Ken Stevens
f11d939131
oops
2019-11-14 14:55:02 -05:00
Ken Stevens
25c094e38a
skip trying to populate resources in search result bundle if no resources were found
2019-11-14 14:55:02 -05:00
James Agnew
497a96ae68
Version bump for next round of development
2019-11-12 22:09:21 -05:00
Anthony Sute
2c22b9d7ef
Added _filter unit tests for date type values.
2019-11-12 17:58:29 -05:00
jamesagnew
f99ad981b5
Version bump to 4.1.0
2019-11-12 16:08:20 -05:00
Anthony Sute
bed0cc4d61
New unit tests to support _filter gt, lt, ge, and le operators for string types.
2019-11-12 15:06:17 -05:00
James Agnew
aa0301084b
Don't succeed validation on unknown codesystem ( #1575 )
...
* Don't succeed validation on unknown codesystem
* Test fixes
* Work on error messages
* Work on code validation API
* work on tests
* Work on validation
* Test fix
* Update DSTU3 validation reources
* Upgrade structures
* Test fixes
2019-11-12 14:35:49 -05:00
Anthony Sute
49ed6b48dc
Merged James' most recent changes.
2019-11-12 13:57:02 -05:00
Anthony Sute
09daf7aacc
Implemented changes/fixes and associated unit tests for following _filter operators for strings:
...
- eq
- ne
- co
- sw
- ew
2019-11-11 21:58:49 -05:00
James Agnew
1a348abaf5
Try to fix 2 intermittent test failures
2019-11-08 08:45:08 -05:00
jamesagnew
3b1d8d1bc0
Add test logging sort
2019-11-08 07:27:25 -05:00
jamesagnew
7c8342dcc1
Add some test logging
2019-11-08 05:53:59 -05:00
James Agnew
c027ff27c3
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-11-07 21:52:31 -05:00
James Agnew
d4aea82460
Add some test logging
2019-11-07 21:50:06 -05:00
James Agnew
056756dbab
Fix paging issue #1300 ( #1584 )
...
* Fix paging issue
* Add changelog with credit
* Add a test
2019-11-07 18:17:09 -05:00
James Agnew
ebc52e6b48
Correctly handle below expansion with missing system
2019-11-07 09:28:24 -05:00
Anthony Sute
92de268f32
Fixes for LGTM warnings
2019-11-06 08:47:53 -05:00
Anthony Sute
3cf8254625
(1) Fixes to address _filter-based _id retrievals not being restricted to the specified resource type
...
(2) Import fix for FhirServerConfig.java in hapi-fhir-jpaserver-example
2019-11-06 08:47:53 -05:00
jamesagnew
9c93d5d7f7
Test fixes
2019-11-04 07:04:26 -05:00
James Agnew
78a323f105
Test fixes
2019-11-03 21:20:22 -05:00
James Agnew
f481e11ad5
Update migration tasks
2019-11-03 18:49:47 -05:00
James Agnew
60628356a8
Version bump spring
2019-11-03 11:29:22 -05:00
jamesagnew
2bf578879a
One more bit of extensibility
2019-11-02 19:03:46 -04:00
jamesagnew
f7ad82d7a8
Add a test
2019-11-02 18:47:02 -04:00
jamesagnew
5ad57d9ea9
Add some API to subscriptionactivating interceptor to make it more
...
extendible
2019-11-02 18:14:50 -04:00
jamesagnew
89b25ce828
License updates
2019-11-02 17:34:05 -04:00
James Agnew
3b6709e1d1
Merge pull request #1566 from jamesagnew/ja_20190928_rationalize_search_param_extractor
...
Rationalize search param extractors across FHIR versions
2019-11-02 16:18:23 -04:00
James Agnew
33a3ea8fca
Fix compile error
2019-10-30 16:23:24 -04:00
James Agnew
cacd243a44
Correctly Expand ValueSets in non-lucene mode ( #1573 )
2019-10-30 16:21:44 -04:00
Ken Stevens
1fd3948b12
Merge pull request #1572 from jamesagnew/ks-source-subscriptions
...
fixed in-memory search by _source for Dstu3
2019-10-30 16:20:14 -04:00
James Agnew
e96500d54f
Add a test
2019-10-30 15:51:46 -04:00
James Agnew
7f62d60c4e
Correctly Expand ValueSets in non-lucene mode
2019-10-30 14:26:31 -04:00
Ken Stevens
21c591eaf2
ready for review
2019-10-30 13:49:10 -04:00
James Agnew
d3e66680f0
Add some testing
2019-10-30 09:49:40 -04:00
James Agnew
b90f285218
Merge branch 'master' into ja_20190928_rationalize_search_param_extractor
2019-10-30 08:41:14 -04:00
James Agnew
007cfaf00e
Don't error out on missing CS ( #1570 )
...
* Don't error out on mi9ssing CS
* Add tests
* Add a bit of test coverage
* One more test
2019-10-30 08:38:39 -04:00
James Agnew
9c852283e9
Correctly handle "special" search params in CS ( #1569 )
...
* Correctly handle "special" search params in CS
* Add another test
2019-10-30 05:31:25 -04:00
James Agnew
84803a02ef
Preserve line numbers in XML validation ( #1567 )
...
* Preserve line numbers in XML validation
* Test fixes
2019-10-29 15:54:49 -04:00
James Agnew
c5f48b6b47
Add tests
2019-10-29 13:24:43 -04:00
James Agnew
3dfb6959c1
Don't reload terminology resources when nothing has changed
2019-10-29 11:35:26 -04:00
James Agnew
2b8426114f
Test fixes
2019-10-28 10:58:14 -04:00
James Agnew
d321a8276a
Fix intermittent
2019-10-28 10:45:39 -04:00
jamesagnew
75ad205bd5
Try to fix intermittent
2019-10-28 07:23:49 -04:00
jamesagnew
51a0006548
Work on rationalizing search param extractor
2019-10-27 20:04:33 -04:00
jamesagnew
ac4d108126
Merge branch 'ja_20190928_rationalize_search_param_extractor' of github.com:jamesagnew/hapi-fhir into ja_20190928_rationalize_search_param_extractor
2019-10-27 18:17:29 -04:00
James Agnew
817f9ae36e
Merge branch 'master' into ja_20190928_rationalize_search_param_extractor
2019-10-27 17:25:20 -04:00
jamesagnew
5a300d2d8e
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-10-26 10:32:16 -04:00
James Agnew
403a3d1889
Correct URI loading in testpage-overlay ( #1565 )
...
* Clean up tests
* Try to fix intermittent
* Fix URI issue
* Add changelog
2019-10-25 16:14:06 -04:00
jamesagnew
cd84af30b1
Merge branch 'master' into ja_20190928_rationalize_search_param_extractor
2019-10-25 05:56:39 -04:00
jamesagnew
935ec9ebc2
License headers
2019-10-25 05:44:51 -04:00
Ken Stevens
f19100cbb3
final cleanup
2019-10-24 20:29:45 -04:00
Ken Stevens
4a2ed62357
review feedback
2019-10-24 20:25:16 -04:00
Ken Stevens
08472c1e3f
ready to merge
2019-10-24 17:56:15 -04:00
Ken Stevens
4fa849a3e5
pre-review cleanup
2019-10-24 16:43:47 -04:00
Ken Stevens
43f17534bb
commiting with FIXMEs so James can review
2019-10-24 16:40:53 -04:00
James Agnew
df4376606d
Validation cleanup ( #1561 )
...
* Validation cleanup
* Test fix
* Fix build
* Test tweaks
2019-10-24 13:09:18 -05:00
James Agnew
385a885abf
Add ability for resource source to be specified by header
2019-10-24 08:32:52 -04:00
James Agnew
0d3f7d4a03
Correctly handle searching by source in JPA server
2019-10-23 06:58:16 -04:00
James Agnew
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
James Agnew
371bf2e5cf
Disable unit test SQL logging
2019-10-22 17:27:36 -04:00
James Agnew
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
James Agnew
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
Ken Stevens
d0704269d7
ready for rereview
2019-10-22 10:13:49 -04:00
Ken Stevens
427f7397da
ready for rereview
2019-10-22 10:13:49 -04:00
Ken Stevens
0f40b2c48f
npe check for binary storage interceptor
2019-10-22 10:13:49 -04:00
James Agnew
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
James Agnew
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
James Agnew
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
James Agnew
985cd49892
Test fixes
2019-10-18 16:36:05 -04:00
James Agnew
0cddb54476
Remove accidental commit
2019-10-18 15:52:03 -04:00
James Agnew
c455a46160
Add missing class
2019-10-18 15:51:20 -04:00
James Agnew
a71d969ba1
Add line numbers to validation failures
2019-10-18 14:10:47 -04:00
James Agnew
50af4bfb19
Merge latest changes
2019-10-18 13:36:26 -04:00
James Agnew
13b80a294a
Test fix
2019-10-18 07:13:11 -04:00
James Agnew
0971998f57
Fix #848 - Pass raw JSON to the validator
2019-10-17 11:28:48 -04:00
James Agnew
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
James Agnew
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
James Agnew
839f935401
remove unnecessary index
2019-10-15 19:07:37 -04:00
James Agnew
fdcf5f5d73
Add a test
2019-10-15 18:16:22 -04:00
James Agnew
bf476b9c32
Handle null returns from search cache methods
2019-10-15 16:25:21 -05:00
James Agnew
9c23959b38
Licene header updates
2019-10-15 15:08:13 -04:00
James Agnew
9a050461a8
Make cache timeout configurable
2019-10-15 09:34:48 -04:00
James Agnew
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
James Agnew
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
James Agnew
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
jamesagnew
150c865f68
License header updates
2019-10-03 21:20:08 -04:00
James Agnew
069db501ee
Fix _has parameter ( #1525 )
...
