Commit Graph

2939 Commits

Author SHA1 Message Date
jamesagnew 5de955c3c2 Licence header updates 2021-11-09 08:44:18 -05:00
TipzCM 59bf8b836f
Issue 3120 support adding retry extension (#3137)
* issue-1134 initial work on adding retry handler

* issue-1134 subdscription creation fixes

* issue-1134 update the test

* issue-1134 retry policy off canonicalsubscription

* issue 1134 base subscription changes

* add failing test

* issue 1134 retry configs on base parameters

* issue 1134 passing forward params

* issue-1134 added more tests for making sure subscriptions create their channels correctly

* issue-1134 updates to get the retry to channels

* issue-1134 updating channel factory

* issue-1134 remove the dlq since it's not defineable

* issue-3120 changelog added

* issue-3120 cleaning up

* issue-3120 test fix

* issue-3120 review fixes

* issue-3120 fixed bad master merge

* issue-3120 updates for new release

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-11-03 18:21:10 -04:00
Tadgh a10c58e839
Bump version, add version to versionenum (#3135) 2021-11-02 09:40:56 -04:00
Tadgh 362c2f30db
Add 5.5.3 to versionenum (#3133) 2021-11-01 13:50:57 -04:00
Tadgh 7c63441663
Revert "Issue 1134 retry mechanic on subscriptions (#3121)" (#3128)
This reverts commit 9b23e9e825.
2021-10-30 19:46:42 +00:00
TipzCM 9b23e9e825
Issue 1134 retry mechanic on subscriptions (#3121)
* issue-1134 initial work on adding retry handler

* issue-1134 subdscription creation fixes

* issue-1134 update the test

* issue-1134 retry policy off canonicalsubscription

* issue 1134 base subscription changes

* add failing test

* issue 1134 retry configs on base parameters

* issue 1134 passing forward params

* issue-1134 added more tests for making sure subscriptions create their channels correctly

* issue-1134 updates to get the retry to channels

* issue-1134 updating channel factory

* issue-1134 remove the dlq since it's not defineable

* issue-3120 changelog added

* issue-3120 cleaning up

* issue-3120 test fix

* issue-3120 review fixes

* issue-3120 fixed bad master merge

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-10-29 11:21:43 -04:00
Tadgh 8a7b5c1b2f
Multiple improvements (#2997)
* Add failing test

* Tidy test for new tokenparam style

* Add removeByQualifier to SearchParameterMap

* Add new property binder for search terms

* Member move, add test for new parser

* whoops missed an add

* Passing test.

Introduced SearchParamTextWrapper to give a type for the binder.
Enhance FulltextSearchSvcImpl to understand TokenParams as well as StringParams.

* Add more to test, change analyzer for template

* Optimize imports

* Minor refactoring

* added eq and gt test cases

* added missing gt search param tests

* Search all CodeableConcepts

* Extract new LuceneRuntimeSearchParam to mediate indexing and searching.

* Fix up broken test with mock

* Add support for identifier type

* Bump for special maven package

* fix-me to todo

* Prevent version check

* FIx version for test

* DSTU2 does not support fluent path

* Don't accidentally strip SPs in DSTU2

* added lt tests

* Add some high-bound test cases

* More test cases and new compressed format

* More test cases

* More test cases

* Re-order columns for easier reading

* Comments

* Cleanup and comments

* Make support :text for all token SPs

* Make support :text for all token SPs

* Fixed incomplete date issue

* Set to the last millisecond 23:59:59.999

* Disabled 4 failed JVM/TZ related test cases

* add test for failing batch bug, remove bounding on queue

* remove parallelism from non-get batch operations

* Fix count for test

* New index layout

* Notes and cleanup

* Notes and cleanup

* remove the jetbrains

* Demote FIXME to WIP

* Change :text search to be lucene simple search and use standardAnalyzer.

* Change :text to require * for prefix match.

* add prefix negative test

* Bump version

* Added changelog

* Add more search parameters to lucene indexing (#3000)

* dirty the branch

* Add oversight to changelog

* Start using jpa indexing for es

* Correct negative search test

* Update templates, index tokens, write new test. TODO gotta modify SB

* Add test for code token search

* add comment

* Flesh out token search

* minor cleanup and comments

* Extract index handling from FulltextSearchSvcImpl

* D'oh.  Actually use elastic to search.

* Move supported query check closer to query builder

* String search test before activating lucene

* Add string:exact to hibernate search.

* Add string:contains search

* cleanup

* demote fixmes to allow build to run.

* Add unmodified string search.

* empty stubs for quantity and reference

* Ignore magic search params in lucene index

* Support full-text on all FHIR releases

* Include reference lookups in ES

* Fix and/or logic in _text

* Test for string with space

* Cherry-pick the NoFT fix

* Disable advanced indexing in a bunch of tests of emitted sql.

* Stub changelog

* Fix :missing flag

* Move DaoConfig up to BaseJpaTest to share teardown

* Disable new indexing for partition test

* Add a different analyzer and field for default string search vs text

* checkstyle for a pre-build

* Index full prefix for string search when using Lucene

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3000-Extend-lucene-indexing.yaml

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

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

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Review feedback.

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Remove double-check

* Version bump

* Fix typo

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Long Ma <longma@Longs-MacBook-Pro.local>
Co-authored-by: Frank Tao <frankjtao@gmail.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-10-28 15:13:16 -04:00
jamesagnew 58071aa1b3 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2021-10-26 16:50:10 -04:00
jamesagnew 1792b74b50 Inforporate version checks 2021-10-26 16:49:49 -04:00
James Agnew 9e057574a6
Allow multi-resource Subscription criteria (#3110)
* Allow start criteria subscriptions

* Rework subscription tests

* Subscription cleanup

* Add changelog

* Test fixes

* Test fix
2021-10-26 16:48:13 -04:00
michaelabuckley f98f3cdaa9
Extend ordinal date search to year and month precision (#3102)
* added eq and gt test cases

* added missing gt search param tests

* added lt tests

* Add some high-bound test cases

* More test cases and new compressed format

* More test cases

* More test cases

* Re-order columns for easier reading

* Comments

* Cleanup and comments

* Fixed incomplete date issue

* Set to the last millisecond 23:59:59.999

* Disabled 4 failed JVM/TZ related test cases

* Added changelog

Co-authored-by: Long Ma <longma@Longs-MacBook-Pro.local>
Co-authored-by: Frank Tao <frankjtao@gmail.com>
2021-10-21 15:32:26 -04:00
Tadgh 3d681134e9
Add SearchBundleEntryParts (#3095)
* Add the ability to parse a search bundle into its component parts

* remove deadspace

* wip
2021-10-19 23:41:33 +00:00
Tadgh b427135b04
Patient/$everything _id parameter (#3077)
* Add tests. Add implementation in R4. Add changelog

* Wip partial fixup of other STU versions

* Updated usages of new patient type everything api

* Partial commit of incomplete documentation

* Remove docs

* Cut to token instead of string

* Bump hapi version due to breaking api changes
2021-10-17 14:34:33 +00:00
Ben Li-Sauerwine 2e5aed4016
Adds a NDJSON parser, in preparation for adding NDJSON $import to HAPI (#3022)
* NDJsonParser with one example test.

* Add test for empty NDJson, and fix bug for empty NDJson.

* Adds multi-Patient test, and fixes bug whereby all multi-line NDJSON would be put into the same line.

* Adds test for NDJson with newlines in it.

* Adds test for converting non-Bundle types to NDJSON failing.

* Confirm that we can only extract to Bundle types in test.

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java

Co-authored-by: James Agnew <jamesagnew@gmail.com>

* Documents behavior of the NDJsonParser in FhirContext.

* Attempt to fix failing build by using TestUtil to clear context in the manner of r4 parser tests instead of dstu

Also clean up indentation.

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-10-17 09:06:31 -04:00
Jing Tang b25b186044
Remove the unused dependency on net.sf.saxon:Saxon-HE (#3043)
* Remove the unused dependency on net.sf.saxon:Saxon-HE

* Remove Saxon-HE dependency in hapi-fhir-jpaserver-base

* Remove unused comment in hapi-fhir-structures-dstu2.1/pom.xml
2021-10-14 16:34:48 -04:00
Tadgh 87e594d416
Bump JENA to deal with CVE-2021-29349 (#3063) 2021-10-13 16:17:43 -04:00
Tadgh d2ea4655a7
Rel 5 5 2 (#3060)
* Add versionenum, bump maven version

* failing tests

* more logs

* Add more test cases, not passing

* fixed the double chain with contained resource second case

* clean up a bit

* add tests for qualifiers

* force the resource table to be the root of the query if we might be traversing a contained reference

* tidy up

* tests for longer chains

* changelog

* code review feedback

* backport changelog

* Add version.yaml

* [2935] Escape "%" in like expression

* Add backport to changelog

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
2021-10-12 14:25:03 +00:00
James Agnew 310a4cdb58
Migrate CLOB columns to LOB (SMILE-3072) (#3016)
* Migration finished

* Work on LOBS

* Add to ClobMigrated annotation

* Deal with lobs

* Work on new approach

* HAPI FHIR version bump

* Add changelog

* Add license header

* Fix intermittent

* CLeanup

* Cleanup
2021-10-11 16:47:37 -04:00
TipzCM a474e88ed4
issue-2397 implementing the mdm expansion on everything and searches (#3044)
* issue-2397 implementing the mdm expansion on everything and searches

* issue-2397 code cleanup and removal of test code

* issue-2397 some tests

* issue-2397 changelog added

* issue-2397 review fixes

* issue-2397 updated change log with example and fixed failing tests

* issue-2397 test fixing

* issue-2397 fixing test

* issue-2397 review fix

* issue 2397 fixing changelog file

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-10-07 10:46:23 -04:00
James Agnew d320b78ae1
Improve synthea ingest performance (#3033)
* Improve synthea ingest performance

