https://github.com/jamesagnew/hapi-fhir

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Revision Author Date Message Commit Date
976f1c8 Resolve merge conflicts 28 July 2020, 22:55:43 UTC
9212872 fix resource link index reuse bug 28 July 2020, 22:55:34 UTC
6a8e09a Ensure that parent structuredefinitions are snapshotted before (#2005) * Ensure that parent structuredefinitions are snapshotted before snapshotting child * Add changelog 28 July 2020, 15:46:58 UTC
20d1ab2 Mark renameTask as deprecated 28 July 2020, 12:38:28 UTC
a6213fe One more tweak for #2002 on Oracle 28 July 2020, 12:27:13 UTC
3a7ac0d Correct invalid decimal numbers stored in DB (#2003) * Correct invalid decimal numbers stored in DB * Add changelog 27 July 2020, 17:33:27 UTC
06fd306 Allow constraints to be deleted by the migrator on H2 (#2002) 27 July 2020, 14:20:27 UTC
a35c97e Add utility method to XmlUtil 26 July 2020, 21:54:45 UTC
c6769ef Add test for #1999 25 July 2020, 19:17:25 UTC
ff1d522 Merge pull request #1997 from jamesagnew/1996-empi-match-bug Allow empty candidateSearchParams in EMPI module config. 24 July 2020, 21:22:29 UTC
df6f028 It is allowed to have empty candidate search params, so validator test is, ironically, invalid 24 July 2020, 18:52:32 UTC
7fd690f Add test in provider with different empi json rules 24 July 2020, 17:42:21 UTC
4e66cb6 Merge pull request #1994 from jamesagnew/fix_mssql_errors Fix mssql errors 24 July 2020, 15:26:23 UTC
b67f30a fix oracle and derby default 24 July 2020, 14:03:21 UTC
31d0ed3 remove question, put in PR instead 24 July 2020, 01:09:10 UTC
698b18e Fix NPE in iterator, fix empi-rules.json, add extra tests 24 July 2020, 01:01:08 UTC
2da6411 Resolve issue with test 24 July 2020, 00:28:20 UTC
6a5b96d Start with broken test for #1996 23 July 2020, 22:52:12 UTC
296ed96 Fix sentence fragment 23 July 2020, 16:57:46 UTC
7b435d6 changelog for mssql changers 23 July 2020, 16:16:11 UTC
08cbac5 fix tests (#1993) 23 July 2020, 15:01:54 UTC
a6fd625 Speed up loinc ingestion (#1991) * Speed up loinc ingestion * Add some logging 23 July 2020, 13:20:33 UTC
9231253 Modify drop index syntax for mssql 22 July 2020, 16:22:08 UTC
6f1d46d modify add index logic to behave like the other jdbc databases 22 July 2020, 16:21:58 UTC
f285318 Add mssql to drop FK constraints when column is dropped 22 July 2020, 16:21:50 UTC
160778d Empi docs (#1989) * Remove lines from image edges. Thanks Max! * fix case 4 docs only mark possible match as eid if it was via an eid match 21 July 2020, 17:07:49 UTC
5f1078a Cleanup of package installer 21 July 2020, 15:43:57 UTC
c44c1ff Wrap NPM loader in a try-catch 21 July 2020, 13:57:10 UTC
4c4d460 Credit for #1848 21 July 2020, 09:40:41 UTC
1c27726 #1817: fix problem with missing resource references when extensions are used (#1848) Co-authored-by: Christian Ohr <christian.ohr@icw.de> 21 July 2020, 09:36:25 UTC
0573590 Fixes to interceptor in order to prevent zombie listeners on restart (#1988) * Fixes to interceptor in order to prevent zombie listeners on restart * Add test * Add license header * Test fixes 20 July 2020, 18:03:46 UTC
5db90d3 Address issues when importing US Core (#1986) * Work on US Core import * Work on US Core * Resolve issues with US Core import * Test fix 17 July 2020, 19:28:16 UTC
c13e17b Add changelog and bump Jetty 17 July 2020, 15:50:45 UTC
