org.projecthusky.communication.xdsmhdconversion.converters.DocumentEntryConverter Maven / Gradle / Ivy
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/*
* This code is made available under the terms of the Eclipse Public License v1.0
* in the github project https://github.com/project-husky/husky there you also
* find a list of the contributors and the license information.
*
* This project has been developed further and modified by the joined working group Husky
* on the basis of the eHealth Connector opensource project from June 28, 2021,
* whereas medshare GmbH is the initial and main contributor/author of the eHealth Connector.
*
*/
package org.projecthusky.communication.xdsmhdconversion.converters;
import org.apache.commons.codec.DecoderException;
import org.apache.commons.codec.binary.Hex;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.DocumentReference.DocumentReferenceContentComponent;
import org.hl7.fhir.r4.model.DocumentReference.DocumentReferenceContextComponent;
import org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus;
import org.hl7.fhir.r4.model.Identifier.IdentifierUse;
import org.projecthusky.common.utils.XdsMetadataUtil;
import org.projecthusky.communication.xdsmhdconversion.utils.ConverterUtils;
import org.openehealth.ipf.commons.ihe.xds.core.metadata.*;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.time.ZoneId;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
/**
* A converter between XDS' DocumentEntry and MHD's DocumentReference.
*
* @author Quentin Ligier
* @see DocumentEntry Attributes
* @see Resource
* Profile: MHD DocumentReference Comprehensive
* @see Resource
* Profile: CH MHD DocumentReference Comprehensive
**/
public class DocumentEntryConverter {
/**
* Constructor.
*/
private DocumentEntryConverter() {}
/**
* Convert an XDS DocumentEntry to an MHD DocumentReference.
*
* @param documentEntry The XDS DocumentEntry to convert.
* @return the equivalent MHD DocumentReference.
*/
public static DocumentReference convertDocumentEntry(final DocumentEntry documentEntry) {
final DocumentReference documentReference = new DocumentReference();
documentReference.setId(ConverterUtils.removePrefixUuid(documentEntry.getEntryUuid()));
// profile | DocumentEntry.limitedMetadata
if (documentEntry.isLimitedMetadata()) {
documentReference.getMeta().addProfile("http://ihe.net/fhir/ihe.mhd.fhir/StructureDefinition/IHE.MHD.Query.Comprehensive.DocumentReference");
} else {
documentReference.getMeta().addProfile("http://ihe.net/fhir/ihe.mhd.fhir/StructureDefinition/IHE.MHD.Comprehensive.DocumentManifest");
}
// masterIdentifier | DocumentEntry.uniqueId
if (documentEntry.getUniqueId() != null) {
final var masterId = new Identifier().setValue(documentEntry.getUniqueId());
documentReference.setMasterIdentifier(masterId);
}
// identifier | DocumentEntry.entryUUID
if (documentEntry.getEntryUuid() != null) {
final var id = new Identifier()
.setSystem("urn:ietf:rfc:3986")
.setValue(ConverterUtils.addPrefixUuid(documentEntry.getEntryUuid()))
.setUse(IdentifierUse.OFFICIAL);
documentReference.addIdentifier(id);
}
// status | DocumentEntry.availabilityStatus
final var status = switch (documentEntry.getAvailabilityStatus()) {
case APPROVED -> DocumentReferenceStatus.CURRENT;
case DEPRECATED -> DocumentReferenceStatus.SUPERSEDED;
default -> null;
};
if (status != null) documentReference.setStatus(status);
// type | DocumentEntry.typeCode
if (documentEntry.getTypeCode() != null) {
documentReference.setType(ConverterUtils.toCodeableConcept(documentEntry.getTypeCode()));
}
// category | DocumentEntry.classCode
if (documentEntry.getClassCode() != null) {
documentReference.addCategory(ConverterUtils.toCodeableConcept(documentEntry.getClassCode()));
}
// subject | DocumentEntry.patientId
if (documentEntry.getPatientId() != null) {
documentReference.setSubject(ConverterUtils.toPatientReference(documentEntry.getPatientId()));
}
// author | DocumentEntry.author
if (documentEntry.getAuthors() != null) {
for (Author author : documentEntry.getAuthors()) {
documentReference.addAuthor(ConverterUtils.toReference(author));
}
}
