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3143 Commits

Author SHA1 Message Date
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
ianmarshall f9f8bf6515 Merge remote-tracking branch 'origin/master' into im_20200728_term_multi_version_support 2020-09-20 22:02:08 -04:00
ianmarshall 302bbca8fd Changes to support multi-versioning in ValueSet $expand operation. 2020-09-20 22:01:21 -04:00
Frank Tao 8f692a4776 CodeSystem/$validate-code not supported for DSTU2, DSTU3 2020-09-19 22:54:39 -04:00
Frank Tao a3a032584b Made Transactional 2020-09-19 15:18:28 -04:00
Frank Tao 01d88a665d Added CodeSystem/$validate-code for R5 2020-09-19 14:13:07 -04:00
Frank Tao 7db9f7475b Changed fetch size to 1 for CodeSystem $validate-code 2020-09-19 12:52:18 -04:00
Frank Tao 05de0c5031 Added more test cases for R4 2020-09-19 12:36:14 -04:00
Frank Tao 64f2bae2e7 Impl CodeSystem $validate-code for R4 with basic test cases 2020-09-18 22:30:59 -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
Tue Toft Nørgård c884f29112
SearchCoordinatorSvcImpl gets ExecutorService from injected ThreadPoolTaskExecutor (#2083) 
* Get ExecutorService from injected ThreadPoolTaskExecutor which enables support of TaskDecorators (e.g. to add/clear ThreadLocal logging context (MDC) variables)

* Properly initialize ThreadPoolTaskExecutor
 2020-09-16 09:05:28 -04:00
ianmarshall 7f7e1f39bc Merge remote-tracking branch 'remotes/origin/im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 22:06:43 -04:00
ianmarshall b2b63cbb02 Fixed JUnit tests. 2020-09-15 22:05:46 -04:00
ianmarshall 3add1320b7 Merge remote-tracking branch 'remotes/origin/im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:52:02 -04:00
ianmarshall ca0bdc8e4c Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-09-15 16:49:06 -04:00
ianmarshall 539ef63fc0 Merge branch 'im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:24:47 -04:00
ianmarshall 7b15f85fa1 Merge remote-tracking branch 'remotes/origin/feature_20200830_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:35:31 -04:00
ianmarshall 087c9e3c3b Merge remote-tracking branch 'remotes/origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:34:11 -04:00
ianmarshall b4cd09a5b6 Further cleanup 2020-09-15 12:30:26 -04:00
ianmarshall fe684ee4c0 Further cleanup 2020-09-15 12:26:17 -04:00
ianmarshall cd104ad635 Revised approach for versioning of ValueSet. 2020-09-15 10:21:42 -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
Frank Tao 0d929d4d19 Updated based on review comments 2020-09-14 09:30:03 -04:00
Frank Tao 8551b33e8a Merge branch 'feature_2020_09_02_term_multi_version_support' into ft_2020_09_11_term_multi_version_support_loader 2020-09-14 09:15:12 -04:00
Frank Tao 701fe81acf
Merge pull request #2072 from jamesagnew/ft_2020_09_10_term_multi_version_support_db_migration 
Term multi version support db migration - ConceptMap table change
 2020-09-14 09:13:12 -04:00
Frank Tao 91c1df7ce4 Supported ConceptMap Version from the properties 2020-09-11 21:38:42 -04:00
Frank Tao 750cbf4ba3 @Deprecated the old findTermConceptMapByUrl method 2020-09-11 09:20:01 -04:00
Frank Tao 16a5f57ae9 Added for ConceptMap DB migration 2020-09-10 21:41:06 -04:00
Frank Tao 972bdbd87d Updated based on code review 2020-09-10 21:17:41 -04:00
Frank Tao c873b6d6dd Fixed ConceptMap $translation without conceptMapVersion issue. 2020-09-09 22:24:02 -04:00
ianmarshall b4a87adc64 Suggested test that includes case where ConceptVersion is not specified in $translate operation. 2020-09-09 16:53:14 -04:00
Frank Tao 2fd692f5bb Updated R5 reverse $translate test case for more coverage 2020-09-07 20:54:35 -04:00
Frank Tao 5e17625a1b Fixed NullPointerException for reverse $translate operation. 2020-09-07 18:09:01 -04:00
Frank Tao 5410042643 Multi-version supported for ConceptMap $translate operation 2020-09-07 10:43:58 -04:00
Frank Tao 81cd73f820 Added test cases to for duplicate url and version of ConceptMap 2020-09-06 15:27:29 -04:00
Frank Tao 1ecec0abc9 Fixed duplicate ConceptMap URL only 2020-09-06 15:23:26 -04:00
Frank Tao 45b88de3b6 Fixed typo 2020-09-06 11:47:07 -04:00
Frank Tao ed2801dbaf ConceptMap multi-version supported 2020-09-06 11:33:55 -04:00
ianmarshall 5b707f97a9 Missing commits 2020-09-04 09:25:35 -04:00
ianmarshall 019d08a064 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-09-03 22:37:39 -04:00
ianmarshall 5f005120c9 Initial changes to support multi-version ValueSets 2020-09-03 22:36:15 -04:00
jamesagnew 5b7e6b593b Avoid startup retry loop 2020-09-02 19:56:57 -04:00
James Agnew d8542899e5
Don't lazy load DAOs (#2061) 
* Don't lazy load DAOs

