Examples with Activity org.orcid.jaxb.model.record_rc2.Activity used on opensource projects

Example 6 with Activity

use of org.orcid.jaxb.model.record_rc2.Activity in project kie-wb-common by kiegroup.

the class Bpmn2JsonUnmarshaller method setCatchEventsInfo.

public void setCatchEventsInfo(FlowElementsContainer container, Definitions def, List<Signal> toAddSignals, Set<Error> toAddErrors, Set<Escalation> toAddEscalations, Set<Message> toAddMessages, Set<ItemDefinition> toAddItemDefinitions) {
    List<FlowElement> flowElements = container.getFlowElements();
    for (FlowElement fe : flowElements) {
        if (fe instanceof CatchEvent) {
            if (((CatchEvent) fe).getEventDefinitions().size() > 0) {
                EventDefinition ed = ((CatchEvent) fe).getEventDefinitions().get(0);
                if (ed instanceof SignalEventDefinition) {
                    SignalEventDefinition sed = (SignalEventDefinition) ed;
                    if (sed.getSignalRef() != null && sed.getSignalRef().length() > 0) {
                        String signalRef = sed.getSignalRef();
                        boolean shouldAddSignal = true;
                        List<RootElement> rootElements = def.getRootElements();
                        for (RootElement re : rootElements) {
                            if (re instanceof Signal) {
                                if (((Signal) re).getName().equals(signalRef)) {
                                    shouldAddSignal = false;
                                    break;
                                }
                            }
                        }
                        if (toAddSignals != null) {
                            for (Signal s : toAddSignals) {
                                if (s.getName().equals(signalRef)) {
                                    shouldAddSignal = false;
                                    break;
                                }
                            }
                        }
                        if (shouldAddSignal) {
                            Signal signal = Bpmn2Factory.eINSTANCE.createSignal();
                            signal.setName(signalRef);
                            toAddSignals.add(signal);
                        }
                    }
                } else if (ed instanceof ErrorEventDefinition) {
                    String errorCode = null;
                    String errorId = null;
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("erefname")) {
                            errorId = (String) entry.getValue();
                            errorCode = (String) entry.getValue();
                        }
                    }
                    Error err = this._errors.get(errorCode);
                    if (err == null) {
                        err = Bpmn2Factory.eINSTANCE.createError();
                        err.setId(errorId);
                        err.setErrorCode(errorCode);
                        this._errors.put(errorCode, err);
                    }
                    toAddErrors.add(err);
                    ((ErrorEventDefinition) ed).setErrorRef(err);
                } else if (ed instanceof EscalationEventDefinition) {
                    String escalationCode = null;
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("esccode")) {
                            escalationCode = (String) entry.getValue();
                            break;
                        }
                    }
                    Escalation escalation = this._escalations.get(escalationCode);
                    if (escalation == null) {
                        escalation = Bpmn2Factory.eINSTANCE.createEscalation();
                        escalation.setEscalationCode(escalationCode);
                        this._escalations.put(escalationCode, escalation);
                    }
                    toAddEscalations.add(escalation);
                    ((EscalationEventDefinition) ed).setEscalationRef(escalation);
                } else if (ed instanceof MessageEventDefinition) {
                    ((MessageEventDefinition) ed).setMessageRef(extractMessage(ed, toAddMessages, toAddItemDefinitions));
                } else if (ed instanceof CompensateEventDefinition) {
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("actrefname")) {
                            String activityNameRef = (String) entry.getValue();
                            // we have to iterate again through all flow elements
                            // in order to find our activity name
                            List<RootElement> re = def.getRootElements();
                            for (RootElement r : re) {
                                if (r instanceof Process) {
                                    Process p = (Process) r;
                                    List<FlowElement> fes = p.getFlowElements();
                                    for (FlowElement f : fes) {
                                        if (f instanceof Activity && ((Activity) f).getName().equals(activityNameRef)) {
                                            ((CompensateEventDefinition) ed).setActivityRef((Activity) f);
                                            ((Activity) f).setIsForCompensation(true);
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
            }
        } else if (fe instanceof FlowElementsContainer) {
            setCatchEventsInfo((FlowElementsContainer) fe, def, toAddSignals, toAddErrors, toAddEscalations, toAddMessages, toAddItemDefinitions);
        }
    }
}

