Commit Graph

2496 Commits

Author SHA1 Message Date
JasonRoberts-smile 20f3420397
define constant for new text/xml+cda content type (#3207) 2021-12-02 14:00:52 +00:00
James Agnew aae53d6ec7
Improve loading performance (#3197)
* Synthea perf work

* Cleanup

* Work on performance

* Ongoing perf work

* More perf work

* Perf work

* Test fixes

* Updates

* Test fix

* Test fixes

* Clean up tests

* Test cleanup

* Cleanup

* Add test

* One more perf tweak

* Fixes

* Add changelog

* Add changelog

* License header update

* License header updates
2021-11-28 10:47:30 -05:00
jmarchionatto d496ca98ad
Issue 3172 support member match operation (#3187)
* Suppress unresolved maven properties errors to avoid IntelliJ complains

* Support for $member-match operation

* Add more reference cases

* Adjust tests

* Add test and handle missed condition

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-11-26 14:20:14 -05:00
Tadgh 41ef7cf961
Support multiple EID systems for MDM. (#3178)
* Add implementation, changelog, docs, and tests

* Fix potential NPE

* Use constant instead of *
2021-11-24 06:05:13 +00:00
Kevin Dougan SmileCDR 3c2b4bb397
3136 - Provide RemoteTerminologyServiceValidationSupport Implementation For Operation $validate-code (#3142)
* 3136 - Send validate-code requests to an Instance of IValidationSupport instead of directly to the DAO.

* 3136 - Added support for R4 validate-code calls to a Remote Terminology Server.

* Added more Unit Tests.

* Added NULL checks based on code analysis.

* Adding some cleanup code to the Unit Tests since some other unrelated Unit Tests were failing when running in an Azure Pipeline.

* Adding @Ignore to both of my Unit Test classes to try and see if this is the cause of other unrelated Unit Test failures in the Azure Pipeline.

* Commented out ALL CODE in my Unit Tests to see if this fixes the other Unit Tests.

* Added 1 Unit Tester called RemoteTerminologyServiceResourceProviderR4Test to see if it causes other Unit Test failures.

* Added a Unit Tester called ResourceProviderR4RemoteTerminologyTest with the code that creates a RemoteTerminologyServiceValidationSupport instance commented out for now, just to see if this allows all other Unit Tests to pass.

* Added a Unit test back in to verify how the RemoteTerminologyServiceValidationSupport works when inserted into the front of the IValidation chain. Lets see if this will mess up any other Unit Tests in the Azure Pipeline...

* Added an @AfterEach method to remove the RemoteTerminologyServiceValidationSupport instance from the ValidationSupportChain to see if it allows all the other Unit Tests to work as before.

* Added more Unit tests.

* Added more Unit Tests to increase code coverage.

* Added some NULL checks.

* Added a changelog for this feature add.

* Removed the decision logic in the REST APIs and also the isRemoteTerminologyServiceConfigured() method, and letting the ValidationSupportChain figure out how to perform the validate-code Operation.

* Removed a NULL check that was not needed.

* Reverting the previous change where I tried using the IValidationSupportChain for each and every incoming Operation request. Splitting the implementation between local and remote seems to be required at this time.
2021-11-23 10:39:56 -05:00
TipzCM 7e291bb469
3163 refactor some base mdm stuff (#3166)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2021-11-16 10:47:44 -05:00
TipzCM 25c025cdee
3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155)
* 3153 updating the unknowncodesystemwarningvalidationsupport class

* 3153 updating version for smile

* 3153 update broken tests

* 3153 adding log

* 3153 cleanup

* 3153 cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2021-11-10 16:06:09 -05:00
jamesagnew 5de955c3c2 Licence header updates 2021-11-09 08:44:18 -05:00
TipzCM 59bf8b836f
Issue 3120 support adding retry extension (#3137)
* issue-1134 initial work on adding retry handler

* issue-1134 subdscription creation fixes

* issue-1134 update the test

* issue-1134 retry policy off canonicalsubscription

* issue 1134 base subscription changes

* add failing test

* issue 1134 retry configs on base parameters

* issue 1134 passing forward params

* issue-1134 added more tests for making sure subscriptions create their channels correctly

