259426b0dd
Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache
...
# Conflicts:
# hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
# src/changes/changes.xml
2019-08-28 10:37:17 -04:00
9ef0519b4c
validate-code operation has been optimized for large ValueSets; submitting pull request.
2019-08-27 21:15:12 -04:00
6b0084fc3b
Merge pull request #1448 from jamesagnew/1447-loinc-filenames-should-be-configurable
...
Resolve "LOINC filenames should be configurable."
2019-08-27 13:47:40 -04:00
94c7fc49fd
Making LOINC filenames configurable; fix implicit ValueSet URL for loinc-all.
2019-08-27 13:46:42 -04:00
1adfda44d9
Making LOINC filenames configurable; ready for review.
2019-08-27 11:19:01 -04:00
70d0a8aa8f
Get patch working ( #1449 )
2019-08-27 05:42:15 -04:00
f4789247b2
Making LOINC filenames configurable; fix IEEE medical device code property key.
2019-08-26 18:46:57 -04:00
0765254024
Making LOINC filenames configurable; initial commit.
2019-08-26 18:32:21 -04:00
0ee15874ca
loinc-all ValueSet is now created automatically when loading LOINC terminology.
2019-08-26 16:42:37 -04:00
073d2a45a4
Multiaxial hierarchy support is implemented; we not populated parent and child properties.
2019-08-26 14:26:38 -04:00
17f58a61c3
Revert "add accessor to search hash"
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This reverts commit 2dc70c92
2019-08-24 14:13:06 -04:00
2dc70c92f1
add accessor to search hash
2019-08-24 14:10:17 -04:00
b41926307c
Completed work on large ValueSet expansion support; ready for review.
2019-08-23 17:40:45 -04:00
10958a8e4d
I think this might work now..
2019-08-23 12:22:27 -04:00
c564052b15
One more test fix
2019-08-23 11:46:56 -04:00
890555a77d
Incremental work on large ValueSet expansion support; transaction boundaries need to be broken up.
2019-08-23 11:46:32 -04:00
c346ba92c8
Revert accidental commit
2019-08-23 11:17:02 -04:00
abc894ce90
A few refactors based on ken's suggestions
2019-08-23 10:57:58 -04:00
6fa27934a8
Tests all seem to be working
2019-08-23 10:14:13 -04:00
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
72dd6b2922
Incremental work on large ValueSet expansion support; fixed broken deletion for TermValueSetConceptDesignation.
2019-08-22 14:00:08 -04:00
4afa55ea26
Initial commit - Not yet compiling
2019-08-22 08:49:34 -04:00
37c1ba44fe
Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump
2019-08-21 15:04:16 -04:00
9428430822
Add support for Resource.meta.source ( #1438 )
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* 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
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
5703b55e88
Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump
2019-08-20 15:08:25 -04:00
df7469731b
turn of sql queries
2019-08-20 15:02:02 -04:00
ce44115152
Handle cascading deletes correctly with circular references ( #1435 )
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* 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
daf45db2be
fixed a test and removed awaitility excludes
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mvn install completed successfully
2019-08-20 09:14:21 -04:00
70aef7fbbb
Incremental work on large ValueSet expansion support; need pageable results while querying TRM_VALUESET_CONCEPT.
2019-08-19 18:43:43 -04:00
53364a3af1
Downgraded FIXMEs to TODOs regarding -code for large ValueSets.
2019-08-19 02:50:01 -04:00
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
dfd098c374
Incremental work on large ValueSet expansion support; added use of terminology tables when expanding.