Example 7 with Activity

use of org.orcid.jaxb.model.record_rc2.Activity in project kie-wb-common by kiegroup.

the class Bpmn2JsonUnmarshaller method setCatchEventsInfoForLanes.

public void setCatchEventsInfoForLanes(Lane lane, Definitions def, List<Signal> toAddSignals, Set<Error> toAddErrors, Set<Escalation> toAddEscalations, Set<Message> toAddMessages, Set<ItemDefinition> toAddItemDefinitions) {
    List<FlowNode> laneFlowNodes = lane.getFlowNodeRefs();
    for (FlowElement fe : laneFlowNodes) {
        if (fe instanceof CatchEvent) {
            if (((CatchEvent) fe).getEventDefinitions().size() > 0) {
                EventDefinition ed = ((CatchEvent) fe).getEventDefinitions().get(0);
                if (ed instanceof SignalEventDefinition) {
                    SignalEventDefinition sed = (SignalEventDefinition) ed;
                    if (sed.getSignalRef() != null && sed.getSignalRef().length() > 0) {
                        String signalRef = sed.getSignalRef();
                        boolean shouldAddSignal = true;
                        List<RootElement> rootElements = def.getRootElements();
                        for (RootElement re : rootElements) {
                            if (re instanceof Signal) {
                                if (((Signal) re).getName().equals(signalRef)) {
                                    shouldAddSignal = false;
                                    break;
                                }
                            }
                        }
                        if (toAddSignals != null) {
                            for (Signal s : toAddSignals) {
                                if (s.getName().equals(signalRef)) {
                                    shouldAddSignal = false;
                                    break;
                                }
                            }
                        }
                        if (shouldAddSignal) {
                            Signal signal = Bpmn2Factory.eINSTANCE.createSignal();
                            signal.setName(signalRef);
                            toAddSignals.add(signal);
                        }
                    }
                } else if (ed instanceof ErrorEventDefinition) {
                    String errorCode = null;
                    String errorId = null;
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("erefname")) {
                            errorId = (String) entry.getValue();
                            errorCode = (String) entry.getValue();
                        }
                    }
                    Error err = this._errors.get(errorCode);
                    if (err == null) {
                        err = Bpmn2Factory.eINSTANCE.createError();
                        err.setId(errorId);
                        err.setErrorCode(errorCode);
                        this._errors.put(errorCode, err);
                    }
                    toAddErrors.add(err);
                    ((ErrorEventDefinition) ed).setErrorRef(err);
                } else if (ed instanceof EscalationEventDefinition) {
                    String escalationCode = null;
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("esccode")) {
                            escalationCode = (String) entry.getValue();
                            break;
                        }
                    }
                    Escalation escalation = this._escalations.get(escalationCode);
                    if (escalation == null) {
                        escalation = Bpmn2Factory.eINSTANCE.createEscalation();
                        escalation.setEscalationCode(escalationCode);
                        this._escalations.put(escalationCode, escalation);
                    }
                    toAddEscalations.add(escalation);
                    ((EscalationEventDefinition) ed).setEscalationRef(escalation);
                } else if (ed instanceof MessageEventDefinition) {
                    ((MessageEventDefinition) ed).setMessageRef(extractMessage(ed, toAddMessages, toAddItemDefinitions));
                } else if (ed instanceof CompensateEventDefinition) {
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("actrefname")) {
                            String activityNameRef = (String) entry.getValue();
                            // we have to iterate again through all flow elements
                            // in order to find our activity name
                            List<RootElement> re = def.getRootElements();
                            for (RootElement r : re) {
                                if (r instanceof Process) {
                                    Process p = (Process) r;
                                    List<FlowElement> fes = p.getFlowElements();
                                    for (FlowElement f : fes) {
                                        if (f instanceof Activity && ((Activity) f).getName().equals(activityNameRef)) {
                                            ((CompensateEventDefinition) ed).setActivityRef((Activity) f);
                                            ((Activity) f).setIsForCompensation(true);
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
            }
        } else if (fe instanceof FlowElementsContainer) {
            setCatchEventsInfo((FlowElementsContainer) fe, def, toAddSignals, toAddErrors, toAddEscalations, toAddMessages, toAddItemDefinitions);
        }
    }
}

Example 8 with Activity

use of org.orcid.jaxb.model.record_rc2.Activity in project ORCID-Source by ORCID.

the class RecordTest method testViewRecordFromMemberAPI.