* More tweaks
 2020-09-01 09:54:50 -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
ianmarshall 94440c849f Ensure that LOINC loader assigns a distinct ID for each version. 2020-08-30 21:53:38 -04:00
ianmarshall 1c55d87b10 Problem found in LOINC loader. 2020-08-30 17:11:48 -04:00
ianmarshall 3fef8f7bef Back out changes relating to validate operations. Cleanup of code 2020-08-30 15:29:57 -04:00
ianmarshall 92313cd770 Tests and fixes to support versioned CodeSystem lookup and subsume operations 2020-08-26 16:23:17 -04:00
ianmarshall 5a0bce9155 Changes to enable request delete of specific Code System version. 2020-08-25 12:45:53 -04:00
ianmarshall 796d2923e0 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-25 12:07:13 -04:00
ianmarshall 749c2bc4be Changes to enable request delete of specific Code System version. 2020-08-25 12:06:07 -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
vedion 31d736915f
- Adding missing null guard (#2049) 
* - Adding missing null guard. Guard needed when reference can't be resolved.

* Adding test for INCLUDE_ALL null guard fix

Co-authored-by: ahn <anders.havn@systematic.com>
 2020-08-22 16:59:36 -04:00
ianmarshall dc786eaff9 Refine model for storing multiple code versions. 2020-08-21 10:16:10 -04:00
ianmarshall 2126c5c556 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-18 11:15:09 -04:00
jamesagnew 30ac44974d Add JPA Starter to componentscan exclusions 2020-08-18 08:06:21 -04:00
ianmarshall c1dcf0442c Fix broken tests. 2020-08-17 21:52:16 -04:00
ianmarshall 4db00fa604 Fix broken test and cleanup. 2020-08-17 18:14:37 -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
ianmarshall bd94ff96cc Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-16 21:38:41 -04:00
Ken Stevens 7dd7f2b923
resource pid userdata fix (#2044) 
* fixed resource UserData RESOURCE_PID for expunge hook (was incorrectly pointing to ResourceHistoryTable pid instead of ResourceTable pid.

* fix merge
 2020-08-16 20:48:39 -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
jamesagnew 90ebaf8549 Add one more test for #2023 2020-08-11 08:54:03 -04:00
jamesagnew f3fbad63e7 Avoid a LOB error when expanding a valueset on Postgres 2020-08-11 08:30:48 -04:00
jamesagnew f0ed640e24 Upgrade core library dependency version 2020-08-10 09:05:04 -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
jamesagnew 096f310cae Increase visibility 2020-08-09 14:23:06 -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
jamesagnew 49f4f3ef62 Add license headers 2020-08-09 13:23:45 -04:00
ianmarshall d39348d7bd Initial changes to support multiple versions for code system. 2020-08-09 11:49:04 -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 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
James Agnew 5d9d4070fb
Fix an issue with binary storage not updating correctly if a retry (#2014) 
interceptor is present
 2020-08-05 09:14:40 -04:00
Tadgh 750d693fc3
Merge pull request #1984 from jamesagnew/batch-empi-job 2020-08-04 13:21:25 -07:00
jamesagnew 03f7289ac8 Add test for #2012 2020-08-04 09:16:47 -04:00
Tadgh 2cf48eb9b9 Move field length into constants 2020-08-01 13:11:33 -07:00
Tadgh 995c188305 implement function for all concrete classe 2020-08-01 13:03:37 -07:00
Tadgh 0a4d81eb85 Move getNextBatch into IResultIterator 2020-08-01 13:00:55 -07:00
Tadgh efaf09fbfa Fix java.lang.string in empiLink entity 2020-08-01 11:47:00 -07:00
Tadgh 48bf78e972 Rename service interface name 2020-07-30 12:17:14 -07:00
Tadgh 102f936156 Rework into new person deleting service 2020-07-29 12:17:07 -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
jamesagnew c6769ef075 Add test for #1999 2020-07-25 15:17:25 -04:00
James Agnew a6fd6254db
Speed up loinc ingestion (#1991) 
* Speed up loinc ingestion

