331 Commits

Author SHA1 Message Date
Diederik Muylwyk
48f7ee5afb Rolling back previous unnecessary changes. 2019-12-31 09:25:56 -05:00
Diederik Muylwyk
170b607992 Added some FIXMEs. 2019-12-30 18:43:15 -05:00
Diederik Muylwyk
4eaeb7ef9e Implemented isDateWithinRange() and supporting methods. 2019-12-30 14:35:51 -05:00
Diederik Muylwyk
d8133487b2 Initial commits. 2019-12-23 17:14:47 -05:00
James Agnew
2b3c775b77 Some cleanup and fix a test 2019-10-26 12:45:57 -04:00
James Agnew
bfbc73caaf
Auto externalize binary contents (#1550)
* Auto externaliZe binary attachments

* Work on externalization

* Auto externalize binary content

* Work on tests

* Fix alert
2019-10-19 09:01:00 -04:00
James Agnew
b51a93a2b5 Intermittent test fix 2019-10-18 15:46:02 -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
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
956bb39327 Resolve an inefficient regex expression 2019-08-29 13:59:31 -04:00
James Agnew
57c6064d89 Another test fix 2019-08-17 12:21:08 -04:00
James Agnew
74c83f6148 Test fixes 2019-08-17 12:01:04 -04:00
James Agnew
1e07fcd2b3
Fix an unintended regression in #1357 (#1429)
* Start working on a tweak to #1357 - Not yet complete

* Tweaks to avoid an unintended regression from #1357
2019-08-15 08:35:50 -04:00
James Agnew
bfaf617142 Add some more chars to the sanitizer function 2019-08-12 08:16:38 -04:00
Ken Stevens
1b17097f62 a couple more int -> long 2019-08-07 13:35:27 -04:00
jamesagnew
46c8c61932 Restore build - May need to roll back the RDF changes 2019-08-01 10:14:56 -04:00
James Agnew
0f4738c1b5
Merge branch 'master' into rdf_parser 2019-08-01 09:25:40 -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
cc20893018 Add hardcoded keys to localizer 2019-07-08 08:58:06 -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
admin
3b35e6add4 Test Classes 2019-06-14 05:24:11 -05:00
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
James Agnew
738c2c1797
Interceptor framework refactoring (#1287)
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
James Agnew
cff79e6aef PortUtil fixes from my working branch to avoid test failures 2019-04-15 10:34:27 -04:00
James Agnew
81de6cca32 Add a bit of documentation 2019-04-01 10:28:26 -04:00
James Agnew
3eeca4a8fd Merge branch 'master' into ja_interceptor_jpa_queries 2019-04-01 09:59:03 -04:00
James Agnew
3c18275b3d Make port delays configurable 2019-03-29 17:19:22 -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
715b451d94 Add some javadocs to PortUtil 2019-03-18 15:27:04 +01:00
James Agnew
c81c5c2497 One more tweak to the port test 2019-03-17 17:54:48 -04:00
jamesagnew
8818a2479c Try to prevent build failure 2019-03-17 16:14:19 -04:00
jamesagnew
3e57fdb491 Improvements to PortUtil to avoid reusing ports 2019-03-17 14:09:21 -04:00
jamesagnew
c482d22cff Improvements to PortUtil 2019-03-17 13:23:48 -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
4138832071 Add a test 2019-03-01 14:03:14 -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
James Agnew
4367e340ae Log the version number and commit on startup 2019-01-17 16:05:54 -05:00
Heinz-Dieter Conradi
734835de96 Add some test demonstrating null pointer problems in the DateRangeParam class 2018-09-27 11:25:56 +02:00
James Agnew
07cfed14b8 Work on migrator 2018-08-27 08:21:20 -04:00
James Agnew
09b1f547d0 Add expunge 2018-04-24 15:11:00 -04:00
James Agnew
9c5e32d7eb Fix up some logging 2018-03-20 07:53:21 -04:00
jamesagnew
4578b3889f Allow for locale differences in StopwatchTest 2018-03-19 05:54:12 -04:00
James Agnew
e31aa760dd Fix stopwatch ETA calculations 2018-03-05 19:06:05 -05:00
James Agnew
2f7751a079 Move stopwatch into hapi-fhir-base and add timing into to client
LoggingInterceptor
2018-03-04 12:13:18 -05:00
James Agnew
6afe6804db Fix #796 - Correctly escape spaces in generated URLs 2017-11-25 17:52:12 -05:00
James
ce720f5601 Add support for Cache-Control header in JPA server and client 2017-10-05 13:38:53 -04:00
James
be5c5ebecd Merge in HAPI 3.0.0 working branch!
Squashed commit of the following:

