Example usage for org.dom4j Element add

Introduction

In this page you can find the example usage for org.dom4j Element add.

Prototype

void add(Namespace namespace);

Source Link

Document

Adds the given Namespace to this element.

Usage

From source file:edu.northwestern.bioinformatics.studycalendar.xml.writers.ScheduledCalendarXmlSerializer.java

License:BSD License

@Override
public Element createElement(ScheduledCalendar scheduledCalendar) {
    if (scheduledCalendar == null) {
        throw new StudyCalendarSystemException("scheduledCalendar is required");
    }//from   www.  j av a2  s  .co  m

    Element elt = SCHEDULED_CALENDAR.create();
    if (scheduledCalendar.getGridId() != null)
        SCHEDULED_CALENDAR_ID.addTo(elt, scheduledCalendar.getGridId());
    if (scheduledCalendar.getAssignment() != null)
        SCHEDULED_CALENDAR_ASSIGNMENT_ID.addTo(elt, scheduledCalendar.getAssignment().getGridId());

    for (ScheduledStudySegment segment : scheduledCalendar.getScheduledStudySegments()) {
        elt.add(segmentSerialzier.createElement(segment));
    }
    return elt;
}

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From source file:edu.northwestern.bioinformatics.studycalendar.xml.writers.ScheduledStudySegmentXmlSerializer.java

License:BSD License

@Override
public Element createElement(ScheduledStudySegment segment) {
    Element elt = SCHEDULED_STUDY_SEGMENT.create();
    SCHEDULED_STUDY_SEGMENT_ID.addTo(elt, segment.getGridId());
    SCHEDULED_STUDY_SEGMENT_START_DATE.addTo(elt, segment.getStartDate());
    SCHEDULED_STUDY_SEGMENT_START_DAY.addTo(elt, segment.getStartDay());
    XsdAttribute.SCHEDULED_STUDY_SEGMENT_STUDY_SEGMENT_ID.addTo(elt, segment.getStudySegment().getGridId());

    for (ScheduledActivity activity : segment.getActivities()) {
        elt.add(scheduledActivitySerializer.createElement(activity));
    }//from  w  w  w  .j a v a  2  s  . c  o  m
    return elt;
}

---

From source file:edu.northwestern.bioinformatics.studycalendar.xml.writers.StudiesXmlSerializer.java

License:BSD License

@Override
protected Element createElement(final Study study, final boolean inCollection) {
    Element studyElement = rootElement().create();
    STUDY_ASSIGNED_IDENTIFIER.addTo(studyElement, study.getNaturalKey());
    if (study.getProvider() != null) {
        STUDY_PROVIDER.addTo(studyElement, study.getProvider());
    }/*  www .  ja v  a 2 s.  c om*/
    if (study.getLongTitle() != null && study.getLongTitle().length() > 0) {
        Element eltLongTitle = XsdElement.LONG_TITLE.create();
        eltLongTitle.addText(study.getLongTitle());
        studyElement.add(eltLongTitle);
    }
    for (StudySecondaryIdentifier studySecondaryIdent : study.getSecondaryIdentifiers()) {
        studyElement.add(studySecondaryIdentifierXmlSerializer.createElement(studySecondaryIdent));
    }
    return studyElement;
}

---

From source file:edu.northwestern.bioinformatics.studycalendar.xml.writers.StudySnapshotXmlSerializer.java

License:BSD License

@Override
public Element createElement(Study study) {
    Element elt = XsdElement.STUDY_SNAPSHOT.create();
    XsdAttribute.STUDY_SNAPSHOT_ASSIGNED_IDENTIFIER.addTo(elt, study.getAssignedIdentifier());
    if (study.getProvider() != null) {
        XsdAttribute.STUDY_PROVIDER.addTo(elt, study.getProvider());
    }// w w w. jav a 2s .  c  om
    if (study.getLongTitle() != null && study.getLongTitle().length() > 0) {
        Element eltLongTitle = XsdElement.LONG_TITLE.create();
        eltLongTitle.addText(study.getLongTitle());
        elt.add(eltLongTitle);
    }
    for (StudySecondaryIdentifier studySecondaryIdent : study.getSecondaryIdentifiers()) {
        elt.add(studySecondaryIdentifierXmlSerializer.createElement(studySecondaryIdent));
    }

    Set<Population> pops = study.getPopulations();
    for (Population pop : pops) {
        elt.add(populationXmlSerializer.createElement(pop));
    }

    elt.add(plannedCalendarXmlSerializer.createElement(study.getPlannedCalendar()));