* Tweaks

* Fix param splitting

* Update to test

* Add changelog

* Test fix

* Add some runtime checks

* Remove useless test

* Test fix
2021-10-04 05:46:06 -04:00
jamesagnew d4f01ac4e7 License header updates 2021-10-03 20:20:04 -04:00
James Agnew eca725afa4
Improve versioned URL support for ValueSet expansion (#2994)
* Add test

* Test fixes

* Work on expansion errors

* Fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Work on fix

* Test fixes

* Test fixes

* Test fix

* Cleanup

* Test fixes

* Remove accidental commit

* Test fixes

* Version bump

* Add changelog

* Fixes

* Test fix

* Fix conflicts
2021-10-03 19:47:23 -04:00
James Agnew 95e853bdf7
Improve parallel model scanning (#3046)
* Improve parallel model scanning

* Add changelog

* Resolve fixme

* Test fix
2021-10-03 19:40:24 -04:00
Ken Stevens b1dd40fdba
Try commenting out clearAllStaticFieldsForUnitTest to see what happens (#3034)
* Try commenting out clearAllStaticFieldsForUnitTest to see what happens

* Rename clearAllStaticFieldsForUnitTest to randomizeLocaleAndTimezone and only do that
2021-09-24 16:01:28 -04:00
Ken Stevens 53c7476dae
hapi storage (#3024)
* first pass moving core storage classes to storage-api

* move term service apis

* nearly done

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* create new SearchConstants class to store platform independent search constants

* move a couple of subscription services

* move transaction processor adapter to storage

* version bump

* move searchparam

* fix test

* fix compile includes

* fix text

* fix docs
2021-09-23 22:04:46 -04:00
Tadgh a12ce73797 Add more tests 2021-09-21 15:31:36 -04:00
James Agnew 7379dee3d8
Merge branch 'master' into add-device-to-patient-compartment 2021-09-21 14:38:39 -04:00
Ken Stevens 060791aeb4
hapi-fhir-storage-api (#3006)
* rename hapi-fhir-jpaserver-migrate to hapi-fhir-sql-migrate and move hapi-tasks into jpaserver-persistence

* rename hapi-fhir-jpaserver-api to hapi-fhir-storage-api

* move bulk import apis

* create hapi-fhir-jpa

* create hapi-fhir-jpa

* move CircularQueueCaptureQueriesListener to japi-fhir-jpa

* move mdm logs to storage-api

* move gziputil to storage-api

* move quartz scheduling to hapi-fhir-jpa

* move default subscription channel factory to storage-api

* consolidated batch constants

* correct accidental Logs change

* remove dependency of cdr-api on cdr-persistence

* fix javadoc

* pom descriptions

* review feedback
2021-09-21 15:36:08 +00:00
Jaison B 8bb9aca8df Merge branch 'master' into 2849_add_new_mdm_param 2021-09-17 10:18:24 -06:00
Tadgh 3d24a4ce16 Refactor to support arbitrary additional SPs based on Type for a compartment 2021-09-14 01:02:19 -04:00
Ken Stevens eee7d7e455
code cleanup (#2986)
* failed attempt to get it to work

* Use simplified FhirContext.forCached methods

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java

Co-authored-by: James Agnew <jamesagnew@gmail.com>

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-09-13 03:09:18 +00:00
James Agnew 5554431146
Avoid dead SearchParameter links in CapabilityStatement (#2790)
* Avoid dead SearchParameter links in CapabilityStatement

* Resolve fixmes

* Build fix

* Test fix

* Test fix

* Test fix

* Work on metadata

* Fixes

* Test fixes

* Test fix

* Test fix

* Test fixes

* Test fix

* Work on test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fix params

* Resolve fixme

* Adjust changelogs

* Version bump to 5.6.0-PRE7

* Add license header

* Bump version to 5.6.0-PRE5-SNAPSHOT
2021-09-11 18:27:18 -04:00
Tadgh 0ccd71faf8
Merge pull request #2963 from hapifhir/custom-elastic-index
Custom elastic index
2021-09-08 14:29:58 -04:00
Tadgh f04cf02be7
Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-08 08:45:47 -04:00
Tadgh 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -04:00
Nick Goupinets 35aaa98431 Merge branch 'master' into 2849_add_new_mdm_param 2021-09-07 11:27:49 -04:00
Ken Stevens 346e29920a
Issue 2927 convert mdm clear to spring batch (#2929)
* initial roughout of mdm clear batch job

* still roughing out classes

* finished first draft of reader

* most tests passing now

* all tests pass.  now FIXMEs

* FIXMEs done.  Time for regression.

* fix test

* changelog and docs

* fix test

* pre-review cleanup

* version bump

* move spring autowire deps for cdr

* move spring autowire deps for cdr

* finally got beans working phew

* rearrange method calls so persistence module can perform clear operation on its own

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* review feedback

* review feedback

* Remove inheritance

* fix beans

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2021-09-03 14:58:19 -04:00
Nick Goupinets ee65a24260 Merge branch 'master' into 2849_add_new_mdm_param 2021-09-02 17:42:41 -04:00
leif stawnyczy 1a7b101d03 Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-02 10:13:04 -04:00
Tadgh 3e288f1dde Merge branch 'master' into rel_5_5_1 2021-09-01 18:16:27 -04:00
Tadgh e1272a3825 Bump version of HAPI-FHIR 2021-08-31 11:43:17 -04:00
Tadgh 87986d3da8 Add versionenum 2021-08-31 11:42:26 -04:00
Nick Goupinets 8403b85429 Merge remote-tracking branch 'origin/master' into 2849_add_new_mdm_param 2021-08-27 09:42:08 -04:00
Frank Tao 090a8b0821
Impl displayLanguage for $lookup (#2908)
* Impl displayLanguage for $lookup - first cut

* Added original lookupCode method

* Added original lookupCode method to IFhirResourceDaoCodeSystem

* Added more test cases and changelog
2021-08-25 14:47:10 -04:00
leif stawnyczy b51c722755 stashing minor refactors 2021-08-25 10:41:58 -04:00
Tadgh 37ad73a422 Bump PRE version so we don't conflict downstream 2021-08-23 15:42:18 -04:00
Tadgh 1acaf325c5 Merge branch 'master' into rel_5_5_0 2021-08-23 14:50:29 -04:00
Nick Goupinets 3a5e391c77 Fixed pointcut def 2021-08-23 11:00:04 -04:00
Nick Goupinets 4cfe11a221 Merge branch 'master' into 2849_add_new_mdm_param 2021-08-16 13:33:57 -04:00
Tadgh cf917d0f82 Version Bump 2021-08-15 16:54:38 -04:00
Tadgh 669cf05b30 Modify SearchParameterMap toNormalizedQueryString to include value of _contained parameter 2021-08-12 14:25:12 -04:00
Tadgh fa2b4ea0d7 Add version number 2021-08-06 14:08:10 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -04:00
Tadgh 0a303a0e11 Add MDM expansion by golden pid 2021-08-06 13:22:08 -04:00
Nick Goupinets d467c1c79b yMerge branch 'master' into 2849_add_new_mdm_param 2021-07-30 11:18:33 -04:00
Ken Stevens f5dfc3a5ed
New reindex spring batch operation (#2845)
* first sweep to add new $reindex job

* first cut done.  next up integration test.

* start roughing out reindex everything

* Failing test

* test passes

* add BundleUtil helper method

* rough in processEverything

* rough in processEverything

* fix mock test

* merge master

* Make BaseJpaTest.mySrd lenient.

* fix test

* reindex everything works with FIXMEs

* reindex everything more tests

* moar tests

* moar tests

* fix test

* fix test

* fix regression and fix test

* fix test cycle

* fixme

* fix test

* test provider layer

* reindex everything partition aware

* yay last fixme!

* run reindex in partitioned threads

* add fixmes for areas that require extra testing

* added transaction and log message

* manual integration testing

* changelog

* reindex all partitions

* bump hapi version

* fix test

* moar test

* pre-review cleanup

* fix javadoc

* review feedback

* review feedback

* review feedback

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2845-reindex-operation.yaml

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* review feedback

* review feedback

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/ResourceSearch.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/IDeleteExpungeJobSubmitter.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-07-29 19:18:49 -04:00
Nick Goupinets a2aa2ca1c3 2849 Added new parameter to MDM processing 2021-07-29 15:52:27 -04:00
James Agnew f957661dda
Patient ID Partition Mode should support conditional create (#2828)
* Fixes

* Test fix

* Add changelog

* Test fixes

* Test fixes

* Docs tweak

* Partitioning fixes

* Import fix

* Fix test data
2021-07-26 14:18:58 -04:00
jamesagnew a5e6674e84 Version bump to 5.5.0-PRE7-SNAPSHOT 2021-07-22 08:41:16 -04:00
James Agnew 6d37749be8
Add non unique combo search params (#2809)
* Start work on nonunique combo search params

* Work on SQL

* Version bump

* A fix

* Test fixes

* Fixes

* Undo version bump

* Test fixes

* Resolve fixme
2021-07-21 19:14:14 -04:00
juan.marchionatto 1e9163c636 Add changelog. Address MR comments. 2021-07-08 14:52:19 -04:00
jmarchionatto ee1f1fb5b8
Merge pull request #2778 from hapifhir/2777-hapi-fhir-cli-Add-option-to-pass-request-headers-to-target-server
Add header-passthrough option to hapi-fhir-cli commands which generate http requests(#2777)
2021-07-07 16:47:28 -04:00
James Agnew 95306c3d64
Add NPM validation support module (#2782)
* Add NPM validation support module

* Add changelog
2021-07-07 16:28:41 -04:00
Tadgh 3e7bc2a81e
Forward port 5 4 2 (#2781)
* Add new version to enum

