Commit Graph

1268 Commits

Author SHA1 Message Date
jamesagnew 3ba194acbe Reject subscriptions in JPA server if status field is not set 2019-06-22 17:03:22 -04:00
jamesagnew 0fbde2a4e5 Fix #1352 - Don't fail to create observation with a value type of
SampledData
2019-06-22 16:43:25 -04:00
jamesagnew 95876ec3cb Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-06-22 16:24:07 -04:00
jamesagnew 638cb976fd Fix #1250 - Don't include Bundle.entry.response on search results 2019-06-22 16:23:32 -04:00
James Agnew 4ad1808da3
Propagate RequestDetails to everything in JPA server (#1358) 2019-06-22 15:18:06 -05:00
jamesagnew 989e26fdb4 Fix #1355 - Failed to call access method: java.lang.NullPointerException in case of bundle entry without resource 2019-06-22 15:51:56 -04:00
Diederik Muylwyk 266384b536 Evaluation of PartTypeName in LoincRsnaPlaybookHandler is not case insensitive. 2019-06-21 15:36:51 -04:00
James Agnew 6724fd0348
Implement the $subsumes operation (#1344)
* Implement the $subsumes operation

* Fix #976
2019-06-17 17:31:24 -04:00
James Agnew 8bef3eddf9 Credit for #1347 2019-06-17 16:50:51 -04:00
James Agnew b2e99cf035
Add support for conditional patch (#1348)
* Add support for conditional patch

* Add changelog

* Test fix
2019-06-17 16:12:05 -04:00
James Agnew f6504ffc44 Credit for #1336 2019-06-14 15:40:28 -07:00
Ken Stevens 2bf680509b
DeleteConflict hook, SearchableHashMapResourceProvider, and in-memory searching (#1341)
* Make IBundle list interface more flexible

* Make matchResourceLinks visible

* Make matchResourceLinks visible

* Pull in-memory matching functionality out of subscription module into dedicated classes in searchparam module

* Added more accessors to version independent resource classes

* improved forcedid matching (needs to be verified by James)
filter out nulls from HashMapProvider.searchAll() (hopefully no tests depend on this)

* add AnyComposition

* cleanup of Any classes

* create searchparam config so people can use that module without using subscriptions

* create searchparam config so people can use that module without using subscriptions

* fix broken test

* added derivedFrom

* renamed daoRegistry.getResourceDaoIfExists to getResourceDaoOrNull
also added method to add a new dao to the registry and retrieve registered types

* TokenParam.equals

* add error check to searchable hashmap resource provider

* added support for R4

* add successor to measure

* delete conflict hook
start with failing test

* test passes.
hook is called.

* added delete conflict hook
all delete conflict tests pass

* added javadoc

* Performance test

* test bad interceptor case

* typo

* rename criteria matcher

* added support for multiple topics

* fix method name

* add effective period

* Temporarily excluding StressTest from build to try to get Travis under time limit

* change log

* review feedback

* review feedback

* review feedback
2019-06-13 13:59:51 -04:00
Ken Stevens dd203ae28f Credit for #1337 2019-06-10 11:14:52 -04:00
James Agnew c2aec5c1a9 Respect the _total parameter for all JPA searches 2019-06-09 05:44:49 -04:00
James Agnew 9500f6e6fe Roll back derby version for now 2019-06-07 16:27:19 -04:00
James Agnew cab44e9626 One more version bump for dependencies 2019-06-07 09:17:07 -04:00
James Agnew a0fa752eac A number of dependency updates 2019-06-07 09:06:30 -04:00
Ken Stevens 5752a6e2b3 reported issue with proposed fix that breaks tests (#1243)
* reported issue with proposed fix that breaks tests

* Fix spelling

* Merge my changes into this

* Correctly check referential integrity on deletes

* Add one more test
2019-06-04 20:40:20 -04:00
Diederik Muylwyk aed5bb8955
Resolve #1320: "import-csv-to-conceptmap is failing unexpectedly." (#1322)
* Reproduced issue in unit test and identified potential solution.

