Commit Graph

1173 Commits

Author SHA1 Message Date
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
Diederik Muylwyk 25798ee3e2 Added changelog entry. 2019-09-23 15:54:42 -04:00
Diederik Muylwyk 9d4b5f3041 Merging master into working branch to resolve conflicts.
# Conflicts:
#	src/changes/changes.xml
2019-09-23 09:08:56 -04:00
James Agnew 0a5eca0821 Work on docs 2019-09-22 13:25:50 -04:00
Diederik Muylwyk 0cc35699b8 Specify full path for LOINC filenames to avoid duplicates. 2019-09-20 18:43:38 -04:00
James Agnew a989a746b0 Fix #1494 - Upgrade to new :recurse syntax for R4 include/revinclude
statements
2019-09-20 09:38:29 -04:00
James Agnew 6e98c02862 Fix #1495 - Avoid NPE in RuleBuilder 2019-09-20 08:57:01 -04:00
James Agnew 20d33afb6f Credit for #1489 2019-09-19 20:48:17 -04:00
James Agnew ad01d7598c Credit for #1489 2019-09-19 20:41:02 -04:00
James Agnew 2be63a1650 Test fixes 2019-09-19 09:45:07 -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 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 38cf830384 Accurately reflect codesystem URL 2019-09-16 15:55:32 -04:00
James Agnew 08835c1615 FIx a failure in FhirTerser when visiting custom types 2019-09-13 09:11:47 -04:00
James Agnew 9420bca341
Merge branch 'master' into ks-in-memory-date-compare 2019-09-10 13:25:29 -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 7cfbf710fe Merge remote-tracking branch 'remotes/origin/master' into ks-in-memory-date-compare
# Conflicts:
#	src/changes/changes.xml
2019-09-09 14:46:25 -04:00
Ken Stevens 9e83f1d40a changelog 2019-09-09 14:22:42 -04:00
James Agnew 718fcb28a5 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-06 14:58:03 -04:00
James Agnew 722c7a8211 Work on GraphQL updates 2019-09-06 14:56:17 -04:00
Ken Stevens bc821a7060 Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache 2019-09-05 15:59:45 -04:00
James Agnew 7105890d2f Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-05 14:49:29 -04:00
James Agnew 7d162c50db Don't guess content type for create/put 2019-09-05 14:47:04 -04:00
Ken Stevens 49bfe9fb0c Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache 2019-09-04 21:08:04 -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
jamesagnew 17a50765dc 4.0.1 release 2019-09-04 05:33:57 -04:00
James Agnew 8ce8f1e864 Credit for #1461 2019-09-01 18:41:17 -04:00
James Agnew f59bdc4afe Reuse FHIRPath across JPA requests 2019-08-29 14:13:31 -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
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
James Agnew 70d0a8aa8f
Get patch working (#1449) 2019-08-27 05:42:15 -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 b01d59d5a0 Added changelog entry. 2019-08-26 14:47:50 -04:00
Diederik Muylwyk 3f14a7a68b Added changelog entry for switch from Derby to H2 for HAPI FHIR CLI server. 2019-08-26 09:54:05 -04:00
James Agnew 6fa27934a8 Tests all seem to be working 2019-08-23 10:14:13 -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
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
James Agnew ce879b3863 Fix versioned API incompatibility with GraphQL 2019-08-20 08:35:27 -04:00
jamesagnew ab5333f370 Fix subscription config file 2019-08-17 16:15:55 -04:00
jamesagnew 34c1879973 Add changelog 2019-08-17 14:31:30 -04:00
James Agnew 9e8af58e81 Fix reference params via filter 2019-08-16 14:56:36 -04:00
James Agnew afb682dfe9 Handle AuthorizationInterceptor rejection of by-type reads on the wrong type earlier in the process 2019-08-15 09:16:45 -04:00
James Agnew 4490c9ca09 Correct the eq operator on the _filter parameter 2019-08-14 14:39:40 -04:00
James Agnew 406808da8d Credit for #1357 2019-08-14 14:37:20 -04:00
James Agnew 9d37972649 Prepare docs for release 2019-08-14 13:33:12 -04:00
James Agnew b4fece0ae9 Add interceptor hook for graphql calls 2019-08-13 14:46:50 -04:00
jamesagnew a1e1cf4e56 Credit for #1375 2019-08-13 05:37:40 -04:00
jamesagnew 23c05ac2a9 Credit for #1388 2019-08-13 05:29:55 -04:00
James Agnew 31e374ded8 Credit for #1220 2019-08-12 13:35:27 -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 a1acd7525e Changelog update for new structures 2019-08-11 10:19:05 -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 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
jamesagnew 39c2a95ce7 Credit for #1321 2019-08-01 09:29:43 -04:00
jamesagnew e20443010d Credit for #1404 2019-08-01 06:38:37 -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
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
jamesagnew 8158292665 Allow operations to better work across multiple versions of FHIR 2019-07-26 05:46:37 -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
jamesagnew 13dae527d1 Fix #1390 - DiagnosticReport template correction 2019-07-19 05:44:08 -04:00
James Agnew 5bf4fa22e7 Allow patching in tranactions 2019-07-18 16:41:07 -04:00
James Agnew ee7cff9445 Rename a few columns to not conflict with res´rved words 2019-07-18 05:47:32 -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
James Agnew 76384abefb Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-07-17 10:57:43 -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
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
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 accf57230b review feedback 2019-07-12 17:13:17 -04:00
Ken Stevens 78aec06c4d changes.xml 2019-07-12 13:38:45 -04:00
Ken Stevens 26ab115ff5 changes.xml 2019-07-12 13:34:32 -04:00
James Agnew 32a8e1aead Omit extensions when encoding in summary mode (except for
CapabilityStatement)
2019-07-11 16:28:50 -04:00
James Agnew 0fb8db11a2 Add new pointcut: PROCESSING_COMPLETED 2019-07-09 14:32:11 -04:00
James Agnew e50caaa899 Credit for #1370 2019-07-08 10:55:01 -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 d23046b8ea Dependency version bumps 2019-07-07 10:14:08 -04:00
James Agnew 190f0a0d5a Bump several dependency versions to latest versions 2019-07-07 09:58:31 -04:00
James Agnew 1c7c83cd8e Add an isEmpty() method to IBundleProvider 2019-07-05 16:16:39 -04:00
James Agnew 2a6436af23 Rename columns in code mapping 2019-07-05 09:03:03 -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
jamesagnew 5c0e54fb86 Improve processing of deletes in AuthorizationInterceptor 2019-06-29 14:40:51 -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
James Agnew fa80223d57 Fix invalid xml 2019-06-28 15:25:11 -04:00
James Agnew 8acaafed36 Credit for #1354 2019-06-28 15:24:43 -04:00
James Agnew 05d004803f Credit for #1330 2019-06-28 15:15:51 -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 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
James Agnew c14f5c1520 Credit for #1361 2019-06-25 18:31:25 -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
jamesagnew 95876ec3cb Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-06-22 16:24:07 -04:00
jamesagnew 638cb976fd Fix #1250 - Don't include Bundle.entry.response on search results 2019-06-22 16:23:32 -04:00
James Agnew 4ad1808da3
Propagate RequestDetails to everything in JPA server (#1358) 2019-06-22 15:18:06 -05:00
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
Diederik Muylwyk 266384b536 Evaluation of PartTypeName in LoincRsnaPlaybookHandler is not case insensitive. 2019-06-21 15:36:51 -04:00