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
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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
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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
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
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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
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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
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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
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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
...
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
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defined in the JPA database
2019-05-10 12:08:40 -04:00
6b37525f2d
Clean up redundant dependencies ( #1306 )
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* 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
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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
Ken Stevens
James Agnew
Clayton Bodendein
Diederik Muylwyk
Sean McIlvenna
Joel Schneider
jvi
Stig Rohde Døssing
Ken Stevens
Ken Stevens