Commit Graph

590 Commits

Author SHA1 Message Date
James Agnew 7a39f8cbaf
Make reference extractor more reusable (#4205)
* Refactor

* Make reference extractor more reusable

* Test fix

* Test fix

* Headers

* Small refactor
2022-10-27 21:31:39 -04:00
Tadgh 78ce2a6344
4182 convert $mdm submit to a batch job (#4188)
* Changelog

* Wip implementation

* Wip

* wip

* wip

* Fix validator

* Fix up implementation

* tidfy

* TIdy up tests

* Add some docs

* Add changelog info:

* Tidy up self review

* License files

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

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

* Review changes

* fixes

* add new method

* Update tests

* Add batch size parameter

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-10-25 12:02:04 -07:00
James Agnew a71b8fad56
Add R4B Support (#4150)
* Add r4b stuff

* Work on R4B

* Core version bump

* Revert some changes

* Add R4B

* Docs

* Test fixes

* Work on R4B

* Tests passgin

* Add config

* Work on merging

* Work

* Work

* Work

* Test fix

* Fixes

* Test fixes

* Test fix

* Work

* Work

* Fixes

* Test fixes

* Fixes

* Test fix

* Test fix

* Test fix

* Version bump

* Test fix

* Test fix

* ompile fixes

* Fix

* Resolve build warnings

* Updates

* Test fixes

* Fix docs
2022-10-20 13:57:06 -07:00
jmarchionatto 0c5b64cce7
Change IG loader check for existence of SearchParameter resources to use same strategy as validator to avoid first one not finding resource and validator finding it later, producing a duplication exception. (#4164)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-10-20 10:47:18 -07:00
KGJ-software 69d55b7184
3052 Changed IBinaryStorageSvc MaximumBinarySize from int to long. (#4123)
* 3052 Changed IBinaryStorageSvc MaximumBinarySize from int to long.

* 3052 Added changelog

* 3052 Bumped version

* 3052 Remove mysterious +1 on maximum binary size causing overflow.

* Bumping version to 6.2.0-PRE16-SNAPSHOT

* Adding + 1L as original implementation.

* Getting all tests to pass dealing with + 1L.

* Getting all tests to pass dealing with + 1L.

* Adding migration definition and removing unnecessary comment.

* Preventing register overflow when setting maxBinaryStorage.

* Mering relevant test.

* Fixing typo in migration script

Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-10-19 06:09:02 -04:00
James Agnew 422ef87a5d
Standardize on one Transactional annotation (#4130)
* Standardize on one Transactional annotation

* Add changelog

* Disable checkstyle rule

* Fix up transactions

* Test fixes

* Test cleanup

* License headers

* One more dep bump

* Resolve commit issue

* Test fixes

* Test fix

* Dep bump

* Fix

* Fix test

* Version bump

* Test fixes
2022-10-13 16:26:11 -04:00
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
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 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
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
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 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 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
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
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
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 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
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
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
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
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
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
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 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
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
JasonRoberts-smile cedeaa04f1
add support for in and not-in qualifiers (#3680)
* add support for in and not-in qualifiers

* fix failing test

* fix broken test

* fix broken tests

* code review comments

* Make dependency on IValidationSupport optional

* create IValidationSupport dependency only if needed

* small design improvements

* changelog

* rework validation support initialization

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

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

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-06-16 20:17:57 +00:00
James Agnew ac8f4f1e56
Apply fix from #3270 (#3712)
* Apply fix from #3270

* Rework compare method
2022-06-16 15:46:14 -04:00
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 df76b0f8f1
improve nickname matcher (#3628)
* improve nickname matcher

* change log

* review feedback and fix test
2022-05-24 17:13:09 +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
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
Mark Iantorno 544ef3de1b
Update to 6 1 (#3582)
* added changelog folder, upped version

* version enum
2022-05-03 20:34:25 +00:00
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
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
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 05bc208192
Fix for path parsing in STU3 SPs (#3503) 2022-03-30 08:40:17 -07:00
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
Jaison Baskaran 3eb3014d25
Revert change to treat Canonical URLs as Locals (#3483)
* Revert change added in MR: https://github.com/hapifhir/hapi-fhir/pull/3050 to add support for treating Canonical Urls as locals. This is no longer needed as the issue reported in #2843 (_include not working for Canonicals) has been addressed in MR: https://github.com/hapifhir/hapi-fhir/pull/3440
2022-03-22 17:46:10 +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
Tadgh a2133f6940
Break a couple Circular Bean Dependencies (#3437)
* Rely on context refresh event instead of postconstruct. Load bean lazily.

