Commit Graph

403 Commits

Author SHA1 Message Date
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
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
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
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
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
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
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
JasonRoberts-smile b9579313ef
Jr 20220519 expunge config params (#3627)
* fix config settings for system-level expunge

* clean up expunge everything interface

* extract common system provider

* changelog

* version bump

* touch changelog to force a fresh pipeline

* re-enable publishing of checkstyle

* back out Gary's Sonatype change entirely
2022-05-23 18:55:42 -04:00
Tadgh 54f578c8b1
Rel 6 0 mergeback (#3597)
* adding version.yaml, updating version in pom.xml

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

* fixed

* remove sout

* add msg.code

* fix failed tests

* fix equal sign

* update msg code

* extract method

* Fix up code numbers

* Clean changelog

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

* Revert final artifact version

* add graphql test (#3585)

* added graphql birthdate test

* fix variable name

* typo

* 3506 mdm log enhancement (#3543)

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

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

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

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

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

* Update MdmMatchLinkSvc.java

#3506 move "narrowed down" log to different place

* #3506 added scores and tests

#3506 added scores and tests

* #3506 formatting

#3506 formatting

* #3506 create changelog file

#3506 create changelog file

* #3506 fix typo

#3506 fix typo

* #3506 fix part 3, minor formatting

#3506 fix part 3, minor formatting

* #3506 fix tests

#3506 fix tests

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

* mdm matching (#3579)

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

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

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

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

* begin with failing test

* fixed

* changelog

* add jira tag

* Update to 6 1 (#3582)

* added changelog folder, upped version

* version enum

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

* revert merge master doh! bad reflexes

* revert merge origin master

* unrevert revert.  ugh what a pain

* merge recovery.  fix poms.

* merge recovery.  more reverting

* merge recovery.  more reverting

* merge recovery.  more reverting

* Revert "merge recovery.  fix poms."

This reverts commit ae6e0ddb06.

* more revert revert reversions

* more revert revert reversions

* pre-review cleanup

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

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

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

* License

* Ks 20220508 log colour (#3592)

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

* change log

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

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

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

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

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

* 3584 case sensitive string elasticsearch (#3596)

* Fix for case-sensitive search with newer elasticsearch

* Test and fix ascii normalization too

* more test cases

* comments

* Docs update empi usecase (#3598)

* Update diagram for use case 5

* Add new page for database support

* Licnese

* Mb norm fix (#3604)

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

* Handle batch2 job cancellation (#3603)

* Handle batch2 job cancellation

* Add CANCELLED status

* Remove unuseful test

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

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

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

* changelog folder

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

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

* fix ne for lastUpdated search param (#3589)

* init/wip

* add implementation, add tests

* add checks and some refactoring

* refactor and simplify tests

* refactor

* get rid of some of the warnings

* add changelog

* remove my todos

* redo ne logic to account for less precise dates

* add tests

* refactoring

* rename to follow convention

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

* Version bump

Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
2022-05-16 22:08:27 +00:00
Mark Iantorno 544ef3de1b
Update to 6 1 (#3582)
* added changelog folder, upped version

* version enum
2022-05-03 20:34:25 +00:00
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
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
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
jmarchionatto f9824d6b15
Freetext search query builder consolidation (#3556)
* Refactor query builder for Reference

* Execute loop for all entries

* Add sandbox disabled test

* Add multiple components tests

* Revert "Refactor query builder for Reference"

This reverts commit 85e0442082.

* Fix imports

* Simplify test

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
2022-04-21 16:50:21 +00:00
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
michaelabuckley 1a8678cb1c
Implement support for Quantity search parameters in the Hibernate Search index (#3477)
* markers for new quantity hibernate search support

* Add quantity search

* Add normalized (canonical) quantity search

* Add comment

* Use double values instead of BigDecimal to avoid scaling

* Remove multiple case labels which are not supported until source version 14

* Remove switch rules which are not supported until source version 14

* Use constant for error message used in tests

* A failing test for multiple indexed quantity paths

* Disallow dirtying context for nested classes

* failing test for normalized units

* Make sp.value-quantity.quantity a nested structure to handle correlated queries for code and value.
Save units for canonical case and consider them when querying.
Collapse normalized sub-structure under *.quantity.

