f19100cbb3
final cleanup
2019-10-24 20:29:45 -04:00
4a2ed62357
review feedback
2019-10-24 20:25:16 -04:00
08472c1e3f
ready to merge
2019-10-24 17:56:15 -04:00
4fa849a3e5
pre-review cleanup
2019-10-24 16:43:47 -04:00
43f17534bb
commiting with FIXMEs so James can review
2019-10-24 16:40:53 -04:00
df4376606d
Validation cleanup ( #1561 )
...
* Validation cleanup
* Test fix
* Fix build
* Test tweaks
2019-10-24 13:09:18 -05:00
385a885abf
Add ability for resource source to be specified by header
2019-10-24 08:32:52 -04:00
0d3f7d4a03
Correctly handle searching by source in JPA server
2019-10-23 06:58:16 -04:00
19247ffb46
Allow updating externalized binary ( #1556 )
...
* Add non working test
* Add a test
* FIx test
* Allow updating existing externalized binary data
* Add test
* Remove unneeded test
* Fix test
2019-10-22 18:10:03 -04:00
371bf2e5cf
Disable unit test SQL logging
2019-10-22 17:27:36 -04:00
9b94e4e26d
Allow uploading term deltas using CS resource ( #1555 )
...
* Work on accepting codesystem reources for delta operations
* Ongoing work on term uploader
* Restore the ability to use CodeSystem resources for the delta
* Add tests
* Fix NPE
* Test fixes
2019-10-22 17:11:39 -04:00
464c6c5b45
Upgrade dependencies and addess Semmle issues ( #1554 )
...
* Version bumps
* FIx build issues
* Address a few Semmle issues
* Work on tests
* Some test fixes
* Test fix
* Fix deletions
* Test fix
* Fix intermittent test failure
* One more dependency bump
* Add some test logging
* Remove bad import
* Add some tests
* Test updates
2019-10-22 17:10:58 -04:00
d0704269d7
ready for rereview
2019-10-22 10:13:49 -04:00
427f7397da
ready for rereview
2019-10-22 10:13:49 -04:00
0f40b2c48f
npe check for binary storage interceptor
2019-10-22 10:13:49 -04:00
73961072a6
Handle invalid chains on custom search params ( #1553 )
...
* Handle invalid chains on custom search params
* Add some more tests
* One more test fix
2019-10-21 21:21:33 -04:00
0af79b84d9
Use webjars instead of including JS deps ( #1551 )
...
* Use webjars instead of including JS deps
* Add changelog
2019-10-21 07:22:55 -04:00
bfbc73caaf
Auto externalize binary contents ( #1550 )
...
* Auto externaliZe binary attachments
* Work on externalization
* Auto externalize binary content
* Work on tests
* Fix alert
2019-10-19 09:01:00 -04:00
985cd49892
Test fixes
2019-10-18 16:36:05 -04:00
0cddb54476
Remove accidental commit
2019-10-18 15:52:03 -04:00
c455a46160
Add missing class
2019-10-18 15:51:20 -04:00
a71d969ba1
Add line numbers to validation failures
2019-10-18 14:10:47 -04:00
50af4bfb19
Merge latest changes
2019-10-18 13:36:26 -04:00
13b80a294a
Test fix
2019-10-18 07:13:11 -04:00
0971998f57
Fix #848 - Pass raw JSON to the validator
2019-10-17 11:28:48 -04:00
12a74e6cbc
Fix term uploads and validate against valueset recalculation ( #1540 )
...
* Start refactoring terminology delta operations
* Work on delta operations
* Work on concept saving
* Split term services into smaller services
* Work on term delta operations
* Work on term svcs
* Work on term operations
* More work on delta uploader
* Add a test
* Wrk on term service
* Fix compile error
* Some refactoring
* Test fix
* Test fix
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Work on delta
* Work on tests#
* Test fixes
* Improve resequencing logic
* Build test
* More testing
* More build testing
* More work on tests
* CHange test logging
* Fix term service PID issue
* Update src/changes/changes.xml
Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>
* Address review comment
* Some cleanup
* Test fix
* Fix some tests
* Work on upload command
* Test fixes
* Work on validation fixes
* Work on validation against pre-expansion
* Work on direct validation
* A bit of cleanup
* Add some javadoc
* Force another build
* Test fixes
* Fix tests
* Fix tests
2019-10-15 21:31:29 -04:00
8b2ab51bc6
Handle canonical questionnaire refs in validator ( #1544 )
...
* Handle canonical questionnaire refs in validator
* FIx changelog
* Fix canonical reference
* Build tweak
* Change to trigger a build
2019-10-15 20:27:53 -04:00
839f935401
remove unnecessary index
2019-10-15 19:07:37 -04:00
fdcf5f5d73
Add a test
2019-10-15 18:16:22 -04:00
bf476b9c32
Handle null returns from search cache methods
2019-10-15 16:25:21 -05:00
9c23959b38
Licene header updates
2019-10-15 15:08:13 -04:00
9a050461a8
Make cache timeout configurable
2019-10-15 09:34:48 -04:00
2725797610
Implement Terminology Delta Operations ( #1536 )
...
* Start refactoring terminology delta operations
* Work on delta operations
* Work on concept saving
* Split term services into smaller services
* Work on term delta operations
* Work on term svcs
* Work on term operations
* More work on delta uploader
* Add a test
* Wrk on term service
* Fix compile error
* Some refactoring
* Test fix
* Test fix
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Work on delta
* Work on tests#
* Test fixes
* Improve resequencing logic
* Build test
* More testing
* More build testing
* More work on tests
* CHange test logging
* Fix term service PID issue
* Update src/changes/changes.xml
Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>
* Address review comment
* Some cleanup
* Test fix
* Fix some tests
* Test fixes
2019-10-14 19:14:41 -04:00
e656863a73
Correct bugs reported by LGTM ( #1533 )
...
* Correct bugs reported by LGTM
* Add some tests
* A few more updates
* YAML update
* Test fixes
* One more test fix
* Test fix
2019-10-09 19:26:57 -05:00
861ed36f00
Allow patches to be authorized for DSTU3 transactions ( #1529 )
...
