5089 cr measure refactor (#5324)
* version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * repository measure refactor * undo bundle edit, add config * embedded library true * undo post of bundle * clear library cache on test * fix sumbit-data test * missing packages from cql * fix test data and test cases for repository api * 3.0.0 clinical reasoning uplift * r4 cql execution provider and tests * fix submitdata provider config * wip cql tests * debugging cql op wip * wip debugging cql * update tests for $cql, fix class names * prep for Pre6 uplift * spotless checks and test fixes * bump to 3.0.0-PRE6 * cleanup * fix version * cleanup * fix exlusions in pom * add in cache invalidation config * search converter bug and test for repository * update searchconverter * version bump, add changelog * remove term config, move IDaoRegistryUser class * Break out dstu3 providers and move config to version folders * CVE-2023-26119 * remove * imports * code review updates --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com>
This commit is contained in:
Justin McKelvy
GitHub
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---
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type: add
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issue: 5089
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title: "Updating storage-cr module to latest CQL 3.0.0, latest cql engine improvements, and Clinical Reasoning operations
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to leverage repository api pattern. This will remove several dependencies from within hapi-fhir to make future maintenance
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simpler and performance more robust."
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|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<artifactId>hapi-fhir-serviceloaders</artifactId>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<artifactId>hapi-fhir-serviceloaders</artifactId>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
@ -21,7 +21,7 @@
|
|||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-caching-api</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
</dependency>
|
||||
<dependency>
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<artifactId>hapi-fhir-serviceloaders</artifactId>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
</parent>
|
||||
|
||||
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-spring-boot</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.9.6-SNAPSHOT</version>
|
||||
<version>6.9.7-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
@ -77,43 +77,12 @@
|
|||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.opencds.cqf.fhir</groupId>
|
||||
<artifactId>cqf-fhir-api</artifactId>
|
||||
<artifactId>cqf-fhir-cr</artifactId>
|
||||
<version>${clinical-reasoning.version}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.opencds.cqf.cql</groupId>
|
||||
<artifactId>evaluator.fhir</artifactId>
|
||||
<version>${clinical-reasoning.version}</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.r4</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.r4b</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.r5</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xpp3</groupId>
|
||||
<artifactId>xpp3</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xpp3</groupId>
|
||||
<artifactId>xpp3_min</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xmlpull</groupId>
|
||||
<artifactId>xmlpull</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.opencds.cqf.cql</groupId>
|
||||
<artifactId>evaluator.spring</artifactId>
|
||||
<groupId>org.opencds.cqf.fhir</groupId>
|
||||
<artifactId>cqf-fhir-jackson</artifactId>
|
||||
<version>${clinical-reasoning.version}</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
|
|
@ -124,40 +93,33 @@
|
|||
<groupId>xmlpull</groupId>
|
||||
<artifactId>xmlpull</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.opencds.cqf.cql</groupId>
|
||||
<artifactId>evaluator.plandefinition</artifactId>
|
||||
<version>${clinical-reasoning.version}</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>xpp3</groupId>
|
||||
<artifactId>xpp3_min</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xmlpull</groupId>
|
||||
<artifactId>xmlpull</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.opencds.cqf.cql</groupId>
|
||||
<artifactId>evaluator.jackson-deps</artifactId>
|
||||
<version>${clinical-reasoning.version}</version>
|
||||
<type>pom</type>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.opencds.cqf.fhir</groupId>
|
||||
<artifactId>cqf-fhir-cql</artifactId>
|
||||
<version>${clinical-reasoning.version}</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>xpp3</groupId>
|
||||
<artifactId>xpp3_min</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xpp3</groupId>
|
||||
<artifactId>xpp3_min</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xmlpull</groupId>
|
||||
<artifactId>xmlpull</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xmlpull</groupId>
|
||||
<artifactId>xmlpull</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
<type>pom</type>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.ogce</groupId>
|
||||
<artifactId>xpp3</artifactId>
|
||||
|
|
|
|||
|
|
@ -1,103 +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 ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
import javax.annotation.concurrent.NotThreadSafe;
|
||||
|
||||
/**
|
||||
* 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;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -25,11 +25,11 @@ import ca.uhn.fhir.jpa.cache.IResourceChangeEvent;
|
|||
import ca.uhn.fhir.jpa.cache.IResourceChangeListener;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import org.cqframework.cql.elm.execution.VersionedIdentifier;
|
||||
import org.hl7.elm.r1.VersionedIdentifier;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.opencds.cqf.cql.engine.runtime.Code;
|
||||
import org.opencds.cqf.cql.evaluator.fhir.util.Reflections;
|
||||
import org.opencds.cqf.fhir.utility.Reflections;
|
||||
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
|
|
|
|||
|
|
@ -1,118 +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.interceptor.api.Hook;
|
||||
import ca.uhn.fhir.interceptor.api.Interceptor;
|
||||
import ca.uhn.fhir.interceptor.api.Pointcut;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
|
||||
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
|
||||
import org.opencds.cqf.cql.engine.exception.CqlException;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.lang.reflect.InvocationTargetException;
|
||||
import javax.servlet.http.HttpServletRequest;
|
||||
import javax.servlet.http.HttpServletResponse;
|
||||
|
||||
/**
|
||||
* This class represents clinical reasoning interceptor used for cql exception handling and logging
|
||||
**/
|
||||
@Interceptor
|
||||
public class CqlExceptionHandlingInterceptor {
|
||||
|
||||
@Hook(Pointcut.SERVER_HANDLE_EXCEPTION)
|
||||
public boolean handleException(
|
||||
RequestDetails theRequestDetails,
|
||||
BaseServerResponseException theException,
|
||||
HttpServletRequest theServletRequest,
|
||||
HttpServletResponse theServletResponse)
|
||||
throws IOException {
|
||||
|
||||
CqlException cqlException = getCqlException(theException);
|
||||
if (cqlException == null) {
|
||||
return true;
|
||||
}
|
||||
|
||||
IBaseOperationOutcome operationOutcome = theException.getOperationOutcome();
|
||||
if (operationOutcome != null) {
|
||||
String cqlMessage = this.getCqlMessage(cqlException);
|
||||
switch (operationOutcome.getStructureFhirVersionEnum()) {
|
||||
case DSTU3:
|
||||
updateOutcome((org.hl7.fhir.dstu3.model.OperationOutcome) operationOutcome, cqlMessage);
|
||||
break;
|
||||
case R4:
|
||||
updateOutcome((org.hl7.fhir.r4.model.OperationOutcome) operationOutcome, cqlMessage);
|
||||
break;
|
||||
case R5:
|
||||
updateOutcome((org.hl7.fhir.r5.model.OperationOutcome) operationOutcome, cqlMessage);
|
||||
break;
|
||||
default:
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
private void updateOutcome(org.hl7.fhir.dstu3.model.OperationOutcome theOperationOutcome, String theCqlCause) {
|
||||
theOperationOutcome.getIssueFirstRep().setDiagnostics(theCqlCause);
|
||||
}
|
||||
|
||||
private void updateOutcome(org.hl7.fhir.r4.model.OperationOutcome theOperationOutcome, String theCqlCause) {
|
||||
theOperationOutcome.getIssueFirstRep().setDiagnostics(theCqlCause);
|
||||
}
|
||||
|
||||
private void updateOutcome(org.hl7.fhir.r5.model.OperationOutcome theOperationOutcome, String theCqlCause) {
|
||||
theOperationOutcome.getIssueFirstRep().setDiagnostics(theCqlCause);
|
||||
}
|
||||
|
||||
private String getCqlMessage(CqlException theCqlException) {
|
||||
String message = theCqlException.getMessage();
|
||||
|
||||
if (theCqlException.getSourceLocator() != null) {
|
||||
message += "\nat CQL source location: "
|
||||
+ theCqlException.getSourceLocator().toString();
|
||||
}
|
||||
|
||||
if (theCqlException.getCause() != null) {
|
||||
message += "\ncaused by: " + theCqlException.getCause().getMessage();
|
||||
}
|
||||
|
||||
return message;
|
||||
}
|
||||
|
||||
private CqlException getCqlException(BaseServerResponseException theException) {
|
||||
if (theException.getCause() instanceof CqlException) {
|
||||
return (CqlException) theException.getCause();
|
||||
} else if (theException.getCause() instanceof InvocationTargetException) {
|
||||
InvocationTargetException ite = (InvocationTargetException) theException.getCause();
|
||||
if (ite.getCause() instanceof CqlException) {
|
||||
return (CqlException) ite.getCause();
|
||||
}
|
||||
|
||||
if (ite.getTargetException() instanceof CqlException) {
|
||||
return (CqlException) ite.getTargetException();
|
||||
}
|
||||
}
|
||||
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,45 +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 java.util.concurrent.ForkJoinPool;
|
||||
import java.util.concurrent.ForkJoinPool.ForkJoinWorkerThreadFactory;
|
||||
import java.util.concurrent.ForkJoinWorkerThread;
|
||||
|
||||
/**
|
||||
* This class resolves issues with loading JAXB in a server environment and using CompletableFutures
|
||||
* https://stackoverflow.com/questions/49113207/completablefuture-forkjoinpool-set-class-loader
|
||||
**/
|
||||
public class CqlForkJoinWorkerThreadFactory implements ForkJoinWorkerThreadFactory {
|
||||
|
||||
@Override
|
||||
public final ForkJoinWorkerThread newThread(ForkJoinPool thePool) {
|
||||
return new CqlForkJoinWorkerThread(thePool);
|
||||
}
|
||||
|
||||
private static class CqlForkJoinWorkerThread extends ForkJoinWorkerThread {
|
||||
|
||||
private CqlForkJoinWorkerThread(final ForkJoinPool thePool) {
|
||||
super(thePool);
|
||||
// set the correct classloader here
|
||||
setContextClassLoader(Thread.currentThread().getContextClassLoader());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -25,11 +25,11 @@ import ca.uhn.fhir.jpa.cache.IResourceChangeEvent;
|
|||
import ca.uhn.fhir.jpa.cache.IResourceChangeListener;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import org.cqframework.cql.elm.execution.Library;
|
||||
import org.cqframework.cql.elm.execution.VersionedIdentifier;
|
||||
import org.cqframework.cql.cql2elm.model.CompiledLibrary;
|
||||
import org.hl7.elm.r1.VersionedIdentifier;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.opencds.cqf.cql.evaluator.fhir.util.Reflections;
|
||||
import org.opencds.cqf.fhir.utility.Reflections;
|
||||
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
|
|
@ -45,12 +45,12 @@ public class ElmCacheResourceChangeListener implements IResourceChangeListener {
|
|||
org.slf4j.LoggerFactory.getLogger(ElmCacheResourceChangeListener.class);
|
||||
|
||||
private final IFhirResourceDao<?> myLibraryDao;
|
||||
private final Map<VersionedIdentifier, Library> myGlobalLibraryCache;
|
||||
private final Map<VersionedIdentifier, CompiledLibrary> myGlobalLibraryCache;
|
||||
private final Function<IBaseResource, String> myNameFunction;
|
||||
private final Function<IBaseResource, String> myVersionFunction;
|
||||
|
||||
public ElmCacheResourceChangeListener(
|
||||
DaoRegistry theDaoRegistry, Map<VersionedIdentifier, Library> theGlobalLibraryCache) {
|
||||
DaoRegistry theDaoRegistry, Map<VersionedIdentifier, CompiledLibrary> theGlobalLibraryCache) {
|
||||
this.myLibraryDao = theDaoRegistry.getResourceDao("Library");
|
||||
this.myGlobalLibraryCache = theGlobalLibraryCache;
|
||||
this.myNameFunction = Reflections.getNameFunction(myLibraryDao.getResourceType());
|
||||
|
|
|
|||
|
|
@ -1,104 +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.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.rest.param.TokenParam;
|
||||
import ca.uhn.fhir.rest.param.UriParam;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.opencds.cqf.cql.evaluator.fhir.dal.FhirDal;
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
/**
|
||||
* This class leverages DaoRegistry from Hapi-fhir to implement CRUD FHIR API operations constrained to provide only the operations necessary for the cql-evaluator modules to function.
|
||||
**/
|
||||
public class HapiFhirDal implements FhirDal {
|
||||
|
||||
protected final DaoRegistry myDaoRegistry;
|
||||
protected final RequestDetails myRequestDetails;
|
||||
|
||||
public HapiFhirDal(DaoRegistry theDaoRegistry) {
|
||||
this(theDaoRegistry, null);
|
||||
}
|
||||
|
||||
public HapiFhirDal(DaoRegistry theDaoRegistry, RequestDetails theRequestDetails) {
|
||||
this.myDaoRegistry = theDaoRegistry;
|
||||
this.myRequestDetails = theRequestDetails;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void create(IBaseResource theResource) {
|
||||
this.myDaoRegistry.getResourceDao(theResource.fhirType()).create(theResource, myRequestDetails);
|
||||
}
|
||||
|
||||
@Override
|
||||
public IBaseResource read(IIdType theId) {
|
||||
return this.myDaoRegistry.getResourceDao(theId.getResourceType()).read(theId, myRequestDetails);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void update(IBaseResource theResource) {
|
||||
this.myDaoRegistry.getResourceDao(theResource.fhirType()).update(theResource, myRequestDetails);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void delete(IIdType theId) {
|
||||
this.myDaoRegistry.getResourceDao(theId.getResourceType()).delete(theId, myRequestDetails);
|
||||
}
|
||||
|
||||
// TODO: the search interfaces need some work
|
||||
@Override
|
||||
public Iterable<IBaseResource> search(String theResourceType) {
|
||||
var b = this.myDaoRegistry.getResourceDao(theResourceType).search(new SearchParameterMap(), myRequestDetails);
|
||||
return new BundleIterable(myRequestDetails, b);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Iterable<IBaseResource> searchByUrl(String theResourceType, String theUrl) {
|
||||
// version example "http://content.smilecdr.com/fhir/dqm/Library/ImmunizationStatusRoutine|2.0.1"
|
||||
if (theUrl.contains("|")) {
|
||||
String[] urlSplit = theUrl.split("\\|");
|
||||
String urlBase = urlSplit[0];
|
||||
String urlVersion = urlSplit[1];
|
||||
|
||||
IBundleProvider versionResource = this.myDaoRegistry
|
||||
.getResourceDao(theResourceType)
|
||||
.search(
|
||||
SearchParameterMap.newSynchronous()
|
||||
.add("url", new UriParam(urlBase))
|
||||
.add("version", new TokenParam(urlVersion)),
|
||||
new SystemRequestDetails());
|
||||
return new BundleIterable(myRequestDetails, versionResource);
|
||||
} else {
|
||||
// standard example "http://content.smilecdr.com/fhir/dqm/Library/ImmunizationStatusRoutine"
|
||||
IBundleProvider standardResource = this.myDaoRegistry
|
||||
.getResourceDao(theResourceType)
|
||||
.search(
|
||||
SearchParameterMap.newSynchronous().add("url", new UriParam(theUrl)),
|
||||
new SystemRequestDetails());
|
||||
return new BundleIterable(myRequestDetails, standardResource);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -1,166 +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.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.model.api.IQueryParameterType;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.opencds.cqf.cql.engine.fhir.retrieve.SearchParamFhirRetrieveProvider;
|
||||
import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterMap;
|
||||
import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.util.Collections;
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.function.BiFunction;
|
||||
|
||||
/**
|
||||
* This class provides an implementation of the cql-engine's RetrieveProvider
|
||||
* interface which is used for loading
|
||||
* data during CQL evaluation.