* Add some logging
 2020-07-23 09:20:33 -04:00
Tadgh bbe6d5600e Address review comments 2020-07-22 11:58:08 -07:00
jamesagnew 5f1078ac13 Cleanup of package installer 2020-07-21 11:43:57 -04:00
Tadgh 4ec2be4ff5 Merge branch 'master' into batch-empi-job 2020-07-21 07:54:18 -07:00
Tadgh e82451533f Move provider logic. Fix tests to reflect. Remove now-dead methods 2020-07-21 07:52:51 -07:00
jamesagnew c44c1ff11f Wrap NPM loader in a try-catch 2020-07-21 09:57:10 -04:00
Tadgh de9621602b Update provider and create test skeletons for empi batch run 2020-07-18 18:18:21 -07:00
Tadgh 62b5221c3f Move Empi Batch work to the BaseHapiResourceProvider, allowing manual EMPI runs on a server/type/ID basis. 2020-07-18 13:36:14 -07:00
Tadgh 4fa4dd1c48 Update Javadocs 2020-07-17 13:39:39 -07:00
James Agnew 5db90d3e6e
Address issues when importing US Core (#1986) 
* Work on US Core import

* Work on US Core

* Resolve issues with US Core import

* Test fix
 2020-07-17 15:28:16 -04:00
Tadgh e540e4b0a2 Minor addition to PointcutLatch to support an inline runnable 2020-07-17 12:06:19 -07:00
Tadgh 1e12c740f6 Merge branch 'master' into batch-empi-job 2020-07-17 09:28:10 -07:00
Tadgh 92461b6346 wip 2020-07-17 09:00:15 -07:00
jamesagnew b57681da59 License header updates 2020-07-17 08:54:20 -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
Tadgh 6bb92717f5 Merge branch 'master' into batch-empi-job 2020-07-16 11:00:32 -07:00
Ibrohim Kholilul Islam 5a79304893
Implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation (#1896) 
* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation

* GraphQLQueryBodyParameter to recognize application/graphql

* fix 500 error on method without @GraphQLQueryBody

* refactor to processGraphQlGetRequest and processGraphQlPostRequest

* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest

* fix imports
 2020-07-16 09:25:26 -04:00
jamesagnew 962055e092 Undo extra logging in tests 2020-07-15 13:47:19 -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 29bf6b8171
Fix a bug validating ValueSets (#1981) 
* Fix a buig validating ValueSets

* Test fix
 2020-07-15 09:25:34 -04:00
jamesagnew addcdc9269 Make method transactional 2020-07-14 19:12:40 -04:00
jamesagnew d6f6ec2d66 License headers 2020-07-13 16:57:24 -04:00
Tadgh 677bc5577b wip 2020-07-13 12:00:19 -07:00
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
James Agnew 5c14a6c217
Revert pointless SQL optimization (#1977) 
* Revert pointless SQL optimization

* Fix tests
 2020-07-09 22:14:25 -04:00
James Agnew 1449b9cb0a
Install NPM resources correctly (#1972) 
* Install NPM resources correctly

* Fix tests
 2020-07-09 18:37:55 -04:00
James Agnew c949349a41
Correctly validate ISO 3166 codes (#1967 update) (#1973) 
* Add tests

* Test fixes

* Fix tests

* Test fix

* One more test fix
 2020-07-09 18:34:26 -04:00
Ibrohim Kholilul Islam 7a44fa3eb3
Fix GraphQL Array of Argument should be ORed (#1966) 
* provide IQueryParameterOr instead of IQueryParameterType to params.add

* add tests
 2020-07-08 10:38:50 -04:00
Tadgh 86f2761580 Merge branch 'master' into batch-empi-job 2020-07-07 07:52:42 -07:00
Tadgh 5b402de581 Add EmpiTargetType to link 2020-07-07 07:51:41 -07:00
Tadgh f82a53e6f9 Merge branch 'master' into batch-empi-job 2020-07-06 13:12:20 -07:00
Tadgh 3081df3cbd
Merge pull request #1969 from jamesagnew/empi-interceptor-bug 
EMPI Storage interceptor bug fix
 2020-07-06 13:10:39 -07:00
jamesagnew 489bd77dd4 Make constraint name comparisons case insensitive 2020-07-06 14:58:03 -04:00
Tadgh 84da932187 fix test 2020-07-06 11:36:47 -07:00
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
Tadgh 25d8668f55 Add Basic provider method, skeleton of tests 2020-07-03 15:21:32 -07:00
James Agnew 290577ff3e
Remove unnecessary type predicate (#1963) 
* Remove unnecessary type predicate

