Commit Graph

444 Commits

Author SHA1 Message Date
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
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
Nick cfc798cb2b Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-22 09:45:04 -05:00
Tadgh edd9769686 Add documentation fixes for MDM-match 2021-01-22 09:17:51 -05:00
Nick b00f47ef81 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-18 09:25:58 -05:00
jamesagnew a08392e6b2 Add license header 2021-01-17 19:10:34 -05:00
James Agnew 29cf20aac3
Add repo validation outcome to response (#2293)
* Add repository validating interceptor outcome to response

* Add a doc

* Add a test and some docs
2021-01-17 12:50:13 -05:00
Nick 759f06ce48 Added optional manual override to link update 2021-01-14 14:24:59 -05:00
Nick 57662eedb3 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-12 09:22:38 -05:00
Ken Stevens 520400d6ea
added IPagingProvider.canSearchByOffset() (#2281)
* init rev

* added IPagingProvider.canSearchByOffset()
consolidated parameters in bundle link methods

* fix refactoring error

* add @Nonnull to BundleLinks parameter

* null check

* fix test

* cleanup

* fix refactoring

* final cleanup

* review feedback

* review feedback

* review feedback
2021-01-11 20:42:41 -05:00
Nick 9338a4e73e Survivorship 5 2021-01-08 19:25:25 -05:00
jamesagnew d20b07c78e Update license headers 2021-01-01 15:50:24 -05:00
jamesagnew f30999b053 License header updates 2021-01-01 15:07:23 -05:00
James Agnew 8f8c5c31f1
Add validation rules interceptor (#2264)
* Start work on validation rules interceptor

* Work on interceptor

* Add tests

* Work on validation interceptor

* Work on interceptor

* Test fix

* Documentation tweaks
2021-01-01 14:29:10 -05:00
Tadgh e79114e2ec
Un-revert the MDM changes, now that issues have been addressed (#2226)
* Backward compatibility changes

* Revert "Revert "Remove all references to Person from EMPI.""

* Updated docs

* Removed mdm channel references

* Initial implementation

* fix coarseness bug. Fix tests. reinitialize silly bean

* Add forgotten json file

* Generic provider PoC

* Refactored provider to use BundleBuilder

* Removed version-specific MDM providers

* Addressed code review comments

* Fixed after merge

* Fixed docs

* MDM SVG for Update Use Cases

* Removed obsolete docs

Co-authored-by: Nick <nick.goupinets@smilecdr.com>
Co-authored-by: Nick Goupinets <73255752+nvg-smile@users.noreply.github.com>
2020-12-17 10:12:53 -05:00
James Agnew 81f6fe9106
Support IBaseBundle as parameetr type for @Transaction method (#2237)
* Support IBaseBundle as parameetr type for @Transaction method

* Add changelog

* Add bundle setter
2020-12-11 18:33:00 -05:00
Tadgh 0938d72b51
Revert "Remove all references to Person from EMPI." 2020-12-09 14:57:00 -05:00
Nick 52fd83c654 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-09 09:14:58 -05:00
jamesagnew 828573b467 Improve synchronization on HashMapResourceProvider 2020-12-09 05:53:47 -05:00
Nick fd90eb699f Review updates 2020-12-07 18:03:56 -05:00
Nick 5c40afb0c9 Updated doc headers 2020-12-03 16:11:10 -05:00
Nick 4352e0a61f Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-03 11:28:21 -05:00
Tadgh a4b2fbd906
Merge pull request #2211 from bdenton/bd-20201202-fix-split-package
Split package: delete 'ca.uhn.fhir.rest.server' package from hapi-fhir-server-empi
2020-12-03 09:02:46 -05:00
James Agnew 1eae5db374
autoCreatePlaceholderReferenceTargets true breaks multitenancy (#2215)
* Fix #2209 - autoCreatePlaceholderReferenceTargets true breaks multi-tenancy

* Add changelog

* Address fixme
2020-12-03 08:53:37 -05:00
James Agnew 7627a86176
Improve version logging (#2213)
* Improve version logging

* Add changelog

* Test fixes
2020-12-02 21:19:04 -05:00
Bill Denton 01ca7f3746 move TransactionLogMessage to hapi-fhir-rest-server bundle (as per
feedback)
2020-12-02 17:22:31 -08:00
Nick Goupinets d63c580e82 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-01 13:18:42 -05:00
James Agnew c309737166
Allow reading from multiple partitions (#2198)
* Partitioning rework

