Commit Graph

735 Commits

Author SHA1 Message Date
Tadgh 6982c4d680
bump version to 6.0.0-PRE1-SNAPSHOT (#3353)
* bump version

* Add new version enum

* Bumped to 6.0.0
2022-02-02 12:11:31 -08:00
Johnson Lu c42ecc5c08
Add error codes to all exceptions (#3278)
* Initial design of adding exception codes to exceptions

* Initial design of adding exception codes to exceptions

* change int module name to string

* add comment

* shorten message

* shorten message

* added checkstyle

* developing checker

* completed checkstyle plugin and unit test for it

* fix NPE

* fix checker so it ignores throws on exceptions that aren't new

* change parameter order in InvalidResponseException

* accept Msg.code() in any parameter since some exceptions like MessageException have the message string as the second parameter

* exclude generated files

* BIG COMMIT added error codes to all exception throws

* example test fix

* Modified tests such that the assert statements would better match the message responses.

* Modified additional tests such that the assert statements would better match the message responses.

* fix test

* merge master

* merge master

* Fourth commit of modified tests such that the assert statements would better match the message response

* Changes made to modify assert statements such that they match the new errors which now use error codes. Also changed ResourceNotFoundException to include error codes in its messages.

* Modified assert messages to better match new error codes

* Time Zone changes DRAFT. Certain tests pass in intellij and fail during mvn install

* Modified assert messages to better match new error codes

* Added comments for time zone fixes. Previous commit comment on time zone fixes was incorrect. By invaliding caches, all tests on both intellij and mvn install passed.

* Reverted changes on azure-pipelines.yml

* updated hapi-fhir version for checkstyle module

* changes to azure-pipelines.yml

* changes to azure-pipelines.yml

* change to pom.xml to include hapi-fhir-checkstyle in ALLMODULES

* changes to azure-piplines (these changes are to be reverted after testing)

* reverted changes to azure-piplines

* reverted change where hapi-fhir-checkstyle was added to pom.xml (hapi-fhir)

* Attempted fix on checkstyle build error

* modified azure-piplines.yml to change maven repository for checkstyle build

* Attempted fix on checkstyle build error

* checkstyle config location change for hapi-depoloyable-pom. (will be reverted if it does not work)

* attempted dependency add for hapi-depoloyable-pom. (will be reverted if it does not work)

* reverted changes for hapi-deployable-pom

* add javadoc

* update last code

* Attempted fix on checkstyle build error

* Finished adding in missing error codes to pass Checkstyle checks

* Test pipelining

* Fixing errors and bumping version (as suggested by Gary)

* Merge

* Fixing Checkstyle error

* Attempted fix for date error

* Add error code onto assert statement

* Add in a couple more error codes

* Fixing assert statements

* Bump to static version for dependency

* Adding error code to message

* Adding error codes to exceptions

* Adding error codes to exceptions

* Change to work with cdr branch

* Update to faulty error message

* Merge changes

* allow checkstyle pom to deploy

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com>
Co-authored-by: Predap <simon.zuccherato@gmail.com>
Co-authored-by: Predap <46201929+Predap@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-01-31 13:10:15 -08:00
James Agnew 3f42414287
Validate include statements for JPA (#3331)
* Validate include statements for JPA

* Add changelog

* Optmize test fix
2022-01-26 09:16:28 -05:00
Ken Stevens ed2ea91f56
concurrent validation performance improvement (#3327) 2022-01-23 15:55:31 -05:00
James Agnew 3fa76a9027
Add support for of-type token modifier (#3309)
* Add support for of-type token modifier

* Add changelog

* Clean up hash calculation logic

* Test fix

* Rework hash generation

* Work on hash generation

* Test fix

* Avoid redundant hash calculations

* Revert some useless changes

* Cleanup

* Test fixes
2022-01-21 16:10:51 +00:00
TipzCM 221d7ed5b7
3274 transactions with full request url should be rejected (#3280)
* 3274 throw if url is full url