* Fixed using BOMInputStream.

* Added changelog.

* Added a missing word in changelog.

* Added a missing word in changelog. Take two.
2019-06-03 10:53:04 -04:00
James Agnew be06c2ee19 Correctly index timing events 2019-05-31 16:42:45 -04:00
James Agnew f6c7ff1dbb Modify expunge everything to use small batches of deletes 2019-05-31 11:05:17 -04:00
James Agnew f2467e5356 Add release notes 2019-05-30 16:36:26 -04:00
James Agnew 5e181fb214 Credit for #1303 2019-05-29 21:47:57 -04:00
James Agnew 13f3c02b2b Credit for #1244 2019-05-29 21:44:30 -04:00
James Agnew 8734af8451 Credit for #1141 2019-05-29 21:34:35 -04:00
James Agnew 96c70f6093 Credit for #1213 2019-05-29 21:22:54 -04:00
James Agnew 15a962aae7 Credit for #1152 2019-05-29 21:19:03 -04:00
James Agnew 78f12b4397 Credit for #1228 2019-05-29 20:49:15 -04:00
James Agnew f17fc4ce82 Credit for #1305 2019-05-23 09:09:44 -04:00
jamesagnew aa88816d9a Credit for #1311 2019-05-22 17:13:33 -04:00
James Agnew 202c798fcd Restore R4 server support in CLI 2019-05-16 11:56:34 +02:00
James Agnew 702ffd631d Fix #1299 - Return an HTTP 201 when creating a previously deleted
resource
2019-05-06 16:33:23 -04:00
James Agnew 8f41159eb1 Fix a potential security vulneability in the testpage overlay 2019-05-02 08:13:22 -04:00
James Agnew 5132f1f4ed COnfirm validation support comntains codesystem 2019-05-02 07:50:59 -04:00
James Agnew 8c7f065440 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-29 14:49:56 -04:00
James Agnew 37b9e1a42c Improve validation of enableWhen questionnaires 2019-04-29 14:43:42 -04:00
Ken Stevens 3a736924f1 fixed delete reference error message 2019-04-29 10:49:32 -04:00
James Agnew 828df1528f Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-26 11:24:00 -04:00
James Agnew 685adf7754 Revert Jetty upgrade, and improve patch error messages 2019-04-26 11:23:22 -04:00
Ken Stevens 130e879d04
Delete performance (#1286)
* move expunge out

* move to prototype

* turns parameters into fields

* cleanup control flow

* moved transactions outside of loops

* add expungeeverything

* moved daos out

* add expungeThreadCount

* add expungeBatchSize

* added partition runner to run in separate threads

* all done.  just need to consolidate test code.

* Moar tests

* consolidated pointcutlatch into hapi-fhir-jpaserver-model

* final cleanup

* update javadoc

* change log

* failing test

* added delete
also @Transactional

* remove unused parameter

* fix compile

* race condition

(cherry picked from commit e1940d2fb20838859a205f2b96c833b0ce9f05eb)

# Conflicts:
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/PartitionRunnerTest.java

* ja feedback

* ja feedback
2019-04-25 15:38:37 -04:00
James Agnew da962b8c10 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-24 14:33:28 -04:00
James Agnew 738c2c1797
Interceptor framework refactoring (#1287)
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
James Agnew f2e382a132 Swap JSON Patch provider 2019-04-24 14:10:21 -04:00
James Agnew 349b16786a Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-17 16:51:47 -04:00
James Agnew 210d99d121 Correct validation of questionnaire enableWhen 2019-04-17 16:50:37 -04:00
Ken Stevens a57e50317d
Websocket cleanup (#1275)
* fix bug in websocket subscription (It wasn't destroying the channel when there are no subscribers)

* add support for removing channel.  Also synchronize removal (there was a race condition between sync and queue)

* keep deprecated method for backwards compatibility

* make websocket endpoint configurable

* make websocket context path configurable

* make websocket context path configurable

* trying mvn clean test instead of mvn clean install to see if the build goes faster

* that didn't work at all.  reverting.

