Commit Graph

1344 Commits

Author SHA1 Message Date
Luke deGruchy 6e8db3626d
Add Device to the list of resource types considered for group bulk export async (#4384)
* Add Device to the list of resource types considered for group bulk export async. New unit test for bulk export.

* Add changelog.
2022-12-20 16:33:25 -05:00
James Agnew 0d5f8da93f
API improvements for MegaScale (#4112)
* Start work on sharded DB

* Work on migrating

* Work

* Ongoing work

* Ongoing work

* Work

* Work

* Ongoing work

* Work

* Work

* Test fix

* Test fix

* Work

* Compile fix

* Test cleanup

* Test fix

* Resolve fixmes

* Resolve fixme

* Resolve compile errors

* Compile fix

* Fixes

* Work

* Add note for later

* Test fix

* Test fixes

* Build fix

* Test fixes

* Fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fixes

* Fixes

* Remove dead code in pom

* More test cleanup

* Docs fix

* Changes

* Fix

* Fixes

* Resolve merge conflicts

* Build update

* Merge build fixes

* Version bump

* Address review comments

* Review comments

* Review comments

* Test fixes

* Test fix

* Cleanup
2022-12-20 12:05:15 -05:00
Luke deGruchy fd94e16ee0
Enable or disable support for JSON fhir_comments depending on the release. Move HapiFhirStorageResponseCode.json to the module in which it's used (#4374)
* First draft of disabling JsonParser "fhir_comment" code.  Unit test assertion that JSON is not generated with "fhir_comment" in the resulting resource String.

* Surround fhir_comments logic with conditional logic.  Set this to false while awaiting final word from stakeholders.  Add unit tests for STU3 and STU2 proving that fhir_comments do not get generated.

* Add conditional logic for JsonParser and fhir_comments and adjust unit tests accordingly.  Also, move the HapiFhirStorageResponseCode.json file to the same module as DefaultProfileValidationSupport, namely, the code that actually reads it.

* Add changelog.

* Add missing change to JsonParser that I thought I had pushed.   Fix changelog.  Fix unit tests assertions to be clearer.

* JsonParser:  Cache value of isSupportsFhirComment.

* Support version DSTU2_1 as well and add a new unit test.

* Fix pipeline unit test failures.
2022-12-19 12:31:21 -05:00
karneet1212 0035677563
Add Payload Search Mode To Message Channel (#4325)
* Added possible solution - needs to be refined

* Small changes

* Refactoring

* Refactoring + Test

* Changelog

* Small edits to changelog

* Small changes

* Changes made based on comments

* Clean up

* Changes made based on comments

* Changes made based on comments

Co-authored-by: qingyixia <cherry.xia@smilecdr.com>
2022-12-15 09:46:10 -05:00
Nathan Doef 7b86eda8a9
Refactor Common SearchParameter Functionality (#4321)
* refactor checkpoint

* clean up

* add method to find runtime search param by id

* new search param cache tests

* extract SearchParameter validation functionality

* create common interface for combo searchparameters

* Remove ResourceTable from extractor interface

* clean up

* move SearchParameterDaoValidator

* resolve code review comments

* remove reflection

* change log

* bump version to 6.3.4-SNAPSHOT

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-12-15 06:46:45 -05:00
StevenXLi 29ebb950e8
4360 bulk export questionnaireresponses should get picked when author is not empty (#4361)
* added failing test

* implemented solution

* added more tests

* added changelog

* changed the implementation, now extended to get all the patient based search params for a given resource instead of 2 in a fixed list of resources

* added test for patient bulk export for resources not in patient compartment, fixed implementation to pass test

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-12-14 18:43:11 -05:00
Luke deGruchy 01b1074808
Fix MDM update link on resources with an old version. (#4362)
* Add a failing unit test if we update a link after the MDM version had been bumped.

* Fix bug with new MdmLinkFactory method:  newMdmLinkVersionless().  Call this new method from MdmLinkDaoSvc.getLinkByGoldenResourceAndSourceResource() only.   Think about other use cases for versionless MDM links.

* Replace all read uses of MdmLinkFactory with newMdmLinkVersionless().  Add detailed documentation about why to do this.

* Add changelog.  Reverse wildcard change.
2022-12-14 08:47:44 -08:00
jmarchionatto 8307264330
Add score to MDM links which match multiple candidates (#4329)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-12-12 10:09:49 -05:00
Tadgh daaa92fdbc
4350 ap sa and eb prefixes are not handled correctly (#4358)
* Add test and implementation

* Add changelog
2022-12-11 18:19:54 -05:00
James Agnew 7747ebae41
Combine postconstruct methods (#4330)
* Combine postconstruct methods

* Add changelog
2022-12-11 18:02:04 +00:00
kateryna-mironova 017cc4e29c
4244 - Deprecate usages of ResourcePersitentId in jpa (#4245)
* init rev

* id to jpa and mongo id

* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods

* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods

* fixed conflicts, pulled from master

* fixed code for passing tests successfully

* changed PersistentId to Jpa in MdmSearchInterceptor

* added the todo comments with questions

* added one more question

* renamed TODO questions

* first pass at converting to generic ResourcePersistentId

* fix test

* fix test

* fix test

* make ResourcePersistentId abstract

* Generic type MdmLink

* Final TODOs

* Final TODOs

* cleanup

* fix test

* fix id to string

* fix cyclic package dep

* add <?> to Base so we can extract interface

* Revert "add <?> to Base so we can extract interface"

This reverts commit a806f3d2bc.

