Java tutorial
/* OpenClinica is distributed under the GNU Lesser General Public License (GNU * LGPL). * * For details see: http://www.openclinica.org/license copyright 2003-2005 Akaza * Research * */ package org.akaza.openclinica.bean.extract.odm; import org.akaza.openclinica.bean.odmbeans.AuditLogBean; import org.akaza.openclinica.bean.odmbeans.AuditLogsBean; import org.akaza.openclinica.bean.odmbeans.ChildNoteBean; import org.akaza.openclinica.bean.odmbeans.DiscrepancyNoteBean; import org.akaza.openclinica.bean.odmbeans.DiscrepancyNotesBean; import org.akaza.openclinica.bean.odmbeans.OdmClinicalDataBean; import org.akaza.openclinica.bean.submit.ItemDataBean; import org.akaza.openclinica.bean.submit.crfdata.ExportFormDataBean; import org.akaza.openclinica.bean.submit.crfdata.ExportStudyEventDataBean; import org.akaza.openclinica.bean.submit.crfdata.ExportSubjectDataBean; import org.akaza.openclinica.bean.submit.crfdata.ImportItemDataBean; import org.akaza.openclinica.bean.submit.crfdata.ImportItemGroupDataBean; import org.akaza.openclinica.bean.submit.crfdata.SubjectGroupDataBean; import org.apache.commons.lang.StringEscapeUtils; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Collections; import java.util.Comparator; import java.util.Date; /** * Create ODM XML ClinicalData Element for a study. * * @author ywang (May, 2008) */ public class ClinicalDataReportBean extends OdmXmlReportBean { private OdmClinicalDataBean clinicalData; public ClinicalDataReportBean(OdmClinicalDataBean clinicaldata) { super(); this.clinicalData = clinicaldata; } /** * has not been implemented yet */ @Override public void createOdmXml(boolean isDataset) { // this.addHeading(); // this.addRootStartLine(); // addNodeClinicalData(); // this.addRootEndLine(); } public void addNodeClinicalData(boolean header, boolean footer) { String ODMVersion = this.getODMVersion(); // when collecting data, only item with value has been collected. StringBuffer xml = this.getXmlOutput(); String indent = this.getIndent(); String nls = System.getProperty("line.separator"); if (header) { xml.append(indent + "<ClinicalData StudyOID=\"" + StringEscapeUtils.escapeXml(clinicalData.getStudyOID()) + "\" MetaDataVersionOID=\"" + StringEscapeUtils.escapeXml(this.clinicalData.getMetaDataVersionOID()) + "\">"); xml.append(nls); } ArrayList<ExportSubjectDataBean> subs = (ArrayList<ExportSubjectDataBean>) this.clinicalData .getExportSubjectData(); for (ExportSubjectDataBean sub : subs) { xml.append(indent + indent + "<SubjectData SubjectKey=\"" + StringEscapeUtils.escapeXml(sub.getSubjectOID())); if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) { xml.append( "\" OpenClinica:StudySubjectID=\"" + StringEscapeUtils.escapeXml(sub.getStudySubjectId())); String uniqueIdentifier = sub.getUniqueIdentifier(); if (uniqueIdentifier != null && uniqueIdentifier.length() > 0) { xml.append( "\" OpenClinica:UniqueIdentifier=\"" + StringEscapeUtils.escapeXml(uniqueIdentifier)); } String status = sub.getStatus(); if (status != null && status.length() > 0) { xml.append("\" OpenClinica:Status=\"" + StringEscapeUtils.escapeXml(status)); } String secondaryId = sub.getSecondaryId(); if (secondaryId != null && secondaryId.length() > 0) { xml.append("\" OpenClinica:SecondaryID=\"" + StringEscapeUtils.escapeXml(secondaryId)); } Integer year = sub.getYearOfBirth(); if (year != null) { xml.append("\" OpenClinica:YearOfBirth=\"" + sub.getYearOfBirth()); } else { if (sub.getDateOfBirth() != null) { xml.append("\" OpenClinica:DateOfBirth=\"" + sub.getDateOfBirth()); } } String gender = sub.getSubjectGender(); if (gender != null && gender.length() > 0) { xml.append("\" OpenClinica:Sex=\"" + StringEscapeUtils.escapeXml(gender)); } String enrollmentDate = sub.getEnrollmentDate(); if (enrollmentDate != null && enrollmentDate.length() > 