8c145d1212
Merge branch 'master' into 3020_Add_documentation_for_$partition-management-create-partition
2021-09-24 13:01:38 -04:00
a40a27bd46
Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology
2021-09-24 12:58:44 -04:00
4c28b1b552
fix npe
2021-09-24 09:46:48 -04:00
4ab60e2f9b
Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology
2021-09-24 08:59:15 -04:00
53c7476dae
hapi storage ( #3024 )
...
* first pass moving core storage classes to storage-api
* move term service apis
* nearly done
* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor
* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor
* create new SearchConstants class to store platform independent search constants
* move a couple of subscription services
* move transaction processor adapter to storage
* version bump
* move searchparam
* fix test
* fix compile includes
* fix text
* fix docs
2021-09-23 22:04:46 -04:00
91d9101785
Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology
2021-09-23 13:45:28 -04:00
d1e9c23c13
Remove loinc.xml file from application. Now it required as input for loinc upload.
2021-09-23 13:43:27 -04:00
4f00b88512
Merge branch 'master' into jr-20210922-narrowing-interceptor
2021-09-23 12:28:16 -04:00
712a6a798f
clean up
2021-09-23 12:27:32 -04:00
9c8fd26692
Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning
2021-09-23 11:56:44 -04:00
751c5d0d05
Implement revision suggestions. Add changelog.
2021-09-23 11:55:50 -04:00
ad9e0f1c9a
Merge branch 'master' into 3014-prevent-delete-expunge-cascade
2021-09-23 09:33:04 -04:00
2489702ab9
[3020] add documentation for $partition-management-read-partition
2021-09-22 16:08:11 -04:00
e52d11b5ba
search narrowing interceptor responds with 403 Forbidden instead of creating an impossible query
2021-09-22 14:00:12 -04:00
26ac649946
changelog
2021-09-22 11:11:10 -04:00
9a18422173
fix review
2021-09-22 11:09:50 -04:00
b8ef2f6763
Add changes
2021-09-21 15:25:46 -04:00
7379dee3d8
Merge branch 'master' into add-device-to-patient-compartment
2021-09-21 14:38:39 -04:00
645386c999
Apply suggestions from code review
...
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-09-21 12:26:21 -04:00
fa96c5b8be
Merge branch 'master' into jr-20210921-mssql-data-migration
2021-09-21 12:22:56 -04:00
060791aeb4
hapi-fhir-storage-api ( #3006 )
...
* rename hapi-fhir-jpaserver-migrate to hapi-fhir-sql-migrate and move hapi-tasks into jpaserver-persistence
* rename hapi-fhir-jpaserver-api to hapi-fhir-storage-api
* move bulk import apis
* create hapi-fhir-jpa
* create hapi-fhir-jpa
* move CircularQueueCaptureQueriesListener to japi-fhir-jpa
* move mdm logs to storage-api
* move gziputil to storage-api
* move quartz scheduling to hapi-fhir-jpa
* move default subscription channel factory to storage-api
* consolidated batch constants
* correct accidental Logs change
* remove dependency of cdr-api on cdr-persistence
* fix javadoc
* pom descriptions
* review feedback
2021-09-21 15:36:08 +00:00
b6c8658f8c
Fix MS SQLServer database migration
2021-09-21 10:42:59 -04:00
f1f9c672ad
3110 zh disallow unknown extensions ( #3009 )
...
* Added allowKnownExtensionsOnly() method such which calls setAnyExtensionsAllowed() to set myAnyExtensionsAllowed to false and modified changelogs to add entry for this ticket.
* Modified docs to remove description for .allowAnyExtensions() and included it within a description for .allowKnownExtensionsOnly() and also added test for .allowKnownExtensionsOnly()
* refactored allowKnownExtensionsOnly() to rejectUnknownExtensions()
2021-09-20 15:40:56 -04:00
624ad3fcab
Merge branch 'master' into jr-20210914-oidc-support-in-swagger
2021-09-17 17:09:19 -04:00
3b1bf7aa09
Merge branch 'master' into 2849_add_new_mdm_param
2021-09-17 13:27:09 -04:00
8bb9aca8df
Merge branch 'master' into 2849_add_new_mdm_param
2021-09-17 10:18:24 -06:00
cb374042f5
Merge branch 'jr-20210914-oidc-support-in-swagger' of github.com:hapifhir/hapi-fhir into jr-20210914-oidc-support-in-swagger
2021-09-17 11:42:34 -04:00
a866feb730
changelog
2021-09-17 11:41:51 -04:00
115056800c
Merge branch 'master' into issue-2995-valuesetcomposeincludeversion-is-not-set-when-uploading-terminology
2021-09-17 11:32:18 -04:00
a56c85f780
Eliminate Search Coordinator ThreadPool ( #2991 )
...