* switch to interface

* javadoc

* replace base with interface

* fix test

* add generic template to mdmdao

* remove unneccessary JpaPid casts

* remove unneccessary JpaPid casts

* remove unneccessary JpaPid casts

* remove unneccessary MongoPid casts

* fix test

* fix regression

* fix compile issues arising from merging master

* fix beans

* bump version to 6.3.3-SNAPSHOT

* change logs

* review feedback

* review feedback

* fixme

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-12-09 09:30:51 -05:00
Nathan Doef d639a2a86d
meta.versionId Incremented After Update Operation With No Changes (DSTU 3) (#4349)
* Tests for R4 (passing) and DSTU3 (failing)

* Fix

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-12-08 20:26:49 -08:00
granadaCoder 16b97bc6e7
Issue 4310 Fix. Add "distinct" and "sorted" to "Server knows how to handle" error message: (#4311)
* Add "distinct" and "sorted" to "Server knows how to handle" error message.

* Add code comments.  No functional changed.

* Add credit for #4311

Co-authored-by: shollid3 <sloan.h.holliday@optum.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-12-08 16:59:53 -05:00
jmarchionatto c7d991c345
Disallow matching a resource to more than one golden record (#4344)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-12-08 12:26:05 -05:00
Ken Stevens f4ce765122
IndexedSearchParamExtractor regression returned wrong number of links pre-persistence (#4341)
* fixed the issue

* change log

* fix regression

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-12-08 05:22:51 +00:00
StevenXLi 0e59665711
4312 add support for member identifier parameter return from $member match operation (#4314)
* added failing test

* implemented solution

* added change log

* removed special character in change log file name

* added check for member identifier of type MB

* changed msg code to latest

* fixed test for updated msg code

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-12-07 15:55:53 -05:00
Etienne Poirier f13b247c74
4324 excessive amount of time required to update large group resources (#4332)
* Initial test.

* Solution implementation with test adjustment.

* Adding changelog.

* Modifications following first code review.

* Moving changelog to 6.4.0

* Further reductions in query counts

* Fix for broken test

* Test fix

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-12-07 15:27:33 +00:00
Tadgh 6ae1672599
Change folder name, add versionenum (#4320) 2022-12-05 19:46:52 +00:00
Luke deGruchy 869d9996b1
Move partition ID up from ResourceModifiedMessage to BaseResourceModifiedMessage (#4313)
* Move partition ID up from ResourceModifiedMessage to BaseResourceModifiedMessage.

* Add a changelog.  Add a new constructor that contains partition ID to ResourceOperationMessage.   Add partition ID to the toString() for BaseResourceModifiedMessage.  Tweak constructors of all classes to make sure ResourceModifiedMessage always sets default partition IDs, but BaseResourceModifiedMessage and ResourceOperationMessage do not.

* Reverse an accidental whitespace change.

* Small code review fixes including removing comments and updating changelog description.

* Restore whitespace to what it was on master.

* Fix YAML error.
2022-12-05 09:21:30 -05:00
TipzCM 08ca687c72
4287 fix mdm golden resource merging (#4290)
* fixed goldenresourcemergersvcimpl to allow merging GoldenResource into SourceResource in PossibleDuplicate links

* added changelog

* adding some notations

* working on tests

* updated test to use new convention as demo

* updated to allow creating patints too

* updating more tests

* updated all tests to use new notation

* updates the tests

* adding more test support

* fix merge directions

* fixed duplicate merging in

* updates

* cleanup

* cleanup

* fix changelog

* changing how tests work

* test cleanup

* added a comment

* fixing build

* fix for multimap

* fixing tests

* minor change

* addressed 2 points

* review fixes

* remove one change

* adding todo

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2022-12-05 09:04:51 -05:00
James Agnew 312128754b
Allow forced id for conceptmap translation (#4304)
* Allow forced id for conceptmap translation

* Test fixes

* Test fix

* Conversion cleanup

* Test fixes

* Test fixes

* Build fixes

* Build fix

* Test fixes

* Test fixes
2022-11-30 05:31:26 -05:00
James Agnew 50ca94eded
Improve JPA response messages (#4293)
* Improve JPA response messages

* FIxes

* Test fixes

* Test fixes

* Ongoing testing

* Work on messages

* Work on messages

* Add valueset

* Add response code enum

* Version bump

* Undo bump

* Improve changelog

* Test fixes

* Add javadocs

* Version bump HAPI

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Account for review changes

* Test fix

* Docs fix

* Work on API

* Improve SqlQuery api
2022-11-28 07:52:12 -05:00
James Agnew c3697a5f87
JPA Cleanup (#4278)
* JPA cleanup