    Element eSources = studyXmlSerializerHelper.generateSourcesElementWithActivities(study);
    elt.add(eSources);

    return elt;
}

---

From source file:edu.northwestern.bioinformatics.studycalendar.xml.writers.StudySubjectAssignmentXmlSerializer.java

License:BSD License

@Override
public Element createElement(StudySubjectAssignment assignment, boolean inCollection) {
    Element elt = SUBJECT_ASSIGNMENT.create();
    ASSIGNMENT_STUDY_NAME.addTo(elt, assignment.getStudySite().getStudy().getName());
    ASSIGNMENT_SITE_NAME.addTo(elt, assignment.getStudySite().getSite().getName());
    ASSIGNMENT_START_DATE.addTo(elt, assignment.getStartDate());
    ASSIGNMENT_END_DATE.addTo(elt, assignment.getEndDate());
    ASSIGNMENT_SUBJECT_COORD.addTo(elt, assignment.getStudySubjectCalendarManager().getName());
    ASSIGNMENT_CURRENT_AMENDMENT.addTo(elt, assignment.getCurrentAmendment().getNaturalKey());
    ASSIGNMENT_ID.addTo(elt, assignment.getGridId());
    if (!subjectCentric) {
        elt.add(subjectXmlSerializer.createElement(assignment.getSubject()));
    }/*  w  w  w .j  a  v a2 s.c om*/
    if (subjectCentric || includeScheduledCalendar) {
        elt.add(scheduledCalendarXmlSerializer.createElement(assignment.getScheduledCalendar()));
    }
    return elt;
}

---

From source file:edu.northwestern.bioinformatics.studycalendar.xml.writers.StudyXmlSerializer.java

License:BSD License

public Element createElement(Study study) {
    Element elt = XsdElement.STUDY.create();
    STUDY_ASSIGNED_IDENTIFIER.addTo(elt, study.getAssignedIdentifier());
    LAST_MODIFIED_DATE.addToDateTime(elt, study.getLastModifiedDate());

    if (study.getProvider() != null) {
        STUDY_PROVIDER.addTo(elt, study.getProvider());
    }//from   w w w  .  j  ava  2 s  . c  o  m
    if (study.getLongTitle() != null && study.getLongTitle().length() > 0) {
        Element eltLongTitle = XsdElement.LONG_TITLE.create();
        eltLongTitle.addText(study.getLongTitle());
        elt.add(eltLongTitle);
    }

    for (StudySecondaryIdentifier studySecondaryIdent : study.getSecondaryIdentifiers()) {
        elt.add(studySecondaryIdentifierXmlSerializer.createElement(studySecondaryIdent));
    }

    Element eCalendar = getPlannedCalendarXmlSerializer().createElement(study.getPlannedCalendar());

    elt.add(eCalendar);

    for (Amendment amendment : study.getAmendmentsList()) {
        Element eAmendment = getAmendmentSerializer(study).createElement(amendment);
        elt.add(eAmendment);
    }

    if (study.getDevelopmentAmendment() != null) {
        Amendment developmentAmendment = study.getDevelopmentAmendment();
        Element developmentAmendmentElement = getDevelopmentAmendmentSerializer(study)
                .createElement(developmentAmendment);
        elt.add(developmentAmendmentElement);
    }

    Element eSources = studyXmlSerializerHelper.generateSourcesElementWithActivities(study);
    elt.add(eSources);

    return elt;
}

---

From source file:edu.northwestern.bioinformatics.studycalendar.xml.writers.SubjectXmlSerializer.java

License:BSD License

@Override
public Element createElement(Subject subject) {
    Element elt = SUBJECT.create();
    SUBJECT_FIRST_NAME.addTo(elt, subject.getFirstName());
    SUBJECT_LAST_NAME.addTo(elt, subject.getLastName());
    SUBJECT_PERSON_ID.addTo(elt, subject.getPersonId());
    SUBJECT_BIRTH_DATE.addTo(elt, subject.getDateOfBirth());
    SUBJECT_GENDER.addTo(elt, subject.getGender().getCode());
    for (SubjectProperty property : subject.getProperties()) {
        Element child = SUBJECT_PROPERTY.create();
        PROPERTY_NAME.addTo(child, property.getName());
        PROPERTY_VALUE.addTo(child, property.getValue());
        elt.add(child);
    }//from w  w  w .  j  a v  a2  s . c  o m
    return elt;
}

---

From source file:edu.northwestern.bioinformatics.studycalendar.xml.writers.UserRoleMembershipsXmlSerializer.java

