Commit Graph

234 Commits

Author SHA1 Message Date
VK-SMILECDR 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
Ken Stevens 0b05c730fb
don't create a channel if subscriptions are disabled. (#2733)
* don't create a channel if subscriptions are disabled.

* review feedback

* fix test

* fix intermittent

* fix intermittent
2021-06-19 00:00:16 -04:00
James Agnew c8c596aff4
Fix date search on period with no end (#2676)
* 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
James Agnew 7a83c76e65
Add validation suppression mode (#2675)
* Add validation suppression mode

* Add changelog

* Compile fix
2021-05-26 17:41:48 -04:00
jamesagnew e359b6d823 Handle missing contained subscription 2021-05-19 09:45:04 -04:00
jamesagnew de56f440cb Version bump 2021-05-18 17:14:14 -04:00
Ken Stevens a4856bba17
fix iBundleProvider.getResources(from,to) throwing a NPE (#2632)
* 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
James Agnew b617c7690d
Search Parameter Infrastructure Cleanup (#2522)
* Search param service cleanup

* Work on collapsing search param

* Search param cleanup

* Work on build

* Test fix

* Test fixes

* Ongoing work

* Test fix

* Compile fix

* Test fixes

* Test fix

* Test fix

* License header updates

* Remove fixme

* Cleanup

* Cleanup
2021-04-05 17:40:10 -04:00
Frank Tao f6d4a40388
UCUM Service Support (#2261)
* Added UcumServiceUtil

* Removed ucum-essense.xml

* Added ucum service existing test cases passed

* Added more test cases

* Merge branch 'master' into ft-ucum-support

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

* Added back extractReferenceParamsAsQueryTokens

* Added changelog and migration script

* Added length for the string type

* Moved UCUM util to hapi-fhir-jpaserver-model

* Renamed UCUM support to Normalized Quantity Search Support

* Moved setNormalizedQuantitySearchNotSupported to AfterEach

* Changed migrate task to 530

* Removed comments

* Fixed in memory search issue and added more test cases

* Fixed the version order

* License header updates

* Updated based on review comments

* Updated the migration task based on review comments

* Fixed RES_TYPE with type String and length 100

* Changed myParamsQuantityNormalizedPopulated type to Boolean class
2021-01-10 21:05:24 -05:00
jamesagnew 57347ddb63 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2021-01-01 15:52:06 -05:00
jamesagnew d20b07c78e Update license headers 2021-01-01 15:50:24 -05:00
jamesagnew ec712e086c Version bump mockito 2021-01-01 15:50:00 -05:00
jamesagnew f30999b053 License header updates 2021-01-01 15:07:23 -05:00
James Agnew 8f8c5c31f1
Add validation rules interceptor (#2264)
* Start work on validation rules interceptor

* Work on interceptor

* Add tests

* Work on validation interceptor

* Work on interceptor

* Test fix

* Documentation tweaks
2021-01-01 14:29:10 -05:00
Tadgh e79114e2ec
Un-revert the MDM changes, now that issues have been addressed (#2226)
* Backward compatibility changes

* Revert "Revert "Remove all references to Person from EMPI.""

* Updated docs

* Removed mdm channel references

* Initial implementation

* fix coarseness bug. Fix tests. reinitialize silly bean

* Add forgotten json file

* Generic provider PoC

* Refactored provider to use BundleBuilder

* Removed version-specific MDM providers

* Addressed code review comments

* Fixed after merge

* Fixed docs

* MDM SVG for Update Use Cases

* Removed obsolete docs

Co-authored-by: Nick <nick.goupinets@smilecdr.com>
Co-authored-by: Nick Goupinets <73255752+nvg-smile@users.noreply.github.com>
2020-12-17 10:12:53 -05:00
James Agnew d958764d49
Partition data leaks across searches (#2220)
* Partition data leaks across searches

* Add changelog

* Resolve FIXME

* Add test logging

* Test fix

* Test fix
2020-12-06 16:32:07 -05:00
Ken Stevens 3d3242cf9a
Resource change listener (#2191)
* init rev

* fix build

* Tweaked the POM config settings and also added some dependency exclusions (commented out for now).

* More re-factoring of the CQL Unit Tests.

* Removed a LogMessages.html file and a minor Unit Test change.

* Unit Tests.

* added debug logging to troubleshoot the dao that has no name

* added debug logging to troubleshoot the dao that has no name

* workaround to get past null dao resourceName issue

* fix jsons to get test to pass.  Test still fails with library id problem

* gitignore

* gitignore

* test passes!  Woohoo!

* undo troubleshooting logging

* added timer and logging.

* added asserts and time multiple evaluations and measure the average

* readme

* adding explanations

* added more explanatory notes

* measure 2 patients

* move pom to use cqf snapshot

* roughed out cache

* roughed out cache

* Added code to VersionChangeCache class.