* Allow patches to be authorized for DSTU3 transactions
* Add changelog
2019-10-08 14:29:27 -05:00
150c865f68
License header updates
2019-10-03 21:20:08 -04:00
069db501ee
Fix _has parameter ( #1525 )
...
* Fix _has parameter
* Bug fixes
* Add a comment
* Test fixes
2019-10-03 21:19:31 -04:00
836fac9a30
Ensure that JPA PRESHOW interceptor broadcasts don't include expunged
...
resources
2019-10-03 15:49:03 -04:00
38ad11be64
Merge pull request #1513 from jamesagnew/ks-subscription-delivery-queue-configurable-name
...
subscription delivery queue configurable name
2019-10-03 15:19:12 -04:00
1b5528a998
Fix compile error
2019-10-03 15:06:14 -04:00
a3b9db1363
Clean up a few unused methods and move test classes into test project
2019-10-03 14:58:02 -04:00
f6db6ff068
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-10-03 13:35:05 -04:00
53f47fbb1e
Merge remote-tracking branch 'remotes/origin/master' into ks-narrow-search-pointcut
2019-10-03 12:20:20 -04:00
d1deedf247
pre-review cleanup
2019-10-03 12:14:11 -04:00
566443d0fe
move BundleUtil back
2019-10-03 12:05:26 -04:00
98c76a4d49
Test passes
2019-10-03 12:03:38 -04:00
29e7cdc476
Added ability to modify URLs in BundleUtil
2019-10-03 09:46:32 -04:00
db668d96b9
Add a few tests and remove some dead code
2019-10-03 09:00:14 -04:00
2193a30b45
CodeSystem Delta Uploader ( #1520 )
...
* Terminology Delta Uploading
* Add delta operations
* Fix up tests
* Improve test coverage a bit
* Improve test coverage reporting
* fix yaml
* A couple of test enhancements
* FIx intermittent test failure
2019-10-03 07:19:00 -04:00
53f949c2d0
pre-review cleanup
2019-10-02 08:36:54 -04:00
5aa4f88da3
Remove ISubscribableChannel interface. We don't need it after all.
2019-10-02 06:35:39 -04:00
ed195f8dab
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-10-02 06:21:12 -04:00
08825a81d9
Add missing @Override annotations
...
Added missing @Override annotations so that if/when methods in superclasses change
there will be a compile-time error if subclasses haven't been changed accordingly.
This was done using IntelliJ IDEA's "Missing @Override annotation" inspection.
2019-10-02 05:45:59 -04:00
f0b2bb8309
fixed triggering subscriptions
2019-10-01 14:57:25 -04:00
ca95791d2e
fix test
2019-10-01 10:52:00 -04:00
ade9e0316e
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-10-01 09:20:00 -04:00
b028337d8f
Merge branch 'master' into ja_20190928_rationalize_search_param_extractor
2019-09-30 21:11:41 -04:00
731be21c9f
Exclude commons-logging from dependencies
2019-09-30 18:58:25 -04:00
6867a57625
null check
2019-09-30 17:15:35 -04:00
f373abf74c
License header updates
2019-09-30 15:32:49 -04:00
a9f83a8c43
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-09-30 15:19:15 -04:00
066c9a7fb7
Improvements to AutohrizationInterceptor create handling
2019-09-30 15:07:23 -04:00
fd8b5206e7
Separated ChannelRegistry from ActiveSubscriptionRegistry so we can support a many-to-one relationship there
...
All tests pass
2019-09-30 15:01:47 -04:00
396f358f2d
Support for long concept property values has been added.
2019-09-30 14:40:31 -04:00
a324e51efa
Merge pull request #1516 from jamesagnew/1512-need-to-implement-the-ancestor-filter-with-in-operator-for-loinc
...
Resolve "Need to implement the ancestor filter with IN operator for LOINC"
2019-09-30 10:37:25 -04:00
dbd5331f5a
Support for ancestor filter with IN operator for LOINC has been added.
2019-09-30 10:25:29 -04:00
0bee7a7b53
Test fix
2019-09-30 10:12:49 -04:00
7eaa5d5574
Merging master into working branch.
2019-09-30 09:41:43 -04:00
1b2892f475
Merge pull request #1505 from jamesagnew/1454-need-to-implement-the-ancestor-and-descendant-filters-for-loinc
...
Resolve "Need to implement the ancestor and descendant filters for LOINC."
2019-09-30 09:39:32 -04:00
557a8ccc66
Add top level support for ElasticSearch ( #1514 )
...
* ElasticSearch work
* Add ElasticSearch properties builder
* Clean up POM
* Remove redundant project
* Try to troubleshoot embedded elasticsearch
* Another test attempt
* Add credentials to elasticsearch config
* Work on lastn
* Address review comments
* A couple of test fixes
2019-09-30 09:30:39 -04:00
0386448b3f
Initial commit for work on ancestor filter with IN operator for LOINC.
2019-09-30 09:21:32 -04:00
c0eb662a21
Rationalize search param extractor
2019-09-28 19:23:21 -04:00
3e173bb07c
Merging master into working branch to resolve conflicts.
...
# Conflicts:
# src/changes/changes.xml
2019-09-26 20:19:22 -04:00
5f17fb30b4
Address review comments.
2019-09-26 20:15:55 -04:00
07286e3b3f
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-09-26 17:50:14 -04:00
ed78a5f06d
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-26 16:56:42 -04:00
77d15a1836
Fix failing tests due to race conditions
...
* Work on failing tests
* Temporary downgrade of fhir core
* Work on failing build
* Fix pom
* Don't upload codecov
* Restore codecov
* Restore all tests
* Keep hammering away at intermittent test failures
* More test fixes
* Keep chipping away at these...
* Add some extra checks
* Work on tests
* More test logging
* More logging
* This might be it!
* Final build fixes?
* Address some review comments
* A couple more corrections
2019-09-26 16:11:15 -04:00
392d7ab000
Extend SubscribableChannel with SubscribableChannelManagement so we can get a handler count so we know when to destroy a channel
2019-09-26 15:46:40 -04:00
cc0df9850c
Make sure the validator can get at codes defined in notpresent
...
codesystems
2019-09-26 14:44:09 -04:00
94f87e7282
Allow term service to return codes
2019-09-26 12:46:41 -04:00
b6400764c4
Removed scratch notes.