|
||||
*/
|
||||
public class HapiFhirRetrieveProvider extends SearchParamFhirRetrieveProvider implements IDaoRegistryUser {
|
||||
|
||||
private static final Logger logger = LoggerFactory.getLogger(HapiFhirRetrieveProvider.class);
|
||||
|
||||
private final DaoRegistry myDaoRegistry;
|
||||
private final RequestDetails myRequestDetails;
|
||||
|
||||
public HapiFhirRetrieveProvider(DaoRegistry theDaoRegistry, SearchParameterResolver theSearchParameterResolver) {
|
||||
this(theDaoRegistry, theSearchParameterResolver, new SystemRequestDetails());
|
||||
}
|
||||
|
||||
public HapiFhirRetrieveProvider(
|
||||
DaoRegistry registry, SearchParameterResolver searchParameterResolver, RequestDetails requestDetails) {
|
||||
super(searchParameterResolver);
|
||||
this.myDaoRegistry = registry;
|
||||
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) {
|
||||
currentResult = loadNext();
|
||||
}
|
||||
// loop through all batches of results
|
||||
// when query results exhaust load next query
|
||||
while (currentResult != null && !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
|
||||
protected Iterable<Object> executeQueries(String dataType, List<SearchParameterMap> queries) {
|
||||
if (queries == null || queries.isEmpty()) {
|
||||
return Collections.emptyList();
|
||||
}
|
||||
|
||||
return new QueryIterable(dataType, queries, this::executeQuery);
|
||||
}
|
||||
|
||||
protected Iterable<IBaseResource> executeQuery(String dataType, SearchParameterMap map) {
|
||||
ca.uhn.fhir.jpa.searchparam.SearchParameterMap hapiMap = new ca.uhn.fhir.jpa.searchparam.SearchParameterMap();
|
||||
try {
|
||||
|
||||
for (Map.Entry<String, List<List<IQueryParameterType>>> entry : map.entrySet()) {
|
||||
hapiMap.put(entry.getKey(), entry.getValue());
|
||||
}
|
||||
|
||||
} catch (Exception e) {
|
||||
logger.warn("Error converting search parameter map", e);
|
||||
}
|
||||
|
||||
return search(getClass(dataType), hapiMap, myRequestDetails);
|
||||
}
|
||||
|
||||
@Override
|
||||
public DaoRegistry getDaoRegistry() {
|
||||
return this.myDaoRegistry;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,85 +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.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.cqframework.cql.cql2elm.LibraryContentType;
|
||||
import org.cqframework.cql.cql2elm.LibrarySourceProvider;
|
||||
import org.hl7.elm.r1.VersionedIdentifier;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.opencds.cqf.cql.evaluator.fhir.util.Libraries;
|
||||
import org.opencds.cqf.cql.evaluator.fhir.util.Versions;
|
||||
|
||||
import java.io.ByteArrayInputStream;
|
||||
import java.io.InputStream;
|
||||
import java.util.ArrayList;
|
||||
|
||||
/**
|
||||
* This class provides an implementation of the cql-translator's LibrarySourceProvider
|
||||
* interface which is used for loading
|
||||
* library resources during CQL evaluation.
|
||||
*/
|
||||
public class HapiLibrarySourceProvider implements LibrarySourceProvider, IDaoRegistryUser {
|
||||
protected final DaoRegistry myDaoRegistry;
|
||||
protected final RequestDetails myRequestDetails;
|
||||
|
||||
public HapiLibrarySourceProvider(DaoRegistry theDaoRegistry) {
|
||||
this(theDaoRegistry, null);
|
||||
}
|
||||
|
||||
public HapiLibrarySourceProvider(DaoRegistry theDaoRegistry, RequestDetails theRequestDetails) {
|
||||
this.myDaoRegistry = theDaoRegistry;
|
||||
this.myRequestDetails = theRequestDetails;
|
||||
}
|
||||
|
||||
@Override
|
||||
public DaoRegistry getDaoRegistry() {
|
||||
return this.myDaoRegistry;
|
||||
}
|
||||
|
||||
@Override
|
||||
public InputStream getLibraryContent(
|
||||
VersionedIdentifier theLibraryIdentifier, LibraryContentType theLibraryContentType) {
|
||||
String name = theLibraryIdentifier.getId();
|
||||
String version = theLibraryIdentifier.getVersion();
|
||||
var libraries = search(getClass("Library"), Searches.byName(name), myRequestDetails);
|
||||
var libraryList = new ArrayList<IBaseResource>();
|
||||
for (var l : libraries) {
|
||||
libraryList.add(l);
|
||||
}
|
||||
IBaseResource library = Versions.selectByVersion(libraryList, version, Libraries::getVersion);
|
||||
|
||||
if (library == null) {
|
||||
return null;
|
||||
}
|
||||
byte[] content = Libraries.getContent(library, theLibraryContentType.mimeType());
|
||||
if (content == null) {
|
||||
return null;
|
||||
}
|
||||
|
||||
return new ByteArrayInputStream(content);
|
||||
}
|
||||
|
||||
@Override
|
||||
public InputStream getLibrarySource(VersionedIdentifier libraryIdentifier) {
|
||||
return this.getLibraryContent(libraryIdentifier, LibraryContentType.CQL);
|
||||
}
|
||||
}
|
||||
|
|
@ -1,196 +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.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.context.support.IValidationSupport;
|
||||
import ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult;
|
||||
import ca.uhn.fhir.context.support.ValidationSupportContext;
|
||||
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
|
||||
import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import org.cqframework.cql.elm.execution.VersionedIdentifier;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.opencds.cqf.cql.engine.runtime.Code;
|
||||
import org.opencds.cqf.cql.engine.terminology.CodeSystemInfo;
|
||||
import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
|
||||
import org.opencds.cqf.cql.engine.terminology.ValueSetInfo;
|
||||
import org.opencds.cqf.cql.evaluator.fhir.util.Canonicals;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
/**
|
||||
* This class provides an implementation of the cql-engine's TerminologyProvider
|
||||
* interface, which is used for Terminology operations
|
||||
* in CQL
|
||||
*/
|
||||
public class HapiTerminologyProvider implements TerminologyProvider {
|
||||
private final IValidationSupport myValidationSupport;
|
||||
private final Map<VersionedIdentifier, List<Code>> myGlobalCodeCache;
|
||||
|
||||
public HapiTerminologyProvider(
|
||||
IValidationSupport theValidationSupport, Map<VersionedIdentifier, List<Code>> theGlobalCodeCache) {
|
||||
this(theValidationSupport, theGlobalCodeCache, null);
|
||||
}
|
||||
|
||||
public HapiTerminologyProvider(
|
||||
IValidationSupport theValidationSupport,
|
||||
Map<VersionedIdentifier, List<Code>> theGlobalCodeCache,
|
||||
RequestDetails theRequestDetails) {
|
||||
myValidationSupport = theValidationSupport;
|
||||
myGlobalCodeCache = theGlobalCodeCache;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean in(Code code, ValueSetInfo valueSet) throws ResourceNotFoundException {
|
||||
for (Code c : expand(valueSet)) {
|
||||
if (c == null) {
|
||||
continue;
|
||||
}
|
||||
if (c.getCode().equals(code.getCode()) && c.getSystem().equals(code.getSystem())) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Iterable<Code> expand(ValueSetInfo theValueSet) throws ResourceNotFoundException {
|
||||
// This could possibly be refactored into a single call to the underlying HAPI
|
||||
// Terminology service. Need to think through that..,
|
||||
|
||||
VersionedIdentifier vsId =
|
||||
new VersionedIdentifier().withId(theValueSet.getId()).withVersion(theValueSet.getVersion());
|
||||
|
||||
if (this.myGlobalCodeCache.containsKey(vsId)) {
|
||||
return this.myGlobalCodeCache.get(vsId);
|
||||
}
|
||||
|
||||
ValueSetExpansionOptions valueSetExpansionOptions = new ValueSetExpansionOptions();
|
||||
valueSetExpansionOptions.setFailOnMissingCodeSystem(false);
|
||||
valueSetExpansionOptions.setCount(Integer.MAX_VALUE);
|
||||
|
||||
if (theValueSet.getVersion() != null
|
||||
&& Canonicals.getUrl(theValueSet.getId()) != null
|
||||
&& Canonicals.getVersion(theValueSet.getId()) == null) {
|
||||
theValueSet.setId(theValueSet.getId() + "|" + theValueSet.getVersion());
|
||||
}
|
||||
|
||||
IValidationSupport.ValueSetExpansionOutcome vs = myValidationSupport.expandValueSet(
|
||||
new ValidationSupportContext(myValidationSupport), valueSetExpansionOptions, theValueSet.getId());
|
||||
|
||||
List<Code> codes = getCodes(vs.getValueSet());
|
||||
this.myGlobalCodeCache.put(vsId, codes);
|
||||
return codes;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Code lookup(Code theCode, CodeSystemInfo theCodeSystem) throws ResourceNotFoundException {
|
||||
|
||||
LookupCodeResult cs = myValidationSupport.lookupCode(
|
||||
new ValidationSupportContext(myValidationSupport), theCodeSystem.getId(), theCode.getCode());
|
||||
|
||||
if (cs != null) {
|
||||
theCode.setDisplay(cs.getCodeDisplay());
|
||||
}
|
||||
theCode.setSystem(theCodeSystem.getId());
|
||||
|
||||
return theCode;
|
||||
}
|
||||
|
||||
protected List<Code> getCodes(IBaseResource theValueSet) {
|
||||
|
||||
FhirVersionEnum version = theValueSet.getStructureFhirVersionEnum();
|
||||
switch (version) {
|
||||
case DSTU2_1:
|
||||
return getCodesDstu21((org.hl7.fhir.dstu2016may.model.ValueSet) theValueSet);
|
||||
case DSTU2_HL7ORG:
|
||||
return getCodesDstu2Hl7((org.hl7.fhir.dstu2.model.ValueSet) theValueSet);
|
||||
case DSTU3:
|
||||
return getCodesDstu3((org.hl7.fhir.dstu3.model.ValueSet) theValueSet);
|
||||
case R4:
|
||||
return getCodesR4((org.hl7.fhir.r4.model.ValueSet) theValueSet);
|
||||
case R4B:
|
||||
return getCodesR4B((org.hl7.fhir.r4b.model.ValueSet) theValueSet);
|
||||
case R5:
|
||||
return getCodesR5((org.hl7.fhir.r5.model.ValueSet) theValueSet);
|
||||
default:
|
||||
throw new IllegalArgumentException(Msg.code(2225)
|
||||
+ String.format("FHIR version %s is unsupported.", version.getFhirVersionString()));
|
||||
}
|
||||
}
|
||||
|
||||
protected List<Code> getCodesDstu2Hl7(org.hl7.fhir.dstu2.model.ValueSet theValueSet) {
|
||||
var codes = new ArrayList<Code>();
|
||||
for (var vse : theValueSet.getExpansion().getContains()) {
|
||||
codes.add(new Code().withCode(vse.getCode()).withSystem(vse.getSystem()));
|
||||
}
|
||||
|
||||
return codes;
|
||||
}
|
||||
|
||||
protected List<Code> getCodesDstu21(org.hl7.fhir.dstu2016may.model.ValueSet theValueSet) {
|
||||
var codes = new ArrayList<Code>();
|
||||
for (var vse : theValueSet.getExpansion().getContains()) {
|
||||
codes.add(new Code().withCode(vse.getCode()).withSystem(vse.getSystem()));
|
||||
}
|
||||
|
||||
return codes;
|
||||
}
|
||||
|
||||
protected List<Code> getCodesDstu3(org.hl7.fhir.dstu3.model.ValueSet theValueSet) {
|
||||
var codes = new ArrayList<Code>();
|
||||
for (var vse : theValueSet.getExpansion().getContains()) {
|
||||
codes.add(new Code().withCode(vse.getCode()).withSystem(vse.getSystem()));
|
||||
}
|
||||
|
||||
return codes;
|
||||
}
|
||||
|
||||
protected List<Code> getCodesR4(org.hl7.fhir.r4.model.ValueSet theValueSet) {
|
||||
var codes = new ArrayList<Code>();
|
||||
for (var vse : theValueSet.getExpansion().getContains()) {
|
||||
codes.add(new Code().withCode(vse.getCode()).withSystem(vse.getSystem()));
|
||||
}
|
||||
|
||||
return codes;
|
||||
}
|
||||
|
||||
protected List<Code> getCodesR4B(org.hl7.fhir.r4b.model.ValueSet theValueSet) {
|
||||
var codes = new ArrayList<Code>();
|
||||
for (var vse : theValueSet.getExpansion().getContains()) {
|
||||
codes.add(new Code().withCode(vse.getCode()).withSystem(vse.getSystem()));
|
||||
}
|
||||
|
||||
return codes;
|
||||
}
|
||||
|
||||
protected List<Code> getCodesR5(org.hl7.fhir.r5.model.ValueSet theValueSet) {
|
||||
var codes = new ArrayList<Code>();
|
||||
for (var vse : theValueSet.getExpansion().getContains()) {
|
||||
codes.add(new Code().withCode(vse.getCode()).withSystem(vse.getSystem()));
|
||||
}
|
||||
|
||||
return codes;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,33 +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.RequestDetails;
|
||||
import org.opencds.cqf.cql.engine.data.DataProvider;
|
||||
import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
|
||||
|
||||
/**
|
||||
* Single abstract method interface to provide ability to create a DataProvider based of
|
||||
* RequestDetails and TerminologyProvider
|
||||
*/
|
||||
@FunctionalInterface
|
||||
public interface IDataProviderFactory {
|
||||
DataProvider create(RequestDetails theRequestDetails, TerminologyProvider theTerminologyProvider);
|
||||
}
|
||||
|
|
@ -1,29 +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 org.cqframework.cql.cql2elm.LibrarySourceProvider;
|
||||
import org.opencds.cqf.cql.engine.execution.LibraryLoader;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
public interface ILibraryLoaderFactory {
|
||||
LibraryLoader create(List<LibrarySourceProvider> theLibraryContentProviders);
|
||||
}
|
||||
|
|
@ -1,29 +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 org.cqframework.cql.cql2elm.LibraryManager;
|
||||
import org.cqframework.cql.cql2elm.LibrarySourceProvider;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
public interface ILibraryManagerFactory {
|
||||
LibraryManager create(List<LibrarySourceProvider> theLibraryContentProviders);
|
||||
}
|
||||
|
|
@ -1,67 +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.context.FhirContext;
|
||||
import ca.uhn.fhir.context.support.IValidationSupport;
|
||||
import ca.uhn.fhir.context.support.ValidationSupportContext;
|
||||
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
|
||||
import javax.annotation.Nonnull;
|
||||
import javax.annotation.Nullable;
|
||||
|
||||
/**
|
||||
* This class provides an implementation of IValidationSupport
|
||||
* interface which is used for validation of terminology services.
