Commit Graph

19 Commits

Author SHA1 Message Date
michaelabuckley 02169f9a6b
Bump to 6.4.3-SNAPSHOT 2023-03-04 12:58:21 -05:00
Tadgh c51aa39d8f Set back to 6.4.2 2023-02-27 16:27:59 -08:00
James Agnew 3a8b42dc39
Improve bulk export performance (#4569)
* Improve performance on bulk export

* Add changelog

* Start working on cleaned up reducer

* Clean up batch calls

* Work on issues

* Build fixes

* Test fixing

* Test fixes

* Work on progress

* Add changelog

* Build tweak

* Fixes

* Fixes

* Fix compile

* Test fixes

* Bump to 6.4.2-SNAPSHOT

* Fix compile

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-02-27 07:32:39 -05:00
markiantorno 31610cd8fb Updating version to: 6.4.2 post release. 2023-02-26 22:29:48 +00:00
Tadgh 4af1a5016c Force pin structs 2023-02-24 10:08:29 -08:00
Tadgh eee61285f3 Exclude pinned core deps 2023-02-24 09:04:39 -08:00
markiantorno 827bbba1e2 Updating version to: 6.4.1 post release. 2023-02-17 04:29:53 +00:00
Tadgh 96855fb943 Reset version 2023-02-16 16:33:56 -08:00
markiantorno b2644c1c60 Updating version to: 6.4.1 post release. 2023-02-16 23:33:58 +00:00
Tadgh 9578610e15 bump ver 2023-02-10 20:42:38 -08:00
Nathan Doef 9754a72046
Bulk Export Bug With Many Resources and Low Max File Size (#4506)
* failing test

* fix + changelog

* tweak

* add method to IJobPersistence to use a Stream

* tweak

* tweak

* decrease test time

* clean up

* code review comments

* version bump

* Increase timeout limit to match BulkExportUseCaseTest

* shorten test

* maintenance pass

* add logging

* Revert "add logging"

This reverts commit b0453fd953.

* Revert "maintenance pass"

This reverts commit bbc7418d51.

* test

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* shorten tests

* logging

* move test location

* fixes a regression caused my change in hapi-fhir

* timeout

* Revert "fixes a regression caused my change in hapi-fhir"

This reverts commit 4b58013149.

* testing

* Revert "testing"

This reverts commit aafc95c2f3.

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-02-10 13:14:29 -05:00
Tadgh 456cc81b32
Rel 6 2 5 mergeback (#4459)
* jm wrong bundle entry url (#4213)

* Bug test

* here you go

* Generate relative URIs for bundle entry.request.url, as specified

* Point jira issue in changelog

* Adjust tests to fixes

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* improved logging (#4217)

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Rel 6 1 3 mergeback (#4215)

* Bump for CVE (#3856)

* Bump for CVE

* Bump spring-data version

* Fix compile

* Cut over to spring bom

* Bump to RC1

* remove RC

* do not contrain reindex for common SP updates (#3876)

* only fast-track jobs with exactly one chunk (#3879)

* Fix illegalstateexception when an exception is thrown during stream response (#3882)

* Finish up changelog, minor refactor

* reset buffer only

* Hack for some replacements

* Failure handling

* wip

* Fixed the issue (#3845)

* Fixed the issue

* Changelog modification

* Changelog modification

* Implemented seventh character extended code and the corresponding dis… (#3709)

* Implemented seventh character extended code and the corresponding display

* Modifications

* Changes on previous test according to modifications made in ICD10-CM XML file

* Subscription sending delete events being skipped (#3888)

* fixed bug and added test

* refactor

* Update for CVE (#3895)

* updated pointcuts to work as intended (#3903)

* updated pointcuts to work as intended

* added changelog

* review fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)

* Add test and implementation

* Add changelog

* 3899 code in limits (#3901)

* Add implementation, changelog, test

* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

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

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

* 3884 overlapping searchparameter undetected rel 6 1 (#3909)

* Applying all changes from previous dev branch to current one pointing to rel_6_1

* Fixing merge conflict related to Msg.code value.

* Fixing Msg.code value.

* Making checkstyle happy.

* Making sure that all tests are passing.