* Add test
* Remove search coordinator thread pool
* Add changelog
* Add docs
* Test fixes
* Test fixes
* Test fixes
* Test fix
2021-09-16 16:37:34 +00:00
3d3bab5102
merge master into branch
2021-09-16 11:02:17 -04:00
5bbe69cd31
Move into data class
2021-09-15 21:17:03 -04:00
2435d77089
Add changelog
2021-09-15 14:46:33 -04:00
9d982c5e08
Merge branch 'master' into conditional-bug
2021-09-14 08:51:58 -04:00
75a16f3b13
Add docs and changelog
2021-09-14 01:54:59 -04:00
3ccadd636e
Merge branch 'master' into 2958-consistent-error-handling
2021-09-13 19:38:57 -04:00
67cf058318
Add changelog
2021-09-13 19:29:49 -04:00
4aa1329e11
Fix up changelog
2021-09-13 13:13:28 -04:00
5554431146
Avoid dead SearchParameter links in CapabilityStatement ( #2790 )
...
* Avoid dead SearchParameter links in CapabilityStatement
* Resolve fixmes
* Build fix
* Test fix
* Test fix
* Test fix
* Work on metadata
* Fixes
* Test fixes
* Test fix
* Test fix
* Test fixes
* Test fix
* Work on test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Fix params
* Resolve fixme
* Adjust changelogs
* Version bump to 5.6.0-PRE7
* Add license header
* Bump version to 5.6.0-PRE5-SNAPSHOT
2021-09-11 18:27:18 -04:00
a02a9e0254
Merge branch 'master' into 2958-consistent-error-handling
2021-09-10 17:02:31 -07:00
77845d66f7
Improved code formatting
2021-09-10 10:54:33 -07:00
86ab77446e
Merge branch 'master' into 2975-attribution
2021-09-10 13:05:38 -04:00
ab3af7af2a
Merge branch 'master' into 2973-CLI_option_help_fails
2021-09-10 11:54:37 -04:00
30834d13ad
Add attribution.
2021-09-10 10:28:54 -04:00
d6d862015b
Address concerns in review for issue 2975
2021-09-10 15:46:27 +02:00
1af7ed6223
[2973] update changelog
2021-09-10 09:40:35 -04:00
032a9155f0
Merge branch 'master' of https://github.com/hapifhir/hapi-fhir into issue_2975
2021-09-10 09:11:06 +02:00
836948010f
Fixes issue ( #2958 ) where Procedure?patient caused inconsistent results and ensured that such requests gave http 400
2021-09-09 16:10:09 -07:00
ed325e9e11
Enable multiple hosts in ElasticsearchHibernatePropertiesBuilder
2021-09-10 00:14:21 +02:00
e6be758d65
Merge branch 'master' into 2973-CLI_option_help_fails
2021-09-09 17:15:20 -04:00
10f0b0877c
[2973] fix "help {command}"
2021-09-09 17:14:51 -04:00
b3e24078ae
Add changelog
2021-09-09 11:01:11 -04:00
0ccd71faf8
Merge pull request #2963 from hapifhir/custom-elastic-index
...
Custom elastic index
2021-09-08 14:29:58 -04:00
fbf6b35d2e
Merge branch 'master' into custom-elastic-index
2021-09-08 08:49:26 -04:00
f04cf02be7
Merge branch 'master' into issue-2901-npe-in-bundle-transaction
2021-09-08 08:45:47 -04:00
34075911ce
Merge branch 'master' into jr-20210831-contained-chained-search
2021-09-07 17:28:24 -04:00
d02e7e0041
changelog
2021-09-07 14:25:06 -04:00
3ec47cb0ba
Bump version as we break the localcontainerentitymanagerfactory bean constructors args
2021-09-07 13:58:22 -04:00
eabe3e7c74
Merge branch 'master' into custom-elastic-index
2021-09-07 13:56:44 -04:00
ecd93c9e8a
Add changelog
2021-09-07 13:54:28 -04:00
35aaa98431
Merge branch 'master' into 2849_add_new_mdm_param
2021-09-07 11:27:49 -04:00
346e29920a
Issue 2927 convert mdm clear to spring batch ( #2929 )
...
* initial roughout of mdm clear batch job
* still roughing out classes
* finished first draft of reader
* most tests passing now
* all tests pass. now FIXMEs
* FIXMEs done. Time for regression.
* fix test
* changelog and docs
* fix test
* pre-review cleanup
* version bump
* move spring autowire deps for cdr
* move spring autowire deps for cdr
* finally got beans working phew
* rearrange method calls so persistence module can perform clear operation on its own
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* review feedback
* review feedback
* Remove inheritance
* fix beans
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2021-09-03 14:58:19 -04:00
1bd1b36668
Merge branch 'master' into 2849_add_new_mdm_param
2021-09-03 11:04:20 -04:00
dc69bfc729
Add changelog
2021-09-02 23:07:07 -04:00
ee65a24260
Merge branch 'master' into 2849_add_new_mdm_param
2021-09-02 17:42:41 -04:00
26ff15f939
Revert "Fix search of :not modifier"
2021-09-02 14:33:30 -04:00
1a7b101d03
Merge branch 'master' into issue-2901-npe-in-bundle-transaction
2021-09-02 10:13:04 -04:00
4c90ffe975
issue-2901 adding changelog
2021-09-02 09:47:55 -04:00
0286eb5278
issue-2901 updated some documentation and added support for autocreated placeholder / autoversioned references at paths when in transactios and have not been created yet
2021-09-02 09:15:39 -04:00
feb34e9bf5
Merge branch 'master' into patch-2
2021-09-02 08:42:41 -04:00
b1d192637d
Merge pull request #2928 from hapifhir/ft-search-with-not-modifier
...