dbe171d Bump jetty_version from 9.4.24.v20191120 to 9.4.29.v20200521 (#1890) Bumps `jetty_version` from 9.4.24.v20191120 to 9.4.29.v20200521. Updates `jetty-http` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Updates `jetty-servlets` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Updates `jetty-io` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Updates `jetty-continuation` from 9.4.24.v20191120 to 9.4.29.v20200521 Updates `jetty-security` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Updates `jetty-servlet` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Updates `jetty-server` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Updates `jetty-util` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Updates `jetty-webapp` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Updates `jetty-xml` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Updates `websocket-api` from 9.4.24.v20191120 to 9.4.29.v20200521 Updates `websocket-client` from 9.4.24.v20191120 to 9.4.29.v20200521 Updates `websocket-server` from 9.4.24.v20191120 to 9.4.29.v20200521 Updates `jetty-maven-plugin` from 9.4.24.v20191120 to 9.4.29.v20200521 - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 17 July 2020, 15:47:06 UTC
b57681d License header updates 17 July 2020, 12:54:20 UTC
ebd6ca4 Empi 3 ruleset version (#1978) * add rule version * add rule version * Rough in model for Golden Record. * Test Link Rule Version * add eid match boolean * added new fields to EmpiLink to provide more information about how the link was created * add logging to check an edge case * all tests pass * wip with failing tests * tests pass * FIXME * optimize imports * test score in provider output * FIXME * FIXME * Fix jpa test app context * fix migration string length * review feedback param name * review feedback javadoc * review feedback javadoc * bean config reorganization for cdr * add more tests 17 July 2020, 12:31:15 UTC
f5222f3 License headeer update 17 July 2020, 12:27:10 UTC
49c08f3 Credit for #1896 16 July 2020, 13:26:41 UTC
5a79304 Implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation (#1896) * implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation * GraphQLQueryBodyParameter to recognize application/graphql * fix 500 error on method without @GraphQLQueryBody * refactor to processGraphQlGetRequest and processGraphQlPostRequest * add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest * fix imports 16 July 2020, 13:25:26 UTC
962055e Undo extra logging in tests 15 July 2020, 17:47:19 UTC
077ee02 Fix validation for enumerated ValueSets (#1982) * Allow code validation against enumerated VS * Work on validation * Work on this * Work on tests * Work on validation * Work on tests * Work on validation * Test fixes * Add changelog * For a change * Test fixes 15 July 2020, 17:38:14 UTC
063bf42 Allow ConceptMap with no explicit group source/target (#1983) * Allow ConceptMap with no explicit group source/target * Add changelog 15 July 2020, 16:57:10 UTC
29bf6b8 Fix a bug validating ValueSets (#1981) * Fix a buig validating ValueSets * Test fix 15 July 2020, 13:25:34 UTC
addcdc9 Make method transactional 14 July 2020, 23:12:40 UTC
d6f6ec2 License headers 13 July 2020, 20:57:24 UTC
baba4cc Avoid version conflicts on current writes (#1971) * Add auto retry of transactions * Experiment in Maven build * Transaction autoretry * Work on transaction retries * Work on transaction retry * Work on transaction retry * Fix tests * Avoid version conflicts * Add changelog * Resolve LGTM issue * FIx transaction scope error * Test fixes * Test fix * Test fixes * Test fix * Test fixes 13 July 2020, 12:51:13 UTC
e565b1c done (#1976) 10 July 2020, 19:08:50 UTC
5c14a6c Revert pointless SQL optimization (#1977) * Revert pointless SQL optimization * Fix tests 10 July 2020, 02:14:25 UTC
50ae07a stub out all migrations if an empty schema was initialized (#1975) 10 July 2020, 00:18:54 UTC
1449b9c Install NPM resources correctly (#1972) * Install NPM resources correctly * Fix tests 09 July 2020, 22:37:55 UTC
c949349 Correctly validate ISO 3166 codes (#1967 update) (#1973) * Add tests * Test fixes * Fix tests * Test fix * One more test fix 09 July 2020, 22:34:26 UTC
c40d152 Credit for #1966 08 July 2020, 14:44:52 UTC
7a44fa3 Fix GraphQL Array of Argument should be ORed (#1966) * provide IQueryParameterOr instead of IQueryParameterType to params.add * add tests 08 July 2020, 14:38:50 UTC
