63218e560d
Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler
2019-12-02 08:59:17 -05:00
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
a58da3b535
name schema initializer to distinguish between different schemas
2019-11-28 12:10:34 -05:00
bf003f0d16
cleaned up cleanup
2019-11-27 21:54:13 -05:00
9693b1736e
fixed quartz sql with a hack. need a better fix.
2019-11-27 17:10:27 -05:00
df57d24333
Add license headers
2019-11-27 04:49:45 -05:00
7593b7f8f7
fix test
2019-11-26 16:57:59 -05:00
82990f3e97
fix test
2019-11-26 10:39:21 -05:00
ef77490c51
fix test
2019-11-26 09:50:40 -05:00
3d00634b16
make migration table name configurable
2019-11-26 09:07:53 -05:00
98d21c4ee3
review feedback
2019-11-23 07:34:49 -05:00
509799095c
don't hash on init script length since it will change. Hash based on class name.
2019-11-04 10:45:02 -05:00
53cedddcab
rename BaseTask constructor parameters
2019-11-04 10:27:34 -05:00
4e2806bea5
add task descriptions
2019-11-04 10:20:54 -05:00
30865588e3
pre-review cleanup
2019-11-04 08:36:24 -05:00
947ac6f096
fix compile error from merge
2019-11-03 21:11:36 -05:00
4c732ce977
Merge remote-tracking branch 'remotes/origin/master' into ks-flyway
2019-11-03 21:07:59 -05:00
f481e11ad5
Update migration tasks
2019-11-03 18:49:47 -05:00
779366ccad
final hashcode equals fix
2019-11-03 15:52:32 -05:00
ea21b59fde
generalize initialize schema interface
2019-11-03 14:02:28 -05:00
5890059362
moar integration tests
2019-11-03 13:46:09 -05:00
de4f909eda
optimize imports
2019-11-02 21:52:35 -04:00
becd6790e8
fix test
2019-11-02 21:51:17 -04:00
8ee06855d7
FIXME cleanup
2019-11-02 21:36:03 -04:00
4cdde60917
FIXME cleanup
2019-11-02 21:32:42 -04:00
8887d41283
added proxy indicator for hash indexes migration having been run (used TRM_CONCEPT_DESIG table existence)
2019-11-02 21:30:40 -04:00
6356205768
fix final task hashcode. Multiple runs now work.
2019-11-02 17:53:21 -04:00
3bfcb42012
fix enum hashcode
2019-11-02 17:48:30 -04:00
0404454167
abort schema initialization if HFJ_RESOURCE table already exists
2019-11-02 17:03:45 -04:00
5577680a85
test hashcodes are consistent (fixed 3 that weren't)
2019-11-02 16:56:39 -04:00
f20fee297a
add hashcode to initializationProvider
2019-11-01 22:02:07 -04:00
071b14cbcc
add hashcode to initializationProvider
2019-11-01 22:00:59 -04:00
7855ce070c
typo
2019-11-01 21:46:15 -04:00
6049ee6f1c
init schema test
2019-11-01 21:40:24 -04:00
3dc2770962
consolidate providers
2019-11-01 21:35:11 -04:00
7066f35e49
persistence migrate from zero works.
2019-11-01 20:39:11 -04:00
49265dea32
added schema initialization but not used yet
2019-11-01 17:18:27 -04:00
5f294f335d
merge
2019-11-01 13:38:18 -04:00
bee993a0ec
Merge remote-tracking branch 'remotes/origin/master' into ks-flyway
...