* Fix _has parameter
* Bug fixes
* Add a comment
* Test fixes
2019-10-03 21:19:31 -04:00
James Agnew
836fac9a30
Ensure that JPA PRESHOW interceptor broadcasts don't include expunged
...
resources
2019-10-03 15:49:03 -04:00
Ken Stevens
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
James Agnew
1b5528a998
Fix compile error
2019-10-03 15:06:14 -04:00
James Agnew
a3b9db1363
Clean up a few unused methods and move test classes into test project
2019-10-03 14:58:02 -04:00
Ken Stevens
f6db6ff068
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-10-03 13:35:05 -04:00
Ken Stevens
53f47fbb1e
Merge remote-tracking branch 'remotes/origin/master' into ks-narrow-search-pointcut
2019-10-03 12:20:20 -04:00
Ken Stevens
d1deedf247
pre-review cleanup
2019-10-03 12:14:11 -04:00
Ken Stevens
566443d0fe
move BundleUtil back
2019-10-03 12:05:26 -04:00
Ken Stevens
98c76a4d49
Test passes
2019-10-03 12:03:38 -04:00
Ken Stevens
29e7cdc476
Added ability to modify URLs in BundleUtil
2019-10-03 09:46:32 -04:00
James Agnew
db668d96b9
Add a few tests and remove some dead code
2019-10-03 09:00:14 -04:00
James Agnew
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
Ken Stevens
53f949c2d0
pre-review cleanup
2019-10-02 08:36:54 -04:00
Ken Stevens
5aa4f88da3
Remove ISubscribableChannel interface. We don't need it after all.
2019-10-02 06:35:39 -04:00
Ken Stevens
ed195f8dab
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-10-02 06:21:12 -04:00
Clayton Bodendein
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
Ken Stevens
f0b2bb8309
fixed triggering subscriptions
2019-10-01 14:57:25 -04:00
Ken Stevens
ca95791d2e
fix test
2019-10-01 10:52:00 -04:00
Ken Stevens
ade9e0316e
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-10-01 09:20:00 -04:00
James Agnew
b028337d8f
Merge branch 'master' into ja_20190928_rationalize_search_param_extractor
2019-09-30 21:11:41 -04:00
James Agnew
731be21c9f
Exclude commons-logging from dependencies
2019-09-30 18:58:25 -04:00
Ken Stevens
6867a57625
null check
2019-09-30 17:15:35 -04:00
jamesagnew
f373abf74c
License header updates
2019-09-30 15:32:49 -04:00
Ken Stevens
a9f83a8c43
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-09-30 15:19:15 -04:00
James Agnew
066c9a7fb7
Improvements to AutohrizationInterceptor create handling
2019-09-30 15:07:23 -04:00
Ken Stevens
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
Diederik Muylwyk
396f358f2d
Support for long concept property values has been added.
2019-09-30 14:40:31 -04:00
Diederik Muylwyk
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
Diederik Muylwyk
dbd5331f5a
Support for ancestor filter with IN operator for LOINC has been added.
2019-09-30 10:25:29 -04:00
James Agnew
0bee7a7b53
Test fix
2019-09-30 10:12:49 -04:00
Diederik Muylwyk
7eaa5d5574
Merging master into working branch.
2019-09-30 09:41:43 -04:00
Diederik Muylwyk
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
James Agnew
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
Diederik Muylwyk
0386448b3f
Initial commit for work on ancestor filter with IN operator for LOINC.
2019-09-30 09:21:32 -04:00
James Agnew
c0eb662a21
Rationalize search param extractor
2019-09-28 19:23:21 -04:00
Diederik Muylwyk
3e173bb07c
Merging master into working branch to resolve conflicts.
...
# Conflicts:
# src/changes/changes.xml
2019-09-26 20:19:22 -04:00
Diederik Muylwyk
5f17fb30b4
Address review comments.
2019-09-26 20:15:55 -04:00
Ken Stevens
07286e3b3f
Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name
2019-09-26 17:50:14 -04:00
James Agnew
ed78a5f06d
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-26 16:56:42 -04:00
James Agnew
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
Ken Stevens
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
James Agnew
cc0df9850c
Make sure the validator can get at codes defined in notpresent
...
codesystems
2019-09-26 14:44:09 -04:00
James Agnew
94f87e7282
Allow term service to return codes
2019-09-26 12:46:41 -04:00
Diederik Muylwyk
b6400764c4
Removed scratch notes.
2019-09-26 11:42:26 -04:00
Diederik Muylwyk
efae77a330
Added changelog entries.
2019-09-26 11:36:55 -04:00
Diederik Muylwyk
a4f9894104
Merging master into working branch.
2019-09-26 10:41:34 -04:00
Diederik Muylwyk
e098cea07f
Throw UnsupportedOperationException for LOINC ancestor filter with IN operator; ignore tests. See #1512 in GitHub.
2019-09-26 10:39:55 -04:00
James Agnew
ddb5605830
Improve test logging
2019-09-25 22:17:47 -04:00
Diederik Muylwyk
4f7db37d8e
Additional progress for ancestor/descendant filters; only ancestor/in remains.
2019-09-25 21:36:36 -04:00
James Agnew
99787d14f1
Add some test logging
2019-09-25 21:20:36 -04:00
James Agnew
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
Diederik Muylwyk
7c5cf9f1f4
Incremental progress for ancestor/descendant filters.
2019-09-25 17:33:45 -04:00
Diederik Muylwyk
9b4671c05e
Added a bunch of tests for ancestor/descendant filters.
2019-09-25 16:52:08 -04:00
Diederik Muylwyk
729d3a3d3b
Fix intermittent test failure.
2019-09-25 15:32:39 -04:00
James Agnew
4570e50c03
Fix nullability on one column
2019-09-25 15:31:26 -04:00
James Agnew
cddaf058a2
Add some extra test logging
2019-09-25 15:27:17 -04:00
Diederik Muylwyk
30588bf8ee
Completed fixing tests after enabling pre-expansion by default.
2019-09-25 14:29:50 -04:00
jamesagnew
b2c13f3018
Work on codecov integration
2019-09-25 13:25:59 -04:00
Diederik Muylwyk
6b22d705c7
Incremental progress fixing tests after enabling pre-expansion by default.
2019-09-25 13:24:50 -04:00
jamesagnew
2efef13528
Another test fix
2019-09-25 05:43:58 -04:00
jamesagnew
4c064186a9
Try to fix intermittent testfailure
2019-09-25 05:39:00 -04:00
Diederik Muylwyk
799848291f
Merging master into working branch.
2019-09-24 16:47:19 -04:00
Diederik Muylwyk
5743efa066
Minor tweak to test.
2019-09-24 16:46:05 -04:00
James Agnew
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
Diederik Muylwyk
bf5d6acef4
More troubleshooting.
2019-09-24 15:36:06 -04:00
Diederik Muylwyk
46a6b7aaef
Troubleshooting lack of ValueSet pre-expansion when updating a ValueSet via transaction bundle.
2019-09-24 15:30:40 -04:00
James Agnew
bd763d728b
Merge branch 'master' into ks-source-request-id-append-bug
2019-09-24 14:49:39 -04:00
James Agnew
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
Ken Stevens
0e90867a65
fixed meta.source request append bug
2019-09-24 14:35:34 -04:00
James Agnew
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
Diederik Muylwyk
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
Diederik Muylwyk
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
James Agnew
6f44d7c360
Fix issue deleting CodeSystem resources ( #1316 )
...
* Fix deleting CodeSystem resources
* Test fixes
* Address review comments
2019-09-23 15:58:57 -04:00
James Agnew
004f42cdcc
Clean up docs
2019-09-23 15:56:02 -04:00
Diederik Muylwyk
59d7ccb99e
Fixed inconsistent IDs and URLs for LOING.
2019-09-23 15:49:58 -04:00
Ken Stevens
614585cc1f
added failing test
2019-09-21 07:42:04 -04:00
Diederik Muylwyk
56e2904029
Removing my name. Whoops!
2019-09-20 18:48:47 -04:00
Diederik Muylwyk
0cc35699b8
Specify full path for LOINC filenames to avoid duplicates.
2019-09-20 18:43:38 -04:00
Diederik Muylwyk
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
jamesagnew
6475146bc9
Add license headers
2019-09-19 18:08:21 -04:00
James Agnew
eddb98084d
Move PreferReturnEnum back to original location to avoid regressions
2019-09-19 15:48:58 -04:00
James Agnew
6fde2879ef
Fix one more intermittent test
2019-09-19 14:53:29 -04:00
James Agnew
47805bceff
Test fixes
2019-09-19 14:42:27 -04:00
James Agnew
a5a0fca065
Test fixes
2019-09-19 11:33:33 -04:00
James Agnew
2be63a1650
Test fixes
2019-09-19 09:45:07 -04:00
jamesagnew
170698562a
Bump to current org.hl7.fhir.core
2019-09-19 08:11:30 -04:00
James Agnew
30dfde645b
Upgrade to Fontawesdome 5 and prevent uploading resources with binary
...
storage extensions
2019-09-19 05:28:05 -04:00
James Agnew
6b21e8cd90
Add some testing to the bulk export service
2019-09-18 14:43:00 -04:00
James Agnew
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
James Agnew
882e0853df
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-16 15:55:49 -04:00
James Agnew
38cf830384
Accurately reflect codesystem URL
2019-09-16 15:55:32 -04:00
Diederik Muylwyk
3a9342913c
Address review comments. Added tests.
