416 Commits

Author SHA1 Message Date
James Agnew
3b6709e1d1
Merge pull request #1566 from jamesagnew/ja_20190928_rationalize_search_param_extractor
Rationalize search param extractors across FHIR versions
2019-11-02 16:18:23 -04:00
Stig Rohde Døssing
80bfb9af37 Issue-1077: Make CapabilityStatementProvider use the closest common superclass of provided resources when generating rest.resource.profile, instead of always using the base definition. 2019-11-01 10:20:16 -04:00
James Agnew
b90f285218 Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-30 08:41:14 -04:00
James Agnew
9c852283e9
Correctly handle "special" search params in CS (#1569)
* Correctly handle "special" search params in CS

* Add another test
2019-10-30 05:31:25 -04:00
James Agnew
817f9ae36e Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-27 17:25:20 -04:00
James Agnew
6580c98ed7 Work on extractor 2019-10-26 16:56:12 -04:00
James Agnew
74c03b5bb7 Add a test 2019-10-24 08:32:52 -04:00
James Agnew
385a885abf Add ability for resource source to be specified by header 2019-10-24 08:32:52 -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
a71d969ba1 Add line numbers to validation failures 2019-10-18 14:10:47 -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
jamesagnew
92c6b88964 Add test 2019-10-10 07:16:18 -04:00
James Agnew
1f1b94a566
Resolve XXE issue in validator (#1530)
* Resolve XXE issue in validator

* Ensure that we're blocking XXE events into validator XML parser

* A bit of cleanup

* Add an LGTM config

* Add one more fix
2019-10-08 13:06:03 -05:00
Ken Stevens
53f47fbb1e Merge remote-tracking branch 'remotes/origin/master' into ks-narrow-search-pointcut 2019-10-03 12:20:20 -04:00
Ken Stevens
d1deedf247 pre-review cleanup 2019-10-03 12:14:11 -04:00
Ken Stevens
566443d0fe move BundleUtil back 2019-10-03 12:05:26 -04:00
Ken Stevens
98c76a4d49 Test passes 2019-10-03 12:03:38 -04:00
Ken Stevens
29e7cdc476 Added ability to modify URLs in BundleUtil 2019-10-03 09:46:32 -04:00
James Agnew
db668d96b9 Add a few tests and remove some dead code 2019-10-03 09:00:14 -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
Clayton Bodendein
08825a81d9 Add missing @Override annotations
Added missing @Override annotations so that if/when methods in superclasses change
there will be a compile-time error if subclasses haven't been changed accordingly.

This was done using IntelliJ IDEA's "Missing @Override annotation" inspection.
2019-10-02 05:45:59 -04:00
James Agnew
fd16b9efca
Merge branch 'master' into oliveregger_#402 2019-09-30 20:19:25 -04:00
James Agnew
066c9a7fb7 Improvements to AutohrizationInterceptor create handling 2019-09-30 15:07:23 -04:00
James Agnew
0bee7a7b53 Test fix 2019-09-30 10:12:49 -04:00
James Agnew
c8ce07c40e Deprecate redundant IVersionSpecificBundleProvider method 2019-09-30 09:45:31 -04:00
James Agnew
557a8ccc66
Add top level support for ElasticSearch (#1514)
* ElasticSearch work

* Add ElasticSearch properties builder

* Clean up POM

* Remove redundant project

* Try to troubleshoot embedded elasticsearch

* Another test attempt

* Add credentials to elasticsearch config

* Work on lastn

* Address review comments

* A couple of test fixes
2019-09-30 09:30:39 -04:00
James Agnew
57377f5557 Fix #1483 - Don't let RP methods handle a request with includes if the
method doesn't understand them
2019-09-25 10:54:37 -04:00
James Agnew
a989a746b0 Fix #1494 - Upgrade to new :recurse syntax for R4 include/revinclude
statements
2019-09-20 09:38:29 -04:00
James Agnew
20d33afb6f Credit for #1489 2019-09-19 20:48:17 -04:00
James Agnew
6f6cc960ad Add timing tests 2019-09-19 20:39:16 -04:00
James Agnew
eddb98084d Move PreferReturnEnum back to original location to avoid regressions 2019-09-19 15:48:58 -04:00
James Agnew
5e74a6f3e8 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-17 16:01:53 -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
James Agnew
d3c8962ae6 Add some tests 2019-09-17 14:04:35 -04:00
James Agnew
08835c1615 FIx a failure in FhirTerser when visiting custom types 2019-09-13 09:11:47 -04:00
James Agnew
722c7a8211 Work on GraphQL updates 2019-09-06 14:56:17 -04:00
James Agnew
7d162c50db Don't guess content type for create/put 2019-09-05 14:47:04 -04:00
James Agnew
ce879b3863 Fix versioned API incompatibility with GraphQL 2019-08-20 08:35:27 -04:00
James Agnew
74c83f6148 Test fixes 2019-08-17 12:01:04 -04:00
James Agnew
afb682dfe9 Handle AuthorizationInterceptor rejection of by-type reads on the wrong type earlier in the process 2019-08-15 09:16:45 -04:00
James Agnew
b127867ef7 Fix responsehighlighterinterceptor to work with graphql 2019-08-13 18:00:30 -04:00
James Agnew
33767b5399 Test fix 2019-08-13 16:12:28 -04:00
James Agnew
94c498a744 A but more tweaking to the graphql interceptor 2019-08-13 16:05:33 -04:00
Stig Rohde Døssing
bb20c2134b Issue-1387: Read version from resource meta when deciding whether to return 304 on read 2019-08-13 05:28:03 -04:00
James Agnew
c04f1d15d8 Fix #1399 - Issue with DiagnosticReport R4 narrative generation template 2019-08-12 17:17:45 -04:00
James Agnew
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
James Agnew
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
James Agnew
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
jamesagnew
46c8c61932 Restore build - May need to roll back the RDF changes 2019-08-01 10:14:56 -04:00