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1970 Commits

Author SHA1 Message Date
Diederik Muylwyk d1cba9f928 Syncing master into working branch. 2019-07-29 19:39:29 -04:00
jamesagnew cf5201c67b Add a constructor 2019-07-29 19:31:47 -04:00
Diederik Muylwyk a8489f4331 Added TRM_VALUESET.EXPANSION_STATUS column, index, fields to entity, and migration tasks. 2019-07-29 19:30:46 -04:00
jamesagnew a3cbdf0956 Make terminologyuploaderprovider not abstract 2019-07-29 19:02:51 -04:00
James Agnew b030d1af31 Test fixes 2019-07-29 18:17:40 -04:00
James Agnew a4ca5374ec
Add terminology delta operations (#1401) 
* Start work on delta operations

* Add changelog

* Some build fixes

* Move upload terminology command to CodeSystem resource

* Updates

* Some test fixes

* Add changelog

* Some test fixes

* More test fixes

* Test fix

* Add additional tests

* Transaction boundary fixes
 2019-07-29 17:46:42 -04:00
Diederik Muylwyk d03fc0f61d
Add null check for shortName before adding designation. (#1396) 2019-07-25 11:06:02 -04:00
Ken Stevens a7817b07ca Pre PR cleanup 2019-07-24 22:00:34 -04:00
Ken Stevens a20b738161 Pre PR cleanup 2019-07-24 22:00:26 -04:00
Ken Stevens 84f5c7d467 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-24 21:54:05 -04:00
Ken Stevens e05387da02 Recover from failed merge again. This time with feeling! 2019-07-24 13:46:20 -04:00
James Agnew ddb8e385bf Test fix 2019-07-24 13:24:48 -04:00
James Agnew b78cd1e62e Merge branch 'add-pid-to-created-resource' 2019-07-24 13:19:38 -04:00
James Agnew e8cf2738f0 Handle oversized payload request 2019-07-24 13:18:30 -04:00
James Agnew b9dbd69e5d Fix limiting on size 2019-07-24 13:11:05 -04:00
Ken Stevens 37411a6ae2 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-24 10:41:11 -04:00
jamesagnew 6b599c29e5 Merge branch 'add-pid-to-created-resource' 2019-07-23 17:36:15 -04:00
James Agnew bff39e4139 Try to deal with an intermittent failure 2019-07-23 15:58:14 -04:00
James Agnew 9094323c43 Add a test 2019-07-23 14:47:27 -04:00
James Agnew b1e409519d Add a test 2019-07-23 14:47:27 -04:00
Ken Stevens 8d86e34bcf Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
 2019-07-23 09:12:08 -04:00
jamesagnew 60ea922e8d Add license headers 2019-07-23 05:38:10 -04:00
James Agnew 7e3d062d15
Switch default client to JSON (#1392) 
* Start work on changing over

* Update tests

* More test fixes

* Work on generalizing binary access provider a bit

* Add expunge capability to binary storage, and also support actual binary
resources

* Work on binary provider

* Get the DB bound binary storage service working

* Test fixes

* Compile fix

* Fix compile error

* Test fix

* Test tweak

* Trying to figure out an intermittent failure

* Work on tests

* More work on tests

* Another test fix
 2019-07-22 21:27:10 -04:00
Ken Stevens 7ba3ceec90 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-19 10:54:56 -04:00
James Agnew 458cfcfa12 Fix intermittent test failure 2019-07-19 10:46:49 -04:00
James Agnew f53746cd63 One more set of migrator tweaks to account for latest changes 2019-07-19 10:10:00 -04:00
Ken Stevens e634aa6d10 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-18 22:06:10 -04:00
James Agnew 5bf4fa22e7 Allow patching in tranactions 2019-07-18 16:41:07 -04:00
Ken Stevens a7fa79331a Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-18 13:14:54 -04:00
James Agnew 87ab796309 Updates to validating interceptor 2019-07-18 12:57:30 -04:00
Ken Stevens ffa008b2dd Fixing a build error 2019-07-18 10:59:11 -04:00
Ken Stevens 72aa4932d6 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-18 10:12:15 -04:00
James Agnew ee7cff9445 Rename a few columns to not conflict with res´rved words 2019-07-18 05:47:32 -04:00
jamesagnew 7488047686 Add license headers 2019-07-17 18:53:23 -04:00
James Agnew 55c0d5b604
Add binary storage for Attachments (#1386) 
* Have this working now

