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
0a5c52122e
added list stresstest
2019-09-04 08:49:18 -04:00
b00b1d2278
Toggle pre-expansion config.
2019-09-03 20:36:54 -04:00
ea19b46f60
Added an indexed order column to TermValueSetConcept for improved fetching.
2019-09-03 20:36:16 -04:00
aa9a984075
Don't trust stored total when determining whether or not to expand.
2019-09-03 18:44:52 -04:00
358f649d1f
Minor tweaks following review.
2019-09-03 17:14:31 -04:00
3e522a7414
Address review comments.
2019-09-03 16:37:28 -04:00
6ebc9572ac
Adjust concept and designation totals as we process.
2019-09-03 16:23:20 -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
1ef70a0fca
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-09-03 07:02:09 -04:00
8b09b3f3eb
Rename config enum for consistency
2019-09-03 07:01:36 -04:00
02a896f31e
Fix NPE for ValueSet operation validate-code when Coding and/or CodeableConcept is null for DSTU3/R5.
2019-09-02 21:28:51 -04:00
c34d8458ef
Refactor getting resource PIDs with utility methods.
2019-09-02 18:16:46 -04:00
16963881b0
Reset pre-expansion schedule.
2019-08-30 19:36:34 -04:00
548647defe
Toggle pre-expansion config.
2019-08-30 19:31:45 -04:00
f29abd7167
Fixed ResourceTable lookups for pre-expansion and code validation.
2019-08-30 19:31:05 -04:00
9f7cf3923b
Merge pull request #1458 from jamesagnew/1457-valueset-pre-expansion-need-to-account-for-existing-valuesets-and-user-assigned-ids
...
Resolve "ValueSet pre-expansion - need to account for existing ValueSets and user-assigned IDs."
2019-08-30 10:48:39 -04:00
8ef9c61b83
Address review comments; improve logging.
2019-08-30 10:47:21 -04:00
8700088c67
Missed a keyword
2019-08-29 22:06:43 -04:00
668af76514
Make method static again
2019-08-29 22:03:58 -04:00
347aada62e
Add a setter for unit tests
2019-08-29 21:43:29 -04:00
dbe86c8669
One more test fix
2019-08-29 21:35:07 -04:00
1b1d80b850
Test fix
2019-08-29 21:02:19 -04:00
e03d6a5d47
Fixed handling of pre-expansion in light of pre-existing, non-pre-expanded ValueSets.
2019-08-29 18:09:30 -04:00
c5a88444b6
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-08-29 14:00:37 -04:00
956bb39327
Resolve an inefficient regex expression
2019-08-29 13:59:31 -04:00
c22bf8b09f
Fixed handling of client-assigned IDs throughout terminology services.
2019-08-29 10:48:54 -04:00
e67a750c4f
validate-code operation now works with client-assigned IDs; added a bunch of failing tests to work on tomorrow.
2019-08-28 18:49:18 -04:00
d2ae3c24a1
FIXME
2019-08-28 16:26:56 -04:00
3e58962ac1
Split search cache api from search result cache api.
2019-08-28 16:24:56 -04:00
eab589bcac
fixed intermittently failing test
2019-08-28 13:11:44 -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
9ef0519b4c
validate-code operation has been optimized for large ValueSets; submitting pull request.
2019-08-27 21:15:12 -04:00
6b0084fc3b
Merge pull request #1448 from jamesagnew/1447-loinc-filenames-should-be-configurable
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Resolve "LOINC filenames should be configurable."
2019-08-27 13:47:40 -04:00
94c7fc49fd
Making LOINC filenames configurable; fix implicit ValueSet URL for loinc-all.
2019-08-27 13:46:42 -04:00
1adfda44d9
Making LOINC filenames configurable; ready for review.
2019-08-27 11:19:01 -04:00
70d0a8aa8f
Get patch working ( #1449 )
2019-08-27 05:42:15 -04:00
f4789247b2
Making LOINC filenames configurable; fix IEEE medical device code property key.
2019-08-26 18:46:57 -04:00
0765254024
Making LOINC filenames configurable; initial commit.
2019-08-26 18:32:21 -04:00
0ee15874ca
loinc-all ValueSet is now created automatically when loading LOINC terminology.
2019-08-26 16:42:37 -04:00
073d2a45a4
Multiaxial hierarchy support is implemented; we not populated parent and child properties.
2019-08-26 14:26:38 -04:00
17f58a61c3
Revert "add accessor to search hash"
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This reverts commit 2dc70c92
2019-08-24 14:13:06 -04:00
2dc70c92f1
add accessor to search hash
2019-08-24 14:10:17 -04:00
b41926307c
Completed work on large ValueSet expansion support; ready for review.
2019-08-23 17:40:45 -04:00
10958a8e4d
I think this might work now..
2019-08-23 12:22:27 -04:00
c564052b15
One more test fix
2019-08-23 11:46:56 -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
c346ba92c8
Revert accidental commit
2019-08-23 11:17:02 -04:00
abc894ce90
A few refactors based on ken's suggestions
2019-08-23 10:57:58 -04:00
6fa27934a8
Tests all seem to be working
2019-08-23 10:14:13 -04:00
97a235ddfc
Merging master into working branch.