2019-09-26 11:42:26 -04:00
efae77a330
Added changelog entries.
2019-09-26 11:36:55 -04:00
a4f9894104
Merging master into working branch.
2019-09-26 10:41:34 -04:00
e098cea07f
Throw UnsupportedOperationException for LOINC ancestor filter with IN operator; ignore tests. See #1512 in GitHub.
2019-09-26 10:39:55 -04:00
ddb5605830
Improve test logging
2019-09-25 22:17:47 -04:00
4f7db37d8e
Additional progress for ancestor/descendant filters; only ancestor/in remains.
2019-09-25 21:36:36 -04:00
99787d14f1
Add some test logging
2019-09-25 21:20:36 -04:00
8657afb01e
Fix intermittent test failures regarding search ( #1509 )
...
* Add some logging
* Add more test logging
* Work on some test logging
* Fix compile error
* Work on codecov
* Work on codecov
* Remove test debug messages
2019-09-25 20:15:21 -04:00
7c5cf9f1f4
Incremental progress for ancestor/descendant filters.
2019-09-25 17:33:45 -04:00
9b4671c05e
Added a bunch of tests for ancestor/descendant filters.
2019-09-25 16:52:08 -04:00
729d3a3d3b
Fix intermittent test failure.
2019-09-25 15:32:39 -04:00
4570e50c03
Fix nullability on one column
2019-09-25 15:31:26 -04:00
cddaf058a2
Add some extra test logging
2019-09-25 15:27:17 -04:00
30588bf8ee
Completed fixing tests after enabling pre-expansion by default.
2019-09-25 14:29:50 -04:00
b2c13f3018
Work on codecov integration
2019-09-25 13:25:59 -04:00
6b22d705c7
Incremental progress fixing tests after enabling pre-expansion by default.
2019-09-25 13:24:50 -04:00
2efef13528
Another test fix
2019-09-25 05:43:58 -04:00
4c064186a9
Try to fix intermittent testfailure
2019-09-25 05:39:00 -04:00
799848291f
Merging master into working branch.
2019-09-24 16:47:19 -04:00
5743efa066
Minor tweak to test.
2019-09-24 16:46:05 -04:00
21b91ac0e7
Make sure we call the updateEntity method on the correct DAO type when
...
processing inside a transaction
2019-09-24 16:16:13 -04:00
bf5d6acef4
More troubleshooting.
2019-09-24 15:36:06 -04:00
46a6b7aaef
Troubleshooting lack of ValueSet pre-expansion when updating a ValueSet via transaction bundle.
2019-09-24 15:30:40 -04:00
bd763d728b
Merge branch 'master' into ks-source-request-id-append-bug
2019-09-24 14:49:39 -04:00
5f563057c0
Set up CI with Azure Pipelines ( #1502 )
...
* Set up CI with Azure Pipelines
[skip ci]
* Update azure-pipelines.yml for Azure Pipelines
* Skip tests for a build
* Work on pipeline
* Update azure-pipelines.yml for Azure Pipelines
* Interceptors docs
* Test fix
* Disable releases from snapshot repo
* Try disabling jitpack
* Fix dependency issue
* A couple of test fixes
* Change to trigger a build
* Force a change to trigger a build
* Force a build
* FIx test
2019-09-24 14:38:38 -04:00
0e90867a65
fixed meta.source request append bug
2019-09-24 14:35:34 -04:00
9b2826f3c6
Handle searches with chained slash value ( #1503 )
...
* Work on test case for bug with searches
* Work on tests
* Fix issue with slashes in reference chain parameter for JPA server
2019-09-24 14:31:05 -04:00
df4b6c798c
Modified LOINC Terms to RadLex RPIDs ID and URL; pattern is mappings of main LOINC terms to say 'loinc' but parts and other codes are specified.
2019-09-24 09:21:42 -04:00
2a2e8e0ab8
Merge pull request #1501 from jamesagnew/1483-need-consistent-assignment-of-fullurl-id-and-url-for-loinc
...
Fixed inconsistent IDs and URLs for LOINC.
2019-09-23 15:59:21 -04:00
6f44d7c360
Fix issue deleting CodeSystem resources ( #1316 )
...
* Fix deleting CodeSystem resources
* Test fixes
* Address review comments
2019-09-23 15:58:57 -04:00
004f42cdcc
Clean up docs
2019-09-23 15:56:02 -04:00
59d7ccb99e
Fixed inconsistent IDs and URLs for LOING.
2019-09-23 15:49:58 -04:00
614585cc1f
added failing test
2019-09-21 07:42:04 -04:00
56e2904029
Removing my name. Whoops!
2019-09-20 18:48:47 -04:00
0cc35699b8
Specify full path for LOINC filenames to avoid duplicates.
2019-09-20 18:43:38 -04:00
e1e8ec981b
Replaced migration task column length constants with literals because they are not necessarily constant across schema versions.
2019-09-20 12:31:54 -04:00
6475146bc9
Add license headers
2019-09-19 18:08:21 -04:00
eddb98084d
Move PreferReturnEnum back to original location to avoid regressions
2019-09-19 15:48:58 -04:00
6fde2879ef
Fix one more intermittent test
2019-09-19 14:53:29 -04:00
47805bceff
Test fixes
2019-09-19 14:42:27 -04:00
a5a0fca065
Test fixes
2019-09-19 11:33:33 -04:00
2be63a1650
Test fixes
2019-09-19 09:45:07 -04:00
170698562a
Bump to current org.hl7.fhir.core
2019-09-19 08:11:30 -04:00
30dfde645b
Upgrade to Fontawesdome 5 and prevent uploading resources with binary
...
storage extensions
2019-09-19 05:28:05 -04:00
6b21e8cd90
Add some testing to the bulk export service
2019-09-18 14:43:00 -04:00
4a751cbfc5
Integrate Bulk Export ( #1487 )
...
