Commit Graph

3830 Commits

Author SHA1 Message Date
jmarchionatto 98cce2a042
3664 fast elastic load (#3769)
* Start direct HSearch path

* Support no HSearch

* Spike out the direct resource query

* Implement hsearch fast load

* Fix last master merge in issues

* Implement revision requests

* Test direct resources (no IDs query) sorting

* Use mock to count freetext searches to avoid implementing interface in test

* Remove fixme

* Make listener optional as it is used only for tests

* Provide new dependency

* Widen fast path test scope and fix previously untested configurations

* Make method transactional as it can be called from outside a TX (at least testObservationLastNAllParamsPopulated does)

* Update test validation

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-07-14 15:21:43 -04:00
jdar8 5575e722d4
3788 FHIR patch on soft deleted resource undeletes resource (#3789)
* failing test

* fix

* refactor

* refactor

* changelog

* changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3788-fix-fhir-patch-on-soft-deleted-resources.yaml

Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
2022-07-14 18:41:36 +00:00
Tadgh 05ebf0286d
3790 remove legacy search builder (#3791)
* Remove legacy SB

* Add changelog

* Fix more messages

* Fix missed hapi message

* Fix up more messages
2022-07-14 16:01:44 +00:00
michaelabuckley 94a1cda512
Fix sort in hsearch - use full millis (#3787)
Fix sort in hsearch - use full millis
2022-07-13 13:32:40 -04:00
Gjergj Sheldija 4684dde6a6
add `displayLanguage` to the `ValueSet/$expand` (#3619)
* add `displayLanguage` to the `ValueSet/$expand`

* fix tests

* fix tests
2022-07-12 15:54:29 -04:00
Tadgh 57ee93251a
Mergeback 2022 07 08 (#3771)
* fix handling of common search parameters

* Revert "fix handling of common search parameters"

This reverts commit 89c45eebdc.

* Fix implementation, add test (#3378)

* Fix implementation, add test

* Tighten test

* Rip out dead modules

* Add changelog

* Jr 20220210 handle common search params in contained searches (#3377)

* fix handling of common search parameters

* add support for reference search parameters with multiple paths

* Issue 3357

* Version bump

* Fixed null pointer exception for re-loading subscription on cdr restart and when there's no partition id in the request, and added tests

* added changelogs for this fix

* Fix broken changelog file

* Can't specify specific resource type permissions for bulk export (#3376)

* deny user from exporting without perms

* add unit tests

* add changelog

Co-authored-by: olivia-you <olivia.you@smilecdr.com>

* Make migration donothing as it was added in error

* Remove ehcache

* Add version.yaml:

* Add to sources/javadocs for dist

* Fix typo

* fix up pom

* wip test removing checkstyle plugin from deployable pom

* remove test pom changes, instead just dont deploy to sonatype

* typo

* Version bump

* Add implementation, testing, and changelog

* Add backport info, make aware of 6_0_0

* add jira ref

* Fix test

* Add versionenum

* Bump dep for spring, add changelog, add versionenum, add changelog folder

* Actually do the version bump

* 3654 postgres lobs (#3656)

* Implementation, test, changelog

* Modify changelog

* Fix changelog

* Add upgrade.md file

* Modify to yaml changes

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_3/3654-lob-problems.yaml

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

* tidy

* more work

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

* Fix bad yaml indent

* Version bump

* Back out the reindex changes introduced in 5.7.3

* update changelog

* version bump

* added fix for subscription in default partition when default partition's id is null

* added changelog

* Add version info and changelog folder

* adding release pipeline yml file fo azure

* Fix parameter count limitation on MSSQL/Oracle large transactions (#3075)

* Fix parameter count limitation on MSSQL/Oracle large transactions

* Changelog fix

* Move changelog

* Force a change to trigger CI

* Test refactoring

* Backport oracle fix

* Fix backport

* upping version to 5.7.5 for release

* add versionenum

* Updating version to: 5.7.6 post release.

