Commit Graph

388 Commits

Author SHA1 Message Date
James Agnew 108e357ca7
Preserve tags on delete (#4128)
* Preserve tags on delete

* Add changelog

* Add changelog

* Test fix

* Build fix

* Address review comments
2022-10-12 11:01:47 +00:00
Luke deGruchy 5831cbedf5
Concurrent cascade delete operations leading to confusing errors (#4126)
* Add unit tests and supporting classes from gitlab issue.

* Commit with changes thus far to be reviewed.   Namely, add savepoint capabilities to HapiTransactionService, inject HapiTransactionService into CascadingDeleteInterceptor, add savepoint capabilities to the TransactionDetails, and catch an Exception in BaseHapiFhirResourceDao.delete() then rollback to the checkpoint.

* Fix compile error.

* hapi transaction service test

* hapi transaction service test

* hapi transaction service test

* First draft of RetryTemplate and flush() logic.  Try unit testing with PointcutLatch.

* hapi transaction service test

* Latest changes including moving RetryTemplate, cleaning up unit tests.

* First attempt at correct design.  Fix compile errors.

* Add failed rollback savepoint test.

* fix propogation

* interesting test failure in SafeDeleterTest

* Latest code

* move delete

* test passing

* all tests pass

* yay we're done just cleanup

* First round of cleanup:  Get rid of all exploratory logging, remove unneeded dependencies, move creation of RetryTemplate to SafeDeleter.

* More cleanup.  Add changelog.

* Bump to 6.2.0-PRE13-SNAPSHOT.

* Code review feedback:  Refactor SafeDeleter to a service and bean.  Add comments.

* Code review feedback:  Comments on unit test assertions.

* Code review feedback:  Rename SafeDeleterSvc to ThreadSafeResourceDeleterSvc.  Add javadoc.  Add logger to DelayListener.   Remove useless commented out code.

* Fix unit test failure in CascadingDeleteInterceptorTest.

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-10-11 16:48:01 -04:00
James Agnew 26fe5e6b8e
Interceptor improvements (#4125)
* Interceptor improvements

* Add changelogs
2022-10-09 15:02:12 -04:00
KGJ-software c5e1effe5b
3240 Added test case. Currently does not reproduce bug. (#4108)
* 3240 Added test case. Currently does not reproduce bug.

* 3552 Fixed test case.

* 3552 Added StrictErrorHandler validation before applying patch.

* 3552 Use logger instead of sysout.

* 3552 Use try blocks.

* 3552 Better test name.

Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2022-10-07 09:50:49 -04:00
Ken Stevens 40163f73d2
Ks 20220916 remove flyway (#4040)
* removed flyway, started coding persistence

* started wiring up new dao service

* replace jpa with sqlbuilder

* down to 16 failed tests

* remove outOfOrder test.  We no longer support validating order.

* Removed noFlyway mode.  It is no longer a thing.

* merge migrator

* down to 1 failing test

* cleanup

* removed unused noflyway cli arguments

* cleanup

* cleanup

* cleanup

* cleanup

* create MigrationTaskList to replace the List<BaseTask> that gets passed around a lot.  This allows us to add a bunch of behaviour to that as a first-order thing

* fix test

* fix test

* improve migration table detection to use the catalogue

* Msg.code()

* cleanup

* save version in same format as flyway

* cleanup

* add migration result to migration result class

* failed migrations stay in the table and don't really affect anything.

* change log

* docs

* ugh Flyway requires lower-case column names

* integration test fixes

* log

* fix oracle issue

* lowercase tablenames for postgres.  fussy fussy!

* Revert "lowercase tablenames for postgres.  fussy fussy!"

This reverts commit 92c9cb263b.

* revert to capital table names.  surround table name by quotes for Postgres.

* added log message before executing find all query

* changed log message from info to debug

* javadoc

* pom cleanup

* review feedback

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

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

* review feedback

* review feedback.  Use prepared statement.

* Change installedOn insert from timestamp to date

* Change installedOn column type from timestamp to date

* bump hapi version

* fix poms

* fix poms and cdr compile

* add exclusions to clean up build

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2022-10-03 22:40:09 -04:00
weiping202209 66baa8263d
Fix bug in history search (#4009)
* add failing test

* Fix history search bug and add tests for two more scenarios

* Fix history search bug and add tests for two more scenarios

* - added failing test condition

* Fix history search bug and add tests for two more scenarios

* Fix build test failures

* Fix build test failures

* Add extra verifications for scenarios of _since

* Refactor dao.history interface to add overload method and shall come back to remove old method once cdr is refactored.