// authenticator | DocumentEntry.legalAuthenticator
if (documentEntry.getLegalAuthenticator() != null) {
final var practitioner = ConverterUtils.toPractitioner(documentEntry.getLegalAuthenticator());
documentReference.setAuthenticator((Reference) new Reference().setResource(practitioner));
}
// description | DocumentEntry.comments
if (documentEntry.getComments() != null) {
documentReference.setDescription(documentEntry.getComments().getValue());
}
// securityLabel | DocumentEntry.confidentialityCode
if (documentEntry.getConfidentialityCodes() != null) {
documentReference.addSecurityLabel(ConverterUtils.toCodeableConcept(documentEntry.getConfidentialityCodes()));
}
// content
final DocumentReferenceContentComponent content = documentReference.addContent();
/// attachment
final Attachment attachment = new Attachment();
content.setAttachment(attachment);
//// contentType | DocumentEntry.mimeType
if (documentEntry.getMimeType() != null) {
attachment.setContentType(documentEntry.getMimeType());
}
//// language | DocumentEntry.languageCode
if (documentEntry.getLanguageCode() != null) {
attachment.setLanguage(documentEntry.getLanguageCode());
}
//// url | DocumentEntry.repositoryUniqueId or DocumentEntry.URI
if (documentEntry.getUri() != null) {
try {
attachment.setUrl(new URI(documentEntry.getUri()).toURL().toString());
if (documentEntry.getRepositoryUniqueId() != null) {
final var url = String.format("%s&repositoryUniqueId=%s", attachment.getUrl(), documentEntry.getRepositoryUniqueId());
attachment.setUrl(url);
}
} catch (URISyntaxException | MalformedURLException ignored) {}
}
//// size | DocumentEntry.size
if (documentEntry.getSize() != null) {
attachment.setSize(documentEntry.getSize().intValue());
}
//// hash | DocumentEntry.hash
if (documentEntry.getHash() != null) {
try {
attachment.setHash(Hex.decodeHex(documentEntry.getHash()));
} catch (DecoderException ignored) {}
}
//// title | DocumentEntry.title
if (documentEntry.getTitle() != null) {
attachment.setTitle(documentEntry.getTitle().getValue());
}
//// creation | DocumentEntry.creationTime
if (documentEntry.getCreationTime() != null) {
attachment.setCreation(XdsMetadataUtil.convertDtmStringToDate(documentEntry.getCreationTime().toHL7()));
}
/// format | DocumentEntry.formatCode
if (documentEntry.getFormatCode() != null) {
content.setFormat(ConverterUtils.toCoding(documentEntry.getFormatCode()));
}
// context
final var context = new DocumentReferenceContextComponent();
documentReference.setContext(context);
/// event | Document.eventCodeList
if (documentEntry.getEventCodeList() != null) {
documentReference.getContext().setEvent(ConverterUtils.toListCodeableConcept(documentEntry.getEventCodeList()));
}
/// period
if (documentEntry.getServiceStartTime() != null || documentEntry.getServiceStopTime() != null) {
Period period = new Period();
//// start | DocumentEntry.serviceStartTime
period.setStartElement(ConverterUtils.toDateTimeType(documentEntry.getServiceStartTime()));
//// stop | DocumentEntry.serviceStopTime
period.setEndElement(ConverterUtils.toDateTimeType(documentEntry.getServiceStopTime()));
documentReference.getContext().setPeriod(period);
}
/// facilityType | DocumentEntry.healthcareFacilityTypeCode
if (documentEntry.getHealthcareFacilityTypeCode() != null) {
context.setFacilityType(ConverterUtils.toCodeableConcept(documentEntry.getHealthcareFacilityTypeCode()));
}
/// practiceSetting | DocumentEntry.practiceSettingCode
if (documentEntry.getPracticeSettingCode() != null) {
context.setPracticeSetting(ConverterUtils.toCodeableConcept(documentEntry.getPracticeSettingCode()));
}
/// sourcePatientInfo
final Patient sourcePatient = ConverterUtils.toPatient(documentEntry.getSourcePatientId(), documentEntry.getSourcePatientInfo());
if (sourcePatient != null) {
context.getSourcePatientInfo().setResource(sourcePatient);
}
/// related | DocumentEntry.referenceIdList
final List refIds = documentEntry.getReferenceIdList();
if (refIds != null) {
for (ReferenceId refId : refIds) {
context.getRelated().add(ConverterUtils.toReference(refId));
}
}
return documentReference;
}
/**
* Convert an MHD DocumentReference to an XDS DocumentEntry.
