Skip to main content

Browse the archive

https://github.com/jamesagnew/hapi-fhir
14 November 2023, 18:36:22 UTC
sort by:
Revision Author Date Message Commit Date
86ba4d5 Tadgh 20 November 2022, 02:05:37 UTC Fix up MDM Search Expansion 20 November 2022, 02:05:37 UTC
d8abf91 Tadgh 20 November 2022, 01:53:46 UTC Fix up search expansion to use new behaviour of idhelper service 20 November 2022, 01:53:46 UTC
01f23cd Tadgh 19 November 2022, 18:32:56 UTC Merge branch 'master' into rel_6_2_1_mergeback 19 November 2022, 18:32:56 UTC
9621738 Tadgh 18 November 2022, 23:04:00 UTC wip 18 November 2022, 23:04:00 UTC
16fedcf Tadgh 18 November 2022, 22:19:49 UTC wip 18 November 2022, 22:19:49 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
565e56c Tadgh 17 November 2022, 17:53:09 UTC fix build 17 November 2022, 17:53:09 UTC
b5a9d8f Tadgh 17 November 2022, 00:46:48 UTC Fix up version 17 November 2022, 00:46:48 UTC
092fd05 Tadgh 17 November 2022, 00:19:26 UTC licenses 17 November 2022, 00:19:26 UTC
2e9607b Tadgh 16 November 2022, 21:25:55 UTC Version bump 16 November 2022, 21:25:55 UTC
2fb5030 Tadgh 16 November 2022, 21:24:17 UTC Remove double import 16 November 2022, 21:24:17 UTC
ee208eb Tadgh 16 November 2022, 21:13:45 UTC log to console 16 November 2022, 21:13:45 UTC
4e54e37 Tadgh 16 November 2022, 20:54:39 UTC Fix up checkstyle 16 November 2022, 20:54:39 UTC
dbdb374 Tadgh 16 November 2022, 20:41:45 UTC Merge branch 'master' into rel_6_2_1_mergeback 16 November 2022, 20:41:45 UTC
df7e3df Tadgh 16 November 2022, 20:00:35 UTC Quiet log 16 November 2022, 20:00:35 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
5e67399 Tadgh 16 November 2022, 17:13:57 UTC Only submit queued chunks 16 November 2022, 17:13:57 UTC
4b2ede2 Tadgh 16 November 2022, 01:07:02 UTC Disable more broken tests 16 November 2022, 01:07:02 UTC
c25bc8e Tadgh 15 November 2022, 23:12:51 UTC DIsable busted test 15 November 2022, 23:12:51 UTC
969266b Tadgh 15 November 2022, 20:16:21 UTC fix test 15 November 2022, 20:16:21 UTC
d2a5eb3 Tadgh 15 November 2022, 19:25:40 UTC add folder 15 November 2022, 19:25:40 UTC
ea66e37 Tadgh 15 November 2022, 19:10:03 UTC re-add version enum 15 November 2022, 19:10:03 UTC
15c328d Tadgh 15 November 2022, 19:08:48 UTC once again on 6.2.1 15 November 2022, 19:08:48 UTC
e244e7a Tadgh 15 November 2022, 19:03:07 UTC Make minor changes 15 November 2022, 19:03:07 UTC
a75ac9b Tadgh 15 November 2022, 18:46:40 UTC Fix version 15 November 2022, 18:46:40 UTC
779867a Tadgh 15 November 2022, 17:38:22 UTC Unpublicize method 15 November 2022, 17:38:22 UTC
1a373c8 Tadgh 15 November 2022, 17:16:52 UTC Fix up logging 15 November 2022, 17:16:52 UTC
59558db Tadgh 15 November 2022, 17:05:33 UTC Strip some logging 15 November 2022, 17:05:33 UTC
4d37441 Ken Stevens 15 November 2022, 16:48:17 UTC remove 10000 limit 15 November 2022, 16:48:17 UTC
483b88b Tadgh 15 November 2022, 05:37:53 UTC expose useful method 15 November 2022, 05:37:53 UTC
92b9270 Tadgh 15 November 2022, 04:11:24 UTC last-second-fetch 15 November 2022, 04:11:24 UTC
8c896fc Tadgh 15 November 2022, 02:36:24 UTC wip 15 November 2022, 02:36:24 UTC
c19d17b Tadgh 15 November 2022, 02:09:15 UTC wip and test 15 November 2022, 02:09:15 UTC
138be3d Tadgh 15 November 2022, 02:06:44 UTC add implementation 15 November 2022, 02:06:44 UTC
a2ea7ff Tadgh 15 November 2022, 01:01:53 UTC wip 15 November 2022, 01:01:53 UTC
2a455c3 Tadgh 14 November 2022, 23:07:56 UTC Add a whack of logging 14 November 2022, 23:07:56 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
c6e7381 markiantorno 12 November 2022, 07:21:24 UTC Updating version to: 6.2.1 post release. 12 November 2022, 07:21:24 UTC
3f46aa1 Tadgh 12 November 2022, 04:09:50 UTC wip 12 November 2022, 04:09:50 UTC
cef36bd Tadgh 12 November 2022, 03:58:02 UTC TEMP FIX FOR BUILD 12 November 2022, 03:58:02 UTC
93ab52c Tadgh 12 November 2022, 00:54:09 UTC Fix more tests 12 November 2022, 00:54:09 UTC
d08a7a9 Tadgh 11 November 2022, 23:00:44 UTC Fix test: 11 November 2022, 23:00:44 UTC
b9dfd43 Tadgh 11 November 2022, 22:11:08 UTC fix numbers 11 November 2022, 22:11:08 UTC