* Start working on subscription processor
* Work on new scheduler
* Test fixes
* Scheduler refactoring
* Fix test failure
* One more test fix
* Updates to scheduler
* More scheduler work
* Tests now all passing
* Ongoing work on export
* Ongoing scheduler work
* Ongoing testing
* Work on export task
* Sync master
* Ongoing work
* Bump xml patch version
* Work on provider
* Work on bulk
* Work on export scheduler
* More test fies
* More test fixes
* Compile fix
* Reduce logging
* Improve logging
* Reuse bulk export jobs
* Export provider
* Improve logging in bulk export
* Work on bulk export service
* One more bugfix
* Ongoing work on Bulk Data
* Add changelog
2019-09-17 16:01:35 -04:00
882e0853df
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-16 15:55:49 -04:00
38cf830384
Accurately reflect codesystem URL
2019-09-16 15:55:32 -04:00
3a9342913c
Address review comments. Added tests.
2019-09-16 11:54:34 -04:00
b05c5f3f71
Implement the parent and child filters for LOINC. #1453
2019-09-15 21:52:33 -04:00
9b1af6b207
Implement both a copyright property and a copyright filter for LOINC. #1451
2019-09-13 16:18:51 -04:00
678d58ab90
Only manually add EXTERNAL_COPYRIGHT_NOTICE to LOINC uploader if it doesn't already exist in loinc.xml
2019-09-13 11:57:19 -04:00
75ddba7f2d
Add EXTERNAL_COPYRIGHT_NOTICE property for LOINC uploader.
2019-09-13 11:49:01 -04:00
7dce29b86e
Merge pull request #1468 from jamesagnew/dm-more-performance-tuning-on-valueset-expansion
...
More performance tuning on ValueSet expansion.
2019-09-10 17:57:13 -04:00
65e029458c
Test fixes.
2019-09-10 17:50:49 -04:00
d4feb5d0b1
Final cleanup before review.
2019-09-10 14:21:42 -04:00
9420bca341
Merge branch 'master' into ks-in-memory-date-compare
2019-09-10 13:25:29 -04:00
57d4cc23ee
More bug-hunting. DSTU3 was missing a null check.
2019-09-10 11:56:07 -04:00
0843a2b02d
Avoid leaking details when canSeeReource rejects a resource from consent
...
service
2019-09-10 11:14:44 -04:00
c974e9283b
added search % now test
2019-09-10 10:11:09 -04:00
67d24eedff
Merging master into working branch.
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
# hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
2019-09-09 19:01:29 -04:00
dbe5a36f26
Reset schedule for pre-expansions. Ready for review.
2019-09-09 18:44:25 -04:00
7e76c1893f
Fixed bug for large ValueSet expansion with URL parameter; return 404 for unknown ValueSets.
2019-09-09 18:41:00 -04:00
2052df3152
Error with a 404 on invalid valueset
2019-09-09 18:01:41 -04:00
19676a01b7
Incremental progress on large ValueSet expansion with URL parameter.
2019-09-09 17:24:01 -04:00
c82c3a093f
Removing gaps from concept order when pre-expanding ValueSets.
2019-09-09 15:24:37 -04:00
95e75d0a7d
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-09 15:02:55 -04:00
4fc0ad6f0a
Cleanup following paired programming with JA.
2019-09-06 17:56:56 -04:00
6ec991cd39
Finally this is fast!
2019-09-06 16:29:09 -04:00
718fcb28a5
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-06 14:58:03 -04:00
0cabc0392f
Incremental progress on large ValueSet expansion.
2019-09-06 14:57:34 -04:00
722c7a8211
Work on GraphQL updates
2019-09-06 14:56:17 -04:00
362c658f9a
License headers
2019-09-06 10:23:36 -04:00
c88e6a6fa7
Merge pull request #1442 from jamesagnew/ja_20190822_1440_infinispan_query_cache
...
Externalize query cache into its own service
2019-09-06 08:28:12 -04:00
785d40a777
Accuont for a few schema changes
2019-09-05 21:29:47 -04:00
b1421b1d60
@NotNull (hope I picked the right one!)
2019-09-05 16:20:24 -04:00
2a08808935
final PR cleanup
2019-09-05 16:11:58 -04:00
6fa9658b24
Incremental progress on large ValueSet expansion.
2019-09-05 15:54:45 -04:00
655222fcac
Merging master into working branch.
2019-09-05 11:59:44 -04:00
91cfecd257
Incremental progress on large ValueSet expansion.
2019-09-05 11:43:31 -04:00
01015bc435
added list stresstest
2019-09-04 21:15:08 -04:00
1f60d85517
Merge branch 'ks-anylist-enhancement' into ja_20190822_1440_infinispan_query_cache
2019-09-04 13:31:19 -04:00
fa62ab9c9e
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
2019-09-04 13:31:00 -04:00
0a5c52122e
added list stresstest
2019-09-04 08:49:18 -04:00
b00b1d2278
Toggle pre-expansion config.
2019-09-03 20:36:54 -04:00
ea19b46f60
Added an indexed order column to TermValueSetConcept for improved fetching.
2019-09-03 20:36:16 -04:00
aa9a984075
Don't trust stored total when determining whether or not to expand.
2019-09-03 18:44:52 -04:00
358f649d1f
Minor tweaks following review.
2019-09-03 17:14:31 -04:00
3e522a7414
Address review comments.
2019-09-03 16:37:28 -04:00
6ebc9572ac
Adjust concept and designation totals as we process.
2019-09-03 16:23:20 -04:00
b42b598d01
Added pre-fetch for concept designations, improved paging for expanded ValueSets, and columns on TermValueSet for number of concepts and designations.
2019-09-03 16:02:28 -04:00
1ef70a0fca
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-03 07:02:09 -04:00
8b09b3f3eb
Rename config enum for consistency
2019-09-03 07:01:36 -04:00
02a896f31e
Fix NPE for ValueSet operation validate-code when Coding and/or CodeableConcept is null for DSTU3/R5.
2019-09-02 21:28:51 -04:00
c34d8458ef
Refactor getting resource PIDs with utility methods.
2019-09-02 18:16:46 -04:00
16963881b0
Reset pre-expansion schedule.
2019-08-30 19:36:34 -04:00
548647defe
Toggle pre-expansion config.
