Examples with SubmissionSet org.openehealth.ipf.commons.ihe.xds.core.metadata.SubmissionSet used on opensource projects

Example 1 with SubmissionSet

use of org.openehealth.ipf.commons.ihe.xds.core.metadata.SubmissionSet in project ipf by oehf.

the class RegisterDocumentSetBuilderTest method basicBuilder.

@Test
public void basicBuilder() throws GSSException {
    Identifiable patientID = new Identifiable("id3", new Oid("1.3"));
    SubmissionSet submissionSet = SampleData.createSubmissionSet(patientID);
    submissionSet.setEntryUuid(null);
    submissionSet.setUniqueId(null);
    DocumentEntry document = SampleData.createDocumentEntry(patientID);
    document.setEntryUuid(null);
    document.setUniqueId(null);
    RegisterDocumentSet registerDocuments = RegisterDocumentSet.builderWith(submissionSet).withDocument(document).build();
    assertEquals(0, registerDocuments.getAssociations().size());
    assertNull(submissionSet.getEntryUuid());
    assertEquals(1, registerDocuments.getDocumentEntries().size());
}

Example 2 with SubmissionSet

use of org.openehealth.ipf.commons.ihe.xds.core.metadata.SubmissionSet in project MobileAccessGateway by i4mi.

the class Iti66ResponseConverter method translateToFhir.

/**
 * convert ITI-18 query response to ITI-66 response bundle
 */
@Override
public List<ListResource> translateToFhir(QueryResponse input, Map<String, Object> parameters) {
    ArrayList<ListResource> list = new ArrayList<ListResource>();
    if (input != null && Status.SUCCESS.equals(input.getStatus())) {
        Map<String, ListResource> targetList = new HashMap<String, ListResource>();
        if (input.getSubmissionSets() != null) {
            for (SubmissionSet submissionSet : input.getSubmissionSets()) {
                ListResource documentManifest = new ListResource();
                documentManifest.setId(noUuidPrefix(submissionSet.getEntryUuid()));
                documentManifest.setCode(new CodeableConcept(new Coding("http://profiles.ihe.net/ITI/MHD/CodeSystem/MHDlistTypes", "submissionset", "Submission Set")));
                targetList.put(documentManifest.getId(), documentManifest);
                list.add(documentManifest);
                // limitedMetadata -> meta.profile canonical [0..*]
                if (submissionSet.isLimitedMetadata()) {
                    documentManifest.getMeta().addProfile("http://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Minimal.SubmissionSet");
                } else {
                    documentManifest.getMeta().addProfile("http://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.SubmissionSet");
                }
                // comment -> text Narrative [0..1]
                LocalizedString comments = submissionSet.getComments();
                if (comments != null) {
                    documentManifest.addNote().setText(comments.getValue());
                }
                // uniqueId -> masterIdentifier Identifier [0..1] [1..1]
                if (submissionSet.getUniqueId() != null) {
                    documentManifest.addIdentifier((new Identifier().setUse(IdentifierUse.USUAL).setSystem("urn:ietf:rfc:3986").setValue("urn:oid:" + submissionSet.getUniqueId())));
                }
                // entryUUID -> identifier Identifier [0..*]
                if (submissionSet.getEntryUuid() != null) {
                    documentManifest.addIdentifier((new Identifier().setUse(IdentifierUse.OFFICIAL).setSystem("urn:ietf:rfc:3986").setValue(asUuid(submissionSet.getEntryUuid()))));
                }
                // approved -> status=current Other status values are allowed but are not defined in this mapping to XDS.
                if (AvailabilityStatus.APPROVED.equals(submissionSet.getAvailabilityStatus())) {
                    documentManifest.setStatus(ListResource.ListStatus.CURRENT);
                }
                documentManifest.setMode(ListMode.WORKING);
                // contentTypeCode -> type CodeableConcept [0..1]
                if (submissionSet.getContentTypeCode() != null) {
                    documentManifest.addExtension().setUrl("http://profiles.ihe.net/ITI/MHD/StructureDefinition/ihe-designationType").setValue(transform(submissionSet.getContentTypeCode()));
                }
                // patientId -> subject Reference(Patient| Practitioner| Group| Device) [0..1], Reference(Patient)
                if (submissionSet.getPatientId() != null) {
                    Identifiable patient = submissionSet.getPatientId();
                    documentManifest.setSubject(transformPatient(patient));
                }
                // submissionTime -> created dateTime [0..1]
                if (submissionSet.getSubmissionTime() != null) {
                    documentManifest.setDate(Date.from(submissionSet.getSubmissionTime().getDateTime().toInstant()));
                }
                // authorInstitution, authorPerson, authorRole, authorSpeciality, authorTelecommunication -> author Reference(Practitioner| PractitionerRole| Organization| Device| Patient| RelatedPerson) [0..*]
                if (submissionSet.getAuthors() != null) {
                    for (Author author : submissionSet.getAuthors()) {
                        documentManifest.setSource(transformAuthor(author));
                    }
                }
                // intendedRecipient -> recipient Reference(Patient| Practitioner| PractitionerRole| RelatedPerson| Organization) [0..*]
                List<Recipient> recipients = submissionSet.getIntendedRecipients();
                for (Recipient recipient : recipients) {
                    Organization org = recipient.getOrganization();
                    Person person = recipient.getPerson();
                    ContactPoint contact = transform(recipient.getTelecom());
                    var organization = transform(org);
                    Practitioner practitioner = transformPractitioner(person);
                    if (organization != null && practitioner == null) {
                        if (contact != null)
                            organization.addTelecom(contact);
                        documentManifest.addExtension().setUrl("http://profiles.ihe.net/ITI/MHD/StructureDefinition/ihe-intendedRecipient").setValue(new Reference().setResource(organization));
                    } else if (organization != null && practitioner != null) {
                        PractitionerRole role = new PractitionerRole();
                        role.setPractitioner((Reference) new Reference().setResource(practitioner));
                        role.setOrganization((Reference) new Reference().setResource(organization));
                        if (contact != null)
                            role.addTelecom(contact);
                        documentManifest.addExtension().setUrl("http://profiles.ihe.net/ITI/MHD/StructureDefinition/ihe-intendedRecipient").setValue(new Reference().setResource(role));
                    } else if (organization == null && practitioner != null) {
                    // May be a patient, related person or practitioner
                    }
                }
                // sourceId -> source uri [0..1] [1..1]
                if (submissionSet.getSourceId() != null) {
                    documentManifest.addExtension().setUrl("http://profiles.ihe.net/ITI/MHD/StructureDefinition/ihe-sourceId").setValue(new Identifier().setValue("urn:oid:" + submissionSet.getSourceId()));
                }
                // title -> description string [0..1]
                LocalizedString title = submissionSet.getTitle();
                if (title != null) {
                    documentManifest.setTitle(title.getValue());
                }
            }
        }
        if (input.getAssociations() != null) {
            for (Association ass : input.getAssociations()) {
                AssociationType tt = ass.getAssociationType();
                String source = ass.getSourceUuid();
                String target = ass.getTargetUuid();
                if (tt == AssociationType.HAS_MEMBER) {
                    ListResource s = targetList.get(noUuidPrefix(source));
                    if (s != null) {
                        s.addEntry().setItem(new Reference().setReference("DocumentReference/" + noUuidPrefix(target)));
                    }
                }
            }
        }
    } else {
        processError(input);
    }
    return list;
}