* 3274 will throw on invalid urls

* 3274 fixing the tests

* 3274 cleanup

* anonymize the data

* review fixes

* 3274 fixed for backward compatibility

* added review fixes

* fixing tests

* some more test fixes

* test fixes

* 3274 fixing the check to only look for resource at begining

* 3274 fixed test

* test fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-01-17 08:46:32 -08:00
James Agnew d610d33ac3
Dependency bumps (#3264)
* Bump a number of versions

* Fixes

* Work on version bump

* Bump

* Test fix

* More version bumps

* Build fixes

* Test fixes

* Fixes

* Fixes

* Test fix

* Bump jacoco

* Test fix

* Test fix

* Test fix

* Build fix

* Build fix

* Remove versioned H2

* Build fix

* Avoid memory issue in validation tests

* JDK bump

* Restore compile with errorprone

* Force coloured output

* Force jansi

* Try again to force jansi

* Fix for hardcoded date that just passed

* Fixes to JPA

* Improve changelog

* Work on failing test

* Test fix

* Compile fix

* One more version bump

* Test fixes
2022-01-04 13:21:14 -05:00
Tadgh 50a3005c23
Fix flag name (#3247)
* Fix flag name

* Bump hapi version
2021-12-14 19:20:03 +00:00
longma1 a56603daa2
2480 partition aware subscription (#3218)
* some fixmes to start

* Added some FIXMEs

* added RequestPartitionId to reosurceDelivryMessage and ResourceModifiedMessage

* ResourceDeliveryMessage and ResourceModifiedMessage tests

* fixed issue with test missing partitionHelperSvc mocked bean

* Added tests and implemented SubscriptionMatchingSubscriber for partition aware subscription

* modified implementation of partitionId in CanonicalSubscription

* Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)

* Revert "Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)"

This reverts commit fe40fb9733.

* Got added partitionId to subscriptions, added changes to make SubscriptionMatchingSubscriberTest work

* added SubscriptionTriggering test, also added partition support to subscriptionLoader

* Changed implementation for storing partition id of subscriptions from messages, refactored tests to new implementation

* added all subscription systemRequestDetails with all partition to subscription reader

* refactored a generic system request details with default all partition request

* Added test for dao subscriptions, fixes to get the test working

* added partition support for latest version delivery

* added doc changes and changelog for multitenancy subscription

* cleanup and added partitioned subscription manually trigger test

* fixed mocked subscriptionDao

* added package-info for subscription module

* some code review changes

* removed AllPartitionSystemRequestDetail, added new text for multitenant subscription

* renamed method for code review

* version bump to 5.7.0PRE7

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
2021-12-13 08:45:30 -07:00
VK-SMILECDR bd89cf022b
Improve mail service (#3230)
* move mail config to mail service constructor

* update subscription email sender

* added license text

* [2669] bump HAPI version to 5.7.0-PRE6-SNAPSHOT

* add changelog
2021-12-09 17:05:42 -05:00
Ken Stevens 9753b66610
2564 contained resource validation flag (#3225)
* First cut at multithreading bundle validation

* javadoc

* change test to a red-green test

* add daoconfig

* move bundle concurrency config from validationsupport to request validator

* Moved concurrent details from ValidationOptions to FhirValidator

* Remove bundleValidationThreadCount (it's set by creating an appropriate executor)

* validate threadpool prefixes

* FIXME cleanup

* reassign FIXMEs to JB

* only create the threadpool if it will be used

* Add the MdcTaskDectorator to all threadpools

* Add bundle path to concurrently validated bundle resource validation messages.

* Add test to check bundle entry path being added to validation messages

* Threaded validation of contained resources initial checkin

* FHIR validator refactored to maintain correct bundle path and async validation task

* Refactored to use validation complete invoke callback to support raw string resource or resource object

* switch from XML to JSON

* # Conflicts:
#	hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Updated to use new HAPI-FHIR version

* merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation

* Updated to use new HAPI-FHIR version

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit 910b7f676b.

* Revert "merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation"

This reverts commit c7d60fc3e6.

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit aa8a7af455.