* Update with new hapi interface

* Add depreciate comment

* Add depreciate comment

* Version bump to mvn 6.2.0-PRE11-SNAPSHOT

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-10-03 09:00:41 -04:00
Ken Stevens 26756a40bb
add message key to all message types (#4101)
* add message key to all message types

* move test

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-10-01 15:36:04 +00:00
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
James Agnew fc82ed4e44
One more tweak to #4093 (#4094)
* One more tweak to #4093

* Add changelog
2022-09-28 16:46:00 +00:00
James Agnew e4a2285f30
Make sure to not mix resource types in bulk export (#4093)
* Make sure to not mix resource types in bulk export

* Avoid dupes

* Add test
2022-09-28 15:16:15 +00:00
StevenXLi 9e1120a47a
4080 support onc requirements for group bulk export (#4081)
* added failing tests

* added include to bulk export processor, added support for different resource types in bulk export fetch id step

* added changelog

* fixed duplication issue, and added null check

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-09-27 14:51:43 +00:00
Tadgh f06f9dc90a
4084 error segment of bulk export job poll status is missing (#4085)
* changelog

* Change serialization rules

* Always populate error field even if no errors
2022-09-27 01:16:33 +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
Luke deGruchy 3435806df5
4058: Fix JpaPersistedResourceValidationSupport to search for resources that it currently doesn't handle (#4062)
* Add failing and passing tests with bundle JSONs for each scenario based on pared down versions of the following JSON bundle: https://smilecdr.com/docs/fhir_repository/clinical_quality_language/measure-bundle-example.json.html

* Add experimental code to handle cases of "Library" and "Measure". Add a measure report to measure unit test with new JSON with a MeasureReport to Measure resource (can't make it pass yet).

* Refine case statements for JpaPersistedResourceValidationSupport.  MeasureReport test passes if -ea is omitted from run configuration.

* Add changelog.  Remove TODOs from validator.

* Remove erroneous whitespace chance.

* Ken feedback:  Handle SearchParameters from the default case casting a wider net than just Library and Resource.  Assume all CanonicalType inputs to the switch statement have a URL.

* Get rid of TODO since it's not relevant.

* Disable test with only MeasureReport and Measure.  Fix case issue with filenames that was only discovered by running the github pipeline.

* Add more context to the Disabled text, including a reference to a new issue:  https://github.com/hapifhir/org.hl7.fhir.core/issues/930.

* Add more context to the Disabled text, including a reference to a new issue:  https://github.com/hapifhir/org.hl7.fhir.core/issues/930.
2022-09-26 10:08:04 -04:00
TipzCM 389bdce372
fixed bug (#4069)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-09-26 13:43:11 +00:00
James Agnew 917cf8d062
Remove ActionRequestDetails (#3527)
* Add test

* Add test

* Start removing unneeded things

* Fixes

* Add changelog

* Test fix

* Address LGTM issues

* Resolve fixme

* Address review comment

* Add changelog

* Update doc

* Test fixes
2022-09-25 21:29:08 +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
Tadgh 6f80206776
Fix transactional issue in everything operation (#4063)
* Fix transactional issue in everything operation

* Add license files

* Add changelog
2022-09-23 08:33:08 -07:00
Tadgh 5a978646c5
Add changelog, test, and implementation (#4055) 2022-09-21 21:18:12 -07:00
Tadgh 392bfb790f
Fix content negotiation on binary streaming (#4053)
* Fix content negotiation on binary streaming

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/4051-content-type-negotiation-binaries.yaml

Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>

* Tidy logic

* Tidy logic

* Naming

* Wip

Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
2022-09-21 19:05:35 +00:00
jdar8 dbe52b429c
fix-matchers-not-contains-in-asserts (#3913)
* test

* replace not(contains())

* make a util class to replace not(hasItems()) and not(containsInAnyOrder())

* replace not(hasItems()) and not(containsInAnyOrder())

* add javadocs to new util class

* test for util class

* Addressing comments from code review.

* Adding static import.

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-09-21 11:54:27 -04:00
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
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
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
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 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
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
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
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
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
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
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