# Conflicts:
# hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTask.java
# hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropTableTask.java
2019-11-01 13:37:00 -04:00
a5dceca075
Work on migrator task support for dropping tables in postgres
2019-11-01 11:04:20 -04:00
d1814947b3
include version number in log message
2019-10-31 17:12:02 -04:00
0cfea8a871
changed to use hibernate auto ddl flag as a check
2019-10-31 15:47:52 -04:00
f95e4d387d
added schema migration validation
2019-10-31 14:56:55 -04:00
29752465c8
add boolean method FliwayMigrator.migrationRequired() so we can test if we have the current version
2019-10-30 20:27:25 -04:00
7bd29d69fd
all done but removing the old migrator
2019-10-29 21:23:55 -04:00
6cd14122cd
moved version number up to root component
2019-10-29 21:21:54 -04:00
b420578cc5
nudged dates within release date ranges
2019-10-29 20:43:56 -04:00
e8673ecb6f
finished reindexing
2019-10-29 20:40:40 -04:00
28e628ec0e
all done but reversioning
2019-10-29 18:03:13 -04:00
6ba3afb489
All tests pass except noShrink case
2019-10-29 15:30:25 -04:00
c7bd11ed0d
migration version validation tested
2019-10-29 14:54:35 -04:00
788f386ce4
added version order validation
2019-10-29 14:30:17 -04:00
c8c89d976f
Flyway integration test passes
2019-10-29 14:18:41 -04:00
94c8f96856
Add equals and hashcode to tasks for flyway
2019-10-29 13:34:11 -04:00
dd2cb39fd1
tests pass but now need to renumber
2019-10-28 17:45:36 -04:00
a123bfe564
All tests pass except createTableByColumns
2019-10-28 17:28:26 -04:00
f8e15ea69e
added final String release field to migration BaseTask
2019-10-28 16:09:18 -04:00
1aabe9bf40
added final String version field to migration BaseTask
2019-10-28 15:34:21 -04:00
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
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
13b80a294a
Test fix
2019-10-18 07:13:11 -04:00
5dcbed0438
Fix foreign key handling when dropping tables
2019-10-17 15:52:35 -04:00
839f935401
remove unnecessary index
2019-10-15 19:07:37 -04:00
e727769988
FIx a migration task
2019-10-15 18:16:22 -04:00
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
3c24e14a71
Fixed test based on wrong assumption.
2019-10-08 13:39:13 -04:00
23264f497f
Added test.
2019-10-08 13:19:35 -04:00
175c0781eb
Add case for handling JDBC type CLOB in JdbcUtils.
2019-10-08 11:55:03 -04:00
790f655a95
flyway initial implementation (with FIXMEs)
2019-10-06 17:55:10 -04:00
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
260cee023a
Account for longer resource type names
2019-10-02 10:00:45 -04:00
826cb0ff10
Fix migration task for TermConceptProperty; should be BLOB, not CLOB. Good job!
2019-09-30 20:18:20 -04:00
396f358f2d
Support for long concept property values has been added.
2019-09-30 14:40:31 -04:00
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
945cc6419f
fixed npe
2019-09-24 18:13:53 -04:00
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
f4252cdeaa
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-21 08:54:59 -04:00
0cbb33eded
Fix up migratiom tasks for 4.1.0
2019-09-21 08:54:33 -04:00
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
6b21e8cd90
Add some testing to the bulk export service
2019-09-18 14:43:00 -04:00
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
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
dded46d220
fixed bug in drop fk migration task
2019-09-06 10:27:20 -04:00
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
785d40a777
Accuont for a few schema changes
2019-09-05 21:29:47 -04:00
b1421b1d60
@NotNull (hope I picked the right one!)
2019-09-05 16:20:24 -04:00
2a08808935
final PR cleanup
2019-09-05 16:11:58 -04:00
14fadd3004
fix drop foreign key task
2019-09-05 15:51:38 -04:00
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
ea19b46f60
Added an indexed order column to TermValueSetConcept for improved fetching.
2019-09-03 20:36:16 -04:00
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
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
890555a77d
Incremental work on large ValueSet expansion support; transaction boundaries need to be broken up.
2019-08-23 11:46:32 -04:00
6fa27934a8
Tests all seem to be working
2019-08-23 10:14:13 -04:00
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
a839a645db
Skip ModifyColumn migration tasks for columns that don't exist
2019-08-12 17:19:25 -04:00
af9fc882c1
fix log message
2019-08-01 19:11:06 -04:00
f05d212a40
Fixed a data migration error KHS & DM
2019-08-01 17:22:18 -04:00
8475aa4cc8
Add TRM_CODESYSTEM_VER.CS_DISPLAY to migration tool.
2019-08-01 14:44:03 -04:00
78842164fd
Addressing review comments.
2019-08-01 13:37:46 -04:00
a8489f4331
Added TRM_VALUESET.EXPANSION_STATUS column, index, fields to entity, and migration tasks.
2019-07-29 19:30:46 -04:00
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
03918fe29a
Add some javadoc
2019-07-19 13:42:01 -04:00
d304a8fb6c
Add a safety check to rename column task
2019-07-19 12:13:35 -04:00
6ff8484914
One migrator tweak
2019-07-19 10:17:42 -04:00
f53746cd63
One more set of migrator tweaks to account for latest changes
2019-07-19 10:10:00 -04:00
fd23190b4c
Fix on drop table task
2019-07-19 09:38:13 -04:00
cf68efb826
Add drop table task to migrator
2019-07-19 09:33:01 -04:00
ee7cff9445
Rename a few columns to not conflict with res´rved words
2019-07-18 05:47:32 -04:00
456aac5e16
Resolve "experimental implementation for storing and expanding large ValuetSets cont'd..." ( #1376 )
...