commit 12f89a423a1691fdbc360706fd94a03bd9144d17
Author: James <jamesagnew@gmail.com>
Date:   Sun Aug 13 14:38:51 2017 -0400

    Minimize validation resources

commit f6868cce5c73b34d5ecd53bf1a220fdccd6b4e09
Merge: 3b80779fd3 1e158311d8
Author: James <jamesagnew@gmail.com>
Date:   Sun Aug 13 14:05:34 2017 -0400

    Forward port fix for #710

    Merge branch 'master' into hapi3_refactor

commit 3b80779fd3905cbf5322e6973334eb0ecb3d8426
Merge: 1f534985e8 356d9acaf7
Author: James <jamesagnew@gmail.com>
Date:   Sun Aug 13 12:31:09 2017 -0400

    Forward port #705, #708, and #710

    Merge branch 'master' into hapi3_refactor

commit 1f534985e8106347d9cc9da2dd8145fdd869547f
Merge: 7c39a47852 dedd3d635b
Author: James <jamesagnew@gmail.com>
Date:   Sun Aug 13 10:52:59 2017 -0400

    Forward port #695

    Merge branch 'master' into hapi3_refactor

commit 7c39a47852142bee398101120678217ab0917c7e
Merge: e0ffb84d21 6efafe62f1
Author: James <jamesagnew@gmail.com>
Date:   Sun Aug 13 09:53:17 2017 -0400

    Forward port #688

    Merge branch 'master' into hapi3_refactor

commit e0ffb84d2129c209ccffc2611038592f37dddfd2
Merge: 52388c11c1 d19b00ff09
Author: James <jamesagnew@gmail.com>
Date:   Sat Aug 12 14:59:46 2017 -0400

    Merge branch 'master' into hapi3_refactor

commit 52388c11c17cf038591244548f2a592f6b655cee
Author: James <jamesagnew@gmail.com>
Date:   Sat Aug 12 06:21:46 2017 -0400

    Cleanup

commit 209752cd638266b39574ae11c5989b624d5e85d3
Author: James <jamesagnew@gmail.com>
Date:   Thu Aug 10 11:18:19 2017 -0400

    Fix tests

commit 4543408dc8d63b5b9682a275e261d3168cdc2196
Author: James <jamesagnew@gmail.com>
Date:   Sat Aug 5 06:55:50 2017 -0400

    Fix a potential deadlock

commit ee360f537692672df473f94dae75c176b2287415
Author: James <jamesagnew@gmail.com>
Date:   Sat Aug 5 06:22:06 2017 -0400

    Add R4 code to CLI

commit 1a95ba3b6529afdaf81232b82cc303718c0187d6
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Aug 3 06:14:01 2017 -0400

    More cleanup

commit f0d88026817296edaa65132accd67d0c8ad8088c
Author: James <jamesagnew@gmail.com>
Date:   Wed Aug 2 11:27:43 2017 -0400

    Tests are working!

commit a4cbda357e8e7d024f24e3ee9a660b5366983ca1
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed Aug 2 10:42:04 2017 -0400

    Connection handling cleanup for new tests

commit 0e2cecfbd0d7a546444a66e8411600040fd9a17b
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed Aug 2 10:16:28 2017 -0400