Fix search of :not modifier
2021-09-02 08:41:16 -04:00
f5de2da6ba
Corrected typo in docs - Plain Providers
...
It was "plan providers" before
2021-09-02 14:52:38 +05:30
3e288f1dde
Merge branch 'master' into rel_5_5_1
2021-09-01 18:16:27 -04:00
ee956929f9
Merge branch 'master' into add-attribution-for-gotoguy
2021-09-01 16:42:19 -04:00
ae2c752c55
Add attribution for 2793
2021-09-01 15:54:28 -04:00
453ef7ec1c
Merge branch 'master' into 2935_Search_with_trailing_percent_sign
2021-09-01 11:33:26 -04:00
44b0d3e9e7
Fixed $lookup with displayLanguage caching issue ( #2932 )
...
* Fixed $lookup with displayLanguage caching issue
* Added changelog and optimized the test cases
2021-08-31 22:18:40 +00:00
a1fbeeacaa
[2935] Escape "%" in like expression
2021-08-31 15:11:06 -04:00
e1272a3825
Bump version of HAPI-FHIR
2021-08-31 11:43:17 -04:00
993b2a2f47
Backport changelog
2021-08-31 11:41:17 -04:00
7fc6a2f16b
Add changelog
2021-08-31 11:39:01 -04:00
cc2e968595
Add version.yaml
2021-08-31 11:04:20 -04:00
37c88392b4
Add changelog
2021-08-31 10:53:14 -04:00
3c0a197407
Added changelog
2021-08-28 16:23:09 -04:00
91a961f9fd
Added changelog
2021-08-27 10:48:19 -04:00
fd6dcf6363
Fix bug in code. Add test. Add changelog
2021-08-25 18:16:47 -04:00
090a8b0821
Impl displayLanguage for $lookup ( #2908 )
...
* Impl displayLanguage for $lookup - first cut
* Added original lookupCode method
* Added original lookupCode method to IFhirResourceDaoCodeSystem
* Added more test cases and changelog
2021-08-25 14:47:10 -04:00
d34b0ff093
Merge pull request #2914 from hapifhir/issue-2904-Swagger-ui-Doesn't-Work-with-Partitions
...
Issue 2904 swagger UI doesn't work with partitions
2021-08-24 17:43:46 -04:00
1211600e25
[2904] update changelog file name
2021-08-24 11:54:41 -04:00
f8fa09ae8e
[2904] add changelog
2021-08-23 16:39:52 -04:00
2fbe7d7443
Strip broken backport line
2021-08-23 16:39:19 -04:00
a0dd79f68e
[2904] add changelog
2021-08-23 16:38:22 -04:00
37ad73a422
Bump PRE version so we don't conflict downstream
2021-08-23 15:42:18 -04:00
1acaf325c5
Merge branch 'master' into rel_5_5_0
2021-08-23 14:50:29 -04:00
4c2ae513d8
Process bundle batch in parallel ( #2905 )
...
* Process batch in parallel
* Added a test case
* Added more test cases
* Default the bundle batch to single thread.
* Tried transaction before multi-thread.
* Updated the test cases
* Update based on review comments and add changelog
* Updated the changelog
* Restore QueueCapacity
2021-08-20 21:14:08 -04:00
bb0552d0db
Changelog tweak
2021-08-19 12:59:51 -04:00
85517c47e2
Include includes on revincludes ( #2902 )
...
* Include includes on revincludes
2021-08-19 12:31:29 -04:00
367b338d85
Updating HAPI to use latest core lib changes.
2021-08-18 11:06:14 -04:00
4baca0a282
[2883] Add changelog
2021-08-16 11:28:30 -04:00
cf917d0f82
Version Bump
2021-08-15 16:54:38 -04:00
669cf05b30
Modify SearchParameterMap toNormalizedQueryString to include value of _contained parameter
2021-08-12 14:25:12 -04:00
41ec1e03c0
Merge pull request #2880 from hapifhir/weird-contained-issue
...
Contained Issue
2021-08-11 08:27:54 -04:00
b34d569443
Fix changelog test
2021-08-10 22:22:57 -04:00
33fbffcff9
Bump issue number
2021-08-10 16:18:40 -04:00
6a46a68e82
Move file
2021-08-10 16:18:03 -04:00
fe98162616
Add changelog
2021-08-10 14:59:03 -04:00
97f88202eb
Fix Changelog typo
2021-08-10 08:12:54 -04:00
1dfaf73066
Merge branch 'master' into 2876-npe-mdm-resource-util
2021-08-09 19:21:58 -04:00
bfd9dffdbe
Allow jira field in changelog
2021-08-09 19:09:40 -04:00
416a52c679
Add changelog, fix code
2021-08-09 16:02:19 -04:00
1e0f843d6c
2852 - Simplify java mail code ( #2874 )
...