* change log
2019-04-17 15:03:35 -04:00
jamesagnew 08a9844066 Work on #1280 2019-04-17 09:10:17 -04:00
Ken Stevens 38dd7f0687 missing tag 2019-04-16 13:28:54 -04:00
Ken Stevens 36f81731be Merge remote-tracking branch 'origin/master' 2019-04-16 12:01:34 -04:00
Ken Stevens dfcdb2b53e updating downloads page 2019-04-16 12:01:17 -04:00
James Agnew 4512c3d895 Credit for #1255 2019-04-15 17:05:56 -04:00
James Agnew c8f2e4bbc9 Return HTTP 400 for missing body on POST and PUT 2019-04-14 12:32:09 -04:00
James Agnew 706af5d579 Don't update modified time when performing NOOP update in JPA 2019-04-05 14:36:18 -04:00
Ken Stevens 081ae89a46 changelog 2019-04-03 13:42:24 -04:00
James Agnew 3eeca4a8fd Merge branch 'master' into ja_interceptor_jpa_queries 2019-04-01 09:59:03 -04:00
James Agnew e6a6c22783 Bump a few project dependencies 2019-03-31 13:57:02 -04:00
James Agnew e85bec2858
Ja inline references (#1252)
* Use a single IN clause for OR reference searches

* Add changelog

* One more attempt at getting the free port util to actually work... sigh

* One more tweak to free ports

* Bundle fix
2019-03-26 10:42:42 +01:00
James Agnew c701de2861 Create a performance interceptor framework for HAPI FHIR 2019-03-22 01:06:03 +01:00
James Agnew d1667487c2 Clean up unique composite search params 2019-03-21 21:57:38 +01:00
James Agnew 08c7afb804 Reduce logging in JPA server 2019-03-14 17:42:13 -04:00
James Agnew a8c76450e5 Re-enable contains searches on the public HAPI FHIR server and improve
message formatting in HapiLocalizer
2019-03-14 13:19:26 -04:00
James Agnew ed4da7c414 Add setting to disable resource type target validation in JPA 2019-03-12 17:45:19 -04:00
James Agnew f934f76c96
Several JPA search fixes (#1231)
* Search fixes

* Add some tests

* CHangelog

* Some cleanup of the query tracker

* FIx XML issue in changelog

* Test fixes

* SOme test fixes

* Address review comments

* Fix test breakage
2019-03-11 15:49:34 -04:00
James Agnew 9bc0f6784d
Search paging timeout with 1500 < n < 2000 results (#1221)
* Avoid paging links when offset is artificially set very high

* Ongoing fixes

* Adding logging and clean up transaction processing

* Add changelog

* More work on queries

* Keep working on getting tests passing

* More test fixes

* More work on tests

* More test works

* One more test attempt

* Ongoing fixes

* One more change

* FIxes to search algorithm

* Add changelog

* Clean up for review

* Fixed NPE in token matcher when system is not null and value is null

* test opposite (null system not null value)

* added null protection to all matchers

* Address review comments

* Address broken test

* Trying to resolve DB ordering issues
2019-03-06 05:45:05 -05:00
James Agnew 43c07077be Automatically remove duplicate conditional creates in JPA 2019-02-22 12:57:07 -05:00
James Agnew 89b08cd627
Improve SQL IN(..) queries (#1214)
* First attempt, probably has compile issues