    Clean up R4 JPA tests

commit 40317a650d72c86e2529d5179cffe63399301de5
Author: James <jamesagnew@gmail.com>
Date:   Wed Aug 2 09:12:38 2017 -0400

    Work on R4 for JPA server

commit e7f8f8c30d72ed30d739979964db38d41c5baec1
Author: James <jamesagnew@gmail.com>
Date:   Tue Aug 1 20:43:47 2017 -0400

    More work on porting tests

commit 43c9003258696ab33e7bb335e882ab1c66fb61aa
Author: James <jamesagnew@gmail.com>
Date:   Tue Aug 1 07:09:29 2017 -0400

    Work on porting DSTU1 tests

commit 602857f1e26a69a2284e176b5e44a860d9b828ff
Author: James Agnew <jamesagnew@gmail.com>
Date:   Mon Jul 31 22:34:08 2017 -0400

    More work on bring unit tests up to date

commit e326a7b0cdb8368009119bba41886838a973e03e
Author: James Agnew <jamesagnew@gmail.com>
Date:   Mon Jul 31 17:36:38 2017 -0400

    Credit for #686 and forward port the fix to R4 validator

commit 96543c3992adcb406df3c8899dab79cf4bd5b4b4
Merge: 3fb75aa61a 9901b802c4
Author: James Agnew <jamesagnew@gmail.com>
Date:   Mon Jul 31 17:12:33 2017 -0400

    Merge branch 'master' into hapi3_refactor

commit 3fb75aa61ad29d9f3876a1c30c912627486147af
Author: James <jamesagnew@gmail.com>
Date:   Mon Jul 31 15:21:30 2017 -0400

    More work on cleanup

commit b02fbb6804127e77c61c4792eefd9fc0d23d63d0
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Jul 30 22:11:07 2017 -0400

    Work on porting STU1 tests

commit 1ae37b0db3929ea4f37955adf8f026e33ccf43b2
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Jul 30 20:56:10 2017 -0400

    Try to get coverage report working

commit 72b88849b30a94a9ff08d3a1ab50a05b2acbdfdd
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Jul 30 20:27:02 2017 -0400

    Fix android tests

commit e5f6c35aeab8bbc056870a038e1862181049a020
Author: James <jamesagnew@gmail.com>
Date:   Sun Jul 30 19:31:18 2017 -0400

    More work on getting legacy code cleaned up

commit 0b513b0845a082b5c20b0033dfab4e29f5e4a934
Author: James <jamesagnew@gmail.com>
Date:   Sun Jul 30 18:41:13 2017 -0400

    Continue work on removing deprecated API

commit defea69aa38a2e0f4137ed9c8527956872ff70bf
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Jul 30 17:10:01 2017 -0400

    More cleanup of legacy code

commit 9ae7295705cb58f5edcf7ee1259f023cbbe2fe51
Author: James <jamesagnew@gmail.com>
Date:   Sun Jul 30 07:11:45 2017 -0400

    More cleanup of legacy code

commit ebd3eeb5ee793cf5805cc726db353f3def35ab00
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Jul 30 06:43:25 2017 -0400

    More work on removing legacy code

commit 92224c2532faf70171473d64429c3ceaf3e3406c
Author: James <jamesagnew@gmail.com>
Date:   Sat Jul 29 18:44:06 2017 -0400

    Remove DSTU1 Bundle

commit c52cacf71bae3f5c02ffae03881c21de1f3aba22
Author: James <jamesagnew@gmail.com>
Date:   Sat Jul 29 14:27:42 2017 -0400

    Now compiling

commit b405e51773baf4ab3a3c387458cdc59541394cd1
Merge: c3ddf04e25 cb2cea54d7
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Jul 28 06:21:02 2017 -0400

    Merge branch 'master' into hapi3_refactor

commit c3ddf04e2598b8d6214975ab0ae795f850396811
Author: James <jamesagnew@gmail.com>
Date:   Thu Jul 27 11:06:06 2017 -0400

    Sync R4 releases in

commit b13333c3c03ddb9a5061c3b22bf011f4592104f8
Author: James <jamesagnew@gmail.com>
Date:   Fri Jul 14 05:52:33 2017 -0400