* Passing all tests after fixing Msg.code

* Passing all tests.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)

* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete

* created unit test for skip of delete operation while processing duplicating create entries

* moved unit test to FhirSystemDaoR4Test

* 3379 mdm fixes (#3906)

* added MdmLinkCreateSvcimplTest

* fixed creating mdm-link not setting the resource type correctly

* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on

* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java

Change order of tests such that assertEquals takes expected value then actual value

Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* added changelog, also changed a setup function in test to beforeeach

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* Fix to the issue (#3855)

* Fix to the issue

* Progress

* fixed the issue

* Addressing suggestions

* add response status code to MethodOutcome

* Addressing suggestions

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)

* Respect caching in bullk export, fix bug with completed date on empty jobs

* add changelog

* Add impl

* Add breaking test

* Complete failing test

* more broken tests

* Fix more tests'

* Fix paging bug

* Fix another brittle test

* 3915 do not collapse rules with filters (#3916)

* do not attempt to merge compartment permissions with filters

* changelog

* Rename to IT for concurrency problems

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Version bump

* fix $mdm-submit output (#3917)

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Gl3407 bundle offset size (#3918)

* begin with failing test

* fixed

* change log

* rollback default count change and corresponding comments

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Offset interceptor now only works for external calls

* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.

* do not reindex searchparam jobs on startup

* Fix oracle non-enterprise attempting online index add (#3925)

* 3922 delete expunge large dataset (#3923)

* lower batchsize of delete requests so that we do not get sql exceptions

* blah

* fix test

* updated tests to not fail

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* add index

* Fix up colun grab

* Revert offset mode change

* Revert fix for null/system request details checks for reindex purposes

* Fix bug and add test for SP Validating Interceptor (#3930)

* wip

* Fix uptests

* Fix index online test

* Fix SP validating interceptor logic

* Updating version to: 6.1.1 post release.

* fix compile error

* Deploy to sonatype (#3934)

* adding sonatype profile to checkstyle module

* adding sonatype profile to tinder module

* adding sonatype profile to base pom

* adding final deployToSonatype profile

* wip

* Revert version enum

* Updating version to: 6.1.1 post release.

* Add test, changelog, and implementation

* Add backport info

* Create failing test

* Implemented the fix, fixed existing unit tests

* added changelog

* added test case for no filter, exclude 1 patient

* wip

* Add backport info

* Add info of new version

* Updating version to: 6.1.2 post release.

* bump info and backport for 6.1.2

* Bump for hapi

* Implement bug fixes, add new tests (#4022)

* Implement bug fixes, add new tests

* tidy

* Tidy

* refactor for cleaning

* More tidying

* Lower logging

* Split into nested tests, rename, add todos

* Typo

* Code review

* add backport info

* Updating version to: 6.1.3 post release.

* Updating version to: 6.1.3 post release.

* removed duplicate mention of ver 6.1.3 in versionEnum

* backport pr 4101

* mdm message key (#4111)

* begin with failing test

* fixed 2 tests

* fix tests

* fix tests

* change log

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* backport 6.1.3 docs changes

* fixed typo on doc backport message

* fix test breaking

* Updating version to: 6.1.4 post release.

* wip

Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>

* pin okio-jvm for kotlin vuln (#4216)

* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)

* First commit:  Failing unit test and a TODO with a vague idea of where the bug happens.

* Don't escape "+" in a URL GET parameter if it starts with "application".

* Remove unnecessary TODO.

* Add changelog.

* Code review feedback on naming.  Also, make logic more robust by putting plus and should escape boolean && in parens.

* Ks 20221031 migration lock (#4224)

* started design

* complete with tests

* changelog

* cleanup

* tyop

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)

* Added test

* Added solution

* Changelog

* Changes made based on comments

* Fix bug with MDM submit

* fix

* Version bump

* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)

* Add constant for interceptor

* add test, changelog

* Allow Batch2 transition from ERRORED to COMPLETE (#4242)

* Allow Batch2 transition from ERRORED to COMPLETE

* Add changelog

* Test fix

Co-authored-by: James Agnew <james@jamess-mbp.lan>

* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)

* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.

* Update test case.

* Cleaned up changelog.

* Added test case for multiple resource types.

* Added failing test case for not returning Binary resource.

* Refactor solution.