*
* @param documentReference The MHD DocumentReference to convert.
* @return the equivalent XDS DocumentEntry.
*/
public static DocumentEntry convertDocumentReference(final DocumentReference documentReference) {
final var documentEntry = new DocumentEntry();
// profile | DocumentEntry.limitedMetadata
// No action
// masterIdentifier | DocumentEntry.uniqueId
documentEntry.setUniqueId(documentReference.getMasterIdentifier().getValue());
// identifier | DocumentEntry.entryUUID
if (documentReference.hasId()) {
documentEntry.setEntryUuid(documentReference.getId());
} else {
documentEntry.assignEntryUuid();
documentReference.setId(documentEntry.getEntryUuid());
}
// status | DocumentEntry.availabilityStatus
final AvailabilityStatus status = switch (documentReference.getStatus()) {
case CURRENT -> AvailabilityStatus.APPROVED;
case SUPERSEDED -> AvailabilityStatus.DEPRECATED;
default -> null;
};
if (status != null) {
documentEntry.setAvailabilityStatus(status);
}
// type | DocumentEntry.typeCode
documentEntry.setTypeCode(ConverterUtils.toCode(documentReference.getType(), documentReference.getLanguage()));
// category | DocumentEntry.classCode
documentEntry.setClassCode(ConverterUtils.toCode(documentReference.getCategory(), documentReference.getLanguage()));
// subject | DocumentEntry.patientId
documentEntry.setPatientId(ConverterUtils.toIdentifiable(documentReference.getSubject(), documentReference.getContained()));
// author | DocumentEntry.author
for (Reference authorRef : documentReference.getAuthor()) {
documentEntry.getAuthors().add(ConverterUtils.toAuthor(authorRef, documentReference.getContained(), null, documentReference.getLanguage()));
}
// authenticator | DocumentEntry.legalAuthenticator
if (documentReference.hasAuthenticator()) {
Resource authenticator = ConverterUtils.findResource(documentReference.getAuthenticator(), documentReference.getContained());
if (authenticator instanceof PractitionerRole practitionerRole) {
authenticator = ConverterUtils.findResource(practitionerRole.getPractitioner(), documentReference.getContained());
}
if (authenticator instanceof Practitioner practitioner) {
documentEntry.setLegalAuthenticator(ConverterUtils.toPerson(practitioner));
}
}
// description | DocumentEntry.comments
if (documentReference.hasDescription()) {
documentEntry.setComments(ConverterUtils.getLocalizedString(documentReference.getDescription(), documentReference.getLanguage()));
}
// securityLabel | DocumentEntry.confidentialityCode
final List confidentialityCode = ConverterUtils.toCodes(documentReference.getSecurityLabel(), documentReference.getLanguage());
if (confidentialityCode != null && !confidentialityCode.isEmpty()) {
documentEntry.getConfidentialityCodes().addAll(confidentialityCode);
}
// content
final DocumentReferenceContentComponent content = documentReference.getContentFirstRep();
if (content != null && content.hasAttachment()) {
/// attachment
final Attachment attachment = content.getAttachment();
//// contentType | DocumentEntry.mimeType
documentEntry.setMimeType(attachment.getContentType());
//// language | DocumentEntry.languageCode
documentEntry.setLanguageCode(attachment.getLanguage());
//// url | DocumentEntry.repositoryUniqueId or DocumentEntry.URI
if (attachment.hasUrl()) {
if (ConverterUtils.isOid(attachment.getUrl())) {
documentEntry.setRepositoryUniqueId(attachment.getUrl());
} else {
try {
documentEntry.setUri(new URL(attachment.getUrl()).toURI().toString());
} catch (MalformedURLException | URISyntaxException ignored) {}
}
}
//// size | DocumentEntry.size
