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14 November 2023, 18:36:22 UTC
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00badbc nathaniel.doef 22 November 2022, 19:02:45 UTC code review comments 22 November 2022, 19:26:27 UTC
524e51d nathaniel.doef 22 November 2022, 16:01:04 UTC point deprecated constants to new values 22 November 2022, 16:01:04 UTC
9eeb154 James Agnew 22 November 2022, 12:48:54 UTC Avoid race condition in ServiceLoader (#4295) * Avoid race condition in ServiceLoader * Changelog 22 November 2022, 12:48:54 UTC
62c630c karneet1212 21 November 2022, 15:08:10 UTC bundle not throwing an error when multiple matches were found (#4283) * Added test + condition to throw error * changelog * changes made based on comments 21 November 2022, 15:08:10 UTC
b1e3468 Tadgh 20 November 2022, 16:14:28 UTC 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 15c74a46bc1fd9797b42ad6ddbe6ba34605975cb. * 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> 20 November 2022, 16:14:28 UTC
84d4097 Ken Stevens 19 November 2022, 23:57:03 UTC fixed GraphQLEngineTest.beforeClass:181 » Runtime HAPI-2200: No Cache Service Provid... (#4292) Co-authored-by: Ken Stevens <ken@smilecdr.com> 19 November 2022, 23:57:03 UTC
61579aa Jens Kristian Villadsen 18 November 2022, 00:15:05 UTC 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> 18 November 2022, 00:15:05 UTC
6c4283e michaelabuckley 16 November 2022, 18:38:52 UTC 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. 16 November 2022, 18:38:52 UTC
d8d8c5f Ken Stevens 14 November 2022, 18:51:03 UTC Consolidate all System Properties into a single class (#4252) * started converting System.setProperty to HapiSystem * added a couple more. renamed class * all the setProperty calls done * finished System.getProperty() * Split HapiSystemProperties into HapiSystemProperties and HapiTestSystemProperties * Javadoc * Javadoc * review feedback Co-authored-by: Ken Stevens <ken@smilecdr.com> 14 November 2022, 18:51:03 UTC
80f1514 Mark Iantorno 14 November 2022, 16:53:59 UTC Adding okio dependency for r4b structures for running DIST profile (#4275) * Adding okio dependency for r4b structures for running DIST profile * adding optional for okio 14 November 2022, 16:53:59 UTC
663538b dependabot[bot] 12 November 2022, 20:55:02 UTC Bump slf4j-simple from 1.6.0 to 2.0.3 (#4268) * Bump slf4j-simple from 1.6.0 to 2.0.3 Bumps [slf4j-simple](https://github.com/qos-ch/slf4j) from 1.6.0 to 2.0.3. - [Release notes](https://github.com/qos-ch/slf4j/releases) - [Commits](https://github.com/qos-ch/slf4j/compare/v_1.6.0...v_2.0.3) --- updated-dependencies: - dependency-name: org.slf4j:slf4j-simple dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * Bump versions 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> 12 November 2022, 20:55:02 UTC
2df09c0 jmarchionatto 11 November 2022, 20:08:41 UTC 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> 11 November 2022, 20:08:41 UTC
e5cf3ef Roel-Scholten 11 November 2022, 15:56:12 UTC 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> 11 November 2022, 15:56:12 UTC
9a45576 James Agnew 09 November 2022, 19:47:23 UTC 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> 09 November 2022, 19:47:23 UTC
f50d350 James Agnew 09 November 2022, 18:28:00 UTC 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> 09 November 2022, 18:28:00 UTC
145f22c dependabot[bot] 09 November 2022, 15:16:36 UTC 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> 09 November 2022, 15:16:36 UTC
b3ebbe7 James Agnew 09 November 2022, 03:18:36 UTC 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> 09 November 2022, 03:18:36 UTC