* Fix qualified searches

* Another test fix

* More test fixes

* Add changelog

* Two more fixes

* Revert SQL logging
2019-02-20 16:38:51 -05:00
James Agnew 87ed00a002 Add ability to generate named parametrrs in a version independent way 2019-02-15 16:27:16 -05:00
James Agnew a35f30b18e
Merge pull request #1208 from jamesagnew/reuse-subscription-channels
Reuse subscription channels
2019-02-15 13:42:54 -05:00
James Agnew 514ace5981 Changelog for #1209 2019-02-15 09:58:53 -05:00
James Agnew 485335e975 Allow terminology service to work without having Lucene enabled for
simple ValueSet expansions
2019-02-14 20:47:28 -05:00
Ken Stevens ffc5966aa3 Merge branch 'master' into reuse-subscription-channels
# Conflicts:
#	src/changes/changes.xml
2019-02-14 19:42:00 -05:00
Ken Stevens badbde7e4a SubscriptionRegistry re-uses channel and handlers if channel type didn't change when subscription is updated 2019-02-14 19:38:31 -05:00
James Agnew 10c348d44f Tweak to elements parametr support 2019-02-14 19:30:10 -05:00
James Agnew 96ad875d3a Credit for #1204 2019-02-11 09:04:57 -05:00
James Agnew 37fc432fed Credit for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/3/ 2019-02-07 20:20:32 -05:00
jamesagnew c01b9ef5ab Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-02-07 16:47:27 -05:00
jamesagnew dc35e500a7 Add additional files to distribution 2019-02-07 16:47:14 -05:00
James Agnew 810f1ad969 Improvements to elements parameter as well as adding attributes to
RequestDetails
2019-02-07 16:45:59 -05:00
jamesagnew 207015c3af Version bump to 3.7.0 2019-02-05 21:36:38 -05:00
James Agnew c6dfbacd7a Credit for #1148 2019-02-05 20:31:28 -05:00
James Agnew e401ec86e4
Enhanced elements (#1192)
Squashed merge: Add elements exclude mode

* Start working on elements enhancement

* Work on elements projection

* Work on elements filter

* Feature is now working

* Just some cleanup

* Address compile issues
2019-02-03 16:41:33 -05:00
jamesagnew 86a12bcf2a Credit for #1114 2019-02-02 11:33:08 -05:00
jamesagnew ea84f2c377 Version bump hibernate search 2019-02-02 11:26:19 -05:00
jamesagnew b46b60798a Credit for #1130 2019-01-31 05:26:14 -05:00
jamesagnew db42609ca7 Credit for #1135 2019-01-31 05:20:43 -05:00
jamesagnew 5f29e4fbf3 Fix #1174 - Prevent serialization exception 2019-01-30 05:49:45 -05:00
jamesagnew 5d540d9208 Query optimization in JPA 2019-01-27 20:03:48 -05:00
Ken Stevens 10c59fceeb
Subscription strategy tag (#1178)
tests pass
2019-01-25 13:01:04 -05:00
Ken Stevens 5a08593abd
_id support (#1176)
* added support for _id in in-memory matcher
2019-01-23 14:37:34 -05:00
James Agnew 68fae08f20 Fix casing in base64Binary type 2019-01-23 08:34:09 -05:00
jamesagnew eee4c75300 Version bump hibernate 2019-01-23 05:57:20 -05:00
James Agnew 9cf64f78d0 Deprecate a bad setter on RetfulServer, fix a paging issue, and add a
disabled unit test to the subscription matcher
2019-01-21 14:46:17 -05:00
jamesagnew 6c4d4e43a1 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-01-18 07:17:04 -05:00
jamesagnew 3d941ed7e3 Credit for #1084 2019-01-18 05:50:30 -05:00
James Agnew 4367e340ae Log the version number and commit on startup 2019-01-17 16:05:54 -05:00
James Agnew b8755615b2 Allow AuthorizationInterceptor to read patients if the user has read
access to the individual instance
2019-01-14 13:53:08 -06:00
James Agnew 38bade0429 Credit for #1118 2019-01-13 17:22:29 -06:00
James Agnew 63b8a70e8a Allow storing ConceptMap with StructureDefinition as a source or target 2019-01-13 12:24:51 -06:00
James Agnew fc09ed6966 Fix #1163 - Correctly handle invalid CapabilityStatement 2019-01-11 08:01:48 -07:00
James Agnew aee7b2b882 Make sure that sub-request transaction searches and reads preserve HTTP
headers
2019-01-10 07:26:04 -07:00