2019-08-30 19:31:45 -04:00
f29abd7167
Fixed ResourceTable lookups for pre-expansion and code validation.
2019-08-30 19:31:05 -04:00
9f7cf3923b
Merge pull request #1458 from jamesagnew/1457-valueset-pre-expansion-need-to-account-for-existing-valuesets-and-user-assigned-ids
...
Resolve "ValueSet pre-expansion - need to account for existing ValueSets and user-assigned IDs."
2019-08-30 10:48:39 -04:00
8ef9c61b83
Address review comments; improve logging.
2019-08-30 10:47:21 -04:00
8700088c67
Missed a keyword
2019-08-29 22:06:43 -04:00
668af76514
Make method static again
2019-08-29 22:03:58 -04:00
347aada62e
Add a setter for unit tests
2019-08-29 21:43:29 -04:00
dbe86c8669
One more test fix
2019-08-29 21:35:07 -04:00
1b1d80b850
Test fix
2019-08-29 21:02:19 -04:00
e03d6a5d47
Fixed handling of pre-expansion in light of pre-existing, non-pre-expanded ValueSets.
2019-08-29 18:09:30 -04:00
c5a88444b6
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-08-29 14:00:37 -04:00
956bb39327
Resolve an inefficient regex expression
2019-08-29 13:59:31 -04:00
c22bf8b09f
Fixed handling of client-assigned IDs throughout terminology services.
2019-08-29 10:48:54 -04:00
e67a750c4f
validate-code operation now works with client-assigned IDs; added a bunch of failing tests to work on tomorrow.
2019-08-28 18:49:18 -04:00
d2ae3c24a1
FIXME
2019-08-28 16:26:56 -04:00
3e58962ac1
Split search cache api from search result cache api.
2019-08-28 16:24:56 -04:00
eab589bcac
fixed intermittently failing test
2019-08-28 13:11:44 -04:00
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"
...
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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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
...
$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 )
...
* 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 )
...
* 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
10c59fceeb
Subscription strategy tag ( #1178 )
...
tests pass
2019-01-25 13:01:04 -05:00
f55be0b6d0
Test fix
2019-01-25 10:56:17 -05:00
38d03ea99a
Invalid ids in subscription queue ( #1175 )
...
* Start work on this
* Work on interceptors
* Attempt fix
* Avoid environment dependency
* Test fixes
* One more test fix
* One more build tweak
* Lots of cleanup
* A bit more cleanup
* Still more cleanup
* Some test fixes
* Add legacy methods temporarily
* Don't auto-scan interceptor beans
* One more test fix
* rsolve merge conflicts
* Address review comments
2019-01-23 21:17:47 -05:00
67eaeb8af1
Merge remote-tracking branch 'origin/windows-fixes' into windows-fixes
2019-01-23 17:14:51 -05:00
e819b83a94
Make busywait more clear
2019-01-23 16:21:13 -05:00
cfd67d88c7
Merge remote-tracking branch 'origin/windows-fixes' into windows-fixes
2019-01-23 16:17:48 -05:00
5c7907dfea
magic number
2019-01-23 16:17:41 -05:00
7d1d5a102c
Attempt to fix a weird lucene indexing issue
2019-01-23 16:14:53 -05:00
2c7eb39b29
final batch of windows fixes (to deal with jumpy windows clock)
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also added semaphore to PointcutLatch
2019-01-22 18:53:54 -05:00
6b22977d7c
fixing more tests for Windows
2019-01-21 22:28:48 -05:00
00320da9dc
Merge branch 'master' into windows-fixes
2019-01-21 20:34:01 -05:00
9cf64f78d0
Deprecate a bad setter on RetfulServer, fix a paging issue, and add a
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disabled unit test to the subscription matcher
2019-01-21 14:46:17 -05:00
29f483d7b4
Merge branch 'master' into windows-fixes
2019-01-21 11:06:42 -05:00
b4350bbdae
Working through failed tests. Consolidating sleep calls
2019-01-21 11:05:53 -05:00
17f03ac843
Allow null return type for interceptors
2019-01-20 19:44:18 -05:00
c3c7d156e9
Interceptor cleanup
2019-01-20 10:16:18 -05:00
b878925884
Try to avoid intermittent test failure
2019-01-19 18:44:09 -05:00
cd1e0e881c
Add headers
2019-01-19 18:31:17 -05:00
b0cbd52ae9
Interceptor cleanup
2019-01-19 18:01:00 -05:00
29c3cee287
Merge pull request #1172 from jamesagnew/ja-subscription-interceptors
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Ja subscription interceptors
2019-01-19 07:13:14 -06:00
3e84173180
Merge branch 'master' into ja-subscription-interceptors
2019-01-18 17:52:23 -05:00
3d07fc1c22
fixed null subscription id ( #1170 )
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* fixed null subscription id
2019-01-18 10:39:35 -05:00
5ce9d444e9
Work on interceptors
2019-01-18 09:04:45 -05:00
5fd084d7cf
Fix a couple of merge conflicts
2019-01-18 05:47:37 -05:00
432ad8e5bc
Subscription without Payload did not contain header.
2019-01-18 05:41:47 -05:00
66dc7f82d5
organize imports
2019-01-15 20:55:00 -05:00
19afcb7e09
all tests pass
2019-01-15 18:22:08 -05:00
a584e15251
Add headers
2019-01-14 14:58:27 -05:00
4f5640e541
Resilient searchparamregistry ( #1165 )
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SearchParamRegistry and SubscriptionRegistry now both poll retrying connection to the server. This will help in particular in the scenario where the subscriptions are managed in a standalone server that depends on a FHIR Server being available to pull search parameters and subscriptions from.
2019-01-14 11:39:28 -05:00
4b48eebe8b
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-01-13 12:27:40 -06:00
63b8a70e8a
Allow storing ConceptMap with StructureDefinition as a source or target
2019-01-13 12:24:51 -06:00
068117138e
Merge branch 'master' into subscription-bugfix
2019-01-11 09:05:37 -06:00
860a8fb7a6
Emergency fix.
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Normally I'd write a test for this, but this startup behaviour is changing in my next PR.