License:BSD License

@Override
protected Element createElement(SuiteRoleMembership userRoleMembership, boolean inCollection) {
    Element userRoleElement = rootElement().create();
    XsdAttribute.USER_ROLE_NAME.addTo(userRoleElement, userRoleMembership.getRole().getDisplayName());
    if (userRoleMembership.hasSiteScope()) {
        Element roleSites = XsdElement.ROLE_SITES.create();
        if (userRoleMembership.isAllSites()) {
            XsdAttribute.ALL.addTo(roleSites, true);
        } else {/*from w  w  w.java2s . c o m*/
            XsdAttribute.ALL.addTo(roleSites, false);
            for (String siteIdentifier : userRoleMembership.getSiteIdentifiers()) {
                Element site = XsdElement.SITE.create();
                XsdAttribute.SITE_ASSIGNED_IDENTIFIER.addTo(site, siteIdentifier);
                roleSites.add(site);
            }
        }
        userRoleElement.add(roleSites);
    }

    if (userRoleMembership.hasStudyScope()) {
        Element roleStudies = XsdElement.ROLE_STUDIES.create();
        if (userRoleMembership.isAllStudies()) {
            XsdAttribute.ALL.addTo(roleStudies, true);
        } else {
            XsdAttribute.ALL.addTo(roleStudies, false);
            for (String studyIdentifier : userRoleMembership.getStudyIdentifiers()) {
                Element study = XsdElement.STUDY.create();
                XsdAttribute.STUDY_ASSIGNED_IDENTIFIER.addTo(study, studyIdentifier);
                roleStudies.add(study);
            }
        }
        userRoleElement.add(roleStudies);
    }
    return userRoleElement;
}

---

From source file:edu.scripps.fl.pubchem.xml.PubChemXMLDoc.java

License:Apache License

public void organizeXMLDoc(Document doc) {
    Element parent = (Element) doc.selectSingleNode(rootString);
    String[] nodesOrder = { name, description, protocol, comment, xref, results, revision, target,
            activityOutcome, dr, grantNumber, projectCategory, isPanel, panelInfo, categorizedComment };
    for (String nodeString : nodesOrder) {
        Node node = parent.selectSingleNode(nodeString);
        if (node != null) {
            Node clone = (Node) node.clone();
            node.detach();//from   w  w  w.j a v a2  s.  c om
            parent.add(clone);
        }
    }
    parent = (Element) doc.selectSingleNode(dbTracking);
    String[] secondNodesOrder = { "PC-DBTracking_name", "PC-DBTracking_source-id", "PC-DBTracking_date" };
    for (String nodeString : secondNodesOrder) {
        Node node = parent.selectSingleNode(nodeString);
        if (node != null) {
            Node clone = (Node) node.clone();
            node.detach();
            parent.add(clone);
        }
    }

}

---

From source file:edu.ucsd.library.dams.api.DAMSAPIServlet.java

public String objectBatch(List<String> objids, TripleStore ts, TripleStore es) throws Exception {
    ArrayList<String> docs = new ArrayList<String>();
    ArrayList<String> errors = new ArrayList<String>();

    // retrieve rdf/xml for each record
    for (int i = 0; i < objids.size(); i++) {
        try {/*ww w  .  j  a  va  2s  .c  o  m*/
            Identifier id = createID(objids.get(i), null, null);
            if (ts.exists(id)) {
                DAMSObject obj = new DAMSObject(ts, es, objids.get(i), nsmap);
                docs.add(obj.getRDFXML(true));
            } else if (es != null && es.exists(id)) {
                DAMSObject obj = new DAMSObject(es, null, objids.get(i), nsmap);
                docs.add(obj.getRDFXML(true));
            } else {
                errors.add(objids.get(i) + ": not found");
            }
        } catch (Exception ex) {
            errors.add(objids.get(i) + ": " + ex.toString());
        }
    }

    // combine xml documents
    String xml = null;
    if (docs.size() == 1) {
        xml = docs.get(0);
    } else if (docs.size() > 1) {
        try {
            Document doc = DocumentHelper.parseText(docs.get(0));
            Element rdf = doc.getRootElement();
            for (int i = 1; i < docs.size(); i++) {
                Document doc2 = DocumentHelper.parseText(docs.get(i));
                Iterator it = doc2.getRootElement().elementIterator();
                if (it.hasNext()) {
                    Element e = (Element) it.next();
                    rdf.add(e.detach());
                }
            }
            xml = doc.asXML();
        } catch (Exception ex) {
            errors.add("Error combining records into a batch: " + ex.toString());
        }
    }

    // check errors
    if (errors.size() > 0) {
        String msg = errors.get(0);
        for (int i = 1; i < errors.size(); i++) {
            msg += "; " + errors.get(i);
        }
        throw new Exception(msg);
    }

    return xml;
}

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