* issue-1134 updates to get the retry to channels

* issue-1134 updating channel factory

* issue-1134 remove the dlq since it's not defineable

* issue-3120 changelog added

* issue-3120 cleaning up

* issue-3120 test fix

* issue-3120 review fixes

* issue-3120 fixed bad master merge

* issue-3120 updates for new release

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-11-03 18:21:10 -04:00
Tadgh a10c58e839
Bump version, add version to versionenum (#3135) 2021-11-02 09:40:56 -04:00
Tadgh 362c2f30db
Add 5.5.3 to versionenum (#3133) 2021-11-01 13:50:57 -04:00
Tadgh 7c63441663
Revert "Issue 1134 retry mechanic on subscriptions (#3121)" (#3128)
This reverts commit 9b23e9e825.
2021-10-30 19:46:42 +00:00
TipzCM 9b23e9e825
Issue 1134 retry mechanic on subscriptions (#3121)
* issue-1134 initial work on adding retry handler

* issue-1134 subdscription creation fixes

* issue-1134 update the test

* issue-1134 retry policy off canonicalsubscription

* issue 1134 base subscription changes

* add failing test

* issue 1134 retry configs on base parameters

* issue 1134 passing forward params

* issue-1134 added more tests for making sure subscriptions create their channels correctly

* issue-1134 updates to get the retry to channels

* issue-1134 updating channel factory

* issue-1134 remove the dlq since it's not defineable

* issue-3120 changelog added

* issue-3120 cleaning up

* issue-3120 test fix

* issue-3120 review fixes

* issue-3120 fixed bad master merge

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-10-29 11:21:43 -04:00
Tadgh 8a7b5c1b2f
Multiple improvements (#2997)
* Add failing test

* Tidy test for new tokenparam style

* Add removeByQualifier to SearchParameterMap

* Add new property binder for search terms

* Member move, add test for new parser

* whoops missed an add

* Passing test.

Introduced SearchParamTextWrapper to give a type for the binder.
Enhance FulltextSearchSvcImpl to understand TokenParams as well as StringParams.

* Add more to test, change analyzer for template

* Optimize imports

* Minor refactoring

* added eq and gt test cases

* added missing gt search param tests

* Search all CodeableConcepts

* Extract new LuceneRuntimeSearchParam to mediate indexing and searching.

* Fix up broken test with mock

* Add support for identifier type

* Bump for special maven package

* fix-me to todo

* Prevent version check

* FIx version for test

* DSTU2 does not support fluent path

* Don't accidentally strip SPs in DSTU2

* added lt tests

* Add some high-bound test cases

* More test cases and new compressed format

* More test cases

* More test cases

* Re-order columns for easier reading

* Comments

* Cleanup and comments

* Make support :text for all token SPs

* Make support :text for all token SPs

* Fixed incomplete date issue

* Set to the last millisecond 23:59:59.999

* Disabled 4 failed JVM/TZ related test cases

* add test for failing batch bug, remove bounding on queue

* remove parallelism from non-get batch operations

* Fix count for test

* New index layout

* Notes and cleanup

* Notes and cleanup

* remove the jetbrains

* Demote FIXME to WIP

* Change :text search to be lucene simple search and use standardAnalyzer.

* Change :text to require * for prefix match.

* add prefix negative test

* Bump version

* Added changelog

* Add more search parameters to lucene indexing (#3000)

* dirty the branch

* Add oversight to changelog

* Start using jpa indexing for es

* Correct negative search test

* Update templates, index tokens, write new test. TODO gotta modify SB

* Add test for code token search

* add comment

* Flesh out token search

* minor cleanup and comments

* Extract index handling from FulltextSearchSvcImpl

* D'oh.  Actually use elastic to search.

* Move supported query check closer to query builder

* String search test before activating lucene

* Add string:exact to hibernate search.

* Add string:contains search

* cleanup

* demote fixmes to allow build to run.

* Add unmodified string search.

* empty stubs for quantity and reference

* Ignore magic search params in lucene index

* Support full-text on all FHIR releases

* Include reference lookups in ES

* Fix and/or logic in _text

* Test for string with space

* Cherry-pick the NoFT fix

* Disable advanced indexing in a bunch of tests of emitted sql.

