Commit Graph

221 Commits

Author SHA1 Message Date
samuelwlee2 1b55f49a60
4153 extend $member match operation to store consent resource if matched (#4165)
* added senstive and regular filter

* add UUID to Consent

* blah

* fix merge with master

* fixing merge

* blah

* fhir tests

* use constructor injection

* put all tests together

* blah

* blah

* finalize

* add consent update patient and performer reference

* fixes after code review

* blah

* refactor to save consent once

* blah

* fix performer and add validation

* code clean up

* add changelog

* add hrex member match flag

* fix PatientMemberMatchOperationR4Test

* adding code fixes after code review

* move changelog file

* bump version

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2022-10-31 13:33:54 -04:00
Tadgh 31a193fbd3
Bump to 6.3.0 (#4211) 2022-10-28 02:40:59 +00:00
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
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
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
Tadgh 18093bf311
Hl7 core bump (#4110)
* Bump to 5.6.67

* wip

* wip

* Remove capabilitystatement2

* Update fhirversion.properties

* Remove xpathusage for r5

* add new structure defs
2022-10-06 17:50:45 +00:00
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
James Agnew 3935b78083
Add operation blocking interceptor (#4057)
* Add operation blocking interceptor

* Work on interceptor

* Work on interceptor

* FIx up docs

* Address CVE

* Tweak changelog

* Address review comments
2022-09-25 14:19:17 -04:00
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
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
Patrick Werner b026ac10e5
Bump fhir.core to latest version (#3593)
* adding version.yaml, updating version in pom.xml

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

* fixed

* remove sout

* add msg.code

* fix failed tests

* fix equal sign

* update msg code

* extract method

* Fix up code numbers

* Clean changelog

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

* Revert final artifact version

* add graphql test (#3585)

* added graphql birthdate test

* fix variable name

* typo

* 3506 mdm log enhancement (#3543)

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

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

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

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

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

* Update MdmMatchLinkSvc.java

#3506 move "narrowed down" log to different place

* #3506 added scores and tests

#3506 added scores and tests

* #3506 formatting

#3506 formatting

* #3506 create changelog file

#3506 create changelog file

* #3506 fix typo

#3506 fix typo

* #3506 fix part 3, minor formatting

#3506 fix part 3, minor formatting

* #3506 fix tests

#3506 fix tests

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

* mdm matching (#3579)

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

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

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

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

* begin with failing test

* fixed

* changelog

* add jira tag

* Update to 6 1 (#3582)

* added changelog folder, upped version

* version enum

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

* revert merge master doh! bad reflexes

* revert merge origin master

* unrevert revert.  ugh what a pain

* merge recovery.  fix poms.

* merge recovery.  more reverting

* merge recovery.  more reverting

* merge recovery.  more reverting

* Revert "merge recovery.  fix poms."

This reverts commit ae6e0ddb06.

* more revert revert reversions

* more revert revert reversions

* pre-review cleanup

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

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

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

* License

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

* remove duplicated Msg.code

* Ks 20220508 log colour (#3592)

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

* change log

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

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

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

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

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

* 3584 case sensitive string elasticsearch (#3596)

* Fix for case-sensitive search with newer elasticsearch

* Test and fix ascii normalization too

* more test cases

* comments

* Docs update empi usecase (#3598)

* Update diagram for use case 5

* Add new page for database support

* Licnese

* Mb norm fix (#3604)

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

* removed duplicated dependency with wrong version

* fixed test file(added a Base64 string)

* fixed tests

* fixed test:
history?_since is an instant

* removing time from date-strings in examples

* fixed more instant strings

* changed filtering of messages to messageId

* fixed messageId filter on missing profiles

* changed messageID system string to Grahames preferred String

* updated MsgIds of unsupported methods

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

* fixed GraphQL Test

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

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

* updated Msg.codes

* updated Msg.codes

* fixed duplicated Msg.codes

* setErrorOnInvalidValue set to false in test

* reverted date precision test changes

* updated r5 resources to latest build version

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

* Try to fix message codes

* Test fixes

* Checkstyle fix

* Test fix

* Try to avoid CME

Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-08-03 16:12:59 -04:00
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
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
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
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 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
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
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 5b413a9135
Package move-around (#3488)
* moved classes

