Commit Graph

2510 Commits

Author SHA1 Message Date
Tadgh 3d24a4ce16 Refactor to support arbitrary additional SPs based on Type for a compartment 2021-09-14 01:02:19 -04:00
Ken Stevens eee7d7e455
code cleanup (#2986)
* failed attempt to get it to work

* Use simplified FhirContext.forCached methods

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

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

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-09-13 03:09:18 +00:00
James Agnew 5554431146
Avoid dead SearchParameter links in CapabilityStatement (#2790)
* Avoid dead SearchParameter links in CapabilityStatement

* Resolve fixmes

* Build fix

* Test fix

* Test fix

* Test fix

* Work on metadata

* Fixes

* Test fixes

* Test fix

* Test fix

* Test fixes

* Test fix

* Work on test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fix params

* Resolve fixme

* Adjust changelogs

* Version bump to 5.6.0-PRE7

* Add license header

* Bump version to 5.6.0-PRE5-SNAPSHOT
2021-09-11 18:27:18 -04:00
Tadgh 0ccd71faf8
Merge pull request #2963 from hapifhir/custom-elastic-index
Custom elastic index
2021-09-08 14:29:58 -04:00
Tadgh f04cf02be7
Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-08 08:45:47 -04:00
Tadgh 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -04:00
Nick Goupinets 35aaa98431 Merge branch 'master' into 2849_add_new_mdm_param 2021-09-07 11:27:49 -04:00
Ken Stevens 346e29920a
Issue 2927 convert mdm clear to spring batch (#2929)
* initial roughout of mdm clear batch job

* still roughing out classes

* finished first draft of reader

* most tests passing now

* all tests pass.  now FIXMEs

* FIXMEs done.  Time for regression.

* fix test

* changelog and docs

* fix test

* pre-review cleanup

* version bump

* move spring autowire deps for cdr

* move spring autowire deps for cdr

* finally got beans working phew

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

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

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

* review feedback

* review feedback

* Remove inheritance

* fix beans

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2021-09-03 14:58:19 -04:00
Nick Goupinets ee65a24260 Merge branch 'master' into 2849_add_new_mdm_param 2021-09-02 17:42:41 -04:00
leif stawnyczy 1a7b101d03 Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-02 10:13:04 -04:00
Tadgh 3e288f1dde Merge branch 'master' into rel_5_5_1 2021-09-01 18:16:27 -04:00
Tadgh e1272a3825 Bump version of HAPI-FHIR 2021-08-31 11:43:17 -04:00
Tadgh 87986d3da8 Add versionenum 2021-08-31 11:42:26 -04:00
Nick Goupinets 8403b85429 Merge remote-tracking branch 'origin/master' into 2849_add_new_mdm_param 2021-08-27 09:42:08 -04:00
Frank Tao 090a8b0821
Impl displayLanguage for $lookup (#2908)
* Impl displayLanguage for $lookup - first cut

* Added original lookupCode method

* Added original lookupCode method to IFhirResourceDaoCodeSystem

* Added more test cases and changelog
2021-08-25 14:47:10 -04:00
leif stawnyczy b51c722755 stashing minor refactors 2021-08-25 10:41:58 -04:00
Tadgh 37ad73a422 Bump PRE version so we don't conflict downstream 2021-08-23 15:42:18 -04:00
Tadgh 1acaf325c5 Merge branch 'master' into rel_5_5_0 2021-08-23 14:50:29 -04:00
Nick Goupinets 3a5e391c77 Fixed pointcut def 2021-08-23 11:00:04 -04:00
Nick Goupinets 4cfe11a221 Merge branch 'master' into 2849_add_new_mdm_param 2021-08-16 13:33:57 -04:00
Tadgh cf917d0f82 Version Bump 2021-08-15 16:54:38 -04:00
Tadgh 669cf05b30 Modify SearchParameterMap toNormalizedQueryString to include value of _contained parameter 2021-08-12 14:25:12 -04:00
Tadgh fa2b4ea0d7 Add version number 2021-08-06 14:08:10 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -04:00
Tadgh 0a303a0e11 Add MDM expansion by golden pid 2021-08-06 13:22:08 -04:00
Nick Goupinets d467c1c79b yMerge branch 'master' into 2849_add_new_mdm_param 2021-07-30 11:18:33 -04:00
Ken Stevens f5dfc3a5ed
New reindex spring batch operation (#2845)
* first sweep to add new $reindex job

* first cut done.  next up integration test.

* start roughing out reindex everything

* Failing test

* test passes

* add BundleUtil helper method

* rough in processEverything

* rough in processEverything

* fix mock test

* merge master

* Make BaseJpaTest.mySrd lenient.