2019-08-19 02:26:12 -04:00
54657214de
FIx issue uploading US Core resources
2019-08-17 18:11:52 -04:00
89aa37ea6a
Add a test
2019-08-17 15:16:11 -04:00
81adc5c99e
Merge master
2019-08-17 14:31:30 -04:00
970c421311
allow urls in batch transactions to start with /
2019-08-17 14:31:30 -04:00
f252cda126
Test fixes
2019-08-17 14:15:28 -04:00
74c83f6148
Test fixes
2019-08-17 12:01:04 -04:00
9e8af58e81
Fix reference params via filter
2019-08-16 14:56:36 -04:00
4490c9ca09
Correct the eq operator on the _filter parameter
2019-08-14 14:39:40 -04:00
b37c4b5ae7
Fixing broken unit tests
2019-08-14 14:35:18 -04:00
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
e1b43d811f
Version bump to 4.1.0-SNAPSHOT
2019-08-14 14:06:06 -04:00
3f22456b0f
Bump version to 4.0.0
2019-08-14 11:06:26 -04:00
b4fece0ae9
Add interceptor hook for graphql calls
2019-08-13 14:46:50 -04:00
e2f0f4ed8b
License header updates
2019-08-13 05:28:35 -04:00
301a8f8432
Merge #1146 - Filter implementation ( #1220 )
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* 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
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
2999a292e6
Get subscriptions working for R5
2019-08-11 18:32:47 -04:00
d316ec1146
Fix NPE
2019-08-11 18:25:02 -04:00
2518d4e0be
Add some tests
2019-08-08 15:23:55 -04:00
4e1bbe681a
Bump supported PGSQL driver
2019-08-08 15:12:29 -04:00
dd0cb10dbb
validate operation ignores parameter profile ( #1417 )
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* 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
b0eb19cf2f
A few fixes resulting from the R5 merge
2019-08-06 17:55:51 -04:00
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
8475aa4cc8
Add TRM_CODESYSTEM_VER.CS_DISPLAY to migration tool.
2019-08-01 14:44:03 -04:00
d67de13708
Syncing master into working branch.
2019-08-01 13:51:26 -04:00
78842164fd
Addressing review comments.
2019-08-01 13:37:46 -04:00
46c8c61932
Restore build - May need to roll back the RDF changes
2019-08-01 10:14:56 -04:00
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
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
3196bc370f
Add a default implementation to new terminology service loader method
2019-07-31 10:07:51 -04:00
b956b7552e
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-07-30 17:52:47 -04:00
04ce9cfc1a
Add support for uploading custom terminology using the
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$upload-external-code-system operation
2019-07-30 17:30:18 -04:00
d1cba9f928
Syncing master into working branch.
2019-07-29 19:39:29 -04:00
cf5201c67b
Add a constructor
2019-07-29 19:31:47 -04:00
a8489f4331
Added TRM_VALUESET.EXPANSION_STATUS column, index, fields to entity, and migration tasks.
2019-07-29 19:30:46 -04:00
a3cbdf0956
Make terminologyuploaderprovider not abstract
2019-07-29 19:02:51 -04:00
b030d1af31
Test fixes
2019-07-29 18:17:40 -04:00
a4ca5374ec
Add terminology delta operations ( #1401 )
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* 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
d03fc0f61d
Add null check for shortName before adding designation. ( #1396 )
2019-07-25 11:06:02 -04:00
a7817b07ca
Pre PR cleanup
2019-07-24 22:00:34 -04:00
a20b738161
Pre PR cleanup
2019-07-24 22:00:26 -04:00
84f5c7d467
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-24 21:54:05 -04:00
e05387da02
Recover from failed merge again. This time with feeling!
2019-07-24 13:46:20 -04:00
ddb8e385bf
Test fix
2019-07-24 13:24:48 -04:00
b78cd1e62e
Merge branch 'add-pid-to-created-resource'
2019-07-24 13:19:38 -04:00
e8cf2738f0
Handle oversized payload request
2019-07-24 13:18:30 -04:00
b9dbd69e5d
Fix limiting on size
2019-07-24 13:11:05 -04:00
37411a6ae2
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-24 10:41:11 -04:00
6b599c29e5
Merge branch 'add-pid-to-created-resource'
2019-07-23 17:36:15 -04:00
bff39e4139
Try to deal with an intermittent failure
2019-07-23 15:58:14 -04:00
9094323c43
Add a test
2019-07-23 14:47:27 -04:00
b1e409519d
Add a test
2019-07-23 14:47:27 -04:00
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
60ea922e8d
Add license headers
2019-07-23 05:38:10 -04:00
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
7ba3ceec90
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-19 10:54:56 -04:00
458cfcfa12
Fix intermittent test failure
2019-07-19 10:46:49 -04:00
f53746cd63
One more set of migrator tweaks to account for latest changes
2019-07-19 10:10:00 -04:00
e634aa6d10
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-18 22:06:10 -04:00
5bf4fa22e7
Allow patching in tranactions
2019-07-18 16:41:07 -04:00
a7fa79331a
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-18 13:14:54 -04:00
87ab796309
Updates to validating interceptor
2019-07-18 12:57:30 -04:00
ffa008b2dd
Fixing a build error
2019-07-18 10:59:11 -04:00
72aa4932d6
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-18 10:12:15 -04:00
ee7cff9445
Rename a few columns to not conflict with res´rved words
2019-07-18 05:47:32 -04:00
7488047686
Add license headers
2019-07-17 18:53:23 -04:00
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
c73aebe0a0
IResource and IAnyResource are mutually exclusive...