* Add query-chunk-aware code

* Add new folder

* Fix up versionenum

* Remove imports

Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-07-12 11:08:46 -07:00
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
Qingyixia 3d4556b70b
Move PATCH to hapi-fhir-storage (#3763)
* Not the final version

* Support PATCH operation

* minor modifications

* minor modifications

* Final version

* Final version
2022-07-11 14:56:22 +00:00
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
Ken Stevens 839a1b53e9
fix batch intermittent and status update atomicity (#3773)
* fix intermittent and status update atomicity

* change log

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-07-09 08:51:04 -04:00
James Agnew 61d34ab695
Add license headers (#3765) 2022-07-07 17:22:38 -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
michaelabuckley a13f2411a1
Implement direct HSearch search path (#3727)
* Start direct HSearch path

* Support no HSearch

* Spike out the direct resource query

* Implement hsearch fast load

* Fix last master merge in issues

* Implement revision requests

* Test direct resources (no IDs query) sorting

* Use mock to count freetext searches to avoid implementing interface in test

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-07-04 22:18:29 +00:00
JasonRoberts-smile c073c0eeb4
ConformanceStatement generation for DSTU3 is out of date (#3737)
* add system SPs to resource

* populate include list

* wip

* wip

* Tighten test

* Chaneglog

* Use old-style collectors

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-06-30 23:42:14 +00:00
Tadgh 3068eb38c4
Rel 6 0 mb 2 (#3747)
* adding version.yaml, updating version in pom.xml

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

* fixed

* remove sout

* add msg.code

* fix failed tests

* fix equal sign

* update msg code

* extract method

* Fix up code numbers

* Clean changelog

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

* Revert final artifact version

* add graphql test (#3585)

* added graphql birthdate test

* fix variable name

* typo

* 3506 mdm log enhancement (#3543)

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

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

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

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

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

* Update MdmMatchLinkSvc.java

#3506 move "narrowed down" log to different place

* #3506 added scores and tests

#3506 added scores and tests

* #3506 formatting

#3506 formatting

* #3506 create changelog file

#3506 create changelog file

* #3506 fix typo

#3506 fix typo

* #3506 fix part 3, minor formatting

#3506 fix part 3, minor formatting

* #3506 fix tests

#3506 fix tests

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

* mdm matching (#3579)

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

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

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

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

* begin with failing test

* fixed

* changelog

* add jira tag

* Update to 6 1 (#3582)

* added changelog folder, upped version

* version enum

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

* revert merge master doh! bad reflexes

* revert merge origin master

* unrevert revert.  ugh what a pain

* merge recovery.  fix poms.

* merge recovery.  more reverting

* merge recovery.  more reverting

* merge recovery.  more reverting

* Revert "merge recovery.  fix poms."

This reverts commit ae6e0ddb06.

* more revert revert reversions

* more revert revert reversions

* pre-review cleanup

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

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

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

* License

* Ks 20220508 log colour (#3592)

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

* change log

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

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

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

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

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

* 3584 case sensitive string elasticsearch (#3596)

* Fix for case-sensitive search with newer elasticsearch

* Test and fix ascii normalization too

* more test cases

* comments

* Docs update empi usecase (#3598)

* Update diagram for use case 5

* Add new page for database support

* Licnese

* Mb norm fix (#3604)

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

* Handle batch2 job cancellation (#3603)

* Handle batch2 job cancellation

* Add CANCELLED status

* Remove unuseful test

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Add batch2 interfaces to obtain recent instances (#3601)

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* changelog folder

* Documentation change, added warning log and change log for ticket (#3609)

Co-authored-by: Steven Li <steven@smilecdr.com>

* fix ne for lastUpdated search param (#3589)

* init/wip

* add implementation, add tests

* add checks and some refactoring

* refactor and simplify tests

* refactor

* get rid of some of the warnings

* add changelog

* remove my todos

* redo ne logic to account for less precise dates

* add tests

* refactoring

* rename to follow convention

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>

* Version bump

* Add skip of checkstyle to upload

* Typo

* upping version enum, upping version number, 6.0.1

* Group Bulk Export rules exiting too early.  (#3643)

* Implementation, test, changelog

* Add jira link

* adding backport in yaml for 3642

* adding folder for 6.0.1 release

* pom changes to publish checkstyle to sonatype

* bad version in pom file

* Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider

* AUtomcplete error code

* updating comment indicating final erorr code

* Bump error code

* fixing version enum so release docs generate correctly, adding additional changelog for 3650

* 3684 subscription for delivering delete events formatted wrong (#3685)

* Fixed issue with delivering delete events Subscriptions

* Extracted deliverer class name to a constant, now shared across tests and interceptor class

* Added change log and doc changes

* moved the constant to a more appropriate place

Co-authored-by: Steven Li <steven@smilecdr.com>

* Version bump

* Add version enum

* Version enum and folder

* duplicate import

* duplicate import

Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
2022-06-29 21:03:52 +00:00
Ken Stevens 069f20a5f7
batch2 management operations api (#3742)
* first test passes.  onto the next one

* two down two to go

* three down one to go

* licenses

* basic admin-json plumbing confirmed with IT

* FIXME

* FIXME

* FIXME

* FIXME

* changelog

* bump hapi version to 6.1.0-PRE6-SNAPSHOT

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-28 23:02:17 -04:00
jmarchionatto 84fe58cc86
Hsearch namespace consolidation (#3733)
* Initial implementation

* Implement job cancellation

* Works for date and token. Cleanup required.