* Add changelog
 2020-07-03 17:54:25 -04:00
IanMMarshall e23e222f80
Merge pull request #1960 from jamesagnew/im_20200630_code_system_load 
Accidentally merged pull request before pushing changes from code review
 2020-07-03 16:29:34 -04:00
Tadgh 6259eada3c Fix parameter names. These are not partitions 2020-07-03 13:18:48 -07:00
ianmarshall b1ff6cbe37 Changes from code review 2020-07-03 14:25:24 -04:00
Tadgh 63bf9cca1b
Merge pull request #1961 from jamesagnew/bulk-intermittent 
Bulk intermittent bug
 2020-07-03 11:19:51 -07:00
Tadgh 4ff63e2493 Remove unnecessary logging. Spring batch already logs this 2020-07-03 10:21:04 -07:00
Tadgh d09f410b4d Tidy logging, increase timeout to 120 because clocks 2020-07-03 10:15:57 -07:00
Tadgh a84a41643d Increase awaitility timeout for bulk export of ALL resources 2020-07-03 10:08:34 -07:00
ianmarshall 4e5ca2ee15 Changes from code review 2020-07-03 13:08:11 -04:00
Tadgh 38cb526696 Add logging 2020-07-03 09:40:52 -07:00
ianmarshall 46abdfafe0 Merge remote-tracking branch 'remotes/origin/master' into im_20200630_code_system_load 2020-07-02 13:29:17 -04:00
ianmarshall 557f732e17 Cleanup and improved Unit tests. 2020-07-02 12:03:15 -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
jamesagnew bb17688680 Add test for #1780 2020-06-30 17:03:16 -04:00
ianmarshall 0788e79d51 Fix to address deferred save of TermConcept when code system version changes prior to save. 2020-06-30 15:07:14 -04:00
jamesagnew 2cdef055aa Missed commit on #1951 
Squashed commit of the following:

commit f820135996
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 14:29:24 2020 -0400

    Address review comments

commit 11c4f9defb
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:38:16 2020 -0400

    Fix LGTM warning

commit b650fdb9ea
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:20:52 2020 -0400

    Test fix

commit 6ebcceeb5c
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:49:01 2020 -0400

    Add changelog

commit 4a1d7383b0
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:46:52 2020 -0400

    Bundle transmission

commit 88bd4abf0c
Merge: 7cde945281 25fc747b9f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:31:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 7cde945281
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:10:33 2020 -0400

    Work on seed bundles

commit ed2e62752e
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 09:39:10 2020 -0400

    Work on subscriptions

commit 52addcff59
Merge: 64a9eaa4de bf8de84801
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Sat Jun 27 18:09:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 64a9eaa4de
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:32:17 2020 -0400

    Start work

commit f74eba5397
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:28:18 2020 -0400

    Terser should create correct Enumeration on create
 2020-06-30 14:31:40 -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 8df0448f88 Fix import 2020-06-29 11:04:03 -07:00
Tadgh 4e789fbf42 Fix import error 2020-06-29 11:01:38 -07:00
Tadgh e365e643ba
Merge pull request #1906 from jamesagnew/spring-batch-integration 
Spring batch integration
 2020-06-28 16:10:43 -07:00
jamesagnew be23eb3cfc Move the flush into the existing transaction 2020-06-27 18:06:37 -04:00
jamesagnew dac516828e Move validation settings bean 2020-06-26 18:31:13 -04:00
Tadgh 16039af110 Fix up samlpe starters 2020-06-26 13:15:31 -07:00
Tadgh b31b6652a9 Add async to the job launcher, fix test to reflect this 2020-06-26 11:51:01 -07:00
Tadgh 21567fdc43 Tidy await 2020-06-25 11:42:17 -07:00
Tadgh ed155e7657 wip 2020-06-25 10:37:02 -07:00
Tadgh 1d9641a736 fix empilinks 2020-06-25 10:28:03 -07:00
Ken Stevens 93da042d19 fix empi tests so they work with Spring Batch 
(all but one test fixed)
 2020-06-25 11:14:42 -04:00
Tadgh 06e1368388 Re-add comment 2020-06-24 21:00:45 -07:00
Tadgh 3da4ad280b undoes merge issues 2020-06-24 20:00:52 -07:00
ianmarshall 55ff15d039 Merge remote-tracking branch 'remotes/origin/master' into im_20200619_mariadb_expand_valueset_fix 2020-06-24 17:43:34 -04:00
Tadgh 64dbd038c9 Increase min thread count for batch. Add new which waits for all bulkexport jobs to be done 2020-06-24 13:16:11 -07:00
ianmarshall 5e3e7c46a8 Changes to support valueset expansion with Elasticsearch. 2020-06-24 15:48:06 -04:00
Tadgh a7740922f9 Specify version 2020-06-24 11:02:52 -07:00
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 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 ce0cb8916e Improve tests. 2020-06-22 17:22:21 -04:00
Diederik Muylwyk 314df43091 BaseValidationSupportWrapper.expandValueSet(...) and ValidationSupportChain.expandValueSet(...) were incorrectly replacing expansion options (i.e. offset and count) with null. 2020-06-22 16:52:52 -04:00
ianmarshall 5bf1e94a23 Fix to accomodate MySQL and MariaDB. 2020-06-19 17:26:45 -04:00
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
James Agnew b6540064ea
Improve TX scoping for validation (#1925) 
* Improve TX scoping for validation

