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273 Commits

Author SHA1 Message Date
James Agnew 05735900fd
Fixes to interceptor in order to prevent zombie listeners on restart (#1988) 
* Fixes to interceptor in order to prevent zombie listeners on restart

* Add test

* Add license header

* Test fixes
 2020-07-20 14:03:46 -04:00
Tadgh 6bb92717f5 Merge branch 'master' into batch-empi-job 2020-07-16 11:00:32 -07:00
James Agnew baba4cc240
Avoid version conflicts on current writes (#1971) 
* Add auto retry of transactions

* Experiment in Maven build

* Transaction autoretry

* Work on transaction retries

* Work on transaction retry

* Work on transaction retry

* Fix tests

* Avoid version conflicts

* Add changelog

* Resolve LGTM issue

* FIx transaction scope error

* Test fixes

* Test fix

* Test fixes

* Test fix

* Test fixes
 2020-07-13 08:51:13 -04:00
Tadgh c3b89b4ad5 Get basic tests running 2020-07-09 15:56:41 -07:00
James Agnew f356c7c385
Migrate to JUnit5 (#1952) 
* Work on junit

* Work on junit 5

* Work on junit 5

* Bump errorprone vcersion

* Work on tests

* Junit 5 tweaks

* Fixes

* Work on tests

* Work on junit5

* Work on tests

* Test fixes

* Work on junit5

* Test work

* Get junit5 working

* Test fix

* Work on tests

* WOrk on tests

* Work on tests

* fixes

* Compile fix

* One more tweak

* Compile fix

* Add changelog

* Fix compile error

* Compile fix
 2020-07-04 18:28:16 -04:00
jamesagnew 2cdef055aa Missed commit on #1951 
Squashed commit of the following:

commit f820135996
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 14:29:24 2020 -0400

    Address review comments

commit 11c4f9defb
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:38:16 2020 -0400

    Fix LGTM warning

commit b650fdb9ea
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:20:52 2020 -0400

    Test fix

commit 6ebcceeb5c
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:49:01 2020 -0400

    Add changelog

commit 4a1d7383b0
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:46:52 2020 -0400

    Bundle transmission

commit 88bd4abf0c
Merge: 7cde945281 25fc747b9f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:31:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 7cde945281
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:10:33 2020 -0400

    Work on seed bundles

commit ed2e62752e
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 09:39:10 2020 -0400

    Work on subscriptions

commit 52addcff59
Merge: 64a9eaa4de bf8de84801
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Sat Jun 27 18:09:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 64a9eaa4de
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:32:17 2020 -0400

    Start work

commit f74eba5397
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:28:18 2020 -0400

    Terser should create correct Enumeration on create
 2020-06-30 14:31:40 -04:00
James Agnew fa4bbe3685
Allow search criteria as subscription delivery mechanism (#1951) 
* Terser should create correct Enumeration on create

* Start work

* Work on subscriptions

* Work on seed bundles

* Bundle transmission

* Add changelog

* Test fix

* Fix LGTM warning
 2020-06-30 14:29:09 -04:00
Ken Stevens 97a1bd40a1
Added TLS parameters to Java Mail Sender (#1666) 
* Added TLS parameters to Java Mail Sender

* changelog
 2020-05-27 19:17:01 -04:00
jamesagnew 056721829d License header updates 2020-05-22 15:56:14 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857) 
EMPI Initial Implementation (still plenty of known gaps)
 2020-05-22 15:03:20 -04:00
James Agnew e07e071130
Avoid deserialization issues in subscription delivery (#1856) 
* Avoid deserialization issues in subscription delivery

* Add changelog
 2020-05-21 05:47:39 -04:00
James Agnew 5b2181a563
Implement FHIR Patch (#1850) 
* Start working on FHIRPatch

* More work on fhirpatch

* Work on FHIR Patch

* Add patch

* Test fixes

* Test fixes

* Get tests fixed

* Chnage to trigger a build

* Compile fix

* Dependency version fixes

* Test fix

* COmpile fix

* Try to fix build

* Test fix attempt

* Another build attempt

* Another build tweak

* Cleanup
 2020-05-20 19:43:55 -04:00
jamesagnew 52c8e3551c Version bump to 5.1.0-SNAPSHOT 2020-05-15 14:43:32 -04:00
jamesagnew fe0e07a313 Bump to 5.0.1 2020-05-15 05:47:01 -04:00
jamesagnew 1d13e29ac0 Version bump to 5.1.0-SNAPSHOT 2020-05-12 20:04:20 -04:00
jamesagnew d631ecff4a Prepare for 5.0.0 2020-05-12 11:49:18 -04:00
James Agnew 0c13a65871
Bump to latest Core version (#1841) 
* Start working on bumping core

