Commit Graph

2560 Commits

Author SHA1 Message Date
seanmikalson-smilecdr 68c8523046
$translate operation implementation for remote terminology (#3552) 2022-04-25 12:37:15 -07:00
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
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
Ibrohim Kholilul Islam d20c6a7d25
Implement GraphQL Connection Approach (#1987)
* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation

* GraphQLQueryBodyParameter to recognize application/graphql

* fix 500 error on method without @GraphQLQueryBody

* refactor to processGraphQlGetRequest and processGraphQlPostRequest

* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest

* fix imports

* implement GraphQL Connection

* add tests

* add cacheControlDirective and requestDetails to registerSearch

* fix tests and fix bugs

* set error code
2022-04-19 17:43:41 +00:00
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
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 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
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
James Agnew f82534ca51
Convert Reindex into Batch2 Job (#3458)
* Start working on reindex job

* Updates

* Ongoing work

* Ongoing work

* Work on reindex

* Reindex work

* Add logging

* Fix typo

* Test fix

* Test fix

* Address fixme

* Liocense header

* Resolve fixme

* Add logging

* Update logs

* Address review comments

* License header

* Test fixes

* Test fix

* Test fixes

* Test fix

* Version bump

* Version bump
2022-03-19 16:07:58 -04:00
jmarchionatto e45f7ee9cb
Issue 3450 there is no way to recreate freetext indexes for terminology entities (#3463)
* Add reindex-terminology batch command

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

* Add required dbcp2 dependency

* Fix test

* Improve ConnectionPoolInfoProvider setup. Handle maximum connections.

* Remove java higher version construction

* Remove unused config

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

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-03-18 08:39:12 -04:00
Tadgh 17cf1ed9ce
Rel 5 7 1 mergeback (#3480)
* 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

* Remove dups

* Remove unnecessary stuff

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>
2022-03-17 22:31:40 -04:00
Ken Stevens dfd99c5471
improve search parameter registry logging (#3452)
* Startup log cleanup.  Use cached fhir contexts.

* improve logging

* improve logging

* add full comparator

* wrap resource search param map

* rename wrapped map methods

* add fixmes

* further searchparam encapsulation

* fix regression found by test

* improve logging

* pre-review cleanup

* pre-review cleanup

* bump hapi version

* license

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

* licenses
2022-03-09 19:57:38 -05:00
James Agnew ac80c7ffaa
Search Narrowing by Code Tweaks (#3453)
* Search narrowing tweaks

* Search narrowing tweaks

* Test

* Test fixes

* Try to fix LGTM

* Add license headers

* Test fixes

* Test fixes
2022-03-07 20:27:21 -05:00
michaelabuckley 20e092ba6d
Better error messages for ValueSet $expand contextDirection=existing (#3446)
* Better error messages for ValueSet $expand contextDirection=existing
* Apply to $lastn too - it uses aggregations
2022-03-03 21:11:08 -07:00
Tadgh a2133f6940
Break a couple Circular Bean Dependencies (#3437)
* Rely on context refresh event instead of postconstruct. Load bean lazily.

* Remove parent autowire

* Break termcodesystem circular dependency with new bean

* Break cycle between BaseTermReadSvcImpl and TermCodeSystemStorageSvcImpl

* move back into helper method

* Rip out scheduling and submission to spring batch away from BulkDataExportSvcImpl

* wip

* Fix bean naming

* Revert

* re-add autowiring

* Reformat

* docs and reformat

* Back out change

* feedback from review

* merge conflicts
2022-03-03 09:37:40 -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
kailiu-smile 1bc6e0e3ae
Smile 2775 package install logs ignore resource validation (#3381)
* Added log to the create() and valiForUpload() methods in the PackageInstallerSvcImpl class

* Added helper methods to extract URL from SearchParameter.Tested and fixed log entries.