* Test fixes

* Cleanup

* Resolve fixme

* Fix bad changelog entry

* A bit of documentation reworking

* Version bump

* POM bump

* Avoid timeout

* Build fix

* HTMLUnit bump
2022-11-24 14:32:56 -05:00
Nathan Doef 028c3ed5c1
Fix Expunge Deleted Resources Race Condition (#4285)
* failing test

* fix race condition

* change log

* refactor

* clean up

* remove ExpungeOptions hard limit enforcement

* nitpick

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-11-22 12:48:06 -05:00
James Agnew 9eeb1545a1
Avoid race condition in ServiceLoader (#4295)
* Avoid race condition in ServiceLoader

* Changelog
2022-11-22 07:48:54 -05:00
karneet1212 62c630c546
bundle not throwing an error when multiple matches were found (#4283)
* Added test + condition to throw error

* changelog

* changes made based on comments
2022-11-21 10:08:10 -05:00
Tadgh b1e3468dcd
Rel 6 2 1 mergeback (#4288)
* 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 up checkstyle

* log to console

* Remove double import

* Version bump

* licenses

* Fix up version

* fix build

* wip

* wip

* Fix up search expansion to use new behaviour of idhelper service

* Fix up MDM Search Expansion

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>
2022-11-20 08:14:28 -08:00
Jens Kristian Villadsen 61579aae7e
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>
2022-11-18 00:15:05 +00:00
michaelabuckley 6c4283e930
Start moving forced-id inline to ResourceTable (#4260)
New fhir_id column in HFJ_RESOURCE.

Migration, changelog, and insert hook for inline fhir_id column.
2022-11-16 13:38:52 -05:00
jmarchionatto 2df09c0cf3
Issue 4214 bulk export group observations missed when search parameter indexing enabled (#4241)
* Add failing test

* Add failing test for hsearch reference without type

* Modify cache to store forcedid type

* Disable failing test until finding out if it is a bug and strategy for fix in that case

* Remove fixmes and commented lines

* Update test. Add changelog.

* Added test that passes on this branch.

* Added Encounters to test case.

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2022-11-11 20:08:41 +00:00
Roel-Scholten e5cf3ef396
4269 implement a toString for OkHttpRestfulRequest to have better log… (#4270)
* 4269 implement a toString for OkHttpRestfulRequest to have better loggin…

Implement a toString for OkHttpRestfulRequest logging to have better logging.
Currently this still differs from the ApacheHttpRequest.java as we do not have the used protocol (http/1.1/alpn) on request creation. This is added to the Response object.

* Add credit for #4269

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-11-11 10:56:12 -05:00
James Agnew 9a45576793
Cache service loaders (#4196)
* Extracting a Cache interface and building service loaders for Caffeine and Guava

* Fix estimated size interface

* Use LoadingCache when needed.

* Removing Caffeine from dependency lists.

* Adding hapi-fhir-cache-caffeine as a test dependency

* Putting caching solutions in a single module.

* Fixing the spacing

* Standardizing the use of TimeUnits

* Making a new module to simplify the switch of the cache library in tests.

* Making sure the Guava design matches the behavior of Caffeine.

* Making sure the Cache structure also does not throw InvalidCacheLoading exception to match the LoadingCache.

* Renaming module names for the caching group.

* Better error handing that informs devs what to do.

* Improving documentation

* Typo

* Matching error message design with Caffeine.

* Matching the behavior of Caffeine with Guava

* Final adjustments for the test dependencies on the cache modules.

* Fixing relative pom path.

* Adding caffeine as a testing requirement for the new modules.

* Add changelog and set JPA server to use caffeine cache

* POM fixes

* Build fix

* Buid fix

* Fixes

* Address review comment

* One more cache

* Move changelog to next release

* Update pom versions

* Build fix

* Build fixes

* Build fix

* Try to get build working

* Experiment with failing build

* Rever change

* Fix POM version

* Build fix

* Build fix

* Add Msg.code to new exceptions

Co-authored-by: Vitor Pamplona <vitor@vitorpamplona.com>
2022-11-09 19:47:23 +00:00
James Agnew f50d350f1f
Post release HAPI FHIR cleanup (#4266)
* POST release deferred cleanup

* Fixes

* One more test fix

* Test fixes

* Test fixes

* Test cleanup

* Test fixes

* Fixes

* ValueSet cleanup

* Test fix

* Test fixes

* Fixes

* Test fixes

* Fixed

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixc

* Build fix

* Fix merge artifact

* Build fix

* Work on tests

* Test fixes

* Work

* Fixes

* Changelog fix

* Add changelog

* Test fix

* Test fixes

* Fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Tests

* Bumps

* Fixes

* Add errorprone

* Drop bz2 bins

* POM fix

* Build fix

* Update

* Test fix

* Fix tests

* Add changelog

* Test fix

* Avoid intermittent

Co-authored-by: James Agnew <james@jamess-mbp.lan>
2022-11-09 13:28:00 -05:00
dependabot[bot] 145f22c3df
Bump log4j-to-slf4j from 2.17.1 to 2.19.0 (#4265)
* Bump log4j-to-slf4j from 2.17.1 to 2.19.0

Bumps log4j-to-slf4j from 2.17.1 to 2.19.0.

