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127 Commits

Author SHA1 Message Date
James Agnew a5dceca075 Work on migrator task support for dropping tables in postgres 2019-11-01 11:04:20 -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 13b80a294a Test fix 2019-10-18 07:13:11 -04:00
James Agnew 5dcbed0438 Fix foreign key handling when dropping tables 2019-10-17 15:52:35 -04:00
James Agnew 839f935401 remove unnecessary index 2019-10-15 19:07:37 -04:00
James Agnew e727769988 FIx a migration task 2019-10-15 18:16:22 -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
Diederik Muylwyk 3c24e14a71 Fixed test based on wrong assumption. 2019-10-08 13:39:13 -04:00
Diederik Muylwyk 23264f497f Added test. 2019-10-08 13:19:35 -04:00
Diederik Muylwyk 175c0781eb Add case for handling JDBC type CLOB in JdbcUtils. 2019-10-08 11:55:03 -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 260cee023a Account for longer resource type names 2019-10-02 10:00:45 -04:00
Diederik Muylwyk 826cb0ff10 Fix migration task for TermConceptProperty; should be BLOB, not CLOB. Good job! 2019-09-30 20:18:20 -04:00
Diederik Muylwyk 396f358f2d Support for long concept property values has been added. 2019-09-30 14:40:31 -04:00
James Agnew 8657afb01e
Fix intermittent test failures regarding search (#1509) 
* Add some logging

* Add more test logging

* Work on some test logging

* Fix compile error

* Work on codecov

* Work on codecov

* Remove test debug messages
 2019-09-25 20:15:21 -04:00
Ken Stevens 945cc6419f fixed npe 2019-09-24 18:13:53 -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 f4252cdeaa Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-21 08:54:59 -04:00
James Agnew 0cbb33eded Fix up migratiom tasks for 4.1.0 2019-09-21 08:54:33 -04:00
Diederik Muylwyk e1e8ec981b Replaced migration task column length constants with literals because they are not necessarily constant across schema versions. 2019-09-20 12:31:54 -04:00
James Agnew 6b21e8cd90 Add some testing to the bulk export service 2019-09-18 14:43:00 -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
Diederik Muylwyk 67d24eedff Merging master into working branch. 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
 2019-09-09 19:01:29 -04:00
Ken Stevens dded46d220 fixed bug in drop fk migration task 2019-09-06 10:27:20 -04:00
Ken Stevens c88e6a6fa7
Merge pull request #1442 from jamesagnew/ja_20190822_1440_infinispan_query_cache 
Externalize query cache into its own service
 2019-09-06 08:28:12 -04:00
James Agnew 785d40a777 Accuont for a few schema changes 2019-09-05 21:29:47 -04:00
Ken Stevens b1421b1d60 @NotNull (hope I picked the right one!) 2019-09-05 16:20:24 -04:00
Ken Stevens 2a08808935 final PR cleanup 2019-09-05 16:11:58 -04:00
Ken Stevens 14fadd3004 fix drop foreign key task 2019-09-05 15:51:38 -04:00
Ken Stevens fa62ab9c9e Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache 
# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	src/changes/changes.xml
 2019-09-04 13:31:00 -04:00
Diederik Muylwyk ea19b46f60 Added an indexed order column to TermValueSetConcept for improved fetching. 2019-09-03 20:36:16 -04:00
Diederik Muylwyk b42b598d01 Added pre-fetch for concept designations, improved paging for expanded ValueSets, and columns on TermValueSet for number of concepts and designations. 2019-09-03 16:02:28 -04:00
Ken Stevens 259426b0dd Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache 
# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	src/changes/changes.xml
 2019-08-28 10:37:17 -04:00
Diederik Muylwyk 890555a77d Incremental work on large ValueSet expansion support; transaction boundaries need to be broken up. 2019-08-23 11:46:32 -04:00
James Agnew 6fa27934a8 Tests all seem to be working 2019-08-23 10:14:13 -04:00
James Agnew 9428430822
Add support for Resource.meta.source (#1438) 
* Work on indexing source

* Work on tests

* Refactor query count tests

* Unit test fixes

* Add some tests

* DAO fix

* Fix compile error

* Unit test fix

* Cleanup

* Test fix

* Fix compile error

* One more test fix
 2019-08-21 11:17:43 -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
Ruslan_Zinovyev a839a645db Skip ModifyColumn migration tasks for columns that don't exist 2019-08-12 17:19:25 -04:00
Ken Stevens af9fc882c1 fix log message 2019-08-01 19:11:06 -04:00
Ken Stevens f05d212a40 Fixed a data migration error KHS & DM 2019-08-01 17:22:18 -04:00
Diederik Muylwyk 8475aa4cc8 Add TRM_CODESYSTEM_VER.CS_DISPLAY to migration tool. 2019-08-01 14:44:03 -04:00
Diederik Muylwyk 78842164fd Addressing review comments. 2019-08-01 13:37:46 -04:00
Diederik Muylwyk a8489f4331 Added TRM_VALUESET.EXPANSION_STATUS column, index, fields to entity, and migration tasks. 2019-07-29 19:30:46 -04:00
James Agnew 7e3d062d15
Switch default client to JSON (#1392) 
* Start work on changing over

* Update tests

* More test fixes

* Work on generalizing binary access provider a bit

* Add expunge capability to binary storage, and also support actual binary
resources

* Work on binary provider

* Get the DB bound binary storage service working

* Test fixes

* Compile fix

* Fix compile error

* Test fix

* Test tweak

* Trying to figure out an intermittent failure

* Work on tests

* More work on tests

* Another test fix
 2019-07-22 21:27:10 -04:00
James Agnew 03918fe29a Add some javadoc 2019-07-19 13:42:01 -04:00
James Agnew d304a8fb6c Add a safety check to rename column task 2019-07-19 12:13:35 -04:00
James Agnew 6ff8484914 One migrator tweak 2019-07-19 10:17:42 -04:00
James Agnew f53746cd63 One more set of migrator tweaks to account for latest changes 2019-07-19 10:10:00 -04:00
James Agnew fd23190b4c Fix on drop table task 2019-07-19 09:38:13 -04:00