|
||||
*/
|
||||
public class PreExpandedValidationSupport implements IValidationSupport {
|
||||
private final FhirContext myFhirContext;
|
||||
|
||||
public PreExpandedValidationSupport(FhirContext theFhirContext) {
|
||||
this.myFhirContext = theFhirContext;
|
||||
}
|
||||
|
||||
@Override
|
||||
public ValueSetExpansionOutcome expandValueSet(
|
||||
ValidationSupportContext theValidationSupportContext,
|
||||
@Nullable ValueSetExpansionOptions theExpansionOptions,
|
||||
@Nonnull IBaseResource theValueSetToExpand) {
|
||||
Validate.notNull(theValueSetToExpand, "theValueSetToExpand must not be null or blank");
|
||||
|
||||
if (!getFhirContext()
|
||||
.getResourceDefinition("ValueSet")
|
||||
.getChildByName("expansion")
|
||||
.getAccessor()
|
||||
.getValues(theValueSetToExpand)
|
||||
.isEmpty()) {
|
||||
return new ValueSetExpansionOutcome(theValueSetToExpand);
|
||||
} else {
|
||||
return IValidationSupport.super.expandValueSet(
|
||||
theValidationSupportContext, theExpansionOptions, theValueSetToExpand);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public FhirContext getFhirContext() {
|
||||
return this.myFhirContext;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,252 +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.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.model.api.IQueryParameterType;
|
||||
import ca.uhn.fhir.rest.param.StringParam;
|
||||
import ca.uhn.fhir.rest.param.TokenOrListParam;
|
||||
import ca.uhn.fhir.rest.param.TokenParam;
|
||||
import ca.uhn.fhir.rest.param.UriOrListParam;
|
||||
import ca.uhn.fhir.rest.param.UriParam;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.instance.model.api.IPrimitiveType;
|
||||
import org.opencds.cqf.cql.evaluator.fhir.util.Canonicals;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import static com.google.common.base.Preconditions.checkArgument;
|
||||
import static com.google.common.base.Preconditions.checkNotNull;
|
||||
|
||||
/**
|
||||
* Utility class for parameter search
|
||||
*/
|
||||
public class Searches {
|
||||
private static final String VERSION_SP = "version";
|
||||
private static final String URL_SP = "url";
|
||||
private static final String NAME_SP = "name";
|
||||
private static final String ID_SP = "_id";
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*/
|
||||
private Searches() {}
|
||||
|
||||
/**
|
||||
* Creates and returns Parameter search results
|
||||
*/
|
||||
public static SearchParameterMap all() {
|
||||
return new SearchParameterMap();
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameters name and type
|
||||
*
|
||||
* @param theParamName String of parameter name
|
||||
* @param theParam IQuery parameter type
|
||||
* @return a SearchParameterMap
|
||||
*/
|
||||
public static SearchParameterMap byParam(String theParamName, IQueryParameterType theParam) {
|
||||
checkNotNull(theParamName);
|
||||
checkNotNull(theParam);
|
||||
|
||||
return all().add(theParamName, theParam);
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameter name
|
||||
*
|
||||
* @param theName String of parameter name
|
||||
* @return a SearchParameterMap
|
||||
*/
|
||||
public static SearchParameterMap byName(String theName) {
|
||||
checkNotNull(theName);
|
||||
|
||||
return byParam(NAME_SP, new StringParam(theName, true));
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameters name and version
|
||||
*
|
||||
* @param theName String of parameter name
|
||||
* @param theVersion String of code version
|
||||
* @return a SearchParameterMap
|
||||
*/
|
||||
public static SearchParameterMap byName(String theName, String theVersion) {
|
||||
checkNotNull(theName);
|
||||
checkNotNull(theVersion);
|
||||
|
||||
return byName(theName).add(VERSION_SP, new TokenParam(theVersion));
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameters url and version
|
||||
*
|
||||
* @param theUrl String of the url
|
||||
* @param theVersion String of code version
|
||||
* @return a SearchParameterMap
|
||||
*/
|
||||
public static SearchParameterMap byUrlAndVersion(String theUrl, String theVersion) {
|
||||
checkNotNull(theUrl);
|
||||
checkNotNull(theVersion);
|
||||
|
||||
return byParam(URL_SP, new UriParam(theUrl)).add(VERSION_SP, new TokenParam(theVersion));
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameter url
|
||||
*
|
||||
* @param theUrl String of the url
|
||||
* @return a SearchParameterMap
|
||||
*/
|
||||
public static SearchParameterMap byUrl(String theUrl) {
|
||||
checkNotNull(theUrl);
|
||||
|
||||
return byParam(URL_SP, new UriParam(theUrl));
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameter of list of urls
|
||||
*
|
||||
* @param theUrls list of URL strings
|
||||
* @return SearchParameterMap
|
||||
*/
|
||||
// TODO: versioned version
|
||||
public static SearchParameterMap byUrls(List<String> theUrls) {
|
||||
checkNotNull(theUrls);
|
||||
UriOrListParam params = new UriOrListParam();
|
||||
|
||||
theUrls.forEach(theUrl -> {
|
||||
checkNotNull(theUrl);
|
||||
params.addOr(new UriParam(theUrl));
|
||||
});
|
||||
|
||||
return all().add(ID_SP, params);
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameter of canonical search string
|
||||
*
|
||||
* @param theCanonical a string representing the canonical
|
||||
* @return SearchParameterMap
|
||||
*/
|
||||
public static SearchParameterMap byCanonical(String theCanonical) {
|
||||
checkNotNull(theCanonical);
|
||||
|
||||
SearchParameterMap search = byUrl(Canonicals.getUrl(theCanonical));
|
||||
String version = Canonicals.getVersion(theCanonical);
|
||||
if (version != null) {
|
||||
search.add(VERSION_SP, new TokenParam(version));
|
||||
}
|
||||
|
||||
return search;
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameter of canonical type
|
||||
*
|
||||
* @param theCanonicalType a variable representing the canonical type
|
||||
* @return SearchParameterMap by canonical type
|
||||
*/
|
||||
public static <C extends IPrimitiveType<String>> SearchParameterMap byCanonical(C theCanonicalType) {
|
||||
checkNotNull(theCanonicalType);
|
||||
checkArgument(theCanonicalType.hasValue());
|
||||
|
||||
return byCanonical(theCanonicalType.getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameters of canonical search string and version
|
||||
*
|
||||
* @param theCanonical a string representing the canonical
|
||||
* @param version a string representing the version
|
||||
* @return SearchParameterMap
|
||||
*/
|
||||
public static SearchParameterMap byCanonical(String theCanonical, String version) {
|
||||
checkNotNull(theCanonical);
|
||||
|
||||
SearchParameterMap search = byUrl(Canonicals.getUrl(theCanonical));
|
||||
if (version != null) {
|
||||
search.add(VERSION_SP, new TokenParam(version));
|
||||
}
|
||||
|
||||
return search;
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameter of list of canonical types
|
||||
*
|
||||
* @param theCanonicalTypes a variable representing list of the canonical type
|
||||
* @return SearchParameterMap by canonical type
|
||||
*/
|
||||
// TODO: use versioned version
|
||||
public static <C extends IPrimitiveType<String>> SearchParameterMap byCanonicals(List<C> theCanonicalTypes) {
|
||||
checkNotNull(theCanonicalTypes);
|
||||
|
||||
List<String> urls = new ArrayList<>();
|
||||
theCanonicalTypes.forEach(canonicalType -> {
|
||||
checkArgument(canonicalType.hasValue());
|
||||
urls.add(canonicalType.getValue());
|
||||
});
|
||||
|
||||
return byUrls(urls);
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameter of IIdType
|
||||
*
|
||||
* @param theId IID Type variable representing measure ID
|
||||
* @return SearchParameterMap matching Id
|
||||
*/
|
||||
public static SearchParameterMap byId(IIdType theId) {
|
||||
checkNotNull(theId);
|
||||
return byParam(ID_SP, new TokenParam(theId.getIdPart()));
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameter of IIdType
|
||||
*
|
||||
* @param theIdPart String representing theID
|
||||
* @return SearchParameterMap matching theID
|
||||
*/
|
||||
public static SearchParameterMap byId(String theIdPart) {
|
||||
checkNotNull(theIdPart);
|
||||
return byParam(ID_SP, new TokenParam(theIdPart));
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to return a SearchParameterMap which has parameter of list of IIdType
|
||||
*
|
||||
* @param theIdParts String representing theID
|
||||
* @return SearchParameterMap matching theID
|
||||
*/
|
||||
public static SearchParameterMap byIds(List<String> theIdParts) {
|
||||
checkNotNull(theIdParts);
|
||||
TokenOrListParam params = new TokenOrListParam();
|
||||
|
||||
theIdParts.forEach(theIdPart -> {
|
||||
checkNotNull(theIdPart);
|
||||
params.addOr(new TokenParam(theIdPart));
|
||||
});
|
||||
|
||||
return all().add(ID_SP, params);
|
||||
}
|
||||
}
|
||||
|
|
@ -1,236 +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.config;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.support.IValidationSupport;
|
||||
import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
|
||||
import ca.uhn.fhir.cr.common.CqlExceptionHandlingInterceptor;
|
||||
import ca.uhn.fhir.cr.common.CqlForkJoinWorkerThreadFactory;
|
||||
import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
|
||||
import ca.uhn.fhir.cr.common.HapiFhirDal;
|
||||
import ca.uhn.fhir.cr.common.HapiFhirRetrieveProvider;
|
||||
import ca.uhn.fhir.cr.common.HapiLibrarySourceProvider;
|
||||
import ca.uhn.fhir.cr.common.HapiTerminologyProvider;
|
||||
import ca.uhn.fhir.cr.common.IDataProviderFactory;
|
||||
import ca.uhn.fhir.cr.common.IFhirDalFactory;
|
||||
import ca.uhn.fhir.cr.common.ILibrarySourceProviderFactory;
|
||||
import ca.uhn.fhir.cr.common.ITerminologyProviderFactory;
|
||||
import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
|
||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import org.cqframework.cql.cql2elm.ModelManager;
|
||||
import org.cqframework.cql.cql2elm.model.Model;
|
||||
import org.hl7.cql.model.ModelIdentifier;
|
||||
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
|
||||
import org.hl7.fhir.instance.model.api.IBaseBundle;
|
||||
import org.opencds.cqf.cql.engine.data.CompositeDataProvider;
|
||||
import org.opencds.cqf.cql.engine.fhir.model.Dstu3FhirModelResolver;
|
||||
import org.opencds.cqf.cql.engine.fhir.model.R4FhirModelResolver;
|
||||
import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
|
||||
import org.opencds.cqf.cql.engine.model.ModelResolver;
|
||||
import org.opencds.cqf.cql.engine.runtime.Code;
|
||||
import org.opencds.cqf.cql.evaluator.builder.DataProviderComponents;
|
||||
import org.opencds.cqf.cql.evaluator.builder.EndpointInfo;
|
||||
import org.opencds.cqf.cql.evaluator.cql2elm.util.LibraryVersionSelector;
|
||||
import org.opencds.cqf.cql.evaluator.engine.model.CachingModelResolverDecorator;
|
||||
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.spring.fhir.adapter.AdapterConfiguration;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.context.annotation.Import;
|
||||
import org.springframework.context.annotation.Primary;
|
||||
import org.springframework.context.annotation.Scope;
|
||||
import org.springframework.security.concurrent.DelegatingSecurityContextExecutor;
|
||||
import org.springframework.security.core.context.SecurityContextHolder;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.concurrent.ConcurrentHashMap;
|
||||
import java.util.concurrent.Executor;
|
||||
import java.util.concurrent.ForkJoinPool;
|
||||
|
||||
@Configuration
|
||||
@Import({AdapterConfiguration.class, BaseRepositoryConfig.class})
|
||||
public abstract class BaseClinicalReasoningConfig {
|
||||
|
||||
private static final Logger ourLogger = LoggerFactory.getLogger(BaseClinicalReasoningConfig.class);
|
||||
|
||||
@Bean
|
||||
@Scope("prototype")
|
||||
public ModelManager modelManager(Map<ModelIdentifier, Model> theGlobalModelCache) {
|
||||
return new ModelManager(theGlobalModelCache);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public CqlExceptionHandlingInterceptor cqlExceptionHandlingInterceptor() {
|
||||
return new CqlExceptionHandlingInterceptor();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public SearchParameterResolver searchParameterResolver(FhirContext theFhirContext) {
|
||||
return new SearchParameterResolver(theFhirContext);
|
||||
}
|
||||
|
||||
@Bean
|
||||
IFhirDalFactory fhirDalFactory(DaoRegistry theDaoRegistry) {
|
||||
return rd -> new HapiFhirDal(theDaoRegistry, rd);
|
||||
}
|
||||
|
||||
@Bean
|
||||
IDataProviderFactory dataProviderFactory(
|
||||
ModelResolver theModelResolver,
|
||||
DaoRegistry theDaoRegistry,
|
||||
SearchParameterResolver theSearchParameterResolver) {
|
||||
return (rd, t) -> {
|
||||
HapiFhirRetrieveProvider provider =
|
||||
new HapiFhirRetrieveProvider(theDaoRegistry, theSearchParameterResolver, rd);
|
||||
if (t != null) {
|
||||
provider.setTerminologyProvider(t);
|
||||
provider.setExpandValueSets(true);
|
||||
provider.setMaxCodesPerQuery(500);
|
||||
provider.setQueryBatchThreshold(500);
|
||||
provider.setModelResolver(theModelResolver);
|
||||
}
|
||||
return new CompositeDataProvider(theModelResolver, provider);
|
||||
};
|
||||
}
|
||||
|
||||
@Bean
|
||||
org.opencds.cqf.cql.evaluator.builder.DataProviderFactory builderDataProviderFactory(
|
||||
FhirContext theFhirContext, ModelResolver theModelResolver) {
|
||||
return new org.opencds.cqf.cql.evaluator.builder.DataProviderFactory() {
|
||||
@Override
|
||||
public DataProviderComponents create(EndpointInfo theEndpointInfo) {
|
||||
// to do implement endpoint
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public DataProviderComponents create(IBaseBundle theDataBundle) {
|
||||
return new DataProviderComponents(
|
||||
Constants.FHIR_MODEL_URI,
|
||||
theModelResolver,
|
||||
new BundleRetrieveProvider(theFhirContext, theDataBundle));
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
@Bean
|
||||
public HapiFhirRetrieveProvider fhirRetrieveProvider(
|
||||
DaoRegistry theDaoRegistry, SearchParameterResolver theSearchParameterResolver) {
|
||||
return new HapiFhirRetrieveProvider(theDaoRegistry, theSearchParameterResolver);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public ITerminologyProviderFactory terminologyProviderFactory(
|
||||
IValidationSupport theValidationSupport,
|
||||
Map<org.cqframework.cql.elm.execution.VersionedIdentifier, List<Code>> theGlobalCodeCache) {
|
||||
return rd -> new HapiTerminologyProvider(theValidationSupport, theGlobalCodeCache, rd);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ILibrarySourceProviderFactory librarySourceProviderFactory(DaoRegistry theDaoRegistry) {
|
||||
return rd -> new HapiLibrarySourceProvider(theDaoRegistry, rd);
|
||||
}
|
||||
|
||||
// TODO: Use something like caffeine caching for this so that growth is limited.
