Tadgh
6129194353
Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export
2021-03-04 16:53:20 -05:00
Tadgh
2f1518344b
Add changelogs, add patientbulkredaer implementation
2021-03-04 16:53:05 -05:00
Tadgh
c2877e84bb
Merge pull request #2439 from hapifhir/issue-2433-mdm-export
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Support MDM expansion in Group Bulk Export
2021-03-04 16:49:19 -05:00
Tadgh
ff1c6e4d27
Start with failling test and partial job config
2021-03-04 16:15:51 -05:00
Tadgh
8021396f4f
Remove unused mdmlink functions
2021-03-04 14:17:02 -05:00
Diederik Muylwyk
5a952ad980
Add more FIXMEs as my understanding grows.
2021-03-04 14:16:14 -05:00
Tadgh
8eb9ebb797
Add space
2021-03-04 14:07:04 -05:00
Tadgh
e5eacdddd6
Fixes bug with uninterpretable string expression in job parameter
2021-03-04 14:06:48 -05:00
Diederik Muylwyk
e8c080bb12
Add initial FIXMEs.
2021-03-04 13:45:09 -05:00
Tadgh
94377c1159
Just use boolean
2021-03-04 13:02:17 -05:00
Tadgh
f7153a609a
Fix formatting error
2021-03-04 10:04:38 -05:00
Tadgh
3d628a4e9c
Add test for exporting patients from group
2021-03-03 21:30:40 -05:00
Tadgh
de09c7e2da
Bit of logic tidying
2021-03-03 19:03:31 -05:00
Tadgh
7b663bfe99
Add constants, fix up some tests
2021-03-03 18:51:03 -05:00
Tadgh
02f38e9532
Fix up other tests for new data reality
2021-03-03 16:16:22 -05:00
Tadgh
3f3e252175
Extract a superclass
2021-03-03 15:48:28 -05:00
Tadgh
57c7d4f3eb
Support MDM expansion in group bulk export, re-add capability to use _typeFilter in Bulk Export
2021-03-03 15:02:41 -05:00
Tue Toft Nørgård
70c2808ecd
Fix https://github.com/hapifhir/hapi-fhir/issues/2435 ( #2436 )
2021-03-03 08:51:27 -05:00
Tadgh
53598c3bdc
Start with failing test
2021-03-02 13:18:43 -05:00
Tadgh
74066a81b6
Merge pull request #2420 from hapifhir/issue-2401-add-support-for-group-id-export
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Issue 2401 add support for group id export
2021-02-26 10:23:42 -05:00
Ken Stevens
7d769e3b05
Issue 2332 create via put for implementationguide that references some placeholders ( #2423 )
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* begin with failing test
* fixed. test passes.
* documentation and changelog
* added ConceptMap
* review feedback
2021-02-26 09:44:48 -05:00
Tadgh
604b5d2060
Fix all broken tests
2021-02-25 19:11:18 -05:00
Tadgh
6c6b959cb5
fix test
2021-02-25 16:54:21 -05:00
Tadgh
b0209fdaac
Fix multi search parameter issue
2021-02-25 16:39:24 -05:00
Tadgh
1a5439fad5
Comment out unused mdm parameter
2021-02-25 16:27:57 -05:00
Tadgh
1663e367a6
Address review comments
2021-02-25 16:23:36 -05:00
Ken Stevens
a2a3ffb7ec
added failing test
2021-02-25 14:35:20 -05:00
Tadgh
f6a913effe
Fix NPE
2021-02-25 09:27:28 -05:00
Tadgh
8e060a05e0
remove fixme
2021-02-24 22:46:51 -05:00
Tadgh
b725c51172
Change tests
2021-02-24 17:28:46 -05:00
Tadgh
a56060a096
Tidy things from preliminary review
2021-02-24 17:16:54 -05:00
Tadgh
3937d2ef01
Remove some dead code
2021-02-24 15:57:55 -05:00
Tadgh
0033827f57
Minor refactor
2021-02-24 15:14:59 -05:00
Kevin Hartmann
26a385a595
Merge remote-tracking branch 'origin/master' into kh-20200222-search-list
2021-02-24 10:29:38 -05:00
Kevin Hartmann
1eab2caf9f
Added _list as a valid parameter in MatchUrlService
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Wrote tests for and/or/both processing in FhirResourceDaoSearchListTest.
