Commit Graph

1218 Commits

Author SHA1 Message Date
Josiah 1f5fa70fb6 Version bump 2021-06-24 11:22:35 -04:00
Josiah 2cc27d9b4f Forgot changelog 2021-06-24 10:19:45 -04:00
jamesagnew 59653759ed Update tests 2021-06-23 15:58:14 -04:00
Nick Goupinets 6feaa12593
Merge pull request #2747 from hapifhir/2746_npe_in_mdm_utils
Added null checks
2021-06-23 09:51:53 -04:00
jamesagnew e3158045aa License header 2021-06-22 23:25:36 -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
Nick Goupinets 9caa5e68fc Added changelog 2021-06-22 15:52:21 -04:00
Josiah 912b44c3fa
Merge pull request #2734 from hapifhir/2732-bump-conceptmap-group-element-display-storage-size
Address #2732
2021-06-21 08:33:36 -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
Ken Stevens 32ac16e2aa
add a limit to mdm candidate searches (#2742)
* done

* verbal review feedback

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2739-max-mdm-matches.yaml

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

* review feedback

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-06-18 20:48:34 -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 097a2f70b3
add partition support to $evaluate-measure (#2736)
* Finished adding partition support to $evaluate-measure

* review feedback
2021-06-18 14:22:57 -04:00
Josiah 164e684d7c Merge branch 'master' into 2732-bump-conceptmap-group-element-display-storage-size 2021-06-17 15:14:05 -04:00
Josiah 324201b105 Make change 2021-06-17 11:28:02 -04:00
James Agnew 659efa786c
ValueSet Expansion Should Preserve Order (#2724)
* Add test

* FIxed

* Add changelog

* Add test

* Intermittent test failure fix

* Build fix

* Build fix

* Test fix

* Test fixes

* Fix checkstyle issue

* Test fix

* Add test logging
2021-06-16 07:20:59 -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
jamesagnew 48eea5a7cc Prepare changelog for 5.4.1 release 2021-06-14 09:13:41 -04:00
jamesagnew 474cca877a Merge branch 'rel_5_4_2' 2021-06-14 09:07:26 -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
jamesagnew 090dc9a2e2 Docs 2021-06-11 15:55:35 -04:00
James Agnew fcb32eacb6
Add support for loinc 2.70 (#2721)
* Add support for loinc 2.70

* Add changelog
2021-06-11 15:15:22 -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
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
Ken Stevens c498522c78
search by source reported incorrect size (#2705)
* issue reproduced in test and fixed

* changelog
2021-06-03 18:19:43 -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
jamesagnew f5c75e80de Credit for #2693 2021-06-01 10:53:53 -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
Patrick Werner 94bd2400e3
Merge pull request #2689 from me-d4l/fix/update-chaelog-for-2682
Add CHANGELOG entry for ticket 2682
2021-05-31 12:16:13 +02:00
morten.ernebjerg b9931dfb03
Add CHANGELOG entry for ticket 2682 2021-05-31 08:43:23 +02:00
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
James Agnew 786112284b
Bump spring version (#2687) 2021-05-30 19:04:14 -04:00
James Agnew 24b3f0f30d
Enable mass ingestion mode (#2681)
* Work on fixes

* Work on counts

* Enable mass ingestion mode

* Add changelog

* Test fix

* Test fix

* Test fixes

* Fixes

* Test fix

* Test fix
2021-05-27 18:43:51 -04:00
James Agnew c8c596aff4
Fix date search on period with no end (#2676)
* Add test

* Working test

* Update test

* Account for date fixes

* Add changelog

* Add setting

* Test fixes

* Test fix
2021-05-26 21:03:53 -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
Ken Stevens af44b9c7a0
Ks 20210526 accurate total (#2677)
* begin with failing test

* fixed

* changelog
2021-05-26 12:20:49 -04:00
ianmarshall 1b387a5740 Add null check on code lookup result. 2021-05-24 22:14:02 -04:00
James Agnew 2c722e64c2
Add support for including qualified star syntax (#2672)
* Add support for including qualified star syntax

* Add changelog

* Add docs

* Build fix
2021-05-23 16:50:37 -04:00
jamesagnew ff2698d4d1 Merge branch 'rel_5_4' 2021-05-19 09:22:11 -04:00
jamesagnew bd372e4bd8 Fix changelog 2021-05-19 08:34:24 -04:00
James Agnew 2badae2097
Avoid contained resource in conditional create (#2665)
* Work on unexpected contained resources

* Avoid contained on conditional create

* Add changelog
2021-05-19 07:49:59 -04:00
jamesagnew b463b072c8 Test fixes 2021-05-18 21:32:13 -04:00
jamesagnew de56f440cb Version bump 2021-05-18 17:14:14 -04:00
Tadgh 22a1a05cfb Add changelog 2021-05-18 10:05:59 -04:00
James Agnew 7a50454350
Correct index init issue (#2662)
* Correct index init issue

* Add changelog
2021-05-17 20:31:44 -04:00
jamesagnew 926bf393d3 Merge branch 'rel_5_4' 2021-05-17 09:10:58 -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
James Agnew b31bb945ad
Add include clause to MSSQL forcedid table index (#2659)
* Add include clause to MSSQL forcedid table index

* Add changelog

* Test fix

* Bump MSSQL version
2021-05-16 19:14:51 -04:00
Tadgh 57bb11797e fix 2021-05-13 15:46:26 -04:00
Tadgh 15ea4fb555 Tidy test 2021-05-13 10:47:26 -04:00
Tadgh 3428d71023 Add toggle. Add test. Add changelog. add docs 2021-05-13 10:29:07 -04:00
Ken Stevens 316e7e0d6d
Ks 20210512 value set expansion id (#2654)
* tested and fixed

* changelog
2021-05-12 21:38:29 -04:00
James Agnew b64346ba1e
Add shcheduled task enablement config (#2652)
* Add shcheduled task enablement config

* Add changelog

* Test fix

* Cleanup
2021-05-12 14:38:30 -04:00
Tadgh d70b1866c1 Remvoe dead space 2021-05-11 10:54:14 -04:00
Tadgh 424ec2118b Add implementation. Add test. Add changelog 2021-05-11 10:31:29 -04:00
jamesagnew 5c4fcac530 Merge branch 'rel_5_4' 2021-05-11 08:40:09 -04:00
James Agnew 3015438a0c
Avoid query cache poisoning (#2647)
* Avoid query cache poisoning

* Test fixes

* Add changelog
2021-05-11 08:39:38 -04:00
James Agnew 26d030f93e
Add language validation (#2644)
* Add language validation

* Add tests

* Test fix
2021-05-10 20:09:45 -04:00
James Agnew 43631d4937
Account for NOPs in Auto-Versioned References (#2643)
* Account for NOPs in auto-versioned references

* Add docs

* Add tests
2021-05-08 18:09:50 -04:00
jamesagnew 176be4df16 Merge branch 'master' into rel_5_4 2021-05-07 17:44:47 -04:00
jamesagnew 0cebbf4fa8 Merge branch 'master' of github.com:hapifhir/hapi-fhir 2021-05-07 17:44:27 -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 5a9f499fbf
Resolve weakness in history operation (#2642)
* Address DOS issue in History operation

* Work on history caching

* Add docs

* Add changelog

* Resolve test failures

* Test fixes

* Test fix

* Test fixes
2021-05-07 12:04:59 -04:00
Tadgh cf864c2078 Merge remote-tracking branch 'origin/master' into issue-2634-increase-src-path-length 2021-05-06 09:10:48 -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
Tadgh d17ee2eb78 Add changelog 2021-05-05 16:01:29 -04:00
KevinIsAProgrammer 75c74a22db
Merge pull request #2619 from hapifhir/2590_preserve_the_ID_value_of_the_resources_in_the_package_loader
2590 preserve the id value of the resources in the package loader
2021-05-03 15:39:14 -04:00
Kevin Hartmann 320e8379b3 Now convert pure numeric ids to "npm-<id>". 2021-05-03 12:55:17 -04:00
jamesagnew 82be821628 Credit for #2577 2021-05-03 08:03:49 -04:00
jamesagnew 573097379d Credit for #2623 2021-05-02 17:20:16 -04:00
James Agnew 0cea403800
Fix vulnerability warning on maven plugin (#2621)
* Fix vulnerability warning on maven plugin

* Compile fixes

* Fix bootstrap dep

* Test fix

* Fix tests

* FIx deps
2021-05-02 12:14:32 -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
Kai Kewley 55ef6f8653
Add Snowstorm to the points map. (#2582) 2021-04-30 19:05:46 -04:00
jamesagnew 12c0bcda47 Credit for #2579 2021-04-30 19:03:47 -04:00
Kevin Hartmann b3afe41de8 Added test to make sure we have loaded the expected package id. 2021-04-30 15:14:19 -04:00
Tadgh 983d811af6
Merge pull request #2587 from hapifhir/issue-2585-enhance-placeholder-targets-logic
Issue 2585 enhance placeholder targets logic
2021-04-30 12:55:27 -04:00
Tadgh 42109e8a4a Add changelog 2021-04-29 18:31:10 -04:00
Nick Goupinets 8cde076f1e Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-29 17:25:32 -04:00
JP 239d2496ea
CQL hardening and Dstu3 unit tests (#2450)
* WIP for elm caching

* Bug fixes and a working DSTU3 unit test

* More tests, Address review feedback, add initial docs

* Update to cql-evaluator 1.2.0

* Fixes for documentation
2021-04-29 14:52:13 -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
KevinIsAProgrammer dd61a8aa2c
Merge pull request #2575 from hapifhir/kh_2526_Add_Operation_Section_to_Conformance_Statements_resource_section
Kh 2526 add operation section to conformance statements resource section
2021-04-27 22:47:30 -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
Kevin Hartmann b9151a4a75 Added Changelog. 2021-04-27 16:34:24 -04:00
Nick Goupinets 024f553fc9 Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-27 09:31:42 -04:00
jamesagnew 00a37deb08 Credit for #2384 2021-04-27 08:43:25 -04:00
Tadgh 798e960bb8 Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-26 15:26:34 -04:00
Nick Goupinets 9e153ddbcd Updated docs 2021-04-26 14:26:21 -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 b200c10ced Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-26 09:48:30 -04:00
jamesagnew 987264b271 Version bump JENA 2021-04-25 17:38:04 -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
Tadgh 9c19a4c087 Add changelog 2021-04-23 09:11:36 -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
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -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
Tadgh 3075a9b5e6 Still minor refactoring 2021-04-16 16:53:23 -04:00
jamesagnew 42c89ccedd Changelog 2021-04-15 08:22:44 -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
Kevin Dougan SmileCDR 2ebc57b8a2
2548 - Add backport changelog Tag to backported fixes for #2533 and #2543. (#2549) 2021-04-14 13:33:07 -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
IanMMarshall 4cd0409bae
Merge pull request #2546 from hapifhir/2535_ignore_logical_structuredefinition_during_package_install
2535 ignore logical structuredefinition during package install
2021-04-14 10:54:37 -04:00
Kevin Dougan SmileCDR b45ddcc3da
2543 - Fix issue where versionned references are not being returned properly. (#2544)
* 2543 - Fix issue where versionned references are not being returned properly.

* 2543 - Added changelog entries for this fix plus a previous fix for 2533.
2021-04-14 08:45:49 -04:00
ianmarshall 0cb95ad556 Change package loader to not generate snapshot for logical StructureDefinition resources. 2021-04-13 22:30:22 -04:00
Tadgh fcbfb11506 Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-13 15:55:01 -04:00
Tadgh a0c11d7c66 Update docs 2021-04-13 10:04:45 -04:00
James Agnew bc4266d3d2
Improve narrative templates for custom structures (#2537)
* Improve narrative templates for custom structures

* Add changelog

* Test fix
2021-04-12 06:00:31 -04:00
Diederik Muylwyk 1bd585162d
Fix typo in docs. (#2536) 2021-04-09 18:50:12 -04:00
Tadgh 99e10de5fb
Merge pull request #2487 from hapifhir/mdm-expansion-interceptor
MDM Expansion Interceptor (poc)
2021-04-09 11:23:04 -04:00
Tadgh 82fc7b7457 Fix typo 2021-04-09 10:51:12 -04:00
Diederik Muylwyk 38436e5c1b
Fix a typo in docs. (#2532)
* Fixed poorly formatted changelog entry.

* Fixed typo.
2021-04-08 14:57:20 -04:00
Diederik Muylwyk ec7cc8fbaa
Fixed poorly formatted changelog entry. (#2531) 2021-04-08 14:07:16 -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 462d9bc6c4
Fix compartment defs for R5 (#2528)
* Fix compartment defs for R5

* Add changelog

* Test fix
2021-04-08 05:59:05 -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 fcffb04c7b
Allow unknown code systems during validation (#2523)
* Allow unknown code systems during validation

* Add changelog

* Test fix
2021-04-05 20:59:59 -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
Nick Goupinets d366558749 Merge branch 'master' into 2515_MDM_survivorship_rules 2021-04-05 09:17:42 -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
Tadgh 383c55e339 Add changelog 2021-04-01 11:33:45 -04:00
Tadgh 67fe940889 Update docs 2021-04-01 11:07:46 -04:00
Nick Goupinets 0cd14b971a Added changelog 2021-04-01 10:59:50 -04:00
Tadgh d8866ec75f Add doc caveats 2021-03-31 16:33:49 -04:00
Tadgh e5de34c51d Update docs 2021-03-31 16:08:09 -04:00
Tadgh f3c706d656 Add page for mdm expansion 2021-03-31 15:33:03 -04:00
Tadgh 696982ce1e Fix bean name. Update docs 2021-03-31 13:45:40 -04:00
Tadgh dbf050e32e pedantism sated 2021-03-31 10:14:18 -04:00
Tadgh aefe37aaf7 Add forgotten changelog 2021-03-31 09:59:06 -04:00
Tadgh 74be6761b1 Merge remote-tracking branch 'origin/master' into mdm-expansion-interceptor 2021-03-31 09:47:57 -04:00
Tadgh 8b69d161bd Update docs 2021-03-30 17:12:55 -04:00
jamesagnew 116bb12a58 Docs fix 2021-03-30 14:27:47 -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
Diederik Muylwyk bddd3f4c92 PointCutLatch now works with IPointcut instead of Pointcut 2021-03-29 18:20:33 -04:00
longma1 494c8e9593
Merge pull request #2483 from hapifhir/2478_add_extension_mdm_matcher
2478 add extension mdm matcher
2021-03-29 08:13:48 -06:00
jamesagnew 1576227fc8 Credit for #2194 2021-03-26 09:19:02 -04:00
Nick Goupinets 644885e91a Fixed typo in the docs 2021-03-25 18:32:08 -04:00
Nick Goupinets 05c3ca2512 Merge branch 'master' into 2478_add_extension_mdm_matcher 2021-03-25 12:22:23 -04:00
James Agnew 8352bc9c01
Correct the path to the select2 library in the testpage overlay (#2505)
* Correct the path to the select2 library in the testpage overlay

* Add changelog
2021-03-25 10:52:15 -04:00
long 6aab327612 modified documentation wording 2021-03-23 14:27:17 -06:00
Nick Goupinets de0399da23 Merge branch 'master' into 2478_add_extension_mdm_matcher 2021-03-22 09:34:32 -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
long 989e9e7903 refactored terserUtil, added equals function in ExtensionUtil 2021-03-17 13:02:59 -06:00
James Agnew d857048207
Preserve meta values in stored resources (#2481)
* Fix #1731

* Test fix

* Test fixes

* Avoid intermittent failure
2021-03-17 09:23:22 -04:00
Kunjan Patel bdee1f1269
Update points.json for adding a point in atlas (#2482) 2021-03-17 05:50:07 -04:00
Tadgh b191f1da2b
Merge pull request #2480 from hapifhir/issue-2479-bad-packages
Have CreatePackageCommand automatically add fhirVersions based on --fhir-version flag
2021-03-16 18:00:27 -04:00
michelgleeson 0a6c61372c
Parameterize term valueset concept view dao (#2477)
* Generic the list type to accomidate different substring queries

* special subquery for Oracle

* change the conceptview dao depending on dialect

* address review comments

* remove generics

* no longer inherits

* copy paste from non Oracle version

* dang copy pasters

* changelog

Co-authored-by: Mike G <michel.gleeson@gmail.com>
2021-03-16 16:26:19 -04:00
Tadgh c3e6de3aff Add changelog 2021-03-16 13:47:29 -04:00
Nick Goupinets 744adb2d08 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-15 10:32:04 -04:00
James Agnew 2e7eb972ff
Avoid NPE in ResourceVersionConflictResolutionStrategy for system request (#2471)
* Avoid NPE in ResourceVersionConflictResolutionStrategy for system
request

* Add changelog
2021-03-12 19:23:49 -05:00
Nick Goupinets e188a95d66 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-12 16:17:25 -05:00
James Agnew 0ad57c51bb
Fix resource reindexing on partitioned seerver (#2468)
* Fix resource reindexing on partitioned seerver

* Add changelog

* Test fix

* Test fix

* Tets fix

* Test fix
2021-03-12 14:14:39 -05:00
Nick Goupinets f9f0b2705d Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-12 10:30:36 -05:00
Nick Goupinets 8b8bbcc91f Refactored based on the code review 2021-03-11 17:14:01 -05:00
James Agnew 2633cbd141
Improve error message for invalid date param (#2466)
* Improve error message for invalid date param

* Add changelog

* Test fixes
2021-03-11 14:23:02 -05:00
Nick Goupinets 8c77882da0 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-11 09:48:39 -05:00
Tadgh 75f756b49f Add changelog 2021-03-10 15:00:54 -05:00
Tadgh b7398cb6f2 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-10 10:33:24 -05:00
Tadgh e26d757ba3 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-09 22:54:24 -05:00
James Agnew 807d9d53f0
Improve performance for large transactions (#2462)
* Performance tweaks

* Work on processing speed

* Disable no longer relevant tests

* Work on performance

* Work on tests

* Work on large transaction performance

* Add changelog

* Perf tweaks

* Test fixes

* Resolve FIXME

* Fixes

* Test cleanup

* Fix broken changelog entry
2021-03-09 18:16:02 -05:00
Nick Goupinets 9056c95865 Updated docs 2021-03-09 16:41:50 -05:00
Nick Goupinets 02eae95c85 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-09 14:06:33 -05:00
James Agnew be50a46d76
Tweaks to contained searches (#2461)
* Tweaks to contained searches

* Add changelog

* Build fix
2021-03-09 11:51:30 -05:00
Frank Tao bf8e890a0c
Supported contained resource search (#2441)
* POC for indexing on contained resource - test case may failed

* Test contained url

* Add a spt to handle contained flag

* Added search option for contained resource

* Impl contained resource search

* fixed typo

* Reworked on creating index based on the review comments

* Added changelog

* Added more test cases

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-03-09 06:50:23 -05:00
Diederik Muylwyk 6cc8a5ce4d
Fix HasParam#doGetQueryParameterQualifier() (#2460)
* Fix HasParam#doGetQueryParameterQualifier(); add changelog entry

* Fix bad test in SearchParameterMapTest
2021-03-09 06:28:40 -05:00
Nick Goupinets ab4f02b2bd Added changelog 2021-03-08 18:02:40 -05:00
James Agnew 62df320ceb
Avoid a crash reading an unknown ID on partitioned server (#2451)
* Avoid a crash reading an unknown ID on partitioned server. Fix #1953.

* Attempt 2 at fixing #1953
2021-03-07 10:16:30 -05:00
Diederik Muylwyk 11ee6dedd3 Address CVE-2020-27223; bumped minor version of Jetty in root POM 2021-03-06 16:33:05 -05:00
Diederik Muylwyk 6035f78ddf Fix typos 2021-03-05 18:46:42 -05:00
Diederik Muylwyk 35645999d7 Add changelog entries. 2021-03-04 19:55:39 -05:00
Tadgh f5372c9f07 Fix typo 2021-03-04 16:53:52 -05:00
Tadgh 6129194353 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-04 16:53:20 -05:00
Tadgh 2f1518344b Add changelogs, add patientbulkredaer implementation 2021-03-04 16:53:05 -05:00
Diederik Muylwyk 8dcac3e8b7
Improved generic client docs to remind of client.search.byUrl for params like _has. (#2440) 2021-03-03 18:34:18 -05:00
James Agnew db44244405
Fix #2426 - Include modifiers in generic search URLs for map (#2428) 2021-02-28 10:33:43 -05:00
Tadgh 74066a81b6
Merge pull request #2420 from hapifhir/issue-2401-add-support-for-group-id-export
Issue 2401 add support for group id export
2021-02-26 10:23:42 -05:00
Ken Stevens 7d769e3b05
Issue 2332 create via put for implementationguide that references some placeholders (#2423)
* begin with failing test

* fixed.  test passes.

* documentation and changelog

* added ConceptMap

* review feedback
2021-02-26 09:44:48 -05:00
Tadgh 1663e367a6 Address review comments 2021-02-25 16:23:36 -05:00
Tadgh 3937d2ef01 Remove some dead code 2021-02-24 15:57:55 -05:00
Tadgh 8e45a84927 Add changelog 2021-02-24 15:28:52 -05:00
Kevin Hartmann 3b60034a08 Added Changelog entry 2021-02-24 15:25:36 -05:00
michaelabuckley ad6431b24c
Merge pull request #2418 from hapifhir/add-changelog-for-mdm-update
Add MDM FHIRPath Changelog
2021-02-24 13:52:22 -05:00
Patrick Werner cf1f2f27db
added nullchecks to prevent NPE (#2417)
* added nullchecks to prevent NPE
fixes #2171

* Add test from #2171 and changelog

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-02-24 10:09:04 -05:00
Ken Stevens 30905aeba7 Merge remote-tracking branch 'origin/master' into issue-2401-add-support-for-group-id-export 2021-02-24 09:38:59 -05:00
Tadgh 66b59ae327 Update issue number 2021-02-24 09:22:10 -05:00
Tadgh 5ee7793ac4 Add MDM Changelog 2021-02-24 09:20:45 -05:00
Tadgh 29eabbd4f0 Add skeleton 2021-02-23 18:42:41 -05:00
Tadgh ecacef0498 Add bulk export md file 2021-02-23 18:39:25 -05:00
Tadgh c92f302d41
Merge pull request #2410 from hapifhir/2409-support-fhirpath-in-field-matchers
Support FHIRPath in field matchers if present
2021-02-23 09:48:14 -05:00
James Agnew b108e43600
Allow partition date for non-partitionable resources (#2407)
* Allow partition date for searchparam resources

* Cleanup

* Test fix

* Documentation update

* Docs tweak
2021-02-22 20:49:09 -05:00
Tadgh 18b61f21d0 re-add only relevant code 2021-02-22 18:23:03 -05:00
Jens Kristian Villadsen 65c9f5fbf8
Update repository_validating_interceptor.md (#2368)
Refined the wording on the repo interceptor
2021-02-22 07:28:49 -05:00
Nick Goupinets 3541249a5e
Fixed docs (#2405) 2021-02-22 05:42:59 -05:00
James Agnew 3eda19c65a
Version bump (#2400)
* Version bump

* Docs changes

* Docs tweaks

* Docs tweak

* Spelling fixes

* Docs tweaks
2021-02-18 11:07:49 -05:00
Kevin Dougan SmileCDR aa05667761
Clarified partitioning docs. (#2396)
* Clarified partitioning docs.

* Added some more ResourceTypes to the list of non-partitioned ones according to the authoritative list found in RequestPartitionHelperSvc.java.
2021-02-17 08:32:37 -05:00
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
James Agnew 65ac0e80fb
Add CapabilityStatement customizer (#2387)
* Add CapabilityStatement customizer

* Fix javadocs
2021-02-15 14:58:34 -05:00
ianmarshall 7413584bff Make LOINC Top2000* files optional in terminology loader. 2021-02-10 22:35:15 -05:00
Tadgh 2759db2a31
Merge pull request #2371 from hapifhir/config-error-on-url-protocol
Throw ConfigurationError if you attempt to provide a Rest URL that contains a protocol.
2021-02-09 20:25:14 -05:00
Tadgh 64878c23d3 Update text, add changelog 2021-02-09 19:03:09 -05:00
James Agnew dd7a156d19
Call startOperation for paging requests (#2370) 2021-02-09 15:47:11 -05:00
jamesagnew 028ef1b088 Credit for #2365 2021-02-08 09:15:04 -05:00
jamesagnew da847ad08a Credit for #2282 2021-02-07 12:32:41 -05:00
James Agnew c69d741b43
Add CapbilityStatement customizing hook (#2364)
* Add CapbilityStatement customizing hook

* Add additional method

* Interceptor service tweak
2021-02-07 09:12:09 -05:00
Michael Buckley 42afcebd11 Merge in ca.uhn.fhir.rest.param.DateParamTest and add changelog. 2021-02-05 09:57:10 -05:00
Kevin Dougan SmileCDR dd13827290
Added changelog entry for -measure operation. (#2347) 2021-02-03 14:01:20 -05:00
jamesagnew c0142a67b1 Credit for #2340 2021-02-02 14:27:42 -05:00
jamesagnew 8c5b54bf54 Fix broken changelog 2021-01-30 19:26:58 -05:00
jamesagnew 5961fde2dd Docs tweak 2021-01-29 16:12:06 -05:00
Ken Stevens ba63f65115
changed $expand filter matching from left-match to contains match (#2327)
* changed $expand filter matching from left-match to contains match

* changelog

* pure substring match is too generous (a regression test checked for that).  Tightened the match up to word boundaries.

* CLean up to avoid intermittent test failure

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-29 12:37:54 -05:00
jamesagnew 589eb3158e Credit for #2310 2021-01-29 11:02:51 -05:00
Nick Goupinets 3be480c9f0 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-27 16:47:40 -05:00
James Agnew 909d9f742c
Enable Auto-reference versions in JPA (#2323)
* Automatic reference versions

* Auto reference versions

* resolve fixmes

* Add changelog

* Test fixes

* Test fixes

* Resolve fixmes

* Work on versioning

* Add support for _includes

* Update headers

* Change visibility

* One more tweak

* One more API tweak

* Fixes

* Account for review comments

* Fix errorprone reported issue

* Test fix

* Test fixes

* Test fixes
2021-01-27 14:49:10 -05:00
Nick Goupinets 04db4ed229 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-26 09:18:20 -05:00
jamesagnew c55410e6b6 Add changelog for #2302 2021-01-23 17:54:51 -05:00
Ken Stevens 749934d5f1
fixed name text indexing (#2309)
* fixed name text indexing

* fixed name text indexing
2021-01-22 15:39:26 -05:00
Nick d783229406 updated docs 2021-01-22 13:28:24 -05:00
Nick cfc798cb2b Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-22 09:45:04 -05:00
Tadgh edd9769686 Add documentation fixes for MDM-match 2021-01-22 09:17:51 -05:00
Nick 82e52750e7 Merge branch 'master' into ng_20201218_survivorship_poc 2021-01-21 09:00:28 -05:00
James Agnew 14b0688f69
Bump core version to 5.2.16 (#2308)
* Bump core library version

* Test fix

* Build fixes

* Some test fixes

* One more bit of docs

* Build fix

* Test fix

* Test fix

* Docs fix
2021-01-21 05:30:23 -05:00
Nick 4b53ef3920 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-20 14:59:38 -05:00
Tadgh 159128109b Add versionenum value 2021-01-20 10:49:08 -05:00
Nick ae9d4a191f Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-19 11:34:01 -05:00
James Agnew 874b16207f
Bundle.entry.resource.id should not be stripped on POST from client #2297 (#2303) 2021-01-19 11:12:42 -05:00
Nick f5e2086cfd Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-19 09:35:31 -05:00
Tadgh 17d74648de
Merge pull request #2300 from hapifhir/2299-bug-with-bulk-export-bean
Add bean to config
2021-01-18 16:53:36 -05:00
Tadgh 141cd14918 Add changelog 2021-01-18 15:04:03 -05:00
ianmarshall 26491f3bc8 Ensure that table indexes are not deleted during DB migration dry-run. 2021-01-18 14:09:06 -05:00
Nick b00f47ef81 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-18 09:25:58 -05:00
jamesagnew 6ff7d579a3 Update changelog 2021-01-17 17:43:42 -05:00
James Agnew 66e1a51e01
Add validation options to RepositoryValidingInterceptor (#2294)
* Add repository validating interceptor outcome to response

* Add a doc

* Add a test and some docs

* Rework validation
2021-01-17 16:40:32 -05:00
dependabot[bot] 391a6d1a3f
Bump ph-schematron from 5.2.0 to 5.6.5 (#2184)
* Bump ph-schematron from 5.2.0 to 5.6.5

Bumps [ph-schematron](https://github.com/phax/ph-schematron) from 5.2.0 to 5.6.5.
- [Release notes](https://github.com/phax/ph-schematron/releases)
- [Commits](https://github.com/phax/ph-schematron/compare/ph-schematron-parent-pom-5.2.0...ph-schematron-parent-pom-5.6.5)

Signed-off-by: dependabot[bot] <support@github.com>

* Fix compile error

* Build fix

* Add test logging

* Test fix

* Resolve classpath duplicates

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-17 14:27:26 -05:00
jamesagnew ae3930f204 Update changelog 2021-01-17 13:30:19 -05:00
James Agnew 29cf20aac3
Add repo validation outcome to response (#2293)
* Add repository validating interceptor outcome to response

* Add a doc

* Add a test and some docs
2021-01-17 12:50:13 -05:00
jamesagnew 9d8bbaf868 Add credit for #2054 2021-01-17 09:44:18 -05:00
jamesagnew a7c9b9d2f3 Changelog 2021-01-16 19:08:55 -05:00
James Agnew 1dc4fb2206
Make quantity indexes use double datatype (#2290)
* Make quantity indexes use double datatype

* Add changelog

* Test fixes

* Test fixes

* Disable test
2021-01-16 18:44:15 -05:00
Nick 6cc40b134e Pre-review commit 2021-01-14 20:35:09 -05:00
Nick 759f06ce48 Added optional manual override to link update 2021-01-14 14:24:59 -05:00
Nick 57662eedb3 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-12 09:22:38 -05:00
Ken Stevens 520400d6ea
added IPagingProvider.canSearchByOffset() (#2281)
* init rev

* added IPagingProvider.canSearchByOffset()
consolidated parameters in bundle link methods

* fix refactoring error

* add @Nonnull to BundleLinks parameter

* null check

* fix test

* cleanup

* fix refactoring

* final cleanup

* review feedback

* review feedback

* review feedback
2021-01-11 20:42:41 -05:00
Nick 5aa85c7e17 Survivorship 6 2021-01-11 17:22:06 -05:00
Frank Tao f6d4a40388
UCUM Service Support (#2261)
* Added UcumServiceUtil

* Removed ucum-essense.xml

* Added ucum service existing test cases passed

* Added more test cases

* Merge branch 'master' into ft-ucum-support

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

* Added back extractReferenceParamsAsQueryTokens

* Added changelog and migration script

* Added length for the string type

* Moved UCUM util to hapi-fhir-jpaserver-model

* Renamed UCUM support to Normalized Quantity Search Support

* Moved setNormalizedQuantitySearchNotSupported to AfterEach

* Changed migrate task to 530

* Removed comments

* Fixed in memory search issue and added more test cases

* Fixed the version order

* License header updates

* Updated based on review comments

* Updated the migration task based on review comments

* Fixed RES_TYPE with type String and length 100

* Changed myParamsQuantityNormalizedPopulated type to Boolean class
2021-01-10 21:05:24 -05:00
IanMMarshall 4b310f0a3c
Merge pull request #2271 from hapifhir/im_2021_01_04_package_load_with_partitioning
Fixed package loading when partitioning is enabled
2021-01-07 13:25:44 -05:00
jamesagnew 128d384153 Credit for #2273 2021-01-07 06:03:31 -05:00
ianmarshall e23e3c660c Merge remote-tracking branch 'origin/master' into im_2021_01_04_package_load_with_partitioning 2021-01-06 12:23:21 -05:00
ianmarshall a4980ad845 Improve wording in documentation. 2021-01-06 10:32:05 -05:00
ianmarshall 659e83f451 Address use case where packages include non-conformance resources. Update documentation as well. 2021-01-06 10:29:10 -05:00
jamesagnew b79d154d81 Dependency version bumps 2021-01-06 10:21:25 -05:00
James Agnew 0bb878e4a8
Repository validation enhancements (#2270) 2021-01-05 18:22:34 -05:00
ianmarshall d01c775b99 Fixed package loading to enable loading of binary package files into the default partition when partitioning is enabled. 2021-01-05 18:12:11 -05:00
Tadgh efc6809ea6
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190)
* Beginning work on converting to hibernate search 6
* replace all out of date properties
* replace all POM references to old versions
* remove the shaded ES jars as HS6 supports 7.9
* Convert "Bridges" to RoutingBinder and RoutingBridge
* Modernize all indexing annotations
* Begin refactoring of search queries (wip)

* Fix spatial API changes, work on BaseTermReadSvcImpl

* Most of the way through the various filter property conversions

* Finished i think with BaseTermReadSvcImpl

* Compiling, but definitely broken

* Start test compilation failures

* All tests compiling (i think)

* remove suggest keywords operation

* Fix bootstrap errors, still have to deal with transient fields

* Rollback CR

* More refactoring, got IDs baked back into docs

* Fix coord util, fix a few more fields which require projection

* merge fixes

* begin refactor of valuesetexpansion tests

* fix another test

* Update tests

* remove todos, add TestContainers

* Fix descendant in

* Add testcontainers, fix another test

* fix more tests, replace embedded es

* Rip out embedded elastic, replace with TestContainer

* merge conflicts for new analyzers

* Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs

* Remove dead deps, update testcontainer

* Remove java-hamcrest

* Pull asserts up, refactor tests to pass in RP tests

* Update V2 check

* Remove suggest keyword tests

* Split line for testing

* Fix perhaps one of the dumbest programming mistakes in my career so far

* Refactor tests which no longer rely on a strict known order

* Fix up test config, disable log test temporarily

* Remove log4j from being transitively pulled in. re-enable test

* Update log4j exclusions with new bridge. Update test to check for core class

* Move dependency to root pom in dep management section

* Update changelog, add changelog for HS6 with ES requirements. Remove dead comment

* update testst, remove todos

* Add hibernate props provider method, add elastic regexp query

* Add todo for high level client builder

* Modify ElasticsearchRestClientFactory to support HTTPS hosts

* Remove protocol extraction from rest url

* do we even need to index this...?

* remove purge of non-indexed resources

* Add longer timeout to testcontainers

* Add task to add docker CLI to azure pipeline via task, for testcontainers

* WIP remove this

* Dont update version

* Add test for duplicate termconcepts

* Use real hibernate ORM methods

* merge issues

* Add partitionsettigns bean to match master

* Trying to debug testcontainers on azure...

* Trying to debug testcontainers on azure...

* Run even on previous failure

* Fix testcontainer port binds

* Add full text logs attaching, and test reporting

* I love yaml

* Remove comment

* Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue

* Modify TX beheaviour

* wip

* Rework to use config and mocked beans for partition-aware lastN

* rework to not use beans and just inject vars i need for test, keps test envs cleaner

* update azure pipeline to only copy test results

* Remove erroneous publish

* Always get test logs

* Make it so indexing works,

* Add todos

* revert deleteByPid

* Work on test fixes

* Test fixes

* Test fixes

* Another test fix

* Test fix

* Work on tests

* Test fixes

* All tests passing locally

* Fix test failure

* FIx build error

* Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider

* Update ngram of token filters

* Tidying

* subvert the purpose of hibernate elastic props builder to inject template

* dead space

* Rename changed class

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-05 17:56:59 -05:00
James Agnew d943260927
Rework valueset index for MySQL (#2269)
* Rework valueset index for MySQL

* Add changelog
2021-01-05 10:03:33 -05:00
IanMMarshall 14fc8f2598
Merge pull request #2262 from hapifhir/2260-fix-sorting-for-mysql
Fix order by clause in search query for MySQL, MSSQL and MariaDB
2021-01-04 21:19:04 -05:00
dependabot[bot] 86f254cd66
Bump datasource-proxy from 1.5.1 to 1.7 (#2267)
* Bump datasource-proxy from 1.5.1 to 1.7

Bumps [datasource-proxy](https://github.com/ttddyy/datasource-proxy) from 1.5.1 to 1.7.
- [Release notes](https://github.com/ttddyy/datasource-proxy/releases)
- [Changelog](https://github.com/ttddyy/datasource-proxy/blob/1.x/CHANGELOG.md)
- [Commits](https://github.com/ttddyy/datasource-proxy/compare/datasource-proxy-1.5.1...datasource-proxy-1.7)

Signed-off-by: dependabot[bot] <support@github.com>

* Add changelog

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-04 10:32:52 -05:00
ianmarshall 8a2dfe86fd Merge remote-tracking branch 'origin/master' into 2260-fix-sorting-for-mysql 2021-01-04 09:00:21 -05:00
jamesagnew 8df8ed7838 Bump hibernate version 2021-01-03 16:56:02 -05:00
James Agnew 3e6d80bdc2
Fix SQL Server paging with new querybuilder (#2265)
* Fix SQL Server paging with new querybuilder

* Add changelog
2021-01-02 11:13:51 -05:00
jamesagnew cbb16ce3af License header updates 2021-01-01 16:40:46 -05:00
jamesagnew ed4d7d7eb6 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2021-01-01 15:07:37 -05:00
jamesagnew f30999b053 License header updates 2021-01-01 15:07:23 -05:00
jamesagnew 4373b47207 Library version bumps 2021-01-01 15:06:55 -05:00
James Agnew 8f8c5c31f1
Add validation rules interceptor (#2264)
* Start work on validation rules interceptor

* Work on interceptor

* Add tests

* Work on validation interceptor

* Work on interceptor

* Test fix

* Documentation tweaks
2021-01-01 14:29:10 -05:00
ianmarshall eb59da3f03 Added changelog. 2020-12-24 15:23:50 -05:00
Tadgh e79114e2ec
Un-revert the MDM changes, now that issues have been addressed (#2226)
* Backward compatibility changes

* Revert "Revert "Remove all references to Person from EMPI.""

* Updated docs

* Removed mdm channel references

* Initial implementation

* fix coarseness bug. Fix tests. reinitialize silly bean

* Add forgotten json file

* Generic provider PoC

* Refactored provider to use BundleBuilder

* Removed version-specific MDM providers

* Addressed code review comments

* Fixed after merge

* Fixed docs

* MDM SVG for Update Use Cases

* Removed obsolete docs

Co-authored-by: Nick <nick.goupinets@smilecdr.com>
Co-authored-by: Nick Goupinets <73255752+nvg-smile@users.noreply.github.com>
2020-12-17 10:12:53 -05:00
jamesagnew d99b67820a Add to changelog 2020-12-14 14:30:20 -05:00
jamesagnew f4ec19f03c Add changelog 2020-12-14 10:50:33 -05:00
Kevin Dougan SmileCDR 9036df25fa
2229 - Remove support for the upload-igpack CLI command. (#2233)
* 2229 - Remove support for the upload-igpack CLI command.

* 2229 - Revert changes made to the ValidateCommand class since it only takes an igpack as a parameter and therefore, should NOT have been removed.

* 2229 - Remove the igpack option from the Validate command.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_0/2229-remove-upload-igpack-command.yaml

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

Co-authored-by: Kevin Dougan <kevindougan@kevins-mbp.lan>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-12-14 09:50:16 -05:00
jamesagnew 0dc0e91766 Credit for #2241 2020-12-14 06:06:07 -05:00
Vladimir Nemergut 5d43f4c35e
Use system properties in ApacheRestfulClientFactory (#2241)
* Use system properties in ApacheRestfulClientFactory

#2192

* Add changelog entry for #2192
2020-12-14 06:01:17 -05:00
James Agnew 81f6fe9106
Support IBaseBundle as parameetr type for @Transaction method (#2237)
* Support IBaseBundle as parameetr type for @Transaction method

* Add changelog

* Add bundle setter
2020-12-11 18:33:00 -05:00
James Agnew e4d6c51290
Allow plus symbol in email address match url (#2224)
* Allow plus symbol in email address match url

* Add changelog
2020-12-09 21:52:03 -05:00
Tadgh 0938d72b51
Revert "Remove all references to Person from EMPI." 2020-12-09 14:57:00 -05:00
Nick aef84c9fe9 Updated docs yet again 2020-12-08 11:24:40 -05:00
Nick d3c0944388 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-07 22:02:45 -05:00
Nick 61c1b6cfb2 Updated docs 2020-12-07 19:30:18 -05:00
Nick fd90eb699f Review updates 2020-12-07 18:03:56 -05:00
James Agnew fd528a0f7d
Improve error message on unsupported resource type (#2221)
* Improve error message on unsupported resource type

* Add changelog
2020-12-07 17:35:51 -05:00
Nick Goupinets af461cd343
Apply doc update suggestions from code review
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-12-07 14:04:04 -05:00
Nick f5f7f2df14 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-07 11:55:51 -05:00
James Agnew d958764d49
Partition data leaks across searches (#2220)
* Partition data leaks across searches

* Add changelog

* Resolve FIXME

* Add test logging

* Test fix

* Test fix
2020-12-06 16:32:07 -05:00
Tadgh 6799973016
Add attribution for split package fix (#2216) 2020-12-03 16:40:23 -05:00
Nick 5c40afb0c9 Updated doc headers 2020-12-03 16:11:10 -05:00
Nick 499a68a093 Reviewed docs and added change entry 2020-12-03 15:53:06 -05:00
Nick 4352e0a61f Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-03 11:28:21 -05:00
James Agnew 1eae5db374
autoCreatePlaceholderReferenceTargets true breaks multitenancy (#2215)
* Fix #2209 - autoCreatePlaceholderReferenceTargets true breaks multi-tenancy

* Add changelog

* Address fixme
2020-12-03 08:53:37 -05:00
James Agnew 35f4d48eee
Fix validating capabilitystatements (#2214)
* Fix validating capabilitystatements

* Add changelog
2020-12-03 05:31:04 -05:00
James Agnew 7627a86176
Improve version logging (#2213)
* Improve version logging

* Add changelog

* Test fixes
2020-12-02 21:19:04 -05:00
Tadgh b11f97d9ef
HOTFIX for invalid changelog type (#2212) 2020-12-02 16:41:37 -05:00
jamesagnew 0f80c2adf9 Update changelog 2020-12-02 14:48:14 -05:00
James Agnew a3ae6c3813
Add partition selector to id parameter (#2208)
* Add partition selector to id parameter

* Add changelog
2020-12-02 14:10:37 -05:00
Nick Goupinets 417ae55cb4 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-02 09:29:47 -05:00
James Agnew 6e72ee8f6b
Fix new searchbuilder on oracle (#2205)
* Fix new searchbuilder on oracle

* Add changelog
2020-12-02 06:22:41 -05:00
Nick Goupinets d63c580e82 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-01 13:18:42 -05:00
jamesagnew 015502e98e Docs tweak 2020-11-30 18:59:53 -05:00
James Agnew c309737166
Allow reading from multiple partitions (#2198)
* Partitioning rework

* Work on partition improvements

* Partition updates

* Work on partitiong

* Test fixes

* Add docs

* Add changelog

* Resolve FIXME

* Test fixes

* Test fixes

* Test fixes

* Compile fix

* Fix compile error

* Test fix

* Test fixes
2020-11-30 17:59:52 -05:00
jamesagnew 283834ed1d Docs tweak 2020-11-30 16:25:15 -05:00
Ken Stevens 3d3242cf9a
Resource change listener (#2191)
* init rev

* fix build

* Tweaked the POM config settings and also added some dependency exclusions (commented out for now).

* More re-factoring of the CQL Unit Tests.

* Removed a LogMessages.html file and a minor Unit Test change.

* Unit Tests.

* added debug logging to troubleshoot the dao that has no name

* added debug logging to troubleshoot the dao that has no name

* workaround to get past null dao resourceName issue

* fix jsons to get test to pass.  Test still fails with library id problem

* gitignore

* gitignore

* test passes!  Woohoo!

* undo troubleshooting logging

* added timer and logging.

* added asserts and time multiple evaluations and measure the average

* readme

* adding explanations

* added more explanatory notes

* measure 2 patients

* move pom to use cqf snapshot

* roughed out cache

* roughed out cache

* Added code to VersionChangeCache class.

* added tests

* added polling test

* wrote init version

* wrote init version

* optimized versioncache

* worked on getting tests to pass

* redesigned interfaces

* all tests pass

* fixmes

* fixmes

* rename param

* Added Unit Tests.

* javadoc

* Fixed the 2-Patient Unit Test.

* More Unit Test work.

* make ResourceVersionMap immutable

* Fixed a Unit Test that was failing intermittently by adding a new way to refresh the cache.

* Use a new method called doRefreshAllCaches(0) to force a refresh and have all Listeners called immediately.

* Cleaned up IVersionChangeListenerRegistry interface to make methods more clear and resolved all Unit Tests.

* disabled tests

* disabled tests

* removed unused test method

* fixed refresh logic and added asserts

* moved cache so it can be used by searchparamregistry

* Updated the Cql Unit Tests to be properly configured for Dstu3 or R4.

* started rewriting SearchParamRegistryImpl to use new cache
added init method to listener interface

* added fixmes

* adding tests

* tests pass

* added tests

* Fixed the way CqlProviderFactory Autowires Beans so it can work with both Dstu3 and R4 contexts.

* moar tests

* fix test

* work tests

* reverting unneccessary refactors

* undo unneccessary import changes to reduce MR size

* undo unneccessary import changes to reduce MR size

* Unit Test fixes...more to come...

* add unregister

* fix tests

* Changed ResourceVersionCache to use a Map of Maps.

* searchparam test

* test passes

* resolved fixme

* fixmies

* strengthen test asserts

* More Unit Test changes and added some FIMXME items.

* changed from long to changeresult

* renamed VersionChange -> ResourceChange

* fixed delete bug

* organize imports

* fix test

* add update test

* add test reset function

* fix stack overflow

* fix startup race condition (might still be intermittent)

* found the problem.  delete doesn't work because we can't look up the deleted resource to find out what its name is

* fixed regression

* abandoned idea of incrementally updating searchparam registry.  Rebuilding every time--it doesn't change that often.

* fix test

* begin with failing test

* test passes

* fixmes and javadoc

* fix test

* fixme

* fix test

* whack-a-mole.  Either subs pass or cql passes.  Something's fishy with the FhirContext

* fix subscription test initialization

* fix method name

* Re-factored the CqlProvider Unit Tests.

* changed ResourceChange API

* add interface

* add interface

* fix test

* add schedule test

* add doc

* init rev

* FIXME

* modify FhirContext change

* change fhirContext.getResourceTypes to lazy load

* converted subscriptions

* converted subscriptions

* begin with failing test

* test passes

* fix test

* test coverage

* test coverage

* test coverage

* test coverage

* good coverage now

* pre-review cleanup.  I think I found a bug.

* moved cache into listener entry
tests pass with fixmes

* fix test

* fix test

* fix test

* fixme

* FIXMEs

* merge cache and registry

* method reorg

* javadoc

* javadoc done.  all FIXMEs resolved.

* change log

* changes needed by cdr

* spring config cleanup

* james feedback

* james feedback

* might not work. Try moving resourcechangeconfig into searchparam config

* merge ResourceChangeListenerRegistryConfig.java into SearchParamConfig

* fix test

* fix SubscriptionLoader

* fix SubscriptionLoader

* create ResourceVersionMap from resources

* added cache handle interface

* fix test

* javadoc

* fix test

* fix test

* James feedback: clone searchparametermap

* fix startup

* fix test

* fix test

* fix intermittent

* pre-review cleanup

* FIXME

* final FIXME yay!

* Address a couple of my own reviw comments

Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2020-11-29 19:42:40 -05:00
James Agnew 1e5def260c
Bump woodstox version (#2199) 2020-11-27 19:49:06 -05:00
Nick Goupinets 2a3b72db17 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-11-27 16:54:04 -05:00
jamesagnew b85fd42ead Add changelog validator 2020-11-27 16:40:31 -05:00
jamesagnew 835c450b63 Fix changelog file 2020-11-27 16:23:57 -05:00
Nick Goupinets 8a7dc4e80b EMPI to MDM 2020-11-27 15:12:21 -05:00
IanMMarshall 722e24d80c
Merge pull request #2175 from jamesagnew/ft-fix-expend-filter-contains-issue
Fixed expand filter issue
2020-11-27 14:47:05 -05:00
Frank Tao a511543e77 Merge branch 'master' into ft-fix-expend-filter-contains-issue
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
2020-11-26 18:47:10 -05:00
jamesagnew da75ff8da2 Credit for #2197 2020-11-26 10:08:56 -05:00
James Agnew fb8658da70
Always apply vs filters correctly (#2195)
* Always apply valueset filters correctly

* Test fix

* Testfix

* Test fix

* Add changelog

* Test fix
2020-11-24 18:12:02 -05:00
Nick Goupinets 5f97428d38 Added schema migration steps for MDM 2020-11-24 15:50:56 -05:00
Tadgh 702cc7762d
2185 doc updates for multitenancy (#2187)
* update to docs to indicate requests to default partition

* update operation docs
2020-11-20 11:08:19 -05:00
Tadgh 99d2bf1f0e
Merge pull request #2170 from jamesagnew/2169-docs-hapi-fhir-cli
2169 - Fixed hapi-fhir-cli doc issues.
2020-11-20 10:43:46 -05:00
Tadgh 8647502da1
update to docs to indicate requests to default partition (#2186) 2020-11-20 10:32:59 -05:00
Frank Tao 5b471602c6 Merge branch 'master' into ft-fix-expend-filter-contains-issue 2020-11-20 10:29:58 -05:00
Frank Tao 2d2add60ec Updated the changelog 2020-11-20 09:02:40 -05:00
James Agnew a01f5ae906
Fix subsumption test direction (#2183)
* Fix subsumption test direction

* Add changelog

* Test fixes
2020-11-19 21:48:54 -05:00
James Agnew 8b65db0c98
Improve error message on unique constraint violation (#2182)
* Improve error message on unique constraint violation

* Add changelog

* Test fixes

* Test fix
2020-11-19 21:20:59 -05:00
Frank Tao e551f1837e Updated based on review 2020-11-19 20:22:13 -05:00
NG 4bbe4a3ef7 Merge branch 'gg_20201105-remove-person-references' of https://github.com/jamesagnew/hapi-fhir into gg_20201105-remove-person-references 2020-11-19 14:56:31 -05:00
NG 4378df7dcb Removed more EMPI refs from the docs 2020-11-19 14:56:18 -05:00
Tadgh 953b662827 Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references 2020-11-19 14:24:51 -05:00
ianmarshall eb0f5e1e5e Add changelog. 2020-11-19 09:37:34 -05:00
Tadgh d97d4b63a0 Merge branch 'gg_20201105-remove-person-references' of github.com:jamesagnew/hapi-fhir into gg_20201105-remove-person-references 2020-11-18 19:53:21 -05:00
Tadgh 75c0c25d7b remove references to EMPI 2020-11-18 19:50:00 -05:00
Nick Goupinets 1f21220e39 Updated MDM create use cases 2020-11-18 15:57:05 -05:00
jamesagnew 0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew 0336e59591 Add changelog 2020-11-18 14:26:37 -05:00
NG 6d50687d4c Renamed EMPI to MDM in the docs 2020-11-18 13:49:17 -05:00
jamesagnew 4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -05:00
Nick Goupinets f470c343c5 Docs - first pass 2020-11-17 17:22:06 -05:00
Tadgh 1048df4d87
Update rest_operations.md 2020-11-13 15:54:43 -05:00
Tadgh 8f95ad4c0f fix typo :) 2020-11-13 15:35:06 -05:00
Tadgh 16003162fd Address #2172 2020-11-13 15:27:58 -05:00
Kevin Dougan 50328abff1 2169 - Fixed hapi-fhir-cli doc issues. 2020-11-10 15:50:43 -05:00
IanMMarshall bf9e02bc16
Merge pull request #2164 from jamesagnew/im_20201029_ig_package_long_description
Truncate package descriptions that are longer than 200 characters.
2020-11-10 12:01:53 -05:00
James Agnew 63b7b379c2
Improve ValueSet filtering (#2162)
* Improve filter search

* Filter improvements

* Tests passing

* Test fixes

* Fix transaction filter

* Add changelog

* Test fix

* Update hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Resolve FIXME

* Test fix

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-11-10 11:01:13 -05:00
ianmarshall 40c34a4518 Truncate package descriptions that are longer than 200 characters. 2020-11-09 16:36:37 -05:00
James Agnew 228e75b501
Bump core to latest versions (#2154)
* Bump core to latest versions

* Compile fix

* Bump to non snapshot core library
2020-11-03 15:43:37 -05:00
James Agnew 5e8ec8d6f3
Resolve crash in InMemory SP resolver for empty source (#2150)
* Resolve crash in InMemory SP resolver for empty source

* Add changelog
2020-10-28 14:30:32 -04:00
jamesagnew 6ccb7c8312 Bump HTTPClient version 2020-10-28 10:28:04 -04:00
jamesagnew 53c23b8d9b Add method to stringutil 2020-10-27 11:29:16 -04:00
James Agnew 72294fc0a0
Suport typeFilter parameter for bulk export (#2147)
* Cleanup

* Fix tests

* Work on bulk export

* Work on export

* Test fixes

* Add changelog

* Address review comments

* Address review comments
2020-10-26 12:28:07 -04:00
jamesagnew 137e215003 Docs fixes 2020-10-26 07:36:46 -04:00
James Agnew 8000d2d0cf
SQL Join Rework (#2086)
* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* added the other six index links

* trying different annotations

* Start testing

* Update resources on package install

* Add changelog

* Join rework

* CLean up SQL builder

* Add docs

* SP rework

* Join work

* Work on params

* Work on refactor

* Work on chains

* Work on joins

* Rework queries

* Work on queries

* Many more tests passing

* Refs test

* Work on sorting

* Work on tests

* More joins work

* Work on tests

* Work on queries

* Tests passing

* More test fixes

* Test fixes

* Work on SQL

* Tests passing

* Add some tests

* Add some tests

* License headers

* Use entity manager to get datasourcd

* One more fix

* Model cleanup

* Ongoing work

* Fixes

* Fixes

* Work on joins

* Ongoing fixes

* Merge conflict

* Cleanup

* clean up unused fields

* Work on join

* COmpile fix

* Rework querying

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java

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

* Address review comments

* Resolve fixmes

* Test fix

* Test fixes

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-10-26 05:24:26 -04:00
James Agnew 4a5f5199b5
Add custom partition interceptor examples (#2145)
* Add custom partition interceptor examples

* Add documentation

* Test fixes

* Remove outdated test

* Test modification
2020-10-25 19:19:40 -04:00
jamesagnew 0fdff3e052 Credit for #2142 2020-10-23 10:33:49 -04:00
IanMMarshall fd46d0965f
Merge pull request #2141 from jamesagnew/im_20201020_package_installer_enhancements
Enable package installer to load non-Conformance resources
2020-10-21 18:28:15 -04:00
ianmarshall 830ad70089 Add changelog for package installer enhancement. 2020-10-21 16:18:10 -04:00
Ken Stevens 3b91873b7c
delete expunge (#2131)
Added delete _expunge=true
2020-10-20 17:21:50 -04:00
jamesagnew 66e36378c1 Add hardcoded anchor name to docs 2020-10-13 12:11:58 -04:00
James Agnew aa3da9b05f
Bump bootstrap version (#2128)
* Bump bootstrap version

* Add changelog

* Resolve fixme

* Rmove test code
2020-10-12 20:47:14 -04:00
jamesagnew 7d150858dc Credit for #2118 2020-10-12 20:45:02 -04:00
jamesagnew 90016b25a2 Credit for #2059 2020-10-12 17:45:01 -04:00
Tuomo Ala-Vannesluoma 1435540320
Improve synchronous searching by providing offset & limit support (#2059)
* Improve synchronous searching by providing offset & limit support

Add support for offset querying which leverages paging at the query level
Add configuration for search default page size and search maximum page size
If using offset, always use synchronous searching to avoid extra database insert/update etc.
When using offset, only calculate count if it's wanted
Validate params closer to provider and handle size if search returned "all" (or last)

* Review and test fixes

Comment _offset as nonstandard parameter
Make synchronous search always count the total value (for now)
Fix issue with FulltextSearchSvcImpl mutating param map
Dirty fix for BaseJpaTest (not sure how to fix the including resources issue)

* Remove temporary count querying fix for synchronous loads

* Fix offsetting of everything operations, do not drop zero offset

* Fix jpa test default and maximum page size, add some fixmes to tests before resolved

* Ignore one failing test, fix others

* Fix Dereferenced variable may be null

* Fix everything paging in R4 by adding DISTINCT if synchronous load is used

Also fix assertion of size when hitting fetchSizeDefaultMaximum

* Add documentation about offset annotation and paging

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-10-12 17:42:03 -04:00
jamesagnew bd6feec2f4 Initial credit for #2118 2020-10-12 17:19:15 -04:00
jamesagnew 81d7a1eae1 Credit for #2112 2020-10-11 15:29:06 -04:00
jamesagnew 576f6efc39 Credit for #1607 2020-10-09 11:58:00 -04:00
James Agnew 2134d40f1c
Account for timezones in lastUpdated search (#2113)
* Add test

* Fix

* Add changelog

* Test fixes

* Test fix

* Test fixes

* Resolve fixme

* Test fixes

* Remove debug logs

* Try to get CI tests passing again
2020-10-09 07:52:46 -04:00
Tadgh 5a29fd9945 rollback the elastic changes 2020-10-06 17:20:11 -04:00
jamesagnew edbd089092 Docs update 2020-10-06 05:52:22 -04:00
IanMMarshall 5ec1284b8a
Apply suggestions from code review
Edits per code review.

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-10-05 15:14:39 -04:00
ianmarshall 30e50ba90c Improvements to terminology documentation. 2020-10-05 14:08:29 -04:00
ianmarshall 4ca739e223 Improvements to terminology documentation. 2020-10-05 12:02:01 -04:00
ianmarshall 03bd94462d Fix typo in changelog. 2020-10-05 10:13:08 -04:00
ianmarshall 2258d37283 Documentation for terminology. 2020-10-05 09:02:00 -04:00
ianmarshall 8613e76659 Documentation for terminology. 2020-10-04 21:20:19 -04:00
IanMMarshall f1710fd0be
Merge pull request #2081 from jamesagnew/feature_2020_09_02_term_multi_version_support
Feature 2020 09 02 term multi version support
2020-10-01 12:24:40 -04:00
ianmarshall dc3443665c Changes per code review. 2020-09-29 21:12:27 -04:00
ianmarshall 8e7b4e8437 Changes per code review. 2020-09-29 21:05:28 -04:00
Ken Stevens d71121e268 oops 2020-09-29 17:37:09 -04:00
Ken Stevens 09d09233ff
empi bugfixes and enhancements (#2104) 2020-09-29 17:27:43 -04:00
ianmarshall 42b4e9ae02 Add change log. 2020-09-28 08:45:59 -04:00
James Agnew ecc09889cb
Avoid duplicate search param defs in generated CapabilityStatement (#2101)
* Avoid duplicate search param defs in generated CapabilityStatement

* Add changelog
2020-09-22 19:21:34 -04:00
jamesagnew 8d9aa417e2 One more file rename 2020-09-22 17:13:06 -04:00
jamesagnew 3debef6cd4 Rename changelog 2020-09-22 12:39:05 -04:00
James Agnew ef4f3df945
Don't install draft package contents (#2099)
* Don't install draft package contents

* Add changelog

* Add changelog
2020-09-22 09:44:36 -04:00
James Agnew 072e63be5a
Avoid a crash on double date chains (#2097)
* Avoid a crash on double date chains

* Add changelog

* Address coverage warning
2020-09-21 15:43:07 -04:00
Ken Stevens 3189819dd5
limit transaction size config (#2087) 2020-09-16 14:13:03 -04:00
jamesagnew b64e982ec3 Credit for #2083 2020-09-16 09:07:33 -04:00
James Agnew 9711b5ed18
Update resources on package reinstall (#2078)
* Start testing

* Update resources on package install

* Add changelog
2020-09-15 08:46:43 -04:00
James Agnew 5b6ee4e475
Dependency version bump (#2074)
* Dependency version bump

* More dependency work

* One more fix
2020-09-14 08:42:28 -04:00
Alan Lescano 800283ae97
Update points.json (#2073)
Update of my contact e-mail and lat./long. points
2020-09-13 16:06:33 -04:00
jamesagnew c73da4d989 Fix SIL-A's name 2020-09-03 14:17:37 -04:00
James Agnew c6777578a8
Avoid DB binary storage deadlock (#2062)
* Avoid DB binary storage deadlock

* Add changelog

* Rework
2020-09-01 09:52:38 -04:00
James Agnew 437e81fc65
Support multiple updates of one resource in a transaction (#2050)
* Support multiple updates of one resource in a transaction

* Test update

* Add changelog

* Test fix
2020-08-25 05:55:54 -04:00
jamesagnew 969a20d9e8 Credit for #2049 2020-08-22 17:01:37 -04:00
James Agnew dbbff1fd16
Allow HTTP 204 response to transaction (#2051)
* Allow HTTP 204 response to transaction

* Add changelog

* Test fix
2020-08-21 21:00:55 -04:00
James Agnew 03cde8c53f
Don't use remote termsvc on implied system validation (#2045)
* Don't use remote termsvc on implied system validation

* Add changelog
2020-08-18 13:56:37 -04:00
James Agnew 1fadaeeff5
Reject nvalid SearchParameter wiith no path expression (#2043)
* Fix some changelog typos

* Reject SearchParameter with invalid path

* Add changelog

* Test fix

* Test fixes

* Test fixes

* Test fix

* One more test fix
2020-08-17 11:21:55 -04:00
James Agnew eab828f47a
Add transactionbuilder (#2041)
* Add transactionbuilder

* Add changelog

* Add creates
2020-08-17 07:47:40 -04:00
jamesagnew 3a5e0ed872 Fix #2042 - Outdated CI link on website 2020-08-16 21:03:27 -04:00
jamesagnew ad12ee4a5c Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-08-16 21:03:13 -04:00
jamesagnew cd65c298fe Fix some changelog typos 2020-08-16 09:01:42 -04:00
jamesagnew a3951b551f Add release details for 5.1.0 2020-08-13 17:36:04 -04:00
jamesagnew 89f68353ee Add changelog 2020-08-13 05:47:56 -04:00
jamesagnew 92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew 5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
Ken Stevens aed97ad1cb
added EMPI change log (#2036) 2020-08-11 15:33:33 -04:00
Jens Kristian Villadsen 39eea88b47
Update interceptors.md (#2033)
Added the mention of public requirement!
2020-08-11 05:25:36 -04:00
James Agnew e61b39fc30
Force a flush of the SearchParameter cache sooner when SPs change (#2030)
* Force a flush of the SearchParameter cache sooner when SPs change

* Add changelog

* Test fixes
2020-08-09 19:30:59 -04:00
James Agnew 8f6d08dd58
Fix #2022 - Invalidate caches on expunge (#2029)
* Fix #2022 - Invalidate caches on expunge

* Rename changelog file
2020-08-09 14:14:28 -04:00
James Agnew 8e0023c385
Disable referential integrity for some paths (#2025)
* Disable referential integrity for some paths

* Add changelog

* Remove unneeded file
2020-08-09 07:09:37 -04:00
James Agnew 0de0b88aa0
Fix TestpageOverlay XSS Vulnerability (#2027)
* Resolve XSS vulnerability

* Add changelog
2020-08-09 07:06:11 -04:00
James Agnew 63ef2ce006
Fix #2012 - Always filter total from search results when consent interceptor in use (#2020)
* consent bug test

* Fix #2012 - Always filter total from search results when consent
interceptor in use

* Add changelog

* Address coverage issues

Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
Co-authored-by: jvi <jvi@trifork.com>
2020-08-07 09:16:02 -04:00
Tadgh 6cb39a14ea
Empi doc updates (#2021)
* Update documentation about EMPI automatic linking

* Further documentation updates
2020-08-06 16:45:04 -04:00
Tadgh 3b9f9e6cc3 Rename operation 2020-08-03 21:35:12 -07:00
Tadgh 0ef1665061 Merge branch 'batch-empi-job' of github.com:jamesagnew/hapi-fhir into batch-empi-job 2020-08-01 11:48:27 -07:00
Tadgh 8b378995b2 Doc updates 2020-08-01 11:45:47 -07:00
Tadgh 4c64cec8fa
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_operations.md
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-08-01 11:40:24 -07:00
Tadgh 9c5b69bb6e
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_operations.md
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-08-01 11:37:11 -07:00
Tadgh dfecca33bc
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_operations.md
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-08-01 11:32:30 -07:00
Tadgh 7299162f10 Update doc phrasing 2020-08-01 11:31:28 -07:00
Tadgh bd22b0239f Add caveat 2020-07-31 09:13:38 -07:00
Gary Graham 9f0af3c21c docs for batch run 2020-07-30 19:25:30 -07:00
Tadgh f731e44303 Partial addition of docs for batch run 2020-07-30 18:21:35 -07:00
Tadgh 07f9e8466b Add documentation for -clear 2020-07-30 15:23:43 -07:00
Tadgh 8b4fa8048f Add changelog 2020-07-30 14:42:25 -07:00
Tadgh 0e88f359f5 Merge remote-tracking branch 'remotes/origin/master' into batch-empi-job 2020-07-29 09:42:12 -07:00
James Agnew 3098affccb
Update path when updating resource links (#2007)
* fix resource link index reuse bug

* Resolve merge conflicts

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-07-28 21:40:56 -04:00
James Agnew 6a8e09addf
Ensure that parent structuredefinitions are snapshotted before (#2005)
* Ensure that parent structuredefinitions are snapshotted before
snapshotting child

* Add changelog
2020-07-28 11:46:58 -04:00
Tadgh 82dcc395ec Merge branch 'master' into batch-empi-job 2020-07-27 14:59:27 -07:00
James Agnew 3a7ac0debc
Correct invalid decimal numbers stored in DB (#2003)
* Correct invalid decimal numbers stored in DB

* Add changelog
2020-07-27 13:33:27 -04:00
michelgleeson 4e66cb6752
Merge pull request #1994 from jamesagnew/fix_mssql_errors
Fix mssql errors
2020-07-24 11:26:23 -04:00
jamesagnew 296ed963cc Fix sentence fragment 2020-07-23 12:57:46 -04:00
Mike G 7b435d6052 changelog for mssql changers 2020-07-23 12:16:11 -04:00
Tadgh bbe6d5600e Address review comments 2020-07-22 11:58:08 -07:00
Ken Stevens 160778d3fd
Empi docs (#1989)
* Remove lines from image edges.  Thanks Max!

* fix case 4 docs
only mark possible match as eid if it was via an eid match
2020-07-21 13:07:49 -04:00
jamesagnew 4c4d46008b Credit for #1848 2020-07-21 05:40:41 -04:00
jamesagnew c13e17b4e6 Add changelog and bump Jetty 2020-07-17 11:50:45 -04:00
Ken Stevens ebd6ca4b64
Empi 3 ruleset version (#1978)
* add rule version

* add rule version

* Rough in model for Golden Record.

* Test Link Rule Version

* add eid match boolean

* added new fields to EmpiLink to provide more information about how the link was created

* add logging to check an edge case

* all tests pass

* wip with failing tests

* tests pass

* FIXME

* optimize imports

* test score in provider output

* FIXME

* FIXME

* Fix jpa test app context

* fix migration string length

* review feedback param name

* review feedback javadoc

* review feedback javadoc

* bean config reorganization for cdr

* add more tests
2020-07-17 08:31:15 -04:00
jamesagnew 49c08f31d8 Credit for #1896 2020-07-16 09:26:41 -04:00
James Agnew 077ee02771
Fix validation for enumerated ValueSets (#1982)
* Allow code validation against enumerated VS

* Work on validation

* Work on this

* Work on tests

* Work on validation

* Work on tests

* Work on validation

* Test fixes

* Add changelog

* For a change

* Test fixes
2020-07-15 13:38:14 -04:00
James Agnew 063bf4237c
Allow ConceptMap with no explicit group source/target (#1983)
* Allow ConceptMap with no explicit group source/target

* Add changelog
2020-07-15 12:57:10 -04:00
James Agnew baba4cc240
Avoid version conflicts on current writes (#1971)
* Add auto retry of transactions

* Experiment in Maven build

* Transaction autoretry

* Work on transaction retries

* Work on transaction retry

* Work on transaction retry

* Fix tests

* Avoid version conflicts

* Add changelog

* Resolve LGTM issue

* FIx transaction scope error

* Test fixes

* Test fix

* Test fixes

* Test fix

* Test fixes
2020-07-13 08:51:13 -04:00
jamesagnew c40d15294d Credit for #1966 2020-07-08 10:44:52 -04:00
jamesagnew b786006183 Credit for #1878 2020-07-06 13:46:30 -04:00
jamesagnew 11ad41d472 Credit for #1893 2020-07-06 05:52:40 -04:00
jamesagnew 2b5c834d96 Merge branch 'atlas-grand-rounds' of https://github.com/ConsultingMD/hapi-fhir into ConsultingMD-atlas-grand-rounds 2020-07-06 05:45:19 -04:00
Sumeet Chhetri 4c883cf741
Added an entry for Ohum/FHIR (#1930) 2020-07-06 05:43:20 -04:00
James Agnew 4b1546f002
Add support for ISO 3166 to validator (#1967)
* Add ISO 3166 support

* Add support for ISO-3166

* Add changelog

* Test fixes
2020-07-06 05:29:48 -04:00
James Agnew 6fb6675b1e
Resolve validation errors to ValueSet with UCUM (#1948)
* Add tests for validation errors

* Work on validation errors

* Bump core version

* Fix validation errors

* Test fixes

* Add changelog

* Test fix

* Test fix

* Test fix
2020-07-05 19:59:21 -04:00
James Agnew f356c7c385
Migrate to JUnit5 (#1952)
* Work on junit

* Work on junit 5

* Work on junit 5

* Bump errorprone vcersion

* Work on tests

* Junit 5 tweaks

* Fixes

* Work on tests

* Work on junit5

* Work on tests

* Test fixes

* Work on junit5

* Test work

* Get junit5 working

* Test fix

* Work on tests

* WOrk on tests

* Work on tests

* fixes

* Compile fix

* One more tweak

* Compile fix

* Add changelog

* Fix compile error

* Compile fix
2020-07-04 18:28:16 -04:00
James Agnew 290577ff3e
Remove unnecessary type predicate (#1963)
* Remove unnecessary type predicate

* Add changelog
2020-07-03 17:54:25 -04:00
Ken Stevens 714bd6216e
Empi 70 phonetic indexing (#1941)
* start with failing test

* test passes with fixmes

* javadoc and config

* pre-review cleanup

* generalize encoding

* test passes, but indexing needs to be optimized

* test passes, but indexing needs to be optimized

* step 1 of optimization.  big refactor of all predicates

* step 2 of optimization: determine phonetic encoder at time of RuntimeSearchParam creation

* integrated new phonetic encoders into empi

* phonetic search implemented

* IT passes

* pre-review cleanup

* final pre-review cleanup

* final pre-review cleanup

* Fix compile error

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-06-30 17:36:54 -04:00
James Agnew fa4bbe3685
Allow search criteria as subscription delivery mechanism (#1951)
* Terser should create correct Enumeration on create

* Start work

* Work on subscriptions

* Work on seed bundles

* Bundle transmission

* Add changelog

* Test fix

* Fix LGTM warning
2020-06-30 14:29:09 -04:00
James Agnew 072f3a422a
Use read partition for finding update candidate on upsert (#1945)
* Use read partition for finding update candidate on upsert

* Add changelog
2020-06-29 18:22:27 -04:00
Tadgh 571589d00d Merge branch 'master' into spring-batch-integration 2020-06-24 13:46:13 -07:00
Tadgh 2bd17806c4 Update changelog 2020-06-24 09:46:56 -07:00
Ken Stevens 38a2b00663
Empi 69 and candidates (#1936)
broaden empi blocking searches to support and searchparams as well as ors
2020-06-24 09:12:56 -04:00
Tadgh bb7a773f41 Merge branch 'master' into spring-batch-integration 2020-06-23 16:02:41 -07:00
James Agnew e65c264927
Support double _has expressions (#1939)
* Support nested _has queries

* Add changelog
2020-06-23 17:58:47 -04:00
James Agnew 6825d2fcf0
Reduce DB roundtrips for revincludes (#1937)
* Reduce DB roundtrips for revincludes

* Add changelog
2020-06-23 16:26:04 -04:00
James Agnew f88298a1fb
Remote terminology service enhancements (#1934)
* Remote terminology service enhancements

* Add changelog
2020-06-23 11:35:26 -04:00
James Agnew 67d363f9e1
Add setting to allow validation of reference targets (#1932)
* Add setting to allow validation of reference targets

* Add changelog

* Add changelog

* License headers

* Plugin version bump

* Experiment with Maven build
2020-06-23 11:35:10 -04:00
Diederik Muylwyk ced376f7ba Add changelog entry; fix typo. 2020-06-22 17:02:08 -04:00
Tadgh 0e86732599 Add changelog 2020-06-19 14:03:22 -07:00
James Agnew 46c00f4efb
Update for Loinc 2.68 (#1917)
* Work on loinc updates

* Work on loinc upload

* Clean up CLI config

* Add changelog

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Clean up imports

* LOINC fixes

* Loinc loader fixes

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
2020-06-18 16:55:11 -04:00
Ken Stevens d164e2d450
Empi 28 matchers (#1918)
* adding matchers

* reorganize resource matching api

* added precision sensitive date matcher

* stricter rules validation

* validate thresholds

* validate paths.  with FIXMES

* validate searchparams

* fix merge compile error

* add soundex, validate no duplicate names

* add normalize substring

* add exact field to matcher

* EXACT -> STRING, exact=true

* cleanup test method

* match test passes with fixmes

* fixed vector matching

* fixed vector matching

* updating documentation and fixing tests

* updated rules documentation with latest matchers

* updated rules documentation with latest matchers

* created eid page

* eid documentation

* pre-review cleanup

* clean up beans

* disentangling beans

* checkstyle

* noop to trigger CI

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_rules.md

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

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2020-06-14 17:15:56 -04:00
James Agnew 622659cbb3
Add type parameter to resource reindexing operation (#1921)
* Add type parameter to resource reindexing operation

* Add changelog

* CLean up reindexing
2020-06-12 16:51:18 -04:00
jamesagnew 756602183b Add changelog for https://github.com/hapifhir/org.hl7.fhir.core/pull/237 2020-06-11 14:03:20 -04:00
James Agnew b8da4f0140
Add package support (#1911)
* Begin rework of package management

* Work on NPM

* Work on package management

* Work on NPM

* NPM rework

* Work on NPM

* NPM package rework

* Updates

* Updates

* Add license

* Work on package server

* Work on package importing

* Work on package management

* Package rework

* Work on packages

* Work on package manager

* Work on pkgs

* NPM work

* NPM rework

* Work on package cache

* Work on NPM

* Work on NPM

* Package fixes

* Add tests

* Tweaks

* Test fixes

* Add changelog

* Avoid snapshot dep
2020-06-10 05:30:20 -04:00
James Agnew 0d3ad622b5
Correct Validation Performance Regression (#1895)
* Validation performance regression

* Optimize validation

* More cleanup

* Add changelog

* Test fixes

* Build fixes
2020-06-10 05:26:21 -04:00
ianmarshall 122bd97344 Changes recommended during code review. 2020-06-09 09:59:03 -04:00
ianmarshall c86e46b196 Add documentation and remove requirement for max parameter (defaulted to 1 now). 2020-06-08 18:08:02 -04:00
Ken Stevens dd84846b94
Empi 56 link merged person (#1902) 2020-06-05 15:50:50 -04:00
Ken Stevens 558f419955
Empi 54 not duplicate (#1900)
add operation to unduplicate persons
2020-06-05 12:21:09 -04:00
James Agnew 21330a0a22
Transaction create performance improvement (#1899)
* Work on perf issue

* Improve write performance for large bundles with tags

* Add changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1899-improve-write-xact-perf-with-tags.yaml

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Test fix

* Test fixes

* Test fixes

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
2020-06-05 05:26:06 -04:00
Ken Stevens 60e420aaa3
resolves #1838 (#1839)
* Added %today that works like %now but with date precision instead of dateTime precision.
2020-06-04 09:52:41 -04:00
Ken Stevens 33753881e2
Empi 55 deactivate merged (#1883) 2020-06-03 13:12:01 -04:00
jamesagnew 201c3a6187 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-06-02 07:47:06 -04:00
jamesagnew 760d19cf89 Prep for 5.0.2 2020-06-02 07:46:57 -04:00
ianmarshall f48214deda Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
# Conflicts:
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
2020-05-29 23:54:11 -04:00
James Agnew 7f72305f57
Improve Period range indexing (#1873)
* Fix #1871 - Handle period range searches better

* Add changelog

* FIx tests

* Add test logging

* Address review comments
2020-05-28 08:56:43 -04:00
Ken Stevens 97a1bd40a1
Added TLS parameters to Java Mail Sender (#1666)
* Added TLS parameters to Java Mail Sender

* changelog
2020-05-27 19:17:01 -04:00
James Agnew 6899604ae4
Correct validation of fragment codesystems (#1865)
* Update validation for fragment codesystem

* Test fixes

* Add changelog

* Test fix
2020-05-25 20:44:09 -04:00
jamesagnew 0175396ee0 Docs fix 2020-05-25 20:28:57 -04:00
ianmarshall b250ac4f3d Add a change log. 2020-05-25 18:42:17 -04:00
jamesagnew 6a4f5b9b3a Credit for #1826 2020-05-24 09:32:44 -04:00
Craig Appl 098c3ad737
Fixing a typo in the performance.md server_jpa doc (#1849) 2020-05-23 17:17:51 -04:00
jamesagnew 9192d41448 Credit for #1637 2020-05-23 17:16:19 -04:00
James Agnew e780a8402e
Use R5 snapshot generator (#1862)
* Use R5 snapshot generator

* Snapshot generator reworking
2020-05-23 12:54:19 -04:00
James Agnew c374383b37
Allow AuthorizationInterceptor to properly authorize GraphQL statements (#1864)
* Allow AuthorizationInterceptor to properly authorize GraphQL statements

* Add changelog
2020-05-22 20:40:37 -04:00
IanMMarshall a1a3d9de38
Merge branch 'master' into im_20200520_cascade_delete 2020-05-22 16:11:38 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857)
EMPI Initial Implementation (still plenty of known gaps)
2020-05-22 15:03:20 -04:00
ianmarshall 6a5c23c36b Adding a proposed change log. 2020-05-22 13:45:17 -04:00
Ken Stevens 2360ed4abe
fix build (#1861) 2020-05-21 19:22:08 -04:00
James Agnew ce5ade53d9
Fix #1855 - StructureDefinition search not working (#1858) 2020-05-21 09:35:37 -04:00
James Agnew e07e071130
Avoid deserialization issues in subscription delivery (#1856)
* Avoid deserialization issues in subscription delivery

* Add changelog
2020-05-21 05:47:39 -04:00
James Agnew 5b2181a563
Implement FHIR Patch (#1850)
* Start working on FHIRPatch

* More work on fhirpatch

* Work on FHIR Patch

* Add patch

* Test fixes

* Test fixes

* Get tests fixed

* Chnage to trigger a build

* Compile fix

* Dependency version fixes

* Test fix

* COmpile fix

* Try to fix build

* Test fix attempt

* Another build attempt

* Another build tweak

* Cleanup
2020-05-20 19:43:55 -04:00
James Agnew 9aaf5ccd63
Fix expunge when using unique search param (#1854)
* Fix expunge when using unique search param

* Add chaneglog
2020-05-20 15:58:53 -04:00
jamesagnew 8ab80e3529 Credit for #1853 2020-05-20 10:54:38 -04:00
James Agnew c9c90b327c
Allow no read interceptor for partition (#1851)
* Allow no read interceptor for partition

* Add changelog

* Test fix
2020-05-19 17:06:56 -04:00
jamesagnew cc92bd7b07 Revert "Start working on FHIRPatch"
This reverts commit b3f6e7d521.
2020-05-17 11:56:50 -04:00
jamesagnew b3f6e7d521 Start working on FHIRPatch 2020-05-17 11:44:06 -04:00
jamesagnew 52c8e3551c Version bump to 5.1.0-SNAPSHOT 2020-05-15 14:43:32 -04:00
jamesagnew fe0e07a313 Bump to 5.0.1 2020-05-15 05:47:01 -04:00
jamesagnew 9b1cd6cd5c Add changelog 2020-05-15 05:45:01 -04:00
James Agnew 79a064dfd9
Optimize chain sql paths (#1844)
* Start cleanup

* Almost workinf

* Possibly working!!

* Fixes

* Test fix

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

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

* Address review comments

* Add changelog

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-05-15 05:36:12 -04:00
jamesagnew 1d13e29ac0 Version bump to 5.1.0-SNAPSHOT 2020-05-12 20:04:20 -04:00
jamesagnew d631ecff4a Prepare for 5.0.0 2020-05-12 11:49:18 -04:00
jamesagnew c7da4b0914 Build Cleanup 2020-05-11 13:25:58 -04:00
James Agnew 0c13a65871
Bump to latest Core version (#1841)
* Start working on bumping core

* Work on tests

* Work on tests

* Bump core definitions

* Bump R5 defs

* Tweak changelog

* Test fix
2020-05-11 12:37:16 -04:00
jamesagnew 386f395e4b Version bump 2 dependencies 2020-05-10 19:10:18 -04:00
jamesagnew 5ea94abde5 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-05-10 12:10:03 -04:00
James Agnew 9d8bd0d51e
Bump R4 definitions to 4.0.1 (#1837)
* Bump R4 definitions to 4.0.1

* Add changelog

* Test fixes
2020-05-08 19:34:13 -04:00
jamesagnew 7f12f80358 Docs correction 2020-05-08 11:48:26 -04:00
James Agnew 6cc07b6689
Make binary storage work for bulk export (#1836)
* Make binary storage work for bulk export

* Add changelog

* Build fixes

* Test fix

* Test fix

* Test fix
2020-05-07 19:20:22 -04:00
Simon Yun e874abad47 Add Grand Rounds to HAPI FHIR Atlas 2020-05-06 13:47:26 -07:00
James Agnew a77aa6a28e
Multitenancy Ticket 2 - #1813 (#1821)
* Work on multitenancy

* Second ticket started

* More multitenancy work

* Work on tenancy security

* Work on multitenancy

* Test fixes

* Add docs

* cs tweak

* Multitenancy fixes

* Add debug log

* Fix build

* Add headers

* Add partition selection interceptor hook

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

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

* Account for review comments

* Resolve FIXMES

* Work on tests

* Test fixes

* A bit more cleanup

* Work on multitenancy

* Update hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientExamples.java

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md

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

* Address review comments

* Allow disabling text modifier indexing

* Add changelog

* Docs fixes

* Address review comment

* Resolve merge conflicts

* Merge master

* Compile fix

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-05-05 15:12:15 -04:00
James Agnew 35c2b7a2c1
Allow disabling text modifier indexing (#1831)
* Allow disabling text modifier indexing

* Add changelog

* Address review comment

* Resolve merge conflicts
2020-05-05 12:16:55 -04:00
James Agnew 91147cf6b0
Scope tag search to correct resource type (#1829)
* failing _tag tests

* cleanup

* Scope tag query to correct resource type

* Changelog

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-05-05 11:09:46 -04:00
jamesagnew ceae417d35 Credit for #1710 2020-05-04 05:42:32 -04:00
jamesagnew 394a47b83a Fix YAML error 2020-05-01 13:03:59 -04:00
jamesagnew 586089fc69 Credit for #1749 2020-05-01 07:38:31 -04:00
jamesagnew a786756169 Credit for #1812 2020-05-01 07:27:12 -04:00
jamesagnew 439a901e30 Credit for #1734 2020-05-01 05:56:47 -04:00
James Agnew 3d5a8bb3f8
Add UCUM support (#1824)
* Add UCUM support

* Add changelog

* Some cleanup

* Test fix

* Add flywayDB callback

* Add hooks to schema migrator
2020-04-30 15:22:41 -04:00
Tadgh 8f8a8a3dc2 Merge branch 'master' into date-match-bug 2020-04-29 16:17:50 -07:00
jamesagnew 885a18e0d8 Credit for #1788 2020-04-29 09:12:36 -04:00
James Agnew ededcc18d2
Add Partitioning / Multitenancy (#1807)
* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Add columns

* Work on multitenancy

* Work on muiltitenancy

* Work on multitenancy

* Work on uniques

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* More work on multitenancy

* Work on multitenancy

* Multitenancy work

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Work on docs

* Work on multitenancy

* Work on docs

* DOcs work

* Tenancy docs

* Work on docs

* Finish docs

* Add changelog

* Rename config

* Add migration tasks

* Fix typo

* Migration fix

* One more migration fix

* A couple more migration fixes

* Docs cleanup

* Work on docs

* Bump boot version

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Work on review comments

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

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

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Compile fx

* Test fixes

* One more bugfix

* Update operation name

* Add one more constant

* Roll back a change that was causing test failures

* Test fixes

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-04-24 05:45:11 -04:00
jamesagnew 37aa11182d Docs fixes 2020-04-23 21:05:23 -04:00
Ken Stevens 0b1a64d093
Merge pull request #1809 from jamesagnew/ks-20200420-changelog
retroactively add changelog for a search database change
2020-04-23 11:39:24 -04:00
Ken Stevens b728c14b98
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1698-remove-search-last-used-column.yaml
Co-Authored-By: James Agnew <jamesagnew@gmail.com>
2020-04-23 11:39:12 -04:00
James Agnew 5f88d87027
Tweak to #1801 - Normalize double leading zeros in database (#1815) 2020-04-23 09:44:08 -04:00
jamesagnew 7efd8a9f6e Merge branch 'ja_20200206_multitenancy' of github.com:jamesagnew/hapi-fhir into ja_20200206_multitenancy 2020-04-21 20:55:09 -04:00
jamesagnew 6226381595 Merge branch 'master' into ja_20200206_multitenancy 2020-04-21 20:54:56 -04:00
jamesagnew 1f37cdd8cf Address review comments 2020-04-21 20:53:10 -04:00
James Agnew 49d15dbbe8
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:32:27 -04:00
James Agnew 45fdd9981e
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:30:50 -04:00
James Agnew 4184268bea
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:30:10 -04:00
James Agnew 50ef7d7afd
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:27:24 -04:00
James Agnew 6e444986bc
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:26:02 -04:00
James Agnew 7d0d7d9ab7
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:20:34 -04:00
James Agnew d10538cdbe
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:20:20 -04:00
James Agnew fb4e620ba8
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:19:50 -04:00
James Agnew 532c830a43
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:19:35 -04:00
James Agnew 4fe7f6e322
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:19:02 -04:00
James Agnew 53695c50a0
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:18:47 -04:00
James Agnew c67cbca8c2
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:18:33 -04:00
jamesagnew c7de85339c Work on review comments 2020-04-21 20:18:06 -04:00
James Agnew 02e5dcb90d
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:17:44 -04:00
James Agnew 138369ede2
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
2020-04-21 20:17:17 -04:00
jamesagnew 11fade2c2e Bump boot version 2020-04-21 15:55:35 -04:00
jamesagnew 4b93a0d724 Credit for #1806 2020-04-21 15:49:43 -04:00