|
||||
@Bean
|
||||
public Map<org.cqframework.cql.elm.execution.VersionedIdentifier, org.cqframework.cql.elm.execution.Library>
|
||||
globalLibraryCache() {
|
||||
return new ConcurrentHashMap<>();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public Map<org.cqframework.cql.elm.execution.VersionedIdentifier, List<Code>> globalCodeCache() {
|
||||
return new ConcurrentHashMap<>();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public Map<ModelIdentifier, Model> globalModelCache() {
|
||||
return new ConcurrentHashMap<>();
|
||||
}
|
||||
|
||||
@Bean
|
||||
@Primary
|
||||
public ElmCacheResourceChangeListener elmCacheResourceChangeListener(
|
||||
IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
|
||||
DaoRegistry theDaoRegistry,
|
||||
Map<org.cqframework.cql.elm.execution.VersionedIdentifier, org.cqframework.cql.elm.execution.Library>
|
||||
theGlobalLibraryCache) {
|
||||
ElmCacheResourceChangeListener listener =
|
||||
new ElmCacheResourceChangeListener(theDaoRegistry, theGlobalLibraryCache);
|
||||
theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
|
||||
"Library", SearchParameterMap.newSynchronous(), listener, 1000);
|
||||
return listener;
|
||||
}
|
||||
|
||||
@Bean
|
||||
@Primary
|
||||
public CodeCacheResourceChangeListener codeCacheResourceChangeListener(
|
||||
IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
|
||||
DaoRegistry theDaoRegistry,
|
||||
Map<org.cqframework.cql.elm.execution.VersionedIdentifier, List<Code>> theGlobalCodeCache) {
|
||||
CodeCacheResourceChangeListener listener =
|
||||
new CodeCacheResourceChangeListener(theDaoRegistry, theGlobalCodeCache);
|
||||
theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
|
||||
"ValueSet", SearchParameterMap.newSynchronous(), listener, 1000);
|
||||
return listener;
|
||||
}
|
||||
|
||||
@Bean
|
||||
public ModelResolver modelResolver(FhirContext theFhirContext) {
|
||||
switch (theFhirContext.getVersion().getVersion()) {
|
||||
case R4:
|
||||
return new CachingModelResolverDecorator(new R4FhirModelResolver());
|
||||
case DSTU3:
|
||||
return new CachingModelResolverDecorator(new Dstu3FhirModelResolver());
|
||||
default:
|
||||
throw new IllegalStateException(
|
||||
Msg.code(2224)
|
||||
+ "CQL support not yet implemented for this FHIR version. Please change versions or disable the CQL plugin.");
|
||||
}
|
||||
}
|
||||
|
||||
@Bean
|
||||
public LibraryVersionSelector libraryVersionSelector(AdapterFactory theAdapterFactory) {
|
||||
return new LibraryVersionSelector(theAdapterFactory);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public Executor cqlExecutor() {
|
||||
CqlForkJoinWorkerThreadFactory factory = new CqlForkJoinWorkerThreadFactory();
|
||||
ForkJoinPool myCommonPool =
|
||||
new ForkJoinPool(Math.min(32767, Runtime.getRuntime().availableProcessors()), factory, null, false);
|
||||
|
||||
return new DelegatingSecurityContextExecutor(myCommonPool, SecurityContextHolder.getContext());
|
||||
}
|
||||
|
||||
@Bean
|
||||
public PreExpandedValidationSupportLoader preExpandedValidationSupportLoader(
|
||||
ValidationSupportChain theSupportChain, FhirContext theFhirContext) {
|
||||
return new PreExpandedValidationSupportLoader(theSupportChain, theFhirContext);
|
||||
}
|
||||
}
|
||||
|
|
@ -1,54 +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.config;
|
||||
|
||||
public class CareGapsProperties {
|
||||
private boolean myThreadedCareGapsEnabled = true;
|
||||
private String myCareGapsReporter;
|
||||
private String myCareGapsCompositionSectionAuthor;
|
||||
|
||||
public boolean getThreadedCareGapsEnabled() {
|
||||
return myThreadedCareGapsEnabled;
|
||||
}
|
||||
|
||||
public void setThreadedCareGapsEnabled(boolean theThreadedCareGapsEnabled) {
|
||||
myThreadedCareGapsEnabled = theThreadedCareGapsEnabled;
|
||||
}
|
||||
|
||||
public boolean isThreadedCareGapsEnabled() {
|
||||
return myThreadedCareGapsEnabled;
|
||||
}
|
||||
|
||||
public String getCareGapsReporter() {
|
||||
return myCareGapsReporter;
|
||||
}
|
||||
|
||||
public void setCareGapsReporter(String theCareGapsReporter) {
|
||||
myCareGapsReporter = theCareGapsReporter;
|
||||
}
|
||||
|
||||
public String getCareGapsCompositionSectionAuthor() {
|
||||
return myCareGapsCompositionSectionAuthor;
|
||||
}
|
||||
|
||||
public void setCareGapsCompositionSectionAuthor(String theCareGapsCompositionSectionAuthor) {
|
||||
myCareGapsCompositionSectionAuthor = theCareGapsCompositionSectionAuthor;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,35 +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.config;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.cr.common.PreExpandedValidationSupport;
|
||||
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
|
||||
|
||||
/**
|
||||
* This class loads the validation of terminology services.
|
||||
*/
|
||||
public class PreExpandedValidationSupportLoader {
|
||||
public PreExpandedValidationSupportLoader(
|
||||
ValidationSupportChain theValidationSupportChain, FhirContext theFhirContext) {
|
||||
var preExpandedValidationSupport = new PreExpandedValidationSupport(theFhirContext);
|
||||
theValidationSupportChain.addValidationSupport(0, preExpandedValidationSupport);
|
||||
}
|
||||
}
|
||||
|
|
@ -27,9 +27,9 @@ import org.springframework.context.annotation.Bean;
|
|||
import org.springframework.context.annotation.Configuration;
|
||||
|
||||
@Configuration
|
||||
public abstract class BaseRepositoryConfig {
|
||||
public class RepositoryConfig {
|
||||
@Bean
|
||||
IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry) {
|
||||
return rd -> new HapiFhirRepository(theDaoRegistry, rd, (RestfulServer) rd.getServer());
|
||||
IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
|
||||
return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,75 @@
|
|||
/*-
|
||||
* #%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.config.dstu3;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
|
||||
public class ApplyOperationConfig {
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.IActivityDefinitionProcessorFactory dstu3ActivityDefinitionProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.activitydefinition.dstu3.ActivityDefinitionProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.IPlanDefinitionProcessorFactory dstu3PlanDefinitionProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.plandefinition.dstu3.PlanDefinitionProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.activitydefinition.ActivityDefinitionApplyProvider dstu3ActivityDefinitionApplyProvider() {
|
||||
return new ca.uhn.fhir.cr.dstu3.activitydefinition.ActivityDefinitionApplyProvider();
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.plandefinition.PlanDefinitionApplyProvider dstu3PlanDefinitionApplyProvider() {
|
||||
return new ca.uhn.fhir.cr.dstu3.plandefinition.PlanDefinitionApplyProvider();
|
||||
}
|
||||
|
||||
@Bean(name = "applyOperationLoader")
|
||||
public ProviderLoader applyOperationLoader(
|
||||
ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
|
||||
|
||||
var selector = new ProviderSelector(
|
||||
theFhirContext,
|
||||
Map.of(
|
||||
FhirVersionEnum.DSTU3,
|
||||
Arrays.asList(
|
||||
ca.uhn.fhir.cr.dstu3.activitydefinition.ActivityDefinitionApplyProvider.class,
|
||||
ca.uhn.fhir.cr.dstu3.plandefinition.PlanDefinitionApplyProvider.class)));
|
||||
|
||||
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
|
||||
}
|
||||
}
|
||||
|
|
@ -21,45 +21,35 @@ package ca.uhn.fhir.cr.config.dstu3;
|
|||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.config.BaseClinicalReasoningConfig;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.cr.config.RepositoryConfig;
|
||||
import ca.uhn.fhir.cr.dstu3.IMeasureServiceFactory;
|
||||
import ca.uhn.fhir.cr.dstu3.measure.MeasureOperationsProvider;
|
||||
import ca.uhn.fhir.cr.dstu3.measure.MeasureService;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.context.annotation.Import;
|
||||
import org.springframework.context.annotation.Scope;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
import java.util.function.Function;
|
||||
|
||||
@Configuration
|
||||
@Import(BaseClinicalReasoningConfig.class)
|
||||
@Import({RepositoryConfig.class})
|
||||
public class CrDstu3Config {
|
||||
|
||||
@Bean
|
||||
public Function<RequestDetails, MeasureService> dstu3MeasureServiceFactory(
|
||||
ApplicationContext theApplicationContext) {
|
||||
return r -> {
|
||||
var ms = theApplicationContext.getBean(MeasureService.class);
|
||||
ms.setRequestDetails(r);
|
||||
return ms;
|
||||
};
|
||||
IMeasureServiceFactory dstu3MeasureServiceFactory(
|
||||
IRepositoryFactory theRepositoryFactory, MeasureEvaluationOptions theEvaluationOptions) {
|
||||
return rd -> new MeasureService(theRepositoryFactory.create(rd), theEvaluationOptions);
|
||||
}
|
||||
|
||||
@Bean
|
||||
@Scope("prototype")
|
||||
public MeasureService dstu3measureService() {
|
||||
return new MeasureService();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public MeasureOperationsProvider dstu3measureOperationsProvider() {
|
||||
MeasureOperationsProvider dstu3MeasureOperationsProvider() {
|
||||
return new MeasureOperationsProvider();
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,63 @@
|
|||
/*-
|
||||
* #%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.config.dstu3;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
|
||||
public class ExtractOperationConfig {
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.IQuestionnaireResponseProcessorFactory dstu3QuestionnaireResponseProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaireresponse.dstu3.QuestionnaireResponseProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.questionnaireresponse.QuestionnaireResponseExtractProvider
|
||||
dstu3QuestionnaireResponseExtractProvider() {
|
||||
return new ca.uhn.fhir.cr.dstu3.questionnaireresponse.QuestionnaireResponseExtractProvider();
|
||||
}
|
||||
|
||||
@Bean(name = "extractOperationLoader")
|
||||
public ProviderLoader extractOperationLoader(
|
||||
ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
|
||||
|
||||
var selector = new ProviderSelector(
|
||||
theFhirContext,
|
||||
Map.of(
|
||||
FhirVersionEnum.DSTU3,
|
||||
Arrays.asList(
|
||||
ca.uhn.fhir.cr.dstu3.questionnaireresponse.QuestionnaireResponseExtractProvider
|
||||
.class)));
|
||||
|
||||
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,74 @@
|
|||
/*-
|
||||
* #%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.config.dstu3;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
|
||||
public class PackageOperationConfig {
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.IPlanDefinitionProcessorFactory dstu3PlanDefinitionProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.plandefinition.dstu3.PlanDefinitionProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.plandefinition.PlanDefinitionPackageProvider dstu3PlanDefinitionPackageProvider() {
|
||||
return new ca.uhn.fhir.cr.dstu3.plandefinition.PlanDefinitionPackageProvider();
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.IQuestionnaireProcessorFactory dstu3QuestionnaireProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaire.dstu3.QuestionnaireProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.questionnaire.QuestionnairePackageProvider dstu3QuestionnairePackageProvider() {
|
||||
return new ca.uhn.fhir.cr.dstu3.questionnaire.QuestionnairePackageProvider();
|
||||
}
|
||||
|
||||
@Bean(name = "packageOperationLoader")
|
||||
public ProviderLoader packageOperationLoader(
|
||||
ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
|
||||
|
||||
var selector = new ProviderSelector(
|
||||
theFhirContext,
|
||||
Map.of(
|
||||
FhirVersionEnum.DSTU3,
|
||||
Arrays.asList(
|
||||
ca.uhn.fhir.cr.dstu3.questionnaire.QuestionnairePackageProvider.class,
|
||||
ca.uhn.fhir.cr.dstu3.plandefinition.PlanDefinitionPackageProvider.class)));
|
||||
|
||||
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
/*-
|
||||
* #%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.config.dstu3;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
|
||||
public class PopulateOperationConfig {
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.IQuestionnaireProcessorFactory dstu3QuestionnaireProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaire.dstu3.QuestionnaireProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.questionnaire.QuestionnairePopulateProvider dstu3QuestionnairePopulateProvider() {
|
||||
return new ca.uhn.fhir.cr.dstu3.questionnaire.QuestionnairePopulateProvider();
|
||||
}
|
||||
|
||||
@Bean(name = "populateOperationLoader")
|
||||
public ProviderLoader populateOperationLoader(
|
||||
ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
|
||||
|
||||
var selector = new ProviderSelector(
|
||||
theFhirContext,
|
||||
Map.of(
|
||||
FhirVersionEnum.DSTU3,
|
||||
Arrays.asList(ca.uhn.fhir.cr.dstu3.questionnaire.QuestionnairePopulateProvider.class)));
|
||||
|
||||
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,75 @@
|
|||
/*-
|
||||
* #%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.config.r4;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
|
||||
public class ApplyOperationConfig {
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.IActivityDefinitionProcessorFactory r4ActivityDefinitionProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.activitydefinition.r4.ActivityDefinitionProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.IPlanDefinitionProcessorFactory r4PlanDefinitionProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.plandefinition.r4.PlanDefinitionProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.activitydefinition.ActivityDefinitionApplyProvider r4ActivityDefinitionApplyProvider() {
|
||||
return new ca.uhn.fhir.cr.r4.activitydefinition.ActivityDefinitionApplyProvider();
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionApplyProvider r4PlanDefinitionApplyProvider() {
|
||||
return new ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionApplyProvider();
|
||||
}
|
||||
|
||||
@Bean(name = "applyOperationLoader")
|
||||
public ProviderLoader applyOperationLoader(
|
||||
ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
|
||||
|
||||
var selector = new ProviderSelector(
|
||||
theFhirContext,
|
||||
Map.of(
|
||||