Co-authored-by: kylejule <kyle.jule@smilecdr.com>

* Add next version

* bulk export permanently reusing cached results (#4249)

* Add test, fix bug, add changelog

* minor refactor

* Fix broken test

* Smile 4892 DocumentReference Attachment url (#4237)

* failing test

* fix

* increase test Attachment url size to new max

* decrease limit to 500

* ci fix

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Overlapping SearchParameter with the same code and base are not allowed (#4253)

* Overlapping SearchParameter with the same code and base are not allowed

* Fix existing tests according to changes

* Cleanup dead code and remove related tests

* Version Bump

* ignore misfires in quartz

* Allowing Failures On Index Drops (#4272)

* Allowing failure on index drops.

* Adding changeLog

* Modification to changelog following code review.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Revert "ignore misfires in quartz"

This reverts commit 15c74a46bc.

* Ignore misfires in quartz (#4273)

* Reindex Behaviour Issues (#4261)

* fixmes for ND

* address FIXME comments

* fix tests

* increase max retries

* fix resource id chunking logic

* fix test

* add modular patient

* change log

* version bump

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Set official Version

* license

* Fix up numbers

* Fix up numbers

* Update numbers

* wip

* fix numbers

* Fix test:

* Fix more tests

* TEMP FIX FOR BUILD

* wip

* Updating version to: 6.2.1 post release.

* Add a whack of logging

* wip

* add implementation

* wip and test

* wip

* last-second-fetch

* expose useful method

* remove 10000 limit

* Strip some logging

* Fix up logging

* Unpublicize method

* Fix version

* Make minor changes

* once again on 6.2.1

* re-add version enum

* add folder

* fix test

* DIsable busted test

* Disable more broken tests

* Only submit queued chunks

* Quiet log

* Fix wrong pinned version

* Updating version to: 6.2.2 post release.

* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https… (#4291)

* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https://github.com/hapifhir/hapi-fhir/issues/4276

* Credit for #4291

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

* backport and changelog for 6.2.2

* Updating version to: 6.2.3 post release.

* fix https://simpaticois.atlassian.net/browse/SMILE-5781

* Version bump to 6.2.3-SNAPSHOT

* Auto retry on MDM Clear conflicts (#4398)

* Auto-retry mdm-clear on conflict

* Add changelog

* Build fix

* Disable failing test

* Update to 6.2.3 again

* Update license dates

* Dont fail on batch2 double delivery (#4400)

* Don't fail on Batch2 double delivery

* Add changelog

* Update docker for release ppipeline

* Updating version to: 6.2.4 post release.

* Add test and implementation to fix potential NPE in pre-show resources (#4388)

* Add test and implementation to fix potential NPE in pre-show resources

* add test

* WIP getting identical test scenario

* More robust solution

* Finalize Code

* Add changelog, move a bunch of changelogs

* Remove not needed test

* Minor refactor and reporting

* Fix up megeback

* update backport info

* update backport info

* Updating version to: 6.2.5 post release.

* Prevent chunk from returning to in-progress unless it is errorred, in-progress, or queued

* changelog

* Update logger

* Indicate backport

* Add version and upgrade info. add backport

* hapi-fhir side done

* cdr side

* add assert

* add test

* Fix import

* prevent multiple reduction step runs in maintenance run (#4423)

* setting job to inprog to prevent multiple maintenance passes from running reduction steps

* added a new status

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* Add backport info

* Fix up tests

* Fix discrepancies

* Fix test

* Version bump

* bump ips

Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-01-24 17:38:35 -08:00
James Agnew d584e14048
Add IPS Generator (#4438)
* Begin IPS refactor

* Commit work so far

* Fix test bug

* Fix typo

* Fix typo

* Narrative generator cleanup

* Narrative generator working

* Add test for bad reference in narrative

* Tests passing

* Start docs

* Tests passing

* Cleanup

* Update cyangelog

* Doc tweaks

* Version bump

* Address review comments

* Address review comments

* Build fix

* Cleanup

* Compile fix

* Test fix

* Test fix

* Version bump

* Build update

* Test fix

* Test fix

* Add one utility method

* Add doc
2023-01-24 12:07:36 -05:00
Ken Stevens 5dda16d467
Reduce postconstruct use (#4445) 2023-01-21 00:37:58 -05:00
Ken Stevens bf53a08b83
Batch2 fastracking configurable (#4453)
* licenses