* Add utility method

* Build fixes

* Add changelog
 2019-07-17 18:31:17 -04:00
Ken Stevens c73aebe0a0 IResource and IAnyResource are mutually exclusive... 2019-07-17 17:59:49 -04:00
Ken Stevens 465b4daa03 Changed IAnyResource to IResource per feedback 2019-07-17 17:59:49 -04:00
Ken Stevens 1d4dc5b3c5 add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_UPDATED hooks are called 2019-07-17 17:59:49 -04:00
Ken Stevens e27685e811 add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_CREATED hooks are called 2019-07-17 17:59:49 -04:00
Ken Stevens 7bc8517fc6 Merge branch 'add-pid-to-created-resource' into expunge-resource-hook 2019-07-17 14:26:00 -04:00
Ken Stevens 6960f1db1c IResource and IAnyResource are mutually exclusive... 2019-07-17 14:25:10 -04:00
Ken Stevens a5da696823 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-17 13:28:29 -04:00
Ken Stevens d21304e771 cleanup 2019-07-17 13:28:17 -04:00
Ken Stevens fe21dba4a6 Added Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE. 
Also added a couple of tests.
 2019-07-17 13:26:50 -04:00
James Agnew 76384abefb Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-07-17 10:57:43 -04:00
Ken Stevens 160b221f5f Changed IAnyResource to IResource per feedback 2019-07-17 10:26:16 -04:00
Ken Stevens 79ce4a30cc Merge remote-tracking branch 'remotes/origin/master' into add-pid-to-created-resource 2019-07-16 20:46:31 -04:00
Diederik Muylwyk 456aac5e16
Resolve "experimental implementation for storing and expanding large ValuetSets cont'd..." (#1376) 
* Added experimental implementation for storing expanded ValueSets in terminology tables.

* Minor tweak to log message for consistency.

* Another minor tweak to log message for consistency.

* Renamed test.

* Initial work on ValueSetCodeAccumulator.

* Renamed addCode() to includeCode(); added excludeCode().

* Incremental work on large ValueSet expansion support; refactoring.

* Incremental work on large ValueSet expansion support; accounting for designations.

* Incremental work on large ValueSet expansion support; fixed missing designation.language in expanded ValueSets.

* Incremental work on large ValueSet expansion support; now actually populating TermConceptDesignation; added TermValueSetConceptDesignation as well.

* Missed a word.

* Tweak changelog entries.
 2019-07-16 17:12:21 -04:00
Ken Stevens 634718c503 add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_UPDATED hooks are called 2019-07-16 16:36:05 -04:00
Ken Stevens fe7d38d0b5 add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_CREATED hooks are called 2019-07-16 15:33:51 -04:00
James Agnew f8444b90c8 Test tweak 2019-07-14 18:11:37 -04:00
James Agnew 7831e8a0ed Add support for $snapshot generation and validation based on snapshots 2019-07-14 16:15:56 -04:00
James Agnew 120b93f204
Use HL7 FHIR Core Structures (#1382) 
* Ongoing work on core structures suport

* Ongoing work on this merge

* Ongoing work to clean up structures

* Credit for #1179

* Address compile issues

* Latest changes

* Work on parallel execution

* Work on getting tests passing

* Add H2 to migrator

* Test fix
 2019-07-14 10:16:40 -04:00
jamesagnew 534c71c1d5 Higher parallel count for JPA tests 2019-07-13 18:24:31 -04:00
James Agnew ba4bb005bc
Switch JPA unit tests to use H2 (#1381) 
* Start working on this

* Ongoing fixes to H2 branch

* Work on fixing tests

* Updated fixes

* Some test fixes

* More work on H2 migration

* Fixes to try and get the H2 migration building

* Test seem to be passing!

* Tweaks to locale randomization

* Add changelog
 2019-07-13 17:22:43 -04:00
Ken Stevens 8d817b364c Merge remote-tracking branch 'remotes/origin/master' into expunge-hooks 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
 2019-07-12 13:27:11 -04:00
jamesagnew a5a9950e77 License header updates 2019-07-12 08:52:47 -04:00
James Agnew afd2b35ff6 Fix an intermittent test failure 2019-07-12 06:32:18 -04:00
James Agnew 1db019b6df Test fix and try to get Travis building again 2019-07-11 20:20:27 -04:00
Diederik Muylwyk 62e1b7e9ea Fixing minor overlooked change from recent pull request. 2019-07-11 17:07:26 -04:00
Diederik Muylwyk 0729e38e6e
Resolve "experimental implementation for storing expanded ValueSets in terminology tables" (#1369) 
* Added experimental implementation for storing expanded ValueSets in terminology tables.

* Minor tweak to log message for consistency.

* Another minor tweak to log message for consistency.

* Renamed test.

* Addressing review comments.