FhirVersionEnum.R4,
|
||||
Arrays.asList(
|
||||
ca.uhn.fhir.cr.r4.activitydefinition.ActivityDefinitionApplyProvider.class,
|
||||
ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionApplyProvider.class)));
|
||||
|
||||
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
|
||||
}
|
||||
}
|
||||
|
|
@ -21,83 +21,89 @@ package ca.uhn.fhir.cr.config.r4;
|
|||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.config.BaseClinicalReasoningConfig;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.cr.config.RepositoryConfig;
|
||||
import ca.uhn.fhir.cr.r4.ICareGapsServiceFactory;
|
||||
import ca.uhn.fhir.cr.r4.ICqlExecutionServiceFactory;
|
||||
import ca.uhn.fhir.cr.r4.IMeasureServiceFactory;
|
||||
import ca.uhn.fhir.cr.r4.ISubmitDataProcessorFactory;
|
||||
import ca.uhn.fhir.cr.r4.cqlexecution.CqlExecutionOperationProvider;
|
||||
import ca.uhn.fhir.cr.r4.measure.CareGapsOperationProvider;
|
||||
import ca.uhn.fhir.cr.r4.measure.CareGapsService;
|
||||
import ca.uhn.fhir.cr.r4.measure.ISubmitDataService;
|
||||
import ca.uhn.fhir.cr.r4.measure.MeasureOperationsProvider;
|
||||
import ca.uhn.fhir.cr.r4.measure.MeasureService;
|
||||
import ca.uhn.fhir.cr.r4.measure.SubmitDataProvider;
|
||||
import ca.uhn.fhir.cr.r4.measure.SubmitDataService;
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.opencds.cqf.fhir.cr.cql.r4.R4CqlExecutionService;
|
||||
import org.opencds.cqf.fhir.cr.measure.CareGapsProperties;
|
||||
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
|
||||
import org.opencds.cqf.fhir.cr.measure.r4.R4CareGapsService;
|
||||
import org.opencds.cqf.fhir.cr.measure.r4.R4SubmitDataService;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.context.annotation.Import;
|
||||
import org.springframework.context.annotation.Scope;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
import java.util.function.Function;
|
||||
import java.util.concurrent.Executor;
|
||||
|
||||
@Configuration
|
||||
@Import(BaseClinicalReasoningConfig.class)
|
||||
@Import({RepositoryConfig.class})
|
||||
public class CrR4Config {
|
||||
|
||||
@Bean
|
||||
public Function<RequestDetails, MeasureService> r4MeasureServiceFactory(ApplicationContext theApplicationContext) {
|
||||
return r -> {
|
||||
var ms = theApplicationContext.getBean(MeasureService.class);
|
||||
ms.setRequestDetails(r);
|
||||
return ms;
|
||||
};
|
||||
IMeasureServiceFactory r4MeasureServiceFactory(
|
||||
IRepositoryFactory theRepositoryFactory, MeasureEvaluationOptions theEvaluationOptions) {
|
||||
return rd -> new MeasureService(theRepositoryFactory.create(rd), theEvaluationOptions);
|
||||
}
|
||||
|
||||
@Bean
|
||||
@Scope("prototype")
|
||||
public MeasureService r4measureService() {
|
||||
return new MeasureService();
|
||||
ISubmitDataProcessorFactory r4SubmitDataProcessorFactory(IRepositoryFactory theRepositoryFactory) {
|
||||
return rd -> new R4SubmitDataService(theRepositoryFactory.create(rd));
|
||||
}
|
||||
|
||||
@Bean
|
||||
public MeasureOperationsProvider r4measureOperationsProvider() {
|
||||
return new MeasureOperationsProvider();
|
||||
ICqlExecutionServiceFactory r4CqlExecutionServiceFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new R4CqlExecutionService(theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public Function<RequestDetails, CareGapsService> r4CareGapsServiceFactory(
|
||||
ApplicationContext theApplicationContext) {
|
||||
return r -> {
|
||||
var cs = theApplicationContext.getBean(CareGapsService.class);
|
||||
cs.setRequestDetails(r);
|
||||
return cs;
|
||||
};
|
||||
CqlExecutionOperationProvider r4CqlExecutionOperationProvider() {
|
||||
return new CqlExecutionOperationProvider();
|
||||
}
|
||||
|
||||
@Bean
|
||||
@Scope("prototype")
|
||||
public CareGapsService r4CareGapsService() {
|
||||
return new CareGapsService();
|
||||
ICareGapsServiceFactory careGapsServiceFactory(
|
||||
IRepositoryFactory theRepositoryFactory,
|
||||
CareGapsProperties theCareGapsProperties,
|
||||
MeasureEvaluationOptions theMeasureEvaluationOptions,
|
||||
@Qualifier("cqlExecutor") Executor theExecutor) {
|
||||
return rd -> new R4CareGapsService(
|
||||
theCareGapsProperties,
|
||||
theRepositoryFactory.create(rd),
|
||||
theMeasureEvaluationOptions,
|
||||
theExecutor,
|
||||
rd.getFhirServerBase());
|
||||
}
|
||||
|
||||
@Bean
|
||||
public CareGapsOperationProvider r4CareGapsProvider(
|
||||
Function<RequestDetails, CareGapsService> theCareGapsServiceFunction) {
|
||||
CareGapsOperationProvider r4CareGapsOperationProvider() {
|
||||
return new CareGapsOperationProvider();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public ISubmitDataService r4SubmitDataService(DaoRegistry theDaoRegistry) {
|
||||
return requestDetails -> new SubmitDataService(theDaoRegistry, requestDetails);
|
||||
SubmitDataProvider r4SubmitDataProvider() {
|
||||
return new SubmitDataProvider();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public SubmitDataProvider r4SubmitDataProvider(ISubmitDataService theSubmitDataService) {
|
||||
return new SubmitDataProvider(theSubmitDataService);
|
||||
MeasureOperationsProvider r4MeasureOperationsProvider() {
|
||||
return new MeasureOperationsProvider();
|
||||
}
|
||||
|
||||
@Bean
|
||||
|
|
@ -111,7 +117,8 @@ public class CrR4Config {
|
|||
Arrays.asList(
|
||||
MeasureOperationsProvider.class,
|
||||
SubmitDataProvider.class,
|
||||
CareGapsOperationProvider.class)));
|
||||
CareGapsOperationProvider.class,
|
||||
CqlExecutionOperationProvider.class)));
|
||||
|
||||
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,62 @@
|
|||
/*-
|
||||
* #%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.config.r4;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
|
||||
public class ExtractOperationConfig {
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.IQuestionnaireResponseProcessorFactory r4QuestionnaireResponseProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaireresponse.r4.QuestionnaireResponseProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.questionnaireresponse.QuestionnaireResponseExtractProvider
|
||||
r4QuestionnaireResponseExtractProvider() {
|
||||
return new ca.uhn.fhir.cr.r4.questionnaireresponse.QuestionnaireResponseExtractProvider();
|
||||
}
|
||||
|
||||
@Bean(name = "extractOperationLoader")
|
||||
public ProviderLoader extractOperationLoader(
|
||||
ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
|
||||
|
||||
var selector = new ProviderSelector(
|
||||
theFhirContext,
|
||||
Map.of(
|
||||
FhirVersionEnum.R4,
|
||||
Arrays.asList(
|
||||
ca.uhn.fhir.cr.r4.questionnaireresponse.QuestionnaireResponseExtractProvider.class)));
|
||||
|
||||
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,74 @@
|
|||
/*-
|
||||
* #%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.config.r4;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
|
||||
public class PackageOperationConfig {
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.IPlanDefinitionProcessorFactory r4PlanDefinitionProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.plandefinition.r4.PlanDefinitionProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionPackageProvider r4PlanDefinitionPackageProvider() {
|
||||
return new ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionPackageProvider();
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.IQuestionnaireProcessorFactory r4QuestionnaireProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaire.r4.QuestionnaireProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePackageProvider r4QuestionnairePackageProvider() {
|
||||
return new ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePackageProvider();
|
||||
}
|
||||
|
||||
@Bean(name = "packageOperationLoader")
|
||||
public ProviderLoader packageOperationLoader(
|
||||
ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
|
||||
|
||||
var selector = new ProviderSelector(
|
||||
theFhirContext,
|
||||
Map.of(
|
||||
FhirVersionEnum.R4,
|
||||
Arrays.asList(
|
||||
ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePackageProvider.class,
|
||||
ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionPackageProvider.class)));
|
||||
|
||||
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
/*-
|
||||
* #%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.config.r4;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.config.ProviderLoader;
|
||||
import ca.uhn.fhir.cr.config.ProviderSelector;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Map;
|
||||
|
||||
public class PopulateOperationConfig {
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.IQuestionnaireProcessorFactory r4QuestionnaireProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaire.r4.QuestionnaireProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
@Bean
|
||||
ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePopulateProvider r4QuestionnairePopulateProvider() {
|
||||
return new ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePopulateProvider();
|
||||
}
|
||||
|
||||
@Bean(name = "populateOperationLoader")
|
||||
public ProviderLoader populateOperationLoader(
|
||||
ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
|
||||
|
||||
var selector = new ProviderSelector(
|
||||
theFhirContext,
|
||||
Map.of(
|
||||
FhirVersionEnum.R4,
|
||||
Arrays.asList(ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePopulateProvider.class)));
|
||||
|
||||
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
|
||||
}
|
||||
}
|
||||
|
|
@ -1,37 +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.constant;
|
||||
|
||||
public class CareCapsConstants {
|
||||
private CareCapsConstants() {}
|
||||
|
||||
public static final String CARE_GAPS_REPORT_PROFILE =
|
||||
"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/indv-measurereport-deqm";
|
||||
public static final String CARE_GAPS_BUNDLE_PROFILE =
|
||||
"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/gaps-bundle-deqm";
|
||||
public static final String CARE_GAPS_COMPOSITION_PROFILE =
|
||||
"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/gaps-composition-deqm";
|
||||
public static final String CARE_GAPS_DETECTED_ISSUE_PROFILE =
|
||||
"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/gaps-detectedissue-deqm";
|
||||
public static final String CARE_GAPS_GAP_STATUS_EXTENSION =
|
||||
"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-gapStatus";
|
||||
public static final String CARE_GAPS_GAP_STATUS_SYSTEM =
|
||||
"http://hl7.org/fhir/us/davinci-deqm/CodeSystem/gaps-status";
|
||||
}
|
||||
|
|
@ -1,29 +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.constant;
|
||||
|
||||
public class HtmlConstants {
|
||||
|
||||
private HtmlConstants() {}
|
||||
|
||||
public static final String HTML_DIV_CONTENT = "<div xmlns=\"http://www.w3.org/1999/xhtml\">%s</div>";
|
||||
public static final String HTML_PARAGRAPH_CONTENT = "<p>%s</p>";
|
||||
public static final String HTML_DIV_PARAGRAPH_CONTENT = String.format(HTML_DIV_CONTENT, HTML_PARAGRAPH_CONTENT);
|
||||
}
|
||||
|
|
@ -1,45 +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.constant;
|
||||
|
||||
import java.sql.Date;
|
||||
import java.time.LocalDate;
|
||||
|
||||
public class MeasureReportConstants {
|
||||
|
||||
private MeasureReportConstants() {}
|
||||
|
||||
public static final String MEASUREREPORT_IMPROVEMENT_NOTATION_SYSTEM =
|
||||
"http://terminology.hl7.org/CodeSystem/measure-improvement-notation";
|
||||
public static final String MEASUREREPORT_MEASURE_POPULATION_SYSTEM =
|
||||
"http://terminology.hl7.org/CodeSystem/measure-population";
|
||||
public static final String MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION =
|
||||
"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-supplementalData";
|
||||
public static final String MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL =
|
||||
"http://hl7.org/fhir/us/davinci-deqm/SearchParameter/measurereport-supplemental-data";
|
||||
public static final String MEASUREREPORT_PRODUCT_LINE_EXT_URL =
|
||||
"http://hl7.org/fhir/us/cqframework/cqfmeasures/StructureDefinition/cqfm-productLine";
|
||||
public static final String MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION = "0.1.0";
|
||||
public static final Date MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_DEFINITION_DATE =
|
||||
Date.valueOf(LocalDate.of(2022, 7, 20));
|
||||
public static final String COUNTRY_CODING_SYSTEM_CODE = "urn:iso:std:iso:3166";
|
||||
public static final String US_COUNTRY_CODE = "US";
|
||||
public static final String US_COUNTRY_DISPLAY = "United States of America";
|
||||
}
|
||||
|
|
@ -19,10 +19,10 @@
|
|||
*/
|
||||
package ca.uhn.fhir.cr.dstu3;
|
||||
|
||||
import org.opencds.cqf.cql.evaluator.activitydefinition.dstu3.ActivityDefinitionProcessor;
|
||||
import org.opencds.cqf.fhir.api.Repository;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.opencds.cqf.fhir.cr.activitydefinition.dstu3.ActivityDefinitionProcessor;
|
||||
|
||||
@FunctionalInterface
|
||||
public interface IActivityDefinitionProcessorFactory {
|
||||
ActivityDefinitionProcessor create(Repository theRepository);
|
||||
ActivityDefinitionProcessor create(RequestDetails theRequestDetails);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -17,11 +17,12 @@
|
|||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
package ca.uhn.fhir.cr.common;
|
||||
package ca.uhn.fhir.cr.dstu3;
|
||||
|
||||
import ca.uhn.fhir.cr.dstu3.measure.MeasureService;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
|
||||
@FunctionalInterface
|
||||
public interface ITerminologyProviderFactory {
|
||||
HapiTerminologyProvider create(RequestDetails theRequestDetails);
|
||||
public interface IMeasureServiceFactory {
|
||||
MeasureService create(RequestDetails theRequestDetails);
|
||||
}
|
||||
|
|
@ -19,10 +19,10 @@
|
|||
*/
|
||||
package ca.uhn.fhir.cr.dstu3;
|
||||
|
||||
import org.opencds.cqf.cql.evaluator.plandefinition.dstu3.PlanDefinitionProcessor;
|
||||
import org.opencds.cqf.fhir.api.Repository;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.opencds.cqf.fhir.cr.plandefinition.dstu3.PlanDefinitionProcessor;
|
||||
|
||||
@FunctionalInterface
|
||||
public interface IPlanDefinitionProcessorFactory {
|
||||
PlanDefinitionProcessor create(Repository theRepository);
|
||||
