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231 Commits

Author SHA1 Message Date
jamesagnew 9d09466c21 Add debug logging to CLI 2020-03-31 10:49:16 -04:00
James Agnew fe48313100
Add response size capturing interceptor (#1776) 
* Work on capturing repsonse sizes

* Interceptor complete

* Add changelog

* Test fix
 2020-03-30 11:24:10 -04:00
jamesagnew 62d867902f Work on multitenancy 2020-03-29 18:16:04 -04:00
jamesagnew 691f2c4e9a Work on muiltitenancy 2020-03-29 13:35:20 -04:00
jamesagnew 9df4c58122 Work on multitenancy 2020-03-27 09:22:00 -04:00
jamesagnew ec6fe70acb Merge branch 'master' into ja_20200206_multitenancy 2020-03-27 05:50:08 -04:00
James Agnew b794618e9d
Avoid a crash encoding contained bundle (#1778) 
* Avoid a crash encoding contained bundle

* Add changelog

* Apply same fix to XML

* Fix typo
 2020-03-25 21:20:10 -04:00
jamesagnew 4b5165b5e2 Docs fix 2020-03-24 20:10:14 -04:00
James Agnew eaaddaf7ca
Fix #1763 - Include bundle type in summary=count responses (#1773) 
* Fix #1763 - Include bundle type in summary=count responses

* Test fix
 2020-03-24 16:24:41 -04:00
James Agnew c6d23a8bc6
Add chain on _type parameter (#1772) 
* Add chain on _type parameter

* Add changelog

* Test fix

* Address review comments

* Fix azure yaml

* Correct HTTPs in pom

* One more pom tweak

* Test fix

* Try azure again
 2020-03-24 09:44:57 -04:00
jamesagnew 13f0e5384b Address review comments 2020-03-24 06:02:55 -04:00
jamesagnew fa29f3e8ab Credit for #1770 2020-03-23 19:12:05 -04:00
jamesagnew 7706600a8c Add changelog 2020-03-23 18:05:48 -04:00
jamesagnew 14316147c5 Resolve some docs issues 2020-03-23 10:34:12 -04:00
James Agnew c2ae5a8326
Add FHIRPath evaluation interceptor (#1769) 
* Add FHIRPath evaluation interceptor

* Add changelog
 2020-03-22 12:57:24 -04:00
Jafer Khan b8b8248133 Merge branch 'master' of https://github.com/jaferkhan/hapi-fhir into cleanup-docs-v2 
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/validation/profile_validator.md
 2020-03-22 02:25:11 +05:00
Tadgh ad46c3173a Add missed attribution to changelog 2020-03-18 10:26:33 -07:00
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
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
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
tungdt 46c67d20cc Add VEIG(Vietnam Ehealth Innovation Group) to points.json 2020-03-06 17:43:56 +07:00
Tadgh 828ddd5185 Update docs 2020-03-04 12:14:55 -08:00
James Agnew 58ee76549c Merge branch 'master' into ja_20200206_multitenancy 2020-03-04 08:19:22 -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 4a160a2df3 Merge branch 'master' into ja_20200206_multitenancy 2020-03-03 09:25:19 -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
Ken Stevens bce1716c6c documentation 2020-03-02 22:13:21 -05:00
James Agnew 8c78e465b1
Defer large term delta adds (#1736) 
* Defer large term delta adds

* Add changelog
 2020-02-28 14:41:15 -05:00
James Agnew 5bc554949b
Remove deleted resources from cached search results (#1732) 
* Remove deleted resources from cached search results

* Add changelog

* Add tests
 2020-02-28 10:57:26 -05:00
James Agnew cb9906580e
Index canonical references (#1728) 
* Index canonical references

* Add changelog

* Fix compile error

* Add whitespace
 2020-02-25 21:45:46 -05:00
Gary Graham df9e86ec66 Merge branch 'master' into date-match-bug 2020-02-25 17:26:53 -05:00
James Agnew b2b0ff22b4
Collapse date joins (#1726) 
* Collapse date joins

* Add changelog

* Address review comments

* Add whitespace

* fix test

Co-authored-by: Ken Stevens <ken.stevens@sympatico.ca>
 2020-02-25 17:17:13 -05:00
Gary Graham 97c98254d0 Extract Common functionality out of CalculateHashesTask, build CalculateOrdinalDatesTask based on it 2020-02-25 16:09:08 -05:00
Gary Graham 512af5b87d Add changelog entry 2020-02-25 14:09:51 -05:00
James Agnew a05c4ce9eb
Don't thrash delta links (#1721) 
* Don't thrash delta links

