Commit Graph

245 Commits

Author SHA1 Message Date
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
jmarchionatto e45f7ee9cb
Issue 3450 there is no way to recreate freetext indexes for terminology entities (#3463)
* Add reindex-terminology batch command

* Handle number of thread throttling and concurrency with other terminology batch operations

* Add required dbcp2 dependency

* Fix test

* Improve ConnectionPoolInfoProvider setup. Handle maximum connections.

* Remove java higher version construction

* Remove unused config

* Add reindex terminology integration test.
Reset termConcept counters before pre-expanding, which otherwise accumulate if it was pre-expanded before.

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-03-18 08:39:12 -04:00
Ken Stevens dfd99c5471
improve search parameter registry logging (#3452)
* Startup log cleanup.  Use cached fhir contexts.

* improve logging

* improve logging

* add full comparator

* wrap resource search param map

* rename wrapped map methods

* add fixmes

* further searchparam encapsulation

* fix regression found by test

* improve logging

* pre-review cleanup

* pre-review cleanup

* bump hapi version

* license

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

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

* ValueSet improvements

* Work on narrowing

* Work on narrowing

* Work on narrowing

* Work on narrowing

* Add test

* Work on narrowing interceptor

* Work on narrowing

* License headers

* Refactor code narrowing

* Add docs

* Version bump

* Test fix

* Test fixes

* Build fix

* Fixes

* Version bump

* Test fix

* License header updates

* Build fix

* Test fixes

* Test fix

* Test fix

* Docs fix

* Test fix

* Test fix

* Resolve fixme

* Bump

* Force a CI build

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

* Work on new batch framework

* Work on new batch framework

* Work on batch

* Compile working

* Work on bulk import

* Adjust import

* Work

* Work on batch

* Bump version

* WOrk on new batch processes

* Work on bath

* Bump to PRE4

* Build fixes

* CLeanup

* Small tweak

* Add exception code

* Test fixes

* Test fixes

* Test fix

* Additional synchronization

* Add license headers

* Test fixes

* Test fixes

* Add changelogs

* Address PG

* Test fix

* Test fix

* Test fixes

* Review notes

* Work on tests

* Test fixes

* Test fix

* Work on tests

* Tets fix

* Test fixes

* Test fixes

* Add missing exception codes

* Test fix

* Test fixes

* More test fixing

* License headers

* Test fix

* Add new test logging

* Work on tests

* Test fixes

* Test fix

* Resolve fixme

* Try to avoid test failure

* Add import command

* Work on storage

* Fix error codes

* Fixes

* License header

* Build fix

* Build fixes

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

* fix poms

* fix batch config

* dependency rearrangement arising from further testing

* fix searchDao bean name

* fixed dstu2 tests

* consolidate validation config

* dstu2 validation regression (man dstu2 support is expensive)

* fix test (with WIP comment)