* Changelog entry

* Update 3384-Package-Install-added-logs-for-resources-validation.yaml

Co-authored-by: Kai Liu <kliu@Kais-MacBook-Pro.local>
2022-02-28 19:52:43 +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
jmarchionatto dbc9427a05
Issue 3391 2588 expand valueset regex include not working (#3410)
* Refactor ValueSet expansion code to simplify property filtering by using new Hibernate search V6 nested classes capabilities; use generic hibernate search queries where possible (mostly everywhere but regex queries) and add R4 integration tests  for both elastic and lucene.

* Refactor ValueSet expansion code to simplify property filtering by using new Hibernate search V6 nested classes capabilities; use generic hibernate search queries where possible (mostly everywhere but regex queries) and add R4 integration tests  for both elastic and lucene.

* Add comment for trick

* Add codes to exception messages

* Add test specific for the fix

* Move changelog to current release. Add upgrade notice.

* Improve fail-fast method

* Update upgrade instructions

* Try luck with new exception codes

* Update hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/search/ElasticsearchNestedQueryBuilderUtilTest.java

Add missed quote

Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
2022-02-24 21:32:11 +00:00
Tadgh ca6381a52a Build fix 2022-02-23 18:43:55 -08:00
James Agnew cc44deee1a
GraphQL Introspection Support (#3348)
* Start working on graphql Schema

* Start testing

* Work on introspection

* Work on introspection

* Use integers for date ordinals

* Add changelog

* GraphQL updates

* Ongoing wrk

* Cleanup

* Bump core lib

* Add changelog

* Clean up dependencies

* CLeanup

* Add missing message

* Test fix

* Change to force CI
2022-02-22 09:48:57 -05:00
James Agnew 058e53616f
Use integers for date ordinals (#3346)
* Use integers for date ordinals

* Add changelog

* Adjust changelog
2022-02-19 18:50:18 -05:00
Tadgh c6122bcb1b Add license files 2022-02-18 19:11:29 -08:00
Patrick Werner 0c5d868f44
encode narratives of contained resources (#3402)
* encode narratives of contained resources
fixes #1466

* encode narratives of contained resources
fixes #1466
2022-02-17 18:54:03 +00:00
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
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
James Agnew 0f2fc7a882
Allow search narrowing and auth interceptor by `token:in` (#3360)
* Optmize valueset expansion

* Working

* Version bump

* Add documentation

* Add test

* Checkstyle message cleanup

* Add reverse rule

* Test ficx

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fix

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

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

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

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

* Test fixes

* Fix conflict

* Add setter

* Test fixes

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-02-09 14:27:14 -05:00
Tadgh 0ccf1bfa52 Merge branch 'rel_5_7' 2022-02-07 12:11:35 -08:00
Patrick Werner 2531e6e57d
feat: added support for package.tgz uri in the "file:/" format (#3347)
* feat: added support for package.zgz uri in the "file:/" format

* added changelog entry

* add error code to thrown message

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-02-05 13:25:50 -05:00
TipzCM f6181fb6ff
3354 fixing flakey tests (#3355)
* 3354 fixing flakey tests

* must fix code

* updating number again

* fixing test

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-02-03 18:30:58 -05:00
michaelabuckley 6b15754b4a
Mb auto complete code (#3330)
New autocomplete extension to ValueSet $expand with contextDirection=existing
2022-02-02 21:03:53 +00:00
Tadgh 6982c4d680
bump version to 6.0.0-PRE1-SNAPSHOT (#3353)
* bump version

* Add new version enum

* Bumped to 6.0.0
2022-02-02 12:11:31 -08:00
michaelabuckley 717ff71695
Simplify JPA Elasticsearch Test Configuration (#3345)
* Delete TestR4WithLuceneDisabledConfig

* Split off the ES and ESClient test configs

* move hibernate search config out to add-ins

* Use addIn for all R4

* Finish R4

* Finish R3

* Finish dstu2

* R5

* Remove property override, and docs

* Apply error code to error

* Fix test to match new error code

* Lighten test

* Disabling broken test.
2022-02-02 16:09:19 +00:00
Johnson Lu c42ecc5c08
Add error codes to all exceptions (#3278)
* Initial design of adding exception codes to exceptions