* Remove parent autowire

* Break termcodesystem circular dependency with new bean

* Break cycle between BaseTermReadSvcImpl and TermCodeSystemStorageSvcImpl

* move back into helper method

* Rip out scheduling and submission to spring batch away from BulkDataExportSvcImpl

* wip

* Fix bean naming

* Revert

* re-add autowiring

* Reformat

* docs and reformat

* Back out change

* feedback from review

* merge conflicts
2022-03-03 09:37:40 -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
michaelabuckley 86f7373f16
Distinguish multi-coded items during token autocomplete (#3429)
Add nested indexing to support autocomplete of multi-coded items.
2022-03-01 00:59:09 +00:00
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
Tadgh 38912423c1
Remove dead modules (#3380)
* 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

Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
2022-02-10 16:44:26 -05:00
StevenXLi 7841e578ab
2789 nullpointerexception rest hook subscription is not being triggered when cross partition is (#3370)
* 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

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-02-10 14:14:41 -05:00
Jaison B 7794113455
2838 lastn refactor to use extended lucene index (#3339)
* Change token and reference search params to 'keyword' field type

* remove normalizer for keyword field

* WIP - refactor lastN operation to use hibernate search generated ES index.

* Add ES native aggregation builder for lastN

* added date search param support for searching resourcetable ES index

* * Added DateSearch parameterized tests to ElasticSearch test suite

* Added more tests cases for Date searches

* WIP refactor LastN test data to central generator class and use it for both hibernate-search and elastic search implementations.

* WIP fix lastNDataGenerator to avoid assertion errors.

* Fixed tests to run test suite on both existing lastN search implementation and newer extended lucene index based search.

* Cleanup json string to avoid carriage return noise

* Fix checkstyle issues

* Fix checkstyle Msg code issues

* Fix checkstyle Msg code issues

* Add more test case for GT, SA precision modifier

* Fix date precision test cases

* Fix Msg Code conflicts

* Add more logging

* Add way more loggging

* even more logging

* fix msg code conflicts

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-02-10 11:05:31 +00:00
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
TipzCM 41193c60db
3335 allow alternative character encoding length in searchparam (#3336)
* added fixme

* 2714 added support for specifying max code lengths for supported phonetic encoders

* 3335git status

* 3335 updated changelog

* 3335 review fixes

* review fixes

* fixing test

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-01-27 17:29:07 +00:00
James Agnew 3fa76a9027
Add support for of-type token modifier (#3309)
* Add support for of-type token modifier

* Add changelog

* Clean up hash calculation logic

* Test fix

* Rework hash generation

* Work on hash generation

* Test fix

* Avoid redundant hash calculations

* Revert some useless changes

* Cleanup

* Test fixes
2022-01-21 16:10:51 +00:00
TipzCM b148121ab3
3242 search content param removed not readded (#3244)
* 3242 initial changes and nonsense tests

* 3242 added changelog

* 3242 cleanup

* cleanup

* 3242 updated for review

* cleanup

* 3242 review fixes

* review fixes

* fix changelog file

* review fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-01-04 19:38:52 +00:00
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
James Agnew aae53d6ec7
Improve loading performance (#3197)
* Synthea perf work

* Cleanup

* Work on performance

* Ongoing perf work

* More perf work

* Perf work

* Test fixes

* Updates

* Test fix

* Test fixes

* Clean up tests

* Test cleanup

* Cleanup

* Add test

* One more perf tweak

* Fixes

* Add changelog

* Add changelog

* License header update

* License header updates
2021-11-28 10:47:30 -05:00
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 8a7b5c1b2f
Multiple improvements (#2997)
* Add failing test

* Tidy test for new tokenparam style

* Add removeByQualifier to SearchParameterMap

* Add new property binder for search terms

* Member move, add test for new parser

* whoops missed an add

* Passing test.

Introduced SearchParamTextWrapper to give a type for the binder.
Enhance FulltextSearchSvcImpl to understand TokenParams as well as StringParams.

* Add more to test, change analyzer for template

* Optimize imports

* Minor refactoring

* added eq and gt test cases

* added missing gt search param tests

* Search all CodeableConcepts

* Extract new LuceneRuntimeSearchParam to mediate indexing and searching.