2019-09-16 11:54:34 -04:00
Diederik Muylwyk
b05c5f3f71
Implement the parent and child filters for LOINC. #1453
2019-09-15 21:52:33 -04:00
Diederik Muylwyk
9b1af6b207
Implement both a copyright property and a copyright filter for LOINC. #1451
2019-09-13 16:18:51 -04:00
Diederik Muylwyk
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
Diederik Muylwyk
75ddba7f2d
Add EXTERNAL_COPYRIGHT_NOTICE property for LOINC uploader.
2019-09-13 11:49:01 -04:00
Diederik Muylwyk
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
Diederik Muylwyk
65e029458c
Test fixes.
2019-09-10 17:50:49 -04:00
Diederik Muylwyk
d4feb5d0b1
Final cleanup before review.
2019-09-10 14:21:42 -04:00
James Agnew
9420bca341
Merge branch 'master' into ks-in-memory-date-compare
2019-09-10 13:25:29 -04:00
Diederik Muylwyk
57d4cc23ee
More bug-hunting. DSTU3 was missing a null check.
2019-09-10 11:56:07 -04:00
James Agnew
0843a2b02d
Avoid leaking details when canSeeReource rejects a resource from consent
...
service
2019-09-10 11:14:44 -04:00
Ken Stevens
c974e9283b
added search % now test
2019-09-10 10:11:09 -04:00
Diederik Muylwyk
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
Diederik Muylwyk
dbe5a36f26
Reset schedule for pre-expansions. Ready for review.
2019-09-09 18:44:25 -04:00
Diederik Muylwyk
7e76c1893f
Fixed bug for large ValueSet expansion with URL parameter; return 404 for unknown ValueSets.
2019-09-09 18:41:00 -04:00
James Agnew
2052df3152
Error with a 404 on invalid valueset
2019-09-09 18:01:41 -04:00
Diederik Muylwyk
19676a01b7
Incremental progress on large ValueSet expansion with URL parameter.
2019-09-09 17:24:01 -04:00
Diederik Muylwyk
c82c3a093f
Removing gaps from concept order when pre-expanding ValueSets.
2019-09-09 15:24:37 -04:00
jamesagnew
95e75d0a7d
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-09 15:02:55 -04:00
Diederik Muylwyk
4fc0ad6f0a
Cleanup following paired programming with JA.
2019-09-06 17:56:56 -04:00
James Agnew
6ec991cd39
Finally this is fast!
2019-09-06 16:29:09 -04:00
James Agnew
718fcb28a5
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-06 14:58:03 -04:00
Diederik Muylwyk
0cabc0392f
Incremental progress on large ValueSet expansion.
2019-09-06 14:57:34 -04:00
James Agnew
722c7a8211
Work on GraphQL updates
2019-09-06 14:56:17 -04:00
jamesagnew
362c658f9a
License headers
2019-09-06 10:23:36 -04:00
Ken Stevens
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
James Agnew
785d40a777
Accuont for a few schema changes
2019-09-05 21:29:47 -04:00
Ken Stevens
b1421b1d60
@NotNull (hope I picked the right one!)
2019-09-05 16:20:24 -04:00
Ken Stevens
2a08808935
final PR cleanup
2019-09-05 16:11:58 -04:00
Diederik Muylwyk
6fa9658b24
Incremental progress on large ValueSet expansion.
2019-09-05 15:54:45 -04:00
Diederik Muylwyk
655222fcac
Merging master into working branch.
2019-09-05 11:59:44 -04:00
Diederik Muylwyk
91cfecd257
Incremental progress on large ValueSet expansion.
2019-09-05 11:43:31 -04:00
Ken Stevens
01015bc435
added list stresstest
2019-09-04 21:15:08 -04:00
Ken Stevens
1f60d85517
Merge branch 'ks-anylist-enhancement' into ja_20190822_1440_infinispan_query_cache
2019-09-04 13:31:19 -04:00
Ken Stevens
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
Ken Stevens
0a5c52122e
added list stresstest
2019-09-04 08:49:18 -04:00
Diederik Muylwyk
b00b1d2278
Toggle pre-expansion config.
2019-09-03 20:36:54 -04:00
Diederik Muylwyk
ea19b46f60
Added an indexed order column to TermValueSetConcept for improved fetching.
2019-09-03 20:36:16 -04:00
Diederik Muylwyk
aa9a984075
Don't trust stored total when determining whether or not to expand.
2019-09-03 18:44:52 -04:00
Diederik Muylwyk
358f649d1f
Minor tweaks following review.
2019-09-03 17:14:31 -04:00
Diederik Muylwyk
3e522a7414
Address review comments.
2019-09-03 16:37:28 -04:00
Diederik Muylwyk
6ebc9572ac
Adjust concept and designation totals as we process.
2019-09-03 16:23:20 -04:00
Diederik Muylwyk
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
jamesagnew
1ef70a0fca
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-03 07:02:09 -04:00
jamesagnew
8b09b3f3eb
Rename config enum for consistency
2019-09-03 07:01:36 -04:00
Diederik Muylwyk
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
Diederik Muylwyk
c34d8458ef
Refactor getting resource PIDs with utility methods.
2019-09-02 18:16:46 -04:00
Diederik Muylwyk
16963881b0
Reset pre-expansion schedule.
2019-08-30 19:36:34 -04:00
Diederik Muylwyk
548647defe
Toggle pre-expansion config.
2019-08-30 19:31:45 -04:00
Diederik Muylwyk
f29abd7167
Fixed ResourceTable lookups for pre-expansion and code validation.
2019-08-30 19:31:05 -04:00
Diederik Muylwyk
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
Diederik Muylwyk
8ef9c61b83
Address review comments; improve logging.
2019-08-30 10:47:21 -04:00
James Agnew
8700088c67
Missed a keyword
2019-08-29 22:06:43 -04:00
James Agnew
668af76514
Make method static again
2019-08-29 22:03:58 -04:00
James Agnew
347aada62e
Add a setter for unit tests
2019-08-29 21:43:29 -04:00
James Agnew
dbe86c8669
One more test fix
2019-08-29 21:35:07 -04:00
James Agnew
1b1d80b850
Test fix
2019-08-29 21:02:19 -04:00
Diederik Muylwyk
e03d6a5d47
Fixed handling of pre-expansion in light of pre-existing, non-pre-expanded ValueSets.
2019-08-29 18:09:30 -04:00
James Agnew
c5a88444b6
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-08-29 14:00:37 -04:00
James Agnew
956bb39327
Resolve an inefficient regex expression
2019-08-29 13:59:31 -04:00
Diederik Muylwyk
c22bf8b09f
Fixed handling of client-assigned IDs throughout terminology services.
2019-08-29 10:48:54 -04:00
Diederik Muylwyk
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
Ken Stevens
d2ae3c24a1
FIXME
2019-08-28 16:26:56 -04:00
Ken Stevens
3e58962ac1
Split search cache api from search result cache api.
2019-08-28 16:24:56 -04:00
Ken Stevens
eab589bcac
fixed intermittently failing test
2019-08-28 13:11:44 -04:00
Ken Stevens
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
Diederik Muylwyk
9ef0519b4c
validate-code operation has been optimized for large ValueSets; submitting pull request.
2019-08-27 21:15:12 -04:00
Diederik Muylwyk
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
Diederik Muylwyk
94c7fc49fd
Making LOINC filenames configurable; fix implicit ValueSet URL for loinc-all.
2019-08-27 13:46:42 -04:00
Diederik Muylwyk
1adfda44d9
Making LOINC filenames configurable; ready for review.
2019-08-27 11:19:01 -04:00
James Agnew
70d0a8aa8f
Get patch working ( #1449 )
2019-08-27 05:42:15 -04:00
Diederik Muylwyk
f4789247b2
Making LOINC filenames configurable; fix IEEE medical device code property key.
2019-08-26 18:46:57 -04:00
Diederik Muylwyk
0765254024
Making LOINC filenames configurable; initial commit.
2019-08-26 18:32:21 -04:00
Diederik Muylwyk
0ee15874ca
loinc-all ValueSet is now created automatically when loading LOINC terminology.
2019-08-26 16:42:37 -04:00
Diederik Muylwyk
073d2a45a4
Multiaxial hierarchy support is implemented; we not populated parent and child properties.
2019-08-26 14:26:38 -04:00
Ken Stevens
17f58a61c3
Revert "add accessor to search hash"
...
This reverts commit 2dc70c92
2019-08-24 14:13:06 -04:00
Ken Stevens
2dc70c92f1
add accessor to search hash
2019-08-24 14:10:17 -04:00
Diederik Muylwyk
b41926307c
Completed work on large ValueSet expansion support; ready for review.
2019-08-23 17:40:45 -04:00
James Agnew
10958a8e4d
I think this might work now..