642afed Tadgh 11 November 2022, 21:55:21 UTC wip 11 November 2022, 21:55:21 UTC
a2d01fc Tadgh 11 November 2022, 21:40:50 UTC Update numbers 11 November 2022, 21:40:50 UTC
434d817 Tadgh 11 November 2022, 20:15:22 UTC Fix up numbers 11 November 2022, 20:15:22 UTC
1bd060e Tadgh 11 November 2022, 20:13:42 UTC Fix up numbers 11 November 2022, 20:13:42 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
cc51bc2 Tadgh 11 November 2022, 06:28:42 UTC license 11 November 2022, 06:28:42 UTC
75cadad Tadgh 11 November 2022, 06:05:35 UTC Set official Version 11 November 2022, 06:05:35 UTC
1722812 Nathan Doef 11 November 2022, 05:43:06 UTC 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> 11 November 2022, 05:43:06 UTC
7f67493 Tadgh 11 November 2022, 01:03:29 UTC Ignore misfires in quartz (#4273) 11 November 2022, 01:03:29 UTC
9cc8be5 Tadgh 11 November 2022, 00:03:03 UTC Revert "ignore misfires in quartz" This reverts commit 15c74a46bc1fd9797b42ad6ddbe6ba34605975cb. 11 November 2022, 00:03:03 UTC
5e02ea1 Etienne Poirier 10 November 2022, 22:03:33 UTC 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> 10 November 2022, 22:03:33 UTC
15c74a4 Tadgh 10 November 2022, 18:35:48 UTC ignore misfires in quartz 10 November 2022, 18:35:48 UTC
2be9e89 Qingyixia 10 November 2022, 16:19:40 UTC 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 10 November 2022, 16:19:40 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
52aa09f Nathan Doef 08 November 2022, 17:14:39 UTC 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> 08 November 2022, 17:14:39 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
590ddf1 Tadgh 07 November 2022, 22:26:27 UTC Fix broken test 07 November 2022, 22:26:27 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
a296299 Tadgh 04 November 2022, 23:04:03 UTC bulk export permanently reusing cached results (#4249) * Add test, fix bug, add changelog * minor refactor 04 November 2022, 23:04:03 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
e6b80d3 Tadgh 04 November 2022, 20:01:43 UTC Add next version 04 November 2022, 20:01:43 UTC
045ceb3 KGJ-software 04 November 2022, 15:43:30 UTC 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> 04 November 2022, 15:43:30 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
b965347 James Agnew 04 November 2022, 11:21:06 UTC 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> 04 November 2022, 11:21:06 UTC
511d3e1 Tadgh 03 November 2022, 20:31:18 UTC Fix bug (#4239) 03 November 2022, 20:31:18 UTC
3199728 Tadgh 03 November 2022, 20:26:28 UTC 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236) * Add constant for interceptor * add test, changelog 03 November 2022, 20:26:28 UTC
220bfeb Tadgh 03 November 2022, 17:54:26 UTC Version bump 03 November 2022, 17:54:26 UTC
eb739e4 Tadgh 03 November 2022, 17:46:27 UTC fix 03 November 2022, 17:46:27 UTC
928ec86 Tadgh 03 November 2022, 17:41:04 UTC Fix bug with MDM submit 03 November 2022, 17:41:04 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
f68d905 karneet1212 02 November 2022, 01:25:21 UTC 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 02 November 2022, 01:25:21 UTC
a018360 Ken Stevens 01 November 2022, 14:38:30 UTC Ks 20221031 migration lock (#4224) * started design * complete with tests * changelog * cleanup * tyop Co-authored-by: Ken Stevens <ken@smilecdr.com> 01 November 2022, 14:38:30 UTC
6a657d4 Luke deGruchy 31 October 2022, 18:49:43 UTC 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. 31 October 2022, 18:49:43 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
92d7126 Tadgh 31 October 2022, 12:28:09 UTC pin okio-jvm for kotlin vuln (#4216) 31 October 2022, 12:28:09 UTC
2ff11d8 Tadgh 31 October 2022, 12:27:15 UTC 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> 31 October 2022, 12:27:15 UTC
bd28730 Ken Stevens 30 October 2022, 18:38:25 UTC improved logging (#4217) Co-authored-by: Ken Stevens <ken@smilecdr.com> 30 October 2022, 18:38:25 UTC
c6c0952 jmarchionatto 28 October 2022, 20:55:39 UTC 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> 28 October 2022, 20:55:39 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
back to top