* Added experimental implementation for storing expanded ValueSets in terminology tables.
* Minor tweak to log message for consistency.
* Another minor tweak to log message for consistency.
* Renamed test.
* Initial work on ValueSetCodeAccumulator.
* Renamed addCode() to includeCode(); added excludeCode().
* Incremental work on large ValueSet expansion support; refactoring.
* Incremental work on large ValueSet expansion support; accounting for designations.
* Incremental work on large ValueSet expansion support; fixed missing designation.language in expanded ValueSets.
* Incremental work on large ValueSet expansion support; now actually populating TermConceptDesignation; added TermValueSetConceptDesignation as well.
* Missed a word.
* Tweak changelog entries.
2019-07-16 17:12:21 -04:00
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
8d817b364c
Merge remote-tracking branch 'remotes/origin/master' into expunge-hooks
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
2019-07-12 13:27:11 -04:00
0729e38e6e
Resolve "experimental implementation for storing expanded ValueSets in terminology tables" ( #1369 )
...
* Added experimental implementation for storing expanded ValueSets in terminology tables.
* Minor tweak to log message for consistency.
* Another minor tweak to log message for consistency.
* Renamed test.
* Addressing review comments.
* Added migration tasks.
2019-07-11 16:52:19 -04:00
dff2fdd3cf
GET RID OF TRAILING LICENSE HEADER SPACES ONCE AND FOR ALL
...
YESSSSSSSSSSSSS
2019-07-05 11:19:51 -04:00
f160fbb36f
License updates
2019-07-05 10:24:56 -04:00
2a6436af23
Rename columns in code mapping
2019-07-05 09:03:03 -04:00
78e6a7ba6f
Add suport for float type to migrator
2019-06-06 09:21:17 -04:00
c7a224c99d
Merge branch 'master' into upgrade-25-to-33
2019-05-29 21:33:02 -04:00
738c2c1797
Interceptor framework refactoring ( #1287 )
...
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
75b6857902
Add ability to execute arbitrary SQL to migrator tool
2019-04-04 09:24:51 -04:00
1311ded7de
Fix compile issue
2019-02-15 14:55:25 -05:00
09920ad545
Reduce thread contention during tests
2019-02-15 14:18:34 -05:00
c4dd06ad0c
Make it easier to add tables with migrator tools
2019-02-15 13:27:07 -05:00
4a6345d7c4
Improve command chaining in migrator tool
2019-02-15 12:54:41 -05:00
a2d0168671
Fix handling of sequences in migrator tool
2019-01-15 11:31:18 -06:00
98d93df12a
License header updates
2019-01-04 16:22:15 -05:00
49e418edf0
Adjust migrator to handle updated Hibernate version
2018-12-23 15:11:44 -05:00
a0cb7edd08
Version bump a few dependencies
2018-12-22 20:13:03 -05:00
5824826eff
Add support for booleans in the migrator
2018-12-20 10:24:17 -05:00
86b3e45a32
License header updates
2018-12-18 14:08:01 -05:00
11b8304cb4
Fix case sensitivity issue
2018-12-13 08:31:35 -05:00
4fea74cfa2
Fix incorrectly grabbed table
2018-12-13 00:49:17 -05:00
a01d6cf302
Add init330() to migrate from 2.5 -> 3.3
2018-12-12 21:00:41 -05:00
8c7f249a21
Migrator enhancements and adjust reindexer to account for missing
...