* Added migration tasks.
 2019-07-11 16:52:19 -04:00
Ken Stevens 7aaa75c255 fixed pointcut 2019-07-10 10:09:43 -04:00
Ken Stevens 5e05703c1a Add expunge-everything hook. Also add RequestDetails to all expunge operations 2019-07-09 10:58:57 -04:00
jamesagnew 9fcbdb0cdc License header updates 2019-07-07 14:41:57 -04:00
James Agnew 6c221efaf6 More test fixes 2019-07-07 14:09:55 -04:00
James Agnew d00304d706 More test fixes 2019-07-07 13:35:39 -04:00
James Agnew 34f7d4ddbd Refactor ServerConformanceProvider so that it no longer keeps any state 2019-07-07 12:57:31 -04:00
James Agnew 4bd60a8447 Roll back one dependency 2019-07-07 11:02:08 -04:00
James Agnew 1c7c83cd8e Add an isEmpty() method to IBundleProvider 2019-07-05 16:16:39 -04:00
jamesagnew dff2fdd3cf GET RID OF TRAILING LICENSE HEADER SPACES ONCE AND FOR ALL 
YESSSSSSSSSSSSS
 2019-07-05 11:19:51 -04:00
James Agnew 4a0bc27602 Test fix 2019-07-05 09:37:48 -04:00
James Agnew 2a473d1825 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-07-05 09:03:23 -04:00
James Agnew 2a6436af23 Rename columns in code mapping 2019-07-05 09:03:03 -04:00
jamesagnew aff88d3ebb License header updates 2019-07-05 07:27:18 -04:00
James Agnew 6e20b53979 Fix a crash in R4 validation 2019-07-04 16:27:04 -04:00
James Agnew 4f7d4aa8d2 Two test fixes 2019-07-04 09:54:26 -04:00
James Agnew 886f3f442b Moving testloggingutil into test utilities 2019-07-04 09:00:30 -04:00
James Agnew f1848fb1ad Include version ID in response for deleted resource 2019-07-03 14:44:12 -04:00
James Agnew 56aaef641c Add request ID 2019-07-02 21:32:28 -04:00
James Agnew 1faf7785c4 Dont filter constraints from the event broadcast - this was not needed 
after all
 2019-07-02 09:21:15 -04:00
jamesagnew 7b7136e3ab Ensure test coverage of JPA entities 2019-07-02 08:37:48 -04:00
jamesagnew 491776a7b8 Fixes to cascading delete 2019-07-02 05:41:38 -04:00
jamesagnew 742389642d Add tests for delete conflicts and authorizationinterceptor 2019-07-01 10:49:38 -04:00
jamesagnew ccf491b3ae Add parent pom to BOM 2019-06-29 13:50:43 -04:00
James Agnew 1fd99dac63
Enable optional cascading deletes on JPA server (#1363) 
* Start working on cascading deleets

* WOrk on cascading deletes

* Work on cascading deletes

* Enable cascading deletes

* Cascade deletes almost working

* FIx test

* Test fix
 2019-06-28 17:32:39 -04:00
Joel Schneider 5c55133275 quick hack to pass unit test (handle files located in subdirectories of zipfile) 2019-06-28 15:11:16 -04:00
Joel Schneider 557c9b66c2 add TerminologyLoaderSvcImgthlaTest 2019-06-28 15:11:16 -04:00
Joel Schneider 5d113c2e8b Remove allele_id property. (If needed, a CodeSystem supplement could define it. Defining a separate allele_id CodeSystem, and related ConceptMap, may also be a reasonable option.) Trying to keep the list of concept properties as straightforward as possible for now. 2019-06-28 15:11:16 -04:00
Joel Schneider 1f5cbc36b3 add stub for HLA nomenclature terminology upload 2019-06-28 15:11:16 -04:00
jamesagnew 5910131319 License header updates 2019-06-27 18:23:45 -04:00
James Agnew 10d969c514
Add Consent Service (#1359) 
* Initial consent svc

* Ongoing consent svc work

* Add docs

* Ongoing consent service work

* Work on consent service

* More work on consent svc

* License header updates

* Ongoing consent svc work

* Some test fixes

* Some test fixes

* More work on consent svc

* Tests working

* Test fix

* Propagate RequestDetails to everything in JPA server

* More interceptor tweaks

* Fix compile error

* One more tweak to captured SQL

* Ongoing interceptor tweaks

* Ongoing interceptor tweaks

* More interceptor tweaks

* Interceptor tweaks

* Tweaks to tests

* Fix tests

* Test fix

* Raise warnings when encoding extensions with missing values

* Consent service work

* More interceptor tweaks

* Consent interceptor tweaks

* Add logging to test
 2019-06-27 16:35:29 -04:00
James Agnew 2bfbea4e6b Remove duplicate test class 2019-06-26 09:24:36 -04:00
James Agnew ce0c84db03
JPA server can't use OR list on _tag:not (#1362) 
* Add a failing test for :not tags

* Add changelog and fix issue
 2019-06-26 08:44:56 -04:00
jamesagnew e76b1dacb3 License header updates 2019-06-22 18:31:16 -04:00
jamesagnew 8bb010bb18 Test fixes 2019-06-22 17:42:02 -04:00
jamesagnew 3ba194acbe Reject subscriptions in JPA server if status field is not set 2019-06-22 17:03:22 -04:00
jamesagnew 0fbde2a4e5 Fix #1352 - Don't fail to create observation with a value type of 
SampledData
 2019-06-22 16:43:25 -04:00
James Agnew 4ad1808da3
Propagate RequestDetails to everything in JPA server (#1358) 2019-06-22 15:18:06 -05:00
jamesagnew 58e6b7f6aa Fix #1011 - Was resolved in #1355 2019-06-22 16:03:35 -04:00
jamesagnew 989e26fdb4 Fix #1355 - Failed to call access method: java.lang.NullPointerException in case of bundle entry without resource 2019-06-22 15:51:56 -04:00