* fix test

* reindex everything works with FIXMEs

* reindex everything more tests

* moar tests

* moar tests

* fix test

* fix test

* fix regression and fix test

* fix test cycle

* fixme

* fix test

* test provider layer

* reindex everything partition aware

* yay last fixme!

* run reindex in partitioned threads

* add fixmes for areas that require extra testing

* added transaction and log message

* manual integration testing

* changelog

* reindex all partitions

* bump hapi version

* fix test

* moar test

* pre-review cleanup

* fix javadoc

* review feedback

* review feedback

* review feedback

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

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

* review feedback

* review feedback

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

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

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

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

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

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

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

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

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

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

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

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

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-07-29 19:18:49 -04:00
Nick Goupinets a2aa2ca1c3 2849 Added new parameter to MDM processing 2021-07-29 15:52:27 -04:00
James Agnew f957661dda
Patient ID Partition Mode should support conditional create (#2828)
* Fixes

* Test fix

* Add changelog

* Test fixes

* Test fixes

* Docs tweak

* Partitioning fixes

* Import fix

* Fix test data
2021-07-26 14:18:58 -04:00
jamesagnew a5e6674e84 Version bump to 5.5.0-PRE7-SNAPSHOT 2021-07-22 08:41:16 -04:00
James Agnew 6d37749be8
Add non unique combo search params (#2809)
* Start work on nonunique combo search params

* Work on SQL

* Version bump

* A fix

* Test fixes

* Fixes

* Undo version bump

* Test fixes

* Resolve fixme
2021-07-21 19:14:14 -04:00
juan.marchionatto 1e9163c636 Add changelog. Address MR comments. 2021-07-08 14:52:19 -04:00
jmarchionatto ee1f1fb5b8
Merge pull request #2778 from hapifhir/2777-hapi-fhir-cli-Add-option-to-pass-request-headers-to-target-server
Add header-passthrough option to hapi-fhir-cli commands which generate http requests(#2777)
2021-07-07 16:47:28 -04:00
James Agnew 95306c3d64
Add NPM validation support module (#2782)
* Add NPM validation support module

* Add changelog
2021-07-07 16:28:41 -04:00
Tadgh 3e7bc2a81e
Forward port 5 4 2 (#2781)
* Add new version to enum

* Add backport tags, new VersionEnum, and new release folder for 5.4.2
2021-07-07 10:10:07 -04:00
juan.marchionatto 5c5bd1ec6c Organize imports 2021-07-06 09:31:53 -04:00
juan.marchionatto 5f36fe56b0 Add header-passthrough option to hapi-fhir-cli commands which generate http requests.
Add class to parent request-generating commands.
Allow ValidationResult to be set number of detected errors to inform.
2021-07-05 16:08:03 -04:00
James Agnew d762a07817
Partition patient interceptor (#2766)
* Start work on interceptor

* Implemented

* Add interceptor and docs

* Add docs

* Compile fix

* Test fixes

* Test cleanup

* Test fixes

* Test fixes

* Improve error message

* Add broken tests

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2766-add-patient-id-compartment-interceptor.yaml

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptor.java

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

* Address review comments

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-07-05 09:15:20 -04:00
jamesagnew 6bb5cbf764 Cleanup logging 2021-07-04 15:31:10 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
Tadgh 8f3cbb0a7f Refactor docs 2021-06-30 14:48:13 -04:00
James Agnew 8379392e16
Add inline tag mode (#2748)
* Start work on tag mode 3

* Add changelog

* Test fix
2021-06-22 23:08:09 -04:00
jamesagnew f0cfb5ad1b License headers 2021-06-21 05:29:02 -04:00
James Agnew 6ea1438f1d
Add transaction write semaphore interceptor (#2743)
* Add transaction write semaphore interceptor

* Add changelog

* Test fix
2021-06-20 12:55:49 -04:00
James Agnew 8b205b23d0
Fix history paging (#2741)
* Fix history paging

* Add changelog

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

* Add operation

* Wire up jpa provider.  Begin with failing test.