2019-08-23 12:22:27 -04:00
James Agnew
c564052b15
One more test fix
2019-08-23 11:46:56 -04:00
Diederik Muylwyk
890555a77d
Incremental work on large ValueSet expansion support; transaction boundaries need to be broken up.
2019-08-23 11:46:32 -04:00
James Agnew
c346ba92c8
Revert accidental commit
2019-08-23 11:17:02 -04:00
James Agnew
abc894ce90
A few refactors based on ken's suggestions
2019-08-23 10:57:58 -04:00
James Agnew
6fa27934a8
Tests all seem to be working
2019-08-23 10:14:13 -04:00
Diederik Muylwyk
97a235ddfc
Merging master into working branch.
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
2019-08-22 14:02:56 -04:00
Diederik Muylwyk
72dd6b2922
Incremental work on large ValueSet expansion support; fixed broken deletion for TermValueSetConceptDesignation.
2019-08-22 14:00:08 -04:00
James Agnew
4afa55ea26
Initial commit - Not yet compiling
2019-08-22 08:49:34 -04:00
Ken Stevens
37c1ba44fe
Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump
2019-08-21 15:04:16 -04:00
James Agnew
9428430822
Add support for Resource.meta.source ( #1438 )
...
* Work on indexing source
* Work on tests
* Refactor query count tests
* Unit test fixes
* Add some tests
* DAO fix
* Fix compile error
* Unit test fix
* Cleanup
* Test fix
* Fix compile error
* One more test fix
2019-08-21 11:17:43 -04:00
Diederik Muylwyk
3218bd7853
Incremental work on large ValueSet expansion support; implemented paging when reading concepts from the terminology tables. Switched from Derby to H2.
2019-08-20 18:11:53 -04:00
Ken Stevens
5703b55e88
Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump
2019-08-20 15:08:25 -04:00
Ken Stevens
df7469731b
turn of sql queries
2019-08-20 15:02:02 -04:00
James Agnew
ce44115152
Handle cascading deletes correctly with circular references ( #1435 )
...
* Handle cascading deletes correctly with circular references
* A bit of cleanup
* Address review comments
* FIx some javadocs
* Fix an incorrect message
2019-08-20 10:08:34 -04:00
Ken Stevens
daf45db2be
fixed a test and removed awaitility excludes
...
mvn install completed successfully
2019-08-20 09:14:21 -04:00
Diederik Muylwyk
70aef7fbbb
Incremental work on large ValueSet expansion support; need pageable results while querying TRM_VALUESET_CONCEPT.
2019-08-19 18:43:43 -04:00
Diederik Muylwyk
53364a3af1
Downgraded FIXMEs to TODOs regarding -code for large ValueSets.
2019-08-19 02:50:01 -04:00
Diederik Muylwyk
8590e0ca4d
Merging master into working branch.
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
2019-08-19 02:28:30 -04:00
Diederik Muylwyk
dfd098c374
Incremental work on large ValueSet expansion support; added use of terminology tables when expanding.
2019-08-19 02:26:12 -04:00
jamesagnew
54657214de
FIx issue uploading US Core resources
2019-08-17 18:11:52 -04:00
jamesagnew
89aa37ea6a
Add a test
2019-08-17 15:16:11 -04:00
jamesagnew
81adc5c99e
Merge master
2019-08-17 14:31:30 -04:00
Ken Stevens
970c421311
allow urls in batch transactions to start with /
2019-08-17 14:31:30 -04:00
jamesagnew
f252cda126
Test fixes
2019-08-17 14:15:28 -04:00
James Agnew
74c83f6148
Test fixes
2019-08-17 12:01:04 -04:00
James Agnew
9e8af58e81
Fix reference params via filter
2019-08-16 14:56:36 -04:00
James Agnew
4490c9ca09
Correct the eq operator on the _filter parameter
2019-08-14 14:39:40 -04:00
Sean McIlvenna
b37c4b5ae7
Fixing broken unit tests
2019-08-14 14:35:18 -04:00
Sean McIlvenna
d92be90789
Changes to subscriptions to include the resource that triggered the subscription in the payload, serialized as JSON or XML depending on the Subscription.channel.payload property's value
2019-08-14 14:35:18 -04:00
jamesagnew
e1b43d811f
Version bump to 4.1.0-SNAPSHOT
2019-08-14 14:06:06 -04:00
jamesagnew
3f22456b0f
Bump version to 4.0.0
2019-08-14 11:06:26 -04:00
James Agnew
b4fece0ae9
Add interceptor hook for graphql calls
2019-08-13 14:46:50 -04:00
jamesagnew
e2f0f4ed8b
License header updates
2019-08-13 05:28:35 -04:00
James Agnew
301a8f8432
Merge #1146 - Filter implementation ( #1220 )
...
* Initial commit of _filter keyword implementation.
* - Completed all search parameter types for _filter.
- Implemented handling for _has, _id, _security, language, _profile, _security, and _tag.
* - Changes to support "ne" matching on resource ID for _filter
* Implemented language
* Commit/push before creation of pull request
* Ongoing merge work
* Ongoing merge work
* Merge master in
* Test fix
2019-08-12 11:59:33 -04:00
James Agnew
0c9e5ec1ea
Support GraphQL for R3/4/5 ( #1424 )
...
* Work on grpahql enhanbcements
* Add some more chars to the sanitizer function
* Add changelog
2019-08-12 08:24:32 -04:00
jamesagnew
2999a292e6
Get subscriptions working for R5
2019-08-11 18:32:47 -04:00
jamesagnew
d316ec1146
Fix NPE
2019-08-11 18:25:02 -04:00
James Agnew
2518d4e0be
Add some tests
2019-08-08 15:23:55 -04:00
jamesagnew
4e1bbe681a
Bump supported PGSQL driver
2019-08-08 15:12:29 -04:00
James Agnew
dd0cb10dbb
validate operation ignores parameter profile ( #1417 )
...
* This should be working now - need to check tests
* Add a changelog and some docs
* One more test fix
* Tests should be passing
* Fix compile
* Test fixes
* Ignore outdated DSTU2 validation test
2019-08-07 15:31:59 -04:00
James Agnew
b0eb19cf2f
A few fixes resulting from the R5 merge
2019-08-06 17:55:51 -04:00
James Agnew
60eab3ad70
Add support for R5 resources ( #1416 )
...
* Work so far on R5 support
* Add support for R5
* Docs changes
2019-08-06 17:30:31 -04:00
Diederik Muylwyk
8475aa4cc8
Add TRM_CODESYSTEM_VER.CS_DISPLAY to migration tool.
2019-08-01 14:44:03 -04:00
Diederik Muylwyk
d67de13708
Syncing master into working branch.
2019-08-01 13:51:26 -04:00
Diederik Muylwyk
78842164fd
Addressing review comments.
2019-08-01 13:37:46 -04:00
jamesagnew
46c8c61932
Restore build - May need to roll back the RDF changes
2019-08-01 10:14:56 -04:00
Diederik Muylwyk
ffda92514a
Incremental work on large ValueSet expansion support; still need to actually use the terminology tables when expanding.
2019-07-31 16:33:50 -04:00
Diederik Muylwyk
0e2dcce841
Incremental work on large ValueSet expansion support; still need to fix asynchronous tests and actually use the terminology tables when expanding.
2019-07-31 15:52:25 -04:00
James Agnew
3196bc370f
Add a default implementation to new terminology service loader method
2019-07-31 10:07:51 -04:00
James Agnew
b956b7552e
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-07-30 17:52:47 -04:00
James Agnew
04ce9cfc1a
Add support for uploading custom terminology using the
...
$upload-external-code-system operation
2019-07-30 17:30:18 -04:00
Diederik Muylwyk
d1cba9f928
Syncing master into working branch.
2019-07-29 19:39:29 -04:00
jamesagnew
cf5201c67b
Add a constructor
2019-07-29 19:31:47 -04:00
Diederik Muylwyk
a8489f4331
Added TRM_VALUESET.EXPANSION_STATUS column, index, fields to entity, and migration tasks.
2019-07-29 19:30:46 -04:00
jamesagnew
a3cbdf0956
Make terminologyuploaderprovider not abstract
2019-07-29 19:02:51 -04:00
James Agnew
b030d1af31
Test fixes
2019-07-29 18:17:40 -04:00
James Agnew
a4ca5374ec
Add terminology delta operations ( #1401 )
...
* Start work on delta operations
* Add changelog
* Some build fixes
* Move upload terminology command to CodeSystem resource
* Updates
* Some test fixes
* Add changelog
* Some test fixes
* More test fixes
* Test fix
* Add additional tests
* Transaction boundary fixes
2019-07-29 17:46:42 -04:00
Diederik Muylwyk
d03fc0f61d
Add null check for shortName before adding designation. ( #1396 )
2019-07-25 11:06:02 -04:00
Ken Stevens
a7817b07ca
Pre PR cleanup
2019-07-24 22:00:34 -04:00
Ken Stevens
a20b738161
Pre PR cleanup
2019-07-24 22:00:26 -04:00
Ken Stevens
84f5c7d467
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-24 21:54:05 -04:00
Ken Stevens
e05387da02
Recover from failed merge again. This time with feeling!