# Conflicts:
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Fix Test dependencies after reverting changes.

* merge 'validate_contains_change' to 2564-contained-resource-validation-flag

* Disable threadpool prefix name validate check.

* merge master

* fix thread regexp

* pre-review cleanup

* change log

* fix test

* revert to XML as default validation serialization

* fix test

* fix test

Co-authored-by: Jaison B <jaisonb@gmail.com>
2021-12-08 15:18:54 -05:00
Mark Iantorno d60d07b697
Validate contains change (#3209)
* wip

* The updated changes to the validator that were pulled in from the core dependencies are not backwards compat. Need to bump HAPI version.

* pointing to stable core version

* review feedback

* Add changelog

Co-authored-by: markiantorno <miantorno@pop-os.localdomain>
2021-12-06 11:25:00 -05:00
James Agnew d072357c2a
Move graphql provider (#3214)
* Move graphql provider

* Version bump
2021-12-05 17:22:20 -05:00
James Agnew aae53d6ec7
Improve loading performance (#3197)
* Synthea perf work

* Cleanup

* Work on performance

* Ongoing perf work

* More perf work

* Perf work

* Test fixes

* Updates

* Test fix

* Test fixes

* Clean up tests

* Test cleanup

* Cleanup

* Add test

* One more perf tweak

* Fixes

* Add changelog

* Add changelog

* License header update

* License header updates
2021-11-28 10:47:30 -05:00
TipzCM 25c025cdee
3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155)
* 3153 updating the unknowncodesystemwarningvalidationsupport class

* 3153 updating version for smile

* 3153 update broken tests

* 3153 adding log

* 3153 cleanup

* 3153 cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2021-11-10 16:06:09 -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 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 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
jamesagnew ec86ac4088 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2021-10-17 08:10:19 -04:00
Tadgh b9266df1fd Add dependency to unbreak master build 2021-10-16 19:05:11 -04:00
jamesagnew d416bc7101 Build fixes 2021-10-16 18:34:08 -04:00
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
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
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
Jason Roberts 39ae66de16 Add tests for invalid inputs 2021-09-28 08:35:04 -04:00
Jason Roberts 58a2f23c0d Merge branch 'master' into jr-20210922-narrowing-interceptor 2021-09-28 07:41:39 -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
Jason Roberts 626c6f855c handle queries on bare ids without explicit types 2021-09-24 14:57:05 -04:00
Jason Roberts 4a53d10c78 Merge branch 'master' into jr-20210922-narrowing-interceptor 2021-09-24 14:39:10 -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
Jason Roberts 9e8164d73a check search parameters for synonyms 2021-09-23 10:03:24 -04:00
Jason Roberts e52d11b5ba search narrowing interceptor responds with 403 Forbidden instead of creating an impossible query 2021-09-22 14:00:12 -04:00
Tadgh a12ce73797 Add more tests 2021-09-21 15:31:36 -04:00
Tadgh b8ef2f6763 Add changes 2021-09-21 15:25:46 -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
Tadgh 5bbe69cd31 Move into data class 2021-09-15 21:17:03 -04:00
Tadgh 0a9d5344e3 remove more NPE, fix old test 2021-09-14 02:10:34 -04:00
Tadgh 75a16f3b13 Add docs and changelog 2021-09-14 01:54:59 -04:00
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 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -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
Tadgh 37ad73a422 Bump PRE version so we don't conflict downstream 2021-08-23 15:42:18 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -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
jamesagnew a5e6674e84 Version bump to 5.5.0-PRE7-SNAPSHOT 2021-07-22 08:41:16 -04:00
Nick Goupinets 7d4c39b953 Fixed bug 2021-07-02 18:18:10 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
James Agnew 7185089c9d
Add forced offset search JPA interceptor (#2756)
* Add support for offset searches

* Tests working

* Add changelog

* Test fixes

* Test fix

* More test fixes

* Add commit counter
2021-06-25 10:40:39 -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
jmarchionatto 39d7d4ad03
Use pageSize variable to hold page size (#2719)
* Use pageSize variable to hold page size as previously used variable has other function, so not always hols intended value required for previous link

