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Merge remote-tracking branch 'origin/hotfix/40_fix-documentreference-…
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…search'

* origin/hotfix/40_fix-documentreference-search:
  filter document references by author after search
  • Loading branch information
@wetret
wetret committed Feb 18, 2025
2 parents 083c468 + 5ecfb84 commit 76ad164
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Showing 3 changed files with 58 additions and 22 deletions.
2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

<groupId>de.medizininformatik-initiative</groupId>
<artifactId>mii-process-data-transfer</artifactId>
<version>1.0.3.0</version>
<version>1.0.3.1</version>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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4 changes: 2 additions & 2 deletions ...dizininformatik_initiative/process/data_transfer/DataTransferProcessPluginDefinition.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@

public class DataTransferProcessPluginDefinition implements ProcessPluginDefinition
{
public static final String VERSION = "1.0.3.0";
public static final LocalDate RELEASE_DATE = LocalDate.of(2024, 11, 8);
public static final String VERSION = "1.0.3.1";
public static final LocalDate RELEASE_DATE = LocalDate.of(2025, 2, 18);

@Override
public String getName()
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74 changes: 55 additions & 19 deletions src/main/java/de/medizininformatik_initiative/process/data_transfer/service/InsertData.java
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Original file line number Diff line number Diff line change
@@ -1,16 +1,15 @@
package de.medizininformatik_initiative.process.data_transfer.service;

import static java.util.stream.Collectors.toList;

import java.util.ArrayList;
import java.util.List;
import java.util.Objects;

import org.camunda.bpm.engine.delegate.BpmnError;
import org.camunda.bpm.engine.delegate.DelegateExecution;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.DocumentReference;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.ResourceType;
import org.hl7.fhir.r4.model.Task;
Expand Down Expand Up @@ -110,7 +109,7 @@ private List<IdType> storeData(FhirClient fhirClient, Bundle bundle, String send

List<IdType> idsOfCreatedResources = stored.getEntry().stream().filter(Bundle.BundleEntryComponent::hasResponse)
.map(Bundle.BundleEntryComponent::getResponse).map(Bundle.BundleEntryResponseComponent::getLocation)
.map(IdType::new).map(id -> setIdBase(id, fhirClient)).collect(toList());
.map(IdType::new).map(this::setIdBase).toList();

idsOfCreatedResources.stream().filter(i -> ResourceType.DocumentReference.name().equals(i.getResourceType()))
.forEach(i -> addOutputToStartTask(variables, i));
Expand All @@ -123,32 +122,29 @@ private List<IdType> storeData(FhirClient fhirClient, Bundle bundle, String send
private Bundle checkAndAdaptBundleForExistingData(FhirClient fhirClient, Bundle bundle, String sendingOrganization,
String projectIdentifier, Task task)
{
Bundle searchResult = fhirClient.getGenericFhirClient().search().forResource(DocumentReference.class)
.where(DocumentReference.IDENTIFIER.exactly()
.systemAndCode(ConstantsBase.NAMINGSYSTEM_MII_PROJECT_IDENTIFIER, projectIdentifier))
.and(DocumentReference.AUTHOR.hasChainedProperty(Organization.IDENTIFIER.exactly()
.systemAndCode(NamingSystems.OrganizationIdentifier.SID, sendingOrganization)))
.returnBundle(Bundle.class).execute();

List<DocumentReference> existingDocumentReferences = searchResult.getEntry().stream()
.filter(Bundle.BundleEntryComponent::hasResource).map(Bundle.BundleEntryComponent::getResource)
.filter(r -> r instanceof DocumentReference).map(r -> (DocumentReference) r).toList();
List<DocumentReference> existingDocumentReferences = searchExistingDocumentReferences(fhirClient,
sendingOrganization, projectIdentifier, task.getId());

if (existingDocumentReferences.size() < 1)
{
logger.info(
"DocumentReference for project-identifier '{}' authored by '{}' does not yet exist, creating a new data-set on FHIR server with baseUrl '{}' in Task with id '{}'",
projectIdentifier, sendingOrganization, fhirClient.getFhirBaseUrl(), task.getId());
return bundle;
}

if (existingDocumentReferences.size() > 1)
logger.warn(
"Found more than one DocumentReference for project-identifier '{}' authored by '{}', using the first",
projectIdentifier, sendingOrganization);