* Add backport tags, new VersionEnum, and new release folder for 5.4.2
2021-07-07 10:10:07 -04:00
juan.marchionatto 5c5bd1ec6c Organize imports 2021-07-06 09:31:53 -04:00
juan.marchionatto 5f36fe56b0 Add header-passthrough option to hapi-fhir-cli commands which generate http requests.
Add class to parent request-generating commands.
Allow ValidationResult to be set number of detected errors to inform.
2021-07-05 16:08:03 -04:00
James Agnew d762a07817
Partition patient interceptor (#2766)
* Start work on interceptor

* Implemented

* Add interceptor and docs

* Add docs

* Compile fix

* Test fixes

* Test cleanup

* Test fixes

* Test fixes

* Improve error message

* Add broken tests

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2766-add-patient-id-compartment-interceptor.yaml

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptor.java

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Address review comments

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-07-05 09:15:20 -04:00
jamesagnew 6bb5cbf764 Cleanup logging 2021-07-04 15:31:10 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
Tadgh 8f3cbb0a7f Refactor docs 2021-06-30 14:48:13 -04:00
James Agnew 8379392e16
Add inline tag mode (#2748)
* Start work on tag mode 3

* Add changelog

* Test fix
2021-06-22 23:08:09 -04:00
jamesagnew f0cfb5ad1b License headers 2021-06-21 05:29:02 -04:00
James Agnew 6ea1438f1d
Add transaction write semaphore interceptor (#2743)
* Add transaction write semaphore interceptor

* Add changelog

* Test fix
2021-06-20 12:55:49 -04:00
James Agnew 8b205b23d0
Fix history paging (#2741)
* Fix history paging

* Add changelog

* Add license header
2021-06-18 17:47:51 -04:00
Ken Stevens 134631fdee
Convert delete expunge to use Spring Batch (#2697)
* prepare to add $delete-expunge operation that will create a spring batch job

* Add operation

* Wire up jpa provider.  Begin with failing test.

* Copy/paste bulk import job as a starting point.
FIXME with proposed design

* delete expunge job parameter validation with test

* implemented reader
stubbed processor, writer

* wip for master merge

* started implementing reader

* started implementing reader

* working with stubs

* happy path batch delete expunge is done

* Provider done but test not passing.  Guessing batch infrastructure not running in that test.

* IT test works now

* add reader test

* Converted delete _expunge=true to use new batch job

* DeleteExpungeDaoTest passes

* Fix test

* Change batch size to integer

* rename search count to batch size

* Make delete expunge partition aware

* updated docs

* pre-review cleanup

* change log

* add partition id to SystemRequestDetails

* Make RequestPartitionId serializable

* Change delete expunge provider to use partition id instead of tenant name

* fix tests

* test pointcut gets called

* assert on pointcut calls

* Add resource type to STORAGE_PARTITION_SELECTED pointcut

* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants

* bump hapi-fhir version

* copyrights

* restore deleteexpungeservice for mdm

* restore deleteexpungeservice for mdm

* fix test

* public constants

* convert instant to date

* Moved expunge constants to ProviderConstants

* final review

* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run

* fix tests

* fix tests

* fix tests

* fix tests

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* improve logging

* bump version

* version bump

* recovering from failed merge

* unzip RequestListJson per Gary's suggestion.  I didn't want to do it at first, but as usual Gary was right.

* fix serialization
2021-06-15 10:36:05 -04:00
jamesagnew 376a84d213 Version bump 2021-06-14 13:12:34 -04:00
jamesagnew 48eea5a7cc Prepare changelog for 5.4.1 release 2021-06-14 09:13:41 -04:00
Nick Goupinets 3863e82a59
Fixed bug with choice children (#2714) 2021-06-08 08:24:13 -04:00
James Agnew dc627dc019
Add bulk export authorization layer (#2712)
* Add bulk export authorization layer

* Add docs

* Version bump

* Authorize any

* Add bulk export - all

* Address lgtm issue
2021-06-06 20:47:43 -04:00
James Agnew 62be623cf5
Add support for ICD-10-CM (#2702)
* Add support for ICD-10-CM

* Have this working

* Fix LGTM issues

* Test fix
2021-06-03 19:55:16 -04:00
James Agnew 1d2b47c9fb
Update endpoint validation interceptors (#2698) 2021-06-02 05:39:01 -04:00
James Agnew fe763dd2d6
Upgrade deps (#2695)
* Upgrade deps

* Fix build error

* Branch tweak

* Build fix

* Build fix

* Undo bump

* Test fixes
2021-06-01 12:03:29 -04:00
James Agnew 05ac88bc21
Add initiate bulk export pointcut (#2692)
* Add initiate bulk export pointcut

* Add changelog

* Test fixes
2021-05-31 16:05:09 -04:00
James Agnew a2950324ef
Avoid SQL based transaction dupe check (#2688)
* Avoid SQL based transaction dupe check

* Add changelog

* Test fixes

* Test fixes
2021-05-30 20:26:36 -04:00
jamesagnew 8636e4f155 Test fix 2021-05-27 07:30:09 -04:00
James Agnew 7a83c76e65
Add validation suppression mode (#2675)
* Add validation suppression mode

* Add changelog

* Compile fix
2021-05-26 17:41:48 -04:00
Nick Goupinets 80be95dd07 Accounted for uninitialized fields - part 3 2021-05-21 13:32:23 -04:00
Nick Goupinets d0d0ff9890 Accounted for uninitialized fields 2021-05-21 12:00:01 -04:00
Nick Goupinets e243674f5d Accounted for uninitialized fields 2021-05-21 11:54:04 -04:00
Nick Goupinets 995ac96f73 Can't think today 2021-05-20 17:21:04 -04:00
Nick Goupinets 8a7fc58e91 Fixed primitive field merging 2021-05-20 15:48:00 -04:00
jamesagnew ff2698d4d1 Merge branch 'rel_5_4' 2021-05-19 09:22:11 -04:00
jamesagnew de56f440cb Version bump 2021-05-18 17:14:14 -04:00
James Agnew 40ecafcd31
Don't unescape plus in match URLs (#2658)
* Don't unescape plus in match URLs

* Perf improvements

* Add changelog

* Test fix

* Work on tests

* Fixes

* Test fix
2021-05-16 21:51:23 -04:00
jamesagnew 2068372998 Version bump 2021-05-07 17:43:54 -04:00
jamesagnew 63c4b22cd3 Undo bump 2021-05-07 17:42:50 -04:00
jamesagnew 17e41520a4 Version bump 2021-05-07 17:41:39 -04:00
James Agnew 970a9884f0
Avoid tag definition constraint (#2620)
* Avoid tag definition constraint failure

* Version bumps

* Add changelog

* Avoid guava issue

* Test fix

* Test fix

* Bump pom
2021-05-01 17:16:15 -04:00
Nick Goupinets d67537231c Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-29 13:55:48 -04:00
James Agnew 95d7ba6fa8
Streamline Search SQLs (#2576)
* Streamline SQL queries

* SQL query tidying

* Add changelog

* Test fixes

* Tests passing

* Ongoing work

* Test fixes

* Test fixes

* Build fix

* Cleanup

* Fixes
2021-04-28 10:29:09 -04:00
Nick Goupinets 21d8cdfefc Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-28 10:16:27 -04:00
Tadgh ac1d4e3e4f
Merge pull request #2542 from hapifhir/issue-2534-new-tx-pointcut
Add new pointcut for transaction processing completed.
2021-04-27 18:42:19 -04:00
Nick Goupinets 024f553fc9 Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-27 09:31:42 -04:00
Nick Goupinets 82bf8cdc9d Code review updates 2021-04-27 09:29:08 -04:00
jamesagnew 1d054054c7 Test fixes 2021-04-27 07:03:24 -04:00
Tadgh a5e734fec8 Handle sorting entries which contain no resources 2021-04-26 22:24:47 -04:00
Tadgh 798e960bb8 Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-26 15:26:34 -04:00
Kevin Dougan SmileCDR 0246e7dd0e
2572 - Add master Branch changes related to backport of fix for #2171… (#2574)
* 2572 - Add master Branch changes related to backport of fix for #2171 for new 5.3.3 release.

* 2572 - Added some missing changelog folders for the v5.3.1 and v5.3.2 releases.

* 2572 - Added a missing backport changelog entry for the v5.3.1 release.

* 2572 - Added a missing VersionEnum entry for the V5_3_1 release.
2021-04-26 14:13:42 -04:00
Tadgh 3adc259348 Productioninizg 2021-04-26 14:08:20 -04:00
Tadgh 9ecb390dae Move tests to proper class. Fix issue with version referencing 2021-04-26 13:40:11 -04:00
Tadgh b200c10ced Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-26 09:48:30 -04:00
James Agnew 2ba1005762
OpenAPI Support (#2560)
* Start work on OpenAPI

