Commit Graph

618 Commits

Author SHA1 Message Date
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
markiantorno 367b338d85 Updating HAPI to use latest core lib changes. 2021-08-18 11:06:14 -04:00
Tadgh cf917d0f82 Version Bump 2021-08-15 16:54:38 -04:00
Vadim Karantayer f68040aae9 fix SimpleJavaMail configuration username and password handling 2021-08-10 10:45:30 -04:00
VK-SMILECDR 1e0f843d6c
2852 - Simplify java mail code (#2874)
* testing

* [2852] adding SimpleJavaEmail

* [2852] refactor email sender code

* [2852] dependency cleanup

* [2852] add missing dependency

* [2852] add missing spring framework test dependency

* [2852] add change log

* [2852] add change log

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2852-simplify-java-mail-code.yaml

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

* [2852] minor test code cleanup

* [2852] add more tests

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-08-09 15:59:47 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -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
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
jamesagnew 9f77c57e5a Widen access for utility methods 2021-07-20 17:30:26 -04:00
Nick Goupinets 7d4c39b953 Fixed bug 2021-07-02 18:18:10 -04:00
Tadgh cfcc939caa Fix broken tests, add license 2021-07-01 18:28:29 -04:00
Tadgh de84e3f98d add test for restfulserverutil link generation 2021-07-01 17:02:44 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
Tadgh d407501071 More docs 2021-06-30 15:04:05 -04:00
Tadgh 61260dd1b1 Slightly more portable solution for paging 2021-06-30 11:54:59 -04:00
Ken Stevens 795fb31a3a
fixed mdm rules (#2764)
* fixed mdm rules

* changelog

* review feedback jetbrains

* review feedback
2021-06-28 23:24:37 -04:00
Ken Stevens 9500a1a7de
fix false rule matches (#2762)
* fixed an issue with matching compartments to lists of ids

* change log

* Added extra guards against false rule matches.

* changelog

* fix inCompartment

* cleanup
2021-06-27 10:34:32 -04:00
Ken Stevens 5565bf9930
fixed an issue with matching compartments to lists of ids (#2761)
* fixed an issue with matching compartments to lists of ids

* change log
2021-06-26 20:24:28 -04:00
Ken Stevens ea98e62656
collapse multiple owners for same compartment into shared compartment (#2760)
* collapse multiple owners for same compartment into shared compartment

* changelog

* fix regression

* fix regression

* pre-review cleanup

* pre-review cleanup
2021-06-26 11:48:47 -04:00
James Agnew 7185089c9d
Add forced offset search JPA interceptor (#2756)
* Add support for offset searches

* Tests working

* Add changelog

* Test fixes

* Test fix

* More test fixes

* Add commit counter
2021-06-25 10:40:39 -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
James Agnew b934abb297
Impropve transaction Performance (#2717)
* Work on changes

* Work on perf

* Work on testing

* Work on perf

* Work on perf

* Work on fix

* Work on perf

* Ongoing work

* Add changelog

* Additional docs

* Test fixes

* Address review comments

* Test fix
2021-06-14 13:08:19 -04:00
jmarchionatto 39d7d4ad03
Use pageSize variable to hold page size (#2719)
* Use pageSize variable to hold page size as previously used variable has other function, so not always hols intended value required for previous link

* Adjust test to standards and use RestfulServerExtension instead of own server

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-06-11 17:29:14 -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
jamesagnew 4f6c1eaedb Add license header 2021-06-04 14:50:10 -04:00
Ken Stevens 94d6b15db9
_filter searchparam should not appear in cap stmt if disabled (#2706)
* issue reproduced and fixed

* changelog

* cleanup
2021-06-03 18:45:49 -04:00
Michael Buckley 4d6c35ac12 Hide constructor for static helper 2021-06-03 09:09:54 -04:00
Michael Buckley 80266a20a2 Pull request tracing out for sharing 2021-06-02 21:25:06 -04:00
James Agnew 1d2b47c9fb
Update endpoint validation interceptors (#2698) 2021-06-02 05:39:01 -04:00
jamesagnew f774653239 License header updates 2021-05-26 18:18:42 -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
ianmarshall f2627959c2 Add null check on code lookup result. 2021-05-24 22:09:44 -04:00
jamesagnew 926bf393d3 Merge branch 'rel_5_4' 2021-05-17 09:10:58 -04:00
Tadgh e6328dbcae Reflect move in comparison 2021-05-11 10:53:36 -04:00
Tadgh d6252526c3 Move member variable 2021-05-11 10:53:10 -04:00
Tadgh 424ec2118b Add implementation. Add test. Add changelog 2021-05-11 10:31:29 -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
Ken Stevens a4856bba17
fix iBundleProvider.getResources(from,to) throwing a NPE (#2632)
* fix iBundleProvider.getResources(from,to) throwing a NPE

* change log

* review feedback

* rename test to IT that has concurrency failures
2021-05-05 21:50:51 -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
Tuomo Ala-Vannesluoma fbca9f8060
Offset query fixes (#2579)
* Fix new searchbuilder limit similar to legacy searchbuilder

* Fix returning includes when using offset query

* Add unit tests for offset query with include

* Only use count param if offset is given (sometimes we want to search synchronously more if DAO is used directly)

* Throw if offset is tried to use with everything operations

* Do not offer offset paging for everything operations and fix tests to assert that
2021-04-30 19:01:27 -04:00
Nick Goupinets d67537231c Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-29 13:55:48 -04:00
Nick Goupinets d45972abed Added geo accuracy code 2021-04-29 11:46:09 -04:00
Nick Goupinets 4050c42bf4 Treating C addresses as valid 2021-04-28 15:31:34 -04:00
Nick Goupinets ae1c26afea Updated docs 2021-04-28 10:45:15 -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
Nick Goupinets 418c1aa2c6 Added avc code to the interceptors 2021-04-28 10:15:38 -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 a1604c95c9 Updated address validating logic 2021-04-27 18:27:38 -04:00
Nick Goupinets 7cef07b0c1 Improved test coverage 2021-04-27 11:47:57 -04:00
Nick Goupinets 29722ad8ec Fixed exception handling 2021-04-27 10:14:30 -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
Jari Maijenburg 348198e7af
Made unknown operation exception return an OperationOutcome with issue code "not-supported" (#2384) 2021-04-27 08:39:17 -04:00
Nick Goupinets 08934d2364 Updated standardization logic and removed obsolete validator 2021-04-26 16:27:44 -04:00
Nick Goupinets f6ed93b343 Updated validation logic 2021-04-26 14:17:05 -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
Nick Goupinets 634522b405 Updated validation ext handling 2021-04-23 10:43:59 -04:00
Tadgh 596196b3e1 Add licenses 2021-04-23 09:08:41 -04:00
Nick Goupinets 902cd94ca2 Updated address and field validation handling 2021-04-22 16:55:34 -04:00
Nick Goupinets 961f16a1be Initial commit 2021-04-22 09:48:40 -04:00
Tadgh a5f81988fc Merge branch 'improve-bundle-builder' into issue-2534-new-tx-pointcut 2021-04-21 16:53:49 -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 ad8921ac4e Add docs, enum, remove prints 2021-04-21 10:39:23 -04:00
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -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
Tadgh 0bc61b72f7 Add new operation type for transcations 2021-04-14 14:04:00 -04:00
Tadgh 63c9e892b6 Fix up the hashmap provider 2021-04-13 11:12:26 -04:00
Tadgh f61d52d199 Should have realized that transactiondetails is an object reference, so we can't change it effectively 2021-04-13 09:26:05 -04:00
Tadgh 28c917b7a2 Flesh out holder object 2021-04-09 11:28:47 -04:00
Tadgh 8f30f7b0f2 Vague skeleton of pointcut 2021-04-09 11:08:47 -04:00
James Agnew edfe1ae8e6
Add lastupdated to capabilitystatement (#2530)
* Add lastupdated to capabilitystatement

* Test fix

* Test fix
2021-04-08 13:23:21 -04:00
James Agnew f70648484a
Avoid a deadlock uploading terminology in postgres (#2529)
* Fix #2493

* Try to fix intermittent test failure
2021-04-08 12:28:42 -04:00
James Agnew a6cbf7eebd
Add support for hierarchycal valueset expansion (#2525)
* Add support for hierarchycal valueset expansion

* Add changelog

* Add tests

* Cleanup

* Test fix

* Test fixes
2021-04-06 17:36:54 -04:00
James Agnew b617c7690d
Search Parameter Infrastructure Cleanup (#2522)
* Search param service cleanup

* Work on collapsing search param

* Search param cleanup

* Work on build

* Test fix

* Test fixes

* Ongoing work

* Test fix

* Compile fix

* Test fixes

* Test fix

* Test fix

* License header updates

* Remove fixme

* Cleanup

* Cleanup
2021-04-05 17:40:10 -04:00
James Agnew 0bf746f23b
Add support for revincludes to CapabilityStatement generator (#2521)
* Add support for revincludes to CapabilotyStatement generator

* Add changelog

* Fixes

* Test fix

* Test fixes

* Test fix

* Test fix

* More fixes to CS cache

* Test fix

* Test fix

* Test fix
2021-04-05 08:29:04 -04:00
jamesagnew 4eb9508e28 One more fix to interceptor 2021-03-30 11:47:03 -04:00
jamesagnew 8759cdae00 Additional cleanup 2021-03-30 08:20:14 -04:00
jamesagnew 06bdefa16c Improve error handling 2021-03-30 07:36:08 -04:00
James Agnew 049097e5b4
Improve CapabilityStatement Generation (#2511)
* Start work

* Work on testing

* Version bump

* Test fix

* Compile fix

* Test Fixes

* Test fix

* Test fix

* Compile fix

* Tst fix

* Test fix

* Test fix

* Test fix
2021-03-30 05:48:03 -04:00
Diederik Muylwyk b720c32c1d Version bump 2021-03-29 18:23:16 -04:00
Nick Goupinets 05c3ca2512 Merge branch 'master' into 2478_add_extension_mdm_matcher 2021-03-25 12:22:23 -04:00
Nick Goupinets bac2e58b90 Added null checks for the request details param 2021-03-24 10:50:26 -04:00
Tadgh 8785a51857 Remove janky interceptor hook 2021-03-23 19:50:05 -04:00
Tadgh a2ab3f5573 rethrow dataformatexception in case of TargetInvocationException 2021-03-23 19:49:06 -04:00
Tadgh 6f669f9ccd wip 2021-03-23 19:29:22 -04:00
Nick Goupinets 8ead3c5f22 Code review fixes 2021-03-23 15:01:22 -04:00
James Agnew dc41d5ad61
Add terminology mapping and display population interceptors (#2488)
* Start work on code mapping interceptors

* Work on generation

* Add terminology mapping and display population interceptors

* Add changelog

* License header updates

* Test fixes

* Fix typo

* Interceptor fixes

* License header update

* Test fixes

* Mapping fixes

* Version bump

* License header updates

* Add null tests

* Add null guard

* Intermittent fix
2021-03-21 12:03:57 -04:00
Nick Goupinets 04a0ecfc2b Added tests 2021-03-15 10:31:38 -04:00
Nick Goupinets 8b8bbcc91f Refactored based on the code review 2021-03-11 17:14:01 -05:00
Nick Goupinets 0013910c53 Removed commented code 2021-03-11 15:48:22 -05:00