PlanDefinitionProcessor create(RequestDetails theRequestDetails);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -19,10 +19,10 @@
|
|||
*/
|
||||
package ca.uhn.fhir.cr.dstu3;
|
||||
|
||||
import org.opencds.cqf.cql.evaluator.questionnaire.dstu3.QuestionnaireProcessor;
|
||||
import org.opencds.cqf.fhir.api.Repository;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.opencds.cqf.fhir.cr.questionnaire.dstu3.QuestionnaireProcessor;
|
||||
|
||||
@FunctionalInterface
|
||||
public interface IQuestionnaireProcessorFactory {
|
||||
QuestionnaireProcessor create(Repository theRepository);
|
||||
QuestionnaireProcessor create(RequestDetails theRequestDetails);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -19,10 +19,10 @@
|
|||
*/
|
||||
package ca.uhn.fhir.cr.dstu3;
|
||||
|
||||
import org.opencds.cqf.cql.evaluator.questionnaireresponse.dstu3.QuestionnaireResponseProcessor;
|
||||
import org.opencds.cqf.fhir.api.Repository;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.opencds.cqf.fhir.cr.questionnaireresponse.dstu3.QuestionnaireResponseProcessor;
|
||||
|
||||
@FunctionalInterface
|
||||
public interface IQuestionnaireResponseProcessorFactory {
|
||||
QuestionnaireResponseProcessor create(Repository theRepository);
|
||||
QuestionnaireResponseProcessor create(RequestDetails theRequestDetails);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -20,7 +20,6 @@ package ca.uhn.fhir.cr.dstu3.activitydefinition;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.dstu3.IActivityDefinitionProcessorFactory;
|
||||
import ca.uhn.fhir.rest.annotation.IdParam;
|
||||
import ca.uhn.fhir.rest.annotation.Operation;
|
||||
|
|
@ -29,6 +28,9 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
|
|||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
|
||||
import org.hl7.fhir.dstu3.model.ActivityDefinition;
|
||||
import org.hl7.fhir.dstu3.model.BooleanType;
|
||||
import org.hl7.fhir.dstu3.model.Bundle;
|
||||
import org.hl7.fhir.dstu3.model.CodeableConcept;
|
||||
import org.hl7.fhir.dstu3.model.Endpoint;
|
||||
import org.hl7.fhir.dstu3.model.IdType;
|
||||
import org.hl7.fhir.dstu3.model.Parameters;
|
||||
|
|
@ -39,20 +41,16 @@ import org.springframework.beans.factory.annotation.Autowired;
|
|||
import org.springframework.stereotype.Component;
|
||||
|
||||
@Component
|
||||
public class ActivityDefinitionOperationsProvider {
|
||||
public class ActivityDefinitionApplyProvider {
|
||||
@Autowired
|
||||
IRepositoryFactory myRepositoryFactory;
|
||||
|
||||
@Autowired
|
||||
IActivityDefinitionProcessorFactory myDstu3ActivityDefinitionServiceFactory;
|
||||
IActivityDefinitionProcessorFactory myDstu3ActivityDefinitionProcessorFactory;
|
||||
|
||||
/**
|
||||
* Implements the <a href=
|
||||
* "http://www.hl7.org/fhir/activitydefinition-operation-apply.html">$apply</a>
|
||||
* operation found in the
|
||||
* <a href="http://www.hl7.org/fhir/clinicalreasoning-module.html">FHIR Clinical
|
||||
* Reasoning Module</a>. This implementation aims to be compatible with the CPG
|
||||
* IG.
|
||||
* Reasoning Module</a>.
|
||||
*
|
||||
* @param theId The id of the ActivityDefinition to apply
|
||||
* @param theCanonical The canonical identifier for the ActivityDefinition to apply (optionally version-specific)
|
||||
|
|
@ -70,6 +68,8 @@ public class ActivityDefinitionOperationsProvider {
|
|||
* @param theSetting The current setting of the request (inpatient, outpatient, etc.)
|
||||
* @param theSettingContext Additional detail about the setting of the request, if any
|
||||
* @param theParameters Any input parameters defined in libraries referenced by the ActivityDefinition.
|
||||
* @param theUseServerData Whether to use data from the server performing the evaluation.
|
||||
* @param theData Data to be made available to the ActivityDefinition evaluation.
|
||||
* @param theDataEndpoint An endpoint to use to access data referenced by retrieve operations in libraries
|
||||
* referenced by the ActivityDefinition.
|
||||
* @param theContentEndpoint An endpoint to use to access content (i.e. libraries) referenced by the ActivityDefinition.
|
||||
|
|
@ -88,19 +88,21 @@ public class ActivityDefinitionOperationsProvider {
|
|||
@OperationParam(name = "encounter") String theEncounter,
|
||||
@OperationParam(name = "practitioner") String thePractitioner,
|
||||
@OperationParam(name = "organization") String theOrganization,
|
||||
@OperationParam(name = "userType") String theUserType,
|
||||
@OperationParam(name = "userLanguage") String theUserLanguage,
|
||||
@OperationParam(name = "userTaskContext") String theUserTaskContext,
|
||||
@OperationParam(name = "setting") String theSetting,
|
||||
@OperationParam(name = "settingContext") String theSettingContext,
|
||||
@OperationParam(name = "userType") CodeableConcept theUserType,
|
||||
@OperationParam(name = "userLanguage") CodeableConcept theUserLanguage,
|
||||
@OperationParam(name = "userTaskContext") CodeableConcept theUserTaskContext,
|
||||
@OperationParam(name = "setting") CodeableConcept theSetting,
|
||||
@OperationParam(name = "settingContext") CodeableConcept theSettingContext,
|
||||
@OperationParam(name = "parameters") Parameters theParameters,
|
||||
@OperationParam(name = "useServerData") BooleanType theUseServerData,
|
||||
@OperationParam(name = "data") Bundle theData,
|
||||
@OperationParam(name = "dataEndpoint") Endpoint theDataEndpoint,
|
||||
@OperationParam(name = "contentEndpoint") Endpoint theContentEndpoint,
|
||||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return this.myDstu3ActivityDefinitionServiceFactory
|
||||
.create(myRepositoryFactory.create(theRequestDetails))
|
||||
return myDstu3ActivityDefinitionProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.apply(
|
||||
theId,
|
||||
new StringType(theCanonical),
|
||||
|
|
@ -115,6 +117,52 @@ public class ActivityDefinitionOperationsProvider {
|
|||
theSetting,
|
||||
theSettingContext,
|
||||
theParameters,
|
||||
theUseServerData == null ? true : theUseServerData.booleanValue(),
|
||||
theData,
|
||||
theDataEndpoint,
|
||||
theContentEndpoint,
|
||||
theTerminologyEndpoint);
|
||||
}
|
||||
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_APPLY, idempotent = true, type = ActivityDefinition.class)
|
||||
public IBaseResource apply(
|
||||
@OperationParam(name = "canonical") String theCanonical,
|
||||
@OperationParam(name = "activityDefinition") ActivityDefinition theActivityDefinition,
|
||||
@OperationParam(name = "subject") String theSubject,
|
||||
@OperationParam(name = "encounter") String theEncounter,
|
||||
@OperationParam(name = "practitioner") String thePractitioner,
|
||||
@OperationParam(name = "organization") String theOrganization,
|
||||
@OperationParam(name = "userType") CodeableConcept theUserType,
|
||||
@OperationParam(name = "userLanguage") CodeableConcept theUserLanguage,
|
||||
@OperationParam(name = "userTaskContext") CodeableConcept theUserTaskContext,
|
||||
@OperationParam(name = "setting") CodeableConcept theSetting,
|
||||
@OperationParam(name = "settingContext") CodeableConcept theSettingContext,
|
||||
@OperationParam(name = "parameters") Parameters theParameters,
|
||||
@OperationParam(name = "useServerData") BooleanType theUseServerData,
|
||||
@OperationParam(name = "data") Bundle theData,
|
||||
@OperationParam(name = "dataEndpoint") Endpoint theDataEndpoint,
|
||||
@OperationParam(name = "contentEndpoint") Endpoint theContentEndpoint,
|
||||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return myDstu3ActivityDefinitionProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.apply(
|
||||
null,
|
||||
new StringType(theCanonical),
|
||||
theActivityDefinition,
|
||||
theSubject,
|
||||
theEncounter,
|
||||
thePractitioner,
|
||||
theOrganization,
|
||||
theUserType,
|
||||
theUserLanguage,
|
||||
theUserTaskContext,
|
||||
theSetting,
|
||||
theSettingContext,
|
||||
theParameters,
|
||||
theUseServerData == null ? true : theUseServerData.booleanValue(),
|
||||
theData,
|
||||
theDataEndpoint,
|
||||
theContentEndpoint,
|
||||
theTerminologyEndpoint);
|
||||
|
|
@ -19,6 +19,7 @@
|
|||
*/
|
||||
package ca.uhn.fhir.cr.dstu3.measure;
|
||||
|
||||
import ca.uhn.fhir.cr.dstu3.IMeasureServiceFactory;
|
||||
import ca.uhn.fhir.rest.annotation.IdParam;
|
||||
import ca.uhn.fhir.rest.annotation.Operation;
|
||||
import ca.uhn.fhir.rest.annotation.OperationParam;
|
||||
|
|
@ -34,12 +35,10 @@ import org.hl7.fhir.exceptions.FHIRException;
|
|||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.stereotype.Component;
|
||||
|
||||
import java.util.function.Function;
|
||||
|
||||
@Component
|
||||
public class MeasureOperationsProvider {
|
||||
@Autowired
|
||||
Function<RequestDetails, MeasureService> myDstu3MeasureServiceFactory;
|
||||
IMeasureServiceFactory myDstu3MeasureProcessorFactory;
|
||||
|
||||
/**
|
||||
* Implements the <a href=
|
||||
|
|
@ -79,8 +78,8 @@ public class MeasureOperationsProvider {
|
|||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return this.myDstu3MeasureServiceFactory
|
||||
.apply(theRequestDetails)
|
||||
return myDstu3MeasureProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.evaluateMeasure(
|
||||
theId,
|
||||
thePeriodStart,
|
||||
|
|
|
|||
|
|
@ -19,16 +19,7 @@
|
|||
*/
|
||||
package ca.uhn.fhir.cr.dstu3.measure;
|
||||
|
||||
import ca.uhn.fhir.cr.common.IDaoRegistryUser;
|
||||
import ca.uhn.fhir.cr.common.IDataProviderFactory;
|
||||
import ca.uhn.fhir.cr.common.IFhirDalFactory;
|
||||
import ca.uhn.fhir.cr.common.ILibrarySourceProviderFactory;
|
||||
import ca.uhn.fhir.cr.common.ITerminologyProviderFactory;
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.client.api.IGenericClient;
|
||||
import ca.uhn.fhir.util.BundleBuilder;
|
||||
import org.cqframework.cql.cql2elm.LibrarySourceProvider;
|
||||
import org.hl7.fhir.dstu3.model.Bundle;
|
||||
import org.hl7.fhir.dstu3.model.CodeableConcept;
|
||||
import org.hl7.fhir.dstu3.model.Coding;
|
||||
|
|
@ -38,32 +29,32 @@ import org.hl7.fhir.dstu3.model.Endpoint;
|
|||
import org.hl7.fhir.dstu3.model.Enumerations;
|
||||
import org.hl7.fhir.dstu3.model.Extension;
|
||||
import org.hl7.fhir.dstu3.model.IdType;
|
||||
import org.hl7.fhir.dstu3.model.Measure;
|
||||
import org.hl7.fhir.dstu3.model.MeasureReport;
|
||||
import org.hl7.fhir.dstu3.model.SearchParameter;
|
||||
import org.hl7.fhir.dstu3.model.StringType;
|
||||
import org.opencds.cqf.cql.engine.data.DataProvider;
|
||||
import org.opencds.cqf.cql.engine.fhir.terminology.Dstu3FhirTerminologyProvider;
|
||||
import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
|
||||
import org.opencds.cqf.cql.evaluator.fhir.dal.FhirDal;
|
||||
import org.opencds.cqf.cql.evaluator.fhir.util.Clients;
|
||||
import org.opencds.cqf.cql.evaluator.library.EvaluationSettings;
|
||||
import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.opencds.cqf.fhir.api.Repository;
|
||||
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
|
||||
import org.opencds.cqf.fhir.cr.measure.dstu3.Dstu3MeasureProcessor;
|
||||
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import static ca.uhn.fhir.cr.constant.MeasureReportConstants.COUNTRY_CODING_SYSTEM_CODE;
|
||||
import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION;
|
||||
import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_DEFINITION_DATE;
|
||||
import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL;
|
||||
import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION;
|
||||
import static ca.uhn.fhir.cr.constant.MeasureReportConstants.US_COUNTRY_CODE;
|
||||
import static ca.uhn.fhir.cr.constant.MeasureReportConstants.US_COUNTRY_DISPLAY;
|
||||
import static org.opencds.cqf.fhir.cr.measure.constant.MeasureReportConstants.COUNTRY_CODING_SYSTEM_CODE;
|
||||
import static org.opencds.cqf.fhir.cr.measure.constant.MeasureReportConstants.MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION;
|
||||
import static org.opencds.cqf.fhir.cr.measure.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_DEFINITION_DATE;
|
||||
import static org.opencds.cqf.fhir.cr.measure.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL;
|
||||
import static org.opencds.cqf.fhir.cr.measure.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION;
|
||||
import static org.opencds.cqf.fhir.cr.measure.constant.MeasureReportConstants.US_COUNTRY_CODE;
|
||||
import static org.opencds.cqf.fhir.cr.measure.constant.MeasureReportConstants.US_COUNTRY_DISPLAY;
|
||||
|
||||
public class MeasureService implements IDaoRegistryUser {
|
||||
public class MeasureService {
|
||||
private final Repository myRepository;
|
||||
private final MeasureEvaluationOptions myMeasureEvaluationOptions;
|
||||
|
||||
public MeasureService(Repository theRepository, MeasureEvaluationOptions theMeasureEvaluationOptions) {
|
||||
myRepository = theRepository;
|
||||
myMeasureEvaluationOptions = theMeasureEvaluationOptions;
|
||||
}
|
||||
|
||||
public static final List<ContactDetail> CQI_CONTACT_DETAIL = Collections.singletonList(new ContactDetail()
|
||||
.addTelecom(new ContactPoint()
|
||||
|
|
@ -96,47 +87,10 @@ public class MeasureService implements IDaoRegistryUser {
|
|||
.setTitle("Supplemental Data")
|
||||
.setId("deqm-measurereport-supplemental-data");
|
||||
|
||||
@Autowired
|
||||
protected ITerminologyProviderFactory myTerminologyProviderFactory;
|
||||
|
||||
@Autowired
|
||||
protected IDataProviderFactory myCqlDataProviderFactory;
|
||||
|
||||
@Autowired
|
||||
protected org.opencds.cqf.cql.evaluator.builder.DataProviderFactory myDataProviderFactory;
|
||||
|
||||
@Autowired
|
||||
protected ILibrarySourceProviderFactory myLibraryContentProviderFactory;
|
||||
|
||||
@Autowired
|
||||
protected IFhirDalFactory myFhirDalFactory;
|
||||
|
||||
@Autowired
|
||||
protected Map<org.cqframework.cql.elm.execution.VersionedIdentifier, org.cqframework.cql.elm.execution.Library>
|
||||
myGlobalLibraryCache;
|
||||
|
||||
@Autowired
|
||||
protected EvaluationSettings myEvaluationSettings;
|
||||
|
||||
@Autowired
|
||||
protected MeasureEvaluationOptions myMeasureEvaluationOptions;
|
||||
|
||||
@Autowired
|
||||
protected DaoRegistry myDaoRegistry;
|
||||
|
||||
protected RequestDetails myRequestDetails;
|
||||
/**
|
||||
* Get The details (such as tenant) of this request. Usually auto-populated HAPI.