2019-07-17 17:59:49 -04:00
465b4daa03
Changed IAnyResource to IResource per feedback
2019-07-17 17:59:49 -04:00
1d4dc5b3c5
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_UPDATED hooks are called
2019-07-17 17:59:49 -04:00
e27685e811
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_CREATED hooks are called
2019-07-17 17:59:49 -04:00
7bc8517fc6
Merge branch 'add-pid-to-created-resource' into expunge-resource-hook
2019-07-17 14:26:00 -04:00
6960f1db1c
IResource and IAnyResource are mutually exclusive...
2019-07-17 14:25:10 -04:00
a5da696823
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-17 13:28:29 -04:00
d21304e771
cleanup
2019-07-17 13:28:17 -04:00
fe21dba4a6
Added Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE.
...
Also added a couple of tests.
2019-07-17 13:26:50 -04:00
76384abefb
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-07-17 10:57:43 -04:00
160b221f5f
Changed IAnyResource to IResource per feedback
2019-07-17 10:26:16 -04:00
79ce4a30cc
Merge remote-tracking branch 'remotes/origin/master' into add-pid-to-created-resource
2019-07-16 20:46:31 -04:00
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
634718c503
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_UPDATED hooks are called
2019-07-16 16:36:05 -04:00
fe7d38d0b5
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_CREATED hooks are called
2019-07-16 15:33:51 -04:00
f8444b90c8
Test tweak
2019-07-14 18:11:37 -04:00
7831e8a0ed
Add support for $snapshot generation and validation based on snapshots
2019-07-14 16:15:56 -04:00
120b93f204
Use HL7 FHIR Core Structures ( #1382 )
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* 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
534c71c1d5
Higher parallel count for JPA tests
2019-07-13 18:24:31 -04:00
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
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
a5a9950e77
License header updates
2019-07-12 08:52:47 -04:00
afd2b35ff6
Fix an intermittent test failure
2019-07-12 06:32:18 -04:00
1db019b6df
Test fix and try to get Travis building again
2019-07-11 20:20:27 -04:00
62e1b7e9ea
Fixing minor overlooked change from recent pull request.
2019-07-11 17:07:26 -04:00
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
7aaa75c255
fixed pointcut
2019-07-10 10:09:43 -04:00
5e05703c1a
Add expunge-everything hook. Also add RequestDetails to all expunge operations
2019-07-09 10:58:57 -04:00
9fcbdb0cdc
License header updates
2019-07-07 14:41:57 -04:00
6c221efaf6
More test fixes
2019-07-07 14:09:55 -04:00
d00304d706
More test fixes
2019-07-07 13:35:39 -04:00
34f7d4ddbd
Refactor ServerConformanceProvider so that it no longer keeps any state
2019-07-07 12:57:31 -04:00
4bd60a8447
Roll back one dependency
2019-07-07 11:02:08 -04:00
1c7c83cd8e
Add an isEmpty() method to IBundleProvider
2019-07-05 16:16:39 -04:00
dff2fdd3cf
GET RID OF TRAILING LICENSE HEADER SPACES ONCE AND FOR ALL
...
YESSSSSSSSSSSSS
2019-07-05 11:19:51 -04:00
4a0bc27602
Test fix
2019-07-05 09:37:48 -04:00
2a473d1825
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-07-05 09:03:23 -04:00
2a6436af23
Rename columns in code mapping
2019-07-05 09:03:03 -04:00
aff88d3ebb
License header updates
2019-07-05 07:27:18 -04:00
6e20b53979
Fix a crash in R4 validation
2019-07-04 16:27:04 -04:00
4f7d4aa8d2
Two test fixes
2019-07-04 09:54:26 -04:00
886f3f442b
Moving testloggingutil into test utilities
2019-07-04 09:00:30 -04:00
f1848fb1ad
Include version ID in response for deleted resource
2019-07-03 14:44:12 -04:00
56aaef641c
Add request ID
2019-07-02 21:32:28 -04:00
1faf7785c4
Dont filter constraints from the event broadcast - this was not needed
...