* Adjust test to standards and use RestfulServerExtension instead of own server

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-06-11 17:29:14 -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 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
Nick Goupinets 2acb3501a5 Removed sout 2021-05-20 16:15:15 -04:00
Nick Goupinets 8a7fc58e91 Fixed primitive field merging 2021-05-20 15:48:00 -04:00
jamesagnew 926bf393d3 Merge branch 'rel_5_4' 2021-05-17 09:10:58 -04:00
Tadgh 424ec2118b Add implementation. Add test. Add changelog 2021-05-11 10:31:29 -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
jamesagnew 5db01f3139 Build fixes 2021-05-03 05:57:45 -04:00
James Agnew 0cea403800
Fix vulnerability warning on maven plugin (#2621)
* Fix vulnerability warning on maven plugin

* Compile fixes

* Fix bootstrap dep

* Test fix

* Fix tests

* FIx deps
2021-05-02 12:14:32 -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 896c8fbd4f Code review 2021-04-29 17:25:06 -04:00
Nick Goupinets d67537231c Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-29 13:55:48 -04:00
Nick Goupinets d45972abed Added geo accuracy code 2021-04-29 11:46:09 -04:00
Nick Goupinets 4050c42bf4 Treating C addresses as valid 2021-04-28 15:31:34 -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
Nick Goupinets 418c1aa2c6 Added avc code to the interceptors 2021-04-28 10:15:38 -04:00
Nick Goupinets 7cef07b0c1 Improved test coverage 2021-04-27 11:47:57 -04:00
Nick Goupinets 29722ad8ec Fixed exception handling 2021-04-27 10:14:30 -04:00
Nick Goupinets 024f553fc9 Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-27 09:31:42 -04:00
Tadgh a5e734fec8 Handle sorting entries which contain no resources 2021-04-26 22:24:47 -04:00
Nick Goupinets 08934d2364 Updated standardization logic and removed obsolete validator 2021-04-26 16:27:44 -04:00
Nick Goupinets f6ed93b343 Updated validation logic 2021-04-26 14:17:05 -04:00
Tadgh b007fecb1d Add comment 2021-04-26 13:40:40 -04:00
Tadgh 9ecb390dae Move tests to proper class. Fix issue with version referencing 2021-04-26 13:40:11 -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
Nick Goupinets 902cd94ca2 Updated address and field validation handling 2021-04-22 16:55:34 -04:00
Nick Goupinets 961f16a1be Initial commit 2021-04-22 09:48:40 -04:00
Tadgh e711dfb07c enhance bundlebuilder to support deletes 2021-04-21 16:44:22 -04:00
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -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
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
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
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
jamesagnew 06bdefa16c Improve error handling 2021-03-30 07:36:08 -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
Eric Prud'hommeaux 939a57960d
+ informative header in structures-r4 RDFParserTest (#2474) 2021-03-30 05:37:02 -04:00
Diederik Muylwyk b720c32c1d Version bump 2021-03-29 18:23:16 -04:00
Nick Goupinets 8ead3c5f22 Code review fixes 2021-03-23 15:01:22 -04:00
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 9b94718cab Added ext util test 2021-03-20 21:22:21 -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 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
Eric Prud'hommeaux d92a6787c5
- remove-JSON-round-trip-guard (#2472)
hapi-fhir-structures-r4/.../RDFParserTest.java included a guard to NOT
report round-trip errors if JSON didn't round-trip due to changed
ordering of contained resources (and entries in Bundles). be50a46
appears to have fixed these issues so the guard is no longer
necessary.
2021-03-17 05:51:29 -04:00
Nick Goupinets d80a9ed848 Fixed test bug 2021-03-16 11:37:49 -04:00
Nick Goupinets f9f703abe2 Added support for additional types 2021-03-16 11:14:40 -04:00
Nick Goupinets 83acb66675 Touch for a rebuild 2021-03-15 16:16:59 -04:00
Nick Goupinets 04a0ecfc2b Added tests 2021-03-15 10:31:38 -04:00
Nick Goupinets 8c80e0838d Fixing line break problem 2021-03-12 17:48:17 -05:00
Nick Goupinets d68ee68b5d Added test 2021-03-12 10:30:12 -05:00
Nick Goupinets efae1b5e5f Added test 2021-03-11 17:44:34 -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
Nick Goupinets 8c77882da0 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-11 09:48:39 -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 052919eb33 Finished tests 2021-03-09 16:17:13 -05:00
Nick Goupinets dd47c71f44 Fixed test failures 2021-03-09 13:17:48 -05:00
Nick Goupinets ccb5b1aaad Addresses #2449 2021-03-08 17:40:16 -05:00
Tadgh 11b413ee9b Rework tests which relied on old behaviour 2021-03-01 14:19:20 -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
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
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
James Agnew 65ac0e80fb
Add CapabilityStatement customizer (#2387)
* Add CapabilityStatement customizer