2019-01-11 09:49:40 -05:00
aee7b2b882
Make sure that sub-request transaction searches and reads preserve HTTP
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headers
2019-01-10 07:26:04 -07:00
d091665ab6
Test fix
2019-01-09 14:40:43 -05:00
f241457bc1
Merge branch 'master' into test-openjdk-11
2019-01-09 13:42:50 -05:00
66dd6dc96c
updated documentation
2019-01-09 13:39:32 -05:00
cdf1cd9144
undoing inadvertent comment changes
2019-01-09 13:39:32 -05:00
3142ebb892
Fixed typo in class name
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Added channel extensions to CanonicalSubscription
2019-01-09 13:39:32 -05:00
d809569a2d
Added new DaoConfig parameter to control whether subscription matching happens on this server.
2019-01-09 13:39:32 -05:00
8beccab9ab
Merge branch 'master' into test-openjdk-11
2019-01-09 10:48:57 -05:00
62ae71c1c6
Allow authorizing delete operations via a transaction in
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AuthorizationInterceptor
2019-01-07 15:43:36 -05:00
a8a97ae6b2
Two test fixes
2019-01-07 09:18:11 -05:00
c104923855
Add an additional test for transaction processing
2019-01-07 09:17:19 -05:00
8f8385627f
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-01-05 11:33:08 -05:00
98d93df12a
License header updates
2019-01-04 16:22:15 -05:00
5b8fee869e
Add config options for default Prefer header and _total param on server
2019-01-04 16:12:45 -05:00
ba76492865
Another test fix
2019-01-04 14:04:26 -05:00
137d39e80f
Another test fix
2019-01-04 13:53:24 -05:00
051074d0bc
Work on tests
2019-01-04 13:05:39 -05:00
a1275874f8
Correct subscription delivery metadata
2019-01-04 10:56:21 -05:00
7ba07d9f02
Avoid search failure on Oracle when performing very large includes
2019-01-04 09:11:11 -05:00
31b8a392b7
Better CLI error handling for unit tests
2019-01-03 12:57:18 -05:00
14a132a937
Squashed commit of the following:
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commit 965965583070da25b76f
2018-12-27 17:58:47 -05:00
28218c9bba
Version bump for build JDK
2018-12-23 15:14:43 -05:00
fedc59a8d6
Subscription module startup changes ( #1154 )
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* Reorganizing packages and dependencies to support standalone subscription running within a CDR container where all hapi modules are on the classpath.
* EXPERIMENTAL: Moved Subscription registry out of interceptor and introduced ISubscriptionLoader that will be either a Database or FhirClient loader.
5 tests fail. Looks like we're getting too many matches--likely because there is now just one list of subscriptions instead of one list per interceptor.
* Created ActiveSubscription and moved cache bits into it
* Compiles. Next step is get app context to load.
* Application context loads. Now fix NullPointer.
* All subscription tests pass
* FIXME cleanup
* jpa-subscription tests
* fixed config so other module tests work
* MAJOR MILESTONE: All hapi-fhir tests pass.
updated READMEs in example projects
* Moved ExecutorQueue stuff out into its own class
* Organize Imports
* FIXME cleanup
* Null check -> Optional
* Add test and supporting code to validate SubscriptionConstants.EXT_SUBSCRIPTION_RESTHOOK_DELIVER_LATEST_VERSION behaviour
* Added SubscriptionCheckingSubscriber test that works without a database
* Moved a few beans to @ComponentScan
* Replaced use of beanFactory with concrete factory classes
* Switched test to use subscribablechannel
* Added SubscriptionLoaderFhirClientTest
* Undid changes that caused SearchParamProviderFhirClientTest to revert to the Database version. It's now calling the FhirClient version again. (oops)
* Confirm that our SubscriptionProviderFhirClient works with a live fhir client
* Organize imports
* Organize imports
* Register interceptors with DaoConfig instead of RestServer.
Also, Rename @VisibleForTesting methods with ForUnitTest
* Ready to go
* organize imports
* add processing queue
* Fixed interface implementation names
* Fix triggering service so it uses new subscriptionmatcherinterceptor
* fixed example
* Renamed "Database" classes to "Dao"
* Tightened up StoppableSubscriber API
* final code review
* processing -> matching naming change
* fix required by CDR
* oops
* Updated changes.xml
* Renamed subscriptioncheckingsubscriber to subscriptionmatchingsubscriber
* Renamed subscriptioncheckingsubscriber to subscriptionmatchingsubscriber
* CDR integration now works
* Changing subscribable channel abstraction layer in preparation for supporting more types of subscribable channels
* Add interface over both types of messages put on queues
* cosmetic change
* added subscription support for r4
* fixed again
* oops
* self code-review
2018-12-23 13:52:26 -05:00
9d3904ef3e
Fix #1142 - Upgrade Spring Boot to latest version
2018-12-23 13:10:03 -05:00
a0cb7edd08
Version bump a few dependencies
2018-12-22 20:13:03 -05:00
1311ef4157
Revert to JDK9 to build on travis temporarily
2018-12-21 09:26:19 -05:00
f5f9dff391
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-12-18 14:09:20 -05:00
bca958564f
Just a javadoc change
2018-12-18 14:09:11 -05:00
86b3e45a32
License header updates
2018-12-18 14:08:01 -05:00
84a34eb3c9
Subscription module support ( #1147 )
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* Reorganizing packages and dependencies to support standalone subscription running within a CDR container where all hapi modules are on the classpath.
Moved Subscription registry out of interceptor and introduced SubscriptionLoader
* Created ActiveSubscription and moved cache bits into it
* Moved ExecutorQueue stuff out into its own class
* Add test and supporting code to validate SubscriptionConstants.EXT_SUBSCRIPTION_RESTHOOK_DELIVER_LATEST_VERSION behaviour
* Added SubscriptionCheckingSubscriber
* Moved a few beans to @ComponentScan
* Replaced use of beanFactory with concrete factory classes
* Switched test to use subscribablechannel
* Added SubscriptionLoaderFhirClientTest
* Confirm that our SubscriptionProviderFhirClient works with a live fhir client
* Register interceptors with DaoConfig instead of RestServer.
