Commit Graph

2156 Commits

Author SHA1 Message Date
James Agnew 3d5a8bb3f8
Add UCUM support (#1824)
* Add UCUM support

* Add changelog

* Some cleanup

* Test fix

* Add flywayDB callback

* Add hooks to schema migrator
2020-04-30 15:22:41 -04:00
Tadgh 8f8a8a3dc2 Merge branch 'master' into date-match-bug 2020-04-29 16:17:50 -07:00
James Agnew ededcc18d2
Add Partitioning / Multitenancy (#1807)
* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Add columns

* Work on multitenancy

* Work on muiltitenancy

* Work on multitenancy

* Work on uniques

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* More work on multitenancy

* Work on multitenancy

* Multitenancy work

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Work on docs

* Work on multitenancy

* Work on docs

* DOcs work

* Tenancy docs

* Work on docs

* Finish docs

* Add changelog

* Rename config

* Add migration tasks

* Fix typo

* Migration fix

* One more migration fix

* A couple more migration fixes

* Docs cleanup

* Work on docs

* Bump boot version

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Work on review comments

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Compile fx

* Test fixes

* One more bugfix

* Update operation name

* Add one more constant

* Roll back a change that was causing test failures

* Test fixes

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-04-24 05:45:11 -04:00
James Agnew 5f88d87027
Tweak to #1801 - Normalize double leading zeros in database (#1815) 2020-04-23 09:44:08 -04:00
jamesagnew 8a2b799df0 Test fixes 2020-04-22 08:43:00 -04:00
jamesagnew 6226381595 Merge branch 'master' into ja_20200206_multitenancy 2020-04-21 20:54:56 -04:00
jamesagnew 1f37cdd8cf Address review comments 2020-04-21 20:53:10 -04:00
jamesagnew c7de85339c Work on review comments 2020-04-21 20:18:06 -04:00
Ibrohim Kholilul Islam 3225075f9e
Fix GraphQL Error (#1791)
* add debug log

* add debug log to value iteration

* fix _filter issue on /$graphql, fix dash and underscore issue on /$graphql, and give helpful error message on wrong argument.

* remove debug logging

* implement JpaStorageServicesTest
2020-04-21 15:28:28 -04:00
James Agnew c716216b34
Adjust return type for fluent delete() operation (#1805)
* Add cascading delete to client

* Add changelog

* Client delete should return MethodOutcome

* Rerturn more appropriate type for delete operations

* Refactor cascade detection to be reusable
2020-04-21 15:23:11 -04:00
jamesagnew 4abebf2247 Docs cleanup 2020-04-21 09:28:52 -04:00
jamesagnew bbab016ca6 Rename config 2020-04-20 12:38:04 -04:00
jamesagnew 95b77af570 Merge branch 'master' into ja_20200206_multitenancy 2020-04-20 11:07:10 -04:00
jamesagnew 7248b4e18e Finish docs 2020-04-20 11:02:27 -04:00
jamesagnew cd3e1c5e72 Tenancy docs 2020-04-19 10:15:51 -04:00
jamesagnew 843de42144 Add license header 2020-04-18 11:45:58 -04:00
James Agnew 42c8cd0e38
Add cascading delete to client (#1804)
* Add cascading delete to client

* Add changelog
2020-04-18 11:16:16 -04:00
David Gileadi 37dcf589de Add millis methods to DateClientParam, #1798 2020-04-18 11:15:32 -04:00
jamesagnew 48057b9d8e Merge branch 'master' into ja_20200206_multitenancy 2020-04-17 17:59:48 -04:00
James Agnew 497757501b
Improve search method binding priority (#1802)
* Work on search method binding priority

* Work on method priority

* Work on binding priority

* Test fixes

* Add changelog

* Test fixes

* compile fix

* One more comple fix

* Test cleanup

* Test fix
2020-04-17 09:28:33 -04:00
jamesagnew 25cdbb15c2 Work on multitenancy 2020-04-16 15:33:48 -04:00
jamesagnew d822867a4a Merge branch 'master' into ja_20200206_multitenancy 2020-04-15 22:12:20 -04:00
James Agnew f95f619bdc
Correct two JPA processing bugs (#1801)
* Work on search params on contained