* Fixes

* Work on OpenAPI

* Cleanup

* Cleanup

* More swagger work

* Build fix

* More work

* More work

* Add documentation

* Docs fixes

* Add changelog

* License updates

* Add API

* Cleanup

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md

Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>

* Work on scripts

* Add docs

* Compile fix

* Work on fixes

* Fix tests

* Test fix

* Test fix

* Build fix

* Tests

* Build fix

* Work on pipeline

* Version bump

* Test fix

* Version bump

* Test fix attempts

* Test fix

* Test fix

* Remove accidentally committed files

* Fixes

* Tets fixes

* Test fix

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fixes

* License header updates

* test fix

* Test fixes

* Test fix

* Test fixes

* Test fix

* Checkstyle bump

Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
2021-04-25 15:40:50 -04:00
Nick Goupinets ac2aac4342 Updated address validation handling 2021-04-23 18:55:51 -04:00
Tadgh 596196b3e1 Add licenses 2021-04-23 09:08:41 -04:00
Tadgh a5f81988fc Merge branch 'improve-bundle-builder' into issue-2534-new-tx-pointcut 2021-04-21 16:53:49 -04:00
Tadgh e711dfb07c enhance bundlebuilder to support deletes 2021-04-21 16:44:22 -04:00
Tadgh b7166735f9 Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-21 12:13:54 -04:00
Tadgh c80d18aca2 Fix test for pointcut 2021-04-21 11:16:10 -04:00
Tadgh ad8921ac4e Add docs, enum, remove prints 2021-04-21 10:39:23 -04:00
Tadgh 3dee0c8ab6 Working in-place bundle sort 2021-04-20 17:48:55 -04:00
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -04:00
Tadgh ff2690b74e Add tests for transaction sorting 2021-04-20 14:12:25 -04:00
Tadgh 1670ed7202 Begin topological sort implementation 2021-04-19 20:01:02 -04:00
Nick Goupinets 1f10a15c35 Merge branch 'master' into 2515_MDM_survivorship_rules 2021-04-19 17:33:53 -04:00
Nick Goupinets 536ca0e73d Code review updates 2021-04-19 16:27:31 -04:00
jamesagnew 6b43410514 Add missing constant 2021-04-14 18:50:47 -04:00
jamesagnew b294f7d208 License headers 2021-04-14 18:00:52 -04:00
James Agnew ca2088f3ad
Add framework for Bulk Import (#2538)
* Start work on bul;k import

* Work on bulk import

* Have batch working

* Working

* Working

* More work

* More work on bulk export

* Address fixmes

* License header updates

* Test fixes

* License header updates

* Test fix

* Test fix

* Version bumps

* Work on config

* Test cleanup

* One more version bump

* Version bump

* CLeanup

* A few additions

* Test fixes

* Test fix

* Test fix

* Migration fix

* Test fix

* Test fix
2021-04-14 17:41:32 -04:00
Ken Stevens 550602b2f1
added numeric matcher (#2547)
* added numeric matcher

* changelog

* performance optimization

* fix test
2021-04-14 13:15:30 -04:00
Tadgh fef9726026 Fix typo in docs 2021-04-14 12:52:30 -04:00
Tadgh fcbfb11506 Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-13 15:55:01 -04:00
Tadgh 346c9d783c Update tests to reflect new reality 2021-04-13 10:36:17 -04:00
Tadgh a0c11d7c66 Update docs 2021-04-13 10:04:45 -04:00
Tadgh f61d52d199 Should have realized that transactiondetails is an object reference, so we can't change it effectively 2021-04-13 09:26:05 -04:00
James Agnew bc4266d3d2
Improve narrative templates for custom structures (#2537)
* Improve narrative templates for custom structures

* Add changelog

* Test fix
2021-04-12 06:00:31 -04:00
Tadgh ac8e012892 wip 2021-04-09 13:07:15 -04:00
Tadgh 99e10de5fb
Merge pull request #2487 from hapifhir/mdm-expansion-interceptor
MDM Expansion Interceptor (poc)
2021-04-09 11:23:04 -04:00
Tadgh 8f30f7b0f2 Vague skeleton of pointcut 2021-04-09 11:08:47 -04:00
Eric Prud'hommeaux fa921a3cc9
~ inspect instant for specific RDF datatype (#2473) 2021-04-09 05:59:26 -04:00
James Agnew 462d9bc6c4
Fix compartment defs for R5 (#2528)
* Fix compartment defs for R5

* Add changelog

* Test fix
2021-04-08 05:59:05 -04:00
James Agnew a6cbf7eebd
Add support for hierarchycal valueset expansion (#2525)
* Add support for hierarchycal valueset expansion

* Add changelog

* Add tests

* Cleanup

* Test fix

* Test fixes
2021-04-06 17:36:54 -04:00
James Agnew b617c7690d
Search Parameter Infrastructure Cleanup (#2522)
* Search param service cleanup

* Work on collapsing search param

* Search param cleanup

* Work on build

* Test fix

* Test fixes

* Ongoing work

* Test fix

* Compile fix

* Test fixes

* Test fix

* Test fix

* License header updates

* Remove fixme

* Cleanup

* Cleanup
2021-04-05 17:40:10 -04:00
Nick Goupinets d366558749 Merge branch 'master' into 2515_MDM_survivorship_rules 2021-04-05 09:17:42 -04:00
James Agnew 0bf746f23b
Add support for revincludes to CapabilityStatement generator (#2521)
* Add support for revincludes to CapabilotyStatement generator

* Add changelog

* Fixes

* Test fix

* Test fixes

* Test fix

* Test fix

* More fixes to CS cache

* Test fix

* Test fix

* Test fix
2021-04-05 08:29:04 -04:00
Nick Goupinets 9629aceff0 Removed obsolete test and added more control to replace fields in TU 2021-04-01 15:52:52 -04:00
Tadgh f3c706d656 Add page for mdm expansion 2021-03-31 15:33:03 -04:00
Tadgh 2ba3c919d5 Fix doGetQueryParameterQualifier on Mdm Expansion 2021-03-31 14:18:57 -04:00
Tadgh 74be6761b1 Merge remote-tracking branch 'origin/master' into mdm-expansion-interceptor 2021-03-31 09:47:57 -04:00
Tadgh 8b69d161bd Update docs 2021-03-30 17:12:55 -04:00
James Agnew 049097e5b4
Improve CapabilityStatement Generation (#2511)
* Start work

* Work on testing

* Version bump

* Test fix

* Compile fix

* Test Fixes

* Test fix

* Test fix

* Compile fix

* Tst fix

* Test fix

* Test fix

* Test fix
2021-03-30 05:48:03 -04:00
Tadgh ab143e34cb Merge remote-tracking branch 'origin/master' into mdm-expansion-interceptor 2021-03-29 19:27:37 -04:00
Diederik Muylwyk b720c32c1d Version bump 2021-03-29 18:23:16 -04:00
Diederik Muylwyk bddd3f4c92 PointCutLatch now works with IPointcut instead of Pointcut 2021-03-29 18:20:33 -04:00
Tadgh 953dd408da
Merge pull request #2508 from hapifhir/issue-2499-identify-golden-resources-in-export
Issue 2499 identify golden resources in export
2021-03-29 16:11:10 -04:00
Tadgh 002d3fcf3c Migrate constant 2021-03-29 11:07:23 -04:00
Tadgh 9f13225aa5 WIP interceptor using reference param modifier 2021-03-26 17:57:38 -04:00
Tadgh bee33f763a Refactors, tidying. Improving docs 2021-03-26 15:54:27 -04:00
Tadgh 4d3b021f12 Add annotating processor and composite processor 2021-03-25 13:53:41 -04:00
Nick Goupinets 8ead3c5f22 Code review fixes 2021-03-23 15:01:22 -04:00
long 8e45a33e2d renamed one more variable 2021-03-22 10:29:36 -06:00
long b5e12473db changed variable name according to coding convention 2021-03-22 08:47:24 -06:00
Nick Goupinets de0399da23 Merge branch 'master' into 2478_add_extension_mdm_matcher 2021-03-22 09:34:32 -04:00
James Agnew dc41d5ad61
Add terminology mapping and display population interceptors (#2488)
* Start work on code mapping interceptors

* Work on generation

* Add terminology mapping and display population interceptors

* Add changelog

* License header updates

* Test fixes

* Fix typo

* Interceptor fixes

* License header update

* Test fixes

* Mapping fixes

* Version bump

* License header updates

* Add null tests

* Add null guard

* Intermittent fix
2021-03-21 12:03:57 -04:00
Nick Goupinets 4928e726cf Added tests for teser utils 2021-03-20 21:14:51 -04:00
Nick Goupinets 5f2c0a55b7 Merge branch '2478_add_extension_mdm_matcher' of github.com:hapifhir/hapi-fhir into 2478_add_extension_mdm_matcher 2021-03-19 18:15:43 -04:00
Nick Goupinets ba835c7cac Merge branch 'ng_resource_flattening' into 2478_add_extension_mdm_matcher 2021-03-19 18:15:25 -04:00
Nick Goupinets 142fd4c108 Updated utils 2021-03-19 18:14:48 -04:00
long 08ab582c36 made getmethod more generic, added static string variable to terserUtil 2021-03-19 08:41:41 -06:00
Nick Goupinets 5747d5d841 Initial commit 2021-03-19 09:58:15 -04:00
long 6c41ded507 fixed based on pull request comments, added tests 2021-03-18 13:59:07 -06:00
long 989e9e7903 refactored terserUtil, added equals function in ExtensionUtil 2021-03-17 13:02:59 -06:00
James Agnew d857048207
Preserve meta values in stored resources (#2481)
* Fix #1731

* Test fix

* Test fixes

* Avoid intermittent failure
2021-03-17 09:23:22 -04:00
Nick Goupinets b51f9b4261 Updated init param type 2021-03-16 13:13:23 -04:00
Nick Goupinets f9f703abe2 Added support for additional types 2021-03-16 11:14:40 -04:00
Nick Goupinets e188a95d66 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-12 16:17:25 -05:00
James Agnew 0ad57c51bb
Fix resource reindexing on partitioned seerver (#2468)
* Fix resource reindexing on partitioned seerver

* Add changelog

* Test fix

* Test fix

* Tets fix

* Test fix
2021-03-12 14:14:39 -05:00
Nick Goupinets 899bef0c39 Headers 2021-03-12 11:19:14 -05:00
Nick Goupinets f9f0b2705d Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-12 10:30:36 -05:00
Nick Goupinets 8b8bbcc91f Refactored based on the code review 2021-03-11 17:14:01 -05:00
Nick Goupinets 23f3cc1f42 Code review 2021-03-11 14:51:13 -05:00
James Agnew 2633cbd141
Improve error message for invalid date param (#2466)
* Improve error message for invalid date param