* Initial design of adding exception codes to exceptions

* change int module name to string

* add comment

* shorten message

* shorten message

* added checkstyle

* developing checker

* completed checkstyle plugin and unit test for it

* fix NPE

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

* change parameter order in InvalidResponseException

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

* exclude generated files

* BIG COMMIT added error codes to all exception throws

* example test fix

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

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

* fix test

* merge master

* merge master

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

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

* Modified assert messages to better match new error codes

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

* Modified assert messages to better match new error codes

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

* Reverted changes on azure-pipelines.yml

* updated hapi-fhir version for checkstyle module

* changes to azure-pipelines.yml

* changes to azure-pipelines.yml

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

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

* reverted changes to azure-piplines

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

* Attempted fix on checkstyle build error

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

* Attempted fix on checkstyle build error

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

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

* reverted changes for hapi-deployable-pom

* add javadoc

* update last code

* Attempted fix on checkstyle build error

* Finished adding in missing error codes to pass Checkstyle checks

* Test pipelining

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

* Merge

* Fixing Checkstyle error

* Attempted fix for date error

* Add error code onto assert statement

* Add in a couple more error codes

* Fixing assert statements

* Bump to static version for dependency

* Adding error code to message

* Adding error codes to exceptions

* Adding error codes to exceptions

* Change to work with cdr branch

* Update to faulty error message

* Merge changes

* allow checkstyle pom to deploy

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com>
Co-authored-by: Predap <simon.zuccherato@gmail.com>
Co-authored-by: Predap <46201929+Predap@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-01-31 13:10:15 -08:00
TipzCM 41193c60db
3335 allow alternative character encoding length in searchparam (#3336)
* added fixme

* 2714 added support for specifying max code lengths for supported phonetic encoders

* 3335git status

* 3335 updated changelog

* 3335 review fixes

* review fixes

* fixing test

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-01-27 17:29:07 +00:00
James Agnew 3f42414287
Validate include statements for JPA (#3331)
* Validate include statements for JPA

* Add changelog

* Optmize test fix
2022-01-26 09:16:28 -05:00
Ken Stevens ed2ea91f56
concurrent validation performance improvement (#3327) 2022-01-23 15:55:31 -05:00
Tadgh 42ff607561
Rel 5 5 5 merge back (#3326)
* Add backport

* Add versions

* remove not real versions
2022-01-22 12:47:34 -05:00
longma1 ab22fd6e82
2718 cross partition support for subscription (#3298)
* added settings for cross-partition to Dao and Model config

* modified subscription validator to validate cross partition subscriptions

* modify subscription matcher to allow matching on all partitions when subscription is set to cross partition

* added cross partition to canonicalSubscription

* end of day commit, changed how we are checking if default partition in subscription validator

* fixed issue with i memory matching for cross partition subscriptions

* added test for parsing legacy CanonicalSubscription

* added changelog and doc changes

* addressed comments in pr

* added assertdoesnotthrow

* test fixes, added new mocks

* added check for if resource can have extension before checking for extensions

* removed unnecessary semicolon

Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Long Ma <long@smilecdr.com>
2022-01-21 15:04:39 -07:00
James Agnew 3fa76a9027
Add support for of-type token modifier (#3309)
* Add support for of-type token modifier

* Add changelog

* Clean up hash calculation logic

* Test fix

* Rework hash generation

* Work on hash generation

* Test fix

* Avoid redundant hash calculations

* Revert some useless changes

* Cleanup

* Test fixes
2022-01-21 16:10:51 +00:00
Tadgh 9f7c454c6b
Issue 2377 missing entry full url in document (#3304)
* start with failing test

* wip

* add changelog

* Add implementation

* Fix DSTU3 impl

* Fix DSTU2 and R5
2022-01-18 10:40:53 -05:00
Tadgh 2054ef65a6
Rel 5 6 mergeback (#3282)
* 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

* Remove worthless import

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>
2022-01-06 18:21:25 +00:00