* Fix javadocs
2021-02-15 14:58:34 -05:00
James Agnew dd7a156d19
Call startOperation for paging requests (#2370) 2021-02-09 15:47:11 -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
James Agnew 273a5bbbd7
Add BundleUtil utility method (#2356) 2021-02-04 13:13:25 -05:00
James Agnew 92669b29da
Add elastic test (#2348)
* Add elastic test

* Rework

* Add test
2021-02-04 11:04:27 -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
dependabot[bot] feff734736
Bump jaxb-runtime from 2.3.1 to 3.0.0 (#2289)
* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

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

* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

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

* Add jakarta bindings

* Dependency cleanup

* More depndency cleanup

* Work on deps

* Replace transaction annotation

* Cleanup

* Another fix

* Build fix

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-22 11:24:23 -05:00
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
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
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
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
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 5dc12b8787 Add test for custom field parsing 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
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 1e5def260c
Bump woodstox version (#2199) 2020-11-27 19:49:06 -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
jamesagnew 7903b2b577 License headers 2020-10-13 11:43:09 -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
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
James Agnew ecc09889cb
Avoid duplicate search param defs in generated CapabilityStatement (#2101)
* Avoid duplicate search param defs in generated CapabilityStatement

* Add changelog
2020-09-22 19:21:34 -04:00
jamesagnew 190f0ccb22 Add test for #2063 2020-09-01 14:12:57 -04:00
James Agnew dbbff1fd16
Allow HTTP 204 response to transaction (#2051)
* Allow HTTP 204 response to transaction

* Add changelog

* Test fix
2020-08-21 21:00:55 -04:00
James Agnew eab828f47a
Add transactionbuilder (#2041)
* Add transactionbuilder

* Add changelog

* Add creates
2020-08-17 07:47:40 -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
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 5f1078ac13 Cleanup of package installer 2020-07-21 11:43:57 -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
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 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
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
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
James Agnew 46c00f4efb
Update for Loinc 2.68 (#1917)
* Work on loinc updates

* Work on loinc upload

* Clean up CLI config

* Add changelog

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

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

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

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

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

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

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

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Clean up imports

* LOINC fixes

* Loinc loader fixes

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
2020-06-18 16:55:11 -04:00
jamesagnew 4119cbb0c4 Terser should create correct Enumeration on create 2020-06-17 18:32:27 -04:00
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
Martin Zacho Grønhøj 9bde517540
Install external ig package at startup (#1826)
* Do not use deprecated methods in structures-r4 test

* beginning development of feature Implementation Guide installer

* fetch IG, generate snapshots of SDs of and persist conformance resources to db

Missing initialization, error-handling and handling of NameSystems and Subscriptions

* Refactor IgInstaller and implement support for R4 and R5

* Error handling and removed logic for invoking IG installation

IgInstaller should be invoked by applications

* Implement pull request comments in IgInstaller

1) Renamed IgInstaller -> IgInstallerSvc for consistency
2) Use field autowiring and @PostConstruct for consistency
3) Use exceptions instead of boolean flags for success indication
4) Use IValidationSuport to generate snapshots of StructureDefinitions
in a version independent way (less maintenance) instead of SnapshotGenerator.java
5) Read IGs for tests from src/main/resources instead of external URL