* Add changelog

* Remove commented out code
 2020-02-19 17:46:54 -05:00
James Agnew ab8dfa5a03
Avoid multi-term for ElasticSearch (#1717) 
* Avoid multi-term for ElasticSearch

* Add changelog

* Remove redundant code
 2020-02-18 16:40:44 -05:00
IanMMarshall fba28950ec
Merge pull request #1693 from jamesagnew/im_20200131_remove_circular_dependency_forcedid 
Changes to schema to loosen dependencies involving Forced ID table
 2020-02-18 14:16:09 -05:00
James Agnew 64f07e4dc0
Includes performance enhancement (#1702) 
* Includes performance enhancement

* Add changelog

* Test fix

* Fix typo

* A few coverage cleanups

* Test fix

* Fix changelog
 2020-02-18 14:11:48 -05:00
ianmarshall 2f4f62b32e Add change log for Resource and Resource History table changes. 2020-02-18 14:09:59 -05:00
James Agnew 60f16dd91d
Update to 4.3.x core JAR (#1715) 
* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Start working on converter

* Account for compile errors

* Test fix

* Work no validator

* Work on getting core working

* Add some test coverage

* Many test fixes

Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
 2020-02-17 14:28:29 -05:00
jamesagnew ddc7b601ee Version bump to 4.3.0-SNAPSHOT 2020-02-16 19:23:22 -05:00
jamesagnew 4fd80cfca7 Bump to 4.2.0 2020-02-16 19:00:15 -05:00
jamesagnew f7ec41ffc5 Work on multitenancy 2020-02-09 08:40:15 -05:00
James Agnew b2d2346228 Work on multitenancy 2020-02-07 15:18:06 -05:00
James Agnew 97289b3a1f Credit for #1692 2020-02-04 17:38:42 -05:00
jamesagnew afd6a2b3a7 Remove entry from atlas 2020-02-01 17:31:57 -05:00
Ken Stevens 2545fc6e3d Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search 
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml
 2020-01-29 17:06:02 -05:00
jamesagnew beab5b3a9c Credit for #1689 2020-01-29 05:56:36 -05:00
dionmcm 95254406bc updated custom narrative generation documentation 
I found that the documented pattern of
 [name].class=[fully qualified classname]
No longer works. The pattern of
 [name].resourceType=[ResourceType]
worked for me, I updated the datatype example as well in kind, but I've not used it that way.

Maybe some extended examples for the other property type extensions would be good - e.g. .profile, .style, .contextPath, .narrative, .title
 2020-01-29 05:53:45 -05:00
James Agnew 471073103f Further reduce memory usage in the terminology delta operations 2020-01-28 14:36:15 -05:00
Ken Stevens cef58b528e added _filter to list of search gaps 2020-01-25 18:46:58 -05:00
Ken Stevens eff4b294df Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search 
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml
 2020-01-25 18:40:55 -05:00
James Agnew ba0048aade
Resolve memory leak (#1685) 
* Work on memory leak

* Work on term delta uploading

* Resolve memoery leak in terminology service

* Fix cache key
 2020-01-25 17:48:26 -05:00
Ken Stevens a63c62b2e1 ensure in-memory matching location search for Dstu3 falls back to a db search 2020-01-25 14:35:20 -05:00
Ken Stevens 78ab01f00b Change log and check in-memory search for location 2020-01-24 21:56:14 -05:00
James Agnew dd01688a90 Credit for #1679 2020-01-24 08:32:19 -05:00
James Agnew 39ff698dd2
Parser performance tweaks (#1660) 
* Parser improvements

* Parser tweaks

* Fix test

* Add changelog

* Bump spring mvc version

* Bump spring version

* Test fix?
 2020-01-22 14:44:12 -05:00
James Agnew 0718f6b52a
Allow schemalocation in XML validation (#1677) 
* Allow schemaLocation declaration in XML when validating

* Add fix for #1676
 2020-01-21 07:14:16 +09:00
James Agnew c0e929dacb
Copy identifiers to placeholder resources (#1675) 
* Copy identifiers to placeholder resources

* Add tests

* Maven cleanup

* Still messing around with azure

* Adding to logging

* More azure work

* One more attempt

* More messing around with azure

* Test fix

* Another caching attempt

* More work on azure pipeline

* Fix pipeline file

* Keep working on pipeline

* More work on azure

* More azure

* More azure work

* More azure
 2020-01-21 06:09:06 +09:00
James Agnew aad5a30a3d
Support count=0 (#1670) 
* Support count=0

