Commit Graph

2124 Commits

Author SHA1 Message Date
Ken Stevens 2dc70c92f1 add accessor to search hash 2019-08-24 14:10:17 -04:00
Diederik Muylwyk b41926307c Completed work on large ValueSet expansion support; ready for review. 2019-08-23 17:40:45 -04:00
James Agnew 10958a8e4d I think this might work now.. 2019-08-23 12:22:27 -04:00
James Agnew c564052b15 One more test fix 2019-08-23 11:46:56 -04:00
Diederik Muylwyk 890555a77d Incremental work on large ValueSet expansion support; transaction boundaries need to be broken up. 2019-08-23 11:46:32 -04:00
James Agnew c346ba92c8 Revert accidental commit 2019-08-23 11:17:02 -04:00
James Agnew abc894ce90 A few refactors based on ken's suggestions 2019-08-23 10:57:58 -04:00
James Agnew 6fa27934a8 Tests all seem to be working 2019-08-23 10:14:13 -04:00
Diederik Muylwyk 97a235ddfc Merging master into working branch.
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
2019-08-22 14:02:56 -04:00
Diederik Muylwyk 72dd6b2922 Incremental work on large ValueSet expansion support; fixed broken deletion for TermValueSetConceptDesignation. 2019-08-22 14:00:08 -04:00
James Agnew 4afa55ea26 Initial commit - Not yet compiling 2019-08-22 08:49:34 -04:00
Ken Stevens 37c1ba44fe Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump 2019-08-21 15:04:16 -04:00
James Agnew 9428430822
Add support for Resource.meta.source (#1438)
* Work on indexing source

* Work on tests

* Refactor query count tests

* Unit test fixes

* Add some tests

* DAO fix

* Fix compile error

* Unit test fix

* Cleanup

* Test fix

* Fix compile error

* One more test fix
2019-08-21 11:17:43 -04:00
Diederik Muylwyk 3218bd7853 Incremental work on large ValueSet expansion support; implemented paging when reading concepts from the terminology tables. Switched from Derby to H2. 2019-08-20 18:11:53 -04:00
Ken Stevens 5703b55e88 Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump 2019-08-20 15:08:25 -04:00
Ken Stevens df7469731b turn of sql queries 2019-08-20 15:02:02 -04:00
James Agnew ce44115152
Handle cascading deletes correctly with circular references (#1435)
* Handle cascading deletes correctly with circular references

* A bit of cleanup

* Address review comments

* FIx some javadocs

* Fix an incorrect message
2019-08-20 10:08:34 -04:00
Ken Stevens daf45db2be fixed a test and removed awaitility excludes
mvn install completed successfully
2019-08-20 09:14:21 -04:00
Diederik Muylwyk 70aef7fbbb Incremental work on large ValueSet expansion support; need pageable results while querying TRM_VALUESET_CONCEPT. 2019-08-19 18:43:43 -04:00
Diederik Muylwyk 53364a3af1 Downgraded FIXMEs to TODOs regarding -code for large ValueSets. 2019-08-19 02:50:01 -04:00
Diederik Muylwyk 8590e0ca4d Merging master into working branch.
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
2019-08-19 02:28:30 -04:00
Diederik Muylwyk dfd098c374 Incremental work on large ValueSet expansion support; added use of terminology tables when expanding. 2019-08-19 02:26:12 -04:00
jamesagnew 54657214de FIx issue uploading US Core resources 2019-08-17 18:11:52 -04:00
jamesagnew 89aa37ea6a Add a test 2019-08-17 15:16:11 -04:00
jamesagnew 81adc5c99e Merge master 2019-08-17 14:31:30 -04:00
Ken Stevens 970c421311 allow urls in batch transactions to start with / 2019-08-17 14:31:30 -04:00
jamesagnew f252cda126 Test fixes 2019-08-17 14:15:28 -04:00
James Agnew 74c83f6148 Test fixes 2019-08-17 12:01:04 -04:00
James Agnew 9e8af58e81 Fix reference params via filter 2019-08-16 14:56:36 -04:00
James Agnew 4490c9ca09 Correct the eq operator on the _filter parameter 2019-08-14 14:39:40 -04:00
Sean McIlvenna b37c4b5ae7 Fixing broken unit tests 2019-08-14 14:35:18 -04:00
Sean McIlvenna d92be90789 Changes to subscriptions to include the resource that triggered the subscription in the payload, serialized as JSON or XML depending on the Subscription.channel.payload property's value 2019-08-14 14:35:18 -04:00
jamesagnew e1b43d811f Version bump to 4.1.0-SNAPSHOT 2019-08-14 14:06:06 -04:00
jamesagnew 3f22456b0f Bump version to 4.0.0 2019-08-14 11:06:26 -04:00
James Agnew b4fece0ae9 Add interceptor hook for graphql calls 2019-08-13 14:46:50 -04:00
jamesagnew e2f0f4ed8b License header updates 2019-08-13 05:28:35 -04:00
James Agnew 301a8f8432
Merge #1146 - Filter implementation (#1220)
* Initial commit of _filter keyword implementation.

