

* fixed missing import in IdHelperService from merging master

* fixed MdmLinkDaoSvcTest importing wrong MdmLinkTuple

* restored JpaIdHelperService and added changelog

* modified msg.code to non-duplicate

* code review changes

* refactored some bulk export batch 2 files to accomodate change in beans being exported

* fixed jpa bulk export failing tests

* removed duplicate bean declaration of MdmLinkImplFactory in BaseMdmR4Test

* merged master and bump version to pre25

* extracted expungeEverythingByType to IExpungeEverythingService

* fixed wiring issue

* messed up merging pom with master

* fixed broken changelog

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Samuel Lee <samuel.lee@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-29 08:58:40 -06:00
jmarchionatto 5586b325ce
Issue 3857 elastic lucene search returns only 50 results when offset0 and count100 (#3858)
* Add logback definition to project to stop debugging all output

* Fix limit definition to include _offset=0 case

* Move test required resources from previous test module

* Add changelog

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-07-28 19:09:31 -04:00
TipzCM 9a1d6f3172
3821 term code system batch jobs (#3826)
* step one

* blah

* no working test

* updated existing tests

* delete code system version and code system jobs

* trying to get terminology fixed

* updating tests

* need to have some movement

* added completion handler

* added clearing code for failsafe

* review points

* fixing tests

* fixing tests

* more test fixes

* fixing more tests

* review fixes

* todo

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-07-27 14:50:42 -04:00
TipzCM 59540ce803
3813 paging job coordinator (#3814)
* added a paging api to ijobcoordinator

* adding changelog

* moved location

* added a comment

* blah

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-07-26 11:29:37 -06:00
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
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
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
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
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
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
Gjergj Sheldija 4684dde6a6
add `displayLanguage` to the `ValueSet/$expand` (#3619)
* add `displayLanguage` to the `ValueSet/$expand`

* fix tests

* fix tests
2022-07-12 15:54:29 -04:00
Tadgh 57ee93251a
Mergeback 2022 07 08 (#3771)
* fix handling of common search parameters

* Revert "fix handling of common search parameters"

This reverts commit 89c45eebdc.

* Fix implementation, add test (#3378)

* Fix implementation, add test

* Tighten test

* Rip out dead modules

* Add changelog

* Jr 20220210 handle common search params in contained searches (#3377)

* fix handling of common search parameters

* add support for reference search parameters with multiple paths

* Issue 3357

* Version bump

* Fixed null pointer exception for re-loading subscription on cdr restart and when there's no partition id in the request, and added tests

* added changelogs for this fix

* Fix broken changelog file

* Can't specify specific resource type permissions for bulk export (#3376)

* deny user from exporting without perms

* add unit tests

* add changelog

Co-authored-by: olivia-you <olivia.you@smilecdr.com>

* Make migration donothing as it was added in error

* Remove ehcache

* Add version.yaml:

* Add to sources/javadocs for dist

* Fix typo

* fix up pom

* wip test removing checkstyle plugin from deployable pom

* remove test pom changes, instead just dont deploy to sonatype

* typo

* Version bump

* Add implementation, testing, and changelog

* Add backport info, make aware of 6_0_0

* add jira ref

* Fix test

* Add versionenum

* Bump dep for spring, add changelog, add versionenum, add changelog folder

* Actually do the version bump

* 3654 postgres lobs (#3656)

* Implementation, test, changelog

* Modify changelog

* Fix changelog

* Add upgrade.md file

* Modify to yaml changes

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_3/3654-lob-problems.yaml

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

* tidy

* more work

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

* Fix bad yaml indent

* Version bump

* Back out the reindex changes introduced in 5.7.3

* update changelog

* version bump

* added fix for subscription in default partition when default partition's id is null

* added changelog

* Add version info and changelog folder

* adding release pipeline yml file fo azure

* Fix parameter count limitation on MSSQL/Oracle large transactions (#3075)

* Fix parameter count limitation on MSSQL/Oracle large transactions

* Changelog fix

* Move changelog

* Force a change to trigger CI

* Test refactoring

* Backport oracle fix

* Fix backport

* upping version to 5.7.5 for release

* add versionenum

* Updating version to: 5.7.6 post release.

* Add query-chunk-aware code

* Add new folder

* Fix up versionenum

* Remove imports

Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-07-12 11:08:46 -07:00
StevenXLi 2bc6c91153
3719 enable map response terminology for bulk export (#3735)
* added failing test for Map Response Terminology for bulk export

* moved logic for terminology translation out of the interceptor to svc, added translation logic to bulk export file writer, added more tests

* added changelog

* Wip refactor dependency fix

* wip terminology translation code refactor

* terminology translation code refactor

* refactor clean up

* Remove circular dependency

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3719-enable-map-response-terminology-for-bulk-export.yaml

* bump version of hapi to 6.1.0-PRE7-SNAPSHOT

* doc update

* fix issue when search param registry doesn't contain search param for the resource type

* fix beans

* hapi version bump from PRE7 to PRE10

* doc update

* add ResponseTerminologyTranslationSvc as a constructor variable to the interceptor

* fixed ResponseTerminologyInterceptorLoaderTest, added IT for cdr side

* version bump to PRE13

* removed unused import

Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-12 12:24:15 -04:00
Ken Stevens 0526da080b
3757 move delete expunge to batch2 (#3759)
* begin with failing test

* begin with failing test

* remove unused Spring Batch classes.
convert service classes

* move provider

* just one test left to fix

* fix test

* msg.code

* change log

* bumping hapi to PRE12

* fix test

* review feedback

* license update

* fix intermittent and status update atomicity

* restore url-level partition selection

* fix tests

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-09 17:25:55 -04:00
Ken Stevens 839a1b53e9
fix batch intermittent and status update atomicity (#3773)
* fix intermittent and status update atomicity

* change log

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-09 08:51:04 -04:00
James Agnew 61d34ab695
Add license headers (#3765) 2022-07-07 17:22:38 -04:00
michaelabuckley 7cf447cda1
Implement query filter auth via tester (#3758)
Use tester instead of new subclass to implement fhir filtering.

The subclass was too complicated to be trusted for authorization.
2022-07-07 16:15:17 +00:00
michaelabuckley 616a126fad
Change the IAuthRuleTester api to a parameter object. (#3756)
* Try using tester to implement fhir filtering.
2022-07-06 02:08:45 +00:00
Nathan Doef b68ccb373a
3693 Search by id is returning a deleted resource with a client-generated id (#3694)
- Added functionality to optionally filter out deleted resources when resolving forced ids to persistent ids
- Bumps version

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-05 12:37:25 -04:00
Ken Stevens 3a28920ea7
Add error-handler callback and ensure batch2 completion handler can't be called twice (#3752)
* rename field that drives everything includes

* discovered design flaw in completion

* fix intermittent

* ensure batch2 completion handler can't be called twice

* changelog

* changelog

* javadoc

* bump hapi version

* licences

* Batch2 job definitions can now optionally provide an error handler callback that will be called when a job
instance fails, errors or is cancelled.

* Changed error handler and completion handler to take a "read-only" copy of an instance instead of just certain fields.