* Fix up broken test with mock

* Add support for identifier type

* Bump for special maven package

* fix-me to todo

* Prevent version check

* FIx version for test

* DSTU2 does not support fluent path

* Don't accidentally strip SPs in DSTU2

* added lt tests

* Add some high-bound test cases

* More test cases and new compressed format

* More test cases

* More test cases

* Re-order columns for easier reading

* Comments

* Cleanup and comments

* Make support :text for all token SPs

* Make support :text for all token SPs

* Fixed incomplete date issue

* Set to the last millisecond 23:59:59.999

* Disabled 4 failed JVM/TZ related test cases

* add test for failing batch bug, remove bounding on queue

* remove parallelism from non-get batch operations

* Fix count for test

* New index layout

* Notes and cleanup

* Notes and cleanup

* remove the jetbrains

* Demote FIXME to WIP

* Change :text search to be lucene simple search and use standardAnalyzer.

* Change :text to require * for prefix match.

* add prefix negative test

* Bump version

* Added changelog

* Add more search parameters to lucene indexing (#3000)

* dirty the branch

* Add oversight to changelog

* Start using jpa indexing for es

* Correct negative search test

* Update templates, index tokens, write new test. TODO gotta modify SB

* Add test for code token search

* add comment

* Flesh out token search

* minor cleanup and comments

* Extract index handling from FulltextSearchSvcImpl

* D'oh.  Actually use elastic to search.

* Move supported query check closer to query builder

* String search test before activating lucene

* Add string:exact to hibernate search.

* Add string:contains search

* cleanup

* demote fixmes to allow build to run.

* Add unmodified string search.

* empty stubs for quantity and reference

* Ignore magic search params in lucene index

* Support full-text on all FHIR releases

* Include reference lookups in ES

* Fix and/or logic in _text

* Test for string with space

* Cherry-pick the NoFT fix

* Disable advanced indexing in a bunch of tests of emitted sql.

* Stub changelog

* Fix :missing flag

* Move DaoConfig up to BaseJpaTest to share teardown

* Disable new indexing for partition test

* Add a different analyzer and field for default string search vs text

* checkstyle for a pre-build

* Index full prefix for string search when using Lucene

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3000-Extend-lucene-indexing.yaml

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/HibernateSearchQueryBuilder.java

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

* Review feedback.

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

* Remove double-check

* Version bump

* Fix typo

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Long Ma <longma@Longs-MacBook-Pro.local>
Co-authored-by: Frank Tao <frankjtao@gmail.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-10-28 15:13:16 -04:00
jamesagnew ccd0d106dc License header updates 2021-10-27 05:57:38 -04:00
James Agnew 9e057574a6
Allow multi-resource Subscription criteria (#3110)
* Allow start criteria subscriptions

* Rework subscription tests

* Subscription cleanup

* Add changelog

* Test fixes

* Test fix
2021-10-26 16:48:13 -04:00
JasonRoberts-smile 20f31e4854
Jr 20211021 chained references 3 (#3107)
* Create index entries for outbound references of contained resources

* build query for chained reference

* fix case where the contained reference is an explicit id rather than a continued chain

* fix contained index to use path names not search param names

* make qualified search work

* cleanup and changelog

* recurse while creating indexes on contained resources

* double link both contained

* longer contained subchains

* adding some failing test cases to illustrate the limitations of qualified searches

* clean up merge cruft

* changelog

* create recursive resource links

* add test coverage for a more complicated case

* changelog

* remove unnecessary check for _contained flag

* fix broken tests
2021-10-25 10:16:10 -04:00
JasonRoberts-smile b267fdb752
Jr 20211018 chained references 2 (#3099)
* Create index entries for outbound references of contained resources

* build query for chained reference

* fix case where the contained reference is an explicit id rather than a continued chain

* fix contained index to use path names not search param names

* make qualified search work

* cleanup and changelog

* recurse while creating indexes on contained resources

* double link both contained

* longer contained subchains

* adding some failing test cases to illustrate the limitations of qualified searches

* clean up merge cruft

* changelog
2021-10-22 12:41:05 +00:00
JasonRoberts-smile d07764e8e5
Jr 20211013 chained references (#3079)
* Create index entries for outbound references of contained resources

* build query for chained reference

* fix case where the contained reference is an explicit id rather than a continued chain