Example 3 with SubmissionSet

use of org.openehealth.ipf.commons.ihe.xds.core.metadata.SubmissionSet in project ipf by oehf.

the class RegisterDocumentSetBuilderTest method supportiveBuilder.

@Test
public void supportiveBuilder() throws GSSException {
    Identifiable patientID = new Identifiable("id3", new Oid("1.3"));
    SubmissionSet submissionSet = SampleData.createSubmissionSet(patientID);
    submissionSet.setEntryUuid(null);
    submissionSet.setUniqueId(null);
    submissionSet.setSubmissionTime((String) null);
    DocumentEntry document = SampleData.createDocumentEntry(patientID);
    document.setEntryUuid(null);
    document.setUniqueId(null);
    Folder folder1 = SampleData.createFolder(patientID);
    folder1.setEntryUuid(null);
    folder1.setUniqueId(null);
    Folder folder2 = SampleData.createFolder(patientID);
    folder2.setEntryUuid("lol");
    folder2.setUniqueId("2.999.2.3.4");
    RegisterDocumentSet registerDocuments = RegisterDocumentSet.supportiveBuilderWith(submissionSet).withDocument(document).withFolders(List.of(folder1, folder2)).build();
    assertEquals(3, registerDocuments.getAssociations().size(), "Expecting 3 Association to be created");
    assertEquals(2, registerDocuments.getFolders().size());
    assertEquals(1, registerDocuments.getDocumentEntries().size());
    assertNotNull(submissionSet.getEntryUuid());
    assertNotNull(submissionSet.getSubmissionTime());
    assertNotNull(folder1.getEntryUuid());
    assertNotNull(document.getEntryUuid());
    assertNotNull(submissionSet.getUniqueId());
    assertNotNull(folder1.getUniqueId());
    assertNotNull(document.getUniqueId());
    assertEquals("lol", folder2.getEntryUuid());
    assertEquals("2.999.2.3.4", folder2.getUniqueId());
}

Example 4 with SubmissionSet

use of org.openehealth.ipf.commons.ihe.xds.core.metadata.SubmissionSet in project MobileAccessGateway by i4mi.

the class Iti65RequestConverter method convert.