* Test fix

* Test fix

* Some cleanup

* Test fixes

* Test fix
 2020-06-17 14:04:12 -04:00
Tadgh d32ad74402 some renaming 2020-06-15 21:49:34 -07:00
Tadgh 9222fa3f59 change transaction call 2020-06-15 15:17:25 -07:00
Tadgh eccd280d71 Fix test error 2020-06-15 11:24:39 -07:00
Tadgh 798fdb9cc2 Merge branch 'master' into spring-batch-integration 2020-06-15 09:10:41 -07:00
jamesagnew ac0d8c0fe1 Test fixes 2020-06-14 15:32:50 -04:00
Tadgh 4270636d43 Merge branch 'master' into spring-batch-integration 2020-06-12 16:20:54 -07:00
Tadgh 928aafba1e Rename bean 2020-06-12 16:18:04 -07:00
Tadgh 0f469c1a56 Rework to allow for job creation inside of batch 2020-06-12 14:20:50 -07:00
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
Tadgh a9c704c06e Merge branch 'master' into spring-batch-integration 2020-06-10 12:24:19 -07:00
Tadgh 4e42a59ad4 Add licenses 2020-06-10 11:52:45 -07:00
Tadgh d698ad7180 Code review comments 2020-06-10 10:46:28 -07:00
jamesagnew d521dc61cc Package fix 2020-06-10 11:59:37 -04:00
jamesagnew 7d6f8fe612 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-06-10 09:57:24 -04:00
jamesagnew 05df4f0827 Migration task updates 2020-06-10 09:56:49 -04:00
jamesagnew 0c100f1aca Test fixes 2020-06-10 08:09:10 -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
Tadgh 6e43c5348c Add missing imports from import reorganization 2020-06-09 19:27:16 -07:00
Tadgh 6fc5b753e5 Readding imports 2020-06-09 19:20:43 -07:00
Tadgh c36e1d2899 More code review comments 2020-06-09 19:18:06 -07:00
Tadgh 942fc313ec Code review comments 2020-06-09 19:00:41 -07:00
Tadgh d90987368a
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/JobExistsParameterValidator.java 
Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-06-09 16:29:15 -07:00
Tadgh b7cea688f6
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/JobExistsParameterValidator.java 
Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-06-09 15:52:37 -07:00
Ken Stevens 7fdd0f1753 Merge remote-tracking branch 'remotes/origin/master' into spring-batch-integration 2020-06-09 15:52:54 -04:00
Ken Stevens 57f2002b84 organize imports 2020-06-09 15:49:11 -04:00
Tadgh b1d2ab7619 Add invalid parameter validator 2020-06-09 11:02:37 -07:00
Tadgh a25a1064f8 remove constant 2020-06-09 10:22:31 -07:00
Tadgh 4f59c38692 Remove comment 2020-06-09 10:20:41 -07:00
Tadgh 7273457ea7 Rework to read and process larger chunks 2020-06-09 09:55:10 -07:00
ianmarshall 0540c9e205 Merge remote-tracking branch 'remotes/origin/master' into im_20200605_db_blob_mssql 2020-06-09 12:43:05 -04:00
ianmarshall 97e6d967e9 Improve updated JUnit test. 2020-06-09 11:52:51 -04:00
ianmarshall 64aa0feb5d Fix for issue of persisting blob data types to MS SQL databases. 2020-06-09 11:06:01 -04:00
ianmarshall 122bd97344 Changes recommended during code review. 2020-06-09 09:59:03 -04:00
Tadgh 278a1070ae :Merge branch 'master' into spring-batch-integration 2020-06-08 17:16:11 -07:00
Tadgh 25fa0377df tidying 2020-06-08 17:02:37 -07:00
Tadgh 864c9c2cb8 Add task executor to partition step 2020-06-08 16:35:15 -07:00
Tadgh 44aa688a20 Final config layout of Bulk Export Batch job 2020-06-08 15:59:08 -07:00
ianmarshall c86e46b196 Add documentation and remove requirement for max parameter (defaulted to 1 now). 2020-06-08 18:08:02 -04:00
ianmarshall 30dd858f17 Add close method for Elasticsearch service. Fix the partial code match. 2020-06-08 15:07:02 -04:00
ianmarshall 4982e67a0f Merge remote-tracking branch 'remotes/origin/master' into im_2020601_lastn_code_text_filter 2020-06-08 09:26:55 -04:00
ianmarshall 56cbc5149b Add support for partial code description matching. 2020-06-08 09:24:09 -04:00
Tadgh 4405e50db9 wip 2020-06-05 15:53:06 -07:00
Ken Stevens 558f419955
Empi 54 not duplicate (#1900) 
add operation to unduplicate persons
 2020-06-05 12:21:09 -04:00
jamesagnew 5483c99e00 License header updates 2020-06-05 05:47:20 -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
Tadgh 7ed65b0080 partially done writer, working out size-based chunking 2020-06-04 20:58:06 -07:00
ianmarshall 549993886d Fix merge conflicts. 2020-06-04 17:57:38 -04:00
ianmarshall 78b7f091ec Merge remote-tracking branch 'remotes/origin/master' into im_2020601_lastn_code_text_filter 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcMultipleObservationsIT.java
 2020-06-04 16:55:18 -04:00
Ken Stevens eb7b8e816b
Empi 58 no match create person (#1898) 2020-06-04 16:07:50 -04:00
ianmarshall 0a2f9d2697 Changes per code review plus fix for possible intermittent JUnit failures. 2020-06-04 15:24:41 -04:00
ianmarshall 9696af5dc0 Changed observation indexing to bypass hibernate search and removed Observation index tables. 2020-06-04 13:20:42 -04:00
ianmarshall 6e507bf642 Changed observation indexing to bypass hibernate search and removed Observation indexing tables. 2020-06-04 13:10:06 -04:00
Tadgh 7d46b3cc10 Partitioning Based on resource type complete. Still no threading 2020-06-03 14:58:42 -07:00
James Agnew 86ef0ec0e2
Correct transaction processing in multitenant server (#1884) 
* Correct transaction processing in multitenant server

