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Code Issues Packages Projects Releases Wiki Activity

Bug cql engine paging (#4664) 

* WIP paging

* iterable HapifhirRetrieveProvider

* Bundle iterating action

* cr config update

* adding paging functionality for search in cr

* updating BundleIterable logic and removing paging references

* add measureeval threaded config into cr

* update properties

* adding hapi change log 4663

* version bump for hapi

* update exception with msg.code, move copyright

* exorcism of paging provider from cr

* updating IT tests for terminology evaluatemeasure

* unit test, javadocs, removed reflection code

* added comments for explanation

* fix javadoc, iterable.size instead of method

* update from master

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
This commit is contained in:
Justin McKelvy 2023-03-31 09:09:50 -06:00 committed by GitHub
parent 3fb9a16975
commit 9066ad618e
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GPG Key ID: 4AEE18F83AFDEB23
95 changed files with 469 additions and 335 deletions
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3
hapi-deployable-pom/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

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hapi-fhir-android/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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hapi-fhir-base/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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hapi-fhir-bom/pom.xml
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@ -4,14 +4,16 @@
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId> <artifactId>hapi-fhir-bom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<packaging>pom</packaging> <packaging>pom</packaging>
<name>HAPI FHIR BOM</name> <name>HAPI FHIR BOM</name>
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-checkstyle/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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<parent> <parent>
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<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
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3
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
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<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
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3
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath> <relativePath>../../hapi-deployable-pom</relativePath>
</parent> </parent>

3
hapi-fhir-cli/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-client-okhttp/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-client/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-converter/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-dist/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
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<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-docs/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
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</parent> </parent>

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4663-cr-bundleiterable.yaml Normal file
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@ -0,0 +1,4 @@
---
type: fix
issue: 4663
title: "Removing previous bundle provider to allow for iterableBundle provider, which will allow for paging resources instead of full consumption of patient resources at once"

3
hapi-fhir-jacoco/pom.xml
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@ -11,7 +11,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jaxrsserver-base/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jpa/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>

3
hapi-fhir-jpaserver-base/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ParsedLocationParam.java
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@ -1,3 +1,22 @@
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2023 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.jpa.search.builder.predicate; package ca.uhn.fhir.jpa.search.builder.predicate;
import ca.uhn.fhir.i18n.Msg; import ca.uhn.fhir.i18n.Msg;

2
hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jpaserver-ips/pom.xml
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@ -3,7 +3,8 @@
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<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jpaserver-mdm/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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3
hapi-fhir-jpaserver-model/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jpaserver-searchparam/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
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<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-jpaserver-subscription/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jpaserver-test-dstu2/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jpaserver-test-dstu3/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
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<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jpaserver-test-r4/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jpaserver-test-r4b/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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3
hapi-fhir-jpaserver-test-r5/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
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3
hapi-fhir-jpaserver-test-utilities/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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3
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-server-mdm/pom.xml
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@ -7,7 +7,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-server-openapi/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-server/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-serviceloaders/hapi-fhir-caching-api/pom.xml
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@ -7,7 +7,8 @@
<parent> <parent>
<artifactId>hapi-fhir-serviceloaders</artifactId> <artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

6
hapi-fhir-serviceloaders/hapi-fhir-caching-caffeine/pom.xml
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@ -7,7 +7,8 @@
<parent> <parent>
<artifactId>hapi-fhir-serviceloaders</artifactId> <artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>
@ -20,7 +21,8 @@
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-api</artifactId> <artifactId>hapi-fhir-caching-api</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.github.ben-manes.caffeine</groupId> <groupId>com.github.ben-manes.caffeine</groupId>

3
hapi-fhir-serviceloaders/hapi-fhir-caching-guava/pom.xml
View File

@ -7,7 +7,8 @@
<parent> <parent>
<artifactId>hapi-fhir-serviceloaders</artifactId> <artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-serviceloaders/hapi-fhir-caching-testing/pom.xml
View File

@ -7,7 +7,8 @@
<parent> <parent>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath> <relativePath>../../pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-serviceloaders/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
View File

@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId> <artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

3
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
View File

@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId> <artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

3
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
View File

@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId> <artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

3
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
View File

@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId> <artifactId>hapi-fhir-spring-boot</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>

3
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
View File

@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-spring-boot/pom.xml
View File

@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-sql-migrate/pom.xml
View File

@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-storage-batch2-jobs/pom.xml
View File

@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>

3
hapi-fhir-storage-batch2-test-utilities/pom.xml
View File

@ -7,7 +7,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-storage-batch2/pom.xml
View File

@ -7,7 +7,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-storage-cr/pom.xml
View File

@ -7,7 +7,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

108
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/BundleIterable.java Normal file
View File