* Add changelog

* Test fixes
2021-03-11 14:23:02 -05:00
Nick Goupinets 97fc19b2ce
Update hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TerserUtil.java
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-03-11 12:12:12 -05:00
Nick Goupinets e4387ea633
Update hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TerserUtil.java
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-03-11 12:12:06 -05:00
Nick Goupinets 26653f66da
Update hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TerserUtil.java
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-03-11 12:11:39 -05:00
Nick Goupinets 8c77882da0 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-11 09:48:39 -05:00
Tadgh b7398cb6f2 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-10 10:33:24 -05:00
jamesagnew 9f5786ba6c License header updates 2021-03-10 05:09:14 -05:00
Tadgh e26d757ba3 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-09 22:54:24 -05:00
James Agnew 807d9d53f0
Improve performance for large transactions (#2462)
* Performance tweaks

* Work on processing speed

* Disable no longer relevant tests

* Work on performance

* Work on tests

* Work on large transaction performance

* Add changelog

* Perf tweaks

* Test fixes

* Resolve FIXME

* Fixes

* Test cleanup

* Fix broken changelog entry
2021-03-09 18:16:02 -05:00
Nick Goupinets 7f8ac36ce0 Headers 2021-03-09 17:31:04 -05:00
Nick Goupinets 02eae95c85 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-09 14:06:33 -05:00
Nick Goupinets dd47c71f44 Fixed test failures 2021-03-09 13:17:48 -05:00
James Agnew be50a46d76
Tweaks to contained searches (#2461)
* Tweaks to contained searches

* Add changelog

* Build fix
2021-03-09 11:51:30 -05:00
Diederik Muylwyk 6cc8a5ce4d
Fix HasParam#doGetQueryParameterQualifier() (#2460)
* Fix HasParam#doGetQueryParameterQualifier(); add changelog entry

* Fix bad test in SearchParameterMapTest
2021-03-09 06:28:40 -05:00
Nick Goupinets ccb5b1aaad Addresses #2449 2021-03-08 17:40:16 -05:00
Diederik Muylwyk 214c7eb45e Remove unnecessary field. 2021-03-05 12:59:26 -05:00
Diederik Muylwyk e3ba4bd1b6 Set default for Populate Identifier in Auto-Created Placeholder Reference Targets to true; update javadocs accordingly 2021-03-04 18:54:04 -05:00
Diederik Muylwyk 1d1d9a2f7c Fix typo in IGenericClient javadocs 2021-03-04 18:02:06 -05:00
Diederik Muylwyk dfdcfa1365 Add failing tests. 2021-03-04 17:01:39 -05:00
Diederik Muylwyk 9a7bd0e775 Add failing tests. 2021-03-04 16:55:16 -05:00
Tadgh 2f1518344b Add changelogs, add patientbulkredaer implementation 2021-03-04 16:53:05 -05:00
Tadgh 9dd42fa605 Remove duplicate constant 2021-03-01 14:00:20 -05:00
Tadgh 27cac16de6 Add custom mimetypes to capability statement 2021-03-01 13:54:21 -05:00
James Agnew db44244405
Fix #2426 - Include modifiers in generic search URLs for map (#2428) 2021-02-28 10:33:43 -05:00
Ken Stevens 7d769e3b05
Issue 2332 create via put for implementationguide that references some placeholders (#2423)
* begin with failing test

* fixed.  test passes.

* documentation and changelog

* added ConceptMap

* review feedback
2021-02-26 09:44:48 -05:00
Kevin Hartmann 62bfa2cdbc Merge remote-tracking branch 'origin/master' into kh-20200222-search-list 2021-02-24 09:20:07 -05:00
Ken Stevens 330cafa83e initial implementation 2021-02-23 11:25:56 -05:00
James Agnew b108e43600
Allow partition date for non-partitionable resources (#2407)
* Allow partition date for searchparam resources

* Cleanup

* Test fix

* Documentation update

* Docs tweak
2021-02-22 20:49:09 -05:00
Nick Goupinets ddd7c0f267
Merge pull request #2397 from hapifhir/ng_codepoint_fix
UTF-16 characters might cause errors when calculating hash values
2021-02-19 17:22:20 -05:00
James Agnew 3eda19c65a
Version bump (#2400)
* Version bump

* Docs changes

* Docs tweaks

* Docs tweak

* Spelling fixes

* Docs tweaks
2021-02-18 11:07:49 -05:00
Nick Goupinets ca3811412b Code review 2021-02-17 10:20:33 -05:00
Nick Goupinets 2ec906afb2 Code review 2021-02-17 09:42:00 -05:00
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
Nick Goupinets c4daefc9fb Initial implementation 2021-02-16 17:19:57 -05:00
James Agnew 65ac0e80fb
Add CapabilityStatement customizer (#2387)
* Add CapabilityStatement customizer

* Fix javadocs
2021-02-15 14:58:34 -05:00
James Agnew b247e8cde7
Avoid NPE in RequestPartitionId on Default Partition (#2382) 2021-02-12 11:04:25 -05:00
James Agnew c69d741b43
Add CapbilityStatement customizing hook (#2364)
* Add CapbilityStatement customizing hook

* Add additional method

* Interceptor service tweak
2021-02-07 09:12:09 -05:00
Michael Buckley eee11c8844 Merge commit 'af5c45531ab59c1374cd99230bd5b8e32c692123' into mb-20210203-date-param-validation 2021-02-05 11:31:04 -05:00
Michael Buckley 42afcebd11 Merge in ca.uhn.fhir.rest.param.DateParamTest and add changelog. 2021-02-05 09:57:10 -05:00
jamesagnew f3c0ecd54d Exception tweak 2021-02-04 17:31:39 -05:00
Michael Buckley cb0f0161be Add support for legacy "=" prefix. 2021-02-04 13:31:56 -05:00
James Agnew 273a5bbbd7
Add BundleUtil utility method (#2356) 2021-02-04 13:13:25 -05:00
Michael Buckley 50acfbede3 Reject invalid param prefix.
An unrecognized param prefix had been silently ignored.
Reject it with a DataFormatException instead.
2021-02-04 10:34:03 -05:00
Marcelo Avancini 0d00954852
Added @Inherited to ResourceDef annotation (#2340)
This change avoids duplication of ResourceDef on custom resources, where there is no changes on resource name or profile.
2021-02-02 14:25:07 -05:00
Kevin Dougan SmileCDR 2308d8f44b
Merge CQL Initial Implementation Into master (#2330)
* CQL initial implementation
2021-01-29 16:35:38 -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
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 82e52750e7 Merge branch 'master' into ng_20201218_survivorship_poc 2021-01-21 09:00:28 -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
Nick 4b53ef3920 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-20 14:59:38 -05:00
Tadgh 159128109b Add versionenum value 2021-01-20 10:49:08 -05:00
Nick ae9d4a191f Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-19 11:34:01 -05:00
James Agnew 874b16207f
Bundle.entry.resource.id should not be stripped on POST from client #2297 (#2303) 2021-01-19 11:12:42 -05:00
Nick b00f47ef81 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-18 09:25:58 -05:00
dependabot[bot] 391a6d1a3f
Bump ph-schematron from 5.2.0 to 5.6.5 (#2184)
* 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
Eric Prud'hommeaux 8b338cd168
rework r4 RDF tests to skip fewer examples (#2159)
+ relative URL resolution in RDFParser
+ test non-DomainResources in RDFParserTest
~ factor/organize RDFParserTest
~ avoid EXTERNAL shapes (for now) in shex-java
- disable the bundle-response.json example as it is apparently malformed
+ added urn:-guard to PreResourceStateHl7Org.wereBack ID update
2021-01-16 19:15:39 -05:00
James Agnew 1dc4fb2206
Make quantity indexes use double datatype (#2290)
* Make quantity indexes use double datatype

* Add changelog

* Test fixes

* Test fixes

* Disable test
2021-01-16 18:44:15 -05:00
Nick 57662eedb3 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-12 09:22:38 -05:00
jamesagnew 5b5023e6ac License headers 2021-01-11 21:00:12 -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 5aa85c7e17 Survivorship 6 2021-01-11 17:22:06 -05:00
Tadgh efc6809ea6
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190)
* Beginning work on converting to hibernate search 6
* replace all out of date properties
* replace all POM references to old versions
* remove the shaded ES jars as HS6 supports 7.9
* Convert "Bridges" to RoutingBinder and RoutingBridge
* Modernize all indexing annotations
* Begin refactoring of search queries (wip)

* Fix spatial API changes, work on BaseTermReadSvcImpl

* Most of the way through the various filter property conversions

* Finished i think with BaseTermReadSvcImpl

* Compiling, but definitely broken

* Start test compilation failures

* All tests compiling (i think)

* remove suggest keywords operation

* Fix bootstrap errors, still have to deal with transient fields

* Rollback CR

* More refactoring, got IDs baked back into docs

* Fix coord util, fix a few more fields which require projection

* merge fixes

* begin refactor of valuesetexpansion tests

* fix another test

* Update tests

* remove todos, add TestContainers

* Fix descendant in

* Add testcontainers, fix another test

* fix more tests, replace embedded es

* Rip out embedded elastic, replace with TestContainer

* merge conflicts for new analyzers

* Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs

* Remove dead deps, update testcontainer

* Remove java-hamcrest

* Pull asserts up, refactor tests to pass in RP tests

* Update V2 check

* Remove suggest keyword tests

* Split line for testing

* Fix perhaps one of the dumbest programming mistakes in my career so far

* Refactor tests which no longer rely on a strict known order

* Fix up test config, disable log test temporarily

* Remove log4j from being transitively pulled in. re-enable test

* Update log4j exclusions with new bridge. Update test to check for core class

* Move dependency to root pom in dep management section

* Update changelog, add changelog for HS6 with ES requirements. Remove dead comment

* update testst, remove todos

* Add hibernate props provider method, add elastic regexp query

* Add todo for high level client builder

* Modify ElasticsearchRestClientFactory to support HTTPS hosts

* Remove protocol extraction from rest url

* do we even need to index this...?