* Stub changelog

* Fix :missing flag

* Move DaoConfig up to BaseJpaTest to share teardown

* Disable new indexing for partition test

* Add a different analyzer and field for default string search vs text

* checkstyle for a pre-build

* Index full prefix for string search when using Lucene

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3000-Extend-lucene-indexing.yaml

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

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

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Review feedback.

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Remove double-check

* Version bump

* Fix typo

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Long Ma <longma@Longs-MacBook-Pro.local>
Co-authored-by: Frank Tao <frankjtao@gmail.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-10-28 15:13:16 -04:00
jamesagnew 58071aa1b3 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2021-10-26 16:50:10 -04:00
jamesagnew 1792b74b50 Inforporate version checks 2021-10-26 16:49:49 -04:00
James Agnew 9e057574a6
Allow multi-resource Subscription criteria (#3110)
* Allow start criteria subscriptions

* Rework subscription tests

* Subscription cleanup

* Add changelog

* Test fixes

* Test fix
2021-10-26 16:48:13 -04:00
michaelabuckley f98f3cdaa9
Extend ordinal date search to year and month precision (#3102)
* added eq and gt test cases

* added missing gt search param tests

* added lt tests

* Add some high-bound test cases

* More test cases and new compressed format

* More test cases

* More test cases

* Re-order columns for easier reading

* Comments

* Cleanup and comments

* Fixed incomplete date issue

* Set to the last millisecond 23:59:59.999

* Disabled 4 failed JVM/TZ related test cases

* Added changelog

Co-authored-by: Long Ma <longma@Longs-MacBook-Pro.local>
Co-authored-by: Frank Tao <frankjtao@gmail.com>
2021-10-21 15:32:26 -04:00
Tadgh 3d681134e9
Add SearchBundleEntryParts (#3095)
* Add the ability to parse a search bundle into its component parts

* remove deadspace

* wip
2021-10-19 23:41:33 +00:00
Tadgh b427135b04
Patient/$everything _id parameter (#3077)
* Add tests. Add implementation in R4. Add changelog

* Wip partial fixup of other STU versions

* Updated usages of new patient type everything api

* Partial commit of incomplete documentation

* Remove docs

* Cut to token instead of string

* Bump hapi version due to breaking api changes
2021-10-17 14:34:33 +00:00
Ben Li-Sauerwine 2e5aed4016
Adds a NDJSON parser, in preparation for adding NDJSON $import to HAPI (#3022)
* NDJsonParser with one example test.

* Add test for empty NDJson, and fix bug for empty NDJson.

* Adds multi-Patient test, and fixes bug whereby all multi-line NDJSON would be put into the same line.

* Adds test for NDJson with newlines in it.

* Adds test for converting non-Bundle types to NDJSON failing.

* Confirm that we can only extract to Bundle types in test.

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java

Co-authored-by: James Agnew <jamesagnew@gmail.com>

* Documents behavior of the NDJsonParser in FhirContext.

* Attempt to fix failing build by using TestUtil to clear context in the manner of r4 parser tests instead of dstu

Also clean up indentation.

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-10-17 09:06:31 -04:00
Jing Tang b25b186044
Remove the unused dependency on net.sf.saxon:Saxon-HE (#3043)
* Remove the unused dependency on net.sf.saxon:Saxon-HE

* Remove Saxon-HE dependency in hapi-fhir-jpaserver-base

* Remove unused comment in hapi-fhir-structures-dstu2.1/pom.xml
2021-10-14 16:34:48 -04:00
Tadgh 87e594d416
Bump JENA to deal with CVE-2021-29349 (#3063) 2021-10-13 16:17:43 -04:00
Tadgh d2ea4655a7
Rel 5 5 2 (#3060)
* Add versionenum, bump maven version

* failing tests

* more logs

* Add more test cases, not passing

* fixed the double chain with contained resource second case

* clean up a bit

* add tests for qualifiers

* force the resource table to be the root of the query if we might be traversing a contained reference

* tidy up

* tests for longer chains

* changelog

* code review feedback

* backport changelog

* Add version.yaml

* [2935] Escape "%" in like expression

* Add backport to changelog

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
2021-10-12 14:25:03 +00:00
James Agnew 310a4cdb58
Migrate CLOB columns to LOB (SMILE-3072) (#3016)
* Migration finished