* fix contained index to use path names not search param names

* make qualified search work

* cleanup and changelog

* code review

* fix broken tests
2021-10-19 18:07:29 +00:00
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
Tadgh 120443e561
Bump core version (#3067)
* Bump core version

* Changes for version bump

* Resolve NPE:

* Test fix

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-10-16 14:13:13 -04:00
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
James Agnew aed718bd6f
Avoid redundant PID lookups in transaction processing (#3061)
* Avoid redundant PID lookups in transaction processing

* Add changelog

* Test fix
2021-10-11 13:45:57 -04:00
TipzCM a474e88ed4
issue-2397 implementing the mdm expansion on everything and searches (#3044)
* issue-2397 implementing the mdm expansion on everything and searches

* issue-2397 code cleanup and removal of test code

* issue-2397 some tests

* issue-2397 changelog added

* issue-2397 review fixes

* issue-2397 updated change log with example and fixed failing tests

* issue-2397 test fixing

* issue-2397 fixing test

* issue-2397 review fix

* issue 2397 fixing changelog file

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-10-07 10:46:23 -04:00
Tadgh 59afbe086c
Allow canonical references to support treating given base URLs as local. (#3050)
* Add failling test, works on #2843

* Partial hack to get this working

* Move implementation into pre-processing

* Add changelog

* Move implementation

* Minify Test

* Remove fixmes

* Tidying

* Ensure this only operates on STU versions which support canonical
2021-10-05 11:09:49 -04:00
James Agnew d320b78ae1
Improve synthea ingest performance (#3033)
* Improve synthea ingest performance

* Tweaks

* Fix param splitting

* Update to test

* Add changelog

* Test fix

* Add some runtime checks

* Remove useless test

* Test fix
2021-10-04 05:46:06 -04:00
James Agnew eca725afa4
Improve versioned URL support for ValueSet expansion (#2994)
* Add test

* Test fixes

* Work on expansion errors

* Fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Work on fix

* Test fixes

* Test fixes

* Test fix

* Cleanup

* Test fixes

* Remove accidental commit

* Test fixes

* Version bump

* Add changelog

* Fixes

* Test fix

* Fix conflicts
2021-10-03 19:47:23 -04:00
Ken Stevens b1dd40fdba
Try commenting out clearAllStaticFieldsForUnitTest to see what happens (#3034)
* Try commenting out clearAllStaticFieldsForUnitTest to see what happens

* Rename clearAllStaticFieldsForUnitTest to randomizeLocaleAndTimezone and only do that
2021-09-24 16:01:28 -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
Tadgh 9d982c5e08
Merge branch 'master' into conditional-bug 2021-09-14 08:51:58 -04:00
Tadgh 3ccadd636e
Merge branch 'master' into 2958-consistent-error-handling 2021-09-13 19:38:57 -04:00
Tadgh 5f86370c98 Merge branch 'master' into conditional-bug 2021-09-13 13:04:10 -04:00
Tadgh 59c8765e6a Add implementation to validate conditional URLs post-transaction 2021-09-13 13:03:44 -04:00
Ken Stevens eee7d7e455
code cleanup (#2986)
* failed attempt to get it to work

* Use simplified FhirContext.forCached methods

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java

Co-authored-by: James Agnew <jamesagnew@gmail.com>

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-09-13 03:09:18 +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
jdar8 a02a9e0254
Merge branch 'master' into 2958-consistent-error-handling 2021-09-10 17:02:31 -07:00
Justin Dar 77845d66f7 Improved code formatting 2021-09-10 10:54:33 -07:00
Justin Dar 836948010f Fixes issue (#2958) where Procedure?patient caused inconsistent results and ensured that such requests gave http 400 2021-09-09 16:10:09 -07:00
Ken Stevens 661ca02a6a revert clobbered code 2021-09-09 09:28:01 -04:00
Ken Stevens 5bc571d97d fix test 2021-09-09 01:00:12 -04:00
Ken Stevens 67c8216d73 cleanup 2021-09-08 20:17:14 -04:00
Ken Stevens 81abe26cda improve api 2021-09-08 20:08:06 -04:00
Ken Stevens 519244a2ea unit test passes 2021-09-08 19:14:50 -04:00
Tadgh 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -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 1acaf325c5 Merge branch 'master' into rel_5_5_0 2021-08-23 14:50:29 -04:00
Tadgh cf917d0f82 Version Bump 2021-08-15 16:54:38 -04:00
Tadgh 3fd5f7d6d4 Omit if set to false 2021-08-12 19:12:09 -04:00
Tadgh 669cf05b30 Modify SearchParameterMap toNormalizedQueryString to include value of _contained parameter 2021-08-12 14:25:12 -04:00
Tadgh 6f3006f2ba Fix NPE 2021-08-10 20:56:54 -04:00
Tadgh daa3bc773e remove dummy test 2021-08-10 16:46:03 -04:00
Tadgh fe98162616 Add changelog 2021-08-10 14:59:03 -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
James Agnew 6d37749be8
Add non unique combo search params (#2809)
* Start work on nonunique combo search params