versions
2018-12-04 17:33:29 -05:00
6baee4dc3f
Standalone subscription ( #1125 )
2018-11-30 17:19:16 -05:00
b2179b1696
Syntax fixes for the JPA migrator
2018-11-30 12:39:37 -05:00
650872cd3e
Address SQL syntax issue
2018-11-29 08:37:50 -05:00
896568c0f7
License updates
2018-11-04 16:06:53 -05:00
bc72093555
Add reindexing support based on table instead of column
2018-11-04 20:00:27 +01:00
8c2d868f16
License updates
2018-11-01 16:13:34 -04:00
9906243d2d
More migrator updates
2018-11-01 13:58:09 -04:00
c8834cd29a
Merge branch 'philips-3.6.0' of github.com:jamesagnew/hapi-fhir into philips-3.6.0
2018-10-31 17:19:28 -04:00
721c1cd405
Drop column that should have been dropped in 3.4 to 3.5 migration
2018-10-31 16:47:40 -04:00
8955a9e54d
Add threading to migrator
2018-10-31 05:50:50 -04:00
8b46257423
Add warm cache module
2018-10-14 09:32:07 -04:00
eb7b5ca02a
One more missing index
2018-10-12 11:07:15 -04:00
7665e472ad
Add missing migration task
2018-10-12 11:02:01 -04:00
970c48ec37
A bit more test cleanup
2018-10-04 13:29:09 -04:00
9d1e8aa246
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-01 21:36:52 -04:00
12b23fbf23
Make JPA searches more efficient by prefetching a much smaller number of
...
resources
2018-10-01 21:36:10 -04:00
caf7c8b2e1
Header updates
2018-10-01 17:04:50 -04:00
3e445faf47
Squashed commit of the following:
...
commit df641506885e09e63f80efc6c658d01a1a3a8142
Author: James Agnew <jamesagnew@gmail.com>
Date: Sat Sep 29 13:47:22 2018 -0400
Shrink validation resources
commit 4c1550eafa26f4235b4b8804741aecc03276b5c6
Author: James Agnew <jamesagnew@gmail.com>
Date: Fri Sep 28 22:45:28 2018 -0400
Updates to get R4 working
commit 8332f15291006691ed9b07ead3e3524b0fc85510
Author: jamesagnew <jamesagnew@gmail.com>
Date: Fri Sep 28 09:02:13 2018 -0400
Ongoing work on gettign R4 working
commit f7146cab7aed937bb625a8aec95744d76db00041
Author: James Agnew <jamesagnew@gmail.com>
Date: Fri Sep 28 05:21:01 2018 -0400
More work on sync
commit f48de4a10b1bab2584fee813017d9b27b237bfa9
Merge: 9e4f3cc722 aacb78b779
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Sep 27 20:11:29 2018 -0400
Merge branch 'sync_r4' of github.com:jamesagnew/hapi-fhir into sync_r4
commit 9e4f3cc722668aae31a77b19bf9b032af3ae01b0
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Sep 27 20:11:19 2018 -0400
Fix compile error
commit 7ec29e0ceda8f9013cbabb95767cbe15b4b81303
Merge: 23f7517325 002c4b3ff7dfb4de86f1
2018-09-29 13:48:35 -04:00
dc4c0809a4
Automatically detect suitable database drivers
2018-09-25 09:58:08 -04:00
706e004b9d
Bump to 3.6.0-SNAPSHOT
2018-09-19 10:24:48 -04:00
3bfce11d2c
Add OSGI dependency for commons-text
2018-09-17 16:06:11 -04:00
7bbe33cffc
Finalizing 3.5.0 release
2018-09-17 16:04:52 -04:00
664fd2fede
Correct foreign key upgrading on PG
2018-09-17 14:37:49 -04:00
125176cd75
Add indexes
2018-09-17 14:34:35 -04:00
efe2b8e93d
Correct PG migrator syntax
2018-09-17 13:52:22 -04:00
798982773a
Restore old driver logic
2018-09-17 13:46:21 -04:00
fd5854ea85
Migrator enhancements
2018-09-17 13:33:44 -04:00
c34dfda413
Update migration tasks
2018-09-17 13:19:40 -04:00
44dccb8e3f
Migrator
2018-09-17 12:53:44 -04:00
2dc6159af5
Fix drop column command
2018-09-17 11:35:05 -04:00
7e4d6afc5f
Migrator enhancements
2018-09-17 09:24:04 -04:00
bb7fca19a3
Work on migrator
2018-09-14 08:34:39 -04:00
4852b0b60f
Work on migration
2018-09-08 07:14:43 +08:00
f5d567cd00
Work on migrator
2018-09-08 03:30:35 +08:00
77305eb570
Work on migrator
2018-09-04 10:32:08 +08:00
07cfed14b8
Work on migrator
2018-08-27 08:21:20 -04:00
1ff8f45a3e
Start working on migrator
2018-08-26 12:29:05 -04:00
67fede9eda
Start work on migrator
2018-08-23 05:24:13 -04:00
Ken Stevens
James Agnew
Diederik Muylwyk
Ruslan_Zinovyev
Graham, Gary
Ken Stevens