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

* delete expunge job parameter validation with test

* implemented reader
stubbed processor, writer

* wip for master merge

* started implementing reader

* started implementing reader

* working with stubs

* happy path batch delete expunge is done

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

* IT test works now

* add reader test

* Converted delete _expunge=true to use new batch job

* DeleteExpungeDaoTest passes

* Fix test

* Change batch size to integer

* rename search count to batch size

* Make delete expunge partition aware

* updated docs

* pre-review cleanup

* change log

* add partition id to SystemRequestDetails

* Make RequestPartitionId serializable

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

* fix tests

* test pointcut gets called

* assert on pointcut calls

* Add resource type to STORAGE_PARTITION_SELECTED pointcut

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

* bump hapi-fhir version

* copyrights

* restore deleteexpungeservice for mdm

* restore deleteexpungeservice for mdm

* fix test

* public constants

* convert instant to date

* Moved expunge constants to ProviderConstants

* final review

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

* fix tests

* fix tests

* fix tests

* fix tests

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* improve logging

* bump version

* version bump

* recovering from failed merge

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

* fix serialization
2021-06-15 10:36:05 -04:00
jamesagnew 376a84d213 Version bump 2021-06-14 13:12:34 -04:00
jamesagnew 48eea5a7cc Prepare changelog for 5.4.1 release 2021-06-14 09:13:41 -04:00
Nick Goupinets 3863e82a59
Fixed bug with choice children (#2714) 2021-06-08 08:24:13 -04:00
James Agnew dc627dc019
Add bulk export authorization layer (#2712)
* Add bulk export authorization layer

* Add docs

* Version bump

* Authorize any

* Add bulk export - all

* Address lgtm issue
2021-06-06 20:47:43 -04:00
James Agnew 62be623cf5
Add support for ICD-10-CM (#2702)
* Add support for ICD-10-CM

* Have this working

* Fix LGTM issues

* Test fix
2021-06-03 19:55:16 -04:00
James Agnew 1d2b47c9fb
Update endpoint validation interceptors (#2698) 2021-06-02 05:39:01 -04:00
James Agnew fe763dd2d6
Upgrade deps (#2695)
* Upgrade deps

* Fix build error

* Branch tweak

* Build fix

* Build fix

* Undo bump

* Test fixes
2021-06-01 12:03:29 -04:00
James Agnew 05ac88bc21
Add initiate bulk export pointcut (#2692)
* Add initiate bulk export pointcut

* Add changelog

* Test fixes
2021-05-31 16:05:09 -04:00
James Agnew a2950324ef
Avoid SQL based transaction dupe check (#2688)
* Avoid SQL based transaction dupe check

* Add changelog

* Test fixes

* Test fixes
2021-05-30 20:26:36 -04:00
jamesagnew 8636e4f155 Test fix 2021-05-27 07:30:09 -04:00
James Agnew 7a83c76e65
Add validation suppression mode (#2675)
* Add validation suppression mode

* Add changelog

* Compile fix
2021-05-26 17:41:48 -04:00
Nick Goupinets 80be95dd07 Accounted for uninitialized fields - part 3 2021-05-21 13:32:23 -04:00
Nick Goupinets d0d0ff9890 Accounted for uninitialized fields 2021-05-21 12:00:01 -04:00
Nick Goupinets e243674f5d Accounted for uninitialized fields 2021-05-21 11:54:04 -04:00
Nick Goupinets 995ac96f73 Can't think today 2021-05-20 17:21:04 -04:00
Nick Goupinets 8a7fc58e91 Fixed primitive field merging 2021-05-20 15:48:00 -04:00
jamesagnew ff2698d4d1 Merge branch 'rel_5_4' 2021-05-19 09:22:11 -04:00
jamesagnew de56f440cb Version bump 2021-05-18 17:14:14 -04:00
James Agnew 40ecafcd31
Don't unescape plus in match URLs (#2658)
* Don't unescape plus in match URLs

* Perf improvements

* Add changelog

* Test fix

* Work on tests

* Fixes

* Test fix
2021-05-16 21:51:23 -04:00
jamesagnew 2068372998 Version bump 2021-05-07 17:43:54 -04:00
jamesagnew 63c4b22cd3 Undo bump 2021-05-07 17:42:50 -04:00
jamesagnew 17e41520a4 Version bump 2021-05-07 17:41:39 -04:00
James Agnew 970a9884f0
Avoid tag definition constraint (#2620)
* Avoid tag definition constraint failure

* Version bumps

* Add changelog

* Avoid guava issue

* Test fix

* Test fix

* Bump pom
2021-05-01 17:16:15 -04:00
Nick Goupinets d67537231c Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-29 13:55:48 -04:00
James Agnew 95d7ba6fa8
Streamline Search SQLs (#2576)
* Streamline SQL queries