* Bump version

* licensing

* Repackage, fix messages

* reject empty streams

* Remove dead import

* Version bump

* Fix up test to actually return a data stream

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

* Updates

* Ongoing work

* Ongoing work

* Work on reindex

* Reindex work

* Add logging

* Fix typo

* Test fix

* Test fix

* Address fixme

* Liocense header

* Resolve fixme

* Add logging

* Update logs

* Address review comments

* License header

* Test fixes

* Test fix

* Test fixes

* Test fix

* Version bump

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

* improve logging

* improve logging

* add full comparator

* wrap resource search param map

* rename wrapped map methods

* add fixmes

* further searchparam encapsulation

* fix regression found by test

* improve logging

* pre-review cleanup

* pre-review cleanup

* bump hapi version

* license

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

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

* ValueSet improvements

* Work on narrowing

* Work on narrowing

* Work on narrowing

* Work on narrowing

* Add test

* Work on narrowing interceptor

* Work on narrowing

* License headers

* Refactor code narrowing

* Add docs

* Version bump

* Test fix

* Test fixes

* Build fix

* Fixes

* Version bump

* Test fix

* License header updates

* Build fix

* Test fixes

* Test fix

* Test fix

* Docs fix

* Test fix

* Test fix

* Resolve fixme

* Bump

* Force a CI build

* Make CI happen again
2022-03-01 09:16:31 -05:00
Tadgh 68c1015552
Bump core to 5.6.36 (#3433)
* Bump version

* Add changelog, make use of theNoInactive flag

* add test

* remove magic strings
2022-03-01 08:23:48 -05:00
James Agnew b7d1ae217d
New batch framework / Bulk Import (#3387)
* Work on new batch framework

* Work on new batch framework

* Work on new batch framework

* Work on batch

* Compile working

* Work on bulk import

* Adjust import

* Work

* Work on batch

* Bump version

* WOrk on new batch processes

* Work on bath

* Bump to PRE4

* Build fixes

* CLeanup

* Small tweak

* Add exception code

* Test fixes

* Test fixes

* Test fix

* Additional synchronization

* Add license headers

* Test fixes

* Test fixes

* Add changelogs

* Address PG

* Test fix

* Test fix

* Test fixes

* Review notes

* Work on tests

* Test fixes

* Test fix

* Work on tests

* Tets fix

* Test fixes

* Test fixes

* Add missing exception codes

* Test fix

* Test fixes

* More test fixing

* License headers

* Test fix

* Add new test logging

* Work on tests

* Test fixes

* Test fix

* Resolve fixme

* Try to avoid test failure

* Add import command

* Work on storage

* Fix error codes

* Fixes

* License header

* Build fix

* Build fixes

* Fix dep
2022-02-27 16:04:49 -05:00
Tadgh ca6381a52a Build fix 2022-02-23 18:43:55 -08:00
James Agnew cc44deee1a
GraphQL Introspection Support (#3348)
* Start working on graphql Schema

* Start testing

* Work on introspection

* Work on introspection

* Use integers for date ordinals

* Add changelog

* GraphQL updates

* Ongoing wrk

* Cleanup

* Bump core lib

* Add changelog

* Clean up dependencies

* CLeanup

* Add missing message

* Test fix

* Change to force CI
2022-02-22 09:48:57 -05:00
Ken Stevens 631391819b
remove hapi jpa spring config hierarchy (#3390)
* initial refactor to remove hapi jpa spring config hierarchy

* fix poms

* fix batch config

* dependency rearrangement arising from further testing

* fix searchDao bean name

* fixed dstu2 tests

* consolidate validation config

* dstu2 validation regression (man dstu2 support is expensive)

* fix test (with WIP comment)