if (attachment.hasSize()) {
documentEntry.setSize((long) attachment.getSize());
}
//// hash | DocumentEntry.hash
if (attachment.hasHash()) {
documentEntry.setHash(Hex.encodeHexString(attachment.getHash()));
}
//// title | DocumentEntry.title
if (attachment.hasTitle()) {
documentEntry.setTitle(ConverterUtils.getLocalizedString(attachment.getTitle(), attachment.getLanguage()));
}
//// creation | DocumentEntry.creationTime
if (attachment.hasCreation()) {
documentEntry.setCreationTime(new Timestamp(
attachment.getCreation().toInstant().atZone(ZoneId.systemDefault()),
Timestamp.Precision.SECOND)
);
}
}
/// format | DocumentEntry.formatCode
if (content != null && content.hasFormat()) {
documentEntry.setFormatCode(ConverterUtils.toCode(content.getFormat(), documentReference.getLanguage()));
}
// context
final DocumentReferenceContextComponent context = documentReference.getContext();
/// event | DocumentEntry.eventCodeList
final List eventCodeList = ConverterUtils.toCodes(context.getEvent(), documentReference.getLanguage());
if (eventCodeList != null && !eventCodeList.isEmpty()) {
documentEntry.getEventCodeList().addAll(eventCodeList);
}
/// period
if (context.hasPeriod()) {
documentEntry.setServiceStartTime(
new Timestamp(
context.getPeriod().getStart().toInstant().atZone(ZoneId.systemDefault()),
Timestamp.Precision.SECOND)
);
documentEntry.setServiceStopTime(
new Timestamp(
context.getPeriod().getEnd().toInstant().atZone(ZoneId.systemDefault()),
Timestamp.Precision.SECOND)
);
}
/// facilityType | DocumentEntry.healthcareFacilityTypeCode
documentEntry.setHealthcareFacilityTypeCode(ConverterUtils.toCode(context.getFacilityType(), documentReference.getLanguage()));
/// practiceSetting | DocumentEntry.practiceSettingCode
documentEntry.setPracticeSettingCode(ConverterUtils.toCode(context.getPracticeSetting(), documentReference.getLanguage()));
/// sourcePatientInfo
if (context.hasSourcePatientInfo()) {
documentEntry.setSourcePatientId(ConverterUtils.toIdentifiable(context.getSourcePatientInfo(), documentReference.getContained()));
documentEntry.setSourcePatientInfo(ConverterUtils.toPatientInfo(context.getSourcePatientInfo(), documentReference.getContained()));
}
/// related | DocumentEntry.referenceIdList
for (Reference ref : context.getRelated()) {
final Identifiable refId = ConverterUtils.toIdentifiable(ref, documentReference.getContained());
if (refId != null) {
documentEntry.getReferenceIdList().add(ConverterUtils.toReferenceId(refId));
}
}
documentEntry.setExtraMetadata(new HashMap<>());
// originalProviderRole
final Extension originalRole = documentReference.getExtensionByUrl("http://fhir.ch/ig/ch-epr-mhealth/StructureDefinition/ch-ext-author-authorrole");
if (originalRole != null && originalRole.getValue() instanceof final Coding coding) {
documentEntry.setExtraMetadata(
Collections.singletonMap(
"urn:e-health-suisse:2020:originalProviderRole",
Collections.singletonList(String.format("%s^^^&%s&ISO", coding.getCode(), ConverterUtils.removePrefixOid(coding.getSystem())))
)
);
}
// deletionStatus
final Extension deletionStatus = documentReference.getExtensionByUrl("http://fhir.ch/ig/ch-epr-mhealth/StructureDefinition/ch-ext-deletionstatus");
if (deletionStatus != null && deletionStatus.getValue() instanceof Coding coding) {
documentEntry.setExtraMetadata(
Collections.singletonMap(
"urn:e-health-suisse:2019:deletionStatus",
Collections.singletonList("urn:e-health-suisse:2019:deletionStatus:" + coding.getCode())
)
);
}
return documentEntry;
}
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