* testing
* [2852] adding SimpleJavaEmail
* [2852] refactor email sender code
* [2852] dependency cleanup
* [2852] add missing dependency
* [2852] add missing spring framework test dependency
* [2852] add change log
* [2852] add change log
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2852-simplify-java-mail-code.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* [2852] minor test code cleanup
* [2852] add more tests
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-08-09 15:59:47 -04:00
4fadc62066
Bump Hapi Version
2021-08-06 13:44:04 -04:00
0a303a0e11
Add MDM expansion by golden pid
2021-08-06 13:22:08 -04:00
35d3e3689b
2829 - Add DSTU3 Support To UploadTerminologyCommand ( #2832 )
2021-08-05 13:07:50 -04:00
1ff1954cba
Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control
2021-07-30 11:20:23 -04:00
f5dfc3a5ed
New reindex spring batch operation ( #2845 )
...
* first sweep to add new $reindex job
* first cut done. next up integration test.
* start roughing out reindex everything
* Failing test
* test passes
* add BundleUtil helper method
* rough in processEverything
* rough in processEverything
* fix mock test
* merge master
* Make BaseJpaTest.mySrd lenient.
* fix test
* reindex everything works with FIXMEs
* reindex everything more tests
* moar tests
* moar tests
* fix test
* fix test
* fix regression and fix test
* fix test cycle
* fixme
* fix test
* test provider layer
* reindex everything partition aware
* yay last fixme!
* run reindex in partitioned threads
* add fixmes for areas that require extra testing
* added transaction and log message
* manual integration testing
* changelog
* reindex all partitions
* bump hapi version
* fix test
* moar test
* pre-review cleanup
* fix javadoc
* review feedback
* review feedback
* review feedback
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2845-reindex-operation.yaml
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* review feedback
* review feedback
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/ResourceSearch.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/IDeleteExpungeJobSubmitter.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-07-29 19:18:49 -04:00
264dfee099
Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control
2021-07-29 16:21:56 -04:00
1fcb36d84a
Fix implementation to work also for use case where version is being updated.
...
Use property instead of parameter.
2021-07-29 15:54:00 -04:00
e076b30eef
bump Jetty for CVEs
2021-07-27 15:49:00 -04:00
f957661dda
Patient ID Partition Mode should support conditional create ( #2828 )
...
* Fixes
* Test fix
* Add changelog
* Test fixes
* Test fixes
* Docs tweak
* Partitioning fixes
* Import fix
* Fix test data
2021-07-26 14:18:58 -04:00
6bbb403fd1
When Client Id Strategy is set to NOT_ALLOWED, permit system requests to create resources ( #2827 )
...
* resolved 2826
* fix regression
2021-07-23 19:10:19 -04:00
92ec113775
fixed bug ( #2824 )
2021-07-23 16:58:53 -04:00
2539f49662
Add detail to changelog
2021-07-23 15:07:36 -04:00
d99f94e665
changelog
2021-07-23 15:00:48 -04:00
ad6f7a204c
Fix changelog syntax. Merge current master.
2021-07-22 10:49:16 -04:00
ae0665131b
Fix syntax.
2021-07-22 09:41:16 -04:00
a5e6674e84
Version bump to 5.5.0-PRE7-SNAPSHOT
2021-07-22 08:41:16 -04:00
8b8db82666
Enable Package Loader when partitioning is enabled with unnamed partitions ( #2808 )
...
* Enable Package Loader when partitioning is enabled with unnamed partitions.
* Enable Package Loader when partitioning is enabled with unnamed partitions.
* Additional package loading problems found with partitioning.
* Additional package loading problems found with partitioning.
Co-authored-by: ianmarshall <ian@simpatico.ai>
2021-07-22 05:17:17 -04:00
6af022062f
Fix issue with partitioning in patient ID compartment mode ( #2810 )
...
* Fix issue with partitioning in patient ID compartment mode
* Add changelog
2021-07-21 17:21:23 -04:00
e0e52c666c
Add current-version parameter to upload-terminology command.
2021-07-21 16:18:35 -04:00
cbb9a4355a
Add details when we fail to load an element of a package definition.
2021-07-19 17:59:54 -04:00
64f1643046
Added LOINC linguistic variants support ( #2803 )
...
* Added linguistic variants for LOINC uploader
* Using static class
* Added the changelog
2021-07-19 14:17:56 -04:00
946080d709
Added ConsumerName to the loinc loader. ( #2800 )
...
* Added ConsumerName to the loinc loader.
* Added extra test for coverage
* Added the changelog for LOINC CONSUMER NAME support
2021-07-16 13:30:42 -04:00
0235296ba7
Add support for bulk export of multiple types ( #2797 )
...
