/** createODMfile, added by tbh, 01/2009 */
public HashMap<String, Integer> createODMFile(
String odmVersion,
long sysTimeBegin,
String generalFileDir,
DatasetBean datasetBean,
StudyBean currentStudy,
String generalFileDirCopy,
ExtractBean eb,
Integer currentStudyId,
Integer parentStudyId,
String studySubjectNumber) {
Integer ssNumber = getStudySubjectNumber(studySubjectNumber);
MetaDataCollector mdc = new MetaDataCollector(ds, datasetBean, currentStudy);
AdminDataCollector adc = new AdminDataCollector(ds, datasetBean, currentStudy);
ClinicalDataCollector cdc = new ClinicalDataCollector(ds, datasetBean, currentStudy);
MetaDataCollector.setTextLength(200);
if (odmVersion != null) {
// by default odmVersion is 1.2
if ("1.3".equals(odmVersion)) {
ODMBean odmb = new ODMBean();
odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 ODM1-3-0.xsd");
ArrayList<String> xmlnsList = new ArrayList<String>();
xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
odmb.setXmlnsList(xmlnsList);
odmb.setODMVersion("1.3");
mdc.setODMBean(odmb);
adc.setOdmbean(odmb);
cdc.setODMBean(odmb);
} else if ("oc1.2".equals(odmVersion)) {
ODMBean odmb = new ODMBean();
// odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.2 OpenClinica-ODM1-2-1.xsd");
odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.2 OpenClinica-ODM1-2-1-OC1.xsd");
ArrayList<String> xmlnsList = new ArrayList<String>();
xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.2\"");
xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.2\"");
odmb.setXmlnsList(xmlnsList);
odmb.setODMVersion("oc1.2");
mdc.setODMBean(odmb);
adc.setOdmbean(odmb);
cdc.setODMBean(odmb);
} else if ("oc1.3".equals(odmVersion)) {
ODMBean odmb = mdc.getODMBean();
// odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0.xsd");
odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0-OC1.xsd");
ArrayList<String> xmlnsList = new ArrayList<String>();
xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.3\"");
odmb.setXmlnsList(xmlnsList);
odmb.setODMVersion("oc1.3");
mdc.setODMBean(odmb);
adc.setOdmbean(odmb);
cdc.setODMBean(odmb);
}
}
//////////////////////////////////////////
////////// MetaData Extraction //////////
mdc.collectFileData();
MetaDataReportBean metaReport = new MetaDataReportBean(mdc.getOdmStudyMap());
metaReport.setODMVersion(odmVersion);
metaReport.setOdmBean(mdc.getODMBean());
metaReport.createChunkedOdmXml(Boolean.TRUE);
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
String ODMXMLFileName = mdc.getODMBean().getFileOID() + ".xml";
int fId =
this.createFileK(
ODMXMLFileName,
generalFileDir,
metaReport.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFileK(
ODMXMLFileName,
generalFileDirCopy,
metaReport.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
}
//////////////////////////////////////////
////////// AdminData Extraction //////////
adc.collectFileData();
AdminDataReportBean adminReport = new AdminDataReportBean(adc.getOdmAdminDataMap());
adminReport.setODMVersion(odmVersion);
adminReport.setOdmBean(mdc.getODMBean());
adminReport.createChunkedOdmXml(Boolean.TRUE);
sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
fId =
this.createFileK(
ODMXMLFileName,
generalFileDir,
adminReport.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFileK(