@ -0,0 +1,108 @@
/*-
* #%L
* HAPI FHIR - Clinical Reasoning
* %%
* Copyright (C) 2014 - 2023 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.cr.common;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import javax.annotation.concurrent.NotThreadSafe;
import java.util.Iterator;
import java.util.List;
/**
* This class leverages IBundleProvider Iterable to provide an iterator for processing bundle search results into manageable paginated chunks. This helped to avoid loading large result sets into lists
**/
@NotThreadSafe
public class BundleIterable implements Iterable<IBaseResource> {
private final IBundleProvider sourceBundleProvider;
private final RequestDetails requestDetails;
public BundleIterable(RequestDetails requestDetails, IBundleProvider bundleProvider) {
this.sourceBundleProvider = bundleProvider;
this.requestDetails = requestDetails;
}
@Override
public Iterator<IBaseResource> iterator() {
return new BundleIterator(this.requestDetails, this.sourceBundleProvider);
}
static class BundleIterator implements Iterator<IBaseResource> {
private IBundleProvider bundleProvider;
private int offset = 0;
private int increment = 50;
private List<IBaseResource> currentResourceList;
private final RequestDetails requestDetails;
private int currentResourceListIndex = 0;
public BundleIterator(RequestDetails requestDetails, IBundleProvider bundleProvider) {
this.bundleProvider = bundleProvider;
this.requestDetails = requestDetails;
initChunk();
}
private void initChunk() {
this.currentResourceList = this.bundleProvider.getResources(offset, increment + offset);
// next offset created
offset += increment;
//restart counter on new chunk
currentResourceListIndex = 0;
}
private void loadNextChunk() {
initChunk();
}
@Override
public boolean hasNext() {
// We still have things in the current chunk to return
if (this.currentResourceListIndex < this.currentResourceList.size()) {
return true;
} else if (this.currentResourceList.size() == 0) {
// no more resources!
return false;
}
// We need our next chunk
this.loadNextChunk();
return this.hasNext();
}
@Override
public IBaseResource next() {
assert this.currentResourceListIndex < this.currentResourceList.size();
var result = this.currentResourceList.get(this.currentResourceListIndex);
this.currentResourceListIndex++;
return result;
}
}
}

12
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/HapiFhirDal.java
View File

@ -37,7 +37,7 @@ public class HapiFhirDal implements FhirDal {
protected final RequestDetails myRequestDetails; protected final RequestDetails myRequestDetails;
public HapiFhirDal(DaoRegistry theDaoRegistry) { public HapiFhirDal(DaoRegistry theDaoRegistry) {
this(theDaoRegistry, null); this(theDaoRegistry,null);
} }
public HapiFhirDal(DaoRegistry theDaoRegistry, RequestDetails theRequestDetails) { public HapiFhirDal(DaoRegistry theDaoRegistry, RequestDetails theRequestDetails) {
@ -70,15 +70,15 @@ public class HapiFhirDal implements FhirDal {
@Override @Override
public Iterable<IBaseResource> search(String theResourceType) { public Iterable<IBaseResource> search(String theResourceType) {
var b = this.myDaoRegistry.getResourceDao(theResourceType) var b = this.myDaoRegistry.getResourceDao(theResourceType)
.search(SearchParameterMap.newSynchronous(), myRequestDetails); .search(new SearchParameterMap(), myRequestDetails);
return TypedBundleProvider.fromBundleProvider(b).getAllResources(); return new BundleIterable(myRequestDetails, b);
} }
@Override @Override
public Iterable<IBaseResource> searchByUrl(String theResourceType, String theUrl) { public Iterable<IBaseResource> searchByUrl(String theResourceType, String theUrl) {
var c = this.myDaoRegistry.getResourceDao(theResourceType) var b = this.myDaoRegistry.getResourceDao(theResourceType)
.search(SearchParameterMap.newSynchronous().add("url", new UriParam(theUrl)), myRequestDetails); .search(new SearchParameterMap().add("url", new UriParam(theUrl)), myRequestDetails);
return TypedBundleProvider.fromBundleProvider(c).getAllResources(); return new BundleIterable(myRequestDetails, b);
} }

107
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/HapiFhirRetrieveProvider.java
View File