---
updated-dependencies:
- dependency-name: org.apache.logging.log4j:log4j-to-slf4j
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Add changelog

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-11-09 10:16:36 -05:00
James Agnew b3ebbe7933
ValueSet cleanup (#4227)
* POST release deferred cleanup

* Fixes

* One more test fix

* Test fixes

* Test fixes

* Test cleanup

* Test fixes

* Fixes

* ValueSet cleanup

* Test fix

* Test fixes

* Fixes

* Test fixes

* Fixed

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixc

* Build fix

* Fix merge artifact

* Build fix

* Work on tests

* Test fixes

* Work

* Fixes

* Changelog fix

* Add changelog

* Test fix

* Test fixes

* Fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Tests

* Bumps

* Fixes

* Add errorprone

* Drop bz2 bins

* POM fix

* Build fix

* Update

* Test fix

Co-authored-by: James Agnew <james@jamess-mbp.lan>
2022-11-08 22:18:36 -05:00
Tadgh d3367cfede
Rel 6 2 mergeback (#4257)
* 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

* Bump HAPI version

* Remove jetbrains

* Fix broken test

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>
2022-11-07 23:57:57 +00:00
jmarchionatto 6c9fe710ee
Issue 4180 process slows down to a crawl while loading uscore ig (#4201)
* Make query synchronous

* Use outer joins only for sorting.

* Adjust test

* Add changelog

* Fix changelog typo

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-11-07 19:20:28 +00:00
James Agnew 5533afb9f5
Allow Batch2 transition from ERRORED to COMPLETE (#4242) (#4243)
* Allow Batch2 transition from ERRORED to COMPLETE

* Add changelog

* Test fix

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

Co-authored-by: James Agnew <james@jamess-mbp.lan>
2022-11-04 09:06:22 -04:00
jmarchionatto 6cf5989d6c
Issue 4106 process map to properties when uploading loinc terminology (#4231)
* Add loinc upload handler to process MAP_TO properties.

* Move test to test folder

* Fix mapto file location property name

* Allow override as full loinc upload tests take (much) longer than defined timeout

* Move handler later to make sure all concepts were added to map

* Update test to check all project enhancements

* Restore project unrelated changes

* Rename base test class properly and move to right package

* Condition MapTo.csv file processing to file presence for backwards as file is optional

* Document and annotate test-only usage for disabling deferred tasks timeout

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-11-03 08:48:02 -04:00
VK-SMILECDR 27ec3bec79
code coverage needs to run only for JACOCO PROFILE (#4230)
* code coverage needs to run only for JACOCO PROFILE

* remove ALLMODULES profile since it is default now
2022-11-02 15:34:27 -04:00
samuelwlee2 1b55f49a60
4153 extend $member match operation to store consent resource if matched (#4165)
* added senstive and regular filter

* add UUID to Consent

* blah

* fix merge with master

* fixing merge

* blah

* fhir tests

* use constructor injection

* put all tests together

* blah

* blah

* finalize

* add consent update patient and performer reference

* fixes after code review

* blah

* refactor to save consent once

* blah

* fix performer and add validation

* code clean up

* add changelog

* add hrex member match flag

* fix PatientMemberMatchOperationR4Test

* adding code fixes after code review

* move changelog file

* bump version

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2022-10-31 13:33:54 -04:00
Tadgh 31a193fbd3
Bump to 6.3.0 (#4211) 2022-10-28 02:40:59 +00:00
James Agnew 7a39f8cbaf
Make reference extractor more reusable (#4205)
* Refactor

* Make reference extractor more reusable

* Test fix

* Test fix

* Headers

* Small refactor
2022-10-27 21:31:39 -04:00
karneet1212 0a160a35ba
4175-$validate-operation-on-a-resource-update-results-in-an-error-stating-resource-has-no-id (#4181)
* Added unit test + solution

* Changelog

* Cleanup

* changelog filename
2022-10-26 10:29:28 -07:00
Tadgh 296ddb8a37
CVE Fixes (#4200)
* CVEs

* bump snakeyaml again

* Add updates to changes.yaml
2022-10-26 17:17:11 +00:00
Tadgh 78ce2a6344
4182 convert $mdm submit to a batch job (#4188)
* Changelog

* Wip implementation

* Wip

* wip

* wip

* Fix validator

* Fix up implementation

* tidfy

* TIdy up tests

* Add some docs

* Add changelog info:

* Tidy up self review

* License files

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md

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

* Review changes

* fixes

* add new method

* Update tests

* Add batch size parameter

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-10-25 12:02:04 -07:00
Ken Stevens e7ac40d050
Add support for clustered database migrations (#4177)
* initial attempt

* cleanup

* add other databases

* fix test

* fix dangling connection

* the HapiMigratorTest passes when all the tests are run, but not individual tests.  Methinks the locking just isn't working.