* comment

* javadoc

* fix test

* change step execution context from taking instance id to instance

* review feedback

* fix test

* replace 20 or so jetbrains annotations

* fixed a few incorrect @NotNull annotations

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-04 23:27:58 -04:00
michaelabuckley a13f2411a1
Implement direct HSearch search path (#3727)
* 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

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-07-04 22:18:29 +00:00
JasonRoberts-smile c073c0eeb4
ConformanceStatement generation for DSTU3 is out of date (#3737)
* add system SPs to resource

* populate include list

* wip

* wip

* Tighten test

* Chaneglog

* Use old-style collectors

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-06-30 23:42:14 +00:00
michaelabuckley 9aac4f9ba8
Introduce memory-matcher based rules (#3677)
Extend rules with filters.

New rule extension, and consent service for post-query filtering.

Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-06-29 18:23:12 +00:00
Ken Stevens 069f20a5f7
batch2 management operations api (#3742)
* first test passes.  onto the next one

* two down two to go

* three down one to go

* licenses

* basic admin-json plumbing confirmed with IT

* FIXME

* FIXME

* FIXME

* FIXME

* changelog

* bump hapi version to 6.1.0-PRE6-SNAPSHOT

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-28 23:02:17 -04:00
jmarchionatto 84fe58cc86
Hsearch namespace consolidation (#3733)
* Initial implementation

* Implement job cancellation

* Works for date and token. Cleanup required.

* Works for string and quantity.Cleanup pending.

* Works for reference and perform cleanup.

* Cleanup configuration and add missing tests

* Eliminate sort property registry (no go for a cluster) for a static property map.

* Missed in previous commit

* Implement HSearch number parameter

* Implement HSearch number sorting

* Unify different hibernate search names (HibernateSearch, Freetext and Lucene) to HSearch

* Move analysis configures for lucene and elastic to same file to enforce the need to keep them in synch

* Use new defined constant

* Rename package too

* Rename additional elastic references

* bump version to 6.1.0-PRE5-SNAPSHOT

* Restore Hap prefix to hapi configurers

* fixing hapi version of new maven module

* fix pom

* fix pom

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-28 18:38:05 -04:00
Ken Stevens 49d298dba1
mdm clear move to batch2 (#3671)
* begin with failing test

* continue building out

* continue building out

* reworking chunk api

* replace ChunkId zippers with proper iterator

* progressing test

* yay test passes!

* switch to idchunk interface

* fixmes

* compiles

* fixme

* fixme

* rename classes

* rename json classes with json suffix

* work towards homogeneous chunks

* fixme

* fixme

* unit test

* fixme

* fixme

* pull out builder

* moar tests

* moar tests

* preserve order

* moar test

* moar test

* fixme

* fixme -> wip to start ci

* msg code

* msg code fix test

* fixme

* change provider implementation

* final WIPs

* IT failing

* IT passes

* java 11

* fix test

* fix test

* fix test

* changelog

* use batch size if provided

* last WIP

* fix test

* fix test

* fix test

* whitespace change to trigger new build

* fix test

* bumping hapi version

* bumping hapi version

* fix test

* review feedback

Co-authored-by: Ken Stevens <ken@Kens-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-25 20:26:44 -04:00
jdar8 ac006ba7d7
Unknown resource type error message contains plain providers (#3711)
* fix and test

* change stream

* change variable name

* modify test

* changlog

* changlog

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
2022-06-22 14:26:15 -04:00
jmarchionatto e7ce41e5b8
Freetext search sort (#3695)
* Works for date and token. Cleanup required.

* Works for string and quantity.Cleanup pending.

* Works for reference and perform cleanup.

* Cleanup configuration and add missing tests

* Eliminate sort property registry (no go for a cluster) for a static property map.

* Missed in previous commit

* Implement HSearch number parameter

* Implement HSearch number sorting

* Replicate new normalizer configuration from HapiElasticsearchAnalysisConfigurer to HapiLuceneAnalysisConfigurer.
Replace deprecated word filter factory

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-06-22 10:31:01 -04:00
Qingyixia dce330eb01
Fix to the issue (#3723) 2022-06-21 16:29:35 +00:00
TipzCM 48c28997e6
3662 batch2 reduction step (#3681)
* adding a bunch of stuff

* most of the steps are working now

* writing more tests

* adding more tests

* updated the batch2 coordinators

* updating version

* some minor test tweaks

* added a new test

* adding more tests

* blah

* blah

* review fixes 1

* fixing tests and refactoring

* review points

* updated for code review

* review fixes

* updated

* step 1 on review step 5

* final touches

* blah

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-20 18:59:01 +00:00
Ken Stevens 427bdf330e
fix 403 on updates when version submitted without rewrite header (#3716)
* fix 403 on updates when version submitted without rewrite header

* change log

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-17 19:51:47 +00:00
Tadgh 4fbbf4366c
Add impl test and changelog (#3713) 2022-06-16 21:11:15 -04:00
James Agnew ac8f4f1e56
Apply fix from #3270 (#3712)
* Apply fix from #3270

* Rework compare method
2022-06-16 15:46:14 -04:00
StevenXLi 3da39aeda3
3658 adding updating with history rewrite feature (#3659)
* Updating With History Rewrite implementation

* Missed new files

* Updated changelog and documentation

* Fixed test failures and doc

* minor fix

* lgtm code refactor

* Fixed test to clear DaoConfig

* Removed unused class

* Code review changes

* Simplified updateHistoryRewrite's fluent, combining with normal update's, also changed logic on custom header error checking, updated tests

* refactored method to extracted common code

* removed `updateHistoryRewrite()` and replaced with `update()`, updated tests accordingly

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-06-15 12:40:58 -04:00
Tadgh bf2f126c91
Add changelog, add test, add implementation to short-circuit logic in group export (#3701) 2022-06-15 11:22:42 -04:00
Tadgh 1eeb6112f6
Fix Patch in bundle to return Response Entry (#3678)
* Refactor test to cause failure

* Handle patch for entry response building

* add changelog

* Update hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java

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

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-06-13 19:11:18 +00:00
StevenXLi 9336af4b0f
3684 subscription for delivering delete events formatted wrong (#3685)
* Fixed issue with delivering delete events Subscriptions

* Extracted deliverer class name to a constant, now shared across tests and interceptor class

* Added change log and doc changes

* moved the constant to a more appropriate place

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-06-13 18:04:49 +00:00
Etienne Poirier 05cb6c241c
3668 fhir patch operation returning 500 when patching in a transaction with a resource query in property request.url (#3675)
* Initial test exerting the issue.

* Providing fix and changelog

* Providing fix and changelog

* Providing a searchUrl or matchUrl based on the requestUrl.

* Providing fix and changelog

* Modification on test

* Modification on test

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: qingyixia <cherry.xia@smilecdr.com>
2022-06-13 09:15:09 -04:00
Etienne Poirier 868a7e5c40
3637 encapsulation of synchronous query execution capabilities into a new service for reuse (#3638)
* Adding test reproducing the issue.

* Providing implementation fixing the issue and strengthening integrated test.

* Cleaning up commended code.

* Preparing code for review.

* Adding test class SynchronousSearchSvcImplTest.

* Addressing first code review comments.

* Addressing first code review comments.

* Forcing one extra processing step to ensure exit condition is met.

* Adding tests

* Clean up in preparation of second code review.

* Addition of setting page size if required.