1e2505e change migration to correct table. (#1970) * change migration to correct table. QUESTION: Do we need to stub this migration and add new ones? * fix variable name 07 July 2020, 09:45:39 UTC
79862c4 add migration cutpoint (#1968) 06 July 2020, 20:12:44 UTC
3081df3 Merge pull request #1969 from jamesagnew/empi-interceptor-bug EMPI Storage interceptor bug fix 06 July 2020, 20:10:39 UTC
489bd77 Make constraint name comparisons case insensitive 06 July 2020, 18:58:03 UTC
2f11a67 change test name 06 July 2020, 18:53:40 UTC
be42929 Change string name 06 July 2020, 18:46:20 UTC
84da932 fix test 06 July 2020, 18:36:47 UTC
b786006 Credit for #1878 06 July 2020, 17:46:30 UTC
1266619 quick fix to avoid including duplicate copies of hapi-fhir-testpage-overlay classes (#1878) 06 July 2020, 17:43:51 UTC
11ad41d Credit for #1893 06 July 2020, 09:52:40 UTC
df133d1 #1892 Add support for :of-type Token Modifier (#1893) 06 July 2020, 09:50:44 UTC
9813c69 Merge branch 'ConsultingMD-atlas-grand-rounds' 06 July 2020, 09:45:35 UTC
2b5c834 Merge branch 'atlas-grand-rounds' of https://github.com/ConsultingMD/hapi-fhir into ConsultingMD-atlas-grand-rounds 06 July 2020, 09:45:19 UTC
4c883cf Added an entry for Ohum/FHIR (#1930) 06 July 2020, 09:43:20 UTC
4b1546f Add support for ISO 3166 to validator (#1967) * Add ISO 3166 support * Add support for ISO-3166 * Add changelog * Test fixes 06 July 2020, 09:29:48 UTC
6fb6675 Resolve validation errors to ValueSet with UCUM (#1948) * Add tests for validation errors * Work on validation errors * Bump core version * Fix validation errors * Test fixes * Add changelog * Test fix * Test fix * Test fix 05 July 2020, 23:59:21 UTC
9e19b87 Fix build 04 July 2020, 23:32:40 UTC
f356c7c Migrate to JUnit5 (#1952) * Work on junit * Work on junit 5 * Work on junit 5 * Bump errorprone vcersion * Work on tests * Junit 5 tweaks * Fixes * Work on tests * Work on junit5 * Work on tests * Test fixes * Work on junit5 * Test work * Get junit5 working * Test fix * Work on tests * WOrk on tests * Work on tests * fixes * Compile fix * One more tweak * Compile fix * Add changelog * Fix compile error * Compile fix 04 July 2020, 22:28:16 UTC
290577f Remove unnecessary type predicate (#1963) * Remove unnecessary type predicate * Add changelog 03 July 2020, 21:54:25 UTC
e23e222 Merge pull request #1960 from jamesagnew/im_20200630_code_system_load Accidentally merged pull request before pushing changes from code review 03 July 2020, 20:29:34 UTC
b1ff6cb Changes from code review 03 July 2020, 18:25:24 UTC
63bf9cc Merge pull request #1961 from jamesagnew/bulk-intermittent Bulk intermittent bug 03 July 2020, 18:19:51 UTC
4ff63e2 Remove unnecessary logging. Spring batch already logs this 03 July 2020, 17:21:04 UTC
d09f410 Tidy logging, increase timeout to 120 because clocks 03 July 2020, 17:15:57 UTC
a84a416 Increase awaitility timeout for bulk export of ALL resources 03 July 2020, 17:08:34 UTC
4e5ca2e Changes from code review 03 July 2020, 17:08:11 UTC
0e88506 Merge pull request #1958 from jamesagnew/im_20200630_code_system_load Im 20200630 code system load 03 July 2020, 17:06:42 UTC
38cb526 Add logging 03 July 2020, 16:40:52 UTC
46abdfa Merge remote-tracking branch 'remotes/origin/master' into im_20200630_code_system_load 02 July 2020, 17:29:17 UTC
aa1e46f Fix public hapi test server 02 July 2020, 17:09:49 UTC
ef86d26 License header updates 02 July 2020, 16:07:02 UTC
a59b25c Fix startup failure on hapi.fhir.org 02 July 2020, 16:06:33 UTC
557f732 Cleanup and improved Unit tests. 02 July 2020, 16:03:15 UTC
fb0029c Bump mysql-connector-java (#1956) Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 6.0.5 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/6.0.5...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 01 July 2020, 22:30:07 UTC
ef4b79d Bump mysql-connector-java in /hapi-fhir-jpaserver-migrate (#1955) Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 6.0.5 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/6.0.5...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 01 July 2020, 22:29:57 UTC