* SQL query tidying

* Add changelog

* Test fixes

* Tests passing

* Ongoing work

* Test fixes

* Test fixes

* Build fix

* Cleanup

* Fixes
2021-04-28 10:29:09 -04:00
Nick Goupinets 21d8cdfefc Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-28 10:16:27 -04:00
Tadgh ac1d4e3e4f
Merge pull request #2542 from hapifhir/issue-2534-new-tx-pointcut
Add new pointcut for transaction processing completed.
2021-04-27 18:42:19 -04:00
Nick Goupinets 024f553fc9 Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-27 09:31:42 -04:00
Nick Goupinets 82bf8cdc9d Code review updates 2021-04-27 09:29:08 -04:00
jamesagnew 1d054054c7 Test fixes 2021-04-27 07:03:24 -04:00
Tadgh a5e734fec8 Handle sorting entries which contain no resources 2021-04-26 22:24:47 -04:00
Tadgh 798e960bb8 Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-26 15:26:34 -04:00
Kevin Dougan SmileCDR 0246e7dd0e
2572 - Add master Branch changes related to backport of fix for #2171… (#2574)
* 2572 - Add master Branch changes related to backport of fix for #2171 for new 5.3.3 release.

* 2572 - Added some missing changelog folders for the v5.3.1 and v5.3.2 releases.

* 2572 - Added a missing backport changelog entry for the v5.3.1 release.

* 2572 - Added a missing VersionEnum entry for the V5_3_1 release.
2021-04-26 14:13:42 -04:00
Tadgh 3adc259348 Productioninizg 2021-04-26 14:08:20 -04:00
Tadgh 9ecb390dae Move tests to proper class. Fix issue with version referencing 2021-04-26 13:40:11 -04:00
Tadgh b200c10ced Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-26 09:48:30 -04:00
James Agnew 2ba1005762
OpenAPI Support (#2560)
* Start work on OpenAPI

* Fixes

* Work on OpenAPI

* Cleanup

* Cleanup

* More swagger work

* Build fix

* More work

* More work

* Add documentation

* Docs fixes

* Add changelog

* License updates

* Add API

* Cleanup

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

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

* Work on scripts

* Add docs

* Compile fix

* Work on fixes

* Fix tests

* Test fix

* Test fix

* Build fix

* Tests

* Build fix

* Work on pipeline

* Version bump

* Test fix

* Version bump

* Test fix attempts

* Test fix

* Test fix

* Remove accidentally committed files

* Fixes

* Tets fixes

* Test fix

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fixes

* License header updates

* test fix

* Test fixes

* Test fix

* Test fixes

* Test fix

* Checkstyle bump

Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
2021-04-25 15:40:50 -04:00
Nick Goupinets ac2aac4342 Updated address validation handling 2021-04-23 18:55:51 -04:00
Tadgh 596196b3e1 Add licenses 2021-04-23 09:08:41 -04:00
Tadgh a5f81988fc Merge branch 'improve-bundle-builder' into issue-2534-new-tx-pointcut 2021-04-21 16:53:49 -04:00
Tadgh e711dfb07c enhance bundlebuilder to support deletes 2021-04-21 16:44:22 -04:00
Tadgh b7166735f9 Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-21 12:13:54 -04:00
Tadgh c80d18aca2 Fix test for pointcut 2021-04-21 11:16:10 -04:00
Tadgh ad8921ac4e Add docs, enum, remove prints 2021-04-21 10:39:23 -04:00
Tadgh 3dee0c8ab6 Working in-place bundle sort 2021-04-20 17:48:55 -04:00
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -04:00
Tadgh ff2690b74e Add tests for transaction sorting 2021-04-20 14:12:25 -04:00
Tadgh 1670ed7202 Begin topological sort implementation 2021-04-19 20:01:02 -04:00
Nick Goupinets 1f10a15c35 Merge branch 'master' into 2515_MDM_survivorship_rules 2021-04-19 17:33:53 -04:00
Nick Goupinets 536ca0e73d Code review updates 2021-04-19 16:27:31 -04:00
jamesagnew 6b43410514 Add missing constant 2021-04-14 18:50:47 -04:00
jamesagnew b294f7d208 License headers 2021-04-14 18:00:52 -04:00
James Agnew ca2088f3ad
Add framework for Bulk Import (#2538)
* Start work on bul;k import

* Work on bulk import

* Have batch working

* Working

* Working

* More work

* More work on bulk export

* Address fixmes

* License header updates

* Test fixes

* License header updates

* Test fix

* Test fix

* Version bumps

* Work on config

* Test cleanup

* One more version bump

* Version bump

* CLeanup

* A few additions

* Test fixes

* Test fix

* Test fix

* Migration fix

* Test fix

* Test fix
2021-04-14 17:41:32 -04:00
Ken Stevens 550602b2f1
added numeric matcher (#2547)
* added numeric matcher

* changelog

* performance optimization

* fix test
2021-04-14 13:15:30 -04:00