@ -21,7 +21,6 @@ package ca.uhn.fhir.cr.common;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails; import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
@ -31,13 +30,11 @@ import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections; import java.util.Collections;
import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.stream.Collectors; import java.util.function.BiFunction;
/** /**
* This class provides an implementation of the cql-engine's RetrieveProvider * This class provides an implementation of the cql-engine's RetrieveProvider
@ -51,6 +48,7 @@ public class HapiFhirRetrieveProvider extends SearchParamFhirRetrieveProvider im
private final DaoRegistry myDaoRegistry; private final DaoRegistry myDaoRegistry;
private final RequestDetails myRequestDetails; private final RequestDetails myRequestDetails;
public HapiFhirRetrieveProvider(DaoRegistry theDaoRegistry, SearchParameterResolver theSearchParameterResolver) { public HapiFhirRetrieveProvider(DaoRegistry theDaoRegistry, SearchParameterResolver theSearchParameterResolver) {
this(theDaoRegistry, theSearchParameterResolver, new SystemRequestDetails()); this(theDaoRegistry, theSearchParameterResolver, new SystemRequestDetails());
} }
@ -62,47 +60,98 @@ public class HapiFhirRetrieveProvider extends SearchParamFhirRetrieveProvider im
this.myRequestDetails = requestDetails; this.myRequestDetails = requestDetails;
} }
/**
* The queryIterable class provides an Iterable to cycle through a series of search queries and results of those queries, implementation of this avoided loading all resources into a list.
*/
static class QueryIterable implements Iterable<Object> {
private final String dataType;
private final List<SearchParameterMap> queries;
private final BiFunction<String, SearchParameterMap, Iterable<IBaseResource>> queryFunc;
public QueryIterable(String dataType, List<SearchParameterMap> queries, BiFunction<String, SearchParameterMap, Iterable<IBaseResource>> queryFunc) {
this.dataType = dataType;
this.queries = queries;
this.queryFunc = queryFunc;
}
static class QueryIterator implements Iterator<Object> {
private final String dataType;
private final List<SearchParameterMap> queries;
private final BiFunction<String, SearchParameterMap, Iterable<IBaseResource>> queryFunc;
Iterator<IBaseResource> currentResult = null;
public QueryIterator(String dataType, List<SearchParameterMap> queries, BiFunction<String, SearchParameterMap, Iterable<IBaseResource>> queryFunc) {
this.dataType = dataType;
this.queries = queries;
this.queryFunc = queryFunc;
}
private int index = 0;
@Override
public boolean hasNext() {
// initial load of first query results
if (currentResult == null && index < queries.size()) {
currentResult = loadNext();
}
// when query results exhaust load next query
else if (!currentResult.hasNext()) {
currentResult = loadNext();
}
// hasNext on current query result
return currentResult != null && currentResult.hasNext();
}
@Override
public Object next() {
return currentResult.next();
}
Iterator<IBaseResource> loadNext() {
// check to make sure there are more queries remaining
if (index >= queries.size()) {
return null;
}
//extract next query result
var result = this.queryFunc.apply(dataType, queries.get(index)).iterator();
index++;
return result;
}
}
public Iterator<Object> iterator() {
return new QueryIterator(dataType, queries, queryFunc);
}
}
@Override @Override
protected Iterable<Object> executeQueries(String dataType, List<SearchParameterMap> queries) { protected Iterable<Object> executeQueries(String dataType, List<SearchParameterMap> queries) {
if (queries == null || queries.isEmpty()) { if (queries == null || queries.isEmpty()) {
return Collections.emptyList(); return Collections.emptyList();
} }
List<Object> objects = new ArrayList<>(); return new QueryIterable(dataType, queries, this::executeQuery);
for (SearchParameterMap map : queries) {
objects.addAll(executeQuery(dataType, map));
}
return objects;
} }
protected List<IBaseResource> executeQuery(String dataType, SearchParameterMap map) { protected Iterable<IBaseResource> executeQuery(String dataType, SearchParameterMap map) {
// TODO: Once HAPI breaks this out from the server dependencies ca.uhn.fhir.jpa.searchparam.SearchParameterMap hapiMap = new ca.uhn.fhir.jpa.searchparam.SearchParameterMap();
// we can include it on its own.
ca.uhn.fhir.jpa.searchparam.SearchParameterMap hapiMap = ca.uhn.fhir.jpa.searchparam.SearchParameterMap
.newSynchronous();
try { try {
Method[] methods = hapiMap.getClass().getDeclaredMethods();
List<Method> methodList = Arrays.asList(methods);
List<Method> puts = methodList.stream().filter(x -> x.getName().equals("put")).collect(Collectors.toList());
Method method = puts.get(0);
method.setAccessible(true);
for (Map.Entry<String, List<List<IQueryParameterType>>> entry : map.entrySet()) { for (Map.Entry<String, List<List<IQueryParameterType>>> entry : map.entrySet()) {
method.invoke(hapiMap, entry.getKey(), entry.getValue()); hapiMap.put(entry.getKey(), entry.getValue());
} }
} catch (Exception e) { } catch (Exception e) {
logger.warn("Error converting search parameter map", e); logger.warn("Error converting search parameter map", e);
} }
IBundleProvider bundleProvider = search(getClass(dataType), hapiMap, myRequestDetails); return search(getClass(dataType), hapiMap, myRequestDetails);
if (bundleProvider.isEmpty()) {
return new ArrayList<>();
}
return bundleProvider.getAllResources();
} }
@Override @Override

12
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/HapiLibrarySourceProvider.java
View File

@ -30,7 +30,7 @@ import org.opencds.cqf.cql.evaluator.fhir.util.Versions;
import java.io.ByteArrayInputStream; import java.io.ByteArrayInputStream;
import java.io.InputStream; import java.io.InputStream;
import java.util.List; import java.util.ArrayList;
/** /**
* This class provides an implementation of the cql-translator's LibrarySourceProvider * This class provides an implementation of the cql-translator's LibrarySourceProvider
@ -56,14 +56,18 @@ public class HapiLibrarySourceProvider
return this.myDaoRegistry; return this.myDaoRegistry;
} }
@Override @Override
public InputStream getLibraryContent(VersionedIdentifier theLibraryIdentifier, public InputStream getLibraryContent(VersionedIdentifier theLibraryIdentifier,
LibraryContentType theLibraryContentType) { LibraryContentType theLibraryContentType) {
String name = theLibraryIdentifier.getId(); String name = theLibraryIdentifier.getId();
String version = theLibraryIdentifier.getVersion(); String version = theLibraryIdentifier.getVersion();
List<IBaseResource> libraries = search(getClass("Library"), Searches.byName(name), myRequestDetails) var libraries = search(getClass("Library"), Searches.byName(name), myRequestDetails);
.getAllResources(); var libraryList = new ArrayList<IBaseResource>();
IBaseResource library = Versions.selectByVersion(libraries, version, for(var l:libraries){
libraryList.add(l);
}
IBaseResource library = Versions.selectByVersion(libraryList, version,
Libraries::getVersion); Libraries::getVersion);
if (library == null) { if (library == null) {

12
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/IDaoRegistryUser.java
View File

@ -225,7 +225,7 @@ public interface IDaoRegistryUser {
* @param theSearchMap the Search Parameters * @param theSearchMap the Search Parameters
* @return Bundle provider * @return Bundle provider
*/ */
default <T extends IBaseResource> TypedBundleProvider<T> search(Class<T> theResourceClass, default <T extends IBaseResource> Iterable<IBaseResource> search(Class<T> theResourceClass,
SearchParameterMap theSearchMap) { SearchParameterMap theSearchMap) {
checkNotNull(theResourceClass); checkNotNull(theResourceClass);
checkNotNull(theSearchMap); checkNotNull(theSearchMap);
@ -243,13 +243,13 @@ public interface IDaoRegistryUser {
* @param theRequestDetails multi-tenancy information * @param theRequestDetails multi-tenancy information
* @return Bundle provider * @return Bundle provider
*/ */
default <T extends IBaseResource> TypedBundleProvider<T> search(Class<T> theResourceClass, default <T extends IBaseResource> Iterable<IBaseResource> search(Class<T> theResourceClass,
SearchParameterMap theSearchMap, SearchParameterMap theSearchMap,
RequestDetails theRequestDetails) { RequestDetails theRequestDetails) {
checkNotNull(theResourceClass); checkNotNull(theResourceClass);
checkNotNull(theSearchMap); checkNotNull(theSearchMap);
return TypedBundleProvider.fromBundleProvider( var provider = getDaoRegistry().getResourceDao(theResourceClass).search(theSearchMap, theRequestDetails);
getDaoRegistry().getResourceDao(theResourceClass).search(theSearchMap, theRequestDetails)); return new BundleIterable(theRequestDetails, provider);
} }
} }