* Grouping synch test in nested test class.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-06-05 20:38:53 -04:00
Ken Stevens 4f4032d892
Issue 3648 fix mdm log messages (#3649)
* fix log messages

* fix log messages

* fix log messages

* fix log messages

* fix log messages

* fix log messages

* review feedback and fix log messages

* improved logging

* improved logging
2022-05-26 18:50:17 +00:00
jmarchionatto ad3294f8e8
Freetext search lastupdated param support (#3630)
* Initial implementation

* Implement job cancellation

* Handle uri, _tag, _security and _profile freetext search parameters

* Fix combined 'and' and 'or' clauses and add tests
Use collection instead of typed array to eliminate warnings

* Eliminate predicate nesting level

* Implement _source freetext search

* Implement _lastUpdated freetext search

* add ITestDataBuilder.withLastUpdated(String theIsoDate) method

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-26 18:41:12 +00:00
jmarchionatto 464a07e284
Freetext search tag types support (#3622)
* Handle uri, _tag, _security and _profile freetext search parameters

* Fix combined 'and' and 'or' clauses and add tests
Use collection instead of typed array to eliminate warnings

* Eliminate predicate nesting level

* Add changelog

* Implement revision suggestions

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-26 15:59:39 +00:00
jmarchionatto 4eb099b900
Freetext search source parameter support (#3641)
* Handle uri, _tag, _security and _profile freetext search parameters

* Fix combined 'and' and 'or' clauses and add tests
Use collection instead of typed array to eliminate warnings

* Eliminate predicate nesting level

* Implement _source freetext search

* Implement suggestions

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-25 20:07:29 +00:00
Ken Stevens fb6e5cf6ce
Batch 2 Maintenance refactor (#3631)
* SRP refactor maintenance

* SRP refactor maintenance

* cache jobDefinition in jobInstance when processing (rather than looking it up in a bunch of different places)

* begin with failing test

* test passes

* tests pass.  still need to add a few more tests

* add comment to trigger new ci

* added positive and negative tests for new behaviour

* fix IJ warnings

* change log

* change log

* fix test race condition

* resolved feedback

* review feedback
2022-05-25 04:16:58 +00:00
Tadgh a19c1ec996
Group Bulk Export rules exiting too early. (#3643)
* Implementation, test, changelog

* Add jira link
2022-05-25 00:14:36 +00:00
JasonRoberts-smile 1c70e97087
fix build failure (#3639)
* fix build failure

* add missing cleanup
2022-05-24 16:24:08 +00:00
JasonRoberts-smile b9579313ef
Jr 20220519 expunge config params (#3627)
* fix config settings for system-level expunge

* clean up expunge everything interface

* extract common system provider

* changelog

* version bump

* touch changelog to force a fresh pipeline

* re-enable publishing of checkstyle

* back out Gary's Sonatype change entirely
2022-05-23 18:55:42 -04:00
Tadgh 3a286c306f
R5 appointment not storing. (#3621)
* Failing test, works on #3459

* Test, changelog

* Remove dead test
2022-05-17 23:31:17 +00:00
Ken Stevens 27024067b0
Batch 2 documentation and SRP cleanup (#3616)
* begin writing documentation.  minor refactor.

* document submitting a job

* single responsibility principle

* single responsibility principle

* single responsibility principle

* reduce method parameter count

* reduce method parameter count

* fix test mocks

* reduce method arguments

* update documentation

* add tests
resolve warnings

* resolve warnings

* moar test

* moar test

* Add @Nonnull and @Nullable annotation to construction parameters

* pre-review cleanup

* pre-review cleanup

* review feedback

* review feedback.  added FIXME

* started writing IT with FIXMES

* started writing IT with FIXMES

* added batch 2 state transition integration tests

* FIXME

* improve readability of test

* improve readability of test

* fix race condition

* pre-merge cleanup
2022-05-17 21:25:43 +00:00
Tadgh 54f578c8b1
Rel 6 0 mergeback (#3597)
* adding version.yaml, updating version in pom.xml

* It is possible to write to a resource in a partition the user is not authorized to. (#3397)

* fixed

* remove sout

* add msg.code

* fix failed tests

* fix equal sign

* update msg code

* extract method

* Fix up code numbers

* Clean changelog

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Revert final artifact version

* add graphql test (#3585)

* added graphql birthdate test

* fix variable name

* typo

* 3506 mdm log enhancement (#3543)

* Providing Fixme's to be reworked at a later time.

* Adding // FIXME Anna to assist our Austrian friend.

* Adding logging test as a first step in addressing issue #2822.

* hapifhir#3506 part 2: enhance logging for (un)successful MDM matching

hapifhir#3506 part 2: enhance logging for (un)successful MDM matching

* Update MdmMatchLinkSvc.java

#3506 move "narrowed down" log to different place

* #3506 added scores and tests

#3506 added scores and tests

* #3506 formatting

#3506 formatting

* #3506 create changelog file

#3506 create changelog file

* #3506 fix typo

#3506 fix typo

* #3506 fix part 3, minor formatting

#3506 fix part 3, minor formatting

* #3506 fix tests

#3506 fix tests

Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>

* mdm matching (#3579)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

* begin with failing test

* fixed

* changelog

* add jira tag

* Update to 6 1 (#3582)

* added changelog folder, upped version

* version enum

* add a few more unit tests to assert proper NO_MATCH exclusion

* revert merge master doh! bad reflexes

* revert merge origin master

* unrevert revert.  ugh what a pain

* merge recovery.  fix poms.

* merge recovery.  more reverting

* merge recovery.  more reverting

* merge recovery.  more reverting

* Revert "merge recovery.  fix poms."

This reverts commit ae6e0ddb06.

* more revert revert reversions

* more revert revert reversions

* pre-review cleanup

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>

* Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586)

* When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller.

* License

* Ks 20220508 log colour (#3592)

* don't use colours when output is redirected to a file

* change log

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

* 3584 case sensitive string elasticsearch (#3596)

* Fix for case-sensitive search with newer elasticsearch

* Test and fix ascii normalization too

* more test cases

* comments

* Docs update empi usecase (#3598)

* Update diagram for use case 5

* Add new page for database support

* Licnese

* Mb norm fix (#3604)

* Normalize query since wildcard searches aren't normalized in elastic

* Handle batch2 job cancellation (#3603)

* Handle batch2 job cancellation

* Add CANCELLED status

* Remove unuseful test

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Add batch2 interfaces to obtain recent instances (#3601)

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* changelog folder

* Documentation change, added warning log and change log for ticket (#3609)

Co-authored-by: Steven Li <steven@smilecdr.com>

* fix ne for lastUpdated search param (#3589)

* init/wip

* add implementation, add tests

* add checks and some refactoring

* refactor and simplify tests

* refactor

* get rid of some of the warnings

* add changelog

* remove my todos

* redo ne logic to account for less precise dates

* add tests

* refactoring

* rename to follow convention

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>

* Version bump

Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
2022-05-16 22:08:27 +00:00
jmarchionatto 231c2659b8
Implement :below qualifier for tag parameters (#3613)
* Initial implementation

* Implement job cancellation

* Implement :below qualifier for tag parameters

* Add changelog

* Add tests

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-16 14:06:48 -04:00
Mark Iantorno 544ef3de1b
Update to 6 1 (#3582)
* added changelog folder, upped version

* version enum
2022-05-03 20:34:25 +00:00
jmarchionatto 3a7ea64a40
As a temporary palliative until we refactor async search, disallow scrolling less than 50 (#3576)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-02 14:52:11 -04:00
Tadgh 581f40f373
Upgrade Hibernate Search (#3572)
* wip

* updated rest high level for lucene mismatch

* Remove custom JNA

* Bump to 13

* License files

* Changelog
2022-05-02 13:38:56 -04:00
Ken Stevens 10ebb082d0
Issue 3563 mdm nickname support (#3565)
* added NicknameMap

* added NicknameSvc

* create NicknameInterceptor

* test interceptor integration

* add nickname matcher

* test nickname matcher

* unit test

* documentation

* unit test

* cleanup

* cleanup

* Msg.code()

* Msg.code() in test

* Msg.code()

* review feedback
2022-04-28 18:02:56 -04:00
Jaison Baskaran e0f1b913b7
Support _total and _count works for hibernate search (#3567)
Add support for _total, _count, and _offset to Lucene backend.

