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528 Commits

Author SHA1 Message Date
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