* - Completed all search parameter types for _filter.
- Implemented handling for _has, _id, _security, language, _profile, _security, and _tag.

* - Changes to support "ne" matching on resource ID for _filter

* Implemented language

* Commit/push before creation of pull request

* Ongoing merge work

* Ongoing merge work

* Merge master in

* Test fix
2019-08-12 11:59:33 -04:00
James Agnew 0c9e5ec1ea
Support GraphQL for R3/4/5 (#1424)
* Work on grpahql enhanbcements

* Add some more chars to the sanitizer function

* Add changelog
2019-08-12 08:24:32 -04:00
jamesagnew 2999a292e6 Get subscriptions working for R5 2019-08-11 18:32:47 -04:00
jamesagnew d316ec1146 Fix NPE 2019-08-11 18:25:02 -04:00
James Agnew 2518d4e0be Add some tests 2019-08-08 15:23:55 -04:00
jamesagnew 4e1bbe681a Bump supported PGSQL driver 2019-08-08 15:12:29 -04:00
James Agnew dd0cb10dbb
validate operation ignores parameter profile (#1417)
* This should be working now - need to check tests

* Add a changelog and some docs

* One more test fix

* Tests should be passing

* Fix compile

* Test fixes

* Ignore outdated DSTU2 validation test
2019-08-07 15:31:59 -04:00
James Agnew b0eb19cf2f A few fixes resulting from the R5 merge 2019-08-06 17:55:51 -04:00
James Agnew 60eab3ad70
Add support for R5 resources (#1416)
* Work so far on R5 support

* Add support for R5

* Docs changes
2019-08-06 17:30:31 -04:00
Diederik Muylwyk 8475aa4cc8 Add TRM_CODESYSTEM_VER.CS_DISPLAY to migration tool. 2019-08-01 14:44:03 -04:00
Diederik Muylwyk d67de13708 Syncing master into working branch. 2019-08-01 13:51:26 -04:00
Diederik Muylwyk 78842164fd Addressing review comments. 2019-08-01 13:37:46 -04:00
jamesagnew 46c8c61932 Restore build - May need to roll back the RDF changes 2019-08-01 10:14:56 -04:00
Diederik Muylwyk ffda92514a Incremental work on large ValueSet expansion support; still need to actually use the terminology tables when expanding. 2019-07-31 16:33:50 -04:00
Diederik Muylwyk 0e2dcce841 Incremental work on large ValueSet expansion support; still need to fix asynchronous tests and actually use the terminology tables when expanding. 2019-07-31 15:52:25 -04:00
James Agnew 3196bc370f Add a default implementation to new terminology service loader method 2019-07-31 10:07:51 -04:00
James Agnew b956b7552e Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-07-30 17:52:47 -04:00
James Agnew 04ce9cfc1a Add support for uploading custom terminology using the
$upload-external-code-system operation
2019-07-30 17:30:18 -04:00
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
James Agnew 2543f27697 Add a test 2019-06-21 15:38:16 -04:00
Diederik Muylwyk 266384b536 Evaluation of PartTypeName in LoincRsnaPlaybookHandler is not case insensitive. 2019-06-21 15:36:51 -04:00
jamesagnew 9e9be00088 License eader updates 2019-06-17 21:59:03 -04:00
James Agnew 6724fd0348
Implement the $subsumes operation (#1344)
* Implement the $subsumes operation