/**
 * convert ITI-65 to ITI-41 request
 * @param requestBundle
 * @return
 */
public ProvideAndRegisterDocumentSet convert(@Body Bundle requestBundle) {
    SubmissionSet submissionSet = new SubmissionSet();
    ProvideAndRegisterDocumentSetBuilder builder = new ProvideAndRegisterDocumentSetBuilder(true, submissionSet);
    // create mapping fullUrl -> resource for each resource in bundle
    Map<String, Resource> resources = new HashMap<String, Resource>();
    ListResource manifestNeu = null;
    for (Bundle.BundleEntryComponent requestEntry : requestBundle.getEntry()) {
        Resource resource = requestEntry.getResource();
        /*if (resource instanceof DocumentManifest) {
            	manifest = (DocumentManifest) resource;            	
            } else*/
        if (resource instanceof DocumentReference) {
            resources.put(requestEntry.getFullUrl(), resource);
        } else if (resource instanceof ListResource) {
            manifestNeu = (ListResource) resource;
        // resources.put(requestEntry.getFullUrl(), resource);
        } else if (resource instanceof Binary) {
            resources.put(requestEntry.getFullUrl(), resource);
        } else {
            throw new IllegalArgumentException(resource + " is not allowed here");
        }
    }
    /*if (manifest != null) {
		  processDocumentManifest(manifest, submissionSet);
	    } else {*/
    processDocumentManifest(manifestNeu, submissionSet);
    // set limited metadata
    for (CanonicalType profile : requestBundle.getMeta().getProfile()) {
        if ("http://ihe.net/fhir/StructureDefinition/IHE_MHD_Provide_Comprehensive_DocumentBundle".equals(profile.getValue())) {
            submissionSet.setLimitedMetadata(false);
        } else if ("http://ihe.net/fhir/StructureDefinition/IHE_MHD_Provide_Minimal_DocumentBundle".equals(profile.getValue())) {
            submissionSet.setLimitedMetadata(true);
        } else if ("http://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.ProvideBundle".equals(profile.getValue())) {
            submissionSet.setLimitedMetadata(false);
        } else if ("http://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Minimal.ProvideBundle".equals(profile.getValue())) {
            submissionSet.setLimitedMetadata(true);
        }
    }
    // process all resources referenced in DocumentManifest.content
    for (ListEntryComponent listEntry : manifestNeu.getEntry()) {
        Reference content = listEntry.getItem();
        String refTarget = content.getReference();
        Resource resource = resources.get(refTarget);
        if (resource instanceof DocumentReference) {
            DocumentReference documentReference = (DocumentReference) resource;
            Document doc = new Document();
            DocumentEntry entry = new DocumentEntry();
            processDocumentReference(documentReference, entry);
            doc.setDocumentEntry(entry);
            entry.setRepositoryUniqueId(config.getRepositoryUniqueId());
            // create associations
            for (DocumentReferenceRelatesToComponent relatesTo : documentReference.getRelatesTo()) {
                Reference target = relatesTo.getTarget();
                DocumentRelationshipType code = relatesTo.getCode();
                Association association = new Association();
                switch(code) {
                    case REPLACES:
                        association.setAssociationType(AssociationType.REPLACE);
                        break;
                    case TRANSFORMS:
                        association.setAssociationType(AssociationType.TRANSFORM);
                        break;
                    case SIGNS:
                        association.setAssociationType(AssociationType.SIGNS);
                        break;
                    case APPENDS:
                        association.setAssociationType(AssociationType.APPEND);
                        break;
                    default:
                }
                association.setSourceUuid(entry.getEntryUuid());
                association.setTargetUuid(transformUriFromReference(target));
                builder.withAssociation(association);
            }
            // get binary content from attachment.data or from referenced Binary resource
            Attachment attachment = documentReference.getContentFirstRep().getAttachment();
            if (attachment.hasData()) {
                doc.setDataHandler(new DataHandler(new ByteArrayDataSource(attachment.getData(), attachment.getContentType())));
                byte[] decoded = attachment.getData();
                entry.setSize((long) decoded.length);
                entry.setHash(SHAsum(decoded));
            } else if (attachment.hasUrl()) {
                String contentURL = attachment.getUrl();
                Resource binaryContent = resources.get(contentURL);
                if (binaryContent instanceof Binary) {
                    String contentType = attachment.getContentType();
                    Binary binary = (Binary) binaryContent;
                    if (binary.hasContentType() && !binary.getContentType().equals(contentType))
                        throw new InvalidRequestException("ContentType in Binary and in DocumentReference must match");
                    doc.setDataHandler(new DataHandler(new ByteArrayDataSource(binary.getData(), contentType)));
                    byte[] decoded = binary.getData();
                    entry.setSize((long) decoded.length);
                    entry.setHash(SHAsum(decoded));
                    Identifier masterIdentifier = documentReference.getMasterIdentifier();
                    binary.setUserData("masterIdentifier", noPrefix(masterIdentifier.getValue()));
                }
            }
            builder.withDocument(doc);
        }
    }
    return builder.build();
}