* Work on SQL

* Version bump

* A fix

* Test fixes

* Fixes

* Undo version bump

* Test fixes

* Resolve fixme
2021-07-21 19:14:14 -04:00
James Agnew 6af022062f
Fix issue with partitioning in patient ID compartment mode (#2810)
* Fix issue with partitioning in patient ID compartment mode

* Add changelog
2021-07-21 17:21:23 -04:00
James Agnew d762a07817
Partition patient interceptor (#2766)
* Start work on interceptor

* Implemented

* Add interceptor and docs

* Add docs

* Compile fix

* Test fixes

* Test cleanup

* Test fixes

* Test fixes

* Improve error message

* Add broken tests

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2766-add-patient-id-compartment-interceptor.yaml

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptor.java

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

* Address review comments

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-07-05 09:15:20 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
James Agnew 7185089c9d
Add forced offset search JPA interceptor (#2756)
* Add support for offset searches

* Tests working

* Add changelog

* Test fixes

* Test fix

* More test fixes

* Add commit counter
2021-06-25 10:40:39 -04:00
Ken Stevens 0b05c730fb
don't create a channel if subscriptions are disabled. (#2733)
* don't create a channel if subscriptions are disabled.

* review feedback

* fix test

* fix intermittent

* fix intermittent
2021-06-19 00:00:16 -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
James Agnew a2950324ef
Avoid SQL based transaction dupe check (#2688)
* Avoid SQL based transaction dupe check

* Add changelog

* Test fixes

* Test fixes
2021-05-30 20:26:36 -04:00
James Agnew 24b3f0f30d
Enable mass ingestion mode (#2681)
* Work on fixes

* Work on counts

* Enable mass ingestion mode

* Add changelog

* Test fix

* Test fix

* Test fixes

* Fixes

* Test fix

* Test fix
2021-05-27 18:43:51 -04:00
jamesagnew d70bbad6f1 Expand access 2021-05-27 12:15:37 -04:00
James Agnew c8c596aff4
Fix date search on period with no end (#2676)
* Add test

* Working test

* Update test

* Account for date fixes

* Add changelog

* Add setting

* Test fixes

* Test fix
2021-05-26 21:03:53 -04:00
James Agnew 7a83c76e65
Add validation suppression mode (#2675)
* Add validation suppression mode

* Add changelog

* Compile fix
2021-05-26 17:41:48 -04:00
James Agnew 2c722e64c2
Add support for including qualified star syntax (#2672)
* Add support for including qualified star syntax

* Add changelog

* Add docs

* Build fix
2021-05-23 16:50:37 -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
James Agnew 0bf746f23b
Add support for revincludes to CapabilityStatement generator (#2521)
* Add support for revincludes to CapabilotyStatement generator

* Add changelog

* Fixes

* Test fix

* Test fixes

* Test fix

* Test fix

* More fixes to CS cache

* Test fix

* Test fix

* Test fix
2021-04-05 08:29:04 -04:00
James Agnew 049097e5b4
Improve CapabilityStatement Generation (#2511)
* Start work

* Work on testing

* Version bump

* Test fix

* Compile fix

* Test Fixes

* Test fix

* Test fix

* Compile fix

* Tst fix

* Test fix

* Test fix

* Test fix
2021-03-30 05:48:03 -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 d857048207
Preserve meta values in stored resources (#2481)
* Fix #1731

* Test fix

* Test fixes

* Avoid intermittent failure
2021-03-17 09:23:22 -04:00
James Agnew 807d9d53f0
Improve performance for large transactions (#2462)
* Performance tweaks