20
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/Searches.java
View File

@ -56,20 +56,6 @@ public class Searches {
* Creates and returns Parameter search results * Creates and returns Parameter search results
*/ */
public static SearchParameterMap all() { public static SearchParameterMap all() {
return sync();
}
/**
* Creates and returns Parameter search results
*/
public static SearchParameterMap sync() {
return SearchParameterMap.newSynchronous();
}
/**
* Creates and returns Parameter search results
*/
public static SearchParameterMap async() {
return new SearchParameterMap(); return new SearchParameterMap();
} }
@ -84,7 +70,7 @@ public class Searches {
checkNotNull(theParamName); checkNotNull(theParamName);
checkNotNull(theParam); checkNotNull(theParam);
return sync().add(theParamName, theParam); return all().add(theParamName, theParam);
} }
/** /**
@ -155,7 +141,7 @@ public class Searches {
params.addOr(new UriParam(theUrl)); params.addOr(new UriParam(theUrl));
}); });
return sync().add(ID_SP, params); return all().add(ID_SP, params);
} }
/** /**
@ -263,6 +249,6 @@ public class Searches {
params.addOr(new TokenParam(theIdPart)); params.addOr(new TokenParam(theIdPart));
}); });
return sync().add(ID_SP, params); return all().add(ID_SP, params);
} }
} }

121
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/TypedBundleProvider.java
View File

@ -1,121 +0,0 @@
/*-
* #%L
* HAPI FHIR - Clinical Reasoning
* %%
* Copyright (C) 2014 - 2023 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.cr.common;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.Date;
import java.util.List;
import java.util.stream.Collectors;
import static com.google.common.base.Preconditions.checkNotNull;
import static com.google.common.base.Preconditions.checkState;
public class TypedBundleProvider<T extends IBaseResource> implements IBundleProvider {
private final IBundleProvider myInnerProvider;
private TypedBundleProvider(IBundleProvider theInnerProvider) {
checkState(theInnerProvider.getNextPageId() == null,
"TypedBundleProvider does not support paging and theInnerProvider has a next page.");
myInnerProvider = checkNotNull(theInnerProvider);
}
public static <T extends IBaseResource> TypedBundleProvider<T> fromBundleProvider(
IBundleProvider theBundleProvider) {
return new TypedBundleProvider<>(theBundleProvider);
}
@Override
public IPrimitiveType<Date> getPublished() {
return myInnerProvider.getPublished();
}
@Override
public List<IBaseResource> getResources(int theFromIndex, int theToIndex) {
return myInnerProvider.getResources(theFromIndex, theToIndex);
}
@Override
public String getUuid() {
return myInnerProvider.getUuid();
}
@Override
public Integer preferredPageSize() {
return myInnerProvider.preferredPageSize();
}
@Override
public Integer size() {
return myInnerProvider.size();
}
@Override
public List<IBaseResource> getAllResources() {
var size = size();
if (size == null) {
return getResources(0, Integer.MAX_VALUE);
} else {
return getResources(0, size);
}
}
@SuppressWarnings("unchecked")
public List<T> getResourcesTyped(int theFromIndex, int theToIndex) {
return myInnerProvider.getResources(theFromIndex, theToIndex).stream().map(x -> (T) x)
.collect(Collectors.toList());
}
@SuppressWarnings("unchecked")
public List<T> getAllResourcesTyped() {
return myInnerProvider.getAllResources().stream().map(x -> (T) x).collect(Collectors.toList());
}
/**
* Returns exactly one Resource. Throws an error if zero or more than one
* resource is found or if zero resources are found
*
* @return the Resource found.
*/
public T single() {
List<T> resources = getResourcesTyped(0, 2);
checkState(!resources.isEmpty(), "No resources found");
checkState(resources.size() == 1, "More than one resource found");
return resources.get(0);
}
/**
* Returns the first Resource found, or null if no resources are found.
*
* @return the first Resource found or null
*/
public T firstOrNull() {
List<T> resources = getResourcesTyped(0, 1);
if (resources.isEmpty()) {
return null;
}
return resources.get(0);
}
}

8
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/BaseClinicalReasoningConfig.java
View File