* omg it was autoCommit all along ugh!  it works now

* cleanup

* cleanup

* cleanup

* cleanup

* cleanup

* documentation

* javadoc

* cleanup

* final cleanup

* simple solution is working

* fix tests

* final fixmes.  this is actually a merge candidate

* pre-review cleanup

* changelog

* pre-review cleanup

* pre-review cleanup

* fix test

* review feedback

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-10-25 15:20:31 +00:00
Kevin Dougan SmileCDR 1190eb96ac
4197 - Fixed header on the server_jpa/elastic docs page. (#4198) 2022-10-25 14:53:26 +00:00
jmarchionatto 3d9dfd4f08
Fix ForcedId criteria query (#4195)
* Fix ForcedId criteria query

* wip parameterizing tests

* Refactor almost all APIs to use ResourcePersistentId. Convert to fhir resource id when necessary (at search time)

* run tests in ANY id mode

* Test fix

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2022-10-25 13:56:08 +00:00
StevenXLi e1e33df38c
4190 offset count and total are wrong for some queries offset produces short pages and repeats results on different pages (#4193)
* created failing test

* implemented the fix, added more tests

* added change log

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-10-25 09:42:54 -04:00
James Agnew 5328951f15
Version Bump a few dependencies (#4191)
* Version bumps

* Test fixes

* Test fix

* Test fix
2022-10-24 15:20:39 -07:00
James Agnew cbd65c794d
Add remove method to jobregistry (#4187)
* Add remove method to jobregistry

* Add changelog
2022-10-24 17:07:32 -04:00
Tadgh fb6bf5b6a4
Attribution (#4183) 2022-10-24 07:57:54 -04:00
Ken Stevens a824ba263b
package loader npe (#4186)
* begin with failing test

* fixed

* change log

* change log

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-10-22 16:16:27 +00:00
michaelabuckley 929767a09b
Change to a minimal first pre-fetch to avoid latency on the async path. (#4174)
* Change to a minimal first pre-fetch to avoid latency on the async path.

The "async" path is now synchronous, and was causing latency for first page by loading 500 results.
We avoid pre-fetch on the first page, and only pre-fetch after users fetch the second page.

* Fix a nasty bug continuing a pre-fetched search.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3664-shorten-first-prefetch.yaml

* Patch up tests that assumed 500 pre-fetch first step
2022-10-21 20:45:30 +00:00
jmarchionatto 2830792c4b
Issue 3992 elastic search mapper parsing exception when uploading loinc terminology (#4141)
* Revert TermConceptProperty indexing to not-nested type to avoid hitting elastic default maximums and
fix regexp issue which was main reason to change indexing way in the first place.

* Add changelog

* Document that terminology reindexing is required.

* Implement revision suggestions. Fix file name typo.

* Adjust and enable test created to reproduce bug

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-10-21 16:19:45 -04:00
Tadgh b04f082991
Move to correct folder (#4176) 2022-10-21 02:28:20 +00:00
James Agnew a71b8fad56
Add R4B Support (#4150)
* Add r4b stuff

* Work on R4B

* Core version bump

* Revert some changes

* Add R4B

* Docs

* Test fixes

* Work on R4B

* Tests passgin

* Add config

* Work on merging

* Work

* Work

* Work

* Test fix

* Fixes

* Test fixes

* Test fix

* Work

* Work

* Fixes

* Test fixes

* Fixes

* Test fix

* Test fix

* Test fix

* Version bump

* Test fix

* Test fix

* ompile fixes

* Fix

* Resolve build warnings

* Updates

* Test fixes

* Fix docs
2022-10-20 13:57:06 -07:00
Luke deGruchy c8312662d7
Set batch export job results count to number of resources processed instead of 0. (#4172)
* Add count to batch export admin page results and new add new unit test.

* Fix failing unit test in WriteBinaryStepTest.

* Add changelog.

* Small changelog fix.
2022-10-20 14:27:01 -04:00
jmarchionatto 0c5b64cce7
Change IG loader check for existence of SearchParameter resources to use same strategy as validator to avoid first one not finding resource and validator finding it later, producing a duplication exception. (#4164)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-10-20 10:47:18 -07:00
Etienne Poirier 4200ccf756
DatabaseBlobBinaryStorage service will only store blob up to Integer.MAX_VALUE (#4167)
* Modification of entity to support long.

* Adding Changelog.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-10-19 21:06:51 +00:00
Luke deGruchy 0798ab35db
ResourceIndexedSearchParamString: equals() and hashCode(): Add normalized String and use same fields for both calls. (#4148)
* Fix hashCode() to reflect equals() contract in ResourceIndexedSearchParamString.  Write ResourceIndexedSearchParamStringTest with new tests for normalized hashCode.

* Add un-hashed normalized value to ResourceIndexedSearchParamString equals() and hashCode() with comments about potential performance implications.

* Add changelog.  Remove TODOs.

* Inline hashCode.

* Fix comment and issue number and rename changelog.
2022-10-19 14:13:21 -04:00
JasonRoberts-smile 5a31ce0386
disable batch job reuse (#4155) 2022-10-19 11:43:51 -04:00
karneet1212 a6ed393969
4140-upload-terminology-does-not-allow-snomed-ct-canada-edition-zip-file-to-load-due-to-a-different-file-name (#4144)
* Test + Implementation of the Solution

* Changes made based on comments
2022-10-19 08:33:21 -07:00
KGJ-software 69d55b7184
3052 Changed IBinaryStorageSvc MaximumBinarySize from int to long. (#4123)
* 3052 Changed IBinaryStorageSvc MaximumBinarySize from int to long.