* remove purge of non-indexed resources

* Add longer timeout to testcontainers

* Add task to add docker CLI to azure pipeline via task, for testcontainers

* WIP remove this

* Dont update version

* Add test for duplicate termconcepts

* Use real hibernate ORM methods

* merge issues

* Add partitionsettigns bean to match master

* Trying to debug testcontainers on azure...

* Trying to debug testcontainers on azure...

* Run even on previous failure

* Fix testcontainer port binds

* Add full text logs attaching, and test reporting

* I love yaml

* Remove comment

* Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue

* Modify TX beheaviour

* wip

* Rework to use config and mocked beans for partition-aware lastN

* rework to not use beans and just inject vars i need for test, keps test envs cleaner

* update azure pipeline to only copy test results

* Remove erroneous publish

* Always get test logs

* Make it so indexing works,

* Add todos

* revert deleteByPid

* Work on test fixes

* Test fixes

* Test fixes

* Another test fix

* Test fix

* Work on tests

* Test fixes

* All tests passing locally

* Fix test failure

* FIx build error

* Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider

* Update ngram of token filters

* Tidying

* subvert the purpose of hibernate elastic props builder to inject template

* dead space

* Rename changed class

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-05 17:56:59 -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
Bill Denton 84d9854e24
OSGi manifest maintenance (#2217)
* manifest cleanup and delete Fragment-Host

* make hapi-fhir-server-empi into an OSGi bundle
2020-12-18 16:48:44 -05:00
James Agnew f228b4a167
Fix an error parsing extensions with a value type of UUID (#2258) 2020-12-18 10:57:31 -05:00
jamesagnew c745fb2561 Avoid deprecated method 2020-12-18 08:49:20 -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
jamesagnew ab64aa540f Fix #2248 - Wrong import for Validate 2020-12-14 09:19:30 -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
James Agnew e4d6c51290
Allow plus symbol in email address match url (#2224)
* Allow plus symbol in email address match url

* Add changelog
2020-12-09 21:52:03 -05:00
Tadgh 0938d72b51
Revert "Remove all references to Person from EMPI." 2020-12-09 14:57:00 -05:00
Nick d3c0944388 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-07 22:02:45 -05:00
James Agnew fd528a0f7d
Improve error message on unsupported resource type (#2221)
* Improve error message on unsupported resource type

* Add changelog
2020-12-07 17:35:51 -05:00
Nick f5f7f2df14 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-07 11:55:51 -05:00
James Agnew d958764d49
Partition data leaks across searches (#2220)
* Partition data leaks across searches

* Add changelog

* Resolve FIXME

* Add test logging

* Test fix

* Test fix
2020-12-06 16:32:07 -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 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
Bill Denton 53bd271717 Split package: delete 'ca.uhn.fhir.rest.server' package from
hapi-fhir-server-empi
2020-12-02 13:24:07 -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
Ken Stevens 3d3242cf9a
Resource change listener (#2191)
* init rev

* fix build

* Tweaked the POM config settings and also added some dependency exclusions (commented out for now).

* More re-factoring of the CQL Unit Tests.

* Removed a LogMessages.html file and a minor Unit Test change.

* Unit Tests.

* added debug logging to troubleshoot the dao that has no name

* added debug logging to troubleshoot the dao that has no name

* workaround to get past null dao resourceName issue

* fix jsons to get test to pass.  Test still fails with library id problem

* gitignore

* gitignore

* test passes!  Woohoo!

* undo troubleshooting logging

* added timer and logging.

* added asserts and time multiple evaluations and measure the average

* readme

* adding explanations

* added more explanatory notes

* measure 2 patients

* move pom to use cqf snapshot

* roughed out cache

* roughed out cache

* Added code to VersionChangeCache class.

* added tests

* added polling test

* wrote init version

* wrote init version

* optimized versioncache

* worked on getting tests to pass

* redesigned interfaces

* all tests pass

* fixmes

* fixmes

* rename param

* Added Unit Tests.

* javadoc

* Fixed the 2-Patient Unit Test.

* More Unit Test work.

* make ResourceVersionMap immutable

* Fixed a Unit Test that was failing intermittently by adding a new way to refresh the cache.

* Use a new method called doRefreshAllCaches(0) to force a refresh and have all Listeners called immediately.

* Cleaned up IVersionChangeListenerRegistry interface to make methods more clear and resolved all Unit Tests.

* disabled tests

* disabled tests

* removed unused test method

* fixed refresh logic and added asserts

* moved cache so it can be used by searchparamregistry

* Updated the Cql Unit Tests to be properly configured for Dstu3 or R4.

* started rewriting SearchParamRegistryImpl to use new cache
added init method to listener interface

* added fixmes

* adding tests

* tests pass

* added tests

* Fixed the way CqlProviderFactory Autowires Beans so it can work with both Dstu3 and R4 contexts.

* moar tests

* fix test

* work tests

* reverting unneccessary refactors

* undo unneccessary import changes to reduce MR size

* undo unneccessary import changes to reduce MR size

* Unit Test fixes...more to come...

* add unregister

* fix tests

* Changed ResourceVersionCache to use a Map of Maps.

* searchparam test

* test passes

* resolved fixme

* fixmies

* strengthen test asserts

* More Unit Test changes and added some FIMXME items.

* changed from long to changeresult

* renamed VersionChange -> ResourceChange

* fixed delete bug

* organize imports

* fix test

* add update test

* add test reset function

* fix stack overflow

* fix startup race condition (might still be intermittent)

* found the problem.  delete doesn't work because we can't look up the deleted resource to find out what its name is

* fixed regression

* abandoned idea of incrementally updating searchparam registry.  Rebuilding every time--it doesn't change that often.

* fix test

* begin with failing test

* test passes

* fixmes and javadoc

* fix test

* fixme

* fix test

* whack-a-mole.  Either subs pass or cql passes.  Something's fishy with the FhirContext

* fix subscription test initialization

* fix method name

* Re-factored the CqlProvider Unit Tests.

* changed ResourceChange API

* add interface

* add interface

* fix test

* add schedule test

* add doc

* init rev

* FIXME

* modify FhirContext change

* change fhirContext.getResourceTypes to lazy load

* converted subscriptions

* converted subscriptions

* begin with failing test

* test passes

* fix test

* test coverage

* test coverage

* test coverage

* test coverage

* good coverage now

* pre-review cleanup.  I think I found a bug.

* moved cache into listener entry
tests pass with fixmes

* fix test

* fix test

* fix test

* fixme

* FIXMEs

* merge cache and registry

* method reorg

* javadoc

* javadoc done.  all FIXMEs resolved.

* change log

* changes needed by cdr

* spring config cleanup

* james feedback

* james feedback

* might not work. Try moving resourcechangeconfig into searchparam config

* merge ResourceChangeListenerRegistryConfig.java into SearchParamConfig

* fix test

* fix SubscriptionLoader

* fix SubscriptionLoader

* create ResourceVersionMap from resources

* added cache handle interface

* fix test

* javadoc

* fix test

* fix test

* James feedback: clone searchparametermap

* fix startup

* fix test

* fix test

* fix intermittent

* pre-review cleanup

* FIXME

* final FIXME yay!

* Address a couple of my own reviw comments

Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2020-11-29 19:42:40 -05:00
James Agnew 1e5def260c
Bump woodstox version (#2199) 2020-11-27 19:49:06 -05:00
Nick Goupinets 2a3b72db17 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-11-27 16:54:04 -05:00
Nick Goupinets 8a7dc4e80b EMPI to MDM 2020-11-27 15:12:21 -05:00
James Agnew fb8658da70
Always apply vs filters correctly (#2195)
* Always apply valueset filters correctly

* Test fix

* Testfix

* Test fix

* Add changelog

* Test fix
2020-11-24 18:12:02 -05:00
James Agnew 8b65db0c98
Improve error message on unique constraint violation (#2182)
* Improve error message on unique constraint violation

* Add changelog

* Test fixes

* Test fix
2020-11-19 21:20:59 -05:00
Tadgh 953b662827 Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references 2020-11-19 14:24:51 -05:00
Tadgh 75c0c25d7b remove references to EMPI 2020-11-18 19:50:00 -05:00
jamesagnew e8f2bca6ef Add 5.3.0 constant 2020-11-18 14:55:45 -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
James Agnew 63b7b379c2
Improve ValueSet filtering (#2162)
* Improve filter search

* Filter improvements

* Tests passing

* Test fixes

* Fix transaction filter

* Add changelog

* Test fix

* Update hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Resolve FIXME

* Test fix

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-11-10 11:01:13 -05:00
Frank Tao ce1caee9fa
Feature 2020 10 28 reverse chain (#2160)
* Added test cases for multiple '_has'

* Fixed composite search for the new SearchBuilder

* Added more test cases
2020-11-05 05:27:11 -05:00
jamesagnew 53c23b8d9b Add method to stringutil 2020-10-27 11:29:16 -04:00
James Agnew 72294fc0a0
Suport typeFilter parameter for bulk export (#2147)
* Cleanup

* Fix tests

* Work on bulk export

* Work on export

* Test fixes

* Add changelog

* Address review comments

* Address review comments
2020-10-26 12:28:07 -04:00
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 3738297354 Test fix 2020-10-19 20:13:31 -04:00
jamesagnew a25aa37e6a Update to #1607 2020-10-16 14:52:40 -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
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
Oliver Egger 8294b8ddb6
add namespace, prefix for attributes (xml:lang) (#2112) 2020-10-11 15:25:37 -04:00
abrsystematic cad3ba5a66
Fix gettimezone performanceissue (#1607)
* [(release_3_7_SSE)] cache timezone since timezone.gettimezone is static synchronized and performs poorly