* # d codethe npm registry for updates every day (weekdays)
 2020-06-03 10:37:47 -04:00
ianmarshall 8d5232bced Merge remote-tracking branch 'remotes/origin/master' into im_2020601_lastn_code_text_filter 2020-06-02 21:28:10 -04:00
Tadgh e8970bce46 Running batch job 2020-06-02 16:08:19 -07:00
jamesagnew 75a74bdd38 License headers 2020-06-02 18:20:56 -04:00
Tadgh 31b7e862d4 Remove extra beans 2020-06-02 15:00:56 -07:00
Tadgh bb863f26fa Initial run through the first part of batch integration 2020-06-02 13:44:23 -07:00
ianmarshall bfc5f93ec8 Enable filtering $lastn operation by Observation effective date. 2020-06-02 16:39:06 -04:00
ianmarshall 2e709a50c0 Enable filtering $lastn operation by Observation effective date. 2020-06-02 16:37:07 -04:00
Tadgh f8d699e13b Initial working commit passing jobs to spring batch 2020-06-01 15:51:09 -07:00
Tadgh 0fc2e04e65 wip 2020-06-01 12:13:55 -07:00
Tadgh aa7d1cbcb7 Wip getting tasks built 2020-06-01 11:32:36 -07:00
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
ianmarshall a4811f1508 Changes per code review. 2020-05-29 23:47:44 -04:00
Tadgh a306825625 moving dependencies around. Get non-persisted batch working 2020-05-28 12:10:52 -07:00
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
Tadgh 81d5ff8f5a Add schema initialization 2020-05-27 17:06:52 -07:00
James Agnew 22af36ae7b
Conditional update on Partitioned Server fails (#1870) 
* Fix #1869

* Remove FIXME

* Test fix

* Test fix
 2020-05-27 10:40:29 -04:00
ianmarshall 5cc77b78d4 Fixed problems with results of chunked queries being incorrectly sorted. 2020-05-26 18:09:54 -04:00
jamesagnew 5482367e37 Remove redundant index - Already covered by FK 2020-05-26 08:54:00 -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
ianmarshall 1e554731bb Additional cleanup and test fixes. 2020-05-25 18:25:25 -04:00
ianmarshall 6ed724e01b Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-25 17:40:53 -04:00
jamesagnew 2bcfe7cdaa Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-05-25 13:20:59 -04:00
jamesagnew bf550f9c27 License header updates 2020-05-25 13:20:32 -04:00
James Agnew 535bf88efe
Fixes to diff operation (#1866) 2020-05-25 13:16:58 -04:00
ianmarshall ee87a2e2d0 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-25 11:37:34 -04:00
ianmarshall 816f409a8a Re-factor lastn entities to locate them is same package as other Search Parameter entities. 2020-05-25 11:37:01 -04:00
jamesagnew 3807640347 Resolve merge conflict 2020-05-24 11:38:52 -04:00
Martin Zacho Grønhøj 9bde517540
Install external ig package at startup (#1826) 
* Do not use deprecated methods in structures-r4 test

* beginning development of feature Implementation Guide installer

* fetch IG, generate snapshots of SDs of and persist conformance resources to db

Missing initialization, error-handling and handling of NameSystems and Subscriptions

* Refactor IgInstaller and implement support for R4 and R5

* Error handling and removed logic for invoking IG installation

IgInstaller should be invoked by applications

* Implement pull request comments in IgInstaller

1) Renamed IgInstaller -> IgInstallerSvc for consistency
2) Use field autowiring and @PostConstruct for consistency
3) Use exceptions instead of boolean flags for success indication
4) Use IValidationSuport to generate snapshots of StructureDefinitions
in a version independent way (less maintenance) instead of SnapshotGenerator.java
5) Read IGs for tests from src/main/resources instead of external URL