0) { xml.append("\" OpenClinica:EnrollmentDate=\"" + enrollmentDate); } } xml.append("\">"); xml.append(nls); // ArrayList<ExportStudyEventDataBean> ses = (ArrayList<ExportStudyEventDataBean>) sub .getExportStudyEventData(); for (ExportStudyEventDataBean se : ses) { xml.append(indent + indent + indent + "<StudyEventData StudyEventOID=\"" + StringEscapeUtils.escapeXml(se.getStudyEventOID())); if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) { String location = se.getLocation(); if (location != null && location.length() > 0) { xml.append("\" OpenClinica:StudyEventLocation=\"" + StringEscapeUtils.escapeXml(location)); } String startDate = se.getStartDate(); if (startDate != null && startDate.length() > 0) { xml.append("\" OpenClinica:StartDate=\"" + startDate); } String endDate = se.getEndDate(); if (endDate != null && endDate.length() > 0) { xml.append("\" OpenClinica:EndDate=\"" + endDate); } String status = se.getStatus(); if (status != null && status.length() > 0) { xml.append("\" OpenClinica:Status=\"" + StringEscapeUtils.escapeXml(status)); } if (se.getAgeAtEvent() != null) { xml.append("\" OpenClinica:SubjectAgeAtEvent=\"" + se.getAgeAtEvent()); } } xml.append("\""); if (!"-1".equals(se.getStudyEventRepeatKey())) { xml.append(" StudyEventRepeatKey=\"" + se.getStudyEventRepeatKey() + "\""); } xml.append(">"); xml.append(nls); // ArrayList<ExportFormDataBean> forms = se.getExportFormData(); for (ExportFormDataBean form : forms) { xml.append(indent + indent + indent + indent + "<FormData FormOID=\"" + StringEscapeUtils.escapeXml(form.getFormOID())); if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) { String crfVersion = form.getCrfVersion(); if (crfVersion != null && crfVersion.length() > 0) { xml.append("\" OpenClinica:Version=\"" + StringEscapeUtils.escapeXml(crfVersion)); } String interviewerName = form.getInterviewerName(); if (interviewerName != null && interviewerName.length() > 0) { xml.append("\" OpenClinica:InterviewerName=\"" + StringEscapeUtils.escapeXml(interviewerName)); } if (form.getInterviewDate() != null && form.getInterviewDate().length() > 0) { xml.append("\" OpenClinica:InterviewDate=\"" + form.getInterviewDate()); } String status = form.getStatus(); if (status != null && status.length() > 0) { xml.append("\" OpenClinica:Status=\"" + StringEscapeUtils.escapeXml(status)); } } xml.append("\">"); xml.append(nls); // ArrayList<ImportItemGroupDataBean> igs = form.getItemGroupData(); sortImportItemGroupDataBeanList(igs); for (ImportItemGroupDataBean ig : igs) { xml.append(indent + indent + indent + indent + indent + "<ItemGroupData ItemGroupOID=\"" + StringEscapeUtils.escapeXml(ig.getItemGroupOID()) + "\" "); if (!"-1".equals(ig.getItemGroupRepeatKey())) { xml.append("ItemGroupRepeatKey=\"" + ig.getItemGroupRepeatKey() + "\" "); } xml.append("TransactionType=\"Insert\">"); xml.append(nls); ArrayList<ImportItemDataBean> items = ig.getItemData(); sortImportItemDataBeanList(items); for (ImportItemDataBean item : items) { boolean printValue = true; xml.append(indent + indent + indent + indent + indent + indent + "<ItemData ItemOID=\"" + StringEscapeUtils.escapeXml(item.getItemOID()) + "\" "); if ("Yes".equals(item.getIsNull())) { xml.append("IsNull=\"Yes\""); if (!item.isHasValueWithNull()) { printValue = false; } if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) { xml.append(" OpenClinica:ReasonForNull=\"" + StringEscapeUtils.escapeXml(item.getReasonForNull()) + "\" "); if (!printValue) { xml.append("/>"); xml.append(nls); } } } if (printValue) { Boolean hasElm = false; xml.append("Value=\"" + StringEscapeUtils.escapeXml(item.getValue()) + "\""); String muRefOid = item.getMeasurementUnitRef().getElementDefOID(); if (muRefOid != null && muRefOid.length() > 0) { if (hasElm) { } else { xml.append(">"); xml.append(nls); hasElm = true; } xml.append(indent + indent + indent + indent + indent + indent + indent + "<MeasurementUnitRef