* Add workaround for stored decimals with leading decimal point

* Add changelog

* Cleanup

* Test fix

* Test fix

* One more test fix
2020-04-15 14:22:47 -04:00
jamesagnew c26a5553e9 Multitenancy work 2020-04-12 20:47:32 -04:00
jamesagnew e55ccf88fc Work on multitenancy 2020-04-10 20:01:59 -04:00
jamesagnew 219332e9e3 Work on multitenancy 2020-04-10 11:11:29 -04:00
jamesagnew 432b249225 Add license headers 2020-04-10 11:11:04 -04:00
jamesagnew e0fcbe1df2 Merge branch 'master' into ja_20200206_multitenancy 2020-04-09 11:52:27 -04:00
jamesagnew 879fbb0bf8 Test fixes 2020-04-09 10:34:18 -04:00
jamesagnew 2a43aa3b6c Improve error message reporting for invalid json - Fix #1793 2020-04-09 09:53:13 -04:00
jamesagnew 6baf1995c9 Work on subscription cleanup 2020-04-02 20:30:19 -04:00
Jafer Khan 0021561fb1 Raise an error on including invalid query string parameter(s) in read operations 2020-03-31 20:05:05 -04:00
James Agnew fe48313100
Add response size capturing interceptor (#1776)
* Work on capturing repsonse sizes

* Interceptor complete

* Add changelog

* Test fix
2020-03-30 11:24:10 -04:00
jamesagnew 62d867902f Work on multitenancy 2020-03-29 18:16:04 -04:00
jamesagnew ec6fe70acb Merge branch 'master' into ja_20200206_multitenancy 2020-03-27 05:50:08 -04:00
James Agnew b794618e9d
Avoid a crash encoding contained bundle (#1778)
* Avoid a crash encoding contained bundle

* Add changelog

* Apply same fix to XML

* Fix typo
2020-03-25 21:20:10 -04:00
James Agnew c6d23a8bc6
Add chain on _type parameter (#1772)
* Add chain on _type parameter

* Add changelog

* Test fix

* Address review comments

* Fix azure yaml

* Correct HTTPs in pom

* One more pom tweak

* Test fix

* Try azure again
2020-03-24 09:44:57 -04:00
August Langhout a9b6864988 remove first attempt to fix 2020-03-23 19:09:54 -04:00
August Langhout 2b23a6f2f0 Fix Xml parse issue: do not override the references with global contained resources if they have already been resolved 2020-03-23 19:09:54 -04:00
jamesagnew 0ac434ea5d Add chain on _type parameter 2020-03-23 17:53:30 -04:00
jamesagnew 14316147c5 Resolve some docs issues 2020-03-23 10:34:12 -04:00
James Agnew f89661526c Missed noe rename in #1769 2020-03-22 13:27:04 -04:00
James Agnew c2ae5a8326
Add FHIRPath evaluation interceptor (#1769)
* Add FHIRPath evaluation interceptor

* Add changelog
2020-03-22 12:57:24 -04:00
jamesagnew b3cf323e07 Add docs 2020-03-20 18:30:14 -04:00
James Agnew bde7c356fe
Implement Jackson parser/serializer (#1733)
* [dev] Integration of a Jackson serializer and deserializer - first stage

* [fix] Fixed some serializing issues
[improve] Improved the processing, removed the loggers

* [clean] Removed the JacksonSerializer class, replaced all the Gson classes with Jackson classes

* [clean] Small cleanup

* [improve] Throw a ConfigurationException if the JsonGenerator cannot be created

* [improve] Use the ObjectMapper's `readTree` instead of `readValue`

* [dev] Latest fixes and improvements

* [dev] Use the Jackson serializer

* [clean] Removed the ObjectMapper configuration, for now

* [fix] Use the GsonStructure also for the parsing of a FHIR resource

* [clean] Removed the LinkedList usage

* Work on preparing for merge of #1673

* Resolve build errors

* Work on parser integration

* Tests passing

* Resolve fixme

* CLeanup

* Fix dependency

Co-authored-by: Bogdan Solga <bogdan.solga@gmail.com>
2020-03-17 17:27:26 -04:00
James Agnew 22413911bf
Validation api changes (#1719)
* Validation enhancements

* Work on validation api reworking

* Keep working on validation API

* Keep working on new term API

* Work on validation api

* Ongoing work on validation

* Work on integrating validation

* Work on validation API

* Add to validation API

* Work on validation

* Work on API

* Work on validation

* Work on validation API

* Work on validation API

* Work on validation api

* Work on validation API

* Work on validation api

* Validation API changes

* Work on API

* More work on validationo API

* Work on validation API

* FIxes

* WOrk on validation api

* Work on validation API

* Tests passing!

