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6195 Commits

Author SHA1 Message Date
James Agnew bde7c356fe
Implement Jackson parser/serializer (#1733) 
* [dev] Integration of a Jackson serializer and deserializer - first stage

* [fix] Fixed some serializing issues
[improve] Improved the processing, removed the loggers

* [clean] Removed the JacksonSerializer class, replaced all the Gson classes with Jackson classes

* [clean] Small cleanup

* [improve] Throw a ConfigurationException if the JsonGenerator cannot be created

* [improve] Use the ObjectMapper's `readTree` instead of `readValue`

* [dev] Latest fixes and improvements

* [dev] Use the Jackson serializer

* [clean] Removed the ObjectMapper configuration, for now

* [fix] Use the GsonStructure also for the parsing of a FHIR resource

* [clean] Removed the LinkedList usage

* Work on preparing for merge of #1673

* Resolve build errors

* Work on parser integration

* Tests passing

* Resolve fixme

* CLeanup

* Fix dependency

Co-authored-by: Bogdan Solga <bogdan.solga@gmail.com>
 2020-03-17 17:27:26 -04:00
Tadgh 4583cb9939
Merge pull request #1760 from jamesagnew/bugfix/1752-support-chained-parameters-inside-reverse-chained-parameter 
Bugfix/1752 support chained parameters inside reverse chained parameter
 2020-03-17 13:27:20 -07:00
jamesagnew 4c1bbd01cb Intermittent test fix 2020-03-17 14:19:36 -04:00
Tadgh 3eb09b15f0 Merge branch 'master' into bugfix/1752-support-chained-parameters-inside-reverse-chained-parameter 2020-03-17 10:32:43 -07:00
James Agnew 22413911bf
Validation api changes (#1719) 
* Validation enhancements

* Work on validation api reworking

* Keep working on validation API

* Keep working on new term API

* Work on validation api

* Ongoing work on validation

* Work on integrating validation

* Work on validation API

* Add to validation API

* Work on validation

* Work on API

* Work on validation

* Work on validation API

* Work on validation API

* Work on validation api

* Work on validation API

* Work on validation api

* Validation API changes

* Work on API

* More work on validationo API

* Work on validation API

* FIxes

* WOrk on validation api

* Work on validation API

* Tests passing!

* More cleanup

* More validation API changes

* Fix intermittent test failure

* Package reorg

* Validation API work

* Work on doocumentation

* Work on API

* More work on new validation API

* Fix errorprone-reported error

* Test fixes

* Documentation updates

* Documentation tweaks

* Work on API

* Bean name adjustments

* Build fixes

* Some test fixes
 2020-03-17 13:28:59 -04:00
James Agnew 9305bef4ef
Remove useless migrator task generics (#1687) 
* Remove useless migrator task generics

* Clean a couple of compile errors

* Try to fix intermittent
 2020-03-17 13:28:43 -04:00
Jens Kristian Villadsen 80139f4800
Update pom.xml (#1709) 
A run on master using https://jeremylong.github.io/DependencyCheck/dependency-check-maven/index.html shows quartz as having a critical security issue in version 2.3.1
 2020-03-17 12:47:12 -04:00
Tadgh 77733b59fa Add changelog 2020-03-17 09:33:58 -07:00
James Agnew 288abe4504
Improve efficiency in search deleting (#1759) 
* Improve efficiency in search deleting

* Changelog

* Address review comments
 2020-03-17 12:33:38 -04:00
James Agnew 5867d62d62
Avoid duplicate predicate in _id queries (#1761) 
* Avoid duplicate predicate in _id queries

* Add changelog

* Change to trigger CI

* Address review comments
 2020-03-17 11:12:58 -04:00
Tadgh 6f872ffb51 Minor refactor 2020-03-13 19:15:46 -07:00
Tadgh a39ac886af Fix error while resolving rebase 2020-03-13 18:43:43 -07:00
Tadgh 4777d75e6b Merge branch 'master' into bugfix/1752-support-chained-parameters-inside-reverse-chained-parameter 2020-03-13 18:40:11 -07:00
Tadgh b80e71773d Tidy, fix up tests 2020-03-13 18:36:43 -07:00
Tadgh d91cb7524c Fix up whitespace 2020-03-13 15:30:49 -07:00
Tadgh 03567c5831 Add perftrace. Remove regex 2020-03-13 15:29:48 -07:00
Ken Stevens 6b019492fe
Merge pull request #1758 from jamesagnew/ks-20200312-json-annotation 
moved common Json annotations out into an interface
 2020-03-13 15:58:21 -04:00
Tadgh 74fd2c1519 wip 2020-03-13 11:28:44 -07:00
jamesagnew 72b9d9a350 FIx spelling mistake 2020-03-13 09:19:45 -04:00
James Agnew 1dc5d89013
Optmize forced ID resolution (#1754) 
* Add forced ID caching