after all
2019-07-02 09:21:15 -04:00
7b7136e3ab
Ensure test coverage of JPA entities
2019-07-02 08:37:48 -04:00
491776a7b8
Fixes to cascading delete
2019-07-02 05:41:38 -04:00
742389642d
Add tests for delete conflicts and authorizationinterceptor
2019-07-01 10:49:38 -04:00
ccf491b3ae
Add parent pom to BOM
2019-06-29 13:50:43 -04:00
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
5c55133275
quick hack to pass unit test (handle files located in subdirectories of zipfile)
2019-06-28 15:11:16 -04:00
557c9b66c2
add TerminologyLoaderSvcImgthlaTest
2019-06-28 15:11:16 -04:00
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
1f5cbc36b3
add stub for HLA nomenclature terminology upload
2019-06-28 15:11:16 -04:00
5910131319
License header updates
2019-06-27 18:23:45 -04:00
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
2bfbea4e6b
Remove duplicate test class
2019-06-26 09:24:36 -04:00
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
e76b1dacb3
License header updates
2019-06-22 18:31:16 -04:00
8bb010bb18
Test fixes
2019-06-22 17:42:02 -04:00
3ba194acbe
Reject subscriptions in JPA server if status field is not set
2019-06-22 17:03:22 -04:00
0fbde2a4e5
Fix #1352 - Don't fail to create observation with a value type of
...
SampledData
2019-06-22 16:43:25 -04:00
4ad1808da3
Propagate RequestDetails to everything in JPA server ( #1358 )
2019-06-22 15:18:06 -05:00
58e6b7f6aa
Fix #1011 - Was resolved in #1355
2019-06-22 16:03:35 -04:00
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
2543f27697
Add a test
2019-06-21 15:38:16 -04:00
266384b536
Evaluation of PartTypeName in LoincRsnaPlaybookHandler is not case insensitive.
2019-06-21 15:36:51 -04:00
9e9be00088
License eader updates
2019-06-17 21:59:03 -04:00
6724fd0348
Implement the $subsumes operation ( #1344 )
...
* Implement the $subsumes operation
* Fix #976
2019-06-17 17:31:24 -04:00
8b4ceb8d5f
changed json patch framework to slightly more maintained fork
2019-06-17 16:45:17 -04:00
b2e99cf035
Add support for conditional patch ( #1348 )
...
* Add support for conditional patch
* Add changelog
* Test fix
2019-06-17 16:12:05 -04:00
087c53286c
License header updates
2019-06-14 18:43:55 -04:00
b56f59542a
Move JettyUtil to new module
2019-06-14 18:34:45 -04:00
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
19dd7ebc2e
try excluding stress tests from build
2019-06-13 15:21:03 -04:00
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
c2aec5c1a9
Respect the _total parameter for all JPA searches
2019-06-09 05:44:49 -04:00
b72f1c4555
Roll back derby upgrade
2019-06-08 09:27:28 -04:00
517b68882c
Fix derby dependencies for tests
2019-06-07 11:11:25 -04:00
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
be06c2ee19
Correctly index timing events
2019-05-31 16:42:45 -04:00
f6c7ff1dbb
Modify expunge everything to use small batches of deletes
2019-05-31 11:05:17 -04:00
95af87f658
Test fix
2019-05-30 21:46:05 -04:00
f2be9f47a0
Add 4.0.0 version enum
2019-05-30 20:59:23 -04:00
50a8c66bf5
Version bump to 4.0.0-SNAPSHOT
2019-05-30 17:13:03 -04:00
73aa53be8f
Release 3.8.0
2019-05-30 16:50:04 -04:00
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
d4d3178621
A couple of test fixes
2019-05-11 15:04:44 -04:00
444730373b
Fix an NPE in validation
2019-05-10 12:49:34 -04:00
92bd2c7173
Fix regression in validator when validating codesystems explicitly
...
defined in the JPA database
2019-05-10 12:08:40 -04:00
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
702ffd631d
Fix #1299 - Return an HTTP 201 when creating a previously deleted
...