* Works for string and quantity.Cleanup pending.

* Works for reference and perform cleanup.

* Cleanup configuration and add missing tests

* Eliminate sort property registry (no go for a cluster) for a static property map.

* Missed in previous commit

* Implement HSearch number parameter

* Implement HSearch number sorting

* Unify different hibernate search names (HibernateSearch, Freetext and Lucene) to HSearch

* Move analysis configures for lucene and elastic to same file to enforce the need to keep them in synch

* Use new defined constant

* Rename package too

* Rename additional elastic references

* bump version to 6.1.0-PRE5-SNAPSHOT

* Restore Hap prefix to hapi configurers

* fixing hapi version of new maven module

* fix pom

* fix pom

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-28 18:38:05 -04:00
Ken Stevens 49d298dba1
mdm clear move to batch2 (#3671)
* begin with failing test

* continue building out

* continue building out

* reworking chunk api

* replace ChunkId zippers with proper iterator

* progressing test

* yay test passes!

* switch to idchunk interface

* fixmes

* compiles

* fixme

* fixme

* rename classes

* rename json classes with json suffix

* work towards homogeneous chunks

* fixme

* fixme

* unit test

* fixme

* fixme

* pull out builder

* moar tests

* moar tests

* preserve order

* moar test

* moar test

* fixme

* fixme -> wip to start ci

* msg code

* msg code fix test

* fixme

* change provider implementation

* final WIPs

* IT failing

* IT passes

* java 11

* fix test

* fix test

* fix test

* changelog

* use batch size if provided

* last WIP

* fix test

* fix test

* fix test

* whitespace change to trigger new build

* fix test

* bumping hapi version

* bumping hapi version

* fix test

* review feedback

Co-authored-by: Ken Stevens <ken@Kens-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-25 20:26:44 -04:00
jmarchionatto e7ce41e5b8
Freetext search sort (#3695)
* 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

* Replicate new normalizer configuration from HapiElasticsearchAnalysisConfigurer to HapiLuceneAnalysisConfigurer.
Replace deprecated word filter factory

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-06-22 10:31:01 -04:00
Qingyixia dce330eb01
Fix to the issue (#3723) 2022-06-21 16:29:35 +00:00
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
Ken Stevens 427bdf330e
fix 403 on updates when version submitted without rewrite header (#3716)
* fix 403 on updates when version submitted without rewrite header

* change log

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-17 19:51:47 +00:00
JasonRoberts-smile a18c83ae13
replace UNION with UNION ALL in chained search query (#3715) 2022-06-17 16:10:21 +00:00
JasonRoberts-smile cedeaa04f1
add support for in and not-in qualifiers (#3680)
* add support for in and not-in qualifiers

* fix failing test

* fix broken test

* fix broken tests

* code review comments

* Make dependency on IValidationSupport optional

* create IValidationSupport dependency only if needed

* small design improvements

* changelog

* rework validation support initialization

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

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

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-06-16 20:17:57 +00:00
kateryna-mironova 93b89b2bd7
3702 mpi link add index (#3708)
* 3702 - added index to mpi_link

* added changelog file
2022-06-16 13:23:23 -04:00
StevenXLi 3da39aeda3
3658 adding updating with history rewrite feature (#3659)
* Updating With History Rewrite implementation

* Missed new files

* Updated changelog and documentation

* Fixed test failures and doc

* minor fix

* lgtm code refactor

* Fixed test to clear DaoConfig

* Removed unused class

* Code review changes

* Simplified updateHistoryRewrite's fluent, combining with normal update's, also changed logic on custom header error checking, updated tests

* refactored method to extracted common code

* removed `updateHistoryRewrite()` and replaced with `update()`, updated tests accordingly

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-06-15 12:40:58 -04:00
Tadgh bf2f126c91
Add changelog, add test, add implementation to short-circuit logic in group export (#3701) 2022-06-15 11:22:42 -04:00
Etienne Poirier 868a7e5c40
3637 encapsulation of synchronous query execution capabilities into a new service for reuse (#3638)
* Adding test reproducing the issue.