2021-02-24 10:27:22 -05:00
Patrick Werner
cf1f2f27db
added nullchecks to prevent NPE ( #2417 )
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* added nullchecks to prevent NPE
fixes #2171
* Add test from #2171 and changelog
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-02-24 10:09:04 -05:00
Ken Stevens
30905aeba7
Merge remote-tracking branch 'origin/master' into issue-2401-add-support-for-group-id-export
2021-02-24 09:38:59 -05:00
Kevin Hartmann
62bfa2cdbc
Merge remote-tracking branch 'origin/master' into kh-20200222-search-list
2021-02-24 09:20:07 -05:00
Tadgh
627d2b9bd0
Tidy test
2021-02-23 18:53:18 -05:00
Tadgh
077225b87c
Add chunking
2021-02-23 16:41:17 -05:00
Tadgh
7561889924
Partially complete groupbulkexportjob
2021-02-23 13:05:58 -05:00
Ken Stevens
fb884f9f15
test infrastructure
2021-02-23 11:32:02 -05:00
Ken Stevens
330cafa83e
initial implementation
2021-02-23 11:25:56 -05:00
Tadgh
b5b8d27b39
Tidy code
2021-02-22 22:51:20 -05:00
Tadgh
66c2b456de
Add more tests
2021-02-22 22:47:08 -05:00
James Agnew
b108e43600
Allow partition date for non-partitionable resources ( #2407 )
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* Allow partition date for searchparam resources
* Cleanup
* Test fix
* Documentation update
* Docs tweak
2021-02-22 20:49:09 -05:00
Tadgh
a3c291336c
partial add of new style of job
2021-02-22 17:00:01 -05:00
Ken Stevens
24efa97b17
begin with failing test
2021-02-22 11:37:32 -05:00
Tadgh
d8ce476e99
Merge branch 'issue-2401-add-support-for-group-id-export' of github.com:jamesagnew/hapi-fhir into issue-2401-add-support-for-group-id-export
2021-02-22 10:25:26 -05:00
Tadgh
d31b04ee65
wip
2021-02-22 10:25:24 -05:00
Ken Stevens
61a7f9ed6a
added mdm flag
2021-02-19 20:51:52 -05:00
Ken Stevens
9bc051c193
added mdm flag
2021-02-19 20:47:43 -05:00
Ken Stevens
3de51103a3
fixed provider
2021-02-19 20:24:56 -05:00
Ken Stevens
1e0981b416
job call
2021-02-19 13:39:50 -05:00
Ken Stevens
00a8e3897a
begin with failing test
2021-02-18 21:54:16 -05:00
Ken Stevens
70b2b83d1a
begin with failing test
2021-02-18 21:47:43 -05:00
James Agnew
3eda19c65a
Version bump ( #2400 )
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* Version bump
* Docs changes
* Docs tweaks
* Docs tweak
* Spelling fixes
* Docs tweaks
2021-02-18 11:07:49 -05:00
jamesagnew
919c1dbddc
Version bump to 5.3.0
2021-02-17 07:10:13 -05:00
James Agnew
65ac0e80fb
Add CapabilityStatement customizer ( #2387 )
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* Add CapabilityStatement customizer
* Fix javadocs
2021-02-15 14:58:34 -05:00
ianmarshall
88d820bf38
Make LOINC Top2000* files optional in terminology loader.
2021-02-11 09:12:08 -05:00
ianmarshall
a383cb94fc
Make LOINC Top2000* files optional in terminology loader.
2021-02-10 22:30:19 -05:00
Tadgh
2759db2a31
Merge pull request #2371 from hapifhir/config-error-on-url-protocol
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Throw ConfigurationError if you attempt to provide a Rest URL that contains a protocol.
2021-02-09 20:25:14 -05:00
Tadgh
64878c23d3
Update text, add changelog
2021-02-09 19:03:09 -05:00
Tadgh
2e3712357f
Throw configueration error when somebody tries to put a protocol in the rest URL
2021-02-09 18:59:11 -05:00
Ken Stevens
7f127f75f9
validate that Terminology beans are proxied so that @Transactional annotated methods are run within transactions ( #2362 )
2021-02-08 13:11:29 -05:00
Hanan Awwad
6384067e50
Customize concept display in value set expansion ( #2282 )
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* fix issue #2280
* revert the indentation back.
* revert-back untouched changes.