* Work on tests

* Work on tests

* Bump core definitions

* Bump R5 defs

* Tweak changelog

* Test fix
 2020-05-11 12:37:16 -04:00
James Agnew 6cc07b6689
Make binary storage work for bulk export (#1836) 
* Make binary storage work for bulk export

* Add changelog

* Build fixes

* Test fix

* Test fix

* Test fix
 2020-05-07 19:20:22 -04:00
James Agnew a77aa6a28e
Multitenancy Ticket 2 - #1813 (#1821) 
* Work on multitenancy

* Second ticket started

* More multitenancy work

* Work on tenancy security

* Work on multitenancy

* Test fixes

* Add docs

* cs tweak

* Multitenancy fixes

* Add debug log

* Fix build

* Add headers

* Add partition selection interceptor hook

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Account for review comments

* Resolve FIXMES

* Work on tests

* Test fixes

* A bit more cleanup

* Work on multitenancy

* Update hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientExamples.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Allow disabling text modifier indexing

* Add changelog

* Docs fixes

* Address review comment

* Resolve merge conflicts

* Merge master

* Compile fix

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-05-05 15:12:15 -04:00
James Agnew ededcc18d2
Add Partitioning / Multitenancy (#1807) 
* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Add columns

* Work on multitenancy

* Work on muiltitenancy

* Work on multitenancy

* Work on uniques

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* More work on multitenancy

* Work on multitenancy

* Multitenancy work

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Work on docs

* Work on multitenancy

* Work on docs

* DOcs work

* Tenancy docs

* Work on docs

* Finish docs

* Add changelog

* Rename config

* Add migration tasks

* Fix typo

* Migration fix

* One more migration fix

* A couple more migration fixes

* Docs cleanup

* Work on docs

* Bump boot version

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Work on review comments

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Compile fx

* Test fixes

* One more bugfix

* Update operation name

* Add one more constant

* Roll back a change that was causing test failures

* Test fixes

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-04-24 05:45:11 -04:00
jamesagnew ccda668d0c Restore subscription loading at startup 2020-04-23 05:28:56 -04:00
jamesagnew 1f37cdd8cf Address review comments 2020-04-21 20:53:10 -04:00
jamesagnew 998c1f7751 Work on docs 2020-04-21 14:32:41 -04:00
jamesagnew bbab016ca6 Rename config 2020-04-20 12:38:04 -04:00
jamesagnew 982b54df57 Work on multitenancy 2020-04-13 11:50:49 -04:00
jamesagnew 8a77d839c3 One more change 2020-04-07 19:09:44 -04:00
jamesagnew edc30568f2 Address review changes 2020-04-07 19:07:07 -04:00
jamesagnew 47786660d5 Test fixes 2020-04-07 13:58:24 -04:00
jamesagnew 347ecc7d51 Tests passing 2020-04-07 09:39:14 -04:00
jamesagnew 826ba6458a Subscription work 2020-04-06 20:15:41 -04:00
jamesagnew b78205c218 Ongoing cleanup 2020-04-06 17:00:45 -04:00
jamesagnew 40d0c27ae3 Work on subscription cleanup 2020-04-05 18:43:27 -04:00
jamesagnew d0884663d2 Work on subscription cleanup 2020-04-05 11:34:47 -04:00
jamesagnew 0a28c0c060 Work on subscription cleanup 2020-04-05 07:21:05 -04:00
jamesagnew 79da1578cb Subscription cleanup 2020-04-04 20:04:32 -04:00
jamesagnew fef447afee Work on subscription cleanup 2020-04-04 16:07:01 -04:00
jamesagnew 68db40d057 Queue factory cleanup 2020-04-03 08:07:39 -04:00
jamesagnew 7c6024fa14 More work on subscriptions 2020-04-03 07:43:21 -04:00
jamesagnew 43b4d8e0e3 Work on subscriptions 2020-04-02 21:15:07 -04:00
jamesagnew 6baf1995c9 Work on subscription cleanup 2020-04-02 20:30:19 -04:00
jamesagnew e1142f4043 Start work on subscription cleanup 2020-04-02 05:31:12 -04:00
jamesagnew 3f20f7b67f Make SubscriptionDeliveryHandlerFactory not abstract 2020-03-22 21:01:19 -04:00
James Agnew 22413911bf
Validation api changes (#1719) 
* Validation enhancements

* Work on validation api reworking

* Keep working on validation API

* Keep working on new term API

* Work on validation api

* Ongoing work on validation

* Work on integrating validation

* Work on validation API

* Add to validation API

* Work on validation

* Work on API

* Work on validation

* Work on validation API

* Work on validation API

* Work on validation api

* Work on validation API

* Work on validation api

* Validation API changes

* Work on API

* More work on validationo API

* Work on validation API

* FIxes

* WOrk on validation api

* Work on validation API

* Tests passing!