* Nest sp.value-quantity instead of sp.value-quantity.quantity for compatibility with other nested types (IE. token)

* Comment out debug statements

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

Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>

* Add test for nested correlated quantity query

* Address MR comments

* Add proper handling of or query predicates

* Use positive conditions for better readability

* Add tests to validate behavior of combined and and or clauses, including some making no sense but still syntactically correct.

* Only consider normalized quantity searching if ModelConfig search level is NORMALIZED_QUANTITY_SEARCH_SUPPORTED

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>
2022-04-08 08:25:27 -06:00
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 b833c13a3c
Improve batch2 error handling (#3482)
* Improve batch2 error handling

* Build fixes

* Work on reindexing

* Test fixes

* Account for gzipped contents

* License header updates

* Register VS operations on public server

* Test fix

* Build fix

* Remove animal sniffer plugin

* Compile fix
2022-03-26 17:40:12 -04:00
michaelabuckley 1dcc64ee44
Fast-path for lucene queries that skip the database (#3468)
* Store resource data inline with lucene/es resourcetable index.
* Use fulltextsearch to load resources if resource inlined in ES/Lucene index
Co-authored-by: Jaison Baskaran <jaisonb@gmail.com>
2022-03-25 16:21:47 +00:00
michaelabuckley 92db526786
Skip database query when hibernate search fully satisfies search (#3478)
If a query is completely satisfied by Hibernate Search, skip the database.

Co-authored-by: Jaison Baskaran <jaisonb@gmail.com>
2022-03-22 22:41:21 +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
michaelabuckley 03b6c589c8
New indexing for number and quantity search parameters (#3464)
* New Add Index forced-INCLUDE columns, and Online option

* Remove forced-include.  Simpler just to add all columns to index.

* New date index definitions.

* Oops.  Remove test for deleted feature.

* Cleanup

* Drop IDX_SP_DATE_UPDATED

* Add online option to drop index

* Update annotations to match and redefine FK

* Push sp->resource FK down to control name

* remove dead end

* Cleanup date tests

* New token query test cases for sql extraction

* New token search param indexing.

* Continue to allow the legacy hibernate names while we update the indexing.

* Fix jpa annotations with overloaded field

* Decide on token sorting - we do it.

* review comments

* fixme

* disable dead data migration too

* review fixups

* Test cases for numeric search

* add ne and ap

* Test for Numeric SP

* start

* finish number

* new indexing for quantity

* Move config

* cleanup
2022-03-11 16:23:06 +00:00
michaelabuckley 80d1a5a6f8
Mb new token search index (#3386)
* New token search param indexing.
* New token query test cases for sql extraction
* Retire JPA fk ugly nams
2022-03-11 00:51:53 +00:00
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
samuelwlee2 cde39dcc6c
3423 include with client assigned id partition (#3448)
* changes to doResolvePersistentIds

* make changes to tests

* Add code changes after the review
2022-03-08 11:48:33 -05:00
James Agnew 2cba62b4e8
Enable search narrowing on large ValueSets (#3405)
* Enable search narrowing on large ValueSets

* ValueSet improvements

* Work on narrowing

* Work on narrowing

* Work on narrowing

* Work on narrowing

* Add test

* Work on narrowing interceptor

* Work on narrowing

* License headers

* Refactor code narrowing

* Add docs

* Version bump

* Test fix

* Test fixes

* Build fix

* Fixes

* Version bump

* Test fix

* License header updates

* Build fix

* Test fixes

* Test fix

* Test fix

* Docs fix

* Test fix

* Test fix

* Resolve fixme

* Bump

* Force a CI build

* Make CI happen again
2022-03-01 09:16:31 -05:00
michaelabuckley 86f7373f16
Distinguish multi-coded items during token autocomplete (#3429)
Add nested indexing to support autocomplete of multi-coded items.
2022-03-01 00:59:09 +00:00
James Agnew b7d1ae217d
New batch framework / Bulk Import (#3387)
* Work on new batch framework