* 3052 Added changelog

* 3052 Bumped version

* 3052 Remove mysterious +1 on maximum binary size causing overflow.

* Bumping version to 6.2.0-PRE16-SNAPSHOT

* Adding + 1L as original implementation.

* Getting all tests to pass dealing with + 1L.

* Getting all tests to pass dealing with + 1L.

* Adding migration definition and removing unnecessary comment.

* Preventing register overflow when setting maxBinaryStorage.

* Mering relevant test.

* Fixing typo in migration script

Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-10-19 06:09:02 -04:00
samuelwlee2 dac266b719
Extend $member match to validate matched patient (#4136)
* added validation for family name and birthdate

* making changes to tests

* update patient identifer return and validatePatientMember

* update patient identifer type for test

* update method name

* update test comment
2022-10-18 12:19:03 -06:00
jmarchionatto bd22b8d1c0
Issue 4145 reindex terminology command is not documented (#4149)
* Add documentation for reindex-terminology command

* Fix fix type

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-10-17 22:07:33 +00:00
jmarchionatto f6fe8dfc4a
Add documentation for reindex-terminology command (#4146)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-10-17 13:40:10 -04:00
Etienne Poirier a5fb87bb1d
4142 resource contents are written to logs on subscription failure (#4143)
* Add test reproducing the issue.

* Adding solution and changelog.

* Modification following code review.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-10-17 11:09:17 -04:00
James Agnew 26ef32c1dd
Fix 2 issues with has reverse chaining (#4139)
* Fix 2 issues with chains

* Add changelog

* Cleanup

* Add comment

* Cleanup
2022-10-14 16:46:18 -04:00
James Agnew 422ef87a5d
Standardize on one Transactional annotation (#4130)
* Standardize on one Transactional annotation

* Add changelog

* Disable checkstyle rule

* Fix up transactions

* Test fixes

* Test cleanup

* License headers

* One more dep bump

* Resolve commit issue

* Test fixes

* Test fix

* Dep bump

* Fix

* Fix test

* Version bump

* Test fixes
2022-10-13 16:26:11 -04:00
MykolaMedynskyiSCDR 2e6b3d16d6
4017 creating a searchparameter with an expression referencing metasecurity will return error hapi 1118 (#4037)
* Adding initial test reproducing the issue.

* some comments and small refactoring to run pipeline to see the extent of the damage that this can cause.

* Parsing dstu3 expression with FHIRpath parser

* fixed code.

* omitting searchParameter expression(xpath) validation for DSTU2

* Added test for search parameter with many expressions

* changed deprecated method.

* removed and modified custom search parameters tests for DSTU3 and DSTU2.

* fixed code

* Added change log

* Test testIndexFailsIfInvalidSearchParameterExists() is back.

* Update createResourceSearchParameter_withExpressionMetaSecurity_succeeds() test

* Update createResourceSearchParameter_withExpressionMetaSecurity_succeeds() test

* Refactoring if statement and exception message.

* Refactoring tests and rewording changelog.

* Fixing tests.

* Fixing more tests.

* Addressing comments from first code review.

* Fixing issue number.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-10-13 11:05:04 -04:00
Etienne Poirier 4cebcfb766
4115 Combining 'indexMissingFields' and 'advancedHSearchIndexing' functionalities will prevent creating a resource (#4122)
* Added Test

* Added Integration Test

* Made changes based on comments

* Implemented solution

* Implemented solution

* Debug

* Changelog

* Changes made based on comments

* Changelog

* Made changes based on comments

* Made changes based on comments

Co-authored-by: Karneet Kaur <karneet.kaur@smilecdr.com>
2022-10-12 16:16:44 +00:00
samuelwlee2 2de9b5aa03
added attribute to Operation annotation (#4120)
* added attribute to Operation annotation

* add find operation id

* update readOperationDefinition method

* add example to canonicalUrl

* adding more examples
2022-10-12 10:06:22 -04:00
Qingyixia 9d7829a404
Implemented a new setting for Bulk Export that changes how many resources are stored in each binary file (#4119)
* Implemented a new setting for Bulk Export that changes how many resources are stored in each binary file

* Addressing suggestions

* Fixing test

* Fixing test
2022-10-12 10:03:54 -04:00
Tadgh b74e12172e
4098 Resultset missing resources when querying with _sort result parameter (#4099)
* Add broken test

* Finished writing test

* Add in parameterized test to show it works with one

* Adding extra test asserting sort results when providing short chain

* Providing fix to search with sorting.4098-sort-missing-parameter

* Adding ChangeLog.

* Improving, cleaning up and commenting tests.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-10-12 08:06:46 -04:00
James Agnew 108e357ca7
Preserve tags on delete (#4128)
* Preserve tags on delete

* Add changelog

* Add changelog

* Test fix

* Build fix

* Address review comments
2022-10-12 11:01:47 +00:00
Luke deGruchy 5831cbedf5
Concurrent cascade delete operations leading to confusing errors (#4126)
* Add unit tests and supporting classes from gitlab issue.