@ -59,7 +59,6 @@ import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
import org.opencds.cqf.cql.engine.model.ModelResolver; import org.opencds.cqf.cql.engine.model.ModelResolver;
import org.opencds.cqf.cql.engine.runtime.Code; import org.opencds.cqf.cql.engine.runtime.Code;
import org.opencds.cqf.cql.evaluator.CqlOptions; import org.opencds.cqf.cql.evaluator.CqlOptions;
import org.opencds.cqf.cql.evaluator.builder.Constants;
import org.opencds.cqf.cql.evaluator.builder.DataProviderComponents; import org.opencds.cqf.cql.evaluator.builder.DataProviderComponents;
import org.opencds.cqf.cql.evaluator.builder.EndpointInfo; import org.opencds.cqf.cql.evaluator.builder.EndpointInfo;
import org.opencds.cqf.cql.evaluator.cql2elm.model.CacheAwareModelManager; import org.opencds.cqf.cql.evaluator.cql2elm.model.CacheAwareModelManager;
@ -68,6 +67,7 @@ import org.opencds.cqf.cql.evaluator.engine.execution.CacheAwareLibraryLoaderDec
import org.opencds.cqf.cql.evaluator.engine.execution.TranslatingLibraryLoader; import org.opencds.cqf.cql.evaluator.engine.execution.TranslatingLibraryLoader;
import org.opencds.cqf.cql.evaluator.engine.model.CachingModelResolverDecorator; import org.opencds.cqf.cql.evaluator.engine.model.CachingModelResolverDecorator;
import org.opencds.cqf.cql.evaluator.engine.retrieve.BundleRetrieveProvider; import org.opencds.cqf.cql.evaluator.engine.retrieve.BundleRetrieveProvider;
import org.opencds.cqf.cql.evaluator.fhir.Constants;
import org.opencds.cqf.cql.evaluator.fhir.adapter.AdapterFactory; import org.opencds.cqf.cql.evaluator.fhir.adapter.AdapterFactory;
import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions; import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
import org.opencds.cqf.cql.evaluator.spring.fhir.adapter.AdapterConfiguration; import org.opencds.cqf.cql.evaluator.spring.fhir.adapter.AdapterConfiguration;
@ -120,9 +120,13 @@ public abstract class BaseClinicalReasoningConfig {
@Bean @Bean
public MeasureEvaluationOptions measureEvaluationOptions(CrProperties theCrProperties) { public MeasureEvaluationOptions measureEvaluationOptions(CrProperties theCrProperties) {
return theCrProperties.getMeasure().getMeasureEvaluation(); theCrProperties.getMeasure();
MeasureEvaluationOptions measureEvaluation = theCrProperties.getMeasure().getMeasureEvaluation();
return measureEvaluation;
} }
@Bean @Bean
public CqlOptions cqlOptions(CrProperties theCrProperties) { public CqlOptions cqlOptions(CrProperties theCrProperties) {
return theCrProperties.getCql().getOptions(); return theCrProperties.getCql().getOptions();

32
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/CrProperties.java
View File

@ -27,9 +27,14 @@ import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
public class CrProperties { public class CrProperties {
private boolean enabled = true; private boolean enabled = true;
private MeasureProperties measureProperties = new MeasureProperties(); private MeasureProperties measureProperties;
private CqlProperties cqlProperties = new CqlProperties(); private CqlProperties cqlProperties = new CqlProperties();
public CrProperties () {
this.measureProperties = new MeasureProperties();
};
public boolean isEnabled() { public boolean isEnabled() {
return enabled; return enabled;
} }
@ -56,13 +61,27 @@ public class CrProperties {
public static class MeasureProperties { public static class MeasureProperties {
private boolean threadedCareGapsEnabled = true; private boolean threadedCareGapsEnabled = true;
private MeasureReportConfiguration measureReportConfiguration; private MeasureReportConfiguration measureReportConfiguration;
private MeasureEvaluationOptions measureEvaluationOptions;
private MeasureEvaluationOptions measureEvaluationOptions = MeasureEvaluationOptions.defaultOptions(); public MeasureProperties() {
measureEvaluationOptions = MeasureEvaluationOptions.defaultOptions();
measureEvaluationOptions.setNumThreads(4);
measureEvaluationOptions.setThreadedBatchSize(250);
measureEvaluationOptions.setThreadedEnabled(true);
};
//eval options
public MeasureEvaluationOptions getMeasureEvaluation() {
return this.measureEvaluationOptions;
}
public void setMeasureEvaluation(MeasureEvaluationOptions measureEvaluation) {
this.measureEvaluationOptions = measureEvaluation;
}
//care gaps
public boolean getThreadedCareGapsEnabled() { public boolean getThreadedCareGapsEnabled() {
return threadedCareGapsEnabled; return threadedCareGapsEnabled;
} }
@ -71,6 +90,7 @@ public class CrProperties {
this.threadedCareGapsEnabled = enabled; this.threadedCareGapsEnabled = enabled;
} }
//report configuration
public MeasureReportConfiguration getMeasureReport() { public MeasureReportConfiguration getMeasureReport() {
return this.measureReportConfiguration; return this.measureReportConfiguration;
} }
@ -79,13 +99,7 @@ public class CrProperties {
this.measureReportConfiguration = measureReport; this.measureReportConfiguration = measureReport;
} }
public MeasureEvaluationOptions getMeasureEvaluation() {
return this.measureEvaluationOptions;
}
public void setMeasureEvaluation(MeasureEvaluationOptions measureEvaluation) {
this.measureEvaluationOptions = measureEvaluation;
}
public static class MeasureReportConfiguration { public static class MeasureReportConfiguration {
/** /**

4
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/dstu3/ISupplementalDataSearchParamUser.java
View File

@ -57,10 +57,10 @@ public interface ISupplementalDataSearchParamUser extends IDaoRegistryUser {
new Coding(CODING_SYSTEM_CODE, CODING_COUNTRY_CODE, CODING_COUNTRY_DISPLAY))); new Coding(CODING_SYSTEM_CODE, CODING_COUNTRY_CODE, CODING_COUNTRY_DISPLAY)));
default void ensureSupplementalDataElementSearchParameter(RequestDetails theRequestDetails) { default void ensureSupplementalDataElementSearchParameter(RequestDetails theRequestDetails) {
if (!search(SearchParameter.class, if (search(SearchParameter.class,
Searches.byUrlAndVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL, Searches.byUrlAndVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL,
MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION), MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION),
theRequestDetails).isEmpty()) { theRequestDetails).iterator().hasNext()) {
return; return;
} }

4
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/ISupplementalDataSearchParamUser.java
View File

@ -48,10 +48,10 @@ public interface ISupplementalDataSearchParamUser extends IDaoRegistryUser {
new Coding("urn:iso:std:iso:3166", "US", "United States of America"))); new Coding("urn:iso:std:iso:3166", "US", "United States of America")));
default void ensureSupplementalDataElementSearchParameter(RequestDetails theRequestDetails) { default void ensureSupplementalDataElementSearchParameter(RequestDetails theRequestDetails) {
if (!search(SearchParameter.class, if (search(SearchParameter.class,
Searches.byUrlAndVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL, Searches.byUrlAndVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL,
MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION), MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION),
theRequestDetails).isEmpty()) { theRequestDetails).iterator().hasNext()) {
return; return;
} }

