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Add changelogs, add patientbulkredaer implementation

This commit is contained in:
Tadgh 2021-03-04 16:53:05 -05:00
parent ff1c6e4d27
commit 2f1518344b
6 changed files with 146 additions and 47 deletions
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1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/SearchParameterUtil.java
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@ -50,6 +50,7 @@ public class SearchParameterUtil {
return retVal;
}
@Nullable
public static String getCode(FhirContext theContext, IBaseResource theResource) {
return getStringChild(theContext, theResource, "code");

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2433-group-bulk-export-support.yaml Normal file
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@ -0,0 +1,5 @@
---
type: add
issue: 2433
title: "Support has been added for MDM expansion during Group bulk export. Calling a group export via `/Group/123/$export?_mdm=true`
will cause Bulk Export to not only match group members, but also any MDM-matched patients, and their related golden record patients"

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2445-support-patient-level-export.yaml Normal file
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@ -0,0 +1,4 @@
---
type: add
issue: 2445
title: "Support has been added for patient type level Bulk export. This can be done via the `/Patient/$export` endpoint."

46
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BaseBulkItemReader.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.bulk.job;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.batch.log.Logs;
@ -53,6 +54,7 @@ public abstract class BaseBulkItemReader implements ItemReader<List<ResourcePers
private RuntimeResourceDefinition myResourceDefinition;
private Iterator<ResourcePersistentId> myPidIterator;
private RuntimeSearchParam myPatientSearchParam;
/**
* Get and cache an ISearchBuilder for the given resource type this partition is responsible for.
@ -137,4 +139,48 @@ public abstract class BaseBulkItemReader implements ItemReader<List<ResourcePers
return outgoing.size() == 0 ? null : outgoing;
}
/**
* Given the resource type, fetch its patient-based search parameter name
* 1. Attempt to find one called 'patient'
* 2. If that fails, find one called 'subject'
* 3. If that fails, find find by Patient Compartment.
* 3.1 If that returns >1 result, throw an error
* 3.2 If that returns 1 result, return it
*/
protected RuntimeSearchParam getPatientSearchParamForCurrentResourceType() {
if (myPatientSearchParam == null) {
RuntimeResourceDefinition runtimeResourceDefinition = myContext.getResourceDefinition(myResourceType);
myPatientSearchParam = runtimeResourceDefinition.getSearchParam("patient");
if (myPatientSearchParam == null) {
myPatientSearchParam = runtimeResourceDefinition.getSearchParam("subject");
if (myPatientSearchParam == null) {
myPatientSearchParam = getRuntimeSearchParamByCompartment(runtimeResourceDefinition);
if (myPatientSearchParam == null) {
String errorMessage = String.format("[%s] has no search parameters that are for patients, so it is invalid for Group Bulk Export!", myResourceType);
throw new IllegalArgumentException(errorMessage);
}
}
}
}
return myPatientSearchParam;
}
/**
* Search the resource definition for a compartment named 'patient' and return its related Search Parameter.
*/
protected RuntimeSearchParam getRuntimeSearchParamByCompartment(RuntimeResourceDefinition runtimeResourceDefinition) {
RuntimeSearchParam patientSearchParam;
List<RuntimeSearchParam> searchParams = runtimeResourceDefinition.getSearchParamsForCompartmentName("Patient");
if (searchParams == null || searchParams.size() == 0) {
String errorMessage = String.format("Resource type [%s] is not eligible for Group Bulk export, as it contains no Patient compartment, and no `patient` or `subject` search parameter", myResourceType);
throw new IllegalArgumentException(errorMessage);
} else if (searchParams.size() == 1) {
patientSearchParam = searchParams.get(0);
} else {
String errorMessage = String.format("Resource type [%s] is not eligible for Group Bulk export, as we are unable to disambiguate which patient search parameter we should be searching by.", myResourceType);
throw new IllegalArgumentException(errorMessage);
}
return patientSearchParam;
}
}

49
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkItemReader.java
View File