Also, Rename @VisibleForTesting methods with ForUnitTest
* Fix triggering service so it uses new subscriptionmatcherinterceptor
* Renamed "Database" classes to "Dao"
* processing -> matching naming change
2018-12-18 13:09:06 -05:00
dc1f48ffed
Test fix
2018-12-14 14:13:02 -05:00
f978bc3039
Always apply new search params to any resource reindexing
2018-12-14 13:43:25 -05:00
11b8304cb4
Fix case sensitivity issue
2018-12-13 08:31:35 -05:00
b442982310
Add media interceptor
2018-12-08 18:49:58 -05:00
5a80e70d93
Correctly reindex string indexes
2018-12-06 14:44:42 -05:00
a5b1f684f7
Try to prevent intermittent test failure
2018-12-05 19:28:37 -05:00
cbaa39fd63
Try to reuse index rows in JPA server ( #1133 )
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* Try to reuse index rows in JPA server
* Address review comments
* One more test fix
* One more test
2018-12-05 19:25:59 -05:00
d150340d53
One more test fix
2018-12-04 19:55:14 -05:00
29af6160d6
Fix typo
2018-12-04 18:54:26 -05:00
1d3bcd9e8f
Fix indexing bug
2018-12-04 18:50:49 -05:00
d9ce0ebf7c
Unit test fix
2018-12-04 18:24:19 -05:00
8c7f249a21
Migrator enhancements and adjust reindexer to account for missing
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versions
2018-12-04 17:33:29 -05:00
c484c69664
Better error message for unqualified search parameter types
2018-12-03 13:14:10 -05:00
82f40f0423
License header updates
2018-12-03 05:22:10 -05:00
6baee4dc3f
Standalone subscription ( #1125 )
2018-11-30 17:19:16 -05:00
b2179b1696
Syntax fixes for the JPA migrator
2018-11-30 12:39:37 -05:00
364b6cc5fd
One more test fix
2018-11-22 18:40:39 -05:00
055478e1f1
Test fixes
2018-11-22 18:22:33 -05:00
ce3b7c82ce
Avoid issues when using subscription delivery in a serializing/queuing
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environment
2018-11-22 17:53:42 -05:00
d0b194f9d7
Fix two test failures
2018-11-22 08:41:12 -05:00
2e030eebaa
Make sure that reindexing happens correctly
2018-11-21 12:06:10 -05:00
e8482f5c87
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-11-20 13:59:51 -05:00
7cbad7f4e3
A bit of cleanup around subscription wiring following in-memory matcher
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landing
2018-11-20 13:59:31 -05:00
4c84b8fc89
Add a bit more test logging
2018-11-20 05:33:32 -05:00
03ebcafdf5
In-memory matcher ( #1116 )
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* Initial refactoring to move database matcher out into its own class
* MAJOR REFACTOR: Pulled indexing code out of BaseHapiFhirDao into a new class ResourceIndexedSearchParams
* Moved calculateHashes
* Replaced @Bean definitions in BaseConfig.java with @ComponentScan
Annotated bean classes with either @Service (if it's stateless) or @Component (if it's stateful). It doesn't really matter which annotation is used, but it's helpful to see at a glance whether a bean is stateful or stateless.
* Move services out of BaseHapiFhirDao
Moved services required by ResourceIndexedSearchParams out of BaseHapiFhirDao and into new classes called LogicalReferenceHelper, IdHelperService, MatchUrlService, and DaoProvider.
Converted SearchBuilder into Prototype Bean
Mark Spring components that depend on daos and entitymanagers with @Lazy so they aren't picked up by hapi-fhir-spring-boot-autoconfigure.
* Added SubscriptionMatcherInMemory
Moved static data out of BaseHapiFhirDao into ResourceMetaParams
Moved translateMatchUrl methods out of BaseHapiFhirDao into MatchUrlService bean
Simplified SubscriptionMatcherInMemory to not depend on entity or dao
Turned all subscribers into prototype beans
* Moved searchParam method out to mySearchParamProvider
Also removed dao and contest parameters from of myMatchUrlService methods
Moved code out of SearchBuilder into SearchParameterMap.clean() so it can be used by inMemoryMatcher
Introduced a new composite subscription matcher that tries to match in memory and if it finds a parameter in the criteria it doesn't support, it falls back to the database matcher.
* Added support for references
Also fixed a small bug in SearchParameterMap that was missing the ";" after "_has" when creating a normalized query from search params.
* Finished implementing all tests from FhirResourceDaoR4SearchNoFtTest
* Make in-memory matcher configurable, disabled by default
* Validate Subscription criteria when they're submitted
Send HTTP 422 UnprocessableEntityException if the criteria fail validation.
* fixed Sonar "Blocker" issues.
* Don't reload the resource before sending it out
Since we can always force a reload using restHookDetails.isDeliverLatestVersion
* Added tests to cover Custom Search param.
* Split ResourceIndexedSearchParam into separate state and service classes
* Cleaned up SearchBuilder.
Removed uses of myCallingDao as an injection mechanism.