resource
2019-05-06 16:33:23 -04:00
61902da527
Tweak to validator
2019-05-06 10:18:55 -04:00
64f57b9736
Fix broken R4 serrver
2019-05-05 09:12:26 -04:00
7a320729a0
One more test fix
2019-05-04 14:57:18 -04:00
9353ea5b06
Enable websockets on public HAPI server
2019-05-04 10:06:10 -04:00
b860269eb9
fix broken test
2019-04-29 11:12:08 -04:00
10f7eb31eb
fixed delete reference error message
2019-04-29 10:20:45 -04:00
ddf12e7c28
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-28 11:17:18 -04:00
c1bf6d0b3c
License headers
2019-04-28 10:46:52 -04:00
828df1528f
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-26 11:24:00 -04:00
685adf7754
Revert Jetty upgrade, and improve patch error messages
2019-04-26 11:23:22 -04:00
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
abd53c0cbe
License header updates
2019-04-24 21:20:11 -04:00
c8c81c2ebc
FIx invalid patch syntax
2019-04-24 15:00:03 -04:00
da962b8c10
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-24 14:33:28 -04:00
738c2c1797
Interceptor framework refactoring ( #1287 )
...
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
f2e382a132
Swap JSON Patch provider
2019-04-24 14:10:21 -04:00
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
08a9844066
Work on #1280
2019-04-17 09:10:17 -04:00
311246e5f0
Merge pull request #1255 from jamesagnew/addFetchValueSet
...
added fetchValueSet to IValidationSupport and made it public
2019-04-15 17:03:56 -04:00
1e4a497181
Add some tests
2019-04-15 14:44:25 -04:00
a9cfce3615
Header updates
2019-04-15 12:31:11 -04:00
f7ad0bc0d8
Fix a test regression
2019-04-15 11:34:13 -04:00
0848fdf1eb
Fix broken test
2019-04-15 10:29:55 -04:00
c8f2e4bbc9
Return HTTP 400 for missing body on POST and PUT
2019-04-14 12:32:09 -04:00
380644d19d
Add a bit of logging for search parameters when they can't be found
2019-04-14 12:32:09 -04:00
bb98ded1fa
Websocket improvements ( #1272 )
...
* subscription loader now only pulls active subscriptions
only allow websocket connections to subscriptions of type websocket
* Added a "flag for deletion" to ActiveSubscription in the SubscriptionRegistry to handle the race condition of a scheduled sync overlapping with a subscription creation. We could have used a package-scoped semaphore or a pre-remove FHIR read, but this seemed like the safest, simplest and most performant way to handle it.
* ActiveSubscriptionCacheTest
* WebsocketConnectionValidatorTest
* fix compile error in jpa example
2019-04-12 08:36:49 -04:00
ca8b6acdf9
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-07 07:52:40 -04:00
884b80c1d7
Improve ability to select active resources
2019-04-07 07:52:21 -04:00
706af5d579
Don't update modified time when performing NOOP update in JPA
2019-04-05 14:36:18 -04:00
5299479143
fix broken test
2019-04-04 10:26:09 -04:00
859bc7d71b
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-03 20:15:19 -04:00
54e3c50ad7
FIx a build failure
2019-04-03 20:15:07 -04:00
1d5f648070
fixed second expunge bug reported by FMCNA
2019-04-03 13:32:10 -04:00
de4cc89568
bug fixed
2019-04-03 12:20:49 -04:00
28ea97ee9a
reproduced failure reported by FMCNA
2019-04-03 11:42:21 -04:00
767a84bddb
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-02 10:56:43 -04:00
8065f0f5fc
Revert one accidental change
2019-04-02 10:56:26 -04:00
8b5143f436
License header updates
2019-04-02 10:44:41 -04:00
588082aee2
Fix broken test
2019-04-02 10:00:56 -04:00
90d163a4e9
Merge branch 'ja_interceptor_jpa_queries' of github.com:jamesagnew/hapi-fhir into ja_interceptor_jpa_queries
2019-04-02 09:33:22 -04:00
7359b77d99
Address review comments
2019-04-02 09:33:01 -04:00
835b89f449
Build fixes
2019-04-01 18:55:55 -04:00
3eeca4a8fd
Merge branch 'master' into ja_interceptor_jpa_queries
2019-04-01 09:59:03 -04:00
1aeb54e94e
added all fetchValueSet Implementations
2019-03-30 21:02:24 +01:00
8791ed5793
Test tweaks
2019-03-29 17:13:41 -04:00
b1d41a8211
named interceptor registries
2019-03-29 14:29:36 -04:00
cf7cd40336
Make sure we properly scope reference queries on external URLs
2019-03-27 13:10:24 -04:00
e85bec2858
Ja inline references ( #1252 )
...