|
||||
*
|
||||
* @return RequestDetails
|
||||
*/
|
||||
public RequestDetails getRequestDetails() {
|
||||
return this.myRequestDetails;
|
||||
}
|
||||
|
||||
public void setRequestDetails(RequestDetails theRequestDetails) {
|
||||
this.myRequestDetails = theRequestDetails;
|
||||
}
|
||||
|
||||
/**
|
||||
* Implements the <a href=
|
||||
|
|
@ -173,46 +127,14 @@ public class MeasureService implements IDaoRegistryUser {
|
|||
|
||||
ensureSupplementalDataElementSearchParameter();
|
||||
|
||||
Measure measure = read(theId, myRequestDetails);
|
||||
var dstu3MeasureProcessor = new Dstu3MeasureProcessor(myRepository, myMeasureEvaluationOptions);
|
||||
|
||||
TerminologyProvider terminologyProvider;
|
||||
|
||||
if (theTerminologyEndpoint != null) {
|
||||
IGenericClient client = Clients.forEndpoint(getFhirContext(), theTerminologyEndpoint);
|
||||
terminologyProvider = new Dstu3FhirTerminologyProvider(client);
|
||||
} else {
|
||||
terminologyProvider = this.myTerminologyProviderFactory.create(myRequestDetails);
|
||||
}
|
||||
|
||||
DataProvider dataProvider = this.myCqlDataProviderFactory.create(myRequestDetails, terminologyProvider);
|
||||
LibrarySourceProvider libraryContentProvider = this.myLibraryContentProviderFactory.create(myRequestDetails);
|
||||
FhirDal fhirDal = this.myFhirDalFactory.create(myRequestDetails);
|
||||
|
||||
var measureProcessor = new org.opencds.cqf.cql.evaluator.measure.dstu3.Dstu3MeasureProcessor(
|
||||
null,
|
||||
this.myDataProviderFactory,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
terminologyProvider,
|
||||
libraryContentProvider,
|
||||
dataProvider,
|
||||
fhirDal,
|
||||
myMeasureEvaluationOptions,
|
||||
myEvaluationSettings.getCqlOptions(),
|
||||
null);
|
||||
|
||||
MeasureReport report = measureProcessor.evaluateMeasure(
|
||||
measure.getUrl(),
|
||||
MeasureReport report = dstu3MeasureProcessor.evaluateMeasure(
|
||||
theId,
|
||||
thePeriodStart,
|
||||
thePeriodEnd,
|
||||
theReportType,
|
||||
theSubject,
|
||||
null,
|
||||
theLastReceivedOn,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
Collections.singletonList(theSubject),
|
||||
theAdditionalData);
|
||||
|
||||
if (theProductLine != null) {
|
||||
|
|
@ -225,17 +147,12 @@ public class MeasureService implements IDaoRegistryUser {
|
|||
return report;
|
||||
}
|
||||
|
||||
@Override
|
||||
public DaoRegistry getDaoRegistry() {
|
||||
return this.myDaoRegistry;
|
||||
}
|
||||
|
||||
protected void ensureSupplementalDataElementSearchParameter() {
|
||||
// create a transaction bundle
|
||||
BundleBuilder builder = new BundleBuilder(getFhirContext());
|
||||
BundleBuilder builder = new BundleBuilder(myRepository.fhirContext());
|
||||
|
||||
// set the request to be condition on code == supplemental data
|
||||
builder.addTransactionCreateEntry(SUPPLEMENTAL_DATA_SEARCHPARAMETER).conditional("code=supplemental-data");
|
||||
transaction(builder.getBundle(), this.myRequestDetails);
|
||||
myRepository.transaction(builder.getBundle());
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -20,7 +20,6 @@ package ca.uhn.fhir.cr.dstu3.plandefinition;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.dstu3.IPlanDefinitionProcessorFactory;
|
||||
import ca.uhn.fhir.rest.annotation.IdParam;
|
||||
import ca.uhn.fhir.rest.annotation.Operation;
|
||||
|
|
@ -28,7 +27,9 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
|
|||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
|
||||
import org.hl7.fhir.dstu3.model.BooleanType;
|
||||
import org.hl7.fhir.dstu3.model.Bundle;
|
||||
import org.hl7.fhir.dstu3.model.CodeableConcept;
|
||||
import org.hl7.fhir.dstu3.model.Endpoint;
|
||||
import org.hl7.fhir.dstu3.model.IdType;
|
||||
import org.hl7.fhir.dstu3.model.Parameters;
|
||||
|
|
@ -40,21 +41,16 @@ import org.springframework.beans.factory.annotation.Autowired;
|
|||
import org.springframework.stereotype.Component;
|
||||
|
||||
@Component
|
||||
public class PlanDefinitionOperationsProvider {
|
||||
public class PlanDefinitionApplyProvider {
|
||||
@Autowired
|
||||
IRepositoryFactory myRepositoryFactory;
|
||||
|
||||
@Autowired
|
||||
IPlanDefinitionProcessorFactory myDstu3PlanDefinitionServiceFactory;
|
||||
IPlanDefinitionProcessorFactory myDstu3PlanDefinitionProcessorFactory;
|
||||
|
||||
/**
|
||||
* Implements the <a href=
|
||||
* "http://www.hl7.org/fhir/plandefinition-operation-apply.html">$apply</a>
|
||||
* operation found in the
|
||||
* <a href="http://www.hl7.org/fhir/clinicalreasoning-module.html">FHIR Clinical
|
||||
* Reasoning Module</a>. This implementation aims to be compatible with the
|
||||
* <a href="https://build.fhir.org/ig/HL7/cqf-recommendations/OperationDefinition-cpg-plandefinition-apply.html">
|
||||
* CPG IG</a>.
|
||||
* Reasoning Module</a>.
|
||||
*
|
||||
* @param theId The id of the PlanDefinition to apply
|
||||
* @param theCanonical The canonical identifier for the PlanDefinition to apply (optionally version-specific)
|
||||
|
|
@ -72,6 +68,7 @@ public class PlanDefinitionOperationsProvider {
|
|||
* @param theSetting The current setting of the request (inpatient, outpatient, etc.)
|
||||
* @param theSettingContext Additional detail about the setting of the request, if any
|
||||
* @param theParameters Any input parameters defined in libraries referenced by the PlanDefinition.
|
||||
* @param theUseServerData Whether to use data from the server performing the evaluation.
|
||||
* @param theData Data to be made available to the PlanDefinition evaluation.
|
||||
* @param theDataEndpoint An endpoint to use to access data referenced by retrieve operations in libraries
|
||||
* referenced by the PlanDefinition.
|
||||
|
|
@ -91,20 +88,21 @@ public class PlanDefinitionOperationsProvider {
|
|||
@OperationParam(name = "encounter") String theEncounter,
|
||||
@OperationParam(name = "practitioner") String thePractitioner,
|
||||
@OperationParam(name = "organization") String theOrganization,
|
||||
@OperationParam(name = "userType") String theUserType,
|
||||
@OperationParam(name = "userLanguage") String theUserLanguage,
|
||||
@OperationParam(name = "userTaskContext") String theUserTaskContext,
|
||||
@OperationParam(name = "setting") String theSetting,
|
||||
@OperationParam(name = "settingContext") String theSettingContext,
|
||||
@OperationParam(name = "userType") CodeableConcept theUserType,
|
||||
@OperationParam(name = "userLanguage") CodeableConcept theUserLanguage,
|
||||
@OperationParam(name = "userTaskContext") CodeableConcept theUserTaskContext,
|
||||
@OperationParam(name = "setting") CodeableConcept theSetting,
|
||||
@OperationParam(name = "settingContext") CodeableConcept theSettingContext,
|
||||
@OperationParam(name = "parameters") Parameters theParameters,
|
||||
@OperationParam(name = "useServerData") BooleanType theUseServerData,
|
||||
@OperationParam(name = "data") Bundle theData,
|
||||
@OperationParam(name = "dataEndpoint") Endpoint theDataEndpoint,
|
||||
@OperationParam(name = "contentEndpoint") Endpoint theContentEndpoint,
|
||||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return this.myDstu3PlanDefinitionServiceFactory
|
||||
.create(myRepositoryFactory.create(theRequestDetails))
|
||||
return myDstu3PlanDefinitionProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.apply(
|
||||
theId,
|
||||
new StringType(theCanonical),
|
||||
|
|
@ -119,7 +117,52 @@ public class PlanDefinitionOperationsProvider {
|
|||
theSetting,
|
||||
theSettingContext,
|
||||
theParameters,
|
||||
true,
|
||||
theUseServerData == null ? true : theUseServerData.booleanValue(),
|
||||
theData,
|
||||
null,
|
||||
theDataEndpoint,
|
||||
theContentEndpoint,
|
||||
theTerminologyEndpoint);
|
||||
}
|
||||
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_APPLY, idempotent = true, type = PlanDefinition.class)
|
||||
public IBaseResource apply(
|
||||
@OperationParam(name = "canonical") String theCanonical,
|
||||
@OperationParam(name = "planDefinition") PlanDefinition thePlanDefinition,
|
||||
@OperationParam(name = "subject") String theSubject,
|
||||
@OperationParam(name = "encounter") String theEncounter,
|
||||
@OperationParam(name = "practitioner") String thePractitioner,
|
||||
@OperationParam(name = "organization") String theOrganization,
|
||||
@OperationParam(name = "userType") CodeableConcept theUserType,
|
||||
@OperationParam(name = "userLanguage") CodeableConcept theUserLanguage,
|
||||
@OperationParam(name = "userTaskContext") CodeableConcept theUserTaskContext,
|
||||
@OperationParam(name = "setting") CodeableConcept theSetting,
|
||||
@OperationParam(name = "settingContext") CodeableConcept theSettingContext,
|
||||
@OperationParam(name = "parameters") Parameters theParameters,
|
||||
@OperationParam(name = "useServerData") BooleanType theUseServerData,
|
||||
@OperationParam(name = "data") Bundle theData,
|
||||
@OperationParam(name = "dataEndpoint") Endpoint theDataEndpoint,
|
||||
@OperationParam(name = "contentEndpoint") Endpoint theContentEndpoint,
|
||||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return myDstu3PlanDefinitionProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.apply(
|
||||
null,
|
||||
new StringType(theCanonical),
|
||||
thePlanDefinition,
|
||||
theSubject,
|
||||
theEncounter,
|
||||
thePractitioner,
|
||||
theOrganization,
|
||||
theUserType,
|
||||
theUserLanguage,
|
||||
theUserTaskContext,
|
||||
theSetting,
|
||||
theSettingContext,
|
||||
theParameters,
|
||||
theUseServerData == null ? true : theUseServerData.booleanValue(),
|
||||
theData,
|
||||
null,
|
||||
theDataEndpoint,
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
/*-
|
||||
* #%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.dstu3.plandefinition;
|
||||
|
||||
import ca.uhn.fhir.cr.dstu3.IPlanDefinitionProcessorFactory;
|
||||
import ca.uhn.fhir.rest.annotation.IdParam;
|
||||
import ca.uhn.fhir.rest.annotation.Operation;
|
||||
import ca.uhn.fhir.rest.annotation.OperationParam;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
|
||||
import org.hl7.fhir.dstu3.model.IdType;
|
||||
import org.hl7.fhir.dstu3.model.PlanDefinition;
|
||||
import org.hl7.fhir.dstu3.model.StringType;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.instance.model.api.IBaseBundle;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
public class PlanDefinitionPackageProvider {
|
||||
@Autowired
|
||||
IPlanDefinitionProcessorFactory mydstu3PlanDefinitionProcessorFactory;
|
||||
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_PACKAGE, idempotent = true, type = PlanDefinition.class)
|
||||
public IBaseBundle packagePlanDefinition(
|
||||
@IdParam IdType theId,
|
||||
@OperationParam(name = "canonical") String theCanonical,
|
||||
@OperationParam(name = "usePut") String theIsPut,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return mydstu3PlanDefinitionProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.packagePlanDefinition(theId, new StringType(theCanonical), null, Boolean.parseBoolean(theIsPut));
|
||||
}
|
||||
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_PACKAGE, idempotent = true, type = PlanDefinition.class)
|
||||
public IBaseBundle packagePlanDefinition(
|
||||
@OperationParam(name = "id") String theId,
|
||||
@OperationParam(name = "canonical") String theCanonical,
|
||||
@OperationParam(name = "usePut") String theIsPut,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return mydstu3PlanDefinitionProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.packagePlanDefinition(
|
||||
new IdType("PlanDefinition", theId),
|
||||
new StringType(theCanonical),
|
||||
null,
|
||||
Boolean.parseBoolean(theIsPut));
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
/*-
|
||||
* #%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.dstu3.questionnaire;
|
||||
|
||||
import ca.uhn.fhir.cr.dstu3.IQuestionnaireProcessorFactory;
|
||||
import ca.uhn.fhir.rest.annotation.IdParam;
|
||||
import ca.uhn.fhir.rest.annotation.Operation;
|
||||
import ca.uhn.fhir.rest.annotation.OperationParam;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
|
||||
import org.hl7.fhir.dstu3.model.Bundle;
|
||||
import org.hl7.fhir.dstu3.model.IdType;
|
||||
import org.hl7.fhir.dstu3.model.Questionnaire;
|
||||
import org.hl7.fhir.dstu3.model.StringType;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
public class QuestionnairePackageProvider {
|
||||
@Autowired
|
||||
IQuestionnaireProcessorFactory myDstu3QuestionnaireProcessorFactory;
|
||||
|
||||
/**
|
||||
* Implements a $package operation following the <a href=
|
||||
* "https://build.fhir.org/ig/HL7/crmi-ig/branches/master/packaging.html">CRMI IG</a>.
