Commit Graph

10014 Commits

Author SHA1 Message Date
MykolaMedynskyiSCDR 3349ad8ca9
3929 batch2 jobs file fetching step strict policy for response header content type (#3945)
* Adding failing tests cases.

* What was done:
-Accepting text/plain and application/json as import response content type.
-Added change log.

* Fixed NDJSON EncodingEnum

* Added content type application/json+fhir to the test

* Fixed code

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3929-batch2-jobs-file-fetching-step-strict-policy-for-response-header-content-type.yaml

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3929-batch2-jobs-file-fetching-step-strict-policy-for-response-header-content-type.yaml

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3929-batch2-jobs-file-fetching-step-strict-policy-for-response-header-content-type.yaml

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

* Changed message

* Fixed code

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-09-21 08:29:32 -07:00
StevenXLi 3b781022c1
4030 bulk export to support fhir basepatientid$export endpoint (#4032)
* Refactored test helper method to be more generic, added new failing test for feature, and changed BulkDataExportOptions to fix compile error

* added field to all objects needed in the bulk export pipeline for adding patient id, added new operation for the feature

* added changelog

* added support for patient parameter to patient export, changed patient id to a list to match the requirements for the patient parameter, added test for multiple id patient export

* refactored methods, added new changes to changelog

* code review changes

* fix test error

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-09-20 10:42:55 -07:00
KGJ-software 4d16a109de
SMILE-3459 Implemented -l parameter in validator. (#3983)
* SMILE-3459 Implemented -l parameter in validator. Added SnapshotGeneratingValidationSupport to R4 support chain.

* SMILE-3459 Removed failing test that I added.

* Revert "SMILE-3459 Removed failing test that I added."

This reverts commit d11abc7ad5.

* SMILE-3459 Added test cases for loading local R4 profile.

* SMILE-3459 Added when clause to test names.

* SMILE-3459 WIP Logging assert isn't working.

* - changes to test for logging

* - change logging level to error

* - capture all logging events in tests

* SMILE-3459 Ensure validation error is logged when resource doesn't comply with profile.

* SMILE-3459 Added changelog.

* SMILE-3459 Made ValidateCommandTest less brittle.

* SMILE-3459 Changed LocalFileValidationSupport to support all resource types.

* SMILE-3459 Added LocalFileValidationSupportTest

* SMILE-3459 Created ValidationSupportChainCreator.

* SMILE-3459 Added new Msg.code for local profile load failure.

Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-09-20 13:36:41 -04:00
Tadgh d1f988f98a
Skip resource updating completely if found in package load. (#4036)
* add ability to skip loading package resources that already exists, to avoid reindex when loading IGs

* Add a test for validating no updates or creates are called on anything but binaries

* Add changelog

Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com>
2022-09-20 08:45:37 -07:00
jmarchionatto 97b82596f6
Add :text handling to StringParam (#4047)
* Add :text handling to StringParam

* Return qualifier when set.
Add changelog.

* Fix changelog file name (duhhh)

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-09-20 11:36:37 -04:00
MykolaMedynskyiSCDR 14253dd0e3
3960 when creating a resource patient where patientmetasource is provided with a hash the hash value is overwritten (#3965)
* Adding failing test.

* What was done:
-Meta source id is not replaced if provided.
-Added change log.

* Fixed code

* More tests for meta source

* Overwriting meta source can be configured.

* Test naming convention uplift and renaming of overwrite flag along with setter/getter

* Fixed when the source did not return if there was no resourceID

* Test naming convention uplift and renaming of overwrite flag along with setter/getter

* WIP in getting search on _source to be returning the correct number of patients.

* Custom requestId now stored on its own column

* Simplified getRequestId method in BaseHapiFhirDao

* Simplified getRequestId method in BaseHapiFhirDao

* An unused variable has been removed

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-09-19 10:17:09 -04:00
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
TipzCM ae3faafc9a
change search method for missing parameter names (#3982)
* handle changing in missing parameters

* added changelog

* refactor step1

* refactor step 2

* refactor step 3

* refactor step 3

* more code review fixes

* tra lala

* tra lala

* blah

* more changes

* review fixes

* review point

* more review points

* blah

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-09-14 09:29:16 -04:00
alackerbauer 1a3de51cfd
removed library immunizationCQLLibrary (#4024)
* removed library immunizationCQLLibrary

* deleted unused resource file

Co-authored-by: Anna <anna@MacBook-Pro.local>
2022-09-14 07:55:35 -04:00
alackerbauer 8fdfcaa9e6
#3738 renamed patient parameter to subject (#4019)
* #3738 renamed patient parameter to subject

to be R4 compliant

* #3738 removed accidental STU3 rename

Co-authored-by: Anna <anna@MacBook-Pro.local>
2022-09-14 07:54:24 -04:00
James Agnew 6021a09288
Avoid NPE when run in IJ (#4018)
* Avoid NPE when run in IJ

* Add changelog
2022-09-13 20:25:15 +00:00
jmarchionatto ad57ebf148
Add disabled test reproducing open bug (#3994)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-09-13 17:56:31 +00:00
James Agnew 6c0c730ebc
ForcedOffsetSearchModeInterceptor should not modify the search when it is already manually marked as synchronous (#4016)
* ForcedOffsetSearchModeInterceptor should not modify the search when it
is already manually marked as synchronous

* Add changelog
2022-09-12 10:48:56 +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
Tadgh 4226cae752
Broken bulk export (#4012)
* Implement test

* wip

* Fixed a bug in bulk export

* add changelog

* typo

* Switch out to debug logs
2022-09-09 23:18:30 +00:00
Qingyixia 306bb8b64a
Handling unexpected response status code of import-poll-status operation (#3939)
* Handling unexpected response status code when executing import-poll-status operation

* Handling unexpected response status code
2022-09-08 08:44:41 -07:00
Tadgh 6d9a19997f
Rel 6 1 1 mergeback (#4004)
* 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

* Fix bad mergback

* Added a couple of missing imports to a unit test.