* restore poms

* fix demo projects

* fix build

* bumping version

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

* Working

* Version bump

* Add documentation

* Add test

* Checkstyle message cleanup

* Add reverse rule

* Test ficx

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fix

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

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

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

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

* Test fixes

* Fix conflict

* Add setter

* Test fixes

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

* Add new version enum

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

* Initial design of adding exception codes to exceptions

* change int module name to string

* add comment

* shorten message

* shorten message

* added checkstyle

* developing checker

* completed checkstyle plugin and unit test for it

* fix NPE

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

* change parameter order in InvalidResponseException

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

* exclude generated files

* BIG COMMIT added error codes to all exception throws

* example test fix

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

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

* fix test

* merge master

* merge master

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

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

* Modified assert messages to better match new error codes

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

* Modified assert messages to better match new error codes

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

* Reverted changes on azure-pipelines.yml

* updated hapi-fhir version for checkstyle module

* changes to azure-pipelines.yml

* changes to azure-pipelines.yml

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

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

* reverted changes to azure-piplines

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

* Attempted fix on checkstyle build error

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

* Attempted fix on checkstyle build error

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

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

* reverted changes for hapi-deployable-pom

* add javadoc

* update last code

* Attempted fix on checkstyle build error

* Finished adding in missing error codes to pass Checkstyle checks

* Test pipelining

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

* Merge

* Fixing Checkstyle error

* Attempted fix for date error

* Add error code onto assert statement

* Add in a couple more error codes

* Fixing assert statements

* Bump to static version for dependency

* Adding error code to message

* Adding error codes to exceptions

* Adding error codes to exceptions

* Change to work with cdr branch

* Update to faulty error message

* Merge changes

* allow checkstyle pom to deploy

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com>
Co-authored-by: Predap <simon.zuccherato@gmail.com>
Co-authored-by: Predap <46201929+Predap@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-01-31 13:10:15 -08:00
Tadgh 3d4a0d89cf
add needed dependendencies for mysql and mssql (#3343)
* add mssql and mysql flyway dependencies

* add exclusions to CQL to prevent duplicate classes on the classpath

* wip

* ad more databases

* finish test
2022-01-28 03:03:13 +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
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
James Agnew 310a4cdb58
Migrate CLOB columns to LOB (SMILE-3072) (#3016)
* Migration finished

* Work on LOBS

* Add to ClobMigrated annotation

* Deal with lobs

* Work on new approach

* HAPI FHIR version bump

* Add changelog

* Add license header

* Fix intermittent

* CLeanup

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

* move term service apis

* nearly done

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

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

* create new SearchConstants class to store platform independent search constants

* move a couple of subscription services

* move transaction processor adapter to storage

* version bump

* move searchparam

* fix test

* fix compile includes

* fix text

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

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

* move bulk import apis

* create hapi-fhir-jpa

* create hapi-fhir-jpa

* move CircularQueueCaptureQueriesListener to japi-fhir-jpa

* move mdm logs to storage-api

* move gziputil to storage-api

* move quartz scheduling to hapi-fhir-jpa

* move default subscription channel factory to storage-api

* consolidated batch constants

* correct accidental Logs change

* remove dependency of cdr-api on cdr-persistence

* fix javadoc

* pom descriptions

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

* Resolve fixmes

* Build fix

* Test fix

* Test fix

* Test fix

* Work on metadata

* Fixes

* Test fixes

* Test fix

* Test fix

* Test fixes

* Test fix

* Work on test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fix params

* Resolve fixme

* Adjust changelogs

* Version bump to 5.6.0-PRE7

* Add license header

* Bump version to 5.6.0-PRE5-SNAPSHOT
2021-09-11 18:27:18 -04:00
Tadgh 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -04:00
Ken Stevens 346e29920a
Issue 2927 convert mdm clear to spring batch (#2929)
* initial roughout of mdm clear batch job

* still roughing out classes

* finished first draft of reader

* most tests passing now

* all tests pass.  now FIXMEs

* FIXMEs done.  Time for regression.

* fix test

* changelog and docs

* fix test

* pre-review cleanup

* version bump

* move spring autowire deps for cdr

* move spring autowire deps for cdr

* finally got beans working phew

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

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

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

* review feedback

* review feedback

* Remove inheritance

* fix beans

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

* first cut done.  next up integration test.

* start roughing out reindex everything

* Failing test

* test passes

* add BundleUtil helper method

* rough in processEverything

* rough in processEverything

* fix mock test

* merge master

* Make BaseJpaTest.mySrd lenient.

* fix test

* reindex everything works with FIXMEs

* reindex everything more tests

* moar tests

* moar tests

* fix test

* fix test

* fix regression and fix test

* fix test cycle

* fixme

* fix test

* test provider layer

* reindex everything partition aware

* yay last fixme!