2019-07-24 13:46:20 -04:00
James Agnew
ddb8e385bf
Test fix
2019-07-24 13:24:48 -04:00
James Agnew
b78cd1e62e
Merge branch 'add-pid-to-created-resource'
2019-07-24 13:19:38 -04:00
James Agnew
e8cf2738f0
Handle oversized payload request
2019-07-24 13:18:30 -04:00
James Agnew
b9dbd69e5d
Fix limiting on size
2019-07-24 13:11:05 -04:00
Ken Stevens
37411a6ae2
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-24 10:41:11 -04:00
jamesagnew
6b599c29e5
Merge branch 'add-pid-to-created-resource'
2019-07-23 17:36:15 -04:00
James Agnew
bff39e4139
Try to deal with an intermittent failure
2019-07-23 15:58:14 -04:00
James Agnew
9094323c43
Add a test
2019-07-23 14:47:27 -04:00
James Agnew
b1e409519d
Add a test
2019-07-23 14:47:27 -04:00
Ken Stevens
8d86e34bcf
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
2019-07-23 09:12:08 -04:00
jamesagnew
60ea922e8d
Add license headers
2019-07-23 05:38:10 -04:00
James Agnew
7e3d062d15
Switch default client to JSON ( #1392 )
...
* Start work on changing over
* Update tests
* More test fixes
* Work on generalizing binary access provider a bit
* Add expunge capability to binary storage, and also support actual binary
resources
* Work on binary provider
* Get the DB bound binary storage service working
* Test fixes
* Compile fix
* Fix compile error
* Test fix
* Test tweak
* Trying to figure out an intermittent failure
* Work on tests
* More work on tests
* Another test fix
2019-07-22 21:27:10 -04:00
Ken Stevens
7ba3ceec90
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-19 10:54:56 -04:00
James Agnew
458cfcfa12
Fix intermittent test failure
2019-07-19 10:46:49 -04:00
James Agnew
f53746cd63
One more set of migrator tweaks to account for latest changes
2019-07-19 10:10:00 -04:00
Ken Stevens
e634aa6d10
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-18 22:06:10 -04:00
James Agnew
5bf4fa22e7
Allow patching in tranactions
2019-07-18 16:41:07 -04:00
Ken Stevens
a7fa79331a
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-18 13:14:54 -04:00
James Agnew
87ab796309
Updates to validating interceptor
2019-07-18 12:57:30 -04:00
Ken Stevens
ffa008b2dd
Fixing a build error
2019-07-18 10:59:11 -04:00
Ken Stevens
72aa4932d6
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-18 10:12:15 -04:00
James Agnew
ee7cff9445
Rename a few columns to not conflict with res´rved words
2019-07-18 05:47:32 -04:00
jamesagnew
7488047686
Add license headers
2019-07-17 18:53:23 -04:00
James Agnew
55c0d5b604
Add binary storage for Attachments ( #1386 )
...
* Have this working now
* Add utility method
* Build fixes
* Add changelog
2019-07-17 18:31:17 -04:00
Ken Stevens
c73aebe0a0
IResource and IAnyResource are mutually exclusive...
2019-07-17 17:59:49 -04:00
Ken Stevens
465b4daa03
Changed IAnyResource to IResource per feedback
2019-07-17 17:59:49 -04:00
Ken Stevens
1d4dc5b3c5
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_UPDATED hooks are called
2019-07-17 17:59:49 -04:00
Ken Stevens
e27685e811
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_CREATED hooks are called
2019-07-17 17:59:49 -04:00
Ken Stevens
7bc8517fc6
Merge branch 'add-pid-to-created-resource' into expunge-resource-hook
2019-07-17 14:26:00 -04:00
Ken Stevens
6960f1db1c
IResource and IAnyResource are mutually exclusive...
2019-07-17 14:25:10 -04:00
Ken Stevens
a5da696823
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-17 13:28:29 -04:00
Ken Stevens
d21304e771
cleanup
2019-07-17 13:28:17 -04:00
Ken Stevens
fe21dba4a6
Added Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE.
...
Also added a couple of tests.
2019-07-17 13:26:50 -04:00
James Agnew
76384abefb
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-07-17 10:57:43 -04:00
Ken Stevens
160b221f5f
Changed IAnyResource to IResource per feedback
2019-07-17 10:26:16 -04:00
Ken Stevens
79ce4a30cc
Merge remote-tracking branch 'remotes/origin/master' into add-pid-to-created-resource
2019-07-16 20:46:31 -04:00
Diederik Muylwyk
456aac5e16
Resolve "experimental implementation for storing and expanding large ValuetSets cont'd..." ( #1376 )
...
* Added experimental implementation for storing expanded ValueSets in terminology tables.
* Minor tweak to log message for consistency.
* Another minor tweak to log message for consistency.
* Renamed test.
* Initial work on ValueSetCodeAccumulator.
* Renamed addCode() to includeCode(); added excludeCode().
* Incremental work on large ValueSet expansion support; refactoring.
* Incremental work on large ValueSet expansion support; accounting for designations.
* Incremental work on large ValueSet expansion support; fixed missing designation.language in expanded ValueSets.
* Incremental work on large ValueSet expansion support; now actually populating TermConceptDesignation; added TermValueSetConceptDesignation as well.
* Missed a word.
* Tweak changelog entries.
2019-07-16 17:12:21 -04:00
Ken Stevens
634718c503
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_UPDATED hooks are called
2019-07-16 16:36:05 -04:00
Ken Stevens
fe7d38d0b5
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_CREATED hooks are called
2019-07-16 15:33:51 -04:00
James Agnew
f8444b90c8
Test tweak
2019-07-14 18:11:37 -04:00
James Agnew
7831e8a0ed
Add support for $snapshot generation and validation based on snapshots
2019-07-14 16:15:56 -04:00
James Agnew
120b93f204
Use HL7 FHIR Core Structures ( #1382 )
...
* Ongoing work on core structures suport
* Ongoing work on this merge
* Ongoing work to clean up structures
* Credit for #1179
* Address compile issues
* Latest changes
* Work on parallel execution
* Work on getting tests passing
* Add H2 to migrator
* Test fix
2019-07-14 10:16:40 -04:00
jamesagnew
534c71c1d5
Higher parallel count for JPA tests
2019-07-13 18:24:31 -04:00
James Agnew
ba4bb005bc
Switch JPA unit tests to use H2 ( #1381 )
...
* Start working on this
* Ongoing fixes to H2 branch
* Work on fixing tests
* Updated fixes
* Some test fixes
* More work on H2 migration
* Fixes to try and get the H2 migration building
* Test seem to be passing!
* Tweaks to locale randomization
* Add changelog
2019-07-13 17:22:43 -04:00
Ken Stevens
8d817b364c
Merge remote-tracking branch 'remotes/origin/master' into expunge-hooks
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
2019-07-12 13:27:11 -04:00
jamesagnew
a5a9950e77
License header updates
2019-07-12 08:52:47 -04:00
James Agnew
afd2b35ff6
Fix an intermittent test failure
2019-07-12 06:32:18 -04:00
James Agnew
1db019b6df
Test fix and try to get Travis building again
2019-07-11 20:20:27 -04:00
Diederik Muylwyk
62e1b7e9ea
Fixing minor overlooked change from recent pull request.
2019-07-11 17:07:26 -04:00
Diederik Muylwyk
0729e38e6e
Resolve "experimental implementation for storing expanded ValueSets in terminology tables" ( #1369 )
...
* Added experimental implementation for storing expanded ValueSets in terminology tables.
* Minor tweak to log message for consistency.
* Another minor tweak to log message for consistency.
* Renamed test.
* Addressing review comments.
* Added migration tasks.
2019-07-11 16:52:19 -04:00
Ken Stevens
7aaa75c255
fixed pointcut
2019-07-10 10:09:43 -04:00
Ken Stevens
5e05703c1a
Add expunge-everything hook. Also add RequestDetails to all expunge operations
2019-07-09 10:58:57 -04:00
jamesagnew
9fcbdb0cdc
License header updates
2019-07-07 14:41:57 -04:00
James Agnew
6c221efaf6
More test fixes
2019-07-07 14:09:55 -04:00
James Agnew
d00304d706
More test fixes
2019-07-07 13:35:39 -04:00
James Agnew
34f7d4ddbd
Refactor ServerConformanceProvider so that it no longer keeps any state
2019-07-07 12:57:31 -04:00
James Agnew
4bd60a8447
Roll back one dependency
2019-07-07 11:02:08 -04:00
James Agnew
1c7c83cd8e
Add an isEmpty() method to IBundleProvider
2019-07-05 16:16:39 -04:00
jamesagnew
dff2fdd3cf
GET RID OF TRAILING LICENSE HEADER SPACES ONCE AND FOR ALL
...