MeasurementUnitOID=\"" + StringEscapeUtils.escapeXml(muRefOid) + "\"/>"); xml.append(nls); } // if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) { if (item.getAuditLogs() != null && item.getAuditLogs().getAuditLogs().size() > 0) { if (hasElm) { } else { xml.append(">"); xml.append(nls); hasElm = true; } this.addAuditLogs(item.getAuditLogs(), indent + indent + indent + indent + indent + indent + indent, "item"); } // if (item.getDiscrepancyNotes() != null && item.getDiscrepancyNotes().getDiscrepancyNotes().size() > 0) { if (hasElm) { } else { xml.append(">"); xml.append(nls); hasElm = true; } this.addDiscrepancyNotes(item.getDiscrepancyNotes(), indent + indent + indent + indent + indent + indent + indent); } } if (hasElm) { xml.append(indent + indent + indent + indent + indent + indent + "</ItemData>"); xml.append(nls); hasElm = false; } else { xml.append("/>"); xml.append(nls); } } } xml.append(indent + indent + indent + indent + indent + "</ItemGroupData>"); xml.append(nls); } // if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) { if (form.getAuditLogs() != null && form.getAuditLogs().getAuditLogs().size() > 0) { this.addAuditLogs(form.getAuditLogs(), indent + indent + indent + indent + indent, "form"); } // if (form.getDiscrepancyNotes() != null && form.getDiscrepancyNotes().getDiscrepancyNotes().size() > 0) { this.addDiscrepancyNotes(form.getDiscrepancyNotes(), indent + indent + indent + indent + indent); } } xml.append(indent + indent + indent + indent + "</FormData>"); xml.append(nls); } // if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) { if (se.getAuditLogs() != null && se.getAuditLogs().getAuditLogs().size() > 0) { this.addAuditLogs(se.getAuditLogs(), indent + indent + indent + indent, "se"); } // if (se.getDiscrepancyNotes() != null && se.getDiscrepancyNotes().getDiscrepancyNotes().size() > 0) { this.addDiscrepancyNotes(se.getDiscrepancyNotes(), indent + indent + indent + indent); } } xml.append(indent + indent + indent + "</StudyEventData>"); xml.append(nls); } if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) { ArrayList<SubjectGroupDataBean> sgddata = (ArrayList<SubjectGroupDataBean>) sub .getSubjectGroupData(); if (sgddata.size() > 0) { for (SubjectGroupDataBean sgd : sgddata) { String cid = sgd.getStudyGroupClassId() != null ? "OpenClinica:StudyGroupClassID=\"" + StringEscapeUtils.escapeXml(sgd.getStudyGroupClassId()) + "\" " : ""; if (cid.length() > 0) { String cn = sgd.getStudyGroupClassName() != null ? "OpenClinica:StudyGroupClassName=\"" + StringEscapeUtils.escapeXml(sgd.getStudyGroupClassName()) + "\" " : ""; String gn = sgd.getStudyGroupName() != null ? "OpenClinica:StudyGroupName=\"" + StringEscapeUtils.escapeXml(sgd.getStudyGroupName()) + "\" " : ""; xml.append(indent + indent + indent + "<OpenClinica:SubjectGroupData " + cid + cn + gn); } xml.append(" />"); xml.append(nls); } } // if (sub.getAuditLogs() != null && sub.getAuditLogs().getAuditLogs().size() > 0) { this.addAuditLogs(sub.getAuditLogs(), indent + indent + indent, "sub"); } // if (sub.getDiscrepancyNotes() != null && sub.getDiscrepancyNotes().getDiscrepancyNotes().size() > 0) { this.addDiscrepancyNotes(sub.getDiscrepancyNotes(), indent + indent + indent); } } xml.append(indent + indent + "</SubjectData>"); xml.append(nls); } if (footer) { xml.append(indent + "</ClinicalData>"); xml.append(nls); } } protected void addAuditLogs(AuditLogsBean auditLogs, String currentIndent, String entity) { int count = 0; if (auditLogs != null) { ArrayList<AuditLogBean> audits = auditLogs.getAuditLogs(); if (audits != null && audits.size() > 0) { for (AuditLogBean audit : audits) { if (entity == "item" && audit.getOldValue().equals("") && audit.getNewValue().equals("")) { count++; } } if (count != audits.size()) { StringBuffer xml = this.getXmlOutput(); String indent = this.getIndent(); String nls = System.getProperty("line.separator"); xml.append( currentIndent + "<OpenClinica:AuditLogs EntityID=\"" + auditLogs.getEntityID() + "\">"); xml.append(nls); for (AuditLogBean audit : audits) { if (!