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* 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 <[email protected]> Co-authored-by: Tadgh <[email protected]> * improved logging (#4217) Co-authored-by: Ken Stevens <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Ken Stevens <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * added changelog, also changed a setup function in test to beforeeach Co-authored-by: Long Ma <[email protected]> Co-authored-by: jdar8 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Version bump * fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <[email protected]> * Gl3407 bundle offset size (#3918) * begin with failing test * fixed * change log * rollback default count change and corresponding comments Co-authored-by: Ken Stevens <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Qingyixia <[email protected]> Co-authored-by: TipzCM <[email protected]> Co-authored-by: leif stawnyczy <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Etienne Poirier <[email protected]> Co-authored-by: peartree <[email protected]> Co-authored-by: kateryna-mironova <[email protected]> Co-authored-by: longma1 <[email protected]> Co-authored-by: Long Ma <[email protected]> Co-authored-by: jdar8 <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: markiantorno <[email protected]> Co-authored-by: Steven Li <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Revert "ignore misfires in quartz" This reverts commit 15c74a4. * 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 <[email protected]> Co-authored-by: nathaniel.doef <[email protected]> * 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 #4277 and https… (#4291) * fixes for #4277 and #4276 * Credit for #4291 Co-authored-by: James Agnew <[email protected]> * 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 <[email protected]> * Add backport info * Fix up tests * Fix discrepancies * Fix test * Version bump * bump ips Co-authored-by: jmarchionatto <[email protected]> Co-authored-by: juan.marchionatto <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: JasonRoberts-smile <[email protected]> Co-authored-by: Qingyixia <[email protected]> Co-authored-by: TipzCM <[email protected]> Co-authored-by: leif stawnyczy <[email protected]> Co-authored-by: Etienne Poirier <[email protected]> Co-authored-by: peartree <[email protected]> Co-authored-by: kateryna-mironova <[email protected]> Co-authored-by: longma1 <[email protected]> Co-authored-by: Long Ma <[email protected]> Co-authored-by: jdar8 <[email protected]> Co-authored-by: markiantorno <[email protected]> Co-authored-by: Steven Li <[email protected]> Co-authored-by: Luke deGruchy <[email protected]> Co-authored-by: karneet1212 <[email protected]> Co-authored-by: James Agnew <[email protected]> Co-authored-by: James Agnew <[email protected]> Co-authored-by: KGJ-software <[email protected]> Co-authored-by: kylejule <[email protected]> Co-authored-by: Nathan Doef <[email protected]> Co-authored-by: nathaniel.doef <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> Co-authored-by: leif stawnyczy <[email protected]>
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