YESSSSSSSSSSSSS
2019-07-05 11:19:51 -04:00
James Agnew
4a0bc27602
Test fix
2019-07-05 09:37:48 -04:00
James Agnew
2a473d1825
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-07-05 09:03:23 -04:00
James Agnew
2a6436af23
Rename columns in code mapping
2019-07-05 09:03:03 -04:00
jamesagnew
aff88d3ebb
License header updates
2019-07-05 07:27:18 -04:00
James Agnew
6e20b53979
Fix a crash in R4 validation
2019-07-04 16:27:04 -04:00
James Agnew
4f7d4aa8d2
Two test fixes
2019-07-04 09:54:26 -04:00
James Agnew
886f3f442b
Moving testloggingutil into test utilities
2019-07-04 09:00:30 -04:00
James Agnew
f1848fb1ad
Include version ID in response for deleted resource
2019-07-03 14:44:12 -04:00
James Agnew
56aaef641c
Add request ID
2019-07-02 21:32:28 -04:00
James Agnew
1faf7785c4
Dont filter constraints from the event broadcast - this was not needed
...
after all
2019-07-02 09:21:15 -04:00
jamesagnew
7b7136e3ab
Ensure test coverage of JPA entities
2019-07-02 08:37:48 -04:00
jamesagnew
491776a7b8
Fixes to cascading delete
2019-07-02 05:41:38 -04:00
jamesagnew
742389642d
Add tests for delete conflicts and authorizationinterceptor
2019-07-01 10:49:38 -04:00
jamesagnew
ccf491b3ae
Add parent pom to BOM
2019-06-29 13:50:43 -04:00
James Agnew
1fd99dac63
Enable optional cascading deletes on JPA server ( #1363 )
...
* Start working on cascading deleets
* WOrk on cascading deletes
* Work on cascading deletes
* Enable cascading deletes
* Cascade deletes almost working
* FIx test
* Test fix
2019-06-28 17:32:39 -04:00
Joel Schneider
5c55133275
quick hack to pass unit test (handle files located in subdirectories of zipfile)
2019-06-28 15:11:16 -04:00
Joel Schneider
557c9b66c2
add TerminologyLoaderSvcImgthlaTest
2019-06-28 15:11:16 -04:00
Joel Schneider
5d113c2e8b
Remove allele_id property. (If needed, a CodeSystem supplement could define it. Defining a separate allele_id CodeSystem, and related ConceptMap, may also be a reasonable option.) Trying to keep the list of concept properties as straightforward as possible for now.
2019-06-28 15:11:16 -04:00
Joel Schneider
1f5cbc36b3
add stub for HLA nomenclature terminology upload
2019-06-28 15:11:16 -04:00
jamesagnew
5910131319
License header updates
2019-06-27 18:23:45 -04:00
James Agnew
10d969c514
Add Consent Service ( #1359 )
...
* Initial consent svc
* Ongoing consent svc work
* Add docs
* Ongoing consent service work
* Work on consent service
* More work on consent svc
* License header updates
* Ongoing consent svc work
* Some test fixes
* Some test fixes
* More work on consent svc
* Tests working
* Test fix
* Propagate RequestDetails to everything in JPA server
* More interceptor tweaks
* Fix compile error
* One more tweak to captured SQL
* Ongoing interceptor tweaks
* Ongoing interceptor tweaks
* More interceptor tweaks
* Interceptor tweaks
* Tweaks to tests
* Fix tests
* Test fix
* Raise warnings when encoding extensions with missing values
* Consent service work
* More interceptor tweaks
* Consent interceptor tweaks
* Add logging to test
2019-06-27 16:35:29 -04:00
James Agnew
2bfbea4e6b
Remove duplicate test class
2019-06-26 09:24:36 -04:00
James Agnew
ce0c84db03
JPA server can't use OR list on _tag:not ( #1362 )
...
* Add a failing test for :not tags
* Add changelog and fix issue
2019-06-26 08:44:56 -04:00
jamesagnew
e76b1dacb3
License header updates
2019-06-22 18:31:16 -04:00
jamesagnew
8bb010bb18
Test fixes
2019-06-22 17:42:02 -04:00
jamesagnew
3ba194acbe
Reject subscriptions in JPA server if status field is not set
2019-06-22 17:03:22 -04:00
jamesagnew
0fbde2a4e5
Fix #1352 - Don't fail to create observation with a value type of
...
SampledData
2019-06-22 16:43:25 -04:00
James Agnew
4ad1808da3
Propagate RequestDetails to everything in JPA server ( #1358 )
2019-06-22 15:18:06 -05:00
jamesagnew
58e6b7f6aa
Fix #1011 - Was resolved in #1355
2019-06-22 16:03:35 -04:00
jamesagnew
989e26fdb4
Fix #1355 - Failed to call access method: java.lang.NullPointerException in case of bundle entry without resource
2019-06-22 15:51:56 -04:00
James Agnew
2543f27697
Add a test
2019-06-21 15:38:16 -04:00
Diederik Muylwyk
266384b536
Evaluation of PartTypeName in LoincRsnaPlaybookHandler is not case insensitive.
2019-06-21 15:36:51 -04:00
jamesagnew
9e9be00088
License eader updates
2019-06-17 21:59:03 -04:00
James Agnew
6724fd0348
Implement the $subsumes operation ( #1344 )
...
* Implement the $subsumes operation
* Fix #976
2019-06-17 17:31:24 -04:00
jvi
8b4ceb8d5f
changed json patch framework to slightly more maintained fork
2019-06-17 16:45:17 -04:00
James Agnew
b2e99cf035
Add support for conditional patch ( #1348 )
...
* Add support for conditional patch
* Add changelog
* Test fix
2019-06-17 16:12:05 -04:00
jamesagnew
087c53286c
License header updates
2019-06-14 18:43:55 -04:00
Stig Rohde Døssing
b56f59542a
Move JettyUtil to new module
2019-06-14 18:34:45 -04:00
Stig Rohde Døssing
aab7bb6b64
Issue-1325: Let OS assign random ports to servers during testing, and let tests get the port of the running server once the OS has assigned a port. Delete PortUtil and similar utilities.
2019-06-14 18:34:45 -04:00
Ken Stevens
19dd7ebc2e
try excluding stress tests from build
2019-06-13 15:21:03 -04:00
Ken Stevens
2bf680509b
DeleteConflict hook, SearchableHashMapResourceProvider, and in-memory searching ( #1341 )
...
* Make IBundle list interface more flexible
* Make matchResourceLinks visible
* Make matchResourceLinks visible
* Pull in-memory matching functionality out of subscription module into dedicated classes in searchparam module
* Added more accessors to version independent resource classes
* improved forcedid matching (needs to be verified by James)
filter out nulls from HashMapProvider.searchAll() (hopefully no tests depend on this)
* add AnyComposition
* cleanup of Any classes
* create searchparam config so people can use that module without using subscriptions
* create searchparam config so people can use that module without using subscriptions
* fix broken test
* added derivedFrom
* renamed daoRegistry.getResourceDaoIfExists to getResourceDaoOrNull
also added method to add a new dao to the registry and retrieve registered types
* TokenParam.equals
* add error check to searchable hashmap resource provider
* added support for R4
* add successor to measure
* delete conflict hook
start with failing test
* test passes.
hook is called.
* added delete conflict hook
all delete conflict tests pass
* added javadoc
* Performance test
* test bad interceptor case
* typo
* rename criteria matcher
* added support for multiple topics
* fix method name
* add effective period
* Temporarily excluding StressTest from build to try to get Travis under time limit
* change log
* review feedback
* review feedback
* review feedback
2019-06-13 13:59:51 -04:00
James Agnew
c2aec5c1a9
Respect the _total parameter for all JPA searches
2019-06-09 05:44:49 -04:00
jamesagnew
b72f1c4555
Roll back derby upgrade
2019-06-08 09:27:28 -04:00
James Agnew
517b68882c
Fix derby dependencies for tests
2019-06-07 11:11:25 -04:00
Ken Stevens
5752a6e2b3
reported issue with proposed fix that breaks tests ( #1243 )
...
* reported issue with proposed fix that breaks tests
* Fix spelling
* Merge my changes into this
* Correctly check referential integrity on deletes
* Add one more test
2019-06-04 20:40:20 -04:00
James Agnew
be06c2ee19
Correctly index timing events
2019-05-31 16:42:45 -04:00
James Agnew
f6c7ff1dbb
Modify expunge everything to use small batches of deletes
2019-05-31 11:05:17 -04:00
James Agnew
95af87f658
Test fix
2019-05-30 21:46:05 -04:00
James Agnew
f2be9f47a0
Add 4.0.0 version enum
2019-05-30 20:59:23 -04:00
James Agnew
50a8c66bf5
Version bump to 4.0.0-SNAPSHOT
2019-05-30 17:13:03 -04:00
jamesagnew
73aa53be8f
Release 3.8.0
2019-05-30 16:50:04 -04:00
James Agnew
cb8634f26f
Ja interceptor callback fix ( #1308 )
...
* Interceptor callback fix
* Ensure that interceptor methods are called after a transaction
2019-05-14 18:47:11 -04:00
James Agnew
d4d3178621
A couple of test fixes
2019-05-11 15:04:44 -04:00
James Agnew
444730373b
Fix an NPE in validation
2019-05-10 12:49:34 -04:00
James Agnew
92bd2c7173
Fix regression in validator when validating codesystems explicitly
...
defined in the JPA database
2019-05-10 12:08:40 -04:00
James Agnew
6b37525f2d
Clean up redundant dependencies ( #1306 )
...