2021-02-07 12:29:05 -05:00
James Agnew
92669b29da
Add elastic test ( #2348 )
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* Add elastic test
* Rework
* Add test
2021-02-04 11:04:27 -05:00
James Agnew
0f31d106e5
Allow empty request details in JPA ( #2343 )
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* Allow empty request details in JPA
* Test fixes
2021-02-02 11:00:14 -05:00
Mike G
f61cb163ae
refactor and modify for prefix and suffix
2021-02-01 12:11:11 -05:00
Frank Tao
1d835d82d6
Fixed Ucum Conversion NullPointerException issue ( #2331 )
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* 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
Ken Stevens
ba63f65115
changed $expand filter matching from left-match to contains match ( #2327 )
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* 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
jamesagnew
8854f344b3
Add test
2021-01-28 16:22:36 -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 )
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* 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
Ken Stevens
86ea0d60ef
reduce _count to the maximum page size rather than throwing an error. ( #2319 )
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* 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
Frank Tao
1d1ebcf5e8
Improved DateQuery and removed 'OR' in the SQL ( #2302 )
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* 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
Ken Stevens
749934d5f1
fixed name text indexing ( #2309 )
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* fixed name text indexing
* fixed name text indexing
2021-01-22 15:39:26 -05:00
dependabot[bot]
feff734736
Bump jaxb-runtime from 2.3.1 to 3.0.0 ( #2289 )
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* 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
Frank Tao
341eb404e6
Improved the performance for multiple _has by exclude previous pids ( #2304 )
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* 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
Nick
ed5727d795
Fixed missing imports
2021-01-21 10:04:16 -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
078a94f1a6
Fix nonnull annotations
2021-01-21 08:47:44 -05:00
James Agnew
14b0688f69
Bump core version to 5.2.16 ( #2308 )
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* 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
Tadgh
3d5255d88c
Bump ES version running in tests
2021-01-20 11:34:51 -05:00
Nick
f5e2086cfd
Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc
2021-01-19 09:35:31 -05:00
Tadgh
edbc789a93
Add annotation to skip test classes which require docker if it is not found on the host
2021-01-18 21:49:43 -05:00
Tadgh
7c6c64bfb7
Remove dead import
2021-01-18 15:53:49 -05:00
Tadgh
5b2530a948
Remove dead beans
2021-01-18 14:55:33 -05:00
Tadgh
8f72970063
Add bean to config
2021-01-18 14:09:38 -05:00
Nick
b00f47ef81
Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc
2021-01-18 09:25:58 -05:00
James Agnew
66e1a51e01
Add validation options to RepositoryValidingInterceptor ( #2294 )
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* Add repository validating interceptor outcome to response
* Add a doc
* Add a test and some docs
* Rework validation
2021-01-17 16:40:32 -05:00
dependabot[bot]
391a6d1a3f
Bump ph-schematron from 5.2.0 to 5.6.5 ( #2184 )
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* Bump ph-schematron from 5.2.0 to 5.6.5
Bumps [ph-schematron](https://github.com/phax/ph-schematron ) from 5.2.0 to 5.6.5.
- [Release notes](https://github.com/phax/ph-schematron/releases )
- [Commits](https://github.com/phax/ph-schematron/compare/ph-schematron-parent-pom-5.2.0...ph-schematron-parent-pom-5.6.5 )
Signed-off-by: dependabot[bot] <support@github.com>
* Fix compile error
* Build fix
* Add test logging
* Test fix
* Resolve classpath duplicates
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-17 14:27:26 -05:00
James Agnew
29cf20aac3
Add repo validation outcome to response ( #2293 )
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* Add repository validating interceptor outcome to response
* Add a doc
* Add a test and some docs
2021-01-17 12:50:13 -05:00
vedion
99b646eed7
Mapping noExtensibleWarnings and noBindingMsgSuppressed between FhirInstanceValidator and InstanceValidator ( #2054 )
...
Co-authored-by: ahn <anders.havn@systematic.com>
2021-01-17 09:21:08 -05:00
James Agnew
1dc4fb2206
Make quantity indexes use double datatype ( #2290 )
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* Make quantity indexes use double datatype
* Add changelog
* Test fixes
* Test fixes
* Disable test
2021-01-16 18:44:15 -05:00
Nick
1d7ec3cc13
Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc
2021-01-15 14:18:27 -05:00
jamesagnew
4791c81aec
Improve package loading logs
2021-01-15 06:19:57 -05:00