* run reindex in partitioned threads

* add fixmes for areas that require extra testing

* added transaction and log message

* manual integration testing

* changelog

* reindex all partitions

* bump hapi version

* fix test

* moar test

* pre-review cleanup

* fix javadoc

* review feedback

* review feedback

* review feedback

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

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

* review feedback

* review feedback

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

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

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

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

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

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

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

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

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

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

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

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

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

* Add changelog

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

* Add operation

* Wire up jpa provider.  Begin with failing test.

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

* delete expunge job parameter validation with test

* implemented reader
stubbed processor, writer

* wip for master merge

* started implementing reader

* started implementing reader

* working with stubs

* happy path batch delete expunge is done

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

* IT test works now

* add reader test

* Converted delete _expunge=true to use new batch job

* DeleteExpungeDaoTest passes

* Fix test

* Change batch size to integer

* rename search count to batch size

* Make delete expunge partition aware

* updated docs

* pre-review cleanup

* change log

* add partition id to SystemRequestDetails

* Make RequestPartitionId serializable

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

* fix tests

* test pointcut gets called

* assert on pointcut calls

* Add resource type to STORAGE_PARTITION_SELECTED pointcut

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

* bump hapi-fhir version

* copyrights

* restore deleteexpungeservice for mdm

* restore deleteexpungeservice for mdm

* fix test

* public constants

* convert instant to date

* Moved expunge constants to ProviderConstants

* final review

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

* fix tests

* fix tests

* fix tests

* fix tests

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* improve logging

* bump version

* version bump

* recovering from failed merge

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

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

* Add docs

* Version bump

* Authorize any

* Add bulk export - all

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

* Version bumps

* Add changelog

* Avoid guava issue

* Test fix

* Test fix

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

* SQL query tidying

* Add changelog

* Test fixes

* Tests passing

* Ongoing work

* Test fixes

* Test fixes

* Build fix

* Cleanup

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

* Fixes

* Work on OpenAPI

* Cleanup

* Cleanup

* More swagger work

* Build fix

* More work

* More work

* Add documentation

* Docs fixes

* Add changelog

* License updates

* Add API

* Cleanup

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

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

* Work on scripts

* Add docs

* Compile fix

* Work on fixes

* Fix tests

* Test fix

* Test fix

* Build fix

* Tests

* Build fix

* Work on pipeline

* Version bump

* Test fix

* Version bump

* Test fix attempts

* Test fix

* Test fix

* Remove accidentally committed files

* Fixes

* Tets fixes

* Test fix

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fixes

* License header updates

* test fix

* Test fixes

* Test fix

* Test fixes

* Test fix

* Checkstyle bump

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

* Work on bulk import

* Have batch working

* Working

* Working

* More work

* More work on bulk export

* Address fixmes

* License header updates

* Test fixes

* License header updates

* Test fix

* Test fix

* Version bumps

* Work on config

* Test cleanup

* One more version bump

* Version bump

* CLeanup

* A few additions

* Test fixes

* Test fix

* Test fix

* Migration fix

* Test fix

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

* Add changelog

* Add tests

* Cleanup

* Test fix

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

* Work on collapsing search param

* Search param cleanup

* Work on build

* Test fix

* Test fixes

* Ongoing work

* Test fix

* Compile fix

* Test fixes

* Test fix

* Test fix

* License header updates

* Remove fixme

* Cleanup

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

* Work on generation

* Add terminology mapping and display population interceptors

* Add changelog

* License header updates

* Test fixes

* Fix typo

* Interceptor fixes

* License header update

* Test fixes

* Mapping fixes

* Version bump

* License header updates

* Add null tests

* Add null guard

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

* Docs changes

* Docs tweaks

* Docs tweak

* Spelling fixes

* Docs tweaks
2021-02-18 11:07:49 -05:00
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
dependabot[bot] feff734736
Bump jaxb-runtime from 2.3.1 to 3.0.0 (#2289)
* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

Signed-off-by: dependabot[bot] <support@github.com>

* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

Signed-off-by: dependabot[bot] <support@github.com>

* Add jakarta bindings

* Dependency cleanup

* More depndency cleanup

* Work on deps

* Replace transaction annotation

* Cleanup

* Another fix

* Build fix

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-22 11:24:23 -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
Kevin Dougan SmileCDR 9036df25fa
2229 - Remove support for the upload-igpack CLI command. (#2233)
* 2229 - Remove support for the upload-igpack CLI command.