|
||||
*
|
||||
* @param theId The id of the Questionnaire.
|
||||
* @param theCanonical The canonical identifier for the questionnaire (optionally version-specific).
|
||||
* @Param theIsPut A boolean value to determine if the Bundle returned uses PUT or POST request methods. Defaults to false.
|
||||
* @param theRequestDetails The details (such as tenant) of this request. Usually
|
||||
* autopopulated by HAPI.
|
||||
* @return A Bundle containing the Questionnaire and all related Library, CodeSystem and ValueSet resources
|
||||
*/
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_PACKAGE, idempotent = true, type = Questionnaire.class)
|
||||
public Bundle packageQuestionnaire(
|
||||
@IdParam IdType theId,
|
||||
@OperationParam(name = "canonical") String theCanonical,
|
||||
@OperationParam(name = "usePut") String theIsPut,
|
||||
RequestDetails theRequestDetails) {
|
||||
return (Bundle) myDstu3QuestionnaireProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.packageQuestionnaire(theId, new StringType(theCanonical), null, Boolean.parseBoolean(theIsPut));
|
||||
}
|
||||
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_PACKAGE, idempotent = true, type = Questionnaire.class)
|
||||
public Bundle packageQuestionnaire(
|
||||
@OperationParam(name = "canonical") String theCanonical,
|
||||
@OperationParam(name = "usePut") String theIsPut,
|
||||
RequestDetails theRequestDetails) {
|
||||
return (Bundle) myDstu3QuestionnaireProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.packageQuestionnaire(null, new StringType(theCanonical), null, Boolean.parseBoolean(theIsPut));
|
||||
}
|
||||
}
|
||||
|
|
@ -20,7 +20,6 @@ package ca.uhn.fhir.cr.dstu3.questionnaire;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.dstu3.IQuestionnaireProcessorFactory;
|
||||
import ca.uhn.fhir.rest.annotation.IdParam;
|
||||
import ca.uhn.fhir.rest.annotation.Operation;
|
||||
|
|
@ -38,12 +37,9 @@ import org.hl7.fhir.dstu3.model.StringType;
|
|||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
public class QuestionnaireOperationsProvider {
|
||||
public class QuestionnairePopulateProvider {
|
||||
@Autowired
|
||||
IRepositoryFactory myRepositoryFactory;
|
||||
|
||||
@Autowired
|
||||
IQuestionnaireProcessorFactory myDstu3QuestionnaireServiceFactory;
|
||||
IQuestionnaireProcessorFactory myDstu3QuestionnaireProcessorFactory;
|
||||
|
||||
/**
|
||||
* Implements a modified version of the <a href=
|
||||
|
|
@ -81,8 +77,8 @@ public class QuestionnaireOperationsProvider {
|
|||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return this.myDstu3QuestionnaireServiceFactory
|
||||
.create(myRepositoryFactory.create(theRequestDetails))
|
||||
return myDstu3QuestionnaireProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.prePopulate(
|
||||
theId,
|
||||
new StringType(theCanonical),
|
||||
|
|
@ -95,6 +91,32 @@ public class QuestionnaireOperationsProvider {
|
|||
theTerminologyEndpoint);
|
||||
}
|
||||
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_PREPOPULATE, idempotent = true, type = Questionnaire.class)
|
||||
public Questionnaire prepopulate(
|
||||
@OperationParam(name = "canonical") String theCanonical,
|
||||
@OperationParam(name = "questionnaire") Questionnaire theQuestionnaire,
|
||||
@OperationParam(name = "subject") String theSubject,
|
||||
@OperationParam(name = "parameters") Parameters theParameters,
|
||||
@OperationParam(name = "bundle") Bundle theBundle,
|
||||
@OperationParam(name = "dataEndpoint") Endpoint theDataEndpoint,
|
||||
@OperationParam(name = "contentEndpoint") Endpoint theContentEndpoint,
|
||||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return myDstu3QuestionnaireProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.prePopulate(
|
||||
null,
|
||||
new StringType(theCanonical),
|
||||
theQuestionnaire,
|
||||
theSubject,
|
||||
theParameters,
|
||||
theBundle,
|
||||
theDataEndpoint,
|
||||
theContentEndpoint,
|
||||
theTerminologyEndpoint);
|
||||
}
|
||||
|
||||
/**
|
||||
* Implements the <a href=
|
||||
* "http://build.fhir.org/ig/HL7/sdc/OperationDefinition-Questionnaire-populate.html">$populate</a>
|
||||
|
|
@ -129,8 +151,8 @@ public class QuestionnaireOperationsProvider {
|
|||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return (QuestionnaireResponse) this.myDstu3QuestionnaireServiceFactory
|
||||
.create(myRepositoryFactory.create(theRequestDetails))
|
||||
return (QuestionnaireResponse) myDstu3QuestionnaireProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.populate(
|
||||
theId,
|
||||
new StringType(theCanonical),
|
||||
|
|
@ -143,24 +165,29 @@ public class QuestionnaireOperationsProvider {
|
|||
theTerminologyEndpoint);
|
||||
}
|
||||
|
||||
/**
|
||||
* Implements a $package operation following the <a href=
|
||||
* "https://build.fhir.org/ig/HL7/crmi-ig/branches/master/packaging.html">CRMI IG</a>.
|
||||
*
|
||||
* @param theId The id of the Questionnaire.
|
||||
* @param theCanonical The canonical identifier for the questionnaire (optionally version-specific).
|
||||
* @param theRequestDetails The details (such as tenant) of this request. Usually
|
||||
* autopopulated by HAPI.
|
||||
* @return A Bundle containing the Questionnaire and all related Library, CodeSystem and ValueSet resources
|
||||
*/
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_PACKAGE, idempotent = true, type = Questionnaire.class)
|
||||
public Bundle packageQuestionnaire(
|
||||
@IdParam IdType theId,
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_POPULATE, idempotent = true, type = Questionnaire.class)
|
||||
public QuestionnaireResponse populate(
|
||||
@OperationParam(name = "canonical") String theCanonical,
|
||||
RequestDetails theRequestDetails) {
|
||||
|
||||
return (Bundle) this.myDstu3QuestionnaireServiceFactory
|
||||
.create(myRepositoryFactory.create(theRequestDetails))
|
||||
.packageQuestionnaire(theId, new StringType(theCanonical), null, false);
|
||||
@OperationParam(name = "questionnaire") Questionnaire theQuestionnaire,
|
||||
@OperationParam(name = "subject") String theSubject,
|
||||
@OperationParam(name = "parameters") Parameters theParameters,
|
||||
@OperationParam(name = "bundle") Bundle theBundle,
|
||||
@OperationParam(name = "dataEndpoint") Endpoint theDataEndpoint,
|
||||
@OperationParam(name = "contentEndpoint") Endpoint theContentEndpoint,
|
||||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return (QuestionnaireResponse) myDstu3QuestionnaireProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.populate(
|
||||
null,
|
||||
new StringType(theCanonical),
|
||||
theQuestionnaire,
|
||||
theSubject,
|
||||
theParameters,
|
||||
theBundle,
|
||||
theDataEndpoint,
|
||||
theContentEndpoint,
|
||||
theTerminologyEndpoint);
|
||||
}
|
||||
}
|
||||
|
|
@ -20,11 +20,10 @@ package ca.uhn.fhir.cr.dstu3.questionnaireresponse;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.cr.common.IRepositoryFactory;
|
||||
import ca.uhn.fhir.cr.dstu3.IQuestionnaireResponseProcessorFactory;
|
||||
import ca.uhn.fhir.rest.annotation.IdParam;
|
||||
import ca.uhn.fhir.rest.annotation.Operation;
|
||||
import ca.uhn.fhir.rest.annotation.ResourceParam;
|
||||
import ca.uhn.fhir.rest.annotation.OperationParam;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
|
||||
|
|
@ -34,12 +33,9 @@ import org.hl7.fhir.exceptions.FHIRException;
|
|||
import org.hl7.fhir.instance.model.api.IBaseBundle;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
public class QuestionnaireResponseOperationsProvider {
|
||||
public class QuestionnaireResponseExtractProvider {
|
||||
@Autowired
|
||||
IRepositoryFactory myRepositoryFactory;
|
||||
|
||||
@Autowired
|
||||
IQuestionnaireResponseProcessorFactory myDstu3QuestionnaireResponseServiceFactory;
|
||||
IQuestionnaireResponseProcessorFactory myDstu3QuestionnaireResponseProcessorFactory;
|
||||
|
||||
/**
|
||||
* Implements the <a href=
|
||||
|
|
@ -56,11 +52,21 @@ public class QuestionnaireResponseOperationsProvider {
|
|||
@Operation(name = ProviderConstants.CR_OPERATION_EXTRACT, idempotent = true, type = QuestionnaireResponse.class)
|
||||
public IBaseBundle extract(
|
||||
@IdParam IdType theId,
|
||||
@ResourceParam QuestionnaireResponse theQuestionnaireResponse,
|
||||
@OperationParam(name = "questionnaire-response") QuestionnaireResponse theQuestionnaireResponse,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return this.myDstu3QuestionnaireResponseServiceFactory
|
||||
.create(myRepositoryFactory.create(theRequestDetails))
|
||||
return myDstu3QuestionnaireResponseProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.extract(theId, theQuestionnaireResponse, null, null, null);
|
||||
}
|
||||
|
||||
@Operation(name = ProviderConstants.CR_OPERATION_EXTRACT, idempotent = true, type = QuestionnaireResponse.class)
|
||||
public IBaseBundle extract(
|
||||
@OperationParam(name = "questionnaire-response") QuestionnaireResponse theQuestionnaireResponse,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return myDstu3QuestionnaireResponseProcessorFactory
|
||||
.create(theRequestDetails)
|
||||
.extract(null, theQuestionnaireResponse, null, null, null);
|
||||
}
|
||||
}
|
||||
|
|
@ -1,55 +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.enumeration;
|
||||
|
||||
import ca.uhn.fhir.i18n.Msg;
|
||||
|
||||
public enum CareGapsStatusCode {
|
||||
OPEN_GAP("open-gap"),
|
||||
CLOSED_GAP("closed-gap"),
|
||||
NOT_APPLICABLE("not-applicable");
|
||||
|
||||
private final String myValue;
|
||||
|
||||
CareGapsStatusCode(final String theValue) {
|
||||
myValue = theValue;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return myValue;
|
||||
}
|
||||
|
||||
public String toDisplayString() {
|
||||
if (myValue.equals("open-gap")) {
|
||||
return "Open Gap";
|
||||
}
|
||||
|
||||
if (myValue.equals("closed-gap")) {
|
||||
return "Closed Gap";
|
||||
}
|
||||
|
||||
if (myValue.equals("not-applicable")) {
|
||||
return "Not Applicable";
|
||||
}
|
||||
|
||||
throw new RuntimeException(Msg.code(2301) + "Error getting display strings for care gaps status codes");
|
||||
}
|
||||
}
|
||||
|
|
@ -19,10 +19,10 @@
|
|||
*/
|
||||
package ca.uhn.fhir.cr.r4;
|
||||
|
||||
import org.opencds.cqf.cql.evaluator.activitydefinition.r4.ActivityDefinitionProcessor;
|
||||
import org.opencds.cqf.fhir.api.Repository;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.opencds.cqf.fhir.cr.activitydefinition.r4.ActivityDefinitionProcessor;
|
||||
|
||||
@FunctionalInterface
|
||||
public interface IActivityDefinitionProcessorFactory {
|
||||
ActivityDefinitionProcessor create(Repository theRepository);
|
||||
ActivityDefinitionProcessor create(RequestDetails theRequestDetails);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -17,10 +17,12 @@
|
|||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
package ca.uhn.fhir.cr.r4.measure;
|
||||
package ca.uhn.fhir.cr.r4;
|
||||
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.opencds.cqf.fhir.cr.measure.r4.R4CareGapsService;
|
||||
|
||||
import java.util.function.Function;
|
||||
|
||||
public interface ISubmitDataService extends Function<RequestDetails, SubmitDataService> {}
|
||||
@FunctionalInterface
|
||||
public interface ICareGapsServiceFactory {
|
||||
R4CareGapsService create(RequestDetails theRequestDetails);
|
||||
}
|
||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue