Commit Graph

1083 Commits

Author SHA1 Message Date
michaelabuckley 92acd9b001
Avoid unsupported features during migrations on MSSQL (#3652)
Avoid unsupported ONLINE index operations on MSSQL Standard
2022-05-31 18:44:42 +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
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
Tadgh a19c1ec996
Group Bulk Export rules exiting too early. (#3643)
* Implementation, test, changelog

* Add jira link
2022-05-25 00:14:36 +00:00
Ken Stevens df76b0f8f1
improve nickname matcher (#3628)
* improve nickname matcher

* change log

* review feedback and fix test
2022-05-24 17:13:09 +00:00
JasonRoberts-smile b9579313ef
Jr 20220519 expunge config params (#3627)
* fix config settings for system-level expunge

* clean up expunge everything interface

* extract common system provider

* changelog

* version bump

* touch changelog to force a fresh pipeline

* re-enable publishing of checkstyle

* back out Gary's Sonatype change entirely
2022-05-23 18:55:42 -04:00
jamesagnew 8da0a70d50 Credits for #3577 2022-05-18 10:04:13 -04:00
Tadgh 3a286c306f
R5 appointment not storing. (#3621)
* Failing test, works on #3459

* Test, changelog

* Remove dead test
2022-05-17 23:31:17 +00:00
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
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
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
Ken Stevens b59f2d05a7
reversed order matching operation bindings are searched so custom ope… (#3568)
* reversed order matching operation bindings are searched so custom operations override builtin ones

* change log

* add test

* reverse finding operations in interfaces and then classes so last-in-wins finds the right provider method
2022-04-30 16:46:37 -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
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
seanmikalson-smilecdr 68c8523046
$translate operation implementation for remote terminology (#3552) 2022-04-25 12:37:15 -07:00
Tadgh f7a31287b6
3558 bulk export premature deletion (#3562)
* Implementation, parameterize test, changelog

* Bump spring framework for a vuln while i'm in here

* Fix number of changelog

* Add IS NOT NULL to query
2022-04-24 01:46:44 +00:00
samuelwlee2 4c9667c92a
3524 export poll status returning the wrong partition in the url (#3526)
* test added and bulk data export provider fixed

* add test and change jira number

* change test

* modify tests
2022-04-23 16:47:04 +00:00
jdar8 5ccb4effb0
3547 Interceptor hook for client-assigned IDs (#3559)
* add pointcut

* draft test

* fix test, change name and location of pointcut

* add changelog

* change check condition, improve changelog wording

* improve changelog wording

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3547-interceptor-hook-for-client-assigned-ids.yaml

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

* change pointcut name

* update test

* fix test

* fix changelog

* renaming variables in test

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-04-22 18:09:25 -04:00
Tadgh 53c8b067d5
Support forward references in Group Bulk Export (#3558)
* Preliminary test work to generate forward-reference data

* Complete implementation

* Permit Practitioner/Organization as forward references in bulk export group params

* Wip

* Fix test

* Add error number

* Address review comments

* Update assert
2022-04-22 05:33:10 +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
Tadgh 612ee0af32
Supported search (#3549)
* wip

* Revert some work

* Add changelog

* refactor method into SeachParamRegistryImpl

* Javadocs
2022-04-21 07:46:58 +00:00
Tadgh 578d42c955
Add implementation and changelog, and test. (#3554)
* Add implementation and changelog, and test.

* Add daoconfig settings

* Updatae test

* Rename deexternalize -> autoinflate
2022-04-20 13:47:02 -04:00
Olivia You e0cc325294
Allowing any client assigned ID throws ResourceNotFoundException when creating a CodeSystem (#3505)
* add test and potential fix

* add changelog

* fix

* add tests again

* oops. missed a file.

* clean up

* fix resolveResourcePersistentIds

* fix RESOURCE_PID constant

* format

* apply suggestion

* get R5 pid key

* better solution

Co-authored-by: olivia-you <olivia.you@smilecdr.com>
2022-04-17 08:02:50 -04:00
James Agnew 7dec2e334d
AuthorizationInterceptor concurrency failure (#3528)
* Fix #3256 - AuthorizationInterceptor concurrency failure

* Test fixes
2022-04-15 15:27:57 -04:00
Ken Stevens 9d2a317446
Issue 3530 terserutil contained failure (#3532)
* License headers

* begin with failing test

* fixed

* changelog

* add jira tag

* review feedback
2022-04-12 20:16:23 -04:00
JasonRoberts-smile f361aa5998
move expunge core classes and interfaces to storage project (#3529)
* move expunge core classes and interfaces to storage project

* post-merge clean-up

* changelog
2022-04-12 14:12:10 -04:00
longma1 01d6e15f90
2579 partitioned support for mdm (#3485)
* committed changes discussed at tasking

* Changed the subscription message to store the request partition

* modified mdm subscription loader to create a cross partition subscription in the default partition if multitenancy is enabled

* Fix errors when running Multitenant IT for mdm

* Added partition id to mdm golden resource search and creating/updating golden resource

* added partition id column to the mdm link table

* Added partition id of the source resource to partition id column of the mdm link table

* broken build

* working -links, missing hapi tests

* Fixed the mdm link db table due to feedback

* added IT for create link mdm operation, also added changes to pass the IT

* Fixed test for create mdm links, added test for update mdm link on partitioned server

* changed mdmLink search from searchbyExample to criteriaBuilder, added partitionHelperSvc to determine partition

* added test for merge golden resource and search golden resource on partitioned server

* added unit test for not duplicate on partitioned and non-partitioned server

* added criteriabuilder search and tests

* code cleanup

* added partition support to -merge-golden-resources operation

* test cleanup

* fixed  operations with multitenancy

* added test for mdm clear operation

* added waiting for batch job to finish in mdm clear operation test

* added query to dao to support partitioned server for mdm clear operation

* resolve mistake from merge conflict

* added mdm-submit operations, also fixed paging for -query

* added partitionIds constant

* fixed build issue where there was no Code.msg in mdm partition exceptions

* code review fixes

* fix broken test, also fix a bug where query link could not query by linkSource properly

* fix test stubbing

* bump hapi version to 6.0.0-PRE10-SNAPSHOT

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Long Ma <long@smilecdr.com>
2022-04-06 15:48:30 -04:00
Tadgh 523fe95820
Rel 5 7 2 mergeback (#3518)
* 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

* remove doubleimport

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>
2022-04-05 22:39:09 +00:00
Tadgh fe53bcb63d
Rel 5 5 7 mergeback (#3520)
* Add versionenum, bump maven version

* failing tests

* more logs

* Add more test cases, not passing

* fixed the double chain with contained resource second case

* clean up a bit

* add tests for qualifiers

* force the resource table to be the root of the query if we might be traversing a contained reference

* tidy up

* tests for longer chains

* changelog

* code review feedback

* backport changelog

* Add version.yaml

* [2935] Escape "%" in like expression

* Add backport to changelog

* Bumping version number. Update VersionEnum to support 5.5.3

* Jr 20211013 chained references (#3079)

* Create index entries for outbound references of contained resources

* build query for chained reference

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

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

* make qualified search work

* cleanup and changelog

* code review

* fix broken tests

* add imports from bad merge

* Add forgotten import from merge

* Jr 20211018 chained references 2 (#3099)

* Create index entries for outbound references of contained resources

* build query for chained reference

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

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

* make qualified search work

* cleanup and changelog

* recurse while creating indexes on contained resources

* double link both contained

* longer contained subchains

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

* clean up merge cruft

* changelog

* Jr 20211021 chained references 3 (#3107)

* Create index entries for outbound references of contained resources

* build query for chained reference

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

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

* make qualified search work

* cleanup and changelog

* recurse while creating indexes on contained resources

* double link both contained

* longer contained subchains

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

* clean up merge cruft

* changelog

* create recursive resource links

* add test coverage for a more complicated case

* changelog

* remove unnecessary check for _contained flag

* fix broken tests

* Add backport information

* Bump version, add version enum

* begin with failing test

* fix bug

* change log

* change log

* Add backport information

* Improve performance of chained queries into contained resources (#3312)

* base restructuring of query

* fix unit tests

* suppress unnecessary resource type parameter

* pass the resource type used to fetch the search param as part of the chain, so later we do not need to guess what it was

* add query structure tests

* changelog

* fix test failures

* got one of the branches wrong in the 3-reference case

* Add backport info

* Bump version

* Fix errors due to merge

* Bump license year

* Add folder for release version

* Version bump

* 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

* Add backport info

* add new folder for version

* Add missing message

* New version enum, and folder

* Version bump

* Bump spring lib version

* Tidy versions

* Remove test

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
2022-04-05 17:15:18 -04:00
samuelwlee2 7dc302b7ef
add addBundleEntry method (#3522)
* add addBundleEntry method

* change method to createNewBundleEntryWithSingleField

* changes to changelog
2022-04-05 10:40:09 -04:00
Tadgh c2f30502b0
Rel 5 6 3 mergeback (#3519)
* 3138 externalized binary packages (#3139)

* Add test and impl

* Add changelog

* Fix test

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3138-support-externalized-binaries.yaml

* add beans to test configs

* Typo

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java

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

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* 3131 - Added support for the lookup operation in the Remote Terminology code (#3134)

* Remove leading underscores from identifiers (#3146)

* Version bump

* License files

* version.yaml

* Add executeRawSql() method to Migrator (#3183)

* Add implementation, add test

* Add javadoc

* Add another helper function

* Bump version

* 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>

* Add backport info

* Avoid creating ResourcePersistentId for placeholder resources with null ID (#3158)

* Add check before mapping storage ID to resource ID in TransactionDetails.

* Add change log.

* Changed to instead prevent creation of ResourcePersistentId with null ID value.

* Changed to instead prevent ResourcePersistentId being created with null resource ID.

Co-authored-by: ianmarshall <ian@simpatico.ai>

* Fix bug loading packages in non-database mode (#3199)

* Add implementation

* Add changelog

* Add backports

* 3164 updating code review points (#3165)

* 3164 updating code review points

* 3164 updating code review points

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Add executeRawSqlStub (#3203)

Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>

* Add new version

* begin with failing test

* fix bug

* change log

* change log

* Add backport informationm

* begin with failing test

* fix issue

* change log

* code review

* Add backport info. Add folder

* fixed

* Add test

* Update test

* Add backport info

* Bump minor version

* 3170 language portion of language code is case insensitive (#3171)

* 3170 language portion of language code is case insensitive

* 3170 adding changelog

* 3170 house keeping

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Add backport info:

* Add version enum

* Bump hapi version to 5.6.3

* Add version enum

* Add changelog folder and version.yaml

* Patch vulnerability, add changelog

* Add new version

* Remove test

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
Co-authored-by: ianmarshall <ian@simpatico.ai>
Co-authored-by: Joanne Mendoza <joannemmendoza@gmail.com>
Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
2022-04-04 11:29:42 -04:00
jamesagnew 60bbe271a5 Changelog for #3510 2022-04-01 19:32:02 -04:00
Etienne Poirier 26784ba7c8
Fixing ValueSet expansion not supporting canonical url. (#3501)
* 2991 - WIP, starting to implement test to reproduce the issue.

* Adding capability to extract url & version from the valueSet.include.url

* parsing codeSystem canonical URL to extra version if required.

* WIP

* Cleaning up the test.

* Replacing hard code value with variable.

* Removing non required test.

* Modifications following first code review.

* Further modifications following first code review.

* Refining the test for better code coverage.

* Prefixing the change log file name with the hapi-fhir issue number.

Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
2022-03-31 18:47:15 +00:00
Tadgh 05bc208192
Fix for path parsing in STU3 SPs (#3503) 2022-03-30 08:40:17 -07:00
Mark Iantorno 179c970144
Issue 3486 (#3487)
* added failing tests

* tests pass

* Added changelog and javadocs

* fixed package tests for resources with no active field

* adding jira ticket number

* feedback from code review'

* switching to old style switch statement'
2022-03-30 08:52:52 -04:00
Tadgh 476e754bff
Update docs (#3499) 2022-03-29 08:35:38 -04:00
Tadgh b1e2d7c104
Add test, add changelog, fix bug (#3494)
* Add test, add changelog, fix bug

* Test fix

* Fix some more test artifacts
2022-03-26 20:34:43 -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
Olivia You 625ed936e9
3470 ne date search (#3471)
* fix mongo date search with the NOT_EQUALS prefix

* add test & changelog

* add some unit tests

* rename unit test names to be more clear

Co-authored-by: olivia-you <olivia.you@smilecdr.com>
2022-03-25 17:51:17 -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
jamesagnew 34eb47aba6 Add changelog 2022-03-25 05:53:05 -04:00
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
Jaison Baskaran 3eb3014d25
Revert change to treat Canonical URLs as Locals (#3483)
* Revert change added in MR: https://github.com/hapifhir/hapi-fhir/pull/3050 to add support for treating Canonical Urls as locals. This is no longer needed as the issue reported in #2843 (_include not working for Canonicals) has been addressed in MR: https://github.com/hapifhir/hapi-fhir/pull/3440
2022-03-22 17:46:10 +00:00
James Agnew f82534ca51
Convert Reindex into Batch2 Job (#3458)
* Start working on reindex job

* Updates

* Ongoing work

* Ongoing work

* Work on reindex

* Reindex work

* Add logging

* Fix typo

* Test fix

* Test fix

* Address fixme

* Liocense header

* Resolve fixme

* Add logging

* Update logs

* Address review comments

* License header

* Test fixes

* Test fix

* Test fixes

* Test fix

* Version bump

* Version bump
2022-03-19 16:07:58 -04:00