* [(fixgettimezoneperformanceissue)] fiximport
2020-10-09 11:51:50 -04:00
James Agnew 2134d40f1c
Account for timezones in lastUpdated search (#2113)
* Add test

* Fix

* Add changelog

* Test fixes

* Test fix

* Test fixes

* Resolve fixme

* Test fixes

* Remove debug logs

* Try to get CI tests passing again
2020-10-09 07:52:46 -04:00
ianmarshall 8e7b4e8437 Changes per code review. 2020-09-29 21:05:28 -04:00
IanMMarshall 26688aac65
Update hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-09-29 12:11:56 -04:00
ianmarshall 47244c54dc Merge remote-tracking branch 'origin/feature_2020_09_02_term_multi_version_support' into im_20200728_term_multi_version_support
# Conflicts:
#	hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
2020-09-25 09:10:07 -04:00
ianmarshall 6f9874468a Merge remote-tracking branch 'origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-25 08:54:17 -04:00
ianmarshall ceb5ec6384 Use canonical identifiers for code systems rather than specifying version separately. 2020-09-23 16:42:29 -04:00
ianmarshall 4216cee8c6 Added and enhanced tests plus fixes arising from tests. 2020-09-22 14:44:32 -04:00
ianmarshall f9f8bf6515 Merge remote-tracking branch 'origin/master' into im_20200728_term_multi_version_support 2020-09-20 22:02:08 -04:00
ianmarshall 302bbca8fd Changes to support multi-versioning in ValueSet $expand operation. 2020-09-20 22:01:21 -04:00
Tadgh 74bba9dbcc Rename to ResourceOperationMessage 2020-09-15 18:57:55 -04:00
ianmarshall 3add1320b7 Merge remote-tracking branch 'remotes/origin/im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:52:02 -04:00
ianmarshall 539ef63fc0 Merge branch 'im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:24:47 -04:00
Tadgh ea64bea1b0 Refactor to use concrete class instead of parent 2020-09-15 15:27:21 -04:00
ianmarshall 7b15f85fa1 Merge remote-tracking branch 'remotes/origin/feature_20200830_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:35:31 -04:00
ianmarshall 087c9e3c3b Merge remote-tracking branch 'remotes/origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:34:11 -04:00
Tadgh 28a9a53917 Rework to keep several things in subscription 2020-09-10 16:05:56 -04:00
ianmarshall d00db11586 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-09-09 17:38:24 -04:00
Frank Tao 5410042643 Multi-version supported for ConceptMap $translate operation 2020-09-07 10:43:58 -04:00
Frank Tao 1ecec0abc9 Fixed duplicate ConceptMap URL only 2020-09-06 15:23:26 -04:00
jamesagnew 2d7c808326 Localizer refactor 2020-09-05 15:47:10 -04:00
ianmarshall 5f005120c9 Initial changes to support multi-version ValueSets 2020-09-03 22:36:15 -04:00
ianmarshall 1c55d87b10 Problem found in LOINC loader. 2020-08-30 17:11:48 -04:00
ianmarshall dc786eaff9 Refine model for storing multiple code versions. 2020-08-21 10:16:10 -04:00
ianmarshall 2126c5c556 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-18 11:15:09 -04:00
James Agnew eab828f47a
Add transactionbuilder (#2041)
* Add transactionbuilder

* Add changelog

* Add creates
2020-08-17 07:47:40 -04:00
ianmarshall bd94ff96cc Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-16 21:38:41 -04:00
jamesagnew 92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew 5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
jamesagnew 90ebaf8549 Add one more test for #2023 2020-08-11 08:54:03 -04:00
James Agnew e61b39fc30
Force a flush of the SearchParameter cache sooner when SPs change (#2030)
* Force a flush of the SearchParameter cache sooner when SPs change

* Add changelog

* Test fixes
2020-08-09 19:30:59 -04:00
ianmarshall d39348d7bd Initial changes to support multiple versions for code system. 2020-08-09 11:49:04 -04:00
James Agnew 0de0b88aa0
Fix TestpageOverlay XSS Vulnerability (#2027)
* Resolve XSS vulnerability

* Add changelog
2020-08-09 07:06:11 -04:00
James Agnew 5d9d4070fb
Fix an issue with binary storage not updating correctly if a retry (#2014)
interceptor is present
2020-08-05 09:14:40 -04:00
jamesagnew a35c97e13d Add utility method to XmlUtil 2020-07-26 17:54:45 -04:00
christian ohr 1c27726055
#1817: fix problem with missing resource references when extensions are used (#1848)
Co-authored-by: Christian Ohr <christian.ohr@icw.de>
2020-07-21 05:36:25 -04:00
James Agnew 5db90d3e6e
Address issues when importing US Core (#1986)
* Work on US Core import

* Work on US Core

* Resolve issues with US Core import

* Test fix
2020-07-17 15:28:16 -04:00
Ken Stevens ebd6ca4b64
Empi 3 ruleset version (#1978)
* add rule version

* add rule version

* Rough in model for Golden Record.

* Test Link Rule Version

* add eid match boolean

* added new fields to EmpiLink to provide more information about how the link was created

* add logging to check an edge case

* all tests pass

* wip with failing tests

* tests pass

* FIXME

* optimize imports

* test score in provider output

* FIXME

* FIXME

* Fix jpa test app context

* fix migration string length

* review feedback param name

* review feedback javadoc

* review feedback javadoc

* bean config reorganization for cdr

* add more tests
2020-07-17 08:31:15 -04:00
jamesagnew f5222f3105 License headeer update 2020-07-17 08:27:10 -04:00
Ibrohim Kholilul Islam 5a79304893
Implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation (#1896)
* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation

* GraphQLQueryBodyParameter to recognize application/graphql

* fix 500 error on method without @GraphQLQueryBody

* refactor to processGraphQlGetRequest and processGraphQlPostRequest

* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest

* fix imports
2020-07-16 09:25:26 -04:00
James Agnew 077ee02771
Fix validation for enumerated ValueSets (#1982)
* Allow code validation against enumerated VS

* Work on validation

* Work on this

* Work on tests

* Work on validation

* Work on tests

* Work on validation

* Test fixes

* Add changelog

* For a change

* Test fixes
2020-07-15 13:38:14 -04:00
James Agnew baba4cc240
Avoid version conflicts on current writes (#1971)
* Add auto retry of transactions

* Experiment in Maven build

* Transaction autoretry

* Work on transaction retries

* Work on transaction retry

* Work on transaction retry

* Fix tests

* Avoid version conflicts

* Add changelog

* Resolve LGTM issue

* FIx transaction scope error

* Test fixes

* Test fix

* Test fixes

* Test fix

* Test fixes
2020-07-13 08:51:13 -04:00
Ken Stevens e565b1c948
done (#1976) 2020-07-10 15:08:50 -04:00
Alexander Lukyanchikov df133d10f2
#1892 Add support for :of-type Token Modifier (#1893) 2020-07-06 05:50:44 -04:00
James Agnew f356c7c385
Migrate to JUnit5 (#1952)
* Work on junit

* Work on junit 5

* Work on junit 5

* Bump errorprone vcersion

* Work on tests

* Junit 5 tweaks

* Fixes

* Work on tests

* Work on junit5

* Work on tests

* Test fixes

* Work on junit5

* Test work

* Get junit5 working

* Test fix

* Work on tests

* WOrk on tests

* Work on tests

* fixes

* Compile fix

* One more tweak

* Compile fix

* Add changelog

* Fix compile error

* Compile fix
2020-07-04 18:28:16 -04:00
jamesagnew ef86d26357 License header updates 2020-07-02 12:07:02 -04:00
Ken Stevens 714bd6216e
Empi 70 phonetic indexing (#1941)
* start with failing test

* test passes with fixmes

* javadoc and config

* pre-review cleanup

* generalize encoding

* test passes, but indexing needs to be optimized

* test passes, but indexing needs to be optimized

* step 1 of optimization.  big refactor of all predicates

* step 2 of optimization: determine phonetic encoder at time of RuntimeSearchParam creation

* integrated new phonetic encoders into empi

* phonetic search implemented

* IT passes

* pre-review cleanup

* final pre-review cleanup

* final pre-review cleanup

* Fix compile error

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-06-30 17:36:54 -04:00
jamesagnew 349c752860 License headers 2020-06-30 15:13:38 -04:00
jamesagnew 2cdef055aa Missed commit on #1951
Squashed commit of the following:

commit f820135996
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 14:29:24 2020 -0400

    Address review comments

commit 11c4f9defb
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:38:16 2020 -0400

    Fix LGTM warning

commit b650fdb9ea
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:20:52 2020 -0400

    Test fix

commit 6ebcceeb5c
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:49:01 2020 -0400

    Add changelog

commit 4a1d7383b0
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:46:52 2020 -0400

    Bundle transmission

commit 88bd4abf0c
Merge: 7cde945281 25fc747b9f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:31:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 7cde945281
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:10:33 2020 -0400

    Work on seed bundles

commit ed2e62752e
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 09:39:10 2020 -0400

    Work on subscriptions

commit 52addcff59
Merge: 64a9eaa4de bf8de84801
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Sat Jun 27 18:09:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 64a9eaa4de
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:32:17 2020 -0400

    Start work

commit f74eba5397
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:28:18 2020 -0400

    Terser should create correct Enumeration on create
2020-06-30 14:31:40 -04:00
James Agnew fa4bbe3685
Allow search criteria as subscription delivery mechanism (#1951)
* Terser should create correct Enumeration on create

* Start work

* Work on subscriptions

* Work on seed bundles

* Bundle transmission

* Add changelog

* Test fix

* Fix LGTM warning
2020-06-30 14:29:09 -04:00
Tadgh bb7a773f41 Merge branch 'master' into spring-batch-integration 2020-06-23 16:02:41 -07:00
James Agnew f88298a1fb
Remote terminology service enhancements (#1934)
* Remote terminology service enhancements