* Work on new batch framework

* Work on new batch framework

* Work on batch

* Compile working

* Work on bulk import

* Adjust import

* Work

* Work on batch

* Bump version

* WOrk on new batch processes

* Work on bath

* Bump to PRE4

* Build fixes

* CLeanup

* Small tweak

* Add exception code

* Test fixes

* Test fixes

* Test fix

* Additional synchronization

* Add license headers

* Test fixes

* Test fixes

* Add changelogs

* Address PG

* Test fix

* Test fix

* Test fixes

* Review notes

* Work on tests

* Test fixes

* Test fix

* Work on tests

* Tets fix

* Test fixes

* Test fixes

* Add missing exception codes

* Test fix

* Test fixes

* More test fixing

* License headers

* Test fix

* Add new test logging

* Work on tests

* Test fixes

* Test fix

* Resolve fixme

* Try to avoid test failure

* Add import command

* Work on storage

* Fix error codes

* Fixes

* License header

* Build fix

* Build fixes

* Fix dep
2022-02-27 16:04:49 -05:00
Ben Li-Sauerwine 65776bbab3
Adds a NDJSON-capable Bulk Data Import Provider (#3039)
* NDJsonParser with one example test.

* Add test for empty NDJson, and fix bug for empty NDJson.

* Adds multi-Patient test, and fixes bug whereby all multi-line NDJSON would be put into the same line.

* Adds test for NDJson with newlines in it.

* Adds test for converting non-Bundle types to NDJSON failing.

* Confirm that we can only extract to Bundle types in test.

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

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

* Documents behavior of the NDJsonParser in FhirContext.

* Attempt to fix failing build by using TestUtil to clear context in the manner of r4 parser tests instead of dstu

Also clean up indentation.

* Adds a BulkDataImportProvider, with a single test.  More tests are forthcoming.

* Adds an additional test.

* Enhance tests to include content of job files.  Fix a bug whereby the content was never actually being added.

* Adds several tests for BulkImportProvider's polling operation.

* Adds requred Msg.code to errors.

* Apparently I can't duplicate Msg.code even if it's the same issue.

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-02-27 11:38:20 -05:00
Tadgh c6122bcb1b Add license files 2022-02-18 19:11:29 -08:00
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
michaelabuckley 1c82d0933c
Mb new date search index (#3368)
* New date index definitions.
* Dropped unused indexes.
* Add online option to drop index and add index
* Push sp->resource FK down to control name
* Update annotations to match and redefine FK
* Continue to allow the legacy hibernate names while we update the indexing.
2022-02-16 22:12:20 +00:00
Tadgh 43f570259e Merge branch 'rel_5_7' 2022-02-10 08:44:07 -08:00
Jaison B 7794113455
2838 lastn refactor to use extended lucene index (#3339)
* Change token and reference search params to 'keyword' field type

* remove normalizer for keyword field

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

* Add ES native aggregation builder for lastN

* added date search param support for searching resourcetable ES index

* * Added DateSearch parameterized tests to ElasticSearch test suite

* Added more tests cases for Date searches

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

* WIP fix lastNDataGenerator to avoid assertion errors.

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

* Cleanup json string to avoid carriage return noise

* Fix checkstyle issues

* Fix checkstyle Msg code issues

* Fix checkstyle Msg code issues

* Add more test case for GT, SA precision modifier

* Fix date precision test cases

* Fix Msg Code conflicts

* Add more logging

* Add way more loggging

* even more logging

* fix msg code conflicts

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-02-10 11:05:31 +00:00
michaelabuckley 3531d9b4fc
Fix exception when contained indexing met hibernate search. (#3372)
* Fix exception when contained indexing met hibernate search.
2022-02-09 20:27:40 -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