d3367cf Tadgh 07 November 2022, 23:57:57 UTC 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> 07 November 2022, 23:57:57 UTC
6c9fe71 jmarchionatto 07 November 2022, 19:20:28 UTC 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> 07 November 2022, 19:20:28 UTC
8ff8704 michaelabuckley 07 November 2022, 18:42:39 UTC use ${project.version} instead of literal string to avoid merge noise (#4255) 07 November 2022, 18:42:39 UTC
02944ba jmarchionatto 04 November 2022, 20:57:19 UTC Fix release pipeline Originally Issue 4106 process map to properties when uploading loinc terminology (#4246) * 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 * Fix alignments to try to make release pipeline work Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 04 November 2022, 20:57:19 UTC
5533afb James Agnew 04 November 2022, 13:06:22 UTC 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> 04 November 2022, 13:06:22 UTC
511d3e1 Tadgh 03 November 2022, 20:31:18 UTC Fix bug (#4239) 03 November 2022, 20:31:18 UTC
6cf5989 jmarchionatto 03 November 2022, 12:48:02 UTC 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> 03 November 2022, 12:48:02 UTC
3053a1d VK-SMILECDR 02 November 2022, 21:30:03 UTC fix snapshot pipeline yml syntax issues (#4235) 02 November 2022, 21:30:03 UTC
27ec3be VK-SMILECDR 02 November 2022, 19:34:27 UTC 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 02 November 2022, 19:34:27 UTC
1b55f49 samuelwlee2 31 October 2022, 17:33:54 UTC 4153 extend $member match operation to store consent resource if matched (#4165) * added senstive and regular filter * add UUID to Consent * blah * fix merge with master * fixing merge * blah * fhir tests * use constructor injection * put all tests together * blah * blah * finalize * add consent update patient and performer reference * fixes after code review * blah * refactor to save consent once * blah * fix performer and add validation * code clean up * add changelog * add hrex member match flag * fix PatientMemberMatchOperationR4Test * adding code fixes after code review * move changelog file * bump version Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> 31 October 2022, 17:33:54 UTC
31a193f Tadgh 28 October 2022, 02:40:59 UTC Bump to 6.3.0 (#4211) 28 October 2022, 02:40:59 UTC
7a39f8c James Agnew 28 October 2022, 01:31:39 UTC Make reference extractor more reusable (#4205) * Refactor * Make reference extractor more reusable * Test fix * Test fix * Headers * Small refactor 28 October 2022, 01:31:39 UTC
d8dd42c StevenXLi 27 October 2022, 19:53:07 UTC added aggregate function to the sort columns (#4208) * added aggregate function to the sort columns, as the sql will not work on other dbs other than H2 that use order by * rename parameter to make it more meaningful * extract parameter to a field Co-authored-by: Steven Li <steven@smilecdr.com> 27 October 2022, 19:53:07 UTC
0a160a3 karneet1212 26 October 2022, 17:29:28 UTC 4175-$validate-operation-on-a-resource-update-results-in-an-error-stating-resource-has-no-id (#4181) * Added unit test + solution * Changelog * Cleanup * changelog filename 26 October 2022, 17:29:28 UTC
296ddb8 Tadgh 26 October 2022, 17:17:11 UTC CVE Fixes (#4200) * CVEs * bump snakeyaml again * Add updates to changes.yaml 26 October 2022, 17:17:11 UTC
78ce2a6 Tadgh 25 October 2022, 19:02:04 UTC 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> 25 October 2022, 19:02:04 UTC
fb3512d Ken Stevens 25 October 2022, 18:01:24 UTC Deprecate dao methods that do not take a RequestDetails parameter (#4199) Co-authored-by: Ken Stevens <ken@smilecdr.com> 25 October 2022, 18:01:24 UTC
e7ac40d Ken Stevens 25 October 2022, 15:20:31 UTC 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> 25 October 2022, 15:20:31 UTC
