de.samply.directory_sync.fhir.FhirApi Maven / Gradle / Ivy
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Syncs Information between the BBMRI-ERIC Biobank Directory and the local bridgehead
package de.samply.directory_sync.fhir;
import static ca.uhn.fhir.rest.api.PreferReturnEnum.OPERATION_OUTCOME;
import static ca.uhn.fhir.rest.api.SummaryEnum.COUNT;
import static java.util.Collections.emptyList;
import static org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.ERROR;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.gclient.ICreateTyped;
import ca.uhn.fhir.rest.gclient.IQuery;
import ca.uhn.fhir.rest.gclient.IUpdateExecutable;
import ca.uhn.fhir.rest.gclient.UriClientParam;
import de.samply.directory_sync.directory.model.BbmriEricId;
import io.vavr.control.Either;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Measure;
import org.hl7.fhir.r4.model.MeasureReport;
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.ResourceType;
import org.hl7.fhir.r4.model.StringType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Provides convenience methods for selected FHIR operations.
*/
public class FhirApi {
private static final String BIOBANK_PROFILE_URI = "https://fhir.bbmri.de/StructureDefinition/Biobank";
private static final String COLLECTION_PROFILE_URI = "https://fhir.bbmri.de/StructureDefinition/Collection";
private static final Logger logger = LoggerFactory.getLogger(FhirApi.class);
/**
* Returns the BBMRI-ERIC identifier of {@code collection} if some valid one could be found.
*
* @param collection the Organization resource, possibly containing a BBMRI-ERIC identifier
* @return the found BBMRI-ERIC identifier or {@link Optional#empty empty}
*/
public static Optional bbmriEricId(Organization collection) {
return collection.getIdentifier().stream()
.filter(i -> "http://www.bbmri-eric.eu/".equals(i.getSystem()))
.findFirst().map(Identifier::getValue).flatMap(BbmriEricId::valueOf);
}
private final IGenericClient fhirClient;
public FhirApi(IGenericClient fhirClient) {
this.fhirClient = Objects.requireNonNull(fhirClient);
}
public OperationOutcome updateResource(IBaseResource theResource) {
try {
return (OperationOutcome) resourceUpdate(theResource).execute().getOperationOutcome();
} catch (Exception e) {
OperationOutcome outcome = new OperationOutcome();
outcome.addIssue().setSeverity(ERROR).setDiagnostics(e.getMessage());
return outcome;
}
}
private IUpdateExecutable resourceUpdate(IBaseResource theResource) {
return fhirClient.update().resource(theResource).prefer(OPERATION_OUTCOME);
}
public Either createResource(IBaseResource resource) {
try {
MethodOutcome outcome = resourceCreate(resource).execute();
if (outcome.getCreated()) {
return Either.right(null);
} else {
return Either.left("error while creating a resource");
}
} catch (Exception e) {
return Either.left(e.getMessage());
}
}
private ICreateTyped resourceCreate(IBaseResource resource) {
return fhirClient.create().resource(resource).prefer(OPERATION_OUTCOME);
}
/**
* Lists all Organization resources with the biobank profile.
*
* @return either a list of {@link Organization} resources or an {@link OperationOutcome} on *
* errors
*/
public Either> listAllBiobanks() {
return listAllOrganizations(BIOBANK_PROFILE_URI)
.map(bundle -> extractOrganizations(bundle, BIOBANK_PROFILE_URI));
}
private Either listAllOrganizations(String profileUri) {
try {
return Either.right((Bundle) fhirClient.search().forResource(Organization.class)
.withProfile(profileUri).execute());
} catch (Exception e) {
OperationOutcome outcome = new OperationOutcome();
outcome.addIssue().setSeverity(ERROR)
.setDiagnostics(e.getMessage());
return Either.left(outcome);
}
}
private static List extractOrganizations(Bundle bundle, String profileUrl) {
return bundle.getEntry().stream()
.map(BundleEntryComponent::getResource)
.filter(r -> r.getResourceType() == ResourceType.Organization)
.filter(r -> r.getMeta().hasProfile(profileUrl))
.map(r -> (Organization) r)
.collect(Collectors.toList());
}
/**
* Lists all Organization resources with the collection profile.
*
* @return either a list of {@link Organization} resources or an {@link OperationOutcome} on
* errors
*/
public Either> listAllCollections() {
return listAllOrganizations(COLLECTION_PROFILE_URI)
.map(bundle -> extractOrganizations(bundle, COLLECTION_PROFILE_URI));
}
/**
* Checks whether a resource of {@code type} and canonical {@code uri} exists.
*
* @param type the resource type
* @param uri the canonical URI
* @return a Right with {@code true} if the resource exists or a Left in case of an error
*/
public Either resourceExists(Class type, String uri) {
logger.debug("Check whether {} with canonical URI {} exists.", type.getSimpleName(), uri);
try {
return Either.right(resourceQuery(type, uri).execute().getTotal() == 1);
} catch (Exception e) {
return Either.left(e.getMessage());
}
}
private IQuery resourceQuery(Class type, String uri) {
return fhirClient.search().forResource(type)
.where(new UriClientParam("url").matches().value(uri))
.summaryMode(COUNT)
.returnBundle(Bundle.class);
}
/**
* Executes the Measure with the given canonical URL.
*
* @param url canonical URL of the Measure to be executed
* @return MeasureReport or OperationOutcome in case of error.
*/
Either evaluateMeasure(String url) {
// Create the input parameters to pass to the server
Parameters inParams = new Parameters();
inParams.addParameter().setName("periodStart").setValue(new DateType("1900"));
inParams.addParameter().setName("periodEnd").setValue(new DateType("2100"));
inParams.addParameter().setName("measure").setValue(new StringType(url));
try {
Parameters outParams = fhirClient
.operation()
.onType(Measure.class)
.named("$evaluate-measure")
.withParameters(inParams)
.useHttpGet()
.execute();
return Either.right((MeasureReport) outParams.getParameter().get(0).getResource());
} catch (Exception e) {
OperationOutcome outcome = new OperationOutcome();
outcome.addIssue().setSeverity(ERROR)
.setDiagnostics(e.getMessage());
return Either.left(outcome);
}
}
/**
* Loads the Organization resource for each of the FHIR ids given.
*
* @param ids logical ids of the Organization resources to load
* @return List of Organization Resources or OperationOutcome in case of failure.
*/
Either> fetchCollections(Set ids) {
if (ids.isEmpty()) {
return Either.right(emptyList());
}
try {
Bundle response = (Bundle) fhirClient.search().forResource(Organization.class)
.where(Organization.RES_ID.exactly().codes(ids)).execute();
return Either.right(response.getEntry().stream()
.filter(e -> ResourceType.Organization == e.getResource().getResourceType())
.map(e -> (Organization) e.getResource())
.collect(Collectors.toList()));
} catch (Exception e) {
OperationOutcome outcome = new OperationOutcome();
outcome.addIssue().setSeverity(ERROR)
.setDiagnostics(e.getMessage());
return Either.left(outcome);
}
}
}