@Test
public void testViewRecordFromMemberAPI() throws InterruptedException, JSONException {
    String accessToken = getAccessToken();
    assertNotNull(accessToken);
    ClientResponse response = memberV2ApiClient.viewRecord(getUser1OrcidId(), accessToken);
    assertNotNull(response);
    assertEquals("invalid " + response, 200, response.getStatus());
    Record record = response.getEntity(Record.class);
    assertNotNull(record);
    assertNotNull(record.getOrcidIdentifier());
    assertEquals(getUser1OrcidId(), record.getOrcidIdentifier().getPath());
    // Check the visibility of every activity that exists
    if (record.getActivitiesSummary() != null) {
        // Educations
        if (record.getActivitiesSummary().getEducations() != null) {
            Educations e = record.getActivitiesSummary().getEducations();
            if (e.getSummaries() != null) {
                for (EducationSummary s : e.getSummaries()) {
                    assertNotNull(s.getSource());
                    assertNotNull(s.getVisibility());
                    Visibility v = s.getVisibility();
                    // If the visibility is PRIVATE the client should be the owner
                    if (Visibility.PRIVATE.equals(v)) {
                        assertEquals(getClient1ClientId(), s.getSource().retrieveSourcePath());
                    }
                }
            }
        }
        // Employments
        if (record.getActivitiesSummary().getEmployments() != null) {
            Employments e = record.getActivitiesSummary().getEmployments();
            if (e.getSummaries() != null) {
                for (EmploymentSummary s : e.getSummaries()) {
                    assertNotNull(s.getSource());
                    assertNotNull(s.getVisibility());
                    Visibility v = s.getVisibility();
                    // If the visibility is PRIVATE the client should be the owner
                    if (Visibility.PRIVATE.equals(v)) {
                        assertEquals(getClient1ClientId(), s.getSource().retrieveSourcePath());
                    }
                }
            }
        }
        // Fundings
        if (record.getActivitiesSummary().getFundings() != null) {
            Fundings f = record.getActivitiesSummary().getFundings();
            List<FundingGroup> groups = f.getFundingGroup();
            if (groups != null) {
                for (FundingGroup fGroup : groups) {
                    List<FundingSummary> summaries = fGroup.getFundingSummary();
                    if (summaries != null) {
                        for (FundingSummary s : summaries) {
                            assertNotNull(s.getSource());
                            assertNotNull(s.getVisibility());
                            Visibility v = s.getVisibility();
                            // If the visibility is PRIVATE the client should be the owner
                            if (Visibility.PRIVATE.equals(v)) {
                                assertEquals(getClient1ClientId(), s.getSource().retrieveSourcePath());
                            }
                        }
                    }
                }
            }
        }
        // PeerReviews
        if (record.getActivitiesSummary().getPeerReviews() != null) {
            PeerReviews p = record.getActivitiesSummary().getPeerReviews();
            List<PeerReviewGroup> groups = p.getPeerReviewGroup();
            if (groups != null) {
                for (PeerReviewGroup pGroup : groups) {
                    List<PeerReviewSummary> summaries = pGroup.getPeerReviewSummary();
                    if (summaries != null) {
                        for (PeerReviewSummary s : summaries) {
                            assertNotNull(s.getSource());
                            assertNotNull(s.getVisibility());
                            Visibility v = s.getVisibility();
                            // If the visibility is PRIVATE the client should be the owner
                            if (Visibility.PRIVATE.equals(v)) {
                                assertEquals(getClient1ClientId(), s.getSource().retrieveSourcePath());
                            }
                        }
                    }
                }
            }
        }
        // Works
        if (record.getActivitiesSummary().getWorks() != null) {
            Works w = record.getActivitiesSummary().getWorks();
            List<WorkGroup> groups = w.getWorkGroup();
            if (groups != null) {
                for (WorkGroup wGroup : groups) {
                    List<WorkSummary> summaries = wGroup.getWorkSummary();
                    if (summaries != null) {
                        for (WorkSummary s : summaries) {
                            assertNotNull(s.getSource());
                            assertNotNull(s.getVisibility());
