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));
}
}
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) {
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();
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();
for (ImportItemDataBean item : items) {
if ("Yes".equals(item.getIsNull())) {
xml.append(
indent
+ indent
+ indent
+ indent
+ indent
+ indent
+ "<ItemData ItemOID=\""
+ StringEscapeUtils.escapeXml(item.getItemOID())
+ "\" IsNull=\"Yes\"");
if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) {
xml.append(
" OpenClinica:ReasonForNull=\""
+ StringEscapeUtils.escapeXml(item.getReasonForNull())
+ "\"");
}
xml.append("/>");
xml.append(nls);
} else {
String muRefOid = item.getMeasurementUnitRef().getElementDefOID();
if (muRefOid != null && muRefOid.length() > 0) {
xml.append(
indent
+ indent
+ indent
+ indent
+ indent
+ indent
+ "<ItemData ItemOID=\""
+ StringEscapeUtils.escapeXml(item.getItemOID())
+ "\" Value=\""
+ StringEscapeUtils.escapeXml(item.getValue())
+ "\">");
xml.append(nls);
xml.append(
indent
+ indent
+ indent
+ indent
+ indent
+ indent
+ indent
+ "<MeasurementUnitRef MeasurementUnitOID=\""
+ StringEscapeUtils.escapeXml(muRefOid)
+ "\"/>");
xml.append(nls);
xml.append(indent + indent + indent + indent + indent + indent + "</ItemData>");
xml.append(nls);
} else {
xml.append(
indent
+ indent
+ indent
+ indent
+ indent
+ indent
+ "<ItemData ItemOID=\""
+ StringEscapeUtils.escapeXml(item.getItemOID())
+ "\" Value=\""
+ StringEscapeUtils.escapeXml(item.getValue())
+ "\"/>");
xml.append(nls);
}
}
}
xml.append(indent + indent + indent + indent + indent + "</ItemGroupData>");
xml.append(nls);
}
xml.append(indent + indent + indent + indent + "</FormData>");
xml.append(nls);
}
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);
}
}
}
xml.append(indent + indent + "</SubjectData>");
xml.append(nls);
}
if (footer) {
xml.append(indent + "</ClinicalData>");
xml.append(nls);
}
}
public String generateHardValidationErrorMessage(
ArrayList<SubjectDataBean> subjectData,
HashMap<String, String> hardValidationErrors,
boolean isValid) {
StringBuffer sb = new StringBuffer();
String studyEventRepeatKey = "1";
String groupRepeatKey = "1";
sb.append("<table border=\'0\' cellpadding=\'0\' cellspacing=\'0\' width=\'100%\'>");
for (SubjectDataBean subjectDataBean : subjectData) {
sb.append(
"<tr valign=\'top\'> <td class=\'table_header_row\' colspan=\'4\'>Study Subject: "
+ subjectDataBean.getSubjectOID()
+ "</td> </tr>");
// next step here
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
sb.append(
"<tr valign=\'top\'> <td class=\'table_header_row\'>Event CRF OID</td> <td class=\'table_header_row\' colspan=\'3\'></td>");
sb.append("</tr> <tr valign=\'top\'> <td class=\'table_cell_left\'>");
sb.append(studyEventDataBean.getStudyEventOID());
if (studyEventDataBean.getStudyEventRepeatKey() != null) {
studyEventRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
sb.append(" (Repeat key " + studyEventDataBean.getStudyEventRepeatKey() + ")");
} else {
// reset
studyEventRepeatKey = "1";
}
sb.append("</td> <td class=\'table_cell\' colspan=\'3\'></td> </tr>");
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
for (FormDataBean formDataBean : formDataBeans) {
sb.append("<tr valign=\'top\'> <td class=\'table_header_row\'></td> ");
sb.append(
"<td class=\'table_header_row\'>CRF Version OID</td> <td class=\'table_header_row\' colspan=\'2\'></td></tr>");
sb.append(
"<tr valign=\'top\'> <td class=\'table_cell_left\'></td> <td class=\'table_cell\'>");
sb.append(formDataBean.getFormOID());
sb.append("</td> <td class=\'table_cell\' colspan=\'2\'></td> </tr>");
ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
sb.append("<tr valign=\'top\'> <td class=\'table_header_row\'></td>");
sb.append(
"<td class=\'table_header_row\'></td> <td class=\'table_header_row\' colspan=\'2\'>");
sb.append(itemGroupDataBean.getItemGroupOID());
if (itemGroupDataBean.getItemGroupRepeatKey() != null) {
groupRepeatKey = itemGroupDataBean.getItemGroupRepeatKey();
sb.append(" (Repeat key " + itemGroupDataBean.getItemGroupRepeatKey() + ")");
} else {
groupRepeatKey = "1";
}
sb.append("</td></tr>");
ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
for (ImportItemDataBean itemDataBean : itemDataBeans) {
String oidKey =
itemDataBean.getItemOID()
+ "_"
+ studyEventRepeatKey
+ "_"
+ groupRepeatKey
+ "_"
+ subjectDataBean.getSubjectOID();
if (!isValid) {
if (hardValidationErrors.containsKey(oidKey)) {
sb.append("<tr valign=\'top\'> <td class=\'table_cell_left\'></td>");
sb.append(
"<td class=\'table_cell\'></td> <td class=\'table_cell\'><font color=\'red\'>");
sb.append(itemDataBean.getItemOID());
sb.append("</font></td> <td class=" + "\'table_cell\'>");
sb.append(itemDataBean.getValue() + "<br/>");
sb.append(hardValidationErrors.get(oidKey));
sb.append("</td></tr>");
/*
* <tr valign="top"> <td
* class="table_cell_left"></td> <td
* class="table_cell"></td> <td
* class="table_cell"><font
* color="red"><c:out
* value="${itemData.itemOID}"/></font></td>
* <td class="table_cell"> <c:out
* value="${itemData.value}"/><br/> <c:out
* value="${hardValidationErrors[oidKey]}"/>
* </td> </tr>
*/
}
} else {
if (!hardValidationErrors.containsKey(oidKey)) {
sb.append("<tr valign=\'top\'> <td class=\'table_cell_left\'></td>");
sb.append("<td class=\'table_cell\'></td> <td class=\'table_cell\'>");
sb.append(itemDataBean.getItemOID());
sb.append("</td> <td class=" + "\'table_cell\'>");
sb.append(itemDataBean.getValue());
sb.append("</td></tr>");
}
}
}
}
}
}
}
sb.append("</table>");
return sb.toString();
}