Left // FIXME KHS cookie crumbs to clean up
* Reduced dependencies on BaseHapiFhirDao
Removed methods from IDao interface that were used for injection
* Updated change log
2018-11-19 16:19:52 -05:00
45a5db6fd8
One more fix
2018-11-19 13:31:01 -05:00
719339fc14
One more test fix
2018-11-19 10:27:16 -05:00
67dbc802be
Better detection of binary content in ResponseHighlighterInterceptor
2018-11-18 14:32:54 +01:00
fad53c6669
Fix a test
2018-11-16 13:15:14 +01:00
6a6451f694
Reduce number of queries on some DB operations
2018-11-16 12:41:50 +01:00
1de0ef405c
Clean up test compile and reenable GraphQL on hapi.fhir.org
2018-11-16 11:15:44 +01:00
84acafe3af
Streamline expunge operation
2018-11-15 11:37:16 +01:00
75210d614b
Bump to 3.7.0-SNAPSHOT
2018-11-12 22:37:52 -05:00
63af04a7b4
Prepare for 3.6.0 release
2018-11-12 05:40:55 -05:00
030b33a0f2
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-11-09 15:59:34 -05:00
4a0c45a494
License updates
2018-11-09 15:59:23 -05:00
c81a59bb9a
Only use FHIRPath to validate searchparameterr paths in R4
2018-11-09 15:57:34 -05:00
7f6f06dddf
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-11-09 15:47:22 -05:00
5834e6aa62
Test fixes
2018-11-09 15:32:55 -05:00
3942f1bb29
License header updates
2018-11-09 14:41:57 -05:00
f61df5c3fe
Use FHIRPath expression parser for custom SP validation
2018-11-09 14:41:20 -05:00
a3e79b5759
License updates only
2018-11-08 15:28:09 -05:00
3ae5f9a3b7
Build tweak
2018-11-08 14:04:21 -05:00
cca49425ae
Some work on collection processing
2018-11-08 08:56:51 -05:00
76cd3f6b47
Allow client assigned IDs to be purely numeric in JPA server if
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configured to do so
2018-11-07 18:25:50 -05:00
62145e1b74
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-11-07 11:02:02 +01:00
4b790eddb6
Add additional authorization test
2018-11-07 11:01:29 +01:00
896568c0f7
License updates
2018-11-04 16:06:53 -05:00
bc72093555
Add reindexing support based on table instead of column
2018-11-04 20:00:27 +01:00
b1283791ca
Allow JPA server to restore resources and link to them in a single
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transaction
2018-11-02 16:45:21 -04:00
1b877ac03e
Add licene headers
2018-11-01 09:15:51 -04:00
4315900ac0
Merge branch 'philips-3.6.0'
2018-11-01 09:15:27 -04:00
3bfdc61866
Fix a couple of test failures
2018-11-01 09:15:03 -04:00
3f6960d82b
Add multithreaded migrator tool
2018-11-01 05:42:51 -04:00
c8834cd29a
Merge branch 'philips-3.6.0' of github.com:jamesagnew/hapi-fhir into philips-3.6.0
2018-10-31 17:19:28 -04:00
041a4c4018
Fix SearchCoordinator tests
2018-10-31 12:36:27 -04:00
31ef4c68e1
Merge branch 'philips-3.6.0' of github.com:jamesagnew/hapi-fhir into philips-3.6.0
2018-10-31 05:51:13 -04:00
8955a9e54d
Add threading to migrator
2018-10-31 05:50:50 -04:00
7acba90d15
Update search logic
2018-10-30 22:43:16 -04:00
3d008aee5d
Make test observation lists thread safe ( #1105 )
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* Initial refactoring to move database matcher out into its own class
* MAJOR REFOACTOR: Pulled indexing code out of BaseHapiFhirDao into a new class ResourceIndexedSearchParams
* made observations lists thread safe to stop intermittent test failures
2018-10-29 15:56:47 -04:00
b66e01ce65
Allow plain server @Operation methods to declare a wildcard so that any
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opeeration invocations will be direected to them
2018-10-29 10:36:32 -04:00
794d9145e9
Move query count tests to consolidate them, and avoid an accidental
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rewrite of existing indexes in some conditions
2018-10-24 17:54:58 -03:00
f601b212ad
Performance enhancements to the JPA server and better retry logic in
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$trigger-subscription
2018-10-20 14:47:37 -04:00
c8db7fe035
Add a test
2018-10-18 15:12:22 -04:00
e00ff641b2
Increase visibility of two methods needed by the HSPC sandbox
2018-10-18 10:17:55 -04:00
da2763d8c8
Merge branch 'master' into philips-3.6.0
2018-10-17 22:38:27 -04:00
f571fc4f92
Rename DAO registry
2018-10-17 22:37:43 -04:00
b78aaea415
FIx up subscription processing
2018-10-17 21:23:52 -04:00
de76f37845
Try to fix an intermittent test failure
2018-10-17 15:49:26 -04:00
99cd4ce5f7
Allow for _total parameter
2018-10-17 09:47:35 -04:00
4b5dcce021
Add a bit of logging to subscription triggering
2018-10-17 08:32:57 -04:00
b220154e9c
Fix error in retriggeer logic
2018-10-17 07:02:51 -04:00
aa1f624132
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-17 05:53:46 -04:00
8130700d68
One more optimization to the subscription retriggering logic
2018-10-17 05:53:07 -04:00
d129d43635
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-16 21:51:50 -04:00
2c05d9c5db
Test cleanup
2018-10-16 21:51:33 -04:00
e2dfaa517f
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-16 20:38:21 -04:00
388bda1fec
Avoid transaction isolation level not supported by Oracle
2018-10-16 20:31:43 -04:00
47a5763fb5
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-16 20:25:12 -04:00
5d7142a972
Avoid intermittent test failures
2018-10-16 20:23:32 -04:00
1c1f601332
License header updates
2018-10-16 19:56:52 -04:00
0fbe897ca4
Add named beans to JPA config
2018-10-16 17:24:17 -04:00
755060f91e
Allow subscription triggering on a block of resources
2018-10-16 15:29:41 -04:00
ba6df6d55a
Handle unqualified ID in delete box for testpage overlay
2018-10-15 10:23:21 -04:00
93c545c42c
License header updates
2018-10-15 09:54:00 -04:00
483c9bff3a
Auto detect whether the appropriate dialect is selected
2018-10-15 09:53:04 -04:00
b44e96a5cd
Merge branch 'philips-3.6.0'
2018-10-15 08:37:00 -04:00
b75226914d
Fix intermittent test failure
2018-10-15 08:19:23 -04:00
6dc2dc1d6f
One more test fix
2018-10-15 07:11:10 -04:00
796b12e33e
Fix bug in $everything processing
2018-10-15 05:44:53 -04:00
8b46257423
Add warm cache module
2018-10-14 09:32:07 -04:00
51a69f0dc9
Fixes to migrator and count logic
2018-10-13 12:02:19 -04:00
a9fcfaf79a
Add a test
2018-10-10 19:11:57 -04:00
0837daecc2
One more recurring failure fix
2018-10-10 13:36:50 -04:00
Ken Stevens
James Agnew
Clayton Bodendein
Diederik Muylwyk
Sean McIlvenna
Joel Schneider
jvi
Stig Rohde Døssing
Ken Stevens
Ken Stevens
patrick-werner
Volker Schmidt