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-04-28 16:35:39 -04:00
seanmikalson-smilecdr 68c8523046
$translate operation implementation for remote terminology (#3552) 2022-04-25 12:37:15 -07:00
Tadgh f7a31287b6
3558 bulk export premature deletion (#3562)
* Implementation, parameterize test, changelog

* Bump spring framework for a vuln while i'm in here

* Fix number of changelog

* Add IS NOT NULL to query
2022-04-24 01:46:44 +00:00
samuelwlee2 4c9667c92a
3524 export poll status returning the wrong partition in the url (#3526)
* test added and bulk data export provider fixed

* add test and change jira number

* change test

* modify tests
2022-04-23 16:47:04 +00:00
jdar8 5ccb4effb0
3547 Interceptor hook for client-assigned IDs (#3559)
* add pointcut

* draft test

* fix test, change name and location of pointcut

* add changelog

* change check condition, improve changelog wording

* improve changelog wording

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3547-interceptor-hook-for-client-assigned-ids.yaml

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* change pointcut name

* update test

* fix test

* fix changelog

* renaming variables in test

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-04-22 18:09:25 -04:00
Tadgh 53c8b067d5
Support forward references in Group Bulk Export (#3558)
* Preliminary test work to generate forward-reference data

* Complete implementation

* Permit Practitioner/Organization as forward references in bulk export group params

* Wip

* Fix test

* Add error number

* Address review comments

* Update assert
2022-04-22 05:33:10 +00:00
jmarchionatto f9824d6b15
Freetext search query builder consolidation (#3556)
* Refactor query builder for Reference

* Execute loop for all entries

* Add sandbox disabled test

* Add multiple components tests

* Revert "Refactor query builder for Reference"

This reverts commit 85e0442082.

* Fix imports

* Simplify test

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
2022-04-21 16:50:21 +00:00
JasonRoberts-smile 1114c72f03
Further expunge refactoring (#3550)
* convert expunge public interfaces to use ResourcePersistentId instead of Long

* changelog

* version bump
2022-04-21 09:51:19 -04:00
Tadgh 612ee0af32
Supported search (#3549)
* wip

* Revert some work

* Add changelog

* refactor method into SeachParamRegistryImpl

* Javadocs
2022-04-21 07:46:58 +00:00
Tadgh 578d42c955
Add implementation and changelog, and test. (#3554)
* Add implementation and changelog, and test.

* Add daoconfig settings

* Updatae test

* Rename deexternalize -> autoinflate
2022-04-20 13:47:02 -04:00
Ibrohim Kholilul Islam d20c6a7d25
Implement GraphQL Connection Approach (#1987)
* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation

* GraphQLQueryBodyParameter to recognize application/graphql

* fix 500 error on method without @GraphQLQueryBody

* refactor to processGraphQlGetRequest and processGraphQlPostRequest

* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest

* fix imports

* implement GraphQL Connection

* add tests

* add cacheControlDirective and requestDetails to registerSearch

* fix tests and fix bugs

* set error code
2022-04-19 17:43:41 +00:00
James Agnew 5dfdc91682
Add gated execution mode for Batch2 (#3545)
* Add gated execution mode for Batcvh2

* Allow for async processing

* Test fixes

* Cleanup

* Add javadoc

* Fixes
2022-04-18 20:20:52 -04:00
Olivia You e0cc325294
Allowing any client assigned ID throws ResourceNotFoundException when creating a CodeSystem (#3505)
* add test and potential fix

* add changelog

* fix

* add tests again

* oops. missed a file.

* clean up

* fix resolveResourcePersistentIds

* fix RESOURCE_PID constant

* format

* apply suggestion

* get R5 pid key

* better solution

Co-authored-by: olivia-you <olivia.you@smilecdr.com>
2022-04-17 08:02:50 -04:00
Jaison Baskaran c29bb462c5
Add support for additional params with lastN operation on Observation (#3533) 2022-04-13 21:38:43 +00:00
JasonRoberts-smile f361aa5998
move expunge core classes and interfaces to storage project (#3529)
* move expunge core classes and interfaces to storage project

* post-merge clean-up

* changelog
2022-04-12 14:12:10 -04:00
James Agnew 8d116b932e
Refactor to restore LGTM functionality (#3455)
* Refactor to restore LGTM functionality

* Compile fix

* Work on cleanup

* Attempt to restore LGTM

* Work on tests

* Fixes

* Build fixes

* Build fix

* Test fix

* Test fixes

* Work on build

* License header updates

* Test fixes

* Test fixes

* License header

* Test fix

* Test fix

* Test fixes

* Restore LGTM

* Fix azure

* Disable test

* Test fixes

* Test cleanup

* Build fix

* Build fix

* Test fix

* Test fix

* Test fixes
2022-04-10 15:54:27 -04:00
longma1 01d6e15f90
2579 partitioned support for mdm (#3485)
* committed changes discussed at tasking

* Changed the subscription message to store the request partition

* modified mdm subscription loader to create a cross partition subscription in the default partition if multitenancy is enabled

* Fix errors when running Multitenant IT for mdm

* Added partition id to mdm golden resource search and creating/updating golden resource

* added partition id column to the mdm link table

* Added partition id of the source resource to partition id column of the mdm link table

* broken build

* working -links, missing hapi tests

* Fixed the mdm link db table due to feedback

* added IT for create link mdm operation, also added changes to pass the IT

* Fixed test for create mdm links, added test for update mdm link on partitioned server

* changed mdmLink search from searchbyExample to criteriaBuilder, added partitionHelperSvc to determine partition

* added test for merge golden resource and search golden resource on partitioned server

* added unit test for not duplicate on partitioned and non-partitioned server

* added criteriabuilder search and tests

* code cleanup

* added partition support to -merge-golden-resources operation

* test cleanup

* fixed  operations with multitenancy

* added test for mdm clear operation

* added waiting for batch job to finish in mdm clear operation test

* added query to dao to support partitioned server for mdm clear operation

* resolve mistake from merge conflict

* added mdm-submit operations, also fixed paging for -query

* added partitionIds constant

* fixed build issue where there was no Code.msg in mdm partition exceptions

* code review fixes

* fix broken test, also fix a bug where query link could not query by linkSource properly

* fix test stubbing

* bump hapi version to 6.0.0-PRE10-SNAPSHOT

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Long Ma <long@smilecdr.com>
2022-04-06 15:48:30 -04:00
Tadgh 5b413a9135
Package move-around (#3488)
* moved classes

* Bump version

* licensing

* Repackage, fix messages

* reject empty streams

* Remove dead import

* Version bump

* Fix up test to actually return a data stream

* Move null binary svc to storage
2022-03-26 22:43:41 +00:00
James Agnew f82534ca51
Convert Reindex into Batch2 Job (#3458)
* Start working on reindex job

* Updates

* Ongoing work

* Ongoing work

* Work on reindex

* Reindex work

* Add logging

* Fix typo

* Test fix

* Test fix

* Address fixme

* Liocense header

* Resolve fixme

* Add logging

* Update logs

* Address review comments

* License header

* Test fixes

* Test fix

* Test fixes

* Test fix

* Version bump

* Version bump
2022-03-19 16:07:58 -04:00
Ken Stevens dfd99c5471
improve search parameter registry logging (#3452)
* Startup log cleanup.  Use cached fhir contexts.