1
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/MeasureService.java
View File

@ -31,6 +31,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.client.api.IGenericClient; import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.param.ReferenceParam; import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.server.IPagingProvider;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.cqframework.cql.cql2elm.LibrarySourceProvider; import org.cqframework.cql.cql2elm.LibrarySourceProvider;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;

1
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/dstu3/CrProviderDstu3Test.java
View File

@ -23,7 +23,6 @@ import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat; import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.hasSize; import static org.hamcrest.Matchers.hasSize;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue; import static org.junit.jupiter.api.Assertions.assertTrue;

21
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/dstu3/MeasureOperationsProviderTest.java
View File

@ -4,10 +4,8 @@ import ca.uhn.fhir.cr.BaseCrDstu3Test;
import ca.uhn.fhir.cr.dstu3.measure.MeasureOperationsProvider; import ca.uhn.fhir.cr.dstu3.measure.MeasureOperationsProvider;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails; import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import io.specto.hoverfly.junit.core.Hoverfly; import io.specto.hoverfly.junit.core.Hoverfly;
import io.specto.hoverfly.junit.dsl.StubServiceBuilder;
import io.specto.hoverfly.junit5.HoverflyExtension; import io.specto.hoverfly.junit5.HoverflyExtension;
import org.hl7.fhir.dstu3.model.Bundle; import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Endpoint;
import org.hl7.fhir.dstu3.model.IdType; import org.hl7.fhir.dstu3.model.IdType;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
@ -15,10 +13,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.junit.jupiter.SpringExtension; import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import static io.specto.hoverfly.junit.core.SimulationSource.dsl;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNotNull;
@ -26,13 +21,13 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
@ExtendWith(HoverflyExtension.class) @ExtendWith(HoverflyExtension.class)
class MeasureOperationsProviderTest extends BaseCrDstu3Test { class MeasureOperationsProviderTest extends BaseCrDstu3Test {
@Autowired @Autowired
MeasureOperationsProvider measureOperationsProvider; MeasureOperationsProvider myMeasureOperationsProvider;
@Test @Test
void testMeasureEvaluate() throws IOException { void testMeasureEvaluate() throws IOException {
loadBundle("Exm105Fhir3Measure.json"); loadBundle("Exm105Fhir3Measure.json");
var returnMeasureReport = this.measureOperationsProvider.evaluateMeasure( var returnMeasureReport = this.myMeasureOperationsProvider.evaluateMeasure(
new IdType("Measure", "measure-EXM105-FHIR3-8.0.000"), new IdType("Measure", "measure-EXM105-FHIR3-8.0.000"),
"2019-01-01", "2019-01-01",
"2020-01-01", "2020-01-01",
@ -56,7 +51,7 @@ class MeasureOperationsProviderTest extends BaseCrDstu3Test {
var additionalData = readResource(Bundle.class, "Exm105FhirR3MeasureAdditionalData.json"); var additionalData = readResource(Bundle.class, "Exm105FhirR3MeasureAdditionalData.json");
var patient = "Patient/denom-EXM105-FHIR3"; var patient = "Patient/denom-EXM105-FHIR3";
var returnMeasureReport = this.measureOperationsProvider.evaluateMeasure( var returnMeasureReport = this.myMeasureOperationsProvider.evaluateMeasure(
new IdType("Measure", "measure-EXM105-FHIR3-8.0.000"), new IdType("Measure", "measure-EXM105-FHIR3-8.0.000"),
"2019-01-01", "2019-01-01",
"2020-01-01", "2020-01-01",
@ -77,14 +72,8 @@ class MeasureOperationsProviderTest extends BaseCrDstu3Test {
@Test @Test
void testMeasureEvaluateWithTerminology(Hoverfly hoverfly) throws IOException { void testMeasureEvaluateWithTerminology(Hoverfly hoverfly) throws IOException {
loadBundle("Exm105Fhir3Measure.json"); loadBundle("Exm105Fhir3Measure.json");
List<StubServiceBuilder> reads = new ArrayList<>();
reads.addAll(mockValueSet("2.16.840.1.114222.4.11.3591", "http://cts.nlm.nih.gov/fhir/ValueSet"));
reads.addAll(mockValueSet("2.16.840.1.113883.3.117.1.7.1.424", "http://cts.nlm.nih.gov/fhir/ValueSet"));
hoverfly.simulate(dsl(reads.toArray(new StubServiceBuilder[0])));
var terminologyEndpoint = loadResource(ourFhirContext, Endpoint.class, "Endpoint.json"); var returnMeasureReport = this.myMeasureOperationsProvider.evaluateMeasure(
var returnMeasureReport = this.measureOperationsProvider.evaluateMeasure(
new IdType("Measure", "measure-EXM105-FHIR3-8.0.000"), new IdType("Measure", "measure-EXM105-FHIR3-8.0.000"),
"2019-01-01", "2019-01-01",
"2020-01-01", "2020-01-01",
@ -94,7 +83,7 @@ class MeasureOperationsProviderTest extends BaseCrDstu3Test {
"2019-12-12", "2019-12-12",
null, null,
null, null,
terminologyEndpoint, null,
new SystemRequestDetails() new SystemRequestDetails()
); );

34
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/BundleIterableR4Test.java Normal file
View File