* 2229 - Revert changes made to the ValidateCommand class since it only takes an igpack as a parameter and therefore, should NOT have been removed.

* 2229 - Remove the igpack option from the Validate command.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_0/2229-remove-upload-igpack-command.yaml

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

Co-authored-by: Kevin Dougan <kevindougan@kevins-mbp.lan>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-12-14 09:50:16 -05:00
jamesagnew 0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew 4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -05:00
jamesagnew 92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew 5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
jamesagnew 52c8e3551c Version bump to 5.1.0-SNAPSHOT 2020-05-15 14:43:32 -04:00
jamesagnew fe0e07a313 Bump to 5.0.1 2020-05-15 05:47:01 -04:00
jamesagnew 1d13e29ac0 Version bump to 5.1.0-SNAPSHOT 2020-05-12 20:04:20 -04:00
jamesagnew d631ecff4a Prepare for 5.0.0 2020-05-12 11:49:18 -04:00
James Agnew 22413911bf
Validation api changes (#1719)
* Validation enhancements

* Work on validation api reworking

* Keep working on validation API

* Keep working on new term API

* Work on validation api

* Ongoing work on validation

* Work on integrating validation

* Work on validation API

* Add to validation API

* Work on validation

* Work on API

* Work on validation

* Work on validation API

* Work on validation API

* Work on validation api

* Work on validation API

* Work on validation api

* Validation API changes

* Work on API

* More work on validationo API

* Work on validation API

* FIxes

* WOrk on validation api

* Work on validation API

* Tests passing!

* More cleanup

* More validation API changes

* Fix intermittent test failure

* Package reorg

* Validation API work

* Work on doocumentation

* Work on API

* More work on new validation API

* Fix errorprone-reported error

* Test fixes

* Documentation updates

* Documentation tweaks

* Work on API

* Bean name adjustments

* Build fixes

* Some test fixes
2020-03-17 13:28:59 -04:00
jamesagnew ddc7b601ee Version bump to 4.3.0-SNAPSHOT 2020-02-16 19:23:22 -05:00
jamesagnew 4fd80cfca7 Bump to 4.2.0 2020-02-16 19:00:15 -05:00
Ken Stevens 6543da1470 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 2019-11-15 09:28:30 -05:00
James Agnew 497a96ae68 Version bump for next round of development 2019-11-12 22:09:21 -05:00
jamesagnew f99ad981b5 Version bump to 4.1.0 2019-11-12 16:08:20 -05:00
Ken Stevens 18e8604494 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
2019-10-27 08:29:52 -04:00
James Agnew 464c6c5b45
Upgrade dependencies and addess Semmle issues (#1554)
* Version bumps