* Work on LOBS

* Add to ClobMigrated annotation

* Deal with lobs

* Work on new approach

* HAPI FHIR version bump

* Add changelog

* Add license header

* Fix intermittent

* CLeanup

* Cleanup
2021-10-11 16:47:37 -04:00
TipzCM a474e88ed4
issue-2397 implementing the mdm expansion on everything and searches (#3044)
* issue-2397 implementing the mdm expansion on everything and searches

* issue-2397 code cleanup and removal of test code

* issue-2397 some tests

* issue-2397 changelog added

* issue-2397 review fixes

* issue-2397 updated change log with example and fixed failing tests

* issue-2397 test fixing

* issue-2397 fixing test

* issue-2397 review fix

* issue 2397 fixing changelog file

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-10-07 10:46:23 -04:00
James Agnew d320b78ae1
Improve synthea ingest performance (#3033)
* Improve synthea ingest performance

* Tweaks

* Fix param splitting

* Update to test

* Add changelog

* Test fix

* Add some runtime checks

* Remove useless test

* Test fix
2021-10-04 05:46:06 -04:00
jamesagnew d4f01ac4e7 License header updates 2021-10-03 20:20:04 -04:00
James Agnew eca725afa4
Improve versioned URL support for ValueSet expansion (#2994)
* Add test

* Test fixes

* Work on expansion errors

* Fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Work on fix

* Test fixes

* Test fixes

* Test fix

* Cleanup

* Test fixes

* Remove accidental commit

* Test fixes

* Version bump

* Add changelog

* Fixes

* Test fix

* Fix conflicts
2021-10-03 19:47:23 -04:00
James Agnew 95e853bdf7
Improve parallel model scanning (#3046)
* Improve parallel model scanning

* Add changelog

* Resolve fixme

* Test fix
2021-10-03 19:40:24 -04:00
Ken Stevens b1dd40fdba
Try commenting out clearAllStaticFieldsForUnitTest to see what happens (#3034)
* Try commenting out clearAllStaticFieldsForUnitTest to see what happens

* Rename clearAllStaticFieldsForUnitTest to randomizeLocaleAndTimezone and only do that
2021-09-24 16:01:28 -04:00
Ken Stevens 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
Tadgh a12ce73797 Add more tests 2021-09-21 15:31:36 -04:00
James Agnew 7379dee3d8
Merge branch 'master' into add-device-to-patient-compartment 2021-09-21 14:38:39 -04:00
Ken Stevens 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
Jaison B 8bb9aca8df Merge branch 'master' into 2849_add_new_mdm_param 2021-09-17 10:18:24 -06:00
Tadgh 3d24a4ce16 Refactor to support arbitrary additional SPs based on Type for a compartment 2021-09-14 01:02:19 -04:00
Ken Stevens eee7d7e455
code cleanup (#2986)
* failed attempt to get it to work

* Use simplified FhirContext.forCached methods

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java

Co-authored-by: James Agnew <jamesagnew@gmail.com>

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-09-13 03:09:18 +00:00
James Agnew 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
Tadgh 0ccd71faf8
Merge pull request #2963 from hapifhir/custom-elastic-index
Custom elastic index
2021-09-08 14:29:58 -04:00
Tadgh f04cf02be7
Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-08 08:45:47 -04:00
Tadgh 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -04:00
Nick Goupinets 35aaa98431 Merge branch 'master' into 2849_add_new_mdm_param 2021-09-07 11:27:49 -04:00
Ken Stevens 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
Nick Goupinets ee65a24260 Merge branch 'master' into 2849_add_new_mdm_param 2021-09-02 17:42:41 -04:00
leif stawnyczy 1a7b101d03 Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-02 10:13:04 -04:00
Tadgh 3e288f1dde Merge branch 'master' into rel_5_5_1 2021-09-01 18:16:27 -04:00
Tadgh e1272a3825 Bump version of HAPI-FHIR 2021-08-31 11:43:17 -04:00
Tadgh 87986d3da8 Add versionenum 2021-08-31 11:42:26 -04:00
Nick Goupinets 8403b85429 Merge remote-tracking branch 'origin/master' into 2849_add_new_mdm_param 2021-08-27 09:42:08 -04:00