* added tests

* added polling test

* wrote init version

* wrote init version

* optimized versioncache

* worked on getting tests to pass

* redesigned interfaces

* all tests pass

* fixmes

* fixmes

* rename param

* Added Unit Tests.

* javadoc

* Fixed the 2-Patient Unit Test.

* More Unit Test work.

* make ResourceVersionMap immutable

* Fixed a Unit Test that was failing intermittently by adding a new way to refresh the cache.

* Use a new method called doRefreshAllCaches(0) to force a refresh and have all Listeners called immediately.

* Cleaned up IVersionChangeListenerRegistry interface to make methods more clear and resolved all Unit Tests.

* disabled tests

* disabled tests

* removed unused test method

* fixed refresh logic and added asserts

* moved cache so it can be used by searchparamregistry

* Updated the Cql Unit Tests to be properly configured for Dstu3 or R4.

* started rewriting SearchParamRegistryImpl to use new cache
added init method to listener interface

* added fixmes

* adding tests

* tests pass

* added tests

* Fixed the way CqlProviderFactory Autowires Beans so it can work with both Dstu3 and R4 contexts.

* moar tests

* fix test

* work tests

* reverting unneccessary refactors

* undo unneccessary import changes to reduce MR size

* undo unneccessary import changes to reduce MR size

* Unit Test fixes...more to come...

* add unregister

* fix tests

* Changed ResourceVersionCache to use a Map of Maps.

* searchparam test

* test passes

* resolved fixme

* fixmies

* strengthen test asserts

* More Unit Test changes and added some FIMXME items.

* changed from long to changeresult

* renamed VersionChange -> ResourceChange

* fixed delete bug

* organize imports

* fix test

* add update test

* add test reset function

* fix stack overflow

* fix startup race condition (might still be intermittent)

* found the problem.  delete doesn't work because we can't look up the deleted resource to find out what its name is

* fixed regression

* abandoned idea of incrementally updating searchparam registry.  Rebuilding every time--it doesn't change that often.

* fix test

* begin with failing test

* test passes

* fixmes and javadoc

* fix test

* fixme

* fix test

* whack-a-mole.  Either subs pass or cql passes.  Something's fishy with the FhirContext

* fix subscription test initialization

* fix method name

* Re-factored the CqlProvider Unit Tests.

* changed ResourceChange API

* add interface

* add interface

* fix test

* add schedule test

* add doc

* init rev

* FIXME

* modify FhirContext change

* change fhirContext.getResourceTypes to lazy load

* converted subscriptions

* converted subscriptions

* begin with failing test

* test passes

* fix test

* test coverage

* test coverage

* test coverage

* test coverage

* good coverage now

* pre-review cleanup.  I think I found a bug.

* moved cache into listener entry
tests pass with fixmes

* fix test

* fix test

* fix test

* fixme

* FIXMEs

* merge cache and registry

* method reorg

* javadoc

* javadoc done.  all FIXMEs resolved.

* change log

* changes needed by cdr

* spring config cleanup

* james feedback

* james feedback

* might not work. Try moving resourcechangeconfig into searchparam config

* merge ResourceChangeListenerRegistryConfig.java into SearchParamConfig

* fix test

* fix SubscriptionLoader

* fix SubscriptionLoader

* create ResourceVersionMap from resources

* added cache handle interface

* fix test

* javadoc

* fix test

* fix test

* James feedback: clone searchparametermap

* fix startup

* fix test

* fix test

* fix intermittent

* pre-review cleanup

* FIXME

* final FIXME yay!

* Address a couple of my own reviw comments

Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2020-11-29 19:42:40 -05:00
James Agnew 5e8ec8d6f3
Resolve crash in InMemory SP resolver for empty source (#2150)
* Resolve crash in InMemory SP resolver for empty source

* Add changelog
2020-10-28 14:30:32 -04:00
Tadgh ea64bea1b0 Refactor to use concrete class instead of parent 2020-09-15 15:27:21 -04:00
Tadgh 5744f7035f Rename to match names across classes 2020-09-14 16:54:09 -04:00
Tadgh a9fb849d49 Moved more into parent class, added javadocs for transactionId 2020-09-14 16:44:50 -04:00
Tadgh 6e0ef035e9 Rename constants. Remove dead comment 2020-09-14 15:35:58 -04:00
Tadgh 9a09a8abf3 Update todos 2020-09-14 13:41:11 -04:00
Tadgh c3ddf59d6f Add HapiMessageHeaders to BaseJsonMessage class 2020-09-14 13:02:32 -04:00
Tadgh 28a9a53917 Rework to keep several things in subscription 2020-09-10 16:05:56 -04:00
Tadgh 2229233749 Move subscription models to legacy, except the ones that are subscription specific 2020-09-09 15:58:41 -04:00
Tadgh df20a04b53 Add test to ensure Messageheaders are serializable 2020-09-09 12:07:22 -04:00
Tadgh 4ec2be4ff5 Merge branch 'master' into batch-empi-job 2020-07-21 07:54:18 -07:00
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
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