                            Visibility v = s.getVisibility();
                            // If the visibility is PRIVATE the client should be the owner
                            if (Visibility.PRIVATE.equals(v)) {
                                assertEquals(getClient1ClientId(), s.getSource().retrieveSourcePath());
                            }
                        }
                    }
                }
            }
        }
    }
    // Check the visibility of every biography elements that exists
    if (record.getPerson() != null) {
        // Address
        if (record.getPerson().getAddresses() != null) {
            Addresses addresses = record.getPerson().getAddresses();
            List<Address> list = addresses.getAddress();
            if (list != null) {
                for (Address o : list) {
                    assertNotNull(o.getSource());
                    assertNotNull(o.getVisibility());
                    Visibility v = o.getVisibility();
                    // If the visibility is PRIVATE the client should be the owner
                    if (Visibility.PRIVATE.equals(v)) {
                        assertEquals(getClient1ClientId(), o.getSource().retrieveSourcePath());
                    }
                }
            }
        }
        // Biography
        if (record.getPerson().getBiography() != null) {
            Biography b = record.getPerson().getBiography();
            if (b != null) {
                assertNotNull(b.getVisibility());
                if (Visibility.PRIVATE.equals(b.getVisibility())) {
                    fail("Visibility is private");
                }
            }
        }
        // Emails
        if (record.getPerson().getEmails() != null) {
            Emails emails = record.getPerson().getEmails();
            List<Email> list = emails.getEmails();
            if (list != null) {
                for (Email e : list) {
                    assertNotNull(e.getVisibility());
                    if (Visibility.PRIVATE.equals(e.getVisibility())) {
                        fail("Email " + e.getEmail() + " is private");
                    }
                }
            }
        }
        // External identifiers
        if (record.getPerson().getExternalIdentifiers() != null) {
            PersonExternalIdentifiers extIds = record.getPerson().getExternalIdentifiers();
            List<PersonExternalIdentifier> list = extIds.getExternalIdentifiers();
            if (list != null) {
                for (PersonExternalIdentifier e : list) {
                    assertNotNull(e.getVisibility());
                    if (Visibility.PRIVATE.equals(e.getVisibility())) {
                        assertEquals(getClient1ClientId(), e.getSource().retrieveSourcePath());
                    }
                }
            }
        }
        // Keywords
        if (record.getPerson().getKeywords() != null) {
            Keywords keywords = record.getPerson().getKeywords();
            List<Keyword> list = keywords.getKeywords();
            if (list != null) {
                for (Keyword e : list) {
                    assertNotNull(e.getVisibility());
                    if (Visibility.PRIVATE.equals(e.getVisibility())) {
                        assertEquals(getClient1ClientId(), e.getSource().retrieveSourcePath());
                    }
                }
            }
        }
        // Name
        if (record.getPerson().getName() != null) {
            Name name = record.getPerson().getName();
            if (Visibility.PRIVATE.equals(name.getVisibility())) {
                fail("Name is private");
            }
        }
        // Other names
        if (record.getPerson().getOtherNames() != null) {
            OtherNames otherNames = record.getPerson().getOtherNames();
            List<OtherName> list = otherNames.getOtherNames();
            if (list != null) {
                for (OtherName e : list) {
                    assertNotNull(e.getVisibility());
                    if (Visibility.PRIVATE.equals(e.getVisibility())) {
                        assertEquals(getClient1ClientId(), e.getSource().retrieveSourcePath());
                    }
                }
            }
        }
        // Researcher urls
        if (record.getPerson().getResearcherUrls() != null) {
            ResearcherUrls rUrls = record.getPerson().getResearcherUrls();
            List<ResearcherUrl> list = rUrls.getResearcherUrls();
            if (list != null) {
                for (ResearcherUrl e : list) {
                    assertNotNull(e.getVisibility());
                    if (Visibility.PRIVATE.equals(e.getVisibility())) {
                        assertEquals(getClient1ClientId(), e.getSource().retrieveSourcePath());
                    }
                }
            }
        }
    }
}