* improve logging

* improve logging

* add full comparator

* wrap resource search param map

* rename wrapped map methods

* add fixmes

* further searchparam encapsulation

* fix regression found by test

* improve logging

* pre-review cleanup

* pre-review cleanup

* bump hapi version

* license

* since I'm bumping hapi-fhir now, improve the api dependency

* licenses
2022-03-09 19:57:38 -05:00
James Agnew 2cba62b4e8
Enable search narrowing on large ValueSets (#3405)
* Enable search narrowing on large ValueSets

* ValueSet improvements

* Work on narrowing

* Work on narrowing

* Work on narrowing

* Work on narrowing

* Add test

* Work on narrowing interceptor

* Work on narrowing

* License headers

* Refactor code narrowing

* Add docs

* Version bump

* Test fix

* Test fixes

* Build fix

* Fixes

* Version bump

* Test fix

* License header updates

* Build fix

* Test fixes

* Test fix

* Test fix

* Docs fix

* Test fix

* Test fix

* Resolve fixme

* Bump

* Force a CI build

* Make CI happen again
2022-03-01 09:16:31 -05:00
James Agnew b7d1ae217d
New batch framework / Bulk Import (#3387)
* Work on new batch framework

* Work on new batch framework

* Work on new batch framework

* Work on batch

* Compile working

* Work on bulk import

* Adjust import

* Work

* Work on batch

* Bump version

* WOrk on new batch processes

* Work on bath

* Bump to PRE4

* Build fixes

* CLeanup

* Small tweak

* Add exception code

* Test fixes

* Test fixes

* Test fix

* Additional synchronization

* Add license headers

* Test fixes

* Test fixes

* Add changelogs

* Address PG

* Test fix

* Test fix

* Test fixes

* Review notes

* Work on tests

* Test fixes

* Test fix

* Work on tests

* Tets fix

* Test fixes

* Test fixes

* Add missing exception codes

* Test fix

* Test fixes

* More test fixing

* License headers

* Test fix

* Add new test logging

* Work on tests

* Test fixes

* Test fix

* Resolve fixme

* Try to avoid test failure

* Add import command

* Work on storage

* Fix error codes

* Fixes

* License header

* Build fix

* Build fixes

* Fix dep
2022-02-27 16:04:49 -05:00
Ken Stevens 631391819b
remove hapi jpa spring config hierarchy (#3390)
* initial refactor to remove hapi jpa spring config hierarchy

* fix poms

* fix batch config

* dependency rearrangement arising from further testing

* fix searchDao bean name

* fixed dstu2 tests

* consolidate validation config

* dstu2 validation regression (man dstu2 support is expensive)

* fix test (with WIP comment)

* restore poms

* fix demo projects

* fix build

* bumping version

* rename generated config class
2022-02-16 20:44:03 -05:00
James Agnew 0f2fc7a882
Allow search narrowing and auth interceptor by `token:in` (#3360)
* Optmize valueset expansion

* Working

* Version bump

* Add documentation

* Add test

* Checkstyle message cleanup

* Add reverse rule

* Test ficx

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fix

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/security/search_narrowing_interceptor.md

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/security/search_narrowing_interceptor.md

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

* Test fixes

* Fix conflict

* Add setter

* Test fixes

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-02-09 14:27:14 -05:00
Tadgh 6982c4d680
bump version to 6.0.0-PRE1-SNAPSHOT (#3353)
* bump version

* Add new version enum

* Bumped to 6.0.0
2022-02-02 12:11:31 -08:00
Johnson Lu c42ecc5c08
Add error codes to all exceptions (#3278)
* Initial design of adding exception codes to exceptions

* Initial design of adding exception codes to exceptions

* change int module name to string

* add comment

* shorten message

* shorten message

* added checkstyle

* developing checker

* completed checkstyle plugin and unit test for it

* fix NPE

* fix checker so it ignores throws on exceptions that aren't new

* change parameter order in InvalidResponseException

* accept Msg.code() in any parameter since some exceptions like MessageException have the message string as the second parameter

* exclude generated files

* BIG COMMIT added error codes to all exception throws

* example test fix

* Modified tests such that the assert statements would better match the message responses.

* Modified additional tests such that the assert statements would better match the message responses.

* fix test

* merge master

* merge master

* Fourth commit of modified tests such that the assert statements would better match the message response

* Changes made to modify assert statements such that they match the new errors which now use error codes. Also changed ResourceNotFoundException to include error codes in its messages.

* Modified assert messages to better match new error codes

* Time Zone changes DRAFT. Certain tests pass in intellij and fail during mvn install

* Modified assert messages to better match new error codes

* Added comments for time zone fixes. Previous commit comment on time zone fixes was incorrect. By invaliding caches, all tests on both intellij and mvn install passed.

* Reverted changes on azure-pipelines.yml

* updated hapi-fhir version for checkstyle module

* changes to azure-pipelines.yml

* changes to azure-pipelines.yml

* change to pom.xml to include hapi-fhir-checkstyle in ALLMODULES

* changes to azure-piplines (these changes are to be reverted after testing)

* reverted changes to azure-piplines

* reverted change where hapi-fhir-checkstyle was added to pom.xml (hapi-fhir)

* Attempted fix on checkstyle build error

* modified azure-piplines.yml to change maven repository for checkstyle build

* Attempted fix on checkstyle build error

* checkstyle config location change for hapi-depoloyable-pom. (will be reverted if it does not work)

* attempted dependency add for hapi-depoloyable-pom. (will be reverted if it does not work)

* reverted changes for hapi-deployable-pom

* add javadoc

* update last code

* Attempted fix on checkstyle build error

* Finished adding in missing error codes to pass Checkstyle checks

* Test pipelining

* Fixing errors and bumping version (as suggested by Gary)

* Merge

* Fixing Checkstyle error

* Attempted fix for date error

* Add error code onto assert statement

* Add in a couple more error codes

* Fixing assert statements

* Bump to static version for dependency

* Adding error code to message

* Adding error codes to exceptions

* Adding error codes to exceptions

* Change to work with cdr branch

* Update to faulty error message

* Merge changes

* allow checkstyle pom to deploy

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com>
Co-authored-by: Predap <simon.zuccherato@gmail.com>
Co-authored-by: Predap <46201929+Predap@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-01-31 13:10:15 -08:00
jamesagnew aafc42fdd8 License header updates 2022-01-04 13:37:10 -05:00
James Agnew d610d33ac3
Dependency bumps (#3264)
* Bump a number of versions

* Fixes

* Work on version bump

* Bump

* Test fix

* More version bumps

* Build fixes

* Test fixes

* Fixes

* Fixes

* Test fix

* Bump jacoco

* Test fix

* Test fix

* Test fix

* Build fix

* Build fix

* Remove versioned H2

* Build fix

* Avoid memory issue in validation tests

* JDK bump

* Restore compile with errorprone

* Force coloured output

* Force jansi

* Try again to force jansi

* Fix for hardcoded date that just passed

* Fixes to JPA

* Improve changelog

* Work on failing test

* Test fix

* Compile fix

* One more version bump

* Test fixes
2022-01-04 13:21:14 -05:00
Tadgh 50a3005c23
Fix flag name (#3247)
* Fix flag name

* Bump hapi version
2021-12-14 19:20:03 +00:00
longma1 a56603daa2
2480 partition aware subscription (#3218)
* some fixmes to start

* Added some FIXMEs

* added RequestPartitionId to reosurceDelivryMessage and ResourceModifiedMessage

* ResourceDeliveryMessage and ResourceModifiedMessage tests

* fixed issue with test missing partitionHelperSvc mocked bean

* Added tests and implemented SubscriptionMatchingSubscriber for partition aware subscription

* modified implementation of partitionId in CanonicalSubscription

* Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)

* Revert "Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)"

This reverts commit fe40fb9733.