* Use a single IN clause for OR reference searches
* Add changelog
* One more attempt at getting the free port util to actually work... sigh
* One more tweak to free ports
* Bundle fix
2019-03-26 10:42:42 +01:00
9a54d7086e
Fix a couple of bugs ( #1251 )
...
* might keep this
* might keep this
* undoing start in interface
* fixed bug that only supported resources with ResourceType/id prefixes
* added standalone subscription support for Dstu2. untested.
* failing test
* fixed cannonicalsubscription.equals for email
* final cleanup
2019-03-26 10:39:40 +01:00
87c0b3778b
More work on threadlocal interceptors
2019-03-22 09:54:02 -04:00
c701de2861
Create a performance interceptor framework for HAPI FHIR
2019-03-22 01:06:03 +01:00
d1667487c2
Clean up unique composite search params
2019-03-21 21:57:38 +01:00
8d49b4e6d2
Add a test (currently ignored)
2019-03-21 15:59:59 +01:00
037ed27497
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-03-17 14:09:37 -04:00
3e57fdb491
Improvements to PortUtil to avoid reusing ports
2019-03-17 14:09:21 -04:00
08c7afb804
Reduce logging in JPA server
2019-03-14 17:42:13 -04:00
6ff92abecc
License header
2019-03-14 13:32:32 -04:00
e15afbc4f0
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-03-14 13:32:03 -04:00
a8c76450e5
Re-enable contains searches on the public HAPI FHIR server and improve
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message formatting in HapiLocalizer
2019-03-14 13:19:26 -04:00
a1046f7729
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-03-12 17:46:03 -04:00
7b1950aeed
License headers
2019-03-12 17:45:51 -04:00
ed4da7c414
Add setting to disable resource type target validation in JPA
2019-03-12 17:45:19 -04:00
6597a928d5
Fix broken test
2019-03-12 15:45:53 -04:00
00a8f8c759
Fix broken build
2019-03-12 13:13:13 -04:00
f934f76c96
Several JPA search fixes ( #1231 )
...
* Search fixes
* Add some tests
* CHangelog
* Some cleanup of the query tracker
* FIx XML issue in changelog
* Test fixes
* SOme test fixes
* Address review comments
* Fix test breakage
2019-03-11 15:49:34 -04:00
dcfacfea49
Has param no in ( #1232 )
2019-03-10 20:50:24 -04:00
5dccf93506
Fix broken test
2019-03-06 17:15:30 -05:00
f8b8f2d1b0
Move process-message to the correct level
2019-03-06 16:12:43 -05:00
a2d4c93922
Subscription matcher transactions ( #1229 )
...
* fix bug in ResourceIndexSearchParamQuantity
Move transaction boundary around SubscriptionMatcherInterceptor so it can be overridden in subclass
Lots of CRLF changes from a mvn -P DIST
* FIXME
2019-03-06 16:12:04 -05:00
fd401165a9
Fix an occassional failure in the stress test
2019-03-06 09:32:37 -05:00
9bc0f6784d
Search paging timeout with 1500 < n < 2000 results ( #1221 )
...
* Avoid paging links when offset is artificially set very high
* Ongoing fixes
* Adding logging and clean up transaction processing
* Add changelog
* More work on queries
* Keep working on getting tests passing
* More test fixes
* More work on tests
* More test works
* One more test attempt
* Ongoing fixes
* One more change
* FIxes to search algorithm
* Add changelog
* Clean up for review
* Fixed NPE in token matcher when system is not null and value is null
* test opposite (null system not null value)
* added null protection to all matchers
* Address review comments
* Address broken test
* Trying to resolve DB ordering issues
2019-03-06 05:45:05 -05:00
7896887f67
Updates to transaction processing
2019-02-28 12:23:48 -05:00
48c10bddc5
Narrative Generator refactoring ( #1219 )
...
* Starting work on this
* Working on narrative templates
* Work on new narrative system
* Account for some failing tests due to refactoring of narrative mode
* Another test fix
* More test fixes
* One more test fix
* Work on searches
* Address review comments
2019-02-27 14:59:57 -05:00
94f9ffa977
Avoid paging links when offset is artificially set very high
2019-02-25 20:44:22 -05:00
fb06664f70
Clean up paging query
2019-02-25 19:05:19 -05:00
820a3d2296
Collapse conditional UPDATES as well in JPA transactions
2019-02-22 13:49:38 -05:00
43c07077be
Automatically remove duplicate conditional creates in JPA
2019-02-22 12:57:07 -05:00
89b08cd627
Improve SQL IN(..) queries ( #1214 )
...