* Commit with changes thus far to be reviewed.   Namely, add savepoint capabilities to HapiTransactionService, inject HapiTransactionService into CascadingDeleteInterceptor, add savepoint capabilities to the TransactionDetails, and catch an Exception in BaseHapiFhirResourceDao.delete() then rollback to the checkpoint.

* Fix compile error.

* hapi transaction service test

* hapi transaction service test

* hapi transaction service test

* First draft of RetryTemplate and flush() logic.  Try unit testing with PointcutLatch.

* hapi transaction service test

* Latest changes including moving RetryTemplate, cleaning up unit tests.

* First attempt at correct design.  Fix compile errors.

* Add failed rollback savepoint test.

* fix propogation

* interesting test failure in SafeDeleterTest

* Latest code

* move delete

* test passing

* all tests pass

* yay we're done just cleanup

* First round of cleanup:  Get rid of all exploratory logging, remove unneeded dependencies, move creation of RetryTemplate to SafeDeleter.

* More cleanup.  Add changelog.

* Bump to 6.2.0-PRE13-SNAPSHOT.

* Code review feedback:  Refactor SafeDeleter to a service and bean.  Add comments.

* Code review feedback:  Comments on unit test assertions.

* Code review feedback:  Rename SafeDeleterSvc to ThreadSafeResourceDeleterSvc.  Add javadoc.  Add logger to DelayListener.   Remove useless commented out code.

* Fix unit test failure in CascadingDeleteInterceptorTest.

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-10-11 16:48:01 -04:00
James Agnew 26fe5e6b8e
Interceptor improvements (#4125)
* Interceptor improvements

* Add changelogs
2022-10-09 15:02:12 -04:00
Ken Stevens 44ed3ee354
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>
2022-10-05 00:37:40 +00:00
Ken Stevens 40163f73d2
Ks 20220916 remove flyway (#4040)
* removed flyway, started coding persistence

* started wiring up new dao service

* replace jpa with sqlbuilder

* down to 16 failed tests

* remove outOfOrder test.  We no longer support validating order.

* Removed noFlyway mode.  It is no longer a thing.

* merge migrator

* down to 1 failing test

* cleanup

* removed unused noflyway cli arguments

* cleanup

* cleanup

* cleanup

* cleanup

* create MigrationTaskList to replace the List<BaseTask> that gets passed around a lot.  This allows us to add a bunch of behaviour to that as a first-order thing

* fix test

* fix test

* improve migration table detection to use the catalogue

* Msg.code()

* cleanup

* save version in same format as flyway

* cleanup

* add migration result to migration result class

* failed migrations stay in the table and don't really affect anything.

* change log

* docs

* ugh Flyway requires lower-case column names

* integration test fixes

* log

* fix oracle issue

* lowercase tablenames for postgres.  fussy fussy!

* Revert "lowercase tablenames for postgres.  fussy fussy!"

This reverts commit 92c9cb263b.

* revert to capital table names.  surround table name by quotes for Postgres.

* added log message before executing find all query

* changed log message from info to debug

* javadoc

* pom cleanup

* review feedback

* Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/MigrationTaskList.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* review feedback

* review feedback.  Use prepared statement.

* Change installedOn insert from timestamp to date

* Change installedOn column type from timestamp to date

* bump hapi version

* fix poms

* fix poms and cdr compile

* add exclusions to clean up build

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2022-10-03 22:40:09 -04:00
weiping202209 66baa8263d
Fix bug in history search (#4009)
* add failing test

* Fix history search bug and add tests for two more scenarios

* Fix history search bug and add tests for two more scenarios

* - added failing test condition

* Fix history search bug and add tests for two more scenarios

* Fix build test failures

* Fix build test failures

* Add extra verifications for scenarios of _since

* Refactor dao.history interface to add overload method and shall come back to remove old method once cdr is refactored.

* Update with new hapi interface

* Add depreciate comment

* Add depreciate comment

* Version bump to mvn 6.2.0-PRE11-SNAPSHOT

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-10-03 09:00:41 -04:00
jmarchionatto 43ed8ca051
Issue 4052 addition of properties to the loinc terminology uploading process (#4100)
* Allow for easier override of DataSource and dialect

* Add debug logging

* Load AskAtOrderEntry and AssociatedObservations properties from loinc.cvs.
Add changelog.

* Add disabled sandbox test used to develop loinc upload modifications

* Add flags to easily select running mode

* Add validation counters and use gziped csv input to save space in repo

* Implement revision suggestions.
As test is a sandbox remove large files and add readme and test notes to locate them before running the test.

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-10-03 08:48:40 -04:00
Ken Stevens e9a855d3f6
remove spring batch (#4064)
* remove spring batch
it compiles
expect test failures

* fix test transaction manager bean name (wow that was quite the hunt the wumpus!)