* Got added partitionId to subscriptions, added changes to make SubscriptionMatchingSubscriberTest work

* added SubscriptionTriggering test, also added partition support to subscriptionLoader

* Changed implementation for storing partition id of subscriptions from messages, refactored tests to new implementation

* added all subscription systemRequestDetails with all partition to subscription reader

* refactored a generic system request details with default all partition request

* Added test for dao subscriptions, fixes to get the test working

* added partition support for latest version delivery

* added doc changes and changelog for multitenancy subscription

* cleanup and added partitioned subscription manually trigger test

* fixed mocked subscriptionDao

* added package-info for subscription module

* some code review changes

* removed AllPartitionSystemRequestDetail, added new text for multitenant subscription

* renamed method for code review

* version bump to 5.7.0PRE7

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
2021-12-13 08:45:30 -07:00
VK-SMILECDR bd89cf022b
Improve mail service (#3230)
* move mail config to mail service constructor

* update subscription email sender

* added license text

* [2669] bump HAPI version to 5.7.0-PRE6-SNAPSHOT

* add changelog
2021-12-09 17:05:42 -05:00
Ken Stevens 9753b66610
2564 contained resource validation flag (#3225)
* First cut at multithreading bundle validation

* javadoc

* change test to a red-green test

* add daoconfig

* move bundle concurrency config from validationsupport to request validator

* Moved concurrent details from ValidationOptions to FhirValidator

* Remove bundleValidationThreadCount (it's set by creating an appropriate executor)

* validate threadpool prefixes

* FIXME cleanup

* reassign FIXMEs to JB

* only create the threadpool if it will be used

* Add the MdcTaskDectorator to all threadpools

* Add bundle path to concurrently validated bundle resource validation messages.

* Add test to check bundle entry path being added to validation messages

* Threaded validation of contained resources initial checkin

* FHIR validator refactored to maintain correct bundle path and async validation task

* Refactored to use validation complete invoke callback to support raw string resource or resource object

* switch from XML to JSON

* # Conflicts:
#	hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Updated to use new HAPI-FHIR version

* merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation

* Updated to use new HAPI-FHIR version

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit 910b7f676b.

* Revert "merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation"

This reverts commit c7d60fc3e6.

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit aa8a7af455.

# Conflicts:
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Fix Test dependencies after reverting changes.

* merge 'validate_contains_change' to 2564-contained-resource-validation-flag

* Disable threadpool prefix name validate check.

* merge master

* fix thread regexp

* pre-review cleanup

* change log

* fix test

* revert to XML as default validation serialization

* fix test

* fix test

Co-authored-by: Jaison B <jaisonb@gmail.com>
2021-12-08 15:18:54 -05:00
James Agnew d072357c2a
Move graphql provider (#3214)
* Move graphql provider

* Version bump
2021-12-05 17:22:20 -05:00
Tadgh 0a64294467
Release 5.6.0 (#3174)
* 3138 externalized binary packages (#3139)

* Add test and impl

* Add changelog

* Fix test

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3138-support-externalized-binaries.yaml

* add beans to test configs

* Typo

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java

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

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* 3131 - Added support for the lookup operation in the Remote Terminology code (#3134)

* Remove leading underscores from identifiers (#3146)

* Version bump

* License files

* version.yaml

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-11-19 15:24:44 +00:00
TipzCM 25c025cdee
3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155)
* 3153 updating the unknowncodesystemwarningvalidationsupport class

* 3153 updating version for smile

* 3153 update broken tests

* 3153 adding log

* 3153 cleanup

* 3153 cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2021-11-10 16:06:09 -05:00
TipzCM 59bf8b836f
Issue 3120 support adding retry extension (#3137)
* issue-1134 initial work on adding retry handler

* issue-1134 subdscription creation fixes

* issue-1134 update the test

* issue-1134 retry policy off canonicalsubscription

* issue 1134 base subscription changes

* add failing test

* issue 1134 retry configs on base parameters

* issue 1134 passing forward params

* issue-1134 added more tests for making sure subscriptions create their channels correctly

* issue-1134 updates to get the retry to channels

* issue-1134 updating channel factory

* issue-1134 remove the dlq since it's not defineable

* issue-3120 changelog added

* issue-3120 cleaning up

* issue-3120 test fix

* issue-3120 review fixes

* issue-3120 fixed bad master merge

* issue-3120 updates for new release

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-11-03 18:21:10 -04:00
Tadgh a10c58e839
Bump version, add version to versionenum (#3135) 2021-11-02 09:40:56 -04:00
Tadgh 7c63441663
Revert "Issue 1134 retry mechanic on subscriptions (#3121)" (#3128)
This reverts commit 9b23e9e825.
2021-10-30 19:46:42 +00:00
TipzCM 9b23e9e825
Issue 1134 retry mechanic on subscriptions (#3121)
* issue-1134 initial work on adding retry handler

* issue-1134 subdscription creation fixes

* issue-1134 update the test

* issue-1134 retry policy off canonicalsubscription

* issue 1134 base subscription changes

* add failing test

* issue 1134 retry configs on base parameters

* issue 1134 passing forward params

* issue-1134 added more tests for making sure subscriptions create their channels correctly

* issue-1134 updates to get the retry to channels

* issue-1134 updating channel factory

* issue-1134 remove the dlq since it's not defineable

* issue-3120 changelog added

* issue-3120 cleaning up

* issue-3120 test fix

* issue-3120 review fixes

* issue-3120 fixed bad master merge

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-10-29 11:21:43 -04:00
Tadgh b427135b04
Patient/$everything _id parameter (#3077)
* Add tests. Add implementation in R4. Add changelog

* Wip partial fixup of other STU versions

* Updated usages of new patient type everything api

* Partial commit of incomplete documentation

* Remove docs

* Cut to token instead of string

* Bump hapi version due to breaking api changes
2021-10-17 14:34:33 +00:00
James Agnew 310a4cdb58
Migrate CLOB columns to LOB (SMILE-3072) (#3016)
* Migration finished

* Work on LOBS

* Add to ClobMigrated annotation

* Deal with lobs

* Work on new approach

* HAPI FHIR version bump

* Add changelog

* Add license header

* Fix intermittent

* CLeanup

* Cleanup
2021-10-11 16:47:37 -04:00
Ken Stevens 53c7476dae
hapi storage (#3024)
* first pass moving core storage classes to storage-api

* move term service apis

* nearly done

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* create new SearchConstants class to store platform independent search constants

* move a couple of subscription services

* move transaction processor adapter to storage

* version bump

* move searchparam

* fix test

* fix compile includes

* fix text

* fix docs
2021-09-23 22:04:46 -04:00
Ken Stevens 060791aeb4
hapi-fhir-storage-api (#3006)
* rename hapi-fhir-jpaserver-migrate to hapi-fhir-sql-migrate and move hapi-tasks into jpaserver-persistence