* Fix #976
2019-06-17 17:31:24 -04:00
jvi 8b4ceb8d5f changed json patch framework to slightly more maintained fork 2019-06-17 16:45:17 -04:00
James Agnew b2e99cf035
Add support for conditional patch (#1348)
* Add support for conditional patch

* Add changelog

* Test fix
2019-06-17 16:12:05 -04:00
jamesagnew 087c53286c License header updates 2019-06-14 18:43:55 -04:00
Stig Rohde Døssing b56f59542a Move JettyUtil to new module 2019-06-14 18:34:45 -04:00
Stig Rohde Døssing aab7bb6b64 Issue-1325: Let OS assign random ports to servers during testing, and let tests get the port of the running server once the OS has assigned a port. Delete PortUtil and similar utilities. 2019-06-14 18:34:45 -04:00
Ken Stevens 19dd7ebc2e try excluding stress tests from build 2019-06-13 15:21:03 -04:00
Ken Stevens 2bf680509b
DeleteConflict hook, SearchableHashMapResourceProvider, and in-memory searching (#1341)
* Make IBundle list interface more flexible

* Make matchResourceLinks visible

* Make matchResourceLinks visible

* Pull in-memory matching functionality out of subscription module into dedicated classes in searchparam module

* Added more accessors to version independent resource classes

* improved forcedid matching (needs to be verified by James)
filter out nulls from HashMapProvider.searchAll() (hopefully no tests depend on this)

* add AnyComposition

* cleanup of Any classes

* create searchparam config so people can use that module without using subscriptions

* create searchparam config so people can use that module without using subscriptions

* fix broken test

* added derivedFrom

* renamed daoRegistry.getResourceDaoIfExists to getResourceDaoOrNull
also added method to add a new dao to the registry and retrieve registered types

* TokenParam.equals

* add error check to searchable hashmap resource provider

* added support for R4

* add successor to measure

* delete conflict hook
start with failing test

* test passes.
hook is called.

* added delete conflict hook
all delete conflict tests pass

* added javadoc

* Performance test

* test bad interceptor case

* typo

* rename criteria matcher

* added support for multiple topics

* fix method name

* add effective period

* Temporarily excluding StressTest from build to try to get Travis under time limit

* change log

* review feedback

* review feedback

* review feedback
2019-06-13 13:59:51 -04:00
James Agnew c2aec5c1a9 Respect the _total parameter for all JPA searches 2019-06-09 05:44:49 -04:00
jamesagnew b72f1c4555 Roll back derby upgrade 2019-06-08 09:27:28 -04:00
James Agnew 517b68882c Fix derby dependencies for tests 2019-06-07 11:11:25 -04:00
Ken Stevens 5752a6e2b3 reported issue with proposed fix that breaks tests (#1243)
* reported issue with proposed fix that breaks tests

* Fix spelling

* Merge my changes into this

* Correctly check referential integrity on deletes

* Add one more test
2019-06-04 20:40:20 -04:00
James Agnew be06c2ee19 Correctly index timing events 2019-05-31 16:42:45 -04:00
James Agnew f6c7ff1dbb Modify expunge everything to use small batches of deletes 2019-05-31 11:05:17 -04:00
James Agnew 95af87f658 Test fix 2019-05-30 21:46:05 -04:00
James Agnew f2be9f47a0 Add 4.0.0 version enum 2019-05-30 20:59:23 -04:00
James Agnew 50a8c66bf5 Version bump to 4.0.0-SNAPSHOT 2019-05-30 17:13:03 -04:00
jamesagnew 73aa53be8f Release 3.8.0 2019-05-30 16:50:04 -04:00
James Agnew cb8634f26f
Ja interceptor callback fix (#1308)
* Interceptor callback fix