d1ceb28 Bump mysql-connector-java (#1954) Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 5.1.40 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/5.1.40...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 01 July 2020, 22:29:45 UTC
714bd62 Empi 70 phonetic indexing (#1941) * start with failing test * test passes with fixmes * javadoc and config * pre-review cleanup * generalize encoding * test passes, but indexing needs to be optimized * test passes, but indexing needs to be optimized * step 1 of optimization. big refactor of all predicates * step 2 of optimization: determine phonetic encoder at time of RuntimeSearchParam creation * integrated new phonetic encoders into empi * phonetic search implemented * IT passes * pre-review cleanup * final pre-review cleanup * final pre-review cleanup * Fix compile error Co-authored-by: James Agnew <jamesagnew@gmail.com> 30 June 2020, 21:36:54 UTC
bb17688 Add test for #1780 30 June 2020, 21:03:16 UTC
349c752 License headers 30 June 2020, 19:13:38 UTC
0788e79 Fix to address deferred save of TermConcept when code system version changes prior to save. 30 June 2020, 19:07:14 UTC
2cdef05 Missed commit on #1951 Squashed commit of the following: commit f820135996bf25d13483012074b38878085e2384 Author: jamesagnew <jamesagnew@gmail.com> Date: Tue Jun 30 14:29:24 2020 -0400 Address review comments commit 11c4f9defba581132a340a2e5f189a934e829b67 Author: jamesagnew <jamesagnew@gmail.com> Date: Tue Jun 30 09:38:16 2020 -0400 Fix LGTM warning commit b650fdb9ea7d09bdc1f9f811727e6d23bbf153ce Author: jamesagnew <jamesagnew@gmail.com> Date: Tue Jun 30 09:20:52 2020 -0400 Test fix commit 6ebcceeb5ca314313c197ff8543a87343e82a7a1 Author: jamesagnew <jamesagnew@gmail.com> Date: Mon Jun 29 18:49:01 2020 -0400 Add changelog commit 4a1d7383b0c7d119acf0f97866be902c61cff0f5 Author: jamesagnew <jamesagnew@gmail.com> Date: Mon Jun 29 18:46:52 2020 -0400 Bundle transmission commit 88bd4abf0cf105765e622a2fedd18b265ec8fbbe Merge: 7cde945281 25fc747b9f Author: jamesagnew <jamesagnew@gmail.com> Date: Mon Jun 29 17:31:23 2020 -0400 Merge branch 'master' into ja_20200617_subscription_send_bundles commit 7cde945281890ce34023a1e954a24503f2741809 Author: jamesagnew <jamesagnew@gmail.com> Date: Mon Jun 29 17:10:33 2020 -0400 Work on seed bundles commit ed2e62752efc828c16e0ca772c76ca1428610777 Author: jamesagnew <jamesagnew@gmail.com> Date: Mon Jun 29 09:39:10 2020 -0400 Work on subscriptions commit 52addcff5916ee3f32b245f464dfa13f4e1c6ac8 Merge: 64a9eaa4de bf8de84801 Author: jamesagnew <jamesagnew@gmail.com> Date: Sat Jun 27 18:09:23 2020 -0400 Merge branch 'master' into ja_20200617_subscription_send_bundles commit 64a9eaa4de38b5b16c0b5d8f3727634c897f06de Author: jamesagnew <jamesagnew@gmail.com> Date: Wed Jun 17 18:32:17 2020 -0400 Start work commit f74eba5397d40f948970c0fc77ef721b021de46a Author: jamesagnew <jamesagnew@gmail.com> Date: Wed Jun 17 18:28:18 2020 -0400 Terser should create correct Enumeration on create 30 June 2020, 18:31:40 UTC
fa4bbe3 Allow search criteria as subscription delivery mechanism (#1951) * Terser should create correct Enumeration on create * Start work * Work on subscriptions * Work on seed bundles * Bundle transmission * Add changelog * Test fix * Fix LGTM warning 30 June 2020, 18:29:09 UTC
cd69a14 Create codeql-analysis.yml 30 June 2020, 15:58:29 UTC
072f3a4 Use read partition for finding update candidate on upsert (#1945) * Use read partition for finding update candidate on upsert * Add changelog 29 June 2020, 22:22:27 UTC
25fc747 Merge pull request #1950 from jamesagnew/hotfix-test-import Hotfix test import 29 June 2020, 20:23:52 UTC
bb7d889 License header updates 29 June 2020, 19:15:51 UTC
8df0448 Fix import 29 June 2020, 18:04:03 UTC
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