* Add support for bulk export of multiple types
* Add changelog
2021-07-15 14:01:10 -04:00
5f2a3af01e
Add Innovattic B.V. to HAPI FHIR Global Atlas ( #2798 )
2021-07-15 14:00:33 -04:00
520cec1e15
Fixed link resolution
2021-07-14 11:30:09 -04:00
554685d142
Fix MDM documentation
2021-07-13 16:08:01 -04:00
0a27b08aad
Merge pull request #2783 from hapifhir/2777-hapi-fhir-cli-Add-option-to-pass-request-headers-to-target-server
...
Add changelog. Address MR comments.
2021-07-09 09:35:56 -04:00
218325b385
Add backport info for full diff between 5.4.1 and 5.4.2 ( #2784 )
2021-07-08 16:25:18 -04:00
1e9163c636
Add changelog. Address MR comments.
2021-07-08 14:52:19 -04:00
95306c3d64
Add NPM validation support module ( #2782 )
...
* Add NPM validation support module
* Add changelog
2021-07-07 16:28:41 -04:00
3e7bc2a81e
Forward port 5 4 2 ( #2781 )
...
* Add new version to enum
* Add backport tags, new VersionEnum, and new release folder for 5.4.2
2021-07-07 10:10:07 -04:00
d762a07817
Partition patient interceptor ( #2766 )
...
* Start work on interceptor
* Implemented
* Add interceptor and docs
* Add docs
* Compile fix
* Test fixes
* Test cleanup
* Test fixes
* Test fixes
* Improve error message
* Add broken tests
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2766-add-patient-id-compartment-interceptor.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptor.java
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Address review comments
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-07-05 09:15:20 -04:00
a4fb72975d
Merge pull request #2767 from hapifhir/2765-mdm-paging
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Paging implementation for MDM query links operation
2021-07-01 23:16:47 -04:00
0a4a50f0a8
update docs
2021-07-01 17:05:14 -04:00
b1334241c7
change out-of-order flag to switch-order flag so the default behaviour reverses ( #2773 )
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* change out-of-order flag to switch-order flag so the default behaviour reverses
* change log
2021-07-01 15:17:39 -04:00
7aba83293a
Merge pull request #2771 from hapifhir/issue-2768-convert-mdm-submit-to-spring-batch
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$mdm-submit operation was only submitting 100 resources ...
2021-06-30 16:14:01 -04:00
f66f9b992e
Bump pre-version as this will break downstream implementations
2021-06-30 15:37:19 -04:00
f33696a165
Add changelog
2021-06-30 15:24:29 -04:00
883337a9f4
Tidying
2021-06-30 14:55:57 -04:00
91dee55279
Correct docs
2021-06-30 14:49:37 -04:00
fa750d209e
$mdm-submit operation was only submitting 100 resources and then stopping.
...
It now correctly submits all requested resources.
2021-06-30 14:48:28 -04:00
8f3cbb0a7f
Refactor docs
2021-06-30 14:48:13 -04:00
4a1b836582
Add Cortico to HAPI FHIR Global Atlas ( #2769 )
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Cortico uses HAPI FHIR to help medical providers engage seamlessly with patients over video, email and SMS.
2021-06-30 08:36:38 -04:00
795fb31a3a
fixed mdm rules ( #2764 )
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* fixed mdm rules
* changelog
* review feedback jetbrains
* review feedback
2021-06-28 23:24:37 -04:00
9500a1a7de
fix false rule matches ( #2762 )
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* fixed an issue with matching compartments to lists of ids
* change log
* Added extra guards against false rule matches.
* changelog
* fix inCompartment
* cleanup
2021-06-27 10:34:32 -04:00
5565bf9930
fixed an issue with matching compartments to lists of ids ( #2761 )
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* fixed an issue with matching compartments to lists of ids
* change log
2021-06-26 20:24:28 -04:00
ea98e62656
collapse multiple owners for same compartment into shared compartment ( #2760 )
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* collapse multiple owners for same compartment into shared compartment
* changelog
* fix regression
* fix regression
* pre-review cleanup
* pre-review cleanup
2021-06-26 11:48:47 -04:00
110173dafb
Merge pull request #2757 from hapifhir/2091-MemoryCacheService-confused-expiry
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Fix units on cache expiry
2021-06-25 14:29:43 -04:00
f1b8802f45
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2758-fix-cache-expiry-units.yaml
...
