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hapi-fhir
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7441 Commits

Author SHA1 Message Date
ianmarshall 40bc754051 Address gaps in migration that can occur with Oracle DB when flyway is disabled. 2021-02-01 15:52:41 -05:00
Frank Tao 1d835d82d6
Fixed Ucum Conversion NullPointerException issue (#2331) 
* Fixed Ucum Conversion NullPointerException issue

* Revoke:save value to the original table if it can't be normalized
 2021-01-30 19:30:12 -05:00
jamesagnew 8c5b54bf54 Fix broken changelog 2021-01-30 19:26:58 -05:00
Kevin Dougan SmileCDR 2308d8f44b
Merge CQL Initial Implementation Into master (#2330) 
* CQL initial implementation
 2021-01-29 16:35:38 -05:00
jamesagnew 5961fde2dd Docs tweak 2021-01-29 16:12:06 -05:00
Ken Stevens ba63f65115
changed $expand filter matching from left-match to contains match (#2327) 
* changed $expand filter matching from left-match to contains match

* changelog

* pure substring match is too generous (a regression test checked for that).  Tightened the match up to word boundaries.

* CLean up to avoid intermittent test failure

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-01-29 12:37:54 -05:00
Marcel P d11515599a
Added FHIRPathResource Generator for R4 including Test. (#2310) 
Signed-off-by: Marcel Parciak <marcel.parciak@gmail.com>
 2021-01-29 11:05:05 -05:00
jamesagnew 589eb3158e Credit for #2310 2021-01-29 11:02:51 -05:00
Tadgh 96b4e5ab38
Merge pull request #2324 from hapifhir/single-threading-mdm 
Ensure Single threading mdm
 2021-01-29 10:01:56 -05:00
James Agnew 947622d25f
CLean up to avoid intermittent test failure (#2329) 
* CLean up to avoid intermittent test failure

* One more intermittent test fix
 2021-01-29 05:28:21 -05:00
jamesagnew 8854f344b3 Add test 2021-01-28 16:22:36 -05:00
Nick Goupinets 0be3f0e4e8
Merge pull request #2286 from hapifhir/ng_20201218_survivorship_poc 
Survivorship proof-of-concept implementation and optional manual override for GR merge
 2021-01-28 09:18:20 -05:00
Nick Goupinets 3be480c9f0 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-27 16:47:40 -05:00
James Agnew 909d9f742c
Enable Auto-reference versions in JPA (#2323) 
* Automatic reference versions

* Auto reference versions

* resolve fixmes

* Add changelog

* Test fixes

* Test fixes

* Resolve fixmes

* Work on versioning

* Add support for _includes

* Update headers

* Change visibility

* One more tweak

* One more API tweak

* Fixes

* Account for review comments

* Fix errorprone reported issue

* Test fix

* Test fixes

* Test fixes
 2021-01-27 14:49:10 -05:00
Nick Goupinets 04db4ed229 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-26 09:18:20 -05:00
Tadgh 170d633181
Merge pull request #2326 from hapifhir/azure-pipelines 
Update snapshot-pipeline.yml for Azure Pipelines
 2021-01-25 14:32:01 -05:00
Tadgh e80e592d80 Skip tests 2021-01-25 14:31:36 -05:00
Tadgh e696262c4a Update snapshot-pipeline.yml for Azure Pipelines 
Add CI,ERRORPRONE profiles.
 2021-01-25 13:08:15 -05:00
Mark Iantorno 1e2f425810
Merge pull request #2322 from hapifhir/README-update 
Just cleaning up the README a little
 2021-01-25 10:30:37 -05:00
Tadgh c572575412 Remove mutator 2021-01-25 09:55:31 -05:00
Tadgh aa37884b2e Worked on #2317, force single consumer 2021-01-25 09:51:50 -05:00
Ken Stevens 86ea0d60ef
reduce _count to the maximum page size rather than throwing an error. (#2319) 
* reduce _count to the maximum page size rather than throwing an error.

Also when setting the paging provider on a restful server, automatically set the default page size and max page sized of the restful server from the paging provider.

* reword log message

* fixing this paging issue has uncovered all sorts of interesting things, including this long hidden bug!