* More cleanup

* More validation API changes

* Fix intermittent test failure

* Package reorg

* Validation API work

* Work on doocumentation

* Work on API

* More work on new validation API

* Fix errorprone-reported error

* Test fixes

* Documentation updates

* Documentation tweaks

* Work on API

* Bean name adjustments

* Build fixes

* Some test fixes
 2020-03-17 13:28:59 -04:00
Ken Stevens ecf5284c87 moved common Json annotations out into an interface 2020-03-12 13:36:34 -04:00
Ken Stevens b2f9dd4578
extend pointcutlatch and simplify FhirClientResourceRetriever (#1737) 
* extend pointcutlatch and simplify FhirClientResourceRetriever

* extend pointcutlatch and simplify FhirClientResourceRetriever
 2020-02-28 16:38:13 -05:00
Ken Stevens b33ad73d46 switch subscriptionchannelfactory to autowire 2020-02-24 14:28:14 -05:00
Ken Stevens 41b5eb2484 Switching cdrsubscribablefactory from @ComponentScan to @Bean 2020-02-23 15:43:30 -05:00
jamesagnew ddc7b601ee Version bump to 4.3.0-SNAPSHOT 2020-02-16 19:23:22 -05:00
jamesagnew 4fd80cfca7 Bump to 4.2.0 2020-02-16 19:00:15 -05:00
Ken Stevens 2bc3181218 ensure in-memory matching location search for Dstu3 falls back to a db search 2020-01-25 13:30:26 -05:00
Ken Stevens 4f14e621ec added failing test for in-memory dstu3 case 2020-01-24 22:03:23 -05:00
jamesagnew 9c7f5e1b9b License header updates 2020-01-12 10:15:08 -05:00
James Agnew 5cfc75eac2 Test fixes 2019-12-25 13:05:33 -05:00
Ken Stevens 625f967688 ready for review 2019-12-20 14:56:44 -05:00
Ken Stevens 993d8220d1 review feedback 2019-12-02 11:18:52 -05:00
Ken Stevens f92c2bb5f9 ensure only one @PostConstruct method to make order explicit 2019-11-29 11:46:03 -05:00
Ken Stevens 37eef4e3e4 rename schedule interface methods 2019-11-29 11:04:35 -05:00
Ken Stevens 321790f6bf standardized job names and how they're scheduled 2019-11-29 10:12:13 -05:00
Ken Stevens a0e363171d replace FireAtInterval class with an interface for now 2019-11-29 09:21:20 -05:00
Ken Stevens 6f9cd56c81 moved scheduler up to hapi-server 2019-11-20 14:30:24 -05:00
Ken Stevens 8fca468e1f remove boolean from scheduling API 2019-11-19 10:13:22 -05:00
James Agnew 74159dcb26
Work on refactoring how PIDs work (#1580) 
* Start work on refactoring how PIDs work

* Some test fixes

* Test fixes

* Test fixes

* Restore accidentally deleted line

* One more tweak

* Rework resource link extraction

* Test fix

* Split out transaction processor

* Updates

* Test fix

* Test fixes

* Test fixes

* Clean up LGTM warning

* Fix compile failure

* One more test fix

* Fix LGTM issue

* Add spot for metadata

* Add test logging

* Remove testing code

* More test logging

* Add some test logging

* Attempty to fix intermittent test failure

* Improve exception tracking

* Work on simplifying search param registry

* Fix compile

* Fix compile errors

* Fix two test bugs
 2019-11-17 14:35:19 -05:00
James Agnew 497a96ae68 Version bump for next round of development 2019-11-12 22:09:21 -05:00
jamesagnew f99ad981b5 Version bump to 4.1.0 2019-11-12 16:08:20 -05:00
Ken Stevens 7525e70bbc added message type to channel api. needed by kafka listeners when more than one message type needs to be supported 2019-11-09 18:31:08 -05:00
James Agnew b90f285218 Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-30 08:41:14 -04:00
James Agnew 007cfaf00e
Don't error out on missing CS (#1570) 
* Don't error out on mi9ssing CS