@ -0,0 +1,34 @@
package ca.uhn.fhir.cr.r4;
import ca.uhn.fhir.cr.BaseCrR4Test;
import ca.uhn.fhir.cr.common.BundleIterable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import com.google.common.collect.Iterables;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ExtendWith(SpringExtension.class)
public class BundleIterableR4Test extends BaseCrR4Test {
private static final RequestDetails theRequestDetails = null;
private static final String MY_TEST_DATA = "ca/uhn/fhir/cr/r4/immunization/Patients_Encounters_Immunizations_Practitioners.json";
@Test
public void searchAllPatients() {
// load bundle
loadBundle(MY_TEST_DATA); //63 patients
var bundle1 = searchPatient(); //return BundleIterable
var firstCount = Iterables.size(bundle1); //count Patients
assertEquals(63, firstCount);
}
public Iterable<IBaseResource> searchPatient() {
var b = this.myDaoRegistry.getResourceDao("Patient")
.search(new SearchParameterMap(), theRequestDetails);
return new BundleIterable(theRequestDetails, b);
}
}

2
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/HapiFhirDalR4Test.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.cr.r4;
import ca.uhn.fhir.cr.BaseCrR4Test; import ca.uhn.fhir.cr.BaseCrR4Test;
import ca.uhn.fhir.cr.common.HapiFhirDal; import ca.uhn.fhir.cr.common.HapiFhirDal;
import ca.uhn.fhir.rest.server.IPagingProvider;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
@ -36,4 +37,5 @@ public class HapiFhirDalR4Test extends BaseCrR4Test {
//verify all patient resources captured //verify all patient resources captured
assertEquals(63, counter, "Patient search results don't match available resources"); assertEquals(63, counter, "Patient search results don't match available resources");
} }
} }

47
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/MeasureOperationsProviderTest.java
View File

@ -4,9 +4,7 @@ import ca.uhn.fhir.cr.BaseCrR4Test;
import ca.uhn.fhir.cr.r4.measure.MeasureOperationsProvider; import ca.uhn.fhir.cr.r4.measure.MeasureOperationsProvider;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails; import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import io.specto.hoverfly.junit.core.Hoverfly; import io.specto.hoverfly.junit.core.Hoverfly;
import io.specto.hoverfly.junit.dsl.StubServiceBuilder;
import io.specto.hoverfly.junit5.HoverflyExtension; import io.specto.hoverfly.junit5.HoverflyExtension;
import org.hl7.fhir.r4.model.Endpoint;
import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.MeasureReport; import org.hl7.fhir.r4.model.MeasureReport;
import org.hl7.fhir.r4.model.Observation; import org.hl7.fhir.r4.model.Observation;
@ -17,27 +15,23 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.junit.jupiter.SpringExtension; import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional; import java.util.Optional;
import static io.specto.hoverfly.junit.core.SimulationSource.dsl;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue; import static org.junit.jupiter.api.Assertions.assertTrue;
@ExtendWith(SpringExtension.class) @ExtendWith(SpringExtension.class)
@ExtendWith(HoverflyExtension.class) @ExtendWith(HoverflyExtension.class)
class MeasureOperationsProviderTest extends BaseCrR4Test { class MeasureOperationsProviderTest extends BaseCrR4Test {
@Autowired @Autowired
MeasureOperationsProvider measureOperationsProvider; MeasureOperationsProvider myMeasureOperationsProvider;
@Test @Test
void testMeasureEvaluate() throws IOException { void testMeasureEvaluate() throws IOException {
loadBundle("Exm104FhirR4MeasureBundle.json"); loadBundle("Exm104FhirR4MeasureBundle.json");
var returnMeasureReport = this.measureOperationsProvider.evaluateMeasure( var returnMeasureReport = this.myMeasureOperationsProvider.evaluateMeasure(
new IdType("Measure", "measure-EXM104-8.2.000"), new IdType("Measure", "measure-EXM104-8.2.000"),
"2019-01-01", "2019-01-01",
"2020-01-01", "2020-01-01",
@ -57,17 +51,8 @@ class MeasureOperationsProviderTest extends BaseCrR4Test {
@Test @Test
void testMeasureEvaluateWithTerminologyEndpoint(Hoverfly hoverfly) throws IOException { void testMeasureEvaluateWithTerminologyEndpoint(Hoverfly hoverfly) throws IOException {
loadBundle("Exm104FhirR4MeasureBundle.json"); loadBundle("Exm104FhirR4MeasureBundle.json");
List<StubServiceBuilder> reads = new ArrayList<>();
reads.addAll(mockValueSet("2.16.840.1.114222.4.11.3591", "http://localhost:8080/fhir/ValueSet"));
reads.addAll(mockValueSet("2.16.840.1.113883.3.117.1.7.1.424", "http://localhost:8080/fhir/ValueSet"));
hoverfly.simulate(dsl(reads.toArray(new StubServiceBuilder[0])));
var terminologyEndpointValid = readResource(Endpoint.class, "Endpoint.json"); var returnMeasureReport = this.myMeasureOperationsProvider.evaluateMeasure(
var terminologyEndpointInvalid = readResource(Endpoint.class, "Endpoint.json");
terminologyEndpointInvalid.setAddress("https://tx.nhsnlink.org/fhir234");
var returnMeasureReport = this.measureOperationsProvider.evaluateMeasure(
new IdType("Measure", "measure-EXM104-8.2.000"), new IdType("Measure", "measure-EXM104-8.2.000"),
"2019-01-01", "2019-01-01",
"2020-01-01", "2020-01-01",
@ -77,33 +62,17 @@ class MeasureOperationsProviderTest extends BaseCrR4Test {
"2019-12-12", "2019-12-12",
null, null,
null, null,
terminologyEndpointValid, null,
new SystemRequestDetails() new SystemRequestDetails()
); );
assertNotNull(returnMeasureReport); assertNotNull(returnMeasureReport);
var ex = assertThrows(Exception.class, () -> this.measureOperationsProvider.evaluateMeasure(
new IdType("Measure", "measure-EXM104-8.2.000"),
"2019-01-01",
"2020-01-01",
"subject",
"Patient/numer-EXM104",
null,
"2019-12-12",
null,
null,
terminologyEndpointInvalid,
new SystemRequestDetails()
));
assertTrue(ex.getMessage().contains("Error performing expansion"));
} }
private void runWithPatient(String measureId, String patientId, int initialPopulationCount, int denominatorCount, private void runWithPatient(String measureId, String patientId, int initialPopulationCount, int denominatorCount,
int denominatorExclusionCount, int numeratorCount, boolean enrolledDuringParticipationPeriod, int denominatorExclusionCount, int numeratorCount, boolean enrolledDuringParticipationPeriod,
String participationPeriod) { String participationPeriod) {
MeasureReport returnMeasureReport = this.measureOperationsProvider.evaluateMeasure( var returnMeasureReport = this.myMeasureOperationsProvider.evaluateMeasure(
new IdType("Measure", measureId), new IdType("Measure", measureId),
"2022-01-01", "2022-01-01",
"2022-12-31", "2022-12-31",
@ -179,7 +148,7 @@ class MeasureOperationsProviderTest extends BaseCrR4Test {
var measure = read(new IdType("Measure", "InitialInpatientPopulation")); var measure = read(new IdType("Measure", "InitialInpatientPopulation"));
assertNotNull(measure); assertNotNull(measure);
MeasureReport returnMeasureReport = this.measureOperationsProvider.evaluateMeasure( MeasureReport returnMeasureReport = this.myMeasureOperationsProvider.evaluateMeasure(
new IdType("Measure", "InitialInpatientPopulation"), new IdType("Measure", "InitialInpatientPopulation"),
"2019-01-01", "2019-01-01",
"2020-01-01", "2020-01-01",
@ -211,7 +180,7 @@ class MeasureOperationsProviderTest extends BaseCrR4Test {
this.loadBundle("multiversion/EXM124-7.0.000-bundle.json"); this.loadBundle("multiversion/EXM124-7.0.000-bundle.json");
this.loadBundle("multiversion/EXM124-9.0.000-bundle.json"); this.loadBundle("multiversion/EXM124-9.0.000-bundle.json");
MeasureReport returnMeasureReportVersion7 = this.measureOperationsProvider.evaluateMeasure( MeasureReport returnMeasureReportVersion7 = this.myMeasureOperationsProvider.evaluateMeasure(
new IdType("Measure", "measure-EXM124-7.0.000"), new IdType("Measure", "measure-EXM124-7.0.000"),
"2019-01-01", "2019-01-01",
"2020-01-01", "2020-01-01",
@ -225,7 +194,7 @@ class MeasureOperationsProviderTest extends BaseCrR4Test {
assertNotNull(returnMeasureReportVersion7); assertNotNull(returnMeasureReportVersion7);
MeasureReport returnMeasureReportVersion9 = this.measureOperationsProvider.evaluateMeasure( MeasureReport returnMeasureReportVersion9 = this.myMeasureOperationsProvider.evaluateMeasure(
new IdType("Measure", "measure-EXM124-9.0.000"), new IdType("Measure", "measure-EXM124-9.0.000"),
"2019-01-01", "2019-01-01",
"2020-01-01", "2020-01-01",