Example 9 with Activity

use of org.orcid.jaxb.model.record_rc2.Activity in project ORCID-Source by ORCID.

the class RecordTest method testViewRecordFromPublicAPI.

@Test
public void testViewRecordFromPublicAPI() {
    ClientResponse response = publicV2ApiClient.viewRecordXML(getUser1OrcidId());
    assertNotNull(response);
    assertEquals("invalid " + response, 200, response.getStatus());
    Record record = response.getEntity(Record.class);
    assertNotNull(record);
    assertNotNull(record.getOrcidIdentifier());
    assertEquals(getUser1OrcidId(), record.getOrcidIdentifier().getPath());
    // Check the visibility of every activity that exists
    if (record.getActivitiesSummary() != null) {
        if (record.getActivitiesSummary() != null) {
            // Educations
            if (record.getActivitiesSummary().getEducations() != null) {
                Educations e = record.getActivitiesSummary().getEducations();
                if (e.getSummaries() != null) {
                    for (EducationSummary s : e.getSummaries()) {
                        assertNotNull(s.getSource());
                        assertEquals(Visibility.PUBLIC, s.getVisibility());
                    }
                }
            }
            // Employments
            if (record.getActivitiesSummary().getEmployments() != null) {
                Employments e = record.getActivitiesSummary().getEmployments();
                if (e.getSummaries() != null) {
                    for (EmploymentSummary s : e.getSummaries()) {
                        assertNotNull(s.getSource());
                        assertEquals(Visibility.PUBLIC, s.getVisibility());
                    }
                }
            }
            // Fundings
            if (record.getActivitiesSummary().getFundings() != null) {
                Fundings f = record.getActivitiesSummary().getFundings();
                List<FundingGroup> groups = f.getFundingGroup();
                if (groups != null) {
                    for (FundingGroup fGroup : groups) {
                        List<FundingSummary> summaries = fGroup.getFundingSummary();
                        if (summaries != null) {
                            for (FundingSummary s : summaries) {
                                assertNotNull(s.getSource());
                                assertEquals(Visibility.PUBLIC, s.getVisibility());
                            }
                        }
                    }
                }
            }
            // PeerReviews
            if (record.getActivitiesSummary().getPeerReviews() != null) {
                PeerReviews p = record.getActivitiesSummary().getPeerReviews();
                List<PeerReviewGroup> groups = p.getPeerReviewGroup();
                if (groups != null) {
                    for (PeerReviewGroup pGroup : groups) {
                        List<PeerReviewSummary> summaries = pGroup.getPeerReviewSummary();
                        if (summaries != null) {
                            for (PeerReviewSummary s : summaries) {
                                assertNotNull(s.getSource());
                                assertEquals(Visibility.PUBLIC, s.getVisibility());
                            }
                        }
                    }
                }
            }
            // Works
            if (record.getActivitiesSummary().getWorks() != null) {
                Works w = record.getActivitiesSummary().getWorks();
                List<WorkGroup> groups = w.getWorkGroup();
                if (groups != null) {
                    for (WorkGroup wGroup : groups) {
                        List<WorkSummary> summaries = wGroup.getWorkSummary();
                        if (summaries != null) {
                            for (WorkSummary s : summaries) {
                                assertNotNull(s.getSource());
                                assertEquals(Visibility.PUBLIC, s.getVisibility());
                            }
                        }
                    }
                }
            }
        }
    }
    // Check the visibility of every biography elements that exists
    if (record.getPerson() != null) {
        // Address
        if (record.getPerson().getAddresses() != null) {
            Addresses addresses = record.getPerson().getAddresses();
            List<Address> list = addresses.getAddress();
            if (list != null) {
                for (Address o : list) {
                    assertNotNull(o.getSource());
                    assertEquals(Visibility.PUBLIC, o.getVisibility());
                }
            }
        }
        // Biography
        if (record.getPerson().getBiography() != null) {
            Biography b = record.getPerson().getBiography();
            if (b != null) {
                assertNotNull(b.getVisibility());
                assertEquals(Visibility.PUBLIC, b.getVisibility());
            }
        }
        // Emails
        if (record.getPerson().getEmails() != null) {
            Emails emails = record.getPerson().getEmails();
            List<Email> list = emails.getEmails();
            if (list != null) {
                for (Email e : list) {
                    assertNotNull(e.getVisibility());
                    assertEquals(Visibility.PUBLIC, e.getVisibility());
                }
            }
        }
        // External identifiers
        if (record.getPerson().getExternalIdentifiers() != null) {
            PersonExternalIdentifiers extIds = record.getPerson().getExternalIdentifiers();
            List<PersonExternalIdentifier> list = extIds.getExternalIdentifiers();
            if (list != null) {
                for (PersonExternalIdentifier e : list) {
                    assertEquals(Visibility.PUBLIC, e.getVisibility());
                }
            }
        }
        // Keywords
        if (record.getPerson().getKeywords() != null) {
            Keywords keywords = record.getPerson().getKeywords();
            List<Keyword> list = keywords.getKeywords();
            if (list != null) {
                for (Keyword e : list) {
                    assertEquals(Visibility.PUBLIC, e.getVisibility());
                }
            }
        }
        // Name
        if (record.getPerson().getName() != null) {
            Name name = record.getPerson().getName();
            assertEquals(Visibility.PUBLIC, name.getVisibility());
        }
        // Other names
        if (record.getPerson().getOtherNames() != null) {
            OtherNames otherNames = record.getPerson().getOtherNames();
            List<OtherName> list = otherNames.getOtherNames();
            if (list != null) {
                for (OtherName e : list) {
                    assertEquals(Visibility.PUBLIC, e.getVisibility());
                }
            }
        }
        // Researcher urls
        if (record.getPerson().getResearcherUrls() != null) {
            ResearcherUrls rUrls = record.getPerson().getResearcherUrls();
            List<ResearcherUrl> list = rUrls.getResearcherUrls();
            if (list != null) {
                for (ResearcherUrl e : list) {
                    assertEquals(Visibility.PUBLIC, e.getVisibility());
                }
            }
        }
    }
}