* More cleanup

* More validation API changes

* Fix intermittent test failure

* Package reorg

* Validation API work

* Work on doocumentation

* Work on API

* More work on new validation API

* Fix errorprone-reported error

* Test fixes

* Documentation updates

* Documentation tweaks

* Work on API

* Bean name adjustments

* Build fixes

* Some test fixes
2020-03-17 13:28:59 -04:00
Ken Stevens 6b019492fe
Merge pull request #1758 from jamesagnew/ks-20200312-json-annotation
moved common Json annotations out into an interface
2020-03-13 15:58:21 -04:00
James Agnew 1dc5d89013
Optmize forced ID resolution (#1754)
* Add forced ID caching

* Work on id optimization

* Test fixes

* More optimization work

* Add some docs

* Work on docs

* Test fixes

* Test fixes

* Test fixes

* Address review comments

* Compile fix
2020-03-12 17:12:50 -04:00
Ken Stevens ecf5284c87 moved common Json annotations out into an interface 2020-03-12 13:36:34 -04:00
Tadgh 828ddd5185 Update docs 2020-03-04 12:14:55 -08:00
James Agnew 4a160a2df3 Merge branch 'master' into ja_20200206_multitenancy 2020-03-03 09:25:19 -05:00
James Agnew ac9a371f18 Add test 2020-03-03 08:28:04 -05:00
James Agnew 5bc554949b
Remove deleted resources from cached search results (#1732)
* Remove deleted resources from cached search results

* Add changelog

* Add tests
2020-02-28 10:57:26 -05:00
Gary Graham b1d7072c42 Add precision checker for ordinal date returning on DateRangeParam 2020-02-26 22:22:42 -05:00
Gary Graham 165f5fd808 fix bugs in calculating ordinal date 2020-02-26 09:32:20 -05:00
Gary Graham 97c98254d0 Extract Common functionality out of CalculateHashesTask, build CalculateOrdinalDatesTask based on it 2020-02-25 16:09:08 -05:00
Gary Graham 3ec772b527 rework ResourceIndexedSearchParamDate constructor to support incoming string values 2020-02-25 14:06:36 -05:00
Gary Graham 34d5925393 Move common work to DateUtils. Rename function for clarity. 2020-02-25 09:37:57 -05:00
Gary Graham 7f5b3394e0 Hacky first-pass of adding ordinal date field to ResourceIndexedSearchParamDate and using it for search 2020-02-24 19:34:16 -05:00
James Agnew 60f16dd91d
Update to 4.3.x core JAR (#1715)
* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Start working on converter

* Account for compile errors

* Test fix

* Work no validator

* Work on getting core working

* Add some test coverage

* Many test fixes

Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
2020-02-17 14:28:29 -05:00
jamesagnew ddc7b601ee Version bump to 4.3.0-SNAPSHOT 2020-02-16 19:23:22 -05:00
jamesagnew 4fd80cfca7 Bump to 4.2.0 2020-02-16 19:00:15 -05:00
James Agnew ebf395bee9 Merge branch 'master' into ja_20200206_multitenancy 2020-02-09 08:40:29 -05:00
jamesagnew f7ec41ffc5 Work on multitenancy 2020-02-09 08:40:15 -05:00
James Agnew c5c1e3196b Resolve FIXMEs (#1705)
* Resolve FIXMEs

* Test fixes

* Test fixes

* Clean up unused code

* Add some test coverage

* Test fix

* Test fix

* Avoid intermittent
2020-02-09 08:39:46 -05:00
James Agnew b2d2346228 Work on multitenancy 2020-02-07 15:18:06 -05:00
Ken Stevens 2545fc6e3d Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml
2020-01-29 17:06:02 -05:00
dionmcm 00fdc978cc narrative gen removed old code and enhanced error message
I ran into an issue trying to use the old .class style property. The validation message was useful, but I spotted some unreachable code investigating which I've removed. I also enhanced the configuration exception to indicate what was wrong with a supplied key and expected extension types.
2020-01-29 05:58:22 -05:00
Ken Stevens f2e8037c90 Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search 2020-01-22 15:06:52 -05:00
James Agnew 39ff698dd2
Parser performance tweaks (#1660)
* Parser improvements

* Parser tweaks

* Fix test

* Add changelog

* Bump spring mvc version

* Bump spring version

* Test fix?
2020-01-22 14:44:12 -05:00
Ken Stevens 9413e8f198 r4 works. But distance calculation still needs to be fixed. 2020-01-22 11:59:03 -05:00
James Agnew c0e929dacb
Copy identifiers to placeholder resources (#1675)
* Copy identifiers to placeholder resources

* Add tests

* Maven cleanup

* Still messing around with azure

* Adding to logging

* More azure work

* One more attempt

* More messing around with azure

* Test fix

* Another caching attempt

* More work on azure pipeline

* Fix pipeline file

* Keep working on pipeline

* More work on azure

* More azure

* More azure work

* More azure
2020-01-21 06:09:06 +09:00
jamesagnew 634458c447 License header update 2020-01-17 00:16:56 -05:00
James Agnew 0385c25aa3 Fix FHIR version defaults 2020-01-15 14:03:59 +08:00
James Agnew 1390ea3c06
Update FHIR R5 structures to 4.2.0 version (#1665)
* Work on upgrading core