* Work on id optimization

* Test fixes

* More optimization work

* Add some docs

* Work on docs

* Test fixes

* Test fixes

* Test fixes

* Address review comments

* Compile fix
 2020-03-12 17:12:50 -04:00
Tadgh fe51c08168
Merge pull request #1753 from dttvn0010/master 
Add VEIG(Vietnam Ehealth Innovation Group) to points.json
 2020-03-12 12:40:31 -07:00
Ken Stevens ecf5284c87 moved common Json annotations out into an interface 2020-03-12 13:36:34 -04:00
Tadgh c3ceffbd72 wip 2020-03-09 16:05:41 -07:00
Tadgh e38ec3e3dd Fix typo 2020-03-09 14:57:53 -07:00
Tadgh 12412a7be9 Add query capturing to query 2020-03-09 13:58:59 -07:00
Tadgh 59d1603597 Some variable renaming. Adds some questions. 2020-03-09 13:51:47 -07:00
James Agnew 9f725892d3
Drop anyresource classes (#1755) 
* Drop anyresource classes

* Drop invalid test
 2020-03-09 14:25:30 -04:00
James Agnew 34d42a17da Add tests 2020-03-09 12:41:46 -04:00
jamesagnew 202b9c9a51 License header 2020-03-08 07:23:57 -04:00
Tadgh aca4bcfaad Minor refactoring for readability 2020-03-06 14:22:31 -08:00
Tadgh b299d0b63f Fix Typos, reduce code duplication 
* Change Two streams into one.
* Fix typos.
* Begin Writing docstrings
* Rename variables for clarity
 2020-03-06 11:39:39 -08:00
tungdt 46c67d20cc Add VEIG(Vietnam Ehealth Innovation Group) to points.json 2020-03-06 17:43:56 +07:00
Tadgh 0acfc51082 Split test into two tests, one of which passes, one of which fails, showing the missing functionality 2020-03-05 16:38:42 -08:00
Ken Stevens 9b37ba35d0
Merge pull request #1747 from jamesagnew/ks-20200303-bulk-export-filter 
fixed a copy/paste error in bulk export with test
 2020-03-03 19:54:26 -05:00
Ken Stevens 2d9dea069d
Merge pull request #1748 from jamesagnew/ks-20200203-near-chain-r4 
fix near chain searching for R4
 2020-03-03 19:40:27 -05:00
Ken Stevens e819d40414 fix near searching for R4 2020-03-03 18:33:19 -05:00
Ken Stevens d104fbdf7d fixed a copy/paste error in bulk export with test 2020-03-03 16:40:31 -05:00
Ken Stevens b42502ae3c
Merge pull request #1744 from jamesagnew/ks-20200302-near-chain 
fix near-distance for chained searches in dstu3
 2020-03-03 14:48:54 -05:00
Ken Stevens ccd983ab42 review feedback: code improvement 2020-03-03 13:46:23 -05:00
Ken Stevens 705735b9c0 review feedback: javadoc 2020-03-03 13:29:10 -05:00
Ken Stevens 5b5ef08500 Merge remote-tracking branch 'remotes/origin/master' into ks-20200302-near-chain 2020-03-03 09:44:52 -05:00
James Agnew 58b5bd9664
Limit type on _has query (#1743) 
* Limit type on _has query

* Add changelog
 2020-03-03 08:28:38 -05:00
James Agnew 3c2c1dab2e
Error on missing profile validation (#1742) 
* Error on missing profile validation

* Add changelog

* Test fixes
 2020-03-03 08:28:26 -05:00
James Agnew ac9a371f18 Add test 2020-03-03 08:28:04 -05:00
jamesagnew 13fbdf418f Add ignored test for #1740 2020-03-03 05:22:16 -05:00
Tadgh 4d7f39cfdc
Merge pull request #1741 from jamesagnew/elastic-apm-integration-for-search 
Create custom span for Search Threads for Elastic APM
 2020-03-02 21:46:45 -08:00
Ken Stevens bce1716c6c documentation 2020-03-02 22:13:21 -05:00
Ken Stevens a56df03055 restrict near-distance extraction to DSTU3 2020-03-02 21:50:57 -05:00
Ken Stevens 4e1be80525 fixme 2020-03-02 21:39:28 -05:00
Ken Stevens d1b54a9668 pre-review cleanup 2020-03-02 21:32:27 -05:00