* Providing implementation fixing the issue and strengthening integrated test.

* Cleaning up commended code.

* Preparing code for review.

* Adding test class SynchronousSearchSvcImplTest.

* Addressing first code review comments.

* Addressing first code review comments.

* Forcing one extra processing step to ensure exit condition is met.

* Adding tests

* Clean up in preparation of second code review.

* Addition of setting page size if required.

* Grouping synch test in nested test class.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-06-05 20:38:53 -04:00
Ken Stevens a3de219a1e
replace search by example. (it caused a cryptic hibernate session error) (#3665) 2022-06-01 19:46:44 +00:00
jmarchionatto ad3294f8e8
Freetext search lastupdated param support (#3630)
* Initial implementation

* Implement job cancellation

* Handle uri, _tag, _security and _profile freetext search parameters

* Fix combined 'and' and 'or' clauses and add tests
Use collection instead of typed array to eliminate warnings

* Eliminate predicate nesting level

* Implement _source freetext search

* Implement _lastUpdated freetext search

* add ITestDataBuilder.withLastUpdated(String theIsoDate) method

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-26 18:41:12 +00:00
jmarchionatto 464a07e284
Freetext search tag types support (#3622)
* Handle uri, _tag, _security and _profile freetext search parameters

* Fix combined 'and' and 'or' clauses and add tests
Use collection instead of typed array to eliminate warnings

* Eliminate predicate nesting level

* Add changelog

* Implement revision suggestions

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-26 15:59:39 +00:00
Tadgh 6f5eea81b7
Jpaserver changes (#3632)
* Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider

* wip

* wip

* wip fix test

* move to override in test class

* Test fixes

* Add failsafe to other projects which have ITs

* Fix test

* Fix test to use transaction

* Move subscription loading

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-05-26 02:52:05 +00:00
jmarchionatto 4eb099b900
Freetext search source parameter support (#3641)
* Handle uri, _tag, _security and _profile freetext search parameters

* Fix combined 'and' and 'or' clauses and add tests
Use collection instead of typed array to eliminate warnings

* Eliminate predicate nesting level

* Implement _source freetext search

* Implement suggestions

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-25 20:07:29 +00:00
Ken Stevens fb6e5cf6ce
Batch 2 Maintenance refactor (#3631)
* SRP refactor maintenance

* SRP refactor maintenance

* cache jobDefinition in jobInstance when processing (rather than looking it up in a bunch of different places)

* begin with failing test

* test passes

* tests pass.  still need to add a few more tests

* add comment to trigger new ci

* added positive and negative tests for new behaviour

* fix IJ warnings

* change log

* change log

* fix test race condition

* resolved feedback

* review feedback
2022-05-25 04:16:58 +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
Joe Shook 4b638bbfee
CockroachDB (#3577)
* Update pom.xml

* Data behavior overrides for CockroachDB

* Unwind two unintended changes

* Update Spring framework version

This is n response to CVE-2022-22968 reported by WhiteSource Security Check ran by GitHub

* Update elasticsearch-rest-high-level-client version

This is n response to CVE-2021-22145 and CVE-2021-22134 reported by WhiteSource Security Check ran by GitHub

Co-authored-by: Shook, Joseph <Joseph.Shook@surescripts.com>
2022-05-18 10:02:11 -04:00
Ken Stevens 27024067b0
Batch 2 documentation and SRP cleanup (#3616)
* begin writing documentation.  minor refactor.

* document submitting a job

* single responsibility principle

* single responsibility principle

* single responsibility principle

* reduce method parameter count

* reduce method parameter count

* fix test mocks

* reduce method arguments

* update documentation

* add tests
resolve warnings

* resolve warnings

* moar test

* moar test

* Add @Nonnull and @Nullable annotation to construction parameters

* pre-review cleanup

* pre-review cleanup

* review feedback

* review feedback.  added FIXME

* started writing IT with FIXMES

* started writing IT with FIXMES

* added batch 2 state transition integration tests

* FIXME

* improve readability of test

* improve readability of test

* fix race condition

* pre-merge cleanup
2022-05-17 21:25:43 +00:00
Tadgh 54f578c8b1
Rel 6 0 mergeback (#3597)
* adding version.yaml, updating version in pom.xml

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

* fixed

* remove sout

* add msg.code

* fix failed tests

* fix equal sign

* update msg code

* extract method

* Fix up code numbers

* Clean changelog

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

* Revert final artifact version

* add graphql test (#3585)