@ -173,7 +173,6 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
return expandedIds;
}
private void queryResourceTypeWithReferencesToPatients(List<ResourcePersistentId> myReadPids, List<String> idChunk) {
//Build SP map
//First, inject the _typeFilters and _since from the export job
@ -198,58 +197,14 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
private void filterSearchByResourceIds(List<String> idChunk, SearchParameterMap expandedSpMap) {
ReferenceOrListParam orList = new ReferenceOrListParam();
idChunk.forEach(id -> orList.add(new ReferenceParam(id)));
expandedSpMap.add(getPatientSearchParam().getName(), orList);
expandedSpMap.add(getPatientSearchParamForCurrentResourceType().getName(), orList);
}
private RuntimeSearchParam validateSearchParameters(SearchParameterMap expandedSpMap) {
RuntimeSearchParam runtimeSearchParam = getPatientSearchParam();
RuntimeSearchParam runtimeSearchParam = getPatientSearchParamForCurrentResourceType();
if (expandedSpMap.get(runtimeSearchParam.getName()) != null) {
throw new IllegalArgumentException(String.format("Group Bulk Export manually modifies the Search Parameter called [%s], so you may not include this search parameter in your _typeFilter!", runtimeSearchParam.getName()));
}
return runtimeSearchParam;
}
/**
* Given the resource type, fetch its patient-based search parameter name
* 1. Attempt to find one called 'patient'
* 2. If that fails, find one called 'subject'
* 3. If that fails, find find by Patient Compartment.
* 3.1 If that returns >1 result, throw an error
* 3.2 If that returns 1 result, return it
*/
private RuntimeSearchParam getPatientSearchParam() {
if (myPatientSearchParam == null) {
RuntimeResourceDefinition runtimeResourceDefinition = myContext.getResourceDefinition(myResourceType);
myPatientSearchParam = runtimeResourceDefinition.getSearchParam("patient");
if (myPatientSearchParam == null) {
myPatientSearchParam = runtimeResourceDefinition.getSearchParam("subject");
if (myPatientSearchParam == null) {
myPatientSearchParam = getRuntimeSearchParamByCompartment(runtimeResourceDefinition);
if (myPatientSearchParam == null) {
String errorMessage = String.format("[%s] has no search parameters that are for patients, so it is invalid for Group Bulk Export!", myResourceType);
throw new IllegalArgumentException(errorMessage);
}
}
}
}
return myPatientSearchParam;
}
/**
* Search the resource definition for a compartment named 'patient' and return its related Search Parameter.
*/
private RuntimeSearchParam getRuntimeSearchParamByCompartment(RuntimeResourceDefinition runtimeResourceDefinition) {
RuntimeSearchParam patientSearchParam;
List<RuntimeSearchParam> searchParams = runtimeResourceDefinition.getSearchParamsForCompartmentName("Patient");
if (searchParams == null || searchParams.size() == 0) {
String errorMessage = String.format("Resource type [%s] is not eligible for Group Bulk export, as it contains no Patient compartment, and no `patient` or `subject` search parameter", myResourceType);
throw new IllegalArgumentException(errorMessage);
} else if (searchParams.size() == 1) {
patientSearchParam = searchParams.get(0);
} else {
String errorMessage = String.format("Resource type [%s] is not eligible for Group Bulk export, as we are unable to disambiguate which patient search parameter we should be searching by.", myResourceType);
throw new IllegalArgumentException(errorMessage);
}
return patientSearchParam;
}
}

88
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/PatientBulkItemReader.java Normal file
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@ -0,0 +1,88 @@
package ca.uhn.fhir.jpa.bulk.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 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%
*/
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.batch.log.Logs;
import ca.uhn.fhir.jpa.dao.IResultIterator;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.StringParam;
import org.slf4j.Logger;
import org.springframework.batch.item.ItemReader;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* Bulk Item reader for the Patient Bulk Export job.
* Instead of performing a normal query on the resource type using type filters, we instead
*
* 1. Determine the resourcetype
* 2. Search for anything that has `patient-compartment-search-param:missing=false`
*/
public class PatientBulkItemReader extends BaseBulkItemReader implements ItemReader<List<ResourcePersistentId>> {
private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
private RuntimeSearchParam validateSearchParameters(SearchParameterMap expandedSpMap) {
RuntimeSearchParam runtimeSearchParam = getPatientSearchParamForCurrentResourceType();
if (expandedSpMap.get(runtimeSearchParam.getName()) != null) {
throw new IllegalArgumentException(String.format("Group Bulk Export manually modifies the Search Parameter called [%s], so you may not include this search parameter in your _typeFilter!", runtimeSearchParam.getName()));
}
return runtimeSearchParam;
}
@Override
Iterator<ResourcePersistentId> getResourcePidIterator() {
List<ResourcePersistentId> myReadPids = new ArrayList<>();
//use _typeFilter and _since and all those fancy bits and bobs to generate our basic SP map.
SearchParameterMap map = createSearchParameterMapForJob();
String patientSearchParam = getPatientSearchParamForCurrentResourceType().getName();
//Ensure users did not monkey with the patient compartment search parameter.
validateSearchParameters(map);
//Skip adding the parameter querying for patient= if we are in fact querying the patient resource type.
if (!myResourceType.equalsIgnoreCase("Patient")) {
//Now that we have our basic built Bulk Export SP map, we inject the condition that the resources returned
//must have a patient= or subject= reference set.
map.add(patientSearchParam, new StringParam().setMissing(false));
}
ISearchBuilder sb = getSearchBuilderForLocalResourceType();
IResultIterator myResultIterator = sb.createQuery(map, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
while (myResultIterator.hasNext()) {
myReadPids.add(myResultIterator.next());
}
return myReadPids.iterator();
}
}