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>
Co-authored-by: Kevin SmileCDR <kevinsmilecdr@Kevins-MacBook-Pro-2.local>
2022-09-08 10:38:42 -04:00
alackerbauer d22651a7c4
3984 rework immunization cql unit test (#4005)
* 3984 added test resources

* 3984 added unit test for ontario immunization POC

* #3084 reworking unit tests to showcase immunization evaluation POC

Co-authored-by: Anna <anna@MacBook-Pro.local>
2022-09-08 08:16:16 -04:00
jmarchionatto 002a7dc670
Issue 3419 elastic search exception while pre expanding valueset with more than 10 000 concepts (#3991)
* Add test reproducing bug

* Refactor ValueSet expansion hsearch queries to use scroll.

* Use void method for never used return value.

* Execute action when transaction is active

* Update tests query counts as the CodeSystemVersion.pid is always queried now

* Enable test after reproduced bug fix.
Add changelog.

* Implement suggestions

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-09-07 15:52:38 -04:00
Nathan Doef 9b50b332a4
:nickname Qualifier Support for Custom SearchParameters (#3969)
* - add failing test

* 4977 Allow any search parameter to have a nickname qualifier.

* IT test to ensure nickname expansion is working on custom SearchParameters

* capture log output in tests

* changelog

* code review changes

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2022-09-07 08:52:37 -07:00
Tadgh cc183c7079
Ensure HS before attempting fulltext reindex. (#3995)
* Do not attempt fulltext reindex if disabled. Validate enabled before using any operation

* attribute
2022-09-07 08:35:57 -07:00
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
Ken Stevens ec5a6adca8
update azure-pipelines.yml to match projects that have tests (#3993) 2022-09-06 14:05:15 -04:00
Qingyixia f3e6837fce
Fixed the issue of bulk export returning the wrong path if "Fixed Value for Endpoint Base URL" is set (#3958)
* Fixed the issue of bulk export returning the wrong path if "Fixed Value for Endpoint Base URL" is set

* Minor modifications according to the suggestions

* Modify the msg code number

* Modify the tests to be parameterized test

* Modifications according to review suggestions

* Update the msg code
2022-09-06 08:40:03 -07:00
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
StevenXLi a4a7fd9344
3987 group bulk export does not apply typefilter searches to members of the group (#3988)
* Create failing test

* Implemented the fix, fixed existing unit tests

* added changelog

* added test case for no filter, exclude 1 patient

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-09-02 13:53:52 -07:00
jdar8 21cce44524
3962 import csv to conceptmap needs status element (#3963)
* wip

* test

* refactor

* doc change and changelog

* add test cases

* edit msg.code

* fix msg code

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
2022-09-02 10:58:57 -07:00
Tadgh 9fd0addec6
Add test, changelog, and implementation (#3981) 2022-09-01 18:00:48 +00:00
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
Tadgh d9134fc553
Permit uplift (#3978)
* Add test and implementation for permitting uplifts

* Add new code paths, error code

* Add license

* Modify to support arbitrary urls

* Modify to support arbitrary urls
2022-09-01 01:03:43 +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
Tadgh 7d478f041e
Fix logging when there are no jobs to start (#3971) 2022-08-30 19:10:47 +00:00
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
Kunjan Patel bd39d65d0e
Update points.json (#2516)
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-08-30 12:39:42 +00:00
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
Tadgh 506966e089
cache pegged to SHa1 (#3968) 2022-08-29 22:55:12 +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
Ken Stevens d9f7c7dc63
back out hl7 version bump (#3955)
* back out hl7 version bump

* bump fhir core to 55

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-08-25 14:10:10 -04:00
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
Jose Arturo Garcia 7f7b7d6303
Update points.json (#3919)
* Update points.json

* Update points.json
2022-08-15 13:45:43 -04:00
dotasek dad1e420fa
3764 Fix NullPointer on validator meta extension (#3910)
* Failing test

* Failing test

* Add necessary package load to test

* WIP add minimum code for passing test

* Use PrePopulatedValidationSupport binaryMap in NpmPackage

* Rename test

* Add test for non-CachingValidationSupport

* Rename Tests + InvalidExtensionValue test

* Revert change to ValidateDirectory

* Gentle reformat

* Fix typo

* Test CachingValidationSupport fetchBinary

* Test for NpmPackageValidationSupport

* Refactor

* Check for nulls when adding Binary

* Test PrePopulatedValidationSupport addBinary

* Test ValidationSupportChain

* Move ValidationSupportChainTest to proper package

* Remove FIXME in VersionSpecificWorkerContextWrapper

* Test VersionSpecificWorkerContextWrapper

* Add example in docs

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-08-12 15:01:07 -04:00
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
James Agnew f4a0397b18
Add test for #3890 (#3891)
* Add test for #3890

* Remove unneeded import

* Add changelog
2022-08-09 17:30:10 -04:00
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