* Remove a bunch of unneedd deps
* Test fix
* Disable useless test
2019-05-09 12:51:13 -04:00
James Agnew
702ffd631d
Fix #1299 - Return an HTTP 201 when creating a previously deleted
...
resource
2019-05-06 16:33:23 -04:00
James Agnew
61902da527
Tweak to validator
2019-05-06 10:18:55 -04:00
James Agnew
64f57b9736
Fix broken R4 serrver
2019-05-05 09:12:26 -04:00
James Agnew
7a320729a0
One more test fix
2019-05-04 14:57:18 -04:00
James Agnew
9353ea5b06
Enable websockets on public HAPI server
2019-05-04 10:06:10 -04:00
Ken Stevens
b860269eb9
fix broken test
2019-04-29 11:12:08 -04:00
Ken Stevens
10f7eb31eb
fixed delete reference error message
2019-04-29 10:20:45 -04:00
jamesagnew
ddf12e7c28
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-28 11:17:18 -04:00
jamesagnew
c1bf6d0b3c
License headers
2019-04-28 10:46:52 -04:00
James Agnew
828df1528f
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-26 11:24:00 -04:00
James Agnew
685adf7754
Revert Jetty upgrade, and improve patch error messages
2019-04-26 11:23:22 -04:00
Ken Stevens
130e879d04
Delete performance ( #1286 )
...
* move expunge out
* move to prototype
* turns parameters into fields
* cleanup control flow
* moved transactions outside of loops
* add expungeeverything
* moved daos out
* add expungeThreadCount
* add expungeBatchSize
* added partition runner to run in separate threads
* all done. just need to consolidate test code.
* Moar tests
* consolidated pointcutlatch into hapi-fhir-jpaserver-model
* final cleanup
* update javadoc
* change log
* failing test
* added delete
also @Transactional
* remove unused parameter
* fix compile
* race condition
(cherry picked from commit e1940d2fb20838859a205f2b96c833b0ce9f05eb)
# Conflicts:
# hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/PartitionRunnerTest.java
* ja feedback
* ja feedback
2019-04-25 15:38:37 -04:00
jamesagnew
abd53c0cbe
License header updates
2019-04-24 21:20:11 -04:00
James Agnew
c8c81c2ebc
FIx invalid patch syntax
2019-04-24 15:00:03 -04:00
James Agnew
da962b8c10
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-24 14:33:28 -04:00
James Agnew
738c2c1797
Interceptor framework refactoring ( #1287 )
...
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
James Agnew
f2e382a132
Swap JSON Patch provider
2019-04-24 14:10:21 -04:00
Ken Stevens
a57e50317d
Websocket cleanup ( #1275 )
...
* fix bug in websocket subscription (It wasn't destroying the channel when there are no subscribers)
* add support for removing channel. Also synchronize removal (there was a race condition between sync and queue)
* keep deprecated method for backwards compatibility
* make websocket endpoint configurable
* make websocket context path configurable
* make websocket context path configurable
* trying mvn clean test instead of mvn clean install to see if the build goes faster
* that didn't work at all. reverting.
* change log
2019-04-17 15:03:35 -04:00
jamesagnew
08a9844066
Work on #1280
2019-04-17 09:10:17 -04:00
James Agnew
311246e5f0
Merge pull request #1255 from jamesagnew/addFetchValueSet
...
added fetchValueSet to IValidationSupport and made it public
2019-04-15 17:03:56 -04:00
James Agnew
1e4a497181
Add some tests
2019-04-15 14:44:25 -04:00
jamesagnew
a9cfce3615
Header updates
2019-04-15 12:31:11 -04:00
James Agnew
f7ad0bc0d8
Fix a test regression
2019-04-15 11:34:13 -04:00
James Agnew
0848fdf1eb
Fix broken test
2019-04-15 10:29:55 -04:00
James Agnew
c8f2e4bbc9
Return HTTP 400 for missing body on POST and PUT
2019-04-14 12:32:09 -04:00
James Agnew
380644d19d
Add a bit of logging for search parameters when they can't be found
2019-04-14 12:32:09 -04:00
Ken Stevens
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
jamesagnew
ca8b6acdf9
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-07 07:52:40 -04:00
jamesagnew
884b80c1d7
Improve ability to select active resources
2019-04-07 07:52:21 -04:00
James Agnew
706af5d579
Don't update modified time when performing NOOP update in JPA
2019-04-05 14:36:18 -04:00
Ken Stevens
5299479143
fix broken test
2019-04-04 10:26:09 -04:00
jamesagnew
859bc7d71b
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-03 20:15:19 -04:00
jamesagnew
54e3c50ad7
FIx a build failure
2019-04-03 20:15:07 -04:00
Ken Stevens
1d5f648070
fixed second expunge bug reported by FMCNA
2019-04-03 13:32:10 -04:00
Ken Stevens
de4cc89568
bug fixed
2019-04-03 12:20:49 -04:00
Ken Stevens
28ea97ee9a
reproduced failure reported by FMCNA
2019-04-03 11:42:21 -04:00
James Agnew
767a84bddb
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-04-02 10:56:43 -04:00
James Agnew
8065f0f5fc
Revert one accidental change
2019-04-02 10:56:26 -04:00
jamesagnew
8b5143f436
License header updates
2019-04-02 10:44:41 -04:00
James Agnew
588082aee2
Fix broken test
2019-04-02 10:00:56 -04:00
James Agnew
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
James Agnew
7359b77d99
Address review comments
2019-04-02 09:33:01 -04:00
jamesagnew
835b89f449
Build fixes
2019-04-01 18:55:55 -04:00
James Agnew
3eeca4a8fd
Merge branch 'master' into ja_interceptor_jpa_queries
2019-04-01 09:59:03 -04:00
patrick-werner
1aeb54e94e
added all fetchValueSet Implementations
2019-03-30 21:02:24 +01:00
jamesagnew
8791ed5793
Test tweaks
2019-03-29 17:13:41 -04:00
Ken Stevens
b1d41a8211
named interceptor registries
2019-03-29 14:29:36 -04:00
James Agnew
cf7cd40336
Make sure we properly scope reference queries on external URLs
2019-03-27 13:10:24 -04:00
James Agnew
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
Ken Stevens
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
James Agnew
87c0b3778b
More work on threadlocal interceptors
2019-03-22 09:54:02 -04:00
James Agnew
c701de2861
Create a performance interceptor framework for HAPI FHIR
2019-03-22 01:06:03 +01:00
James Agnew
d1667487c2
Clean up unique composite search params
2019-03-21 21:57:38 +01:00
James Agnew
8d49b4e6d2
Add a test (currently ignored)
2019-03-21 15:59:59 +01:00
jamesagnew
037ed27497
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-03-17 14:09:37 -04:00
jamesagnew
3e57fdb491
Improvements to PortUtil to avoid reusing ports
2019-03-17 14:09:21 -04:00
James Agnew
08c7afb804
Reduce logging in JPA server
2019-03-14 17:42:13 -04:00
jamesagnew
6ff92abecc
License header
2019-03-14 13:32:32 -04:00
James Agnew
e15afbc4f0
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-03-14 13:32:03 -04:00
James Agnew
a8c76450e5
Re-enable contains searches on the public HAPI FHIR server and improve
...
message formatting in HapiLocalizer
2019-03-14 13:19:26 -04:00
jamesagnew
a1046f7729
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-03-12 17:46:03 -04:00
jamesagnew
7b1950aeed
License headers
2019-03-12 17:45:51 -04:00
James Agnew
ed4da7c414
Add setting to disable resource type target validation in JPA
2019-03-12 17:45:19 -04:00
James Agnew
6597a928d5
Fix broken test
2019-03-12 15:45:53 -04:00
James Agnew
00a8f8c759
Fix broken build
2019-03-12 13:13:13 -04:00
James Agnew
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
Ken Stevens
dcfacfea49
Has param no in ( #1232 )
2019-03-10 20:50:24 -04:00
James Agnew
5dccf93506
Fix broken test
2019-03-06 17:15:30 -05:00
James Agnew
f8b8f2d1b0
Move process-message to the correct level
2019-03-06 16:12:43 -05:00
Ken Stevens
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
James Agnew
fd401165a9
Fix an occassional failure in the stress test
2019-03-06 09:32:37 -05:00
James Agnew
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
James Agnew
7896887f67
Updates to transaction processing
2019-02-28 12:23:48 -05:00
James Agnew
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
James Agnew
94f9ffa977
Avoid paging links when offset is artificially set very high
2019-02-25 20:44:22 -05:00
James Agnew
fb06664f70
Clean up paging query
2019-02-25 19:05:19 -05:00
James Agnew
820a3d2296
Collapse conditional UPDATES as well in JPA transactions
2019-02-22 13:49:38 -05:00
James Agnew
43c07077be
Automatically remove duplicate conditional creates in JPA
2019-02-22 12:57:07 -05:00
James Agnew
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
James Agnew
28b4b812ac
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-02-20 15:07:08 -05:00
James Agnew
e7b7ba1a6d
Add caching test
2019-02-20 11:18:02 -05:00
Ken Stevens
01568ab0b5
Fix test race condition.
2019-02-19 21:14:11 -05:00
Ken Stevens
3af0bc7206
changes needed to support different number of consumers in matching vs delivery
2019-02-17 15:23:01 -05:00
James Agnew
c6fcb4fcbf
Allow canonical subscription to hold multiple extensions with the same
...
URL
2019-02-16 15:28:39 -05:00
jamesagnew
1311ded7de
Fix compile issue
2019-02-15 14:55:25 -05:00
James Agnew
c0970ed46d
Fix typo in test
2019-02-15 14:30:38 -05:00
James Agnew
a35f30b18e
Merge pull request #1208 from jamesagnew/reuse-subscription-channels
...