(entity == "item" && audit.getOldValue().equals("") && audit.getNewValue().equals(""))) { this.addOneAuditLog(audit, currentIndent + indent); } } xml.append(currentIndent + "</OpenClinica:AuditLogs>"); xml.append(nls); } } } } protected void addOneAuditLog(AuditLogBean audit, String currentIndent) { if (audit != null) { StringBuffer xml = this.getXmlOutput(); String indent = this.getIndent(); String nls = System.getProperty("line.separator"); String i = audit.getOid(); String u = audit.getUserId(); String userName = audit.getUserName(); String name = audit.getName(); Date d = audit.getDatetimeStamp(); String t = audit.getType(); String r = audit.getReasonForChange(); String o = audit.getOldValue(); String n = audit.getNewValue(); String vt = audit.getValueType(); Boolean p = i.length() > 0 || u.length() > 0 || d != null || t.length() > 0 || r.length() > 0 || o.length() > 0 || n.length() > 0 ? true : false; if (p) { xml.append(currentIndent + "<OpenClinica:AuditLog "); if (i.length() > 0) { xml.append("ID=\"" + StringEscapeUtils.escapeXml(i) + "\" "); } if (u.length() > 0) { xml.append("UserID=\"" + StringEscapeUtils.escapeXml(u) + "\" "); } if (userName.length() > 0) { xml.append("UserName=\"" + StringEscapeUtils.escapeXml(userName) + "\" "); } if (name.length() > 0) { xml.append("Name=\"" + StringEscapeUtils.escapeXml(name) + "\" "); } if (d != null) { xml.append( "DateTimeStamp=\"" + new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss").format(d) + "\" "); } if (t.length() > 0) { xml.append(nls); xml.append(currentIndent + " AuditType=\"" + t + "\" "); } if (r.length() > 0) { xml.append(nls); xml.append(currentIndent + " ReasonForChange=\"" + StringEscapeUtils.escapeXml(r) + "\" "); } if (o.length() > 0) { xml.append(nls); xml.append(currentIndent + " OldValue=\"" + StringEscapeUtils.escapeXml(o) + "\" "); } if (n.length() > 0) { xml.append(nls); xml.append(currentIndent + " NewValue=\"" + StringEscapeUtils.escapeXml(n) + "\""); } if (vt.length() > 0) { xml.append(nls); xml.append(currentIndent + " ValueType=\"" + StringEscapeUtils.escapeXml(vt) + "\""); } xml.append("/>"); xml.append(nls); } } } protected void addDiscrepancyNotes(DiscrepancyNotesBean DNs, String currentIndent) { if (DNs != null) { ArrayList<DiscrepancyNoteBean> dns = DNs.getDiscrepancyNotes(); if (dns != null && dns.size() > 0) { StringBuffer xml = this.getXmlOutput(); String indent = this.getIndent(); String nls = System.getProperty("line.separator"); xml.append(currentIndent + "<OpenClinica:DiscrepancyNotes EntityID=\"" + DNs.getEntityID() + "\">"); xml.append(nls); for (DiscrepancyNoteBean dn : dns) { this.addOneDN(dn, currentIndent + indent); } xml.append(currentIndent + "</OpenClinica:DiscrepancyNotes>"); xml.append(nls); } } } protected void addOneDN(DiscrepancyNoteBean dn, String currentIndent) { StringBuffer xml = this.getXmlOutput(); String indent = this.getIndent(); String nls = System.getProperty("line.separator"); //Boolean p = s.length()>0||i.length()>0||d.toString().length()>0||n>0 ? true : false; xml.append(currentIndent + "<OpenClinica:DiscrepancyNote "); if (dn.getOid() != null) { String i = dn.getOid(); if (i.length() > 0) { xml.append("ID=\"" + StringEscapeUtils.escapeXml(i) + "\" "); } } if (dn.getStatus() != null) { String s = dn.getStatus(); if (s.length() > 0) { xml.append("Status=\"" + s + "\" "); } } if (dn.getNoteType() != null) { String s = dn.getNoteType(); if (s.length() > 0) { xml.append("NoteType=\"" + s + "\" "); } } if (dn.getDateUpdated() != null) { Date d = dn.getDateUpdated(); if (d.toString().length() > 0) { xml.append("DateUpdated=\"" + new SimpleDateFormat("yyyy-MM-dd").format(d) + "\" "); } } if (dn.getEntityName() != null) { String s = dn.getEntityName(); if (s.length() > 0) { xml.append("EntityName=\"" + s + "\" "); } } int n = dn.getNumberOfChildNotes(); if (n > 0) { xml.append("NumberOfChildNotes=\"" + dn.getNumberOfChildNotes() + "\""); } xml.append(">"); xml.append(nls); if (dn.getChildNotes() != null && dn.getChildNotes().size() > 0) { for (ChildNoteBean cn : dn.getChildNotes()) { xml.append(currentIndent + indent + "<OpenClinica:ChildNote "); if (cn.getOid() != null) { String s = cn.getOid(); if (s.length() > 0) { xml.append("ID=\"" + s + "\" "); } } if (cn.getStatus() != null) { String s = cn.getStatus(); if (s.length() > 0) { xml.append("Status=\"" + s + "\" "); } } if (cn.getDateCreated() != null) { Date d = cn.getDateCreated(); if (d.toString().length() > 0) { xml.append("DateCreated=\"" + new SimpleDateFormat("yyyy-MM-dd").format(d) + "\" "); } } if (cn.getOwnerUserName() != "") { String ownerUserName = cn.getOwnerUserName(); if (ownerUserName.length() > 0) { xml.append("UserName=\"" + ownerUserName + "\" "); } } if (cn.getOwnerFirstName() != "" || cn.getOwnerLastName() != "") { String ownerLastName = cn.getOwnerLastName(); String ownerFirstName = cn.getOwnerFirstName(); if (ownerLastName.length() > 0 || ownerFirstName.length() > 0) { xml.append("Name=\"" + ownerFirstName + " " + ownerLastName + "\""); } } xml.append(">"); xml.append(nls); if (cn.getDescription() != null) { String dc = cn.getDescription(); if (dc.length() > 0) { xml.append(currentIndent + indent + indent + "<OpenClinica:Description>" + StringEscapeUtils.escapeXml(dc) + "</OpenClinica:Description>"); xml.append(nls); } } if (cn.getDetailedNote() != null) { String nt = cn.getDetailedNote(); if (nt.length() > 0) { xml.append(currentIndent + indent + indent + "<OpenClinica:DetailedNote>" + StringEscapeUtils.escapeXml(nt) + "</OpenClinica:DetailedNote>"); xml.append(nls); } } if (cn.getUserRef() != null) { String uid = cn.getUserRef().getElementDefOID(); String userName = cn.getUserRef().getUserName(); String fullName = cn.getUserRef().getFullName(); String temp = ""; if (userName.length() > 0) { temp += " OpenClinica:UserName=\"" + StringEscapeUtils.escapeXml(userName) + "\""; } if (fullName.length() > 0) { temp += " OpenClinica:FullName=\"" + StringEscapeUtils.escapeXml(fullName) + "\""; } if (uid.length() > 0) { xml.append(currentIndent + indent + indent + "<UserRef UserOID=\"" + StringEscapeUtils.escapeXml(uid) + " \"" + temp + "/>"); xml.append(nls); } } xml.append(currentIndent + indent + "</OpenClinica:ChildNote>"); xml.append(nls); } } xml.append(currentIndent + "</OpenClinica:DiscrepancyNote>"); xml.append(nls); } public void setClinicalData(OdmClinicalDataBean clinicaldata) { this.clinicalData = clinicaldata; } public OdmClinicalDataBean getClinicalData() { return this.clinicalData; } @SuppressWarnings("unchecked") private void sortImportItemGroupDataBeanList(ArrayList<ImportItemGroupDataBean> igs) { Collections.sort(igs, new Comparator() { public int compare(Object o1, Object o2) { String x1 = ((ImportItemGroupDataBean) o1).getItemGroupOID(); String x2 = ((ImportItemGroupDataBean) o2).getItemGroupOID(); int sComp = x1.compareTo(x2); if (sComp != 0) { return sComp; } else { Integer i1 = Integer.valueOf(((ImportItemGroupDataBean) o1).getItemGroupRepeatKey()); Integer i2 = Integer.valueOf(((ImportItemGroupDataBean) o2).getItemGroupRepeatKey()); return i1.compareTo(i2); } } }); } @SuppressWarnings("unchecked") private void sortImportItemDataBeanList(ArrayList<ImportItemDataBean> items) { Collections.sort(items, new Comparator() { public int compare(Object o1, Object o2) { String i1 = ((ImportItemDataBean) o1).getItemOID(); String i2 = ((ImportItemDataBean) o2).getItemOID(); // Integer i1 = ((ImportItemDataBean) o1).getItemId(); // Integer i2 = ((ImportItemDataBean) o2).getItemId(); return i1.compareTo(i2); } }); } }