* Work on processing speed

* Disable no longer relevant tests

* Work on performance

* Work on tests

* Work on large transaction performance

* Add changelog

* Perf tweaks

* Test fixes

* Resolve FIXME

* Fixes

* Test cleanup

* Fix broken changelog entry
2021-03-09 18:16:02 -05:00
James Agnew be50a46d76
Tweaks to contained searches (#2461)
* Tweaks to contained searches

* Add changelog

* Build fix
2021-03-09 11:51:30 -05:00
Frank Tao bf8e890a0c
Supported contained resource search (#2441)
* POC for indexing on contained resource - test case may failed

* Test contained url

* Add a spt to handle contained flag

* Added search option for contained resource

* Impl contained resource search

* fixed typo

* Reworked on creating index based on the review comments

* Added changelog

* Added more test cases

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-03-09 06:50:23 -05:00
Diederik Muylwyk 6cc8a5ce4d
Fix HasParam#doGetQueryParameterQualifier() (#2460)
* Fix HasParam#doGetQueryParameterQualifier(); add changelog entry

* Fix bad test in SearchParameterMapTest
2021-03-09 06:28:40 -05:00
Ken Stevens 7d769e3b05
Issue 2332 create via put for implementationguide that references some placeholders (#2423)
* begin with failing test

* fixed.  test passes.

* documentation and changelog

* added ConceptMap

* review feedback
2021-02-26 09:44:48 -05:00
Kevin Hartmann 26a385a595 Merge remote-tracking branch 'origin/master' into kh-20200222-search-list 2021-02-24 10:29:38 -05:00
Kevin Hartmann 1eab2caf9f Added _list as a valid parameter in MatchUrlService
Wrote tests for and/or/both processing in FhirResourceDaoSearchListTest.
2021-02-24 10:27:22 -05:00
Patrick Werner cf1f2f27db
added nullchecks to prevent NPE (#2417)
* added nullchecks to prevent NPE
fixes #2171

* Add test from #2171 and changelog

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-02-24 10:09:04 -05:00
Ken Stevens 0e314a9382
fix searchparam not found failure at startup (#2408)
* reproduced and fixed issue reported by Adi

* undoing rearrange
2021-02-22 15:09:59 -05:00
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
Jari Maijenburg 0ec64cfab1
Fixed bug where AND resource search-params were matched as OR params (#2365)
* Fixed bug where AND resource search-params were matched as OR params

* Added InMemoryResourceMatcher test to test searching in a period
2021-02-08 10:23:07 -05:00
Mike G f61cb163ae refactor and modify for prefix and suffix 2021-02-01 12:11:11 -05:00
James Agnew 909d9f742c
Enable Auto-reference versions in JPA (#2323)
* Automatic reference versions

* Auto reference versions

* resolve fixmes

* Add changelog

* Test fixes

* Test fixes

* Resolve fixmes

* Work on versioning

* Add support for _includes

* Update headers

* Change visibility

* One more tweak

* One more API tweak

* Fixes

* Account for review comments

* Fix errorprone reported issue

* Test fix

* Test fixes

* Test fixes
2021-01-27 14:49:10 -05:00
Ken Stevens 749934d5f1
fixed name text indexing (#2309)
* fixed name text indexing

* fixed name text indexing
2021-01-22 15:39:26 -05:00
jamesagnew 4913c33fdf Test fix 2021-01-17 07:24:00 -05:00
James Agnew 1dc4fb2206
Make quantity indexes use double datatype (#2290)
* Make quantity indexes use double datatype

* Add changelog

* Test fixes

* Test fixes

* Disable test
2021-01-16 18:44:15 -05:00
Frank Tao f6d4a40388
UCUM Service Support (#2261)
* Added UcumServiceUtil

* Removed ucum-essense.xml

* Added ucum service existing test cases passed

* Added more test cases

* Merge branch 'master' into ft-ucum-support

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

* Added back extractReferenceParamsAsQueryTokens

* Added changelog and migration script

* Added length for the string type

* Moved UCUM util to hapi-fhir-jpaserver-model

* Renamed UCUM support to Normalized Quantity Search Support

* Moved setNormalizedQuantitySearchNotSupported to AfterEach

* Changed migrate task to 530

* Removed comments

* Fixed in memory search issue and added more test cases

* Fixed the version order

* License header updates

* Updated based on review comments

* Updated the migration task based on review comments

* Fixed RES_TYPE with type String and length 100

* Changed myParamsQuantityNormalizedPopulated type to Boolean class
2021-01-10 21:05:24 -05:00
jamesagnew 12d366c86e License header updates 2021-01-05 18:13:14 -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 d20b07c78e Update license headers 2021-01-01 15:50:24 -05:00
jamesagnew f30999b053 License header updates 2021-01-01 15:07:23 -05:00
James Agnew e4d6c51290
Allow plus symbol in email address match url (#2224)
* Allow plus symbol in email address match url