* FIx build issues

* Address a few Semmle issues

* Work on tests

* Some test fixes

* Test fix

* Fix deletions

* Test fix

* Fix intermittent test failure

* One more dependency bump

* Add some test logging

* Remove bad import

* Add some tests

* Test updates
2019-10-22 17:10:58 -04:00
Ken Stevens 790f655a95 flyway initial implementation (with FIXMEs) 2019-10-06 17:55:10 -04:00
jamesagnew e1b43d811f Version bump to 4.1.0-SNAPSHOT 2019-08-14 14:06:06 -04:00
jamesagnew 3f22456b0f Bump version to 4.0.0 2019-08-14 11:06:26 -04:00
Ken Stevens 48c8497086 Changed migration test from derby to h2
Added a new test from 340 to latest version.
2019-08-02 16:00:43 -04:00
Stig Rohde Døssing b56f59542a Move JettyUtil to new module 2019-06-14 18:34:45 -04:00
James Agnew 50a8c66bf5 Version bump to 4.0.0-SNAPSHOT 2019-05-30 17:13:03 -04:00
jamesagnew 73aa53be8f Release 3.8.0 2019-05-30 16:50:04 -04:00
James Agnew 0f8c8d18e2 Bump version to 3.8.0-SNAPSHOT 2019-02-06 20:02:28 -05:00
jamesagnew 207015c3af Version bump to 3.7.0 2019-02-05 21:36:38 -05:00
James Agnew a0cb7edd08 Version bump a few dependencies 2018-12-22 20:13:03 -05:00
James Agnew 84acafe3af Streamline expunge operation 2018-11-15 11:37:16 +01:00
James Agnew 75210d614b Bump to 3.7.0-SNAPSHOT 2018-11-12 22:37:52 -05:00
James Agnew bbcbcbf5d6 Don't hardcode commons-compress version 2018-11-12 12:26:17 -05:00
James Agnew 63af04a7b4 Prepare for 3.6.0 release 2018-11-12 05:40:55 -05:00
James Agnew 706e004b9d Bump to 3.6.0-SNAPSHOT 2018-09-19 10:24:48 -04:00
James Agnew daef975734 Version bump to 3.5.0 2018-09-08 07:22:21 +08:00
James Agnew 4852b0b60f Work on migration 2018-09-08 07:14:43 +08:00
James Agnew f5d567cd00 Work on migrator 2018-09-08 03:30:35 +08:00
jamesagnew abcf7852b1 Tests pasing locally 2018-05-31 09:10:34 -04:00
jamesagnew 35a827eac3 Support for JDK10 working now 2018-05-30 08:54:16 -04:00
James Agnew a52805e504 Work on JDK9 support 2018-05-30 05:45:08 -04:00
Diederik Muylwyk 0e2c57fa60 Bumping version. 2018-05-28 17:44:38 -04:00
Diederik Muylwyk 2871920734 Preparing release. 2018-05-28 10:45:47 -04:00
patrick-werner 58e231d299 removed duplicated hapi-fhir-igpacks dependency 2018-05-15 11:56:56 +02:00
James Agnew a3ff08d9ec
Replace phloc with ph for #775 (#930)
* Replace phloc with ph

* Enable schematron tests

* Make HAPI-FHIR ph-schematron on OSGI

* Work on getting tests passing

* Another test fix

* Fix up transaction handling for DSTU2

* Add changelog

* Avoid double transaction

* Dont use readonly

* One more test fix

* Update to snapshow build

* Resolve a circular dependency

* Try to fix tests

* Solve recurring NPE in DSTU2 tests

* Fix one more test

* Test fix

* More test threading fixes

* One more attempt to get tests passing

* Refactoring for tests

* Refactoring for tests
2018-05-14 17:38:40 -04:00
James Agnew b17eebd8d2 Squashed commit of the following:
commit 2be11651c2
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 11:50:53 2018 -0400

    Update changelog

commit b3bb5f9052
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 11:19:28 2018 -0400

    Parameter updates

commit f6b1082ba4
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 07:24:30 2018 -0400

    More test fixes

commit 81a69c265f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:26:48 2018 -0400

    Fix compile error

commit 935938e92c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:25:18 2018 -0400

    Another test fix

commit 43568a1f8d
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:18:06 2018 -0400

    Fix compile error

commit e95894e643
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:13:50 2018 -0400

    More work on tests

commit 9393fb8f4f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 05:36:27 2018 -0400

    One more fix

commit 437f5051e4
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 21:32:10 2018 -0400

    Work on validator

commit 20c51add4f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 19:34:10 2018 -0400

    Validator fix

commit 7bf2b0a0e9
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 18:44:04 2018 -0400

    Fix test

commit adc73e75c9
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 17:22:34 2018 -0400

    Merge validator
2018-05-10 11:53:32 -04:00
James Agnew 392feb7082 Refactor CLI to extract commands 2018-04-30 15:04:35 -04:00