* added graphql birthdate test

* fix variable name

* typo

* 3506 mdm log enhancement (#3543)

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

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

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

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

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

* Update MdmMatchLinkSvc.java

#3506 move "narrowed down" log to different place

* #3506 added scores and tests

#3506 added scores and tests

* #3506 formatting

#3506 formatting

* #3506 create changelog file

#3506 create changelog file

* #3506 fix typo

#3506 fix typo

* #3506 fix part 3, minor formatting

#3506 fix part 3, minor formatting

* #3506 fix tests

#3506 fix tests

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

* mdm matching (#3579)

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

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

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

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

* begin with failing test

* fixed

* changelog

* add jira tag

* Update to 6 1 (#3582)

* added changelog folder, upped version

* version enum

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

* revert merge master doh! bad reflexes

* revert merge origin master

* unrevert revert.  ugh what a pain

* merge recovery.  fix poms.

* merge recovery.  more reverting

* merge recovery.  more reverting

* merge recovery.  more reverting

* Revert "merge recovery.  fix poms."

This reverts commit ae6e0ddb06.

* more revert revert reversions

* more revert revert reversions

* pre-review cleanup

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

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

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

* License

* Ks 20220508 log colour (#3592)

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

* change log

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

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

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

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

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

* 3584 case sensitive string elasticsearch (#3596)

* Fix for case-sensitive search with newer elasticsearch

* Test and fix ascii normalization too

* more test cases

* comments

* Docs update empi usecase (#3598)

* Update diagram for use case 5

* Add new page for database support

* Licnese

* Mb norm fix (#3604)

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

* Handle batch2 job cancellation (#3603)

* Handle batch2 job cancellation

* Add CANCELLED status

* Remove unuseful test

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Add batch2 interfaces to obtain recent instances (#3601)

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* changelog folder

* Documentation change, added warning log and change log for ticket (#3609)

Co-authored-by: Steven Li <steven@smilecdr.com>

* fix ne for lastUpdated search param (#3589)

* init/wip

* add implementation, add tests

* add checks and some refactoring

* refactor and simplify tests

* refactor

* get rid of some of the warnings

* add changelog

* remove my todos

* redo ne logic to account for less precise dates

* add tests

* refactoring

* rename to follow convention

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>

* Version bump

Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
2022-05-16 22:08:27 +00:00
jmarchionatto 231c2659b8
Implement :below qualifier for tag parameters (#3613)
* Initial implementation

* Implement job cancellation

* Implement :below qualifier for tag parameters

* Add changelog

* Add tests

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-16 14:06:48 -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
Jens Kristian Villadsen eb4732a59e
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>
2022-05-03 05:44:47 -04:00
michaelabuckley d6702f956b
Fix tag db migration (#3578)
* Fix tag db migration

PG doesn't support drop index online

* changelog
2022-05-02 17:59:07 -04:00
jmarchionatto 3a7ea64a40
As a temporary palliative until we refactor async search, disallow scrolling less than 50 (#3576)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-02 14:52:11 -04:00
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
michaelabuckley 5aef3cec9e
New tag indexing (#3570)
* New tag indexing

* Migration for tag indexing
2022-04-30 16:51:59 -04:00
michaelabuckley 06030094c8
Add res_id, and partition_id to string norm and exact indexes (#3569)
Add res_id, and partition_id to string norm and exact indexes to avoid random row reads.
2022-04-29 08:12:29 -04:00
Ken Stevens 10ebb082d0
Issue 3563 mdm nickname support (#3565)
* added NicknameMap

* added NicknameSvc

* create NicknameInterceptor

* test interceptor integration

* add nickname matcher

* test nickname matcher

* unit test

* documentation

* unit test

* cleanup

* cleanup

* Msg.code()

* Msg.code() in test

* Msg.code()

* review feedback
2022-04-28 18:02:56 -04:00
Jaison Baskaran e0f1b913b7
Support _total and _count works for hibernate search (#3567)
Add support for _total, _count, and _offset to Lucene backend.

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-04-28 16:35:39 -04:00
Kevin Dougan SmileCDR dd5ab4ede7
Add New Index On HFJ_RESOURCE For $reindex Operation (#3536)
* 3534 - Added new multi-column Index and removed existing single-column Index.
* 3534 - Added PARTITION_ID to the new Index.
* Change migrations to have no timeout. 

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
2022-04-26 17:19:05 +00:00