* Fix LGTM issue
 2020-01-15 14:52:32 +08:00
James Agnew 201ec34db4
Fix expunge issue when no tags present (#1671) 
* Fix expunge issue when no tags present

* Add changelog

* Try to clean up POMs that are failing CI

* Rework dependencies

* Roll back change that did not work
 2020-01-15 14:47:22 +08:00
James Agnew 1390ea3c06
Update FHIR R5 structures to 4.2.0 version (#1665) 
* Work on upgrading core

* Work on R5 updates

* Work on core updates

* Test fix

* Update model version properties file for R5

* Bump core version

* Test fixes

* Add 4.2.0-SNAPSHOT version to versions page in docs
 2020-01-14 10:27:01 +08:00
James Agnew 62b50f06ad Documentation fix 2020-01-14 04:44:10 +08:00
James Agnew 114e8f5f15 Credit for #1655 2020-01-13 13:39:47 +08:00
James Agnew 0c008e11be License header version bump 2020-01-10 13:15:14 -05:00
James Agnew ca3b4297e1 FIx #1649 - Account for LOINC file format changes in 2.67 2020-01-03 14:19:22 -05:00
James Agnew 2f3018c56e Credit for #1603 2020-01-03 13:43:16 -05:00
James Agnew 82921472d4 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-01-03 13:43:11 -05:00
Diederik Muylwyk e65363f74d Fix typo. 2020-01-03 12:31:11 -05:00
James Agnew 3edcb04fb1 Add atlas entry 2020-01-03 11:08:48 -05:00
Diederik Muylwyk 48f7ee5afb Rolling back previous unnecessary changes. 2019-12-31 09:25:56 -05:00
Diederik Muylwyk 856993edf8 Moved changelog entry, and added clarifying comments to DateRangeParam. 2019-12-30 15:29:35 -05:00
jamesagnew 3788136194 Credit for #1650 2019-12-27 10:02:00 -05:00
James Agnew baa8eaf728
Merge pull request #1650 from jaferkhan/fix-modifier-typo 
Correct typos in code snippets across three different files
 2019-12-27 10:00:33 -05:00
jamesagnew 4c923c6e92 Atlas update 2019-12-27 08:16:17 -05:00
Jafer Khan 27a084f061 Correct typo in code's comment. Fixes gh-1617 2019-12-27 16:25:45 +05:00
Jafer Khan 8039d68608 Fixed various typos and other minor issues in docs 2019-12-26 01:36:18 +05:00
Jafer Khan 35fbe69589 Add more text to the incomplete paragraph. Fixes gh-1638 2019-12-25 20:31:57 +05:00
James Agnew ecb8da7aea Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-12-21 11:57:51 -05:00
James Agnew 5aa961ade7 Docs tweak 2019-12-21 11:56:31 -05:00
jamesagnew c03e470fcd Credit for #1588 2019-12-21 11:37:02 -05:00
jamesagnew 736b066884 Update David's email 2019-12-21 09:35:44 -05:00
James Agnew 8a1fa3ea3c
Merge pull request #1643 from jamesagnew/ja_20191219_improve_validator 
Handle standalone validation of custom VS/CS
 2019-12-19 16:38:29 -05:00
James Agnew d050b7b3c2 Add changelog 2019-12-19 15:03:30 -05:00
jamesagnew d7240019c3 Points update from Jens 2019-12-18 19:26:48 -05:00
jamesagnew 5db231bae1 Add style guide 2019-12-18 05:50:55 -05:00
James Agnew f77428c05b Update text on changelog 2019-12-17 11:16:16 -05:00
James Agnew 04b79a7b6f Documentation updates 2019-12-16 18:52:28 -05:00
James Agnew e1f2d044ed Add errorprone back into build 2019-12-15 09:42:51 -05:00
jamesagnew 89f819ae74 A bit more work on docs 2019-12-15 08:07:23 -05:00
jamesagnew ba8f50f0c8 Docs updates 2019-12-14 18:19:09 -05:00
Jafer Khan a1a50ad257 Fixed typo in docs 2019-12-14 18:55:49 +05:00
jamesagnew d232f4267e Docs tweak 2019-12-12 09:33:00 -05:00
James Agnew 2054b409ff Fix compile error 2019-12-10 16:47:50 -05:00
James Agnew 8049215d07 A couple more docs updates 2019-12-10 16:41:43 -05:00
James Agnew d277d3fed5 Docs updates 2019-12-10 16:10:09 -05:00
Ken Stevens bd1b41ff82 change out-of-order-permitted from environment variablet to flag to work like dont-use-flyway 2019-12-09 16:44:24 -05:00
Ken Stevens 5117b93add document new environment variable 2019-12-09 11:49:43 -05:00
Ken Stevens c1aec7c0e4 document new environment variable 2019-12-09 11:45:30 -05:00
James Agnew 5e69fcdc5f Fix compile error 2019-12-06 17:06:53 -05:00
James Agnew 438ef70fdb Reuse connections in brute force migrator 2019-12-06 16:52:26 -05:00
James Agnew d91617e923
Account for review changes (#1623) 2019-12-05 18:01:45 -05:00
James Agnew b2e2cb88d7 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-12-03 10:53:19 -05:00
James Agnew f277819830 Add map points JSON 2019-12-03 10:53:06 -05:00
James Agnew f58fba6f04
Some test cleanup (#1616) 
* Some test cleanup