* Add tests

* Add a bit of test coverage

* One more test
 2019-10-30 08:38:39 -04:00
jamesagnew 51a0006548 Work on rationalizing search param extractor 2019-10-27 20:04:33 -04:00
James Agnew 817f9ae36e Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-27 17:25:20 -04:00
James Agnew 464c6c5b45
Upgrade dependencies and addess Semmle issues (#1554) 
* Version bumps

* FIx build issues

* Address a few Semmle issues

* Work on tests

* Some test fixes

* Test fix

* Fix deletions

* Test fix

* Fix intermittent test failure

* One more dependency bump

* Add some test logging

* Remove bad import

* Add some tests

* Test updates
 2019-10-22 17:10:58 -04:00
James Agnew 73961072a6
Handle invalid chains on custom search params (#1553) 
* Handle invalid chains on custom search params

* Add some more tests

* One more test fix
 2019-10-21 21:21:33 -04:00
Ken Stevens 9a580de6c4 fix subscription logging for delete 2019-10-06 15:10:19 -04:00
jamesagnew 150c865f68 License header updates 2019-10-03 21:20:08 -04:00
Ken Stevens 38ad11be64
Merge pull request #1513 from jamesagnew/ks-subscription-delivery-queue-configurable-name 
subscription delivery queue configurable name
 2019-10-03 15:19:12 -04:00
James Agnew a3b9db1363 Clean up a few unused methods and move test classes into test project 2019-10-03 14:58:02 -04:00
Ken Stevens 6451b9691e review feedback 2019-10-03 13:53:54 -04:00
Ken Stevens 66618ec6bd review feedback 2019-10-03 13:52:54 -04:00
Ken Stevens 5b05e9cda0 review feedback 2019-10-03 13:49:13 -04:00
Ken Stevens 53f949c2d0 pre-review cleanup 2019-10-02 08:36:54 -04:00
Ken Stevens ba37ce0588 test cleanup 2019-10-02 07:31:16 -04:00
Ken Stevens 82543c01d6 fix test 2019-10-02 06:55:27 -04:00
Ken Stevens 5aa4f88da3 Remove ISubscribableChannel interface. We don't need it after all. 2019-10-02 06:35:39 -04:00
Ken Stevens 4c534a8d7e await cleanup 2019-10-01 22:10:07 -04:00
Ken Stevens 028febfe45 await cleanup 2019-10-01 21:16:06 -04:00
Ken Stevens f0b2bb8309 fixed triggering subscriptions 2019-10-01 14:57:25 -04:00
Ken Stevens 718b2c793d fixed asymmetry between add and remove 2019-10-01 11:22:09 -04:00
Ken Stevens ca95791d2e fix test 2019-10-01 10:52:00 -04:00
Ken Stevens 082dff71c2 added tests 2019-09-30 21:07:37 -04:00
Ken Stevens b757d95d64 added tests 2019-09-30 21:04:29 -04:00
Ken Stevens 4c8e330669 change channel cache to us id instead of object 2019-09-30 17:50:12 -04:00
Ken Stevens 6867a57625 null check 2019-09-30 17:15:35 -04:00
Ken Stevens 6196f528d9 fix synchronization channel removal 2019-09-30 16:48:48 -04:00
Ken Stevens 99fee443fd test 2019-09-30 15:19:01 -04:00
Ken Stevens fd8b5206e7 Separated ChannelRegistry from ActiveSubscriptionRegistry so we can support a many-to-one relationship there 
All tests pass
 2019-09-30 15:01:47 -04:00
Ken Stevens 392d7ab000 Extend SubscribableChannel with SubscribableChannelManagement so we can get a handler count so we know when to destroy a channel 2019-09-26 15:46:40 -04:00
Ken Stevens a3a7174c63 Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name 2019-09-26 09:17:53 -04:00
James Agnew 8657afb01e
Fix intermittent test failures regarding search (#1509) 
* Add some logging

* Add more test logging

* Work on some test logging

* Fix compile error

* Work on codecov

* Work on codecov

* Remove test debug messages
 2019-09-25 20:15:21 -04:00
Ken Stevens 2c21d72c03 added queue naming service 2019-09-25 16:45:50 -04:00
jamesagnew 473fa3456e Work on adding codecov 2019-09-25 14:12:42 -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