1190eb9 Kevin Dougan SmileCDR 25 October 2022, 14:53:26 UTC 4197 - Fixed header on the server_jpa/elastic docs page. (#4198) 25 October 2022, 14:53:26 UTC
3d9dfd4 jmarchionatto 25 October 2022, 13:56:08 UTC 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> 25 October 2022, 13:56:08 UTC
e1e33df StevenXLi 25 October 2022, 13:42:54 UTC 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> 25 October 2022, 13:42:54 UTC
51627fb William Denton 24 October 2022, 22:42:29 UTC fix generate-multi-file and generate-single-file goals with R5 (#4134) * fix generate-multi-file and generate-single-file goals with R5 structures * clean up Javadoc & fix R5 issue when generating for all resources 24 October 2022, 22:42:29 UTC
5328951 James Agnew 24 October 2022, 22:20:39 UTC Version Bump a few dependencies (#4191) * Version bumps * Test fixes * Test fix * Test fix 24 October 2022, 22:20:39 UTC
cbd65c7 James Agnew 24 October 2022, 21:07:32 UTC Add remove method to jobregistry (#4187) * Add remove method to jobregistry * Add changelog 24 October 2022, 21:07:32 UTC
fb6bf5b Tadgh 24 October 2022, 11:57:54 UTC Attribution (#4183) 24 October 2022, 11:57:54 UTC
a824ba2 Ken Stevens 22 October 2022, 16:16:27 UTC package loader npe (#4186) * begin with failing test * fixed * change log * change log Co-authored-by: Ken Stevens <ken@smilecdr.com> 22 October 2022, 16:16:27 UTC
929767a michaelabuckley 21 October 2022, 20:45:30 UTC 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 21 October 2022, 20:45:30 UTC
2830792 jmarchionatto 21 October 2022, 20:19:45 UTC 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> 21 October 2022, 20:19:45 UTC
1dba939 Tue Toft Nørgård 21 October 2022, 20:08:21 UTC #4078 Fix BinaryAccessProvider empty stream check (#4170) * Fix #4078 by using theRequestDetails.loadRequestContents() to check if the input stream is empty or not * Remove unused imports 21 October 2022, 20:08:21 UTC
b04f082 Tadgh 21 October 2022, 02:28:20 UTC Move to correct folder (#4176) 21 October 2022, 02:28:20 UTC
a71b8fa James Agnew 20 October 2022, 20:57:06 UTC 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 20 October 2022, 20:57:06 UTC
c831266 Luke deGruchy 20 October 2022, 18:27:01 UTC 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. 20 October 2022, 18:27:01 UTC
0c5b64c jmarchionatto 20 October 2022, 17:47:18 UTC 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> 20 October 2022, 17:47:18 UTC
4200ccf Etienne Poirier 19 October 2022, 21:06:51 UTC 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> 19 October 2022, 21:06:51 UTC
0798ab3 Luke deGruchy 19 October 2022, 18:13:21 UTC 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. 19 October 2022, 18:13:21 UTC
5a31ce0 JasonRoberts-smile 19 October 2022, 15:43:51 UTC disable batch job reuse (#4155) 19 October 2022, 15:43:51 UTC
a6ed393 karneet1212 19 October 2022, 15:33:21 UTC 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 19 October 2022, 15:33:21 UTC
69d55b7 KGJ-software 19 October 2022, 10:09:02 UTC 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> 19 October 2022, 10:09:02 UTC
dac266b samuelwlee2 18 October 2022, 18:19:03 UTC 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 18 October 2022, 18:19:03 UTC
bd22b8d jmarchionatto 17 October 2022, 22:07:33 UTC 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> 17 October 2022, 22:07:33 UTC
f6fe8df jmarchionatto 17 October 2022, 17:40:10 UTC Add documentation for reindex-terminology command (#4146) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 17 October 2022, 17:40:10 UTC
a5fb87b Etienne Poirier 17 October 2022, 15:09:17 UTC 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> 17 October 2022, 15:09:17 UTC