Reuse subscription channels
2019-02-15 13:42:54 -05:00
James Agnew
485335e975
Allow terminology service to work without having Lucene enabled for
...
simple ValueSet expansions
2019-02-14 20:47:28 -05:00
Ken Stevens
ffc5966aa3
Merge branch 'master' into reuse-subscription-channels
...
# Conflicts:
# src/changes/changes.xml
2019-02-14 19:42:00 -05:00
James Agnew
10c348d44f
Tweak to elements parametr support
2019-02-14 19:30:10 -05:00
Ken Stevens
508e15956e
added a couple of subscription tests and un@Ignored another
2019-02-14 15:30:25 -05:00
Ken Stevens
7b3fedc642
sonar
2019-02-13 20:41:11 -05:00
Ken Stevens
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
James Agnew
a5e10740c0
Merge pull request #1194 from jamesagnew/ja_more_subscription_logger
...
More subscription logger work
2019-02-09 11:45:25 -05:00
Ken Stevens
f40614a1aa
fixed bug in in-memory matching for reference id when searchparam has two components
2019-02-08 16:37:08 -05:00
Ken Stevens
52c62884fb
Merge branch 'master' into reuse-subscription-channels
2019-02-08 10:39:00 -05:00
James Agnew
ce840ecb6e
Fix broken test
2019-02-07 17:48:08 -05:00
James Agnew
810f1ad969
Improvements to elements parameter as well as adding attributes to
...
RequestDetails
2019-02-07 16:45:59 -05:00
Ken Stevens
b3e80f8da7
Merge branch 'master' into reuse-subscription-channels
2019-02-07 10:10:10 -05:00
Ken Stevens
4592184c34
fixed typo in logs
2019-02-07 10:06:41 -05:00
James Agnew
0f8c8d18e2
Bump version to 3.8.0-SNAPSHOT
2019-02-06 20:02:28 -05:00
jamesagnew
207015c3af
Version bump to 3.7.0
2019-02-05 21:36:38 -05:00
James Agnew
e3dd296db7
Fix flaky test hopefully?
2019-02-05 15:36:21 -05:00
James Agnew
87a6c24bde
More subscription logger work
2019-02-04 13:49:10 -05:00
James Agnew
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
James Agnew
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
Ken Stevens
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
jamesagnew
5f29e4fbf3
Fix #1174 - Prevent serialization exception
2019-01-30 05:49:45 -05:00
jamesagnew
5d540d9208
Query optimization in JPA
2019-01-27 20:03:48 -05:00
Ken Stevens
10c59fceeb
Subscription strategy tag ( #1178 )
...
tests pass
2019-01-25 13:01:04 -05:00
James Agnew
f55be0b6d0
Test fix
2019-01-25 10:56:17 -05:00
James Agnew
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
Ken Stevens
67eaeb8af1
Merge remote-tracking branch 'origin/windows-fixes' into windows-fixes
2019-01-23 17:14:51 -05:00
James Agnew
e819b83a94
Make busywait more clear
2019-01-23 16:21:13 -05:00
Ken Stevens
cfd67d88c7
Merge remote-tracking branch 'origin/windows-fixes' into windows-fixes
2019-01-23 16:17:48 -05:00
Ken Stevens
5c7907dfea
magic number
2019-01-23 16:17:41 -05:00
James Agnew
7d1d5a102c
Attempt to fix a weird lucene indexing issue
2019-01-23 16:14:53 -05:00
Ken Stevens
2c7eb39b29
final batch of windows fixes (to deal with jumpy windows clock)
...
also added semaphore to PointcutLatch
2019-01-22 18:53:54 -05:00
Ken Stevens
6b22977d7c
fixing more tests for Windows
2019-01-21 22:28:48 -05:00
Ken Stevens
00320da9dc
Merge branch 'master' into windows-fixes
2019-01-21 20:34:01 -05:00
James Agnew
9cf64f78d0
Deprecate a bad setter on RetfulServer, fix a paging issue, and add a
...
disabled unit test to the subscription matcher
2019-01-21 14:46:17 -05:00
Ken Stevens
29f483d7b4
Merge branch 'master' into windows-fixes
2019-01-21 11:06:42 -05:00
Ken Stevens
b4350bbdae
Working through failed tests. Consolidating sleep calls
2019-01-21 11:05:53 -05:00
James Agnew
17f03ac843
Allow null return type for interceptors
2019-01-20 19:44:18 -05:00
James Agnew
c3c7d156e9
Interceptor cleanup
2019-01-20 10:16:18 -05:00
jamesagnew
b878925884
Try to avoid intermittent test failure
2019-01-19 18:44:09 -05:00
jamesagnew
cd1e0e881c
Add headers
2019-01-19 18:31:17 -05:00
jamesagnew
b0cbd52ae9
Interceptor cleanup
2019-01-19 18:01:00 -05:00
James Agnew
29c3cee287
Merge pull request #1172 from jamesagnew/ja-subscription-interceptors
...
Ja subscription interceptors
2019-01-19 07:13:14 -06:00
James Agnew
3e84173180
Merge branch 'master' into ja-subscription-interceptors
2019-01-18 17:52:23 -05:00
Ken Stevens
3d07fc1c22
fixed null subscription id ( #1170 )
...
* fixed null subscription id
2019-01-18 10:39:35 -05:00
James Agnew
5ce9d444e9
Work on interceptors
2019-01-18 09:04:45 -05:00
jamesagnew
5fd084d7cf
Fix a couple of merge conflicts
2019-01-18 05:47:37 -05:00
Volker Schmidt
432ad8e5bc
Subscription without Payload did not contain header.
2019-01-18 05:41:47 -05:00
Ken Stevens
66dc7f82d5
organize imports
2019-01-15 20:55:00 -05:00
Ken Stevens
19afcb7e09
all tests pass
2019-01-15 18:22:08 -05:00
jamesagnew
a584e15251
Add headers
2019-01-14 14:58:27 -05:00
Ken Stevens
4f5640e541
Resilient searchparamregistry ( #1165 )
...
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
James Agnew
4b48eebe8b
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-01-13 12:27:40 -06:00
James Agnew
63b8a70e8a
Allow storing ConceptMap with StructureDefinition as a source or target
2019-01-13 12:24:51 -06:00
James Agnew
068117138e
Merge branch 'master' into subscription-bugfix
2019-01-11 09:05:37 -06:00
Ken Stevens
860a8fb7a6
Emergency fix.
...
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
James Agnew
aee7b2b882
Make sure that sub-request transaction searches and reads preserve HTTP
...
headers
2019-01-10 07:26:04 -07:00
James Agnew
d091665ab6
Test fix
2019-01-09 14:40:43 -05:00
James Agnew
f241457bc1
Merge branch 'master' into test-openjdk-11
2019-01-09 13:42:50 -05:00
Ken Stevens
66dd6dc96c
updated documentation
2019-01-09 13:39:32 -05:00
Ken Stevens
cdf1cd9144
undoing inadvertent comment changes
2019-01-09 13:39:32 -05:00
Ken Stevens
3142ebb892
Fixed typo in class name
...
Added channel extensions to CanonicalSubscription
2019-01-09 13:39:32 -05:00
Ken Stevens
d809569a2d
Added new DaoConfig parameter to control whether subscription matching happens on this server.
2019-01-09 13:39:32 -05:00
James Agnew
8beccab9ab
Merge branch 'master' into test-openjdk-11
2019-01-09 10:48:57 -05:00
James Agnew
62ae71c1c6
Allow authorizing delete operations via a transaction in
...
AuthorizationInterceptor
2019-01-07 15:43:36 -05:00
jamesagnew
a8a97ae6b2
Two test fixes
2019-01-07 09:18:11 -05:00
James Agnew
c104923855
Add an additional test for transaction processing
2019-01-07 09:17:19 -05:00
jamesagnew
8f8385627f
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-01-05 11:33:08 -05:00
jamesagnew
98d93df12a
License header updates
2019-01-04 16:22:15 -05:00
James Agnew
5b8fee869e
Add config options for default Prefer header and _total param on server
2019-01-04 16:12:45 -05:00
James Agnew
ba76492865
Another test fix
2019-01-04 14:04:26 -05:00
James Agnew
137d39e80f
Another test fix
2019-01-04 13:53:24 -05:00
James Agnew
051074d0bc
Work on tests
2019-01-04 13:05:39 -05:00
James Agnew
a1275874f8
Correct subscription delivery metadata
2019-01-04 10:56:21 -05:00
James Agnew
7ba07d9f02
Avoid search failure on Oracle when performing very large includes
2019-01-04 09:11:11 -05:00
James Agnew
31b8a392b7
Better CLI error handling for unit tests
2019-01-03 12:57:18 -05:00
James Agnew
14a132a937
Squashed commit of the following:
...
commit 9659655830
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Dec 27 17:54:25 2018 -0500
Finish sync
commit 70da25b76f
Author: jamesagnew <jamesagnew@gmail.com>
Date: Thu Dec 27 10:32:51 2018 -0500
Work on RI4 sync
2018-12-27 17:58:47 -05:00
jamesagnew
28218c9bba
Version bump for build JDK
2018-12-23 15:14:43 -05:00
Ken Stevens
fedc59a8d6
Subscription module startup changes ( #1154 )
...
* 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
James Agnew
9d3904ef3e
Fix #1142 - Upgrade Spring Boot to latest version
2018-12-23 13:10:03 -05:00