* Ensure that interceptor methods are called after a transaction
2019-05-14 18:47:11 -04:00
James Agnew d4d3178621 A couple of test fixes 2019-05-11 15:04:44 -04:00
James Agnew 444730373b Fix an NPE in validation 2019-05-10 12:49:34 -04:00
James Agnew 92bd2c7173 Fix regression in validator when validating codesystems explicitly
defined in the JPA database
2019-05-10 12:08:40 -04:00
James Agnew 6b37525f2d
Clean up redundant dependencies (#1306)
* Remove a bunch of unneedd deps

* Test fix

* Disable useless test
2019-05-09 12:51:13 -04:00
James Agnew 702ffd631d Fix #1299 - Return an HTTP 201 when creating a previously deleted
resource
2019-05-06 16:33:23 -04:00
James Agnew 61902da527 Tweak to validator 2019-05-06 10:18:55 -04:00
James Agnew 64f57b9736 Fix broken R4 serrver 2019-05-05 09:12:26 -04:00
James Agnew 7a320729a0 One more test fix 2019-05-04 14:57:18 -04:00
James Agnew 9353ea5b06 Enable websockets on public HAPI server 2019-05-04 10:06:10 -04:00
Ken Stevens b860269eb9 fix broken test 2019-04-29 11:12:08 -04:00
Ken Stevens 10f7eb31eb fixed delete reference error message 2019-04-29 10:20:45 -04:00
jamesagnew ddf12e7c28 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-28 11:17:18 -04:00
jamesagnew c1bf6d0b3c License headers 2019-04-28 10:46:52 -04:00
James Agnew 828df1528f Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-26 11:24:00 -04:00
James Agnew 685adf7754 Revert Jetty upgrade, and improve patch error messages 2019-04-26 11:23:22 -04:00
Ken Stevens 130e879d04
Delete performance (#1286)
* move expunge out

* move to prototype

* turns parameters into fields

* cleanup control flow

* moved transactions outside of loops

* add expungeeverything

* moved daos out

* add expungeThreadCount

* add expungeBatchSize

* added partition runner to run in separate threads

* all done.  just need to consolidate test code.

* Moar tests

* consolidated pointcutlatch into hapi-fhir-jpaserver-model

* final cleanup

* update javadoc

* change log

* failing test

* added delete
also @Transactional

* remove unused parameter

* fix compile

* race condition

(cherry picked from commit e1940d2fb20838859a205f2b96c833b0ce9f05eb)

# Conflicts:
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/PartitionRunnerTest.java

* ja feedback

* ja feedback
2019-04-25 15:38:37 -04:00
jamesagnew abd53c0cbe License header updates 2019-04-24 21:20:11 -04:00
James Agnew c8c81c2ebc FIx invalid patch syntax 2019-04-24 15:00:03 -04:00
James Agnew da962b8c10 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-24 14:33:28 -04:00
James Agnew 738c2c1797
Interceptor framework refactoring (#1287)
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
James Agnew f2e382a132 Swap JSON Patch provider 2019-04-24 14:10:21 -04:00
Ken Stevens a57e50317d
Websocket cleanup (#1275)
* fix bug in websocket subscription (It wasn't destroying the channel when there are no subscribers)

* add support for removing channel.  Also synchronize removal (there was a race condition between sync and queue)

* keep deprecated method for backwards compatibility

* make websocket endpoint configurable

* make websocket context path configurable

* make websocket context path configurable

* trying mvn clean test instead of mvn clean install to see if the build goes faster

* that didn't work at all.  reverting.

* change log
2019-04-17 15:03:35 -04:00
jamesagnew 08a9844066 Work on #1280 2019-04-17 09:10:17 -04:00
James Agnew 311246e5f0
Merge pull request #1255 from jamesagnew/addFetchValueSet
added fetchValueSet to IValidationSupport and made it public
2019-04-15 17:03:56 -04:00