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
2019-08-22 14:02:56 -04:00
72dd6b2922
Incremental work on large ValueSet expansion support; fixed broken deletion for TermValueSetConceptDesignation.
2019-08-22 14:00:08 -04:00
4afa55ea26
Initial commit - Not yet compiling
2019-08-22 08:49:34 -04:00
37c1ba44fe
Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump
2019-08-21 15:04:16 -04:00
9428430822
Add support for Resource.meta.source ( #1438 )
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* 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
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
5703b55e88
Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump
2019-08-20 15:08:25 -04:00
df7469731b
turn of sql queries
2019-08-20 15:02:02 -04:00
ce44115152
Handle cascading deletes correctly with circular references ( #1435 )
...
* Handle cascading deletes correctly with circular references
* A bit of cleanup
* Address review comments
* FIx some javadocs
* Fix an incorrect message
2019-08-20 10:08:34 -04:00
daf45db2be
fixed a test and removed awaitility excludes
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mvn install completed successfully
2019-08-20 09:14:21 -04:00
70aef7fbbb
Incremental work on large ValueSet expansion support; need pageable results while querying TRM_VALUESET_CONCEPT.
2019-08-19 18:43:43 -04:00
53364a3af1
Downgraded FIXMEs to TODOs regarding -code for large ValueSets.
2019-08-19 02:50:01 -04:00
8590e0ca4d
Merging master into working branch.
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
2019-08-19 02:28:30 -04:00
dfd098c374
Incremental work on large ValueSet expansion support; added use of terminology tables when expanding.
2019-08-19 02:26:12 -04:00
54657214de
FIx issue uploading US Core resources
2019-08-17 18:11:52 -04:00
89aa37ea6a
Add a test
2019-08-17 15:16:11 -04:00
81adc5c99e
Merge master
2019-08-17 14:31:30 -04:00
970c421311
allow urls in batch transactions to start with /
2019-08-17 14:31:30 -04:00
f252cda126
Test fixes
2019-08-17 14:15:28 -04:00
74c83f6148
Test fixes
2019-08-17 12:01:04 -04:00
9e8af58e81
Fix reference params via filter
2019-08-16 14:56:36 -04:00
4490c9ca09
Correct the eq operator on the _filter parameter
2019-08-14 14:39:40 -04:00
b37c4b5ae7
Fixing broken unit tests
2019-08-14 14:35:18 -04:00
d92be90789
Changes to subscriptions to include the resource that triggered the subscription in the payload, serialized as JSON or XML depending on the Subscription.channel.payload property's value
2019-08-14 14:35:18 -04:00
e1b43d811f
Version bump to 4.1.0-SNAPSHOT
2019-08-14 14:06:06 -04:00
3f22456b0f
Bump version to 4.0.0
2019-08-14 11:06:26 -04:00
b4fece0ae9
Add interceptor hook for graphql calls
2019-08-13 14:46:50 -04:00
e2f0f4ed8b
License header updates
2019-08-13 05:28:35 -04:00
301a8f8432
Merge #1146 - Filter implementation ( #1220 )
...
* Initial commit of _filter keyword implementation.
* - Completed all search parameter types for _filter.
- Implemented handling for _has, _id, _security, language, _profile, _security, and _tag.
* - Changes to support "ne" matching on resource ID for _filter
* Implemented language
* Commit/push before creation of pull request
* Ongoing merge work
* Ongoing merge work
* Merge master in
* Test fix
2019-08-12 11:59:33 -04:00
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
2999a292e6
Get subscriptions working for R5
2019-08-11 18:32:47 -04:00
d316ec1146
Fix NPE
2019-08-11 18:25:02 -04:00
2518d4e0be
Add some tests
2019-08-08 15:23:55 -04:00
4e1bbe681a
Bump supported PGSQL driver
2019-08-08 15:12:29 -04:00
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
b0eb19cf2f
A few fixes resulting from the R5 merge
2019-08-06 17:55:51 -04:00
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
8475aa4cc8
Add TRM_CODESYSTEM_VER.CS_DISPLAY to migration tool.
2019-08-01 14:44:03 -04:00
d67de13708
Syncing master into working branch.
2019-08-01 13:51:26 -04:00
78842164fd
Addressing review comments.
2019-08-01 13:37:46 -04:00
46c8c61932
Restore build - May need to roll back the RDF changes
2019-08-01 10:14:56 -04:00
ffda92514a
Incremental work on large ValueSet expansion support; still need to actually use the terminology tables when expanding.
2019-07-31 16:33:50 -04:00
0e2dcce841
Incremental work on large ValueSet expansion support; still need to fix asynchronous tests and actually use the terminology tables when expanding.
2019-07-31 15:52:25 -04:00
3196bc370f
Add a default implementation to new terminology service loader method
2019-07-31 10:07:51 -04:00
b956b7552e
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-07-30 17:52:47 -04:00
04ce9cfc1a
Add support for uploading custom terminology using the
...