* rename hapi-fhir-jpaserver-api to hapi-fhir-storage-api

* move bulk import apis

* create hapi-fhir-jpa

* create hapi-fhir-jpa

* move CircularQueueCaptureQueriesListener to japi-fhir-jpa

* move mdm logs to storage-api

* move gziputil to storage-api

* move quartz scheduling to hapi-fhir-jpa

* move default subscription channel factory to storage-api

* consolidated batch constants

* correct accidental Logs change

* remove dependency of cdr-api on cdr-persistence

* fix javadoc

* pom descriptions

* review feedback
2021-09-21 15:36:08 +00:00
James Agnew 5554431146
Avoid dead SearchParameter links in CapabilityStatement (#2790)
* Avoid dead SearchParameter links in CapabilityStatement

* Resolve fixmes

* Build fix

* Test fix

* Test fix

* Test fix

* Work on metadata

* Fixes

* Test fixes

* Test fix

* Test fix

* Test fixes

* Test fix

* Work on test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fix params

* Resolve fixme

* Adjust changelogs

* Version bump to 5.6.0-PRE7

* Add license header

* Bump version to 5.6.0-PRE5-SNAPSHOT
2021-09-11 18:27:18 -04:00
Tadgh 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -04:00
Tadgh eabe3e7c74 Merge branch 'master' into custom-elastic-index 2021-09-07 13:56:44 -04:00
Tadgh 16752f393c Finalize implementation 2021-09-07 13:33:03 -04:00
Ken Stevens 346e29920a
Issue 2927 convert mdm clear to spring batch (#2929)
* initial roughout of mdm clear batch job

* still roughing out classes

* finished first draft of reader

* most tests passing now

* all tests pass.  now FIXMEs

* FIXMEs done.  Time for regression.

* fix test

* changelog and docs

* fix test

* pre-review cleanup

* version bump

* move spring autowire deps for cdr

* move spring autowire deps for cdr

* finally got beans working phew

* rearrange method calls so persistence module can perform clear operation on its own

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* review feedback

* review feedback

* Remove inheritance

* fix beans

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2021-09-03 14:58:19 -04:00
Tadgh 37ad73a422 Bump PRE version so we don't conflict downstream 2021-08-23 15:42:18 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -04:00
Ken Stevens f5dfc3a5ed
New reindex spring batch operation (#2845)
* first sweep to add new $reindex job

* first cut done.  next up integration test.

* start roughing out reindex everything

* Failing test

* test passes

* add BundleUtil helper method

* rough in processEverything

* rough in processEverything

* fix mock test

* merge master

* Make BaseJpaTest.mySrd lenient.

* fix test

* reindex everything works with FIXMEs

* reindex everything more tests

* moar tests

* moar tests

* fix test

* fix test

* fix regression and fix test

* fix test cycle

* fixme

* fix test

* test provider layer

* reindex everything partition aware

* yay last fixme!

* run reindex in partitioned threads

* add fixmes for areas that require extra testing

* added transaction and log message

* manual integration testing

* changelog

* reindex all partitions

* bump hapi version

* fix test

* moar test

* pre-review cleanup

* fix javadoc

* review feedback

* review feedback

* review feedback

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2845-reindex-operation.yaml

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

* review feedback

* review feedback

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

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

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

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

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

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

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

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

* Update hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/ResourceSearch.java

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

* Update hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/IDeleteExpungeJobSubmitter.java

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

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-07-29 19:18:49 -04:00
jamesagnew a5e6674e84 Version bump to 5.5.0-PRE7-SNAPSHOT 2021-07-22 08:41:16 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
James Agnew 8b205b23d0
Fix history paging (#2741)
* Fix history paging

* Add changelog

* Add license header
2021-06-18 17:47:51 -04:00
Ken Stevens 134631fdee
Convert delete expunge to use Spring Batch (#2697)
* prepare to add $delete-expunge operation that will create a spring batch job

* Add operation

* Wire up jpa provider.  Begin with failing test.

* Copy/paste bulk import job as a starting point.
FIXME with proposed design

* delete expunge job parameter validation with test

* implemented reader
stubbed processor, writer

* wip for master merge

* started implementing reader

* started implementing reader

* working with stubs

* happy path batch delete expunge is done

* Provider done but test not passing.  Guessing batch infrastructure not running in that test.

* IT test works now

* add reader test

* Converted delete _expunge=true to use new batch job

* DeleteExpungeDaoTest passes

* Fix test

* Change batch size to integer

* rename search count to batch size

* Make delete expunge partition aware

* updated docs

* pre-review cleanup

* change log

* add partition id to SystemRequestDetails

* Make RequestPartitionId serializable

* Change delete expunge provider to use partition id instead of tenant name

* fix tests

* test pointcut gets called

* assert on pointcut calls

* Add resource type to STORAGE_PARTITION_SELECTED pointcut

* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants

* bump hapi-fhir version

* copyrights

* restore deleteexpungeservice for mdm

* restore deleteexpungeservice for mdm

* fix test

* public constants

* convert instant to date

* Moved expunge constants to ProviderConstants

* final review

* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run

* fix tests

* fix tests

* fix tests

* fix tests

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* improve logging

* bump version

* version bump

* recovering from failed merge

* unzip RequestListJson per Gary's suggestion.  I didn't want to do it at first, but as usual Gary was right.

* fix serialization
2021-06-15 10:36:05 -04:00
jamesagnew 376a84d213 Version bump 2021-06-14 13:12:34 -04:00
James Agnew dc627dc019
Add bulk export authorization layer (#2712)
* Add bulk export authorization layer

* Add docs

* Version bump

* Authorize any

* Add bulk export - all

* Address lgtm issue
2021-06-06 20:47:43 -04:00
jamesagnew 2068372998 Version bump 2021-05-07 17:43:54 -04:00
James Agnew 970a9884f0
Avoid tag definition constraint (#2620)
* Avoid tag definition constraint failure

* Version bumps

* Add changelog

* Avoid guava issue

* Test fix

* Test fix

* Bump pom
2021-05-01 17:16:15 -04:00
James Agnew 95d7ba6fa8
Streamline Search SQLs (#2576)
* Streamline SQL queries

* SQL query tidying

* Add changelog

* Test fixes

* Tests passing

* Ongoing work

* Test fixes

* Test fixes

* Build fix

* Cleanup

* Fixes
2021-04-28 10:29:09 -04:00
James Agnew 2ba1005762
OpenAPI Support (#2560)
* Start work on OpenAPI

* Fixes

* Work on OpenAPI

* Cleanup

* Cleanup

* More swagger work

* Build fix

* More work

* More work

* Add documentation

* Docs fixes

* Add changelog

* License updates

* Add API

* Cleanup

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md

Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>

* Work on scripts

* Add docs

* Compile fix

* Work on fixes

* Fix tests

* Test fix

* Test fix

* Build fix

* Tests

* Build fix

* Work on pipeline

* Version bump

* Test fix

* Version bump

* Test fix attempts

* Test fix

* Test fix

* Remove accidentally committed files

* Fixes

* Tets fixes

* Test fix

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fixes

* License header updates

* test fix

* Test fixes

* Test fix

* Test fixes

* Test fix

* Checkstyle bump

Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
2021-04-25 15:40:50 -04:00
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -04:00
James Agnew ca2088f3ad
Add framework for Bulk Import (#2538)
* Start work on bul;k import