* IG installation: Wrap exceptions during resource creation in custom class

* IG installation: Improved logging

* IG installation: Search for existing resources in a version independent way
2020-05-24 09:25:46 -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
Tadgh d1b963321a
MVP EMPI implementation (#1857)
EMPI Initial Implementation (still plenty of known gaps)
2020-05-22 15:03:20 -04:00
James Agnew ce5ade53d9
Fix #1855 - StructureDefinition search not working (#1858) 2020-05-21 09:35:37 -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
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
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 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
jamesagnew 36a7e9c980 Test fixes 2020-04-22 14:56:13 -04:00
jamesagnew 6226381595 Merge branch 'master' into ja_20200206_multitenancy 2020-04-21 20:54:56 -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 33b8e82f79 Compile fix 2020-04-21 09:29:23 -04:00
jamesagnew 544d9fbc6c Add migration tasks 2020-04-20 16:58:48 -04:00
jamesagnew 95b77af570 Merge branch 'master' into ja_20200206_multitenancy 2020-04-20 11:07:10 -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 461739fb32 Add test for millisecond precision 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
jamesagnew e0b419354f Bump up hamcrest version and force the use of the latest version 2020-04-17 13:59:22 -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 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 c1d682ed02 Test fixes 2020-04-09 12:36:33 -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
James Agnew 8cdc3a72ce
Fix #1794 - Client ID and Server ID mode clash (#1795)
* Fix #1794 - Client ID and Server ID mode clash

* Try to track down intermittent test failure
2020-04-09 09:31:13 -04:00
jamesagnew c0df88739a Intermittent test fix 2020-04-08 19:19:30 -04:00
jamesagnew 40d0c27ae3 Work on subscription cleanup 2020-04-05 18:43:27 -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
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 eaaddaf7ca
Fix #1763 - Include bundle type in summary=count responses (#1773)
* Fix #1763 - Include bundle type in summary=count responses

* Test fix
2020-03-24 16:24:41 -04:00
August Langhout 2c1ec8fb0d add test to check that json parsing also fails with identically named contained resources 2020-03-23 19:09:54 -04:00
August Langhout a75bf948c1 Remove personal data 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 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
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
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
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 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 e6d3897700 Add tests 2020-01-30 08:49:40 -05:00
James Agnew a6f3ee8319 Add a unit test 2020-01-29 09:35:22 -05:00
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
James Agnew 0e1f03b999 Work on validation 2019-12-19 14:41:35 -05:00
jamesagnew 549b1c85c3 Test fix 2019-12-12 05:43:05 -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 7745dc4ad4 Don't require fhir core javadocs by default 2019-11-26 02:22:09 -03:00
James Agnew 5f803f7e68 Documentation updates 2019-11-26 02:00:22 -03:00
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 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
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
Stig Rohde Døssing 80bfb9af37 Issue-1077: Make CapabilityStatementProvider use the closest common superclass of provided resources when generating rest.resource.profile, instead of always using the base definition. 2019-11-01 10:20:16 -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 9c852283e9
Correctly handle "special" search params in CS (#1569)
* Correctly handle "special" search params in CS

* Add another test
2019-10-30 05:31:25 -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
James Agnew 74c03b5bb7 Add a test 2019-10-24 08:32:52 -04:00
James Agnew 385a885abf Add ability for resource source to be specified by header 2019-10-24 08:32:52 -04:00
James Agnew 464c6c5b45
Upgrade dependencies and addess Semmle issues (#1554)
* Version bumps

* FIx build issues

* Address a few Semmle issues

* Work on tests

* Some test fixes

* Test fix

* Fix deletions

* Test fix

* Fix intermittent test failure

* One more dependency bump

* Add some test logging

* Remove bad import

* Add some tests

* Test updates
2019-10-22 17:10:58 -04:00
James Agnew a71d969ba1 Add line numbers to validation failures 2019-10-18 14:10:47 -04:00