Example 10 with Activity

use of org.orcid.jaxb.model.record_rc2.Activity in project libSBOLj by SynBioDex.

the class Provenance_SpecifyBuildOperations method specifyJoinOperation.

/**
 * specifies a join operation, which joins two linear DNA constructs
 *
 * NOTE! at this point, we do not specify any further information
 * about how to execute the join operation!
 *
 * @throws Exception
 */
public static void specifyJoinOperation() throws Exception {
    // instantiate a document
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(BUILD_PREFIX);
    // the first linear DNA construct
    ComponentDefinition cdPart1 = document.createComponentDefinition("dna_part_1", LINEAR_DOUBLE_STRANDED_DNA);
    cdPart1.setName("dna_part_1");
    // the second linear DNA construct
    ComponentDefinition cdPart2 = document.createComponentDefinition("dna_part_2", LINEAR_DOUBLE_STRANDED_DNA);
    cdPart2.setName("dna_part_2");
    // Create the generic top level entity for the join operation
    Activity joinOperation = document.createActivity("join_" + cdPart1.getName() + "_with_" + cdPart2.getName());
    joinOperation.setName("join(" + cdPart1.getName() + ", " + cdPart2.getName() + ")");
    // specify the "inputs" to the join operation
    joinOperation.createUsage("dna_part_1", cdPart1.getIdentity()).addRole(UPSTREAM);
    joinOperation.createUsage("dna_part_2", cdPart2.getIdentity()).addRole(DOWNSTREAM);
    // specify the "output" of the join operation
    ComponentDefinition cdJoinedPart = document.createComponentDefinition("joined_dna_part", LINEAR_DOUBLE_STRANDED_DNA);
    cdJoinedPart.setName("joined_dna_part");
    cdJoinedPart.addWasGeneratedBy(joinOperation.getIdentity());
    // serialize the document to a file
    SBOLWriter.write(document, System.out);
}