* Work on bulk import

* Have batch working

* Working

* Working

* More work

* More work on bulk export

* Address fixmes

* License header updates

* Test fixes

* License header updates

* Test fix

* Test fix

* Version bumps

* Work on config

* Test cleanup

* One more version bump

* Version bump

* CLeanup

* A few additions

* Test fixes

* Test fix

* Test fix

* Migration fix

* Test fix

* Test fix
2021-04-14 17:41:32 -04:00
James Agnew a6cbf7eebd
Add support for hierarchycal valueset expansion (#2525)
* Add support for hierarchycal valueset expansion

* Add changelog

* Add tests

* Cleanup

* Test fix

* Test fixes
2021-04-06 17:36:54 -04:00
James Agnew b617c7690d
Search Parameter Infrastructure Cleanup (#2522)
* Search param service cleanup

* Work on collapsing search param

* Search param cleanup

* Work on build

* Test fix

* Test fixes

* Ongoing work

* Test fix

* Compile fix

* Test fixes

* Test fix

* Test fix

* License header updates

* Remove fixme

* Cleanup

* Cleanup
2021-04-05 17:40:10 -04:00
Diederik Muylwyk b720c32c1d Version bump 2021-03-29 18:23:16 -04:00
James Agnew dc41d5ad61
Add terminology mapping and display population interceptors (#2488)
* Start work on code mapping interceptors

* Work on generation

* Add terminology mapping and display population interceptors

* Add changelog

* License header updates

* Test fixes

* Fix typo

* Interceptor fixes

* License header update

* Test fixes

* Mapping fixes

* Version bump

* License header updates

* Add null tests

* Add null guard

* Intermittent fix
2021-03-21 12:03:57 -04:00
James Agnew 3eda19c65a
Version bump (#2400)
* Version bump

* Docs changes

* Docs tweaks

* Docs tweak

* Spelling fixes

* Docs tweaks
2021-02-18 11:07:49 -05:00
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
jamesagnew 1c6592b9fa License header updates 2021-02-02 11:26:45 -05:00
Kevin Dougan SmileCDR 2308d8f44b
Merge CQL Initial Implementation Into master (#2330)
* CQL initial implementation
2021-01-29 16:35:38 -05:00
Tadgh edbc789a93 Add annotation to skip test classes which require docker if it is not found on the host 2021-01-18 21:49:43 -05:00
Tadgh efc6809ea6
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190)
* Beginning work on converting to hibernate search 6
* replace all out of date properties
* replace all POM references to old versions
* remove the shaded ES jars as HS6 supports 7.9
* Convert "Bridges" to RoutingBinder and RoutingBridge
* Modernize all indexing annotations
* Begin refactoring of search queries (wip)

* Fix spatial API changes, work on BaseTermReadSvcImpl

* Most of the way through the various filter property conversions

* Finished i think with BaseTermReadSvcImpl

* Compiling, but definitely broken

* Start test compilation failures

* All tests compiling (i think)

* remove suggest keywords operation

* Fix bootstrap errors, still have to deal with transient fields

* Rollback CR

* More refactoring, got IDs baked back into docs

* Fix coord util, fix a few more fields which require projection

* merge fixes

* begin refactor of valuesetexpansion tests

* fix another test

* Update tests

* remove todos, add TestContainers

* Fix descendant in

* Add testcontainers, fix another test

* fix more tests, replace embedded es

* Rip out embedded elastic, replace with TestContainer

* merge conflicts for new analyzers

* Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs

* Remove dead deps, update testcontainer

* Remove java-hamcrest

* Pull asserts up, refactor tests to pass in RP tests

* Update V2 check

* Remove suggest keyword tests

* Split line for testing

* Fix perhaps one of the dumbest programming mistakes in my career so far

* Refactor tests which no longer rely on a strict known order

* Fix up test config, disable log test temporarily

* Remove log4j from being transitively pulled in. re-enable test

* Update log4j exclusions with new bridge. Update test to check for core class

* Move dependency to root pom in dep management section

* Update changelog, add changelog for HS6 with ES requirements. Remove dead comment

* update testst, remove todos

* Add hibernate props provider method, add elastic regexp query

* Add todo for high level client builder

* Modify ElasticsearchRestClientFactory to support HTTPS hosts

* Remove protocol extraction from rest url

* do we even need to index this...?

* remove purge of non-indexed resources

* Add longer timeout to testcontainers

* Add task to add docker CLI to azure pipeline via task, for testcontainers

* WIP remove this

* Dont update version

* Add test for duplicate termconcepts

* Use real hibernate ORM methods

* merge issues

* Add partitionsettigns bean to match master

* Trying to debug testcontainers on azure...

* Trying to debug testcontainers on azure...

* Run even on previous failure

* Fix testcontainer port binds

* Add full text logs attaching, and test reporting

* I love yaml

* Remove comment

* Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue

* Modify TX beheaviour

* wip

* Rework to use config and mocked beans for partition-aware lastN

* rework to not use beans and just inject vars i need for test, keps test envs cleaner

* update azure pipeline to only copy test results

* Remove erroneous publish

* Always get test logs

* Make it so indexing works,

* Add todos

* revert deleteByPid

* Work on test fixes

* Test fixes

* Test fixes

* Another test fix

* Test fix

* Work on tests

* Test fixes

* All tests passing locally

* Fix test failure

* FIx build error

* Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider

* Update ngram of token filters

* Tidying

* subvert the purpose of hibernate elastic props builder to inject template

* dead space

* Rename changed class

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-05 17:56:59 -05:00
jamesagnew cbb16ce3af License header updates 2021-01-01 16:40:46 -05:00
jamesagnew f30999b053 License header updates 2021-01-01 15:07:23 -05:00
jamesagnew 0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew 4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -05:00
jamesagnew 92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew 5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
Tadgh 7fd690f830 Add test in provider with different empi json rules 2020-07-24 10:42:21 -07:00
James Agnew f356c7c385
Migrate to JUnit5 (#1952)
* Work on junit

* Work on junit 5

* Work on junit 5

* Bump errorprone vcersion

* Work on tests

* Junit 5 tweaks

* Fixes

* Work on tests

* Work on junit5

* Work on tests

* Test fixes

* Work on junit5

* Test work

* Get junit5 working

* Test fix

* Work on tests

* WOrk on tests

* Work on tests

* fixes

* Compile fix

* One more tweak

* Compile fix

* Add changelog

* Fix compile error

* Compile fix
2020-07-04 18:28:16 -04:00
Tadgh e51c5b5263 change transactionmanager name so it doesnt shadow the batchprocessing one 2020-06-24 21:03:02 -07:00
Tadgh 06e1368388 Re-add comment 2020-06-24 21:00:45 -07:00
Tadgh 3da4ad280b undoes merge issues 2020-06-24 20:00:52 -07:00
Ken Stevens 57f2002b84 organize imports 2020-06-09 15:49:11 -04:00
Tadgh 278a1070ae :Merge branch 'master' into spring-batch-integration 2020-06-08 17:16:11 -07:00
James Agnew 21330a0a22
Transaction create performance improvement (#1899)
* Work on perf issue

* Improve write performance for large bundles with tags

* Add changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1899-improve-write-xact-perf-with-tags.yaml

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Test fix

* Test fixes

* Test fixes

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
2020-06-05 05:26:06 -04:00
Tadgh 81d5ff8f5a Add schema initialization 2020-05-27 17:06:52 -07:00
Tadgh d1b963321a
MVP EMPI implementation (#1857)
EMPI Initial Implementation (still plenty of known gaps)
2020-05-22 15:03:20 -04:00