26ef32c James Agnew 14 October 2022, 20:46:18 UTC Fix 2 issues with has reverse chaining (#4139) * Fix 2 issues with chains * Add changelog * Cleanup * Add comment * Cleanup 14 October 2022, 20:46:18 UTC
f00f65a jmarchionatto 14 October 2022, 12:12:12 UTC Issue 4052 addition of properties to the loinc terminology uploading process (#4135) * 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. * Add new CODING property handler to run after all TermConcepts are created, to have them accessible for extracting display value * Add small test file to ease setup Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 14 October 2022, 12:12:12 UTC
422ef87 James Agnew 13 October 2022, 20:26:11 UTC 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 13 October 2022, 20:26:11 UTC
2e6b3d1 MykolaMedynskyiSCDR 13 October 2022, 15:05:04 UTC 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> 13 October 2022, 15:05:04 UTC
4cebcfb Etienne Poirier 12 October 2022, 16:16:44 UTC 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> 12 October 2022, 16:16:44 UTC
2de9b5a samuelwlee2 12 October 2022, 14:06:22 UTC 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 12 October 2022, 14:06:22 UTC
9d7829a Qingyixia 12 October 2022, 14:03:54 UTC 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 12 October 2022, 14:03:54 UTC
379220f alackerbauer 12 October 2022, 12:13:17 UTC removed link (#4132) Co-authored-by: Anna <anna.lin@smilecdr.com> 12 October 2022, 12:13:17 UTC
b74e121 Tadgh 12 October 2022, 12:06:46 UTC 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> 12 October 2022, 12:06:46 UTC
108e357 James Agnew 12 October 2022, 11:01:47 UTC Preserve tags on delete (#4128) * Preserve tags on delete * Add changelog * Add changelog * Test fix * Build fix * Address review comments 12 October 2022, 11:01:47 UTC
5831cbe Luke deGruchy 11 October 2022, 20:48:01 UTC 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> 11 October 2022, 20:48:01 UTC
26fe5e6 James Agnew 09 October 2022, 19:02:12 UTC Interceptor improvements (#4125) * Interceptor improvements * Add changelogs 09 October 2022, 19:02:12 UTC
c5e1eff KGJ-software 07 October 2022, 13:50:49 UTC 3240 Added test case. Currently does not reproduce bug. (#4108) * 3240 Added test case. Currently does not reproduce bug. * 3552 Fixed test case. * 3552 Added StrictErrorHandler validation before applying patch. * 3552 Use logger instead of sysout. * 3552 Use try blocks. * 3552 Better test name. Co-authored-by: kylejule <kyle.jule@smilecdr.com> 07 October 2022, 13:50:49 UTC
18093bf Tadgh 06 October 2022, 17:50:45 UTC Hl7 core bump (#4110) * Bump to 5.6.67 * wip * wip * Remove capabilitystatement2 * Update fhirversion.properties * Remove xpathusage for r5 * add new structure defs 06 October 2022, 17:50:45 UTC
44ed3ee Ken Stevens 05 October 2022, 00:37:40 UTC 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> 05 October 2022, 00:37:40 UTC
40163f7 Ken Stevens 04 October 2022, 02:40:09 UTC 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 92c9cb263b90cff2190cc327fab051dc3bb2f83f. * 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> 04 October 2022, 02:40:09 UTC
66baa82 weiping202209 03 October 2022, 13:00:41 UTC 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> 03 October 2022, 13:00:41 UTC
43ed8ca jmarchionatto 03 October 2022, 12:48:40 UTC 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> 03 October 2022, 12:48:40 UTC
26756a4 Ken Stevens 01 October 2022, 15:36:04 UTC add message key to all message types (#4101) * add message key to all message types * move test Co-authored-by: Ken Stevens <ken@smilecdr.com> 01 October 2022, 15:36:04 UTC
e9a855d Ken Stevens 30 September 2022, 17:18:48 UTC 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> 30 September 2022, 17:18:48 UTC