$upload-external-code-system operation
2019-07-30 17:30:18 -04:00
d1cba9f928
Syncing master into working branch.
2019-07-29 19:39:29 -04:00
cf5201c67b
Add a constructor
2019-07-29 19:31:47 -04:00
a8489f4331
Added TRM_VALUESET.EXPANSION_STATUS column, index, fields to entity, and migration tasks.
2019-07-29 19:30:46 -04:00
a3cbdf0956
Make terminologyuploaderprovider not abstract
2019-07-29 19:02:51 -04:00
b030d1af31
Test fixes
2019-07-29 18:17:40 -04:00
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
d03fc0f61d
Add null check for shortName before adding designation. ( #1396 )
2019-07-25 11:06:02 -04:00
a7817b07ca
Pre PR cleanup
2019-07-24 22:00:34 -04:00
a20b738161
Pre PR cleanup
2019-07-24 22:00:26 -04:00
84f5c7d467
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-24 21:54:05 -04:00
e05387da02
Recover from failed merge again. This time with feeling!
2019-07-24 13:46:20 -04:00
ddb8e385bf
Test fix
2019-07-24 13:24:48 -04:00
b78cd1e62e
Merge branch 'add-pid-to-created-resource'
2019-07-24 13:19:38 -04:00
e8cf2738f0
Handle oversized payload request
2019-07-24 13:18:30 -04:00
b9dbd69e5d
Fix limiting on size
2019-07-24 13:11:05 -04:00
37411a6ae2
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-24 10:41:11 -04:00
6b599c29e5
Merge branch 'add-pid-to-created-resource'
2019-07-23 17:36:15 -04:00
bff39e4139
Try to deal with an intermittent failure
2019-07-23 15:58:14 -04:00
9094323c43
Add a test
2019-07-23 14:47:27 -04:00
b1e409519d
Add a test
2019-07-23 14:47:27 -04:00
8d86e34bcf
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
2019-07-23 09:12:08 -04:00
60ea922e8d
Add license headers
2019-07-23 05:38:10 -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
7ba3ceec90
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-19 10:54:56 -04:00
458cfcfa12
Fix intermittent test failure
2019-07-19 10:46:49 -04:00
f53746cd63
One more set of migrator tweaks to account for latest changes
2019-07-19 10:10:00 -04:00
e634aa6d10
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-18 22:06:10 -04:00
5bf4fa22e7
Allow patching in tranactions
2019-07-18 16:41:07 -04:00
a7fa79331a
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-18 13:14:54 -04:00
87ab796309
Updates to validating interceptor
2019-07-18 12:57:30 -04:00
ffa008b2dd
Fixing a build error
2019-07-18 10:59:11 -04:00
72aa4932d6
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-18 10:12:15 -04:00
ee7cff9445
Rename a few columns to not conflict with res´rved words
2019-07-18 05:47:32 -04:00
7488047686
Add license headers
2019-07-17 18:53:23 -04:00
55c0d5b604
Add binary storage for Attachments ( #1386 )
...
* Have this working now
* Add utility method
* Build fixes
* Add changelog
2019-07-17 18:31:17 -04:00
c73aebe0a0
IResource and IAnyResource are mutually exclusive...
2019-07-17 17:59:49 -04:00
465b4daa03
Changed IAnyResource to IResource per feedback
2019-07-17 17:59:49 -04:00
1d4dc5b3c5
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_UPDATED hooks are called
2019-07-17 17:59:49 -04:00
e27685e811
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_CREATED hooks are called
2019-07-17 17:59:49 -04:00
7bc8517fc6
Merge branch 'add-pid-to-created-resource' into expunge-resource-hook
2019-07-17 14:26:00 -04:00
6960f1db1c
IResource and IAnyResource are mutually exclusive...
2019-07-17 14:25:10 -04:00
a5da696823
Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
2019-07-17 13:28:29 -04:00
d21304e771
cleanup
2019-07-17 13:28:17 -04:00
fe21dba4a6
Added Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE.
...
Also added a couple of tests.
2019-07-17 13:26:50 -04:00
76384abefb
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-07-17 10:57:43 -04:00
160b221f5f
Changed IAnyResource to IResource per feedback
2019-07-17 10:26:16 -04:00
79ce4a30cc
Merge remote-tracking branch 'remotes/origin/master' into add-pid-to-created-resource
2019-07-16 20:46:31 -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
634718c503
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_UPDATED hooks are called
2019-07-16 16:36:05 -04:00
fe7d38d0b5
add RESOURCE_PID to resource UserData before STORAGE_PRECOMMIT_RESOURCE_CREATED hooks are called
2019-07-16 15:33:51 -04:00
f8444b90c8
Test tweak
2019-07-14 18:11:37 -04:00
7831e8a0ed
Add support for $snapshot generation and validation based on snapshots
2019-07-14 16:15:56 -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
534c71c1d5
Higher parallel count for JPA tests
2019-07-13 18:24:31 -04:00
Ken Stevens
Diederik Muylwyk
jamesagnew
Sean McIlvenna