* fix tests in sub-optimal way

* fix NPE

* fix test

* fixed a couple of bugs in SearchCoordinatorSvcImpl that surfaced when i added a default page size to RestfulServer
 2021-01-25 08:19:29 -05:00
James Agnew 5d2e830b15
Fix android tests (#2321) 2021-01-24 12:09:50 -05:00
Mark Iantorno 9e5d0790fb
Just cleaning up the README a little 2021-01-24 11:49:53 -05:00
Frank Tao 66e6cab21f
Fixed xml.bind conflict between jakakax and javax (#2320) 2021-01-24 09:56:45 -05:00
jamesagnew 42d12403f9 Try to restore codecov 2021-01-23 18:50:27 -05:00
jamesagnew c55410e6b6 Add changelog for #2302 2021-01-23 17:54:51 -05:00
Frank Tao 1d1ebcf5e8
Improved DateQuery and removed 'OR' in the SQL (#2302) 
* improved DateQuery and removed 'OR' in the SQL

* improved DateQuery and removed 'OR' in the SQL

* Date handling cleanup (#2316)

* Date handling cleanup

* Fix codecov

* One more fix

* Fix tests

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2021-01-23 17:53:18 -05:00
James Agnew 522efc87d9
Reusable interceptor service (#2318) 
* Reusable interceptor service

* Azure fix
 2021-01-22 19:17:08 -05:00
Nick 10382c4915 Added a few more tests 2021-01-22 16:46:18 -05:00
Ken Stevens 749934d5f1
fixed name text indexing (#2309) 
* fixed name text indexing

* fixed name text indexing
 2021-01-22 15:39:26 -05:00
Nick d783229406 updated docs 2021-01-22 13:28:24 -05:00
dependabot[bot] feff734736
Bump jaxb-runtime from 2.3.1 to 3.0.0 (#2289) 
* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

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

* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

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

* Add jakarta bindings

* Dependency cleanup

* More depndency cleanup

* Work on deps

* Replace transaction annotation

* Cleanup

* Another fix

* Build fix

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-01-22 11:24:23 -05:00
Nick cfc798cb2b Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-22 09:45:04 -05:00
Tadgh 71c76e3ea1
Merge pull request #2314 from hapifhir/2313/error-in-mdm-docs 
Add documentation fixes for MDM-match
 2021-01-22 09:26:20 -05:00
Tadgh edd9769686 Add documentation fixes for MDM-match 2021-01-22 09:17:51 -05:00
Nick cdda12ef8e Added empty matcher 2021-01-21 17:42:28 -05:00
Mark Iantorno d5250e6f1a Adding back in test runs. 2021-01-21 16:40:17 -05:00
Mark Iantorno c09b1394fc Variable name fix. 2021-01-21 16:01:36 -05:00
Mark Iantorno 560d960ec9 I am a dummy who puts typos everywhere in his code. 2021-01-21 15:53:29 -05:00
Mark Iantorno 7f3e0726c8 Initial setup for snapshot pipeline 
Still have to enable tests. They are only disabled now so I can run this multiple times quickly to test deployment. [skip ci]
 2021-01-21 15:39:26 -05:00
Frank Tao 341eb404e6
Improved the performance for multiple _has by exclude previous pids (#2304) 
* Improved the performance for multiple _has by exclude prev pids

* Removed extra import

* Added test case for SQL contains RES_ID NOT IN ()
 2021-01-21 14:42:10 -05:00
Tadgh e7bc2f0e2d
Merge pull request #2311 from hapifhir/cve-fix-2021-20190 
bump databind version for CVE
 2021-01-21 10:48:24 -05:00
Nick ed5727d795 Fixed missing imports 2021-01-21 10:04:16 -05:00
Tadgh 7159d65902 bump databind version for CVE 2021-01-21 10:03:16 -05:00
jamesagnew 7cf41a7e85 One more build fix (grrrrrr) 2021-01-21 09:24:42 -05:00
Nick 82e52750e7 Merge branch 'master' into ng_20201218_survivorship_poc 2021-01-21 09:00:28 -05:00
jamesagnew 656dd33ba8 FIx javadoc build 2021-01-21 08:58:23 -05:00
jamesagnew 078a94f1a6 Fix nonnull annotations 2021-01-21 08:47:44 -05:00
James Agnew 14b0688f69
Bump core version to 5.2.16 (#2308) 
* Bump core library version

* Test fix

* Build fixes

* Some test fixes

* One more bit of docs

* Build fix

* Test fix

* Test fix

* Docs fix
 2021-01-21 05:30:23 -05:00