* Add changelog
2020-12-09 21:52:03 -05:00
James Agnew 30b6244988
Avoid blocking on shutdown (#2206) 2020-12-02 08:44:06 -05:00
jamesagnew 74aed5d107 License headers 2020-11-29 20:53:19 -05:00
Ken Stevens 3d3242cf9a
Resource change listener (#2191)
* init rev

* fix build

* Tweaked the POM config settings and also added some dependency exclusions (commented out for now).

* More re-factoring of the CQL Unit Tests.

* Removed a LogMessages.html file and a minor Unit Test change.

* Unit Tests.

* added debug logging to troubleshoot the dao that has no name

* added debug logging to troubleshoot the dao that has no name

* workaround to get past null dao resourceName issue

* fix jsons to get test to pass.  Test still fails with library id problem

* gitignore

* gitignore

* test passes!  Woohoo!

* undo troubleshooting logging

* added timer and logging.

* added asserts and time multiple evaluations and measure the average

* readme

* adding explanations

* added more explanatory notes

* measure 2 patients

* move pom to use cqf snapshot

* roughed out cache

* roughed out cache

* Added code to VersionChangeCache class.

* added tests

* added polling test

* wrote init version

* wrote init version

* optimized versioncache

* worked on getting tests to pass

* redesigned interfaces

* all tests pass

* fixmes

* fixmes

* rename param

* Added Unit Tests.

* javadoc

* Fixed the 2-Patient Unit Test.

* More Unit Test work.

* make ResourceVersionMap immutable

* Fixed a Unit Test that was failing intermittently by adding a new way to refresh the cache.

* Use a new method called doRefreshAllCaches(0) to force a refresh and have all Listeners called immediately.

* Cleaned up IVersionChangeListenerRegistry interface to make methods more clear and resolved all Unit Tests.

* disabled tests

* disabled tests

* removed unused test method

* fixed refresh logic and added asserts

* moved cache so it can be used by searchparamregistry

* Updated the Cql Unit Tests to be properly configured for Dstu3 or R4.

* started rewriting SearchParamRegistryImpl to use new cache
added init method to listener interface

* added fixmes

* adding tests

* tests pass

* added tests

* Fixed the way CqlProviderFactory Autowires Beans so it can work with both Dstu3 and R4 contexts.

* moar tests

* fix test

* work tests

* reverting unneccessary refactors

* undo unneccessary import changes to reduce MR size

* undo unneccessary import changes to reduce MR size

* Unit Test fixes...more to come...

* add unregister

* fix tests

* Changed ResourceVersionCache to use a Map of Maps.

* searchparam test

* test passes

* resolved fixme

* fixmies

* strengthen test asserts

* More Unit Test changes and added some FIMXME items.

* changed from long to changeresult

* renamed VersionChange -> ResourceChange

* fixed delete bug

* organize imports

* fix test

* add update test

* add test reset function

* fix stack overflow

* fix startup race condition (might still be intermittent)

* found the problem.  delete doesn't work because we can't look up the deleted resource to find out what its name is

* fixed regression

* abandoned idea of incrementally updating searchparam registry.  Rebuilding every time--it doesn't change that often.

* fix test

* begin with failing test

* test passes

* fixmes and javadoc

* fix test

* fixme

* fix test

* whack-a-mole.  Either subs pass or cql passes.  Something's fishy with the FhirContext

* fix subscription test initialization

* fix method name

* Re-factored the CqlProvider Unit Tests.

* changed ResourceChange API

* add interface

* add interface

* fix test

* add schedule test

* add doc

* init rev

* FIXME

* modify FhirContext change

* change fhirContext.getResourceTypes to lazy load

* converted subscriptions

* converted subscriptions

* begin with failing test

* test passes

* fix test

* test coverage

* test coverage

* test coverage

* test coverage

* good coverage now

* pre-review cleanup.  I think I found a bug.