* First attempt, probably has compile issues
* Fix qualified searches
* Another test fix
* More test fixes
* Add changelog
* Two more fixes
* Revert SQL logging
2019-02-20 16:38:51 -05:00
28b4b812ac
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-02-20 15:07:08 -05:00
e7b7ba1a6d
Add caching test
2019-02-20 11:18:02 -05:00
01568ab0b5
Fix test race condition.
2019-02-19 21:14:11 -05:00
3af0bc7206
changes needed to support different number of consumers in matching vs delivery
2019-02-17 15:23:01 -05:00
c6fcb4fcbf
Allow canonical subscription to hold multiple extensions with the same
...
URL
2019-02-16 15:28:39 -05:00
1311ded7de
Fix compile issue
2019-02-15 14:55:25 -05:00
c0970ed46d
Fix typo in test
2019-02-15 14:30:38 -05:00
a35f30b18e
Merge pull request #1208 from jamesagnew/reuse-subscription-channels
...
Reuse subscription channels
2019-02-15 13:42:54 -05:00
485335e975
Allow terminology service to work without having Lucene enabled for
...
simple ValueSet expansions
2019-02-14 20:47:28 -05:00
ffc5966aa3
Merge branch 'master' into reuse-subscription-channels
...
# Conflicts:
# src/changes/changes.xml
2019-02-14 19:42:00 -05:00
10c348d44f
Tweak to elements parametr support
2019-02-14 19:30:10 -05:00
508e15956e
added a couple of subscription tests and un@Ignored another
2019-02-14 15:30:25 -05:00
7b3fedc642
sonar
2019-02-13 20:41:11 -05:00
f34926bb18
fixed a bug matching long ids in searchparams ( #1203 )
...
* fixed a bug matching long ids in searchparams
2019-02-09 13:45:51 -05:00
a5e10740c0
Merge pull request #1194 from jamesagnew/ja_more_subscription_logger
...
More subscription logger work
2019-02-09 11:45:25 -05:00
f40614a1aa
fixed bug in in-memory matching for reference id when searchparam has two components
2019-02-08 16:37:08 -05:00
52c62884fb
Merge branch 'master' into reuse-subscription-channels
2019-02-08 10:39:00 -05:00
ce840ecb6e
Fix broken test
2019-02-07 17:48:08 -05:00
810f1ad969
Improvements to elements parameter as well as adding attributes to
...
RequestDetails
2019-02-07 16:45:59 -05:00
b3e80f8da7
Merge branch 'master' into reuse-subscription-channels
2019-02-07 10:10:10 -05:00
4592184c34
fixed typo in logs
2019-02-07 10:06:41 -05:00
0f8c8d18e2
Bump version to 3.8.0-SNAPSHOT
2019-02-06 20:02:28 -05:00
207015c3af
Version bump to 3.7.0
2019-02-05 21:36:38 -05:00
e3dd296db7
Fix flaky test hopefully?
2019-02-05 15:36:21 -05:00
87a6c24bde
More subscription logger work
2019-02-04 13:49:10 -05:00
e401ec86e4
Enhanced elements ( #1192 )
...
Squashed merge: Add elements exclude mode
* Start working on elements enhancement
* Work on elements projection
* Work on elements filter
* Feature is now working
* Just some cleanup
* Address compile issues
2019-02-03 16:41:33 -05:00
447c394cac
Ja subscription debug logger ( #1190 )
...
Squashed commit adding subscription debug logger
* Work on subscription debug logger
* Add subscription logging interceptor
* Remove unneeded variables
* A bit of cleanup
* Tweak the output logs a bit
* Address review comments
2019-02-03 16:33:54 -05:00
9280cde491
Subscription only registers active ( #1189 )
...
* Fixed a bug in standalone subscription subscriber: It was adding REQUESTED subscriptions to the active subscription registry. (Only ACTIVE subscriptions should be added.)
2019-02-01 10:14:46 -05:00
5f29e4fbf3
Fix #1174 - Prevent serialization exception
2019-01-30 05:49:45 -05:00
5d540d9208
Query optimization in JPA
2019-01-27 20:03:48 -05:00
Ken Stevens
Diederik Muylwyk
James Agnew
Sean McIlvenna
Joel Schneider
jvi
Stig Rohde Døssing
Ken Stevens
Ken Stevens
patrick-werner