* restore poms

* fix demo projects

* fix build

* bumping version

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

* Working

* Version bump

* Add documentation

* Add test

* Checkstyle message cleanup

* Add reverse rule

* Test ficx

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fix

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

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

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

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

* Test fixes

* Fix conflict

* Add setter

* Test fixes

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

* Add new version enum

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

* Initial design of adding exception codes to exceptions

* change int module name to string

* add comment

* shorten message

* shorten message

* added checkstyle

* developing checker

* completed checkstyle plugin and unit test for it

* fix NPE

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

* change parameter order in InvalidResponseException

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

* exclude generated files

* BIG COMMIT added error codes to all exception throws

* example test fix

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

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

* fix test

* merge master

* merge master

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

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

* Modified assert messages to better match new error codes

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

* Modified assert messages to better match new error codes

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

* Reverted changes on azure-pipelines.yml

* updated hapi-fhir version for checkstyle module

* changes to azure-pipelines.yml

* changes to azure-pipelines.yml

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

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

* reverted changes to azure-piplines

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

* Attempted fix on checkstyle build error

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

* Attempted fix on checkstyle build error

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

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

* reverted changes for hapi-deployable-pom

* add javadoc

* update last code

* Attempted fix on checkstyle build error

* Finished adding in missing error codes to pass Checkstyle checks

* Test pipelining

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

* Merge

* Fixing Checkstyle error

* Attempted fix for date error

* Add error code onto assert statement

* Add in a couple more error codes

* Fixing assert statements

* Bump to static version for dependency

* Adding error code to message

* Adding error codes to exceptions

* Adding error codes to exceptions

* Change to work with cdr branch

* Update to faulty error message

* Merge changes

* allow checkstyle pom to deploy

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com>
Co-authored-by: Predap <simon.zuccherato@gmail.com>
Co-authored-by: Predap <46201929+Predap@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-01-31 13:10:15 -08:00
Tadgh 0df332763e Add okhttp dep 2022-01-27 14:03:37 -08:00
Tadgh cd29d369b6
Add okhttp dep to r5 and indicate which deps need to be included (#3332) 2022-01-25 18:39:32 +00:00
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
Mark Iantorno d60d07b697
Validate contains change (#3209)
* wip

* The updated changes to the validator that were pulled in from the core dependencies are not backwards compat. Need to bump HAPI version.

* pointing to stable core version

* review feedback

* Add changelog

Co-authored-by: markiantorno <miantorno@pop-os.localdomain>
2021-12-06 11:25:00 -05:00
James Agnew d072357c2a
Move graphql provider (#3214)
* Move graphql provider

* Version bump
2021-12-05 17:22:20 -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 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
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
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
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
markiantorno 367b338d85 Updating HAPI to use latest core lib changes. 2021-08-18 11:06:14 -04:00
Tadgh cf917d0f82 Version Bump 2021-08-15 16:54:38 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -04:00
Ken Stevens f5dfc3a5ed
New reindex spring batch operation (#2845)
* first sweep to add new $reindex job

* first cut done.  next up integration test.

* start roughing out reindex everything

* Failing test

* test passes

* add BundleUtil helper method

* rough in processEverything

* rough in processEverything

* fix mock test

* merge master

* Make BaseJpaTest.mySrd lenient.

* fix test

* reindex everything works with FIXMEs

* reindex everything more tests

* moar tests

* moar tests

* fix test

* fix test

* fix regression and fix test

* fix test cycle

* fixme

* fix test

* test provider layer

* reindex everything partition aware

* yay last fixme!

* run reindex in partitioned threads

* add fixmes for areas that require extra testing

* added transaction and log message

* manual integration testing

* changelog

* reindex all partitions

* bump hapi version

* fix test

* moar test

* pre-review cleanup

* fix javadoc

* review feedback

* review feedback

* review feedback

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

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

* review feedback

* review feedback

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

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

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

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

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

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

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

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

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

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

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

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

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

* Add changelog

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

* Add operation

* Wire up jpa provider.  Begin with failing test.

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

* delete expunge job parameter validation with test

* implemented reader
stubbed processor, writer

* wip for master merge

* started implementing reader

* started implementing reader

* working with stubs

* happy path batch delete expunge is done

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

* IT test works now

* add reader test

* Converted delete _expunge=true to use new batch job

* DeleteExpungeDaoTest passes

* Fix test

* Change batch size to integer

* rename search count to batch size

* Make delete expunge partition aware

* updated docs

* pre-review cleanup

* change log

* add partition id to SystemRequestDetails

* Make RequestPartitionId serializable

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

* fix tests

* test pointcut gets called

* assert on pointcut calls

* Add resource type to STORAGE_PARTITION_SELECTED pointcut

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

* bump hapi-fhir version

* copyrights

* restore deleteexpungeservice for mdm

* restore deleteexpungeservice for mdm

* fix test

* public constants

* convert instant to date

* Moved expunge constants to ProviderConstants

* final review

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

* fix tests

* fix tests

* fix tests

* fix tests

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* improve logging

* bump version

* version bump

* recovering from failed merge

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

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

* Add docs

* Version bump

* Authorize any

* Add bulk export - all

* Address lgtm issue
2021-06-06 20:47:43 -04:00
jamesagnew ff2698d4d1 Merge branch 'rel_5_4' 2021-05-19 09:22:11 -04:00
jamesagnew de56f440cb Version bump 2021-05-18 17:14:14 -04:00
jamesagnew 2068372998 Version bump 2021-05-07 17:43:54 -04:00
jamesagnew 63c4b22cd3 Undo bump 2021-05-07 17:42:50 -04:00
jamesagnew 17e41520a4 Version bump 2021-05-07 17:41:39 -04:00
jamesagnew 5db01f3139 Build fixes 2021-05-03 05:57:45 -04:00
James Agnew 0cea403800
Fix vulnerability warning on maven plugin (#2621)
* Fix vulnerability warning on maven plugin

* Compile fixes

* Fix bootstrap dep

* Test fix

* Fix tests

* FIx deps
2021-05-02 12:14:32 -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