b472c4b Tadgh 29 September 2022, 17:24:05 UTC 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 29 September 2022, 17:24:05 UTC
fc82ed4 James Agnew 28 September 2022, 16:46:00 UTC One more tweak to #4093 (#4094) * One more tweak to #4093 * Add changelog 28 September 2022, 16:46:00 UTC
31e13e6 Nathan Doef 28 September 2022, 15:17:01 UTC 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> 28 September 2022, 15:17:01 UTC
e4a2285 James Agnew 28 September 2022, 15:16:15 UTC 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 28 September 2022, 15:16:15 UTC
d63d71e Ken Stevens 28 September 2022, 01:37:51 UTC add remove method to field list mutator (#4088) * add remove method to field list mutator * add test and Msg.code * test passes Co-authored-by: Ken Stevens <ken@smilecdr.com> 28 September 2022, 01:37:51 UTC
bcdbb51 Luke deGruchy 27 September 2022, 19:39:10 UTC 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. 27 September 2022, 19:39:10 UTC
9e1120a StevenXLi 27 September 2022, 14:51:43 UTC 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> 27 September 2022, 14:51:43 UTC
f06f9dc Tadgh 27 September 2022, 01:16:33 UTC 4084 error segment of bulk export job poll status is missing (#4085) * changelog * Change serialization rules * Always populate error field even if no errors 27 September 2022, 01:16:33 UTC
96b9215 michaelabuckley 27 September 2022, 00:20:06 UTC 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> 27 September 2022, 00:20:06 UTC
641007f James Agnew 26 September 2022, 19:33:12 UTC Fix DSTU2 conformance statement (#4082) * Fix DSTU2 conformance statement * Add changelog and test 26 September 2022, 19:33:12 UTC
3435806 Luke deGruchy 26 September 2022, 14:08:04 UTC 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. 26 September 2022, 14:08:04 UTC
389bdce TipzCM 26 September 2022, 13:43:11 UTC fixed bug (#4069) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 26 September 2022, 13:43:11 UTC
917cf8d James Agnew 25 September 2022, 21:29:08 UTC 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 25 September 2022, 21:29:08 UTC
3bab354 James Agnew 25 September 2022, 19:22:06 UTC 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 25 September 2022, 19:22:06 UTC
3935b78 James Agnew 25 September 2022, 18:19:17 UTC 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 25 September 2022, 18:19:17 UTC
2770295 Tadgh 24 September 2022, 01:40:13 UTC 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> 24 September 2022, 01:40:13 UTC
ee1cb4e michaelabuckley 24 September 2022, 00:47:25 UTC Cleanup and utilities from composite work (#4066) Utilities and cleanup from composite work #4066 24 September 2022, 00:47:25 UTC
6f80206 Tadgh 23 September 2022, 15:33:08 UTC Fix transactional issue in everything operation (#4063) * Fix transactional issue in everything operation * Add license files * Add changelog 23 September 2022, 15:33:08 UTC
ac673b5 StevenXLi 22 September 2022, 18:00:03 UTC changed the comment in Msg class (#4061) Co-authored-by: Steven Li <steven@smilecdr.com> 22 September 2022, 18:00:03 UTC
31462c0 James Agnew 22 September 2022, 15:52:23 UTC Revert "changed the comment in Msg class, and added changelog (#4049)" (#4059) This reverts commit 612c8a730f74cac6d06cd1a9c89172c6bca132c6. 22 September 2022, 15:52:23 UTC
612c8a7 StevenXLi 22 September 2022, 14:08:26 UTC changed the comment in Msg class, and added changelog (#4049) * changed the comment in Msg class, and added changelog * removed log files, as this change is not client related Co-authored-by: Steven Li <steven@smilecdr.com> 22 September 2022, 14:08:26 UTC
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