* Add changelog
2020-06-23 11:35:26 -04:00
jamesagnew 4119cbb0c4 Terser should create correct Enumeration on create 2020-06-17 18:32:27 -04:00
Tadgh a9c704c06e Merge branch 'master' into spring-batch-integration 2020-06-10 12:24:19 -07:00
James Agnew b8da4f0140
Add package support (#1911)
* Begin rework of package management

* Work on NPM

* Work on package management

* Work on NPM

* NPM rework

* Work on NPM

* NPM package rework

* Updates

* Updates

* Add license

* Work on package server

* Work on package importing

* Work on package management

* Package rework

* Work on packages

* Work on package manager

* Work on pkgs

* NPM work

* NPM rework

* Work on package cache

* Work on NPM

* Work on NPM

* Package fixes

* Add tests

* Tweaks

* Test fixes

* Add changelog

* Avoid snapshot dep
2020-06-10 05:30:20 -04:00
James Agnew 0d3ad622b5
Correct Validation Performance Regression (#1895)
* Validation performance regression

* Optimize validation

* More cleanup

* Add changelog

* Test fixes

* Build fixes
2020-06-10 05:26:21 -04:00
Tadgh 278a1070ae :Merge branch 'master' into spring-batch-integration 2020-06-08 17:16:11 -07:00
Tadgh 44aa688a20 Final config layout of Bulk Export Batch job 2020-06-08 15:59:08 -07:00
Diederik Muylwyk eda806babd Fix typo. 2020-06-08 13:48:44 -04:00
Ken Stevens 60e420aaa3
resolves #1838 (#1839)
* Added %today that works like %now but with date precision instead of dateTime precision.
2020-06-04 09:52:41 -04:00
James Agnew 86ef0ec0e2
Correct transaction processing in multitenant server (#1884)
* Correct transaction processing in multitenant server

* # d codethe npm registry for updates every day (weekdays)
2020-06-03 10:37:47 -04:00
jamesagnew 201c3a6187 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-06-02 07:47:06 -04:00
jamesagnew 760d19cf89 Prep for 5.0.2 2020-06-02 07:46:57 -04:00
ianmarshall 6ed724e01b Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-25 17:40:53 -04:00
jamesagnew bf550f9c27 License header updates 2020-05-25 13:20:32 -04:00
ianmarshall 35b75f8ffb Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-23 15:54:23 -04:00
James Agnew e780a8402e
Use R5 snapshot generator (#1862)
* Use R5 snapshot generator

* Snapshot generator reworking
2020-05-23 12:54:19 -04:00
ianmarshall 4d378ee0ed Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
#	hapi-fhir-jpaserver-base/pom.xml
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java
2020-05-22 17:04:01 -04:00
IanMMarshall a1a3d9de38
Merge branch 'master' into im_20200520_cascade_delete 2020-05-22 16:11:38 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857)
EMPI Initial Implementation (still plenty of known gaps)
2020-05-22 15:03:20 -04:00
IanMMarshall 44869856da
Update hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-05-22 13:50:24 -04:00
ianmarshall a60e5809b2 Changes to enable adjusting limits on delete conflict handling through configuration. 2020-05-22 10:15:04 -04:00
James Agnew 63ff0ede9c
Make diff operation work securely (#1859)
* Make diff operation work securely

* Build tweak

* FIx tests
2020-05-21 19:20:48 -04:00
James Agnew 5b2181a563
Implement FHIR Patch (#1850)
* Start working on FHIRPatch

* More work on fhirpatch

* Work on FHIR Patch

* Add patch

* Test fixes

* Test fixes

* Get tests fixed

* Chnage to trigger a build

* Compile fix

* Dependency version fixes

* Test fix

* COmpile fix

* Try to fix build

* Test fix attempt

* Another build attempt

* Another build tweak

* Cleanup
2020-05-20 19:43:55 -04:00
Tue Toft Nørgård 2f48c7d7fe
Make @Interceptor @Inherited so InterceptorService.determineOrder accepts Spring proxies of @Interceptor annotated classes. (#1853)
See https://groups.google.com/forum/#!topic/hapi-fhir/7Z_FKDBTJSE
2020-05-20 10:52:56 -04:00
jamesagnew cc92bd7b07 Revert "Start working on FHIRPatch"
This reverts commit b3f6e7d521.
2020-05-17 11:56:50 -04:00
jamesagnew b3f6e7d521 Start working on FHIRPatch 2020-05-17 11:44:06 -04:00
jamesagnew 52c8e3551c Version bump to 5.1.0-SNAPSHOT 2020-05-15 14:43:32 -04:00
jamesagnew fe0e07a313 Bump to 5.0.1 2020-05-15 05:47:01 -04:00
ianmarshall 529e1e1f5e Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-14 12:09:24 -04:00
ianmarshall eb1d1c2b27 Changes to better support chunking of queries and paging of results for lastn operation and to monitor performance. 2020-05-14 12:08:55 -04:00
jamesagnew 8a360ebd5b Fix version enum 2020-05-12 20:16:21 -04:00
jamesagnew 1d13e29ac0 Version bump to 5.1.0-SNAPSHOT 2020-05-12 20:04:20 -04:00
jamesagnew d631ecff4a Prepare for 5.0.0 2020-05-12 11:49:18 -04:00
James Agnew 0c13a65871
Bump to latest Core version (#1841)
* Start working on bumping core

* Work on tests

* Work on tests

* Bump core definitions

* Bump R5 defs

* Tweak changelog

* Test fix
2020-05-11 12:37:16 -04:00
James Agnew 6cc07b6689
Make binary storage work for bulk export (#1836)
* Make binary storage work for bulk export

* Add changelog

* Build fixes

* Test fix

* Test fix

* Test fix
2020-05-07 19:20:22 -04:00
James Agnew b67509d7ff
Transaction write performance fix (#1832)
* Performance fix for transactions

* Test fix

* Fixes

* Add docs

* Test fixes
2020-05-07 10:56:41 -04:00
James Agnew a77aa6a28e
Multitenancy Ticket 2 - #1813 (#1821)
* Work on multitenancy

* Second ticket started

* More multitenancy work

* Work on tenancy security

* Work on multitenancy

* Test fixes

* Add docs

* cs tweak

* Multitenancy fixes

* Add debug log

* Fix build

* Add headers

* Add partition selection interceptor hook

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

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

* Account for review comments

* Resolve FIXMES

* Work on tests

* Test fixes

* A bit more cleanup

* Work on multitenancy

* Update hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientExamples.java

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md

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

* Address review comments

* Allow disabling text modifier indexing

* Add changelog

* Docs fixes

* Address review comment

* Resolve merge conflicts

* Merge master

* Compile fix

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-05-05 15:12:15 -04:00
James Agnew 35c2b7a2c1
Allow disabling text modifier indexing (#1831)
* Allow disabling text modifier indexing

* Add changelog

* Address review comment

* Resolve merge conflicts
2020-05-05 12:16:55 -04:00
Ian 41c715dc2d
Make BaseOrListParam and BaseParam visible outside of the package (#1710) 2020-05-04 05:39:10 -04:00
jamesagnew 8b49142b94 Clean up migrator tasks 2020-05-01 15:03:36 -04:00
Bert Roos c8ad3e80e6
Correction in comment (#1734)
The description for SERVER_INCOMING_REQUEST_PRE_HANDLED referred to itself rather than to SERVER_INCOMING_REQUEST_PRE_PROCESSED. Along with this corrected begin into begun.
2020-05-01 05:36:28 -04:00
jamesagnew 41056092ed License header updates 2020-04-30 18:24:07 -04:00
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
James Agnew 0b9f921c3e Fix NPE in xml parser 2019-11-04 09:49:49 -05:00
jamesagnew 9c93d5d7f7 Test fixes 2019-11-04 07:04:26 -05:00
James Agnew 3b6709e1d1
Merge pull request #1566 from jamesagnew/ja_20190928_rationalize_search_param_extractor
Rationalize search param extractors across FHIR versions
2019-11-02 16:18:23 -04:00
James Agnew 48930de31c Attempt to resolve #1356 2019-11-02 16:15:37 -04:00
Ken Stevens 1fd3948b12
Merge pull request #1572 from jamesagnew/ks-source-subscriptions
fixed in-memory search by _source for Dstu3
2019-10-30 16:20:14 -04:00
James Agnew e96500d54f Add a test 2019-10-30 15:51:46 -04:00
Ken Stevens 97f4de553a fix test. this is better 2019-10-30 15:24:43 -04:00
Ken Stevens 3ceb4085cb fix test (not super happy about this fix, but I think it's the right thing to do) 2019-10-30 15:21:21 -04:00
Ken Stevens 21c591eaf2 ready for review 2019-10-30 13:49:10 -04:00
James Agnew b90f285218 Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-30 08:41:14 -04:00
James Agnew 007cfaf00e
Don't error out on missing CS (#1570)
* Don't error out on mi9ssing CS

* Add tests

* Add a bit of test coverage

* One more test
2019-10-30 08:38:39 -04:00
jamesagnew 8b227a59fc Add some tests 2019-10-28 06:02:19 -04:00
jamesagnew ac4d108126 Merge branch 'ja_20190928_rationalize_search_param_extractor' of github.com:jamesagnew/hapi-fhir into ja_20190928_rationalize_search_param_extractor 2019-10-27 18:17:29 -04:00
James Agnew d18550b96f Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-27 18:00:31 -04:00
James Agnew a82da8de1c Override enum factory interfaces 2019-10-27 17:51:57 -04:00
James Agnew 817f9ae36e Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-27 17:25:20 -04:00
James Agnew 6580c98ed7 Work on extractor 2019-10-26 16:56:12 -04:00