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250 Commits

Author SHA1 Message Date
Ken Stevens 8c7c4fc56f configurable table name 2019-11-26 13:40:03 -05:00
Ken Stevens 01ebe9ae8c Revert "fix test" 
This reverts commit 3b35724b
 2019-11-26 12:07:31 -05:00
Ken Stevens 3b35724bdd fix test 2019-11-26 11:36:25 -05:00
Ken Stevens 3d00634b16 make migration table name configurable 2019-11-26 09:07:53 -05:00
Ken Stevens 6543da1470 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 2019-11-15 09:28:30 -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
Ken Stevens 30865588e3 pre-review cleanup 2019-11-04 08:36:24 -05:00
Ken Stevens 5890059362 moar integration tests 2019-11-03 13:46:09 -05:00
Ken Stevens de4f909eda optimize imports 2019-11-02 21:52:35 -04:00
Ken Stevens bb0f71f271 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 2019-11-02 21:51:47 -04:00
Ken Stevens fd9d61018c FIXME 2019-10-31 17:14:54 -04:00
Ken Stevens f95e4d387d added schema migration validation 2019-10-31 14:56:55 -04:00
Ken Stevens d29e112e26 removed old migration command 2019-10-30 17:32:46 -04:00
James Agnew d3e66680f0 Add some testing 2019-10-30 09:49:40 -04:00
Ken Stevens c8c89d976f Flyway integration test passes 2019-10-29 14:18:41 -04:00
Ken Stevens 18e8604494 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
 2019-10-27 08:29:52 -04:00
James Agnew 9b94e4e26d
Allow uploading term deltas using CS resource (#1555) 
* Work on accepting codesystem reources for delta operations

* Ongoing work on term uploader

* Restore the ability to use CodeSystem resources for the delta

* Add tests

* Fix NPE

* Test fixes
 2019-10-22 17:11:39 -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 12a74e6cbc
Fix term uploads and validate against valueset recalculation (#1540) 
* Start refactoring terminology delta operations

* Work on delta operations

* Work on concept saving

* Split term services into smaller services

* Work on term delta operations

* Work on term svcs

* Work on term operations

* More work on delta uploader

* Add a test

* Wrk on term service

* Fix compile error

* Some refactoring

* Test fix

* Test fix

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Work on delta

* Work on tests#

* Test fixes

* Improve resequencing logic

* Build test

* More testing

* More build testing

* More work on tests

* CHange test logging

* Fix term service PID issue

* Update src/changes/changes.xml

Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Address review comment

* Some cleanup

* Test fix

* Fix some tests

* Work on upload command

* Test fixes

* Work on validation fixes

* Work on validation against pre-expansion

* Work on direct validation

* A bit of cleanup

* Add some javadoc

* Force another build

* Test fixes

* Fix tests

* Fix tests
 2019-10-15 21:31:29 -04:00
James Agnew 2725797610
Implement Terminology Delta Operations (#1536) 
* Start refactoring terminology delta operations

* Work on delta operations

* Work on concept saving

* Split term services into smaller services

* Work on term delta operations

* Work on term svcs

* Work on term operations

* More work on delta uploader

* Add a test

* Wrk on term service

* Fix compile error

* Some refactoring

* Test fix

* Test fix

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Work on delta

* Work on tests#

* Test fixes

* Improve resequencing logic

* Build test

* More testing

* More build testing

* More work on tests

* CHange test logging

* Fix term service PID issue

* Update src/changes/changes.xml

Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Address review comment

* Some cleanup

* Test fix

* Fix some tests

* Test fixes
 2019-10-14 19:14:41 -04:00
Ken Stevens 790f655a95 flyway initial implementation (with FIXMEs) 2019-10-06 17:55:10 -04:00
James Agnew 2193a30b45
CodeSystem Delta Uploader (#1520) 
* Terminology Delta Uploading

* Add delta operations

* Fix up tests

* Improve test coverage a bit

* Improve test coverage reporting

* fix yaml

* A couple of test enhancements

* FIx intermittent test failure
 2019-10-03 07:19:00 -04:00
James Agnew c8ce07c40e Deprecate redundant IVersionSpecificBundleProvider method 2019-09-30 09:45:31 -04:00
James Agnew f5788341f2
Add no-shrink-columns option to migrator (#1500) 
* Add no-shrink-columns option to migrator

* Address review comments
 2019-09-23 18:44:51 -04:00
James Agnew 4a751cbfc5
Integrate Bulk Export (#1487) 
* Start working on subscription processor