* Add test

* More test logging

* More docs cleanup

* Add test logging
 2019-12-02 11:00:18 -05:00
James Agnew 86bd9a28fe
Fix to valueset expansion logic (#1613) 
* Fox to valueset expansion logic

* Work on docs

* Docs tweaks

* Docs tweaks

* Fix test

* Remove unused class

* Add changelog
 2019-12-01 21:21:19 -05:00
Jafer Khan 2115721940 Corrected typos and fixed grammatical mistakes in documentation 2019-12-01 03:35:35 +05:00
James Agnew 5f803f7e68 Documentation updates 2019-11-26 02:00:22 -03:00
James Agnew 5becb613fe Add some documentation 2019-11-24 19:09:34 -05:00
James Agnew 497a96ae68 Version bump for next round of development 2019-11-12 22:09:21 -05:00
jamesagnew f99ad981b5 Version bump to 4.1.0 2019-11-12 16:08:20 -05:00
James Agnew aa0301084b
Don't succeed validation on unknown codesystem (#1575) 
* Don't succeed validation on unknown codesystem

* Test fixes

* Work on error messages

* Work on code validation API

* work on tests

* Work on validation

* Test fix

* Update DSTU3 validation reources

* Upgrade structures

* Test fixes
 2019-11-12 14:35:49 -05:00
John Poth 969174136e Rename org.hl7.fhir.convertors package as it's already used 2019-10-24 12:23:38 -05:00
Stig Rohde Døssing 79e97b24e5 Fix #1481 - Add missing dependency to hapi-fhir-docs 2019-10-17 13:57:58 -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 c8ce07c40e Deprecate redundant IVersionSpecificBundleProvider method 2019-09-30 09:45:31 -04:00
James Agnew 663431f571 Fix docs issue 2019-09-27 16:57:14 -04:00
James Agnew 27c637b8d7 Docs fix 2019-09-27 14:02:42 -04:00
James Agnew 5f563057c0
Set up CI with Azure Pipelines (#1502) 
* Set up CI with Azure Pipelines

[skip ci]

* Update azure-pipelines.yml for Azure Pipelines

* Skip tests for a build

* Work on pipeline

* Update azure-pipelines.yml for Azure Pipelines

* Interceptors docs

* Test fix

* Disable releases from snapshot repo

* Try disabling jitpack

* Fix dependency issue

* A couple of test fixes

* Change to trigger a build

* Force a change to trigger a build

* Force a build

* FIx test
 2019-09-24 14:38:38 -04:00
James Agnew 004f42cdcc Clean up docs 2019-09-23 15:56:02 -04:00
James Agnew 2bcb1c9c1c Work on docs 2019-09-23 09:56:29 -04:00
James Agnew e05ea676e9 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-22 15:55:06 -04:00
James Agnew 520b50dfdc Ongoing work on docs migration 2019-09-22 15:54:52 -04:00
jamesagnew 936587df6e Work on migrating docs 2019-09-22 15:52:49 -04:00
James Agnew 0a5eca0821 Work on docs 2019-09-22 13:25:50 -04:00
James Agnew d43c1760ef Adjust docs 2019-09-22 08:59:54 -04:00
James Agnew 58b7e3a923 Start splitting docs into separate project 2019-09-22 08:58:17 -04:00