* Work on partition improvements

* Partition updates

* Work on partitiong

* Test fixes

* Add docs

* Add changelog

* Resolve FIXME

* Test fixes

* Test fixes

* Test fixes

* Compile fix

* Fix compile error

* Test fix

* Test fixes
2020-11-30 17:59:52 -05:00
Nick Goupinets 8a7dc4e80b EMPI to MDM 2020-11-27 15:12:21 -05:00
Tadgh 953b662827 Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references 2020-11-19 14:24:51 -05:00
Tadgh 3209faf2fb Rename package and module 2020-11-18 21:55:29 -05:00
jamesagnew 0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew 4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -05:00
Tadgh c0bef70e12 Add optional resource type to EMPI provider method 2020-11-13 16:42:09 -05:00
Tadgh 331acc1b55 Attempting to perform MDM on a new resource type 2020-11-11 14:15:35 -05:00
Tadgh ffbe35e2cd Partial refactor of Provider 2020-11-10 12:26:20 -05:00
Tadgh a67b3a8298 Fixed possible-matcher 2020-11-10 10:46:43 -05:00
James Agnew 8000d2d0cf
SQL Join Rework (#2086)
* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* added the other six index links

* trying different annotations

* Start testing

* Update resources on package install

* Add changelog

* Join rework

* CLean up SQL builder

* Add docs

* SP rework

* Join work

* Work on params

* Work on refactor

* Work on chains

* Work on joins

* Rework queries

* Work on queries

* Many more tests passing

* Refs test

* Work on sorting

* Work on tests

* More joins work

* Work on tests

* Work on queries

* Tests passing

* More test fixes

* Test fixes

* Work on SQL

* Tests passing

* Add some tests

* Add some tests

* License headers

* Use entity manager to get datasourcd

* One more fix

* Model cleanup

* Ongoing work

* Fixes

* Fixes

* Work on joins

* Ongoing fixes

* Merge conflict

* Cleanup

* clean up unused fields

* Work on join

* COmpile fix

* Rework querying

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Resolve fixmes

* Test fix

* Test fixes

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-10-26 05:24:26 -04:00
Ken Stevens 3b91873b7c
delete expunge (#2131)
Added delete _expunge=true
2020-10-20 17:21:50 -04:00
jamesagnew 7903b2b577 License headers 2020-10-13 11:43:09 -04:00
Tuomo Ala-Vannesluoma 1435540320
Improve synchronous searching by providing offset & limit support (#2059)
* Improve synchronous searching by providing offset & limit support

Add support for offset querying which leverages paging at the query level
Add configuration for search default page size and search maximum page size
If using offset, always use synchronous searching to avoid extra database insert/update etc.
When using offset, only calculate count if it's wanted
Validate params closer to provider and handle size if search returned "all" (or last)

* Review and test fixes

Comment _offset as nonstandard parameter
Make synchronous search always count the total value (for now)
Fix issue with FulltextSearchSvcImpl mutating param map
Dirty fix for BaseJpaTest (not sure how to fix the including resources issue)

* Remove temporary count querying fix for synchronous loads

* Fix offsetting of everything operations, do not drop zero offset

* Fix jpa test default and maximum page size, add some fixmes to tests before resolved

* Ignore one failing test, fix others

* Fix Dereferenced variable may be null

* Fix everything paging in R4 by adding DISTINCT if synchronous load is used

Also fix assertion of size when hitting fetchSizeDefaultMaximum

* Add documentation about offset annotation and paging

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-10-12 17:42:03 -04:00
Joel Schneider (NMDP) a32397d993
add CorsInterceptorTest (#2126)
* add simple CorsInterceptorTest

* add relevant exposedHeaders to custom CorsConfiguration

* use SLF4J Logger.info() instead of System.err.println(), and run the test assertions first

* Add logback-classic dependency to test scope, to enable SLF4J logging within unit tests.  (SLF4J defaults to NOP binding if no binding found on classpath, see also http://www.slf4j.org/codes.html#StaticLoggerBinder)
2020-10-12 17:38:31 -04:00
Josh Collins 844624b6dd
RDF Support in HAPI FHIR (#2118)
* RDF Support in HAPI FHIR

* Ability to read/write FHIR resources as RDF (turtle serialization)
* Test suite to test roundtrip-ability of RDF parser

* Add null checks to appease LGTM

* Correct null check logic
2020-10-12 17:16:00 -04:00
James Agnew d2aae361bf
Rewrite deferred interceptor callback framework (#2121)
* Rewrite deferred interceptor callback framework

* Improve deferred handling

* Null guard

* Test fix
2020-10-07 20:08:18 -04:00
jamesagnew edbd089092 Docs update 2020-10-06 05:52:22 -04:00
Tadgh 66a0115340 Missed a space 2020-09-30 11:13:40 -04:00
Tadgh ca52268249 Rename accessors, fix whitespace 2020-09-30 11:11:56 -04:00
Ken Stevens 09d09233ff
empi bugfixes and enhancements (#2104) 2020-09-29 17:27:43 -04:00