* Work on new scheduler

* Test fixes

* Scheduler refactoring

* Fix test failure

* One more test fix

* Updates to scheduler

* More scheduler work

* Tests now all passing

* Ongoing work on export

* Ongoing scheduler work

* Ongoing testing

* Work on export task

* Sync master

* Ongoing work

* Bump xml patch version

* Work on provider

* Work on bulk

* Work on export scheduler

* More test fies

* More test fixes

* Compile fix

* Reduce logging

* Improve logging

* Reuse bulk export jobs

* Export provider

* Improve logging in bulk export

* Work on bulk export service

* One more bugfix

* Ongoing work on Bulk Data

* Add changelog
 2019-09-17 16:01:35 -04:00
jamesagnew 8b09b3f3eb Rename config enum for consistency 2019-09-03 07:01:36 -04:00
James Agnew 1b1d80b850 Test fix 2019-08-29 21:02:19 -04:00
Diederik Muylwyk 3218bd7853 Incremental work on large ValueSet expansion support; implemented paging when reading concepts from the terminology tables. Switched from Derby to H2. 2019-08-20 18:11:53 -04:00
Diederik Muylwyk b84d6c7061 Fix deprecated references to versioned TerminologyUploaderProvider. 2019-08-19 10:28:05 -04:00
jamesagnew e1b43d811f Version bump to 4.1.0-SNAPSHOT 2019-08-14 14:06:06 -04:00
jamesagnew 3f22456b0f Bump version to 4.0.0 2019-08-14 11:06:26 -04:00
James Agnew 0c9e5ec1ea
Support GraphQL for R3/4/5 (#1424) 
* Work on grpahql enhanbcements

* Add some more chars to the sanitizer function

* Add changelog
 2019-08-12 08:24:32 -04:00
James Agnew dd0cb10dbb
validate operation ignores parameter profile (#1417) 
* This should be working now - need to check tests

* Add a changelog and some docs

* One more test fix

* Tests should be passing

* Fix compile

* Test fixes

* Ignore outdated DSTU2 validation test
 2019-08-07 15:31:59 -04:00
James Agnew 60eab3ad70
Add support for R5 resources (#1416) 
* Work so far on R5 support

* Add support for R5

* Docs changes
 2019-08-06 17:30:31 -04:00
Ken Stevens 808da73854
Merge pull request #1413 from jamesagnew/ks-migration-tests 
test all migrations to latest version
 2019-08-02 16:13:24 -04:00
Ken Stevens 48c8497086 Changed migration test from derby to h2 
Added a new test from 340 to latest version.
 2019-08-02 16:00:43 -04:00
Diederik Muylwyk 345ce880ce Address review comments. 2019-08-02 14:45:59 -04:00
Diederik Muylwyk ca01f31ca9 Enable support of DSTU3 for upload-terminology command. 2019-08-02 14:00:56 -04:00
James Agnew 04ce9cfc1a Add support for uploading custom terminology using the 
$upload-external-code-system operation
 2019-07-30 17:30:18 -04:00
James Agnew a4ca5374ec
Add terminology delta operations (#1401) 
* Start work on delta operations

* Add changelog

* Some build fixes

* Move upload terminology command to CodeSystem resource

* Updates

* Some test fixes

* Add changelog

* Some test fixes

* More test fixes

* Test fix

* Add additional tests

* Transaction boundary fixes
 2019-07-29 17:46:42 -04:00
James Agnew 33531f9010 Add some test logging 2019-07-14 16:56:43 -04:00
James Agnew 7831e8a0ed Add support for $snapshot generation and validation based on snapshots 2019-07-14 16:15:56 -04:00
James Agnew 120b93f204
Use HL7 FHIR Core Structures (#1382) 
* Ongoing work on core structures suport

* Ongoing work on this merge

* Ongoing work to clean up structures

* Credit for #1179

* Address compile issues

* Latest changes

* Work on parallel execution

* Work on getting tests passing

* Add H2 to migrator

* Test fix
 2019-07-14 10:16:40 -04:00
jamesagnew dff2fdd3cf GET RID OF TRAILING LICENSE HEADER SPACES ONCE AND FOR ALL 
YESSSSSSSSSSSSS
 2019-07-05 11:19:51 -04:00
James Agnew af7de15b0f Add cascading deletes to CLI 2019-06-30 13:04:26 -04:00
James Agnew 10d969c514
Add Consent Service (#1359) 
* Initial consent svc

* Ongoing consent svc work

* Add docs

* Ongoing consent service work

* Work on consent service

* More work on consent svc

* License header updates

* Ongoing consent svc work

* Some test fixes

* Some test fixes

* More work on consent svc

* Tests working

* Test fix

* Propagate RequestDetails to everything in JPA server

* More interceptor tweaks

* Fix compile error

* One more tweak to captured SQL

* Ongoing interceptor tweaks

* Ongoing interceptor tweaks

* More interceptor tweaks

* Interceptor tweaks

* Tweaks to tests

* Fix tests

* Test fix

* Raise warnings when encoding extensions with missing values

* Consent service work

* More interceptor tweaks

* Consent interceptor tweaks

* Add logging to test
 2019-06-27 16:35:29 -04:00
Stig Rohde Døssing b56f59542a Move JettyUtil to new module 2019-06-14 18:34:45 -04:00
Stig Rohde Døssing aab7bb6b64 Issue-1325: Let OS assign random ports to servers during testing, and let tests get the port of the running server once the OS has assigned a port. Delete PortUtil and similar utilities. 2019-06-14 18:34:45 -04:00
jamesagnew b72f1c4555 Roll back derby upgrade 2019-06-08 09:27:28 -04:00