* IG installation: Wrap exceptions during resource creation in custom class

* IG installation: Improved logging

* IG installation: Search for existing resources in a version independent way
 2020-05-24 09:25:46 -04:00
Jacob Stampe Mikkelsen 262a964a31
Add index on CONCEPT_PID on TRM_CONCEPT_PROPERTY to optimize a full-reindex of lucene index which can be needed when running in a docker container where the lucene files are discarded on redeploy. (#1637) 
Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-05-23 17:11:21 -04:00
ianmarshall 35b75f8ffb Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-23 15:54:23 -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
ianmarshall 4d378ee0ed Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
#	hapi-fhir-jpaserver-base/pom.xml
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java
 2020-05-22 17:04:01 -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 b501a601b7 Some final cleanup minor updates. 2020-05-22 13:36:08 -04:00
ianmarshall a60e5809b2 Changes to enable adjusting limits on delete conflict handling through configuration. 2020-05-22 10:15:04 -04:00
jamesagnew 5ba7f1525f Test fix 2020-05-21 20:38:11 -04:00
James Agnew 63ff0ede9c
Make diff operation work securely (#1859) 
* Make diff operation work securely

* Build tweak

* FIx tests
 2020-05-21 19:20:48 -04:00
James Agnew ce5ade53d9
Fix #1855 - StructureDefinition search not working (#1858) 2020-05-21 09:35:37 -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
jamesagnew b044d05332 Add a disabled test 2020-05-20 17:26:24 -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
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
ianmarshall 3b7f106052 Fixed latest merge conflicts. 2020-05-19 16:34:05 -04:00
ianmarshall d2b54d6203 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
 2020-05-19 15:20:06 -04:00
ianmarshall 6a27192a96 Fixed sorting with chunked and paged queries. 2020-05-19 14:48:26 -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
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
ianmarshall 529e1e1f5e Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-14 12:09:24 -04:00
ianmarshall eb1d1c2b27 Changes to better support chunking of queries and paging of results for lastn operation and to monitor performance. 2020-05-14 12:08:55 -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
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
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
ianmarshall 8fcdc78077 Fix issues resulting from latest merge. 2020-05-08 09:31:05 -04:00
ianmarshall e56cb049f7 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-08 09:19:44 -04:00
ianmarshall c290fa3493 Fixes to enable $lastn to return more than 32K records. 2020-05-08 09:19:14 -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
James Agnew b67509d7ff
Transaction write performance fix (#1832) 
* Performance fix for transactions

* Test fix

* Fixes

* Add docs

* Test fixes
 2020-05-07 10:56:41 -04:00
ianmarshall 4cced40b54 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
 2020-05-05 17:19:32 -04:00
ianmarshall 4db5beeabf Additional changes to enable processing of lastn operations with large numbers of parameters. 2020-05-05 16:53:47 -04:00
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 dada217966
Clean up hash code calculation (#1830) 
* Clean up hash code calculation

* Test fixes

* Test fix

* Test fixes

* Compile fix

* Test fix
 2020-05-05 11:11:24 -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 41056092ed License header updates 2020-04-30 18:24:07 -04:00
Tadgh 8f8a8a3dc2 Merge branch 'master' into date-match-bug 2020-04-29 16:17:50 -07:00
jamesagnew e439891ea2 Add test 2020-04-29 15:21:54 -04:00
ianmarshall 3e49e5615f Fixing merge conflicts after merge from Master. 2020-04-25 22:14:55 -04:00
ianmarshall dd749791db 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
 2020-04-24 16:55:45 -04:00
ianmarshall 0e45db0ba9 More cleanup and test fixes. 2020-04-24 16:23:59 -04:00
jamesagnew e219c1774b Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-04-24 05:45:26 -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
ianmarshall 197bf2b6a8 Further refinements and test fixes. 2020-04-23 23:21:45 -04:00
jamesagnew c994f48ccd Add test case 2020-04-23 10:37:05 -04:00
James Agnew 5f88d87027
Tweak to #1801 - Normalize double leading zeros in database (#1815) 2020-04-23 09:44:08 -04:00
jamesagnew ccda668d0c Restore subscription loading at startup 2020-04-23 05:28:56 -04:00
Andrew Fitzgerald 99b9ec0b1c Fix compilation error 2020-04-22 09:57:52 -04:00
jamesagnew be5f8191dc One more bugfix 2020-04-22 09:08:46 -04:00
jamesagnew 8a2b799df0 Test fixes 2020-04-22 08:43:00 -04:00
jamesagnew 009d6443f5 Compile fx 2020-04-21 21:34:15 -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 cc2b7452be
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:36:19 -04:00
jamesagnew c7de85339c Work on review comments 2020-04-21 20:18:06 -04:00
Maciej Kucharek f69fb1a39b
Set ES username and password only if they're not blank (#1806) 
This is important for AWS-hosted ES, as it does not accept HTTP requests with Basic authentication (even if the username/passwords are blank). Skipping those settings in case they're blank solves the issue.

