Commit Graph

2235 Commits

Author SHA1 Message Date
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
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