* fix test and fix build

* fix test and fix build

* fix test

* remove spring batch schema initialization

* bump hapi version

* fix schema migrator

* bump to PRE-10

* merge master

* change logs

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-09-30 13:18:48 -04:00
Tadgh b472c4bb54
4083 batch permissions (#4095)
* Move threadpool factory into a bean

* Move threadpool factory into a bean

* change return type

* Add license files

* Version bump

* Fix test
2022-09-29 17:24:05 +00:00
James Agnew fc82ed4e44
One more tweak to #4093 (#4094)
* One more tweak to #4093

* Add changelog
2022-09-28 16:46:00 +00:00
Nathan Doef 31e13e6adb
Upload Terminology with Endpoint Validation (#4035)
* add failing test

* Fix doc upload issue

* Add change log yaml file

* update due to review from Nathan

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: weiping202209 <weiping.yang@smilecdr.com>
2022-09-28 11:17:01 -04:00
James Agnew e4a2285f30
Make sure to not mix resource types in bulk export (#4093)
* Make sure to not mix resource types in bulk export

* Avoid dupes

* Add test
2022-09-28 15:16:15 +00:00
Luke deGruchy bcdbb51fde
Fix hashCode() to reflect the equals() contract by passing in getValu… (#4086)
* Fix hashCode() to reflect the equals() contract by passing in getValue() instead of getHashIdentity().  Fix bug with DaoSearchParamSynchronizer setting wrong count on AddRemoveCount.addToCount().

* Add hashIdentity to both equals and hashCode.  Rename unit test to be more descriptive.

* Add changelog and fix changelog for previous MR.

* Add newline to changelog file.
2022-09-27 12:39:10 -07:00
StevenXLi 9e1120a47a
4080 support onc requirements for group bulk export (#4081)
* added failing tests

* added include to bulk export processor, added support for different resource types in bulk export fetch id step

* added changelog

* fixed duplication issue, and added null check

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-09-27 14:51:43 +00:00
Tadgh f06f9dc90a
4084 error segment of bulk export job poll status is missing (#4085)
* changelog

* Change serialization rules

* Always populate error field even if no errors
2022-09-27 01:16:33 +00:00
michaelabuckley 96b92153f6
Implement composite search parameters in HibernateSearch for JPA (#3839)
Implement composite search parameters in Lucene/Elasticsearch Hibernate Search indexing

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-09-27 00:20:06 +00:00
James Agnew 641007f5b6
Fix DSTU2 conformance statement (#4082)
* Fix DSTU2 conformance statement

* Add changelog and test
2022-09-26 12:33:12 -07:00
Luke deGruchy 3435806df5
4058: Fix JpaPersistedResourceValidationSupport to search for resources that it currently doesn't handle (#4062)
* Add failing and passing tests with bundle JSONs for each scenario based on pared down versions of the following JSON bundle: https://smilecdr.com/docs/fhir_repository/clinical_quality_language/measure-bundle-example.json.html

* Add experimental code to handle cases of "Library" and "Measure". Add a measure report to measure unit test with new JSON with a MeasureReport to Measure resource (can't make it pass yet).

* Refine case statements for JpaPersistedResourceValidationSupport.  MeasureReport test passes if -ea is omitted from run configuration.

* Add changelog.  Remove TODOs from validator.

* Remove erroneous whitespace chance.

* Ken feedback:  Handle SearchParameters from the default case casting a wider net than just Library and Resource.  Assume all CanonicalType inputs to the switch statement have a URL.

* Get rid of TODO since it's not relevant.

* Disable test with only MeasureReport and Measure.  Fix case issue with filenames that was only discovered by running the github pipeline.

* Add more context to the Disabled text, including a reference to a new issue:  https://github.com/hapifhir/org.hl7.fhir.core/issues/930.

* Add more context to the Disabled text, including a reference to a new issue:  https://github.com/hapifhir/org.hl7.fhir.core/issues/930.
2022-09-26 10:08:04 -04:00
TipzCM 389bdce372
fixed bug (#4069)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-09-26 13:43:11 +00:00
James Agnew 917cf8d062
Remove ActionRequestDetails (#3527)
* Add test

* Add test

* Start removing unneeded things

* Fixes

* Add changelog

* Test fix

* Address LGTM issues

* Resolve fixme

* Address review comment

* Add changelog

* Update doc

* Test fixes
2022-09-25 21:29:08 +00:00
James Agnew 3bab3544ec
Reduce SQL queries for _include (#4007)
* Rework includes processing for reuse

* Optimize include

* Test fixes

* Bump version down

* Fixed

* Update

* Test fixes

* Start to add javadoc

* Test fixes
2022-09-25 15:22:06 -04:00
James Agnew 3935b78083
Add operation blocking interceptor (#4057)
* Add operation blocking interceptor

* Work on interceptor

* Work on interceptor

* FIx up docs

* Address CVE

* Tweak changelog

* Address review comments
2022-09-25 14:19:17 -04:00
Tadgh 2770295638
Add MDM Expansion Docs (#4068)
* Add docs

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_expansion.md

Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_expansion.md

Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>

Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
2022-09-24 01:40:13 +00:00
Tadgh 6f80206776
Fix transactional issue in everything operation (#4063)
* Fix transactional issue in everything operation

* Add license files

* Add changelog
2022-09-23 08:33:08 -07:00