* moved cache into listener entry
tests pass with fixmes

* fix test

* fix test

* fix test

* fixme

* FIXMEs

* merge cache and registry

* method reorg

* javadoc

* javadoc done.  all FIXMEs resolved.

* change log

* changes needed by cdr

* spring config cleanup

* james feedback

* james feedback

* might not work. Try moving resourcechangeconfig into searchparam config

* merge ResourceChangeListenerRegistryConfig.java into SearchParamConfig

* fix test

* fix SubscriptionLoader

* fix SubscriptionLoader

* create ResourceVersionMap from resources

* added cache handle interface

* fix test

* javadoc

* fix test

* fix test

* James feedback: clone searchparametermap

* fix startup

* fix test

* fix test

* fix intermittent

* pre-review cleanup

* FIXME

* final FIXME yay!

* Address a couple of my own reviw comments

Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2020-11-29 19:42:40 -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
James Agnew 228e75b501
Bump core to latest versions (#2154)
* Bump core to latest versions

* Compile fix

* Bump to non snapshot core library
2020-11-03 15:43:37 -05:00
James Agnew 5e8ec8d6f3
Resolve crash in InMemory SP resolver for empty source (#2150)
* Resolve crash in InMemory SP resolver for empty source

* Add changelog
2020-10-28 14:30:32 -04:00
James Agnew 8000d2d0cf
SQL Join Rework (#2086)
* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* added the other six index links

* trying different annotations

* Start testing

* Update resources on package install

* Add changelog

* Join rework

* CLean up SQL builder

* Add docs

* SP rework

* Join work

* Work on params

* Work on refactor

* Work on chains

* Work on joins

* Rework queries

* Work on queries

* Many more tests passing

* Refs test

* Work on sorting

* Work on tests

* More joins work

* Work on tests

* Work on queries

* Tests passing

* More test fixes

* Test fixes

* Work on SQL

* Tests passing

* Add some tests

* Add some tests

* License headers

* Use entity manager to get datasourcd

* One more fix

* Model cleanup

* Ongoing work

* Fixes

* Fixes

* Work on joins

* Ongoing fixes

* Merge conflict

* Cleanup

* clean up unused fields

* Work on join

* COmpile fix

* Rework querying

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java

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

* Address review comments

* Resolve fixmes

* Test fix

* Test fixes

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-10-26 05:24:26 -04:00
Ken Stevens 3b91873b7c
delete expunge (#2131)
Added delete _expunge=true
2020-10-20 17:21:50 -04:00
Tuomo Ala-Vannesluoma 1435540320
Improve synchronous searching by providing offset & limit support (#2059)
* Improve synchronous searching by providing offset & limit support

Add support for offset querying which leverages paging at the query level
Add configuration for search default page size and search maximum page size
If using offset, always use synchronous searching to avoid extra database insert/update etc.
When using offset, only calculate count if it's wanted
Validate params closer to provider and handle size if search returned "all" (or last)

* Review and test fixes

Comment _offset as nonstandard parameter
Make synchronous search always count the total value (for now)
Fix issue with FulltextSearchSvcImpl mutating param map
Dirty fix for BaseJpaTest (not sure how to fix the including resources issue)

* Remove temporary count querying fix for synchronous loads

* Fix offsetting of everything operations, do not drop zero offset

* Fix jpa test default and maximum page size, add some fixmes to tests before resolved

* Ignore one failing test, fix others

* Fix Dereferenced variable may be null

* Fix everything paging in R4 by adding DISTINCT if synchronous load is used

Also fix assertion of size when hitting fetchSizeDefaultMaximum

* Add documentation about offset annotation and paging

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-10-12 17:42:03 -04:00
James Agnew 2134d40f1c
Account for timezones in lastUpdated search (#2113)
* Add test

* Fix

* Add changelog

* Test fixes

* Test fix

* Test fixes

* Resolve fixme

* Test fixes

* Remove debug logs

* Try to get CI tests passing again
2020-10-09 07:52:46 -04:00
James Agnew ef4f3df945
Don't install draft package contents (#2099)
* Don't install draft package contents

* Add changelog

* Add changelog
2020-09-22 09:44:36 -04:00
James Agnew 437e81fc65
Support multiple updates of one resource in a transaction (#2050)
* Support multiple updates of one resource in a transaction

* Test update

* Add changelog

* Test fix
2020-08-25 05:55:54 -04:00
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