DocumentReference existingDocumentReference = existingDocumentReferences.get(0);
String existingDocumentReferenceId = existingDocumentReference.getIdElement().getIdPart();

logger.info(
"DocumentReference for project-identifier '{}' authored by '{}' already exists, updating data-set on FHIR server with baseUrl '{}' in Task with id '{}'",
projectIdentifier, sendingOrganization, fhirClient.getFhirBaseUrl(), task.getId());

DocumentReference existingDocumentReference = existingDocumentReferences.get(0);
String existingDocumentReferenceId = existingDocumentReference.getIdElement().getIdPart();

bundle.getEntry().stream().filter(Bundle.BundleEntryComponent::hasResource)
.filter(e -> e.getResource() instanceof DocumentReference)
.filter(Bundle.BundleEntryComponent::hasRequest).filter(Bundle.BundleEntryComponent::hasResource)
Expand All @@ -162,6 +158,46 @@ private Bundle checkAndAdaptBundleForExistingData(FhirClient fhirClient, Bundle
return bundle;
}

private List<DocumentReference> searchExistingDocumentReferences(FhirClient fhirClient, String sendingOrganization,
String projectIdentifier, String taskId)
{
// workaround since not all fhir server used in MII support DocumentReference.author:identifier or
// DocumentReference.author:Organization.identifier search parameters. Therefore filtering for author
// after loading all DocumentReferences for given project-identifier
try
{
List<Bundle.BundleEntryComponent> entries = new ArrayList<>();

Bundle searchResult = fhirClient.getGenericFhirClient().search().forResource(DocumentReference.class)
.where(DocumentReference.IDENTIFIER.exactly()
.systemAndCode(ConstantsBase.NAMINGSYSTEM_MII_PROJECT_IDENTIFIER, projectIdentifier))
.returnBundle(Bundle.class).execute();
entries.addAll(searchResult.getEntry());

while (searchResult.getLink(IBaseBundle.LINK_NEXT) != null)
{
searchResult = fhirClient.getGenericFhirClient().loadPage().next(searchResult).execute();
entries.addAll(searchResult.getEntry());
}

return entries.stream().filter(Bundle.BundleEntryComponent::hasResource)
.map(Bundle.BundleEntryComponent::getResource).filter(r -> r instanceof DocumentReference)
.map(r -> (DocumentReference) r)
.filter(d -> d.getAuthor().stream().anyMatch(a -> a.hasIdentifier()
&& NamingSystems.OrganizationIdentifier.SID.equals(a.getIdentifier().getSystem())
&& sendingOrganization != null && sendingOrganization.equals(a.getIdentifier().getValue())))
.toList();
}
catch (Exception exception)
{
logger.warn(
"Error while searching for existing DocumentReferences for project-identifier '{}' authored by '{}' on FHIR server with baseUrl '{}' in Task with id '{}'- {}",
projectIdentifier, sendingOrganization, fhirClient.getFhirBaseUrl(), taskId,
exception.getMessage());
return List.of();
}
}

private void sendMail(Task task, List<IdType> createdIds, String sendingOrganization, String projectIdentifier)
{
String subject = "New data-set received in process '" + ConstantsDataTransfer.PROCESS_NAME_FULL_DATA_RECEIVE
Expand All @@ -178,9 +214,9 @@ private void sendMail(Task task, List<IdType> createdIds, String sendingOrganiza
api.getMailService().send(subject, message.toString());
}

private IdType setIdBase(IdType idType, FhirClient fhirClient)
private IdType setIdBase(IdType idType)
{
String fhirBaseUrl = fhirClient.getFhirBaseUrl();
String fhirBaseUrl = fhirClientFactory.getFhirClient().getFhirBaseUrl();
return new IdType(fhirBaseUrl, idType.getResourceType(), idType.getIdPart(), idType.getVersionIdPart());
}

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