Co-authored-by: Maciej Kucharek <maciej@oraoncology.com>
 2020-04-21 15:32:12 -04:00
Ibrohim Kholilul Islam 3225075f9e
Fix GraphQL Error (#1791) 
* add debug log

* add debug log to value iteration

* fix _filter issue on /$graphql, fix dash and underscore issue on /$graphql, and give helpful error message on wrong argument.

* remove debug logging

* implement JpaStorageServicesTest
 2020-04-21 15:28:28 -04:00
James Agnew c716216b34
Adjust return type for fluent delete() operation (#1805) 
* Add cascading delete to client

* Add changelog

* Client delete should return MethodOutcome

* Rerturn more appropriate type for delete operations

* Refactor cascade detection to be reusable
 2020-04-21 15:23:11 -04:00
jamesagnew 998c1f7751 Work on docs 2020-04-21 14:32:41 -04:00
jamesagnew e6c806283e Merge branch 'ja_20200206_multitenancy' of github.com:jamesagnew/hapi-fhir into ja_20200206_multitenancy 2020-04-20 16:58:59 -04:00
jamesagnew 544d9fbc6c Add migration tasks 2020-04-20 16:58:48 -04:00
jamesagnew bbab016ca6 Rename config 2020-04-20 12:38:04 -04:00
jamesagnew 7248b4e18e Finish docs 2020-04-20 11:02:27 -04:00
jamesagnew cd3e1c5e72 Tenancy docs 2020-04-19 10:15:51 -04:00
jamesagnew 48057b9d8e Merge branch 'master' into ja_20200206_multitenancy 2020-04-17 17:59:48 -04:00
ianmarshall 540375a7eb Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-04-17 17:39:27 -04:00
ianmarshall 4a89860f9b Additional tests and cleanup. 2020-04-17 17:38:42 -04:00
jamesagnew e0b419354f Bump up hamcrest version and force the use of the latest version 2020-04-17 13:59:22 -04:00
James Agnew 497757501b
Improve search method binding priority (#1802) 
* Work on search method binding priority

* Work on method priority

* Work on binding priority

* Test fixes

* Add changelog

* Test fixes

* compile fix

* One more comple fix

* Test cleanup

* Test fix
 2020-04-17 09:28:33 -04:00
jamesagnew 81723c30d8 Work on multitenancy 2020-04-16 15:52:15 -04:00
jamesagnew 25cdbb15c2 Work on multitenancy 2020-04-16 15:33:48 -04:00
jamesagnew 8873749d9c Add license headers 2020-04-16 10:06:56 -04:00
jamesagnew cd06137745 Work on multitenancy 2020-04-15 22:12:28 -04:00
jamesagnew d822867a4a Merge branch 'master' into ja_20200206_multitenancy 2020-04-15 22:12:20 -04:00
James Agnew f95f619bdc
Correct two JPA processing bugs (#1801) 
* Work on search params on contained

* Add workaround for stored decimals with leading decimal point

* Add changelog

* Cleanup

* Test fix

* Test fix

* One more test fix
 2020-04-15 14:22:47 -04:00
ianmarshall d03ce6533e Fixed conflicts after merging latest from Master. 2020-04-13 20:01:34 -04:00
ianmarshall 925bbbbcdc Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java
#	hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
#	pom.xml
 2020-04-13 18:35:15 -04:00
ianmarshall 0f9bdbd3af Undid previous re-factoring and fixed a bug introduced in last commit. 2020-04-13 16:14:38 -04:00
jamesagnew 982b54df57 Work on multitenancy 2020-04-13 11:50:49 -04:00
jamesagnew f2fa8659c4 Test fix 2020-04-13 09:35:51 -04:00
ianmarshall af11763dee Fixes to command line tool, clean-up and minor re-factoring. 2020-04-13 08:56:56 -04:00
jamesagnew c26a5553e9 Multitenancy work 2020-04-12 20:47:32 -04:00
jamesagnew e55ccf88fc Work on multitenancy 2020-04-10 20:01:59 -04:00
ianmarshall e64d67f429 Consolidate changes to Command Line Tool and add/improve tests. 2020-04-10 16:58:00 -04:00
jamesagnew 8d8c657ce2 More work on multitenancy 2020-04-10 13:05:17 -04:00
jamesagnew 219332e9e3 Work on multitenancy 2020-04-10 11:11:29 -04:00
jamesagnew e0fcbe1df2 Merge branch 'master' into ja_20200206_multitenancy 2020-04-09 11:52:27 -04:00
James Agnew 8cdc3a72ce
Fix #1794 - Client ID and Server ID mode clash (#1795) 
* Fix #1794 - Client ID and Server ID mode clash

* Try to track down intermittent test failure
 2020-04-09 09:31:13 -04:00