* Work on R5 updates

* Work on core updates

* Test fix

* Update model version properties file for R5

* Bump core version

* Test fixes

* Add 4.2.0-SNAPSHOT version to versions page in docs
2020-01-14 10:27:01 +08:00
Petro Mykhaylyshyn 8ed3dcc9ac [(fixjsongenerationtomaster)] Remove unused import. 2020-01-13 13:37:54 +08:00
Petro Mykhaylyshyn fdab81361c [(fixjsongenerationtomaster)] When max cardinality in profile is changed to 1 output JSON contain an array. 2020-01-13 13:37:54 +08:00
Petro Mykhaylyshyn a234b1f8a9 [(fixjsongeneration)] When max cardinality in profile is changed to 1 output JSON should still contain an array. 2020-01-13 13:37:54 +08:00
jamesagnew 3ac4172bc4 License header versions 2020-01-11 23:23:02 -05:00
Diederik Muylwyk 8615d10730 Fix typo. 2019-12-31 09:27:26 -05:00
Diederik Muylwyk 48f7ee5afb Rolling back previous unnecessary changes. 2019-12-31 09:25:56 -05:00
Diederik Muylwyk 170b607992 Added some FIXMEs. 2019-12-30 18:43:15 -05:00
Diederik Muylwyk 856993edf8 Moved changelog entry, and added clarifying comments to DateRangeParam. 2019-12-30 15:29:35 -05:00
Diederik Muylwyk 4eaeb7ef9e Implemented isDateWithinRange() and supporting methods. 2019-12-30 14:35:51 -05:00
Diederik Muylwyk d8133487b2 Initial commits. 2019-12-23 17:14:47 -05:00
James Agnew e1f2d044ed Add errorprone back into build 2019-12-15 09:42:51 -05:00
jamesagnew ba8f50f0c8 Docs updates 2019-12-14 18:19:09 -05:00
James Agnew d277d3fed5 Docs updates 2019-12-10 16:10:09 -05:00
James Agnew f58fba6f04
Some test cleanup (#1616)
* Some test cleanup

* Add test

* More test logging

* More docs cleanup

* Add test logging
2019-12-02 11:00:18 -05:00
James Agnew 86bd9a28fe
Fix to valueset expansion logic (#1613)
* Fox to valueset expansion logic

* Work on docs

* Docs tweaks

* Docs tweaks

* Fix test

* Remove unused class

* Add changelog
2019-12-01 21:21:19 -05:00
James Agnew ca620d652f
Add tests (#1606)
* Support chained HAS

* Add some tests

* Add some cleanup

* Work on intermittent tests
2019-11-24 10:11:49 +01:00
James Agnew 51b608188b
Some CI surefire improvements (#1602)
* Some CI surefire improvements

* Build tweak

* More tweak

* Update azure-pipelines.yml for Azure Pipelines

* Update azure-pipelines.yml for Azure Pipelines

* One more CI attempt

* Update azure-pipelines.yml for Azure Pipelines

* Tweak command line

* Another build test fixc

* More build cleanup
2019-11-23 19:51:02 +01:00
James Agnew a2f77b23d2
Fix #1583 - Index local refs in canonical types (#1593)
* Fix #1583 - Index local refs in canonical types

* Add fix to pre-expansion

* Test fix

* Rework ID handling

* Test fixes

* Fix test
2019-11-23 16:32:37 +01:00
James Agnew 74159dcb26
Work on refactoring how PIDs work (#1580)
* Start work on refactoring how PIDs work

* Some test fixes

* Test fixes

* Test fixes

* Restore accidentally deleted line

* One more tweak

* Rework resource link extraction

* Test fix

* Split out transaction processor

* Updates

* Test fix

* Test fixes

* Test fixes

* Clean up LGTM warning

* Fix compile failure

* One more test fix

* Fix LGTM issue

* Add spot for metadata

* Add test logging

* Remove testing code

* More test logging

* Add some test logging

* Attempty to fix intermittent test failure

* Improve exception tracking

* Work on simplifying search param registry

* Fix compile

* Fix compile errors

* Fix two test bugs
2019-11-17 14:35:19 -05:00
James Agnew 497a96ae68 Version bump for next round of development 2019-11-12 22:09:21 -05:00
jamesagnew f99ad981b5 Version bump to 4.1.0 2019-11-12 16:08:20 -05:00
James Agnew aa0301084b
Don't succeed validation on unknown codesystem (#1575)
* Don't succeed validation on unknown codesystem

* Test fixes

* Work on error messages

* Work on code validation API

* work on tests

* Work on validation

* Test fix

* Update DSTU3 validation reources

* Upgrade structures

* Test fixes
2019-11-12 14:35:49 -05:00
James Agnew 1a348abaf5 Try to fix 2 intermittent test failures 2019-11-08 08:45:08 -05:00
jamesagnew 7c8342dcc1 Add some test logging 2019-11-08 05:53:59 -05:00
James Agnew ebc52e6b48 Correctly handle below expansion with missing system 2019-11-07 09:28:24 -05:00