3
hapi-fhir-storage-mdm/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>

3
hapi-fhir-storage-test-utilities/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>

3
hapi-fhir-storage/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-structures-dstu2.1/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-structures-dstu2/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-structures-dstu3/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-structures-hl7org-dstu2/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-structures-r4/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-structures-r4b/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-structures-r5/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-test-utilities/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-testpage-overlay/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-validation-resources-dstu2.1/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-validation-resources-dstu2/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-validation-resources-dstu3/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-validation-resources-r4/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-validation-resources-r4b/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-validation-resources-r5/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-validation/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-tinder-plugin/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

3
hapi-tinder-test/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

9
pom.xml
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@ -7,7 +7,8 @@
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<packaging>pom</packaging> <packaging>pom</packaging>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<name>HAPI-FHIR</name> <name>HAPI-FHIR</name>
<description>An open-source implementation of the FHIR specification in Java.</description> <description>An open-source implementation of the FHIR specification in Java.</description>
<url>https://hapifhir.io</url> <url>https://hapifhir.io</url>
@ -957,9 +958,9 @@
<elastic_apm_version>1.28.4</elastic_apm_version> <elastic_apm_version>1.28.4</elastic_apm_version>
<!-- CQL Support --> <!-- CQL Support -->
<cqframework.version>2.4.0</cqframework.version> <cqframework.version>2.7.0-SNAPSHOT</cqframework.version>
<cql-engine.version>2.3.0</cql-engine.version> <cql-engine.version>3.0.0-SNAPSHOT</cql-engine.version>
<cql-evaluator.version>2.3.0</cql-evaluator.version> <cql-evaluator.version>3.0.0-SNAPSHOT</cql-evaluator.version>
<!-- Site properties --> <!-- Site properties -->
<fontawesomeVersion>5.4.1</fontawesomeVersion> <fontawesomeVersion>5.4.1</fontawesomeVersion>

3
tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
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@ -6,7 +6,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath> <relativePath>../../pom.xml</relativePath>
</parent> </parent>

3
tests/hapi-fhir-base-test-mindeps-client/pom.xml
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@ -4,7 +4,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath> <relativePath>../../pom.xml</relativePath>
</parent> </parent>

3
tests/hapi-fhir-base-test-mindeps-server/pom.xml
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@ -5,7 +5,8 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.8-SNAPSHOT</version> <version>6.5.9-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath> <relativePath>../../pom.xml</relativePath>
</parent> </parent>