* hapi-fhir side done

* cdr side

* add assert

* add test

* bump hapi version

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-01-20 19:03:13 -05:00
Qingyixia 663834ddfe
Added resourceType as a parameter to $mdm-duplicate-golden-resources operation (#4434)
* Solution + changelog

* Addressing suggestions

* Minor changes

* Version Bump
2023-01-19 08:43:44 -05:00
TipzCM 23b593aa17
breaking up package installer and package config (#4319)
* breaking up package installer and package config

* breaking out parsing of resources

* wrong nullable

* added an integration test

* adding a changelog

* added a few minor tests

* review fixes

* unit test fixes

* fixing code checkstyle

* moving fetching local package data to package loader svc

* updating the method name

* splitting the fhirversion parsing

* updating table creation task for pretty printing and use in RTE

* adding foreign keys

* Adding mroe info

* minor prettiness changes

* fixing fk generation

* minor changes

* update version

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-01-17 01:58:14 +00:00
Ken Stevens 04c28b6c08
Schedule jobs via IJobScheduler instead of in @PostConstruct (#4415)
* parameterizing BinaryStorageInterceptor

* parameterizing BinaryStorageInterceptor

* changed jobs scheduling from @PostConstruct to coordinated by HapiLifecycleService events

* fix test

* remove events for now

* fix test

* simplify design

* FIXME

* changelog

* fix compile issue

* review feedback.  partially implemented

* review feedback

* review feedback

* bump hapi version to 6.3.8-SNAPSHOT

* fix test

* mirror contextclosedevent handlers with contextrefreshedevent

* version bump

* licenses

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-01-14 23:51:04 -05:00
Justin McKelvy 8c48a6fb91
Clinical reasoning module (#4347)
* Add new Clinical Reasoning module

* Add config to get test up and running

* Removed FhirClient from tests

* First passing test

* Remove unused utilities

* Build updates

* exclude xxp3 and substitute with unbundled version

* Refactor to use provider factory and loader pattern

* First passing dstu3 test

* CR r4 test config and immunization tests

* Add base test classes

* Exclude transitive dependency xmlpull

* More dependency cleanup

* Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr

* Fixes for duplicate xpp3 classes

* Remove more references to jpa

* Add mock FHIR server for terminology endpoint tests

* fix cql file for making providerr4 tests pass

* fix pom

* fix generic

* Adding r4 test cases for measure operations.

* Fix endpoint tests

* javadoc comment, temporarily comment out test results for practitioner sync

* javadoc typo fix

* adding java docs for cr module WIP

* Updates to clinical reasoning documentation

* More documentation updates

* docs now compile

* fix test

* DqmR4IT now successfully starts up, but the test does not pass

* Fix additionalData test

* Make measure service bean overridable

* adding clinical reasoning javadoc information

* Rename interfaces to start with I

* More styleguide updates

* Reformat all code in the storage-cr module

* More coding convention updates

* Remove bunches of unused code, reogranize so that fhir version in package name is consistent

* Clean up some static array initializations

* add practitioner patient list

* refactor product-line constant

* test dependency update

* add change log for cr module

* Add hapi-validation to the pom

* Exclude dependencies that are causing duplicates

* More dependencies and exclusions

* Make some base MeasureService components protected

* Update to latest cql compiler release

* fix measure service for null subject & practitioner and open up practitioner test

* Rev to release versions

* Add remaining Dstu3 tests

* update hedis bundle from policyHolder to beneficiary

* update snapshot

* Delete old CQL module

* Post-master-merge recovery

* Fix Java 17 feature usage issue

* update changelog with more information about new functionality

* Remove support chain wrapper usage

* Add javadocs to IResourceLoader

* added the property versioning for antlr jar.

* addressing code review comments.

* addressing code review comments.

* Fix typos in changelog

* Remove azure pipeline for cql module, add it for cr module

* Address exception comments, add Msg.code calls to exceptions

* Fix self-assignment bug

* Add storage-cr module to bom

* addressing coding comments.

* Addressed the variable naming convention to camelCase.

* Snapshot version bump

Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 19:49:57 +00:00