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-06-25 14:19:04 -04:00
7185089c9d
Add forced offset search JPA interceptor ( #2756 )
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* Add support for offset searches
* Tests working
* Add changelog
* Test fixes
* Test fix
* More test fixes
* Add commit counter
2021-06-25 10:40:39 -04:00
1367e61c93
changelog
2021-06-24 19:13:54 -04:00
a9208a88da
Revert "Version bump"
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This reverts commit 1f5fa70fb6
2021-06-24 11:48:31 -04:00
1f5fa70fb6
Version bump
2021-06-24 11:22:35 -04:00
2cc27d9b4f
Forgot changelog
2021-06-24 10:19:45 -04:00
59653759ed
Update tests
2021-06-23 15:58:14 -04:00
6feaa12593
Merge pull request #2747 from hapifhir/2746_npe_in_mdm_utils
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Added null checks
2021-06-23 09:51:53 -04:00
e3158045aa
License header
2021-06-22 23:25:36 -04:00
8379392e16
Add inline tag mode ( #2748 )
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* Start work on tag mode 3
* Add changelog
* Test fix
2021-06-22 23:08:09 -04:00
9caa5e68fc
Added changelog
2021-06-22 15:52:21 -04:00
912b44c3fa
Merge pull request #2734 from hapifhir/2732-bump-conceptmap-group-element-display-storage-size
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Address #2732
2021-06-21 08:33:36 -04:00
6ea1438f1d
Add transaction write semaphore interceptor ( #2743 )
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* Add transaction write semaphore interceptor
* Add changelog
* Test fix
2021-06-20 12:55:49 -04:00
32ac16e2aa
add a limit to mdm candidate searches ( #2742 )
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* done
* verbal review feedback
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2739-max-mdm-matches.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* review feedback
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-06-18 20:48:34 -04:00
8b205b23d0
Fix history paging ( #2741 )
...
* Fix history paging
* Add changelog
* Add license header
2021-06-18 17:47:51 -04:00
097a2f70b3
add partition support to $evaluate-measure ( #2736 )
...
* Finished adding partition support to $evaluate-measure
* review feedback
2021-06-18 14:22:57 -04:00
164e684d7c
Merge branch 'master' into 2732-bump-conceptmap-group-element-display-storage-size
2021-06-17 15:14:05 -04:00
324201b105
Make change
2021-06-17 11:28:02 -04:00
659efa786c
ValueSet Expansion Should Preserve Order ( #2724 )
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* Add test
* FIxed
* Add changelog
* Add test
* Intermittent test failure fix
* Build fix
* Build fix
* Test fix
* Test fixes
* Fix checkstyle issue
* Test fix
* Add test logging
2021-06-16 07:20:59 -04:00
134631fdee
Convert delete expunge to use Spring Batch ( #2697 )
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* prepare to add $delete-expunge operation that will create a spring batch job
* Add operation
* Wire up jpa provider. Begin with failing test.
* Copy/paste bulk import job as a starting point.
FIXME with proposed design
* delete expunge job parameter validation with test
* implemented reader
stubbed processor, writer
* wip for master merge
* started implementing reader
* started implementing reader
* working with stubs
* happy path batch delete expunge is done
* Provider done but test not passing. Guessing batch infrastructure not running in that test.
* IT test works now
* add reader test
* Converted delete _expunge=true to use new batch job
* DeleteExpungeDaoTest passes
* Fix test
* Change batch size to integer
* rename search count to batch size
* Make delete expunge partition aware
* updated docs
* pre-review cleanup
* change log
* add partition id to SystemRequestDetails
* Make RequestPartitionId serializable
* Change delete expunge provider to use partition id instead of tenant name
* fix tests
* test pointcut gets called
* assert on pointcut calls
* Add resource type to STORAGE_PARTITION_SELECTED pointcut
* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants
* bump hapi-fhir version
* copyrights
* restore deleteexpungeservice for mdm
* restore deleteexpungeservice for mdm
* fix test
* public constants
* convert instant to date
* Moved expunge constants to ProviderConstants
* final review
* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run
* fix tests
* fix tests
* fix tests
* fix tests
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* improve logging
* bump version
* version bump
* recovering from failed merge
* unzip RequestListJson per Gary's suggestion. I didn't want to do it at first, but as usual Gary was right.
* fix serialization
2021-06-15 10:36:05 -04:00
376a84d213
Version bump
2021-06-14 13:12:34 -04:00
b934abb297
Impropve transaction Performance ( #2717 )
...
* Work on changes
* Work on perf
* Work on testing
* Work on perf
* Work on perf
* Work on fix
* Work on perf
* Ongoing work
* Add changelog
* Additional docs
* Test fixes
* Address review comments
* Test fix
2021-06-14 13:08:19 -04:00
48eea5a7cc
Prepare changelog for 5.4.1 release
2021-06-14 09:13:41 -04:00
474cca877a
Merge branch 'rel_5_4_2'
2021-06-14 09:07:26 -04:00
39d7d4ad03
Use pageSize variable to hold page size ( #2719 )
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* Use pageSize variable to hold page size as previously used variable has other function, so not always hols intended value required for previous link
* Adjust test to standards and use RestfulServerExtension instead of own server
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-06-11 17:29:14 -04:00
090dc9a2e2
Docs
2021-06-11 15:55:35 -04:00
fcb32eacb6
Add support for loinc 2.70 ( #2721 )
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* Add support for loinc 2.70
* Add changelog
2021-06-11 15:15:22 -04:00
dc627dc019
Add bulk export authorization layer ( #2712 )
...