    JPA server is now able to handle placeholder IDs (e.g. urn:uuid:00....000) being used in Bundle.entry.request.url as a part of the conditional URL within transactions.

commit 2e60ff7521b42890a32b97c2dda88ab233f5c91e
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Jul 13 20:02:46 2017 -0400

    Fix imports

commit a92ace2e0dac6e24f6dada53bf97d03861fd21a1
Merge: 3196db96d1 1a6b3ea867
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Jul 13 12:02:27 2017 -0400

    Merge branch 'master' into hapi3_refactor

commit 3196db96d1c485310e746833df59c0e010b5b161
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Jul 13 11:48:10 2017 -0400

    Don't add false paging link to request

commit bd4e1d338855a664045caa271d41616aed973a4d
Author: James <jamesagnew@gmail.com>
Date:   Sun Jul 9 21:32:16 2017 -0400

    Finally building correctly!

commit 6464ce9304703cb3c5ecc58491282ddacc900853
Author: James <jamesagnew@gmail.com>
Date:   Sun Jul 9 16:38:28 2017 -0400

    Work on refactor

commit 0059f2e48e9d7c812c1d42a57c5b6059814f5155
Author: James <jamesagnew@gmail.com>
Date:   Sat Jul 8 07:16:20 2017 -0400

    Keep working on refactor

commit 6c2e87e8cc19863a811c11623d1c878c8b48f031
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Jul 6 22:35:13 2017 -0400

    Lots of work on refactor

commit 11cab975047a0c28190e6533074fd3f11ddde240
Merge: 34ec6b8807 6c47bd4c51
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Jul 6 21:43:57 2017 -0400

    Merge branch 'master' into hapi3_refactor

commit 34ec6b8807946aa6c97f0b5581dca9bd5f7b7a3e
Merge: f8e647511b c520e60ac1
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Jul 6 21:43:49 2017 -0400

    Merge branch 'hapi3_refactor' of github.com:jamesagnew/hapi-fhir into hapi3_refactor

commit f8e647511b4a82e7fde71a8850b8800e3d698b1f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Jul 6 18:46:55 2017 -0400

    Work on hapi3 changes

commit c520e60ac1198f340cfb9090a7a33f91aa2d1e61
Author: James <jamesagnew@gmail.com>
Date:   Wed Jul 5 08:08:40 2017 -0400

    Keep working on refactor

commit f1d2ee90926f7db900a5b3b4ab9a8948d18e49f2
Author: James Agnew <jamesagnew@gmail.com>
Date:   Mon Jul 3 22:10:59 2017 -0400

    Continue refactor for HAPI 3

commit 9281ccafc32354222932c5a9f5ee8b0f206ebc05
Merge: ea1264cd8e 294d080bd3
Author: James Agnew <jamesagnew@gmail.com>
Date:   Mon Jul 3 20:34:16 2017 -0400

    Merge branch 'master' into hapi3_refactor

commit ea1264cd8e9b8c5297d218e91cf14bd48d0a92c7
Author: James <jamesagnew@gmail.com>
Date:   Wed Jun 28 10:26:01 2017 -0400

    Continue work on refactor

commit fbe2f98a0238f3d4e065db4550dd2ef1b460c0d8
Merge: b2bef47100 0a4dcc32ec
Author: James <jamesagnew@gmail.com>
Date:   Wed Jun 28 06:21:22 2017 -0400

    Merge branch 'master' into hapi3_refactor

commit b2bef47100370e1248834523d73a630950032d7a
Author: James <jamesagnew@gmail.com>
Date:   Tue Jun 27 21:13:23 2017 -0400

    Work on refactor

commit 8f76e4e46385daa9ce3442e2d9342453ce373ba3
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Jun 25 21:55:35 2017 -0400

    Lots of work on refactoring
2017-08-13 14:39:47 -04:00
James
78643981f6 Credit and test for #636 2017-05-20 18:12:34 -04:00