* Add bulk export authorization layer
* Add docs
* Version bump
* Authorize any
* Add bulk export - all
* Address lgtm issue
2021-06-06 20:47:43 -04:00
62be623cf5
Add support for ICD-10-CM ( #2702 )
...
* Add support for ICD-10-CM
* Have this working
* Fix LGTM issues
* Test fix
2021-06-03 19:55:16 -04:00
94d6b15db9
_filter searchparam should not appear in cap stmt if disabled ( #2706 )
...
* issue reproduced and fixed
* changelog
* cleanup
2021-06-03 18:45:49 -04:00
c498522c78
search by source reported incorrect size ( #2705 )
...
* issue reproduced in test and fixed
* changelog
2021-06-03 18:19:43 -04:00
fe763dd2d6
Upgrade deps ( #2695 )
...
* Upgrade deps
* Fix build error
* Branch tweak
* Build fix
* Build fix
* Undo bump
* Test fixes
2021-06-01 12:03:29 -04:00
f5c75e80de
Credit for #2693
2021-06-01 10:53:53 -04:00
05ac88bc21
Add initiate bulk export pointcut ( #2692 )
...
* Add initiate bulk export pointcut
* Add changelog
* Test fixes
2021-05-31 16:05:09 -04:00
94bd2400e3
Merge pull request #2689 from me-d4l/fix/update-chaelog-for-2682
...
Add CHANGELOG entry for ticket 2682
2021-05-31 12:16:13 +02:00
b9931dfb03
Add CHANGELOG entry for ticket 2682
2021-05-31 08:43:23 +02:00
a2950324ef
Avoid SQL based transaction dupe check ( #2688 )
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* Avoid SQL based transaction dupe check
* Add changelog
* Test fixes
* Test fixes
2021-05-30 20:26:36 -04:00
786112284b
Bump spring version ( #2687 )
2021-05-30 19:04:14 -04:00
24b3f0f30d
Enable mass ingestion mode ( #2681 )
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* Work on fixes
* Work on counts
* Enable mass ingestion mode
* Add changelog
* Test fix
* Test fix
* Test fixes
* Fixes
* Test fix
* Test fix
2021-05-27 18:43:51 -04:00
c8c596aff4
Fix date search on period with no end ( #2676 )
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* Add test
* Working test
* Update test
* Account for date fixes
* Add changelog
* Add setting
* Test fixes
* Test fix
2021-05-26 21:03:53 -04:00
7a83c76e65
Add validation suppression mode ( #2675 )
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* Add validation suppression mode
* Add changelog
* Compile fix
2021-05-26 17:41:48 -04:00
af44b9c7a0
Ks 20210526 accurate total ( #2677 )
...
* begin with failing test
* fixed
* changelog
2021-05-26 12:20:49 -04:00
1b387a5740
Add null check on code lookup result.
2021-05-24 22:14:02 -04:00
2c722e64c2
Add support for including qualified star syntax ( #2672 )
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* Add support for including qualified star syntax
* Add changelog
* Add docs
* Build fix
2021-05-23 16:50:37 -04:00
ff2698d4d1
Merge branch 'rel_5_4'
2021-05-19 09:22:11 -04:00
bd372e4bd8
Fix changelog
2021-05-19 08:34:24 -04:00
2badae2097
Avoid contained resource in conditional create ( #2665 )
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* Work on unexpected contained resources
* Avoid contained on conditional create
* Add changelog
2021-05-19 07:49:59 -04:00
b463b072c8
Test fixes
2021-05-18 21:32:13 -04:00
de56f440cb
Version bump
2021-05-18 17:14:14 -04:00
22a1a05cfb
Add changelog
2021-05-18 10:05:59 -04:00
7a50454350
Correct index init issue ( #2662 )
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* Correct index init issue
* Add changelog
2021-05-17 20:31:44 -04:00
926bf393d3
Merge branch 'rel_5_4'
2021-05-17 09:10:58 -04:00
40ecafcd31
Don't unescape plus in match URLs ( #2658 )
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* Don't unescape plus in match URLs
* Perf improvements
* Add changelog
* Test fix
* Work on tests
* Fixes
* Test fix
2021-05-16 21:51:23 -04:00
b31bb945ad
Add include clause to MSSQL forcedid table index ( #2659 )
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* Add include clause to MSSQL forcedid table index
* Add changelog
* Test fix
* Bump MSSQL version
2021-05-16 19:14:51 -04:00
57bb11797e
fix
2021-05-13 15:46:26 -04:00
15ea4fb555
Tidy test
2021-05-13 10:47:26 -04:00
3428d71023
Add toggle. Add test. Add changelog. add docs
2021-05-13 10:29:07 -04:00
316e7e0d6d
Ks 20210512 value set expansion id ( #2654 )
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* tested and fixed
* changelog
2021-05-12 21:38:29 -04:00
b64346ba1e
Add shcheduled task enablement config ( #2652 )
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* Add shcheduled task enablement config
* Add changelog
* Test fix
* Cleanup
2021-05-12 14:38:30 -04:00
d70b1866c1
Remvoe dead space
2021-05-11 10:54:14 -04:00
424ec2118b
Add implementation. Add test. Add changelog
2021-05-11 10:31:29 -04:00
5c4fcac530
Merge branch 'rel_5_4'
2021-05-11 08:40:09 -04:00
3015438a0c
Avoid query cache poisoning ( #2647 )
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* Avoid query cache poisoning
* Test fixes
* Add changelog
2021-05-11 08:39:38 -04:00
26d030f93e
Add language validation ( #2644 )
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* Add language validation
* Add tests
* Test fix
2021-05-10 20:09:45 -04:00
43631d4937
Account for NOPs in Auto-Versioned References ( #2643 )
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* Account for NOPs in auto-versioned references
* Add docs
* Add tests
2021-05-08 18:09:50 -04:00
176be4df16
Merge branch 'master' into rel_5_4
2021-05-07 17:44:47 -04:00
0cebbf4fa8
Merge branch 'master' of github.com:hapifhir/hapi-fhir
2021-05-07 17:44:27 -04:00
2068372998
Version bump
2021-05-07 17:43:54 -04:00
63c4b22cd3
Undo bump
2021-05-07 17:42:50 -04:00
17e41520a4
Version bump
2021-05-07 17:41:39 -04:00
5a9f499fbf
Resolve weakness in history operation ( #2642 )
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* Address DOS issue in History operation
* Work on history caching
* Add docs
* Add changelog
* Resolve test failures
* Test fixes
* Test fix
* Test fixes
2021-05-07 12:04:59 -04:00
cf864c2078
Merge remote-tracking branch 'origin/master' into issue-2634-increase-src-path-length
2021-05-06 09:10:48 -04:00
a4856bba17
fix iBundleProvider.getResources(from,to) throwing a NPE ( #2632 )
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* fix iBundleProvider.getResources(from,to) throwing a NPE
* change log
* review feedback
* rename test to IT that has concurrency failures
2021-05-05 21:50:51 -04:00
d17ee2eb78
Add changelog
2021-05-05 16:01:29 -04:00
75c74a22db
Merge pull request #2619 from hapifhir/2590_preserve_the_ID_value_of_the_resources_in_the_package_loader
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2590 preserve the id value of the resources in the package loader
2021-05-03 15:39:14 -04:00
320e8379b3
Now convert pure numeric ids to "npm-<id>".
2021-05-03 12:55:17 -04:00
82be821628
Credit for #2577
2021-05-03 08:03:49 -04:00
573097379d
Credit for #2623
2021-05-02 17:20:16 -04:00
0cea403800
Fix vulnerability warning on maven plugin ( #2621 )
...
* Fix vulnerability warning on maven plugin
* Compile fixes
* Fix bootstrap dep
* Test fix
* Fix tests
* FIx deps
2021-05-02 12:14:32 -04:00
970a9884f0
Avoid tag definition constraint ( #2620 )
...
* Avoid tag definition constraint failure
* Version bumps
* Add changelog
* Avoid guava issue
* Test fix
* Test fix
* Bump pom
2021-05-01 17:16:15 -04:00
55ef6f8653
Add Snowstorm to the points map. ( #2582 )
2021-04-30 19:05:46 -04:00
12c0bcda47
Credit for #2579
2021-04-30 19:03:47 -04:00
b3afe41de8
Added test to make sure we have loaded the expected package id.
2021-04-30 15:14:19 -04:00
983d811af6
Merge pull request #2587 from hapifhir/issue-2585-enhance-placeholder-targets-logic
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Issue 2585 enhance placeholder targets logic
2021-04-30 12:55:27 -04:00
42109e8a4a
Add changelog
2021-04-29 18:31:10 -04:00
8cde076f1e
Merge branch 'master' into 2566_update_s13n_and_validation_handling
2021-04-29 17:25:32 -04:00
239d2496ea
CQL hardening and Dstu3 unit tests ( #2450 )
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* WIP for elm caching
* Bug fixes and a working DSTU3 unit test
* More tests, Address review feedback, add initial docs
* Update to cql-evaluator 1.2.0
* Fixes for documentation
2021-04-29 14:52:13 -04:00
d67537231c
Merge branch 'master' into 2566_update_s13n_and_validation_handling
2021-04-29 13:55:48 -04:00
95d7ba6fa8
Streamline Search SQLs ( #2576 )
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* Streamline SQL queries
* SQL query tidying
* Add changelog
* Test fixes
* Tests passing
* Ongoing work
* Test fixes
* Test fixes
* Build fix
* Cleanup
* Fixes
2021-04-28 10:29:09 -04:00
21d8cdfefc
Merge branch 'master' into 2566_update_s13n_and_validation_handling
2021-04-28 10:16:27 -04:00
dd61a8aa2c
Merge pull request #2575 from hapifhir/kh_2526_Add_Operation_Section_to_Conformance_Statements_resource_section
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Kh 2526 add operation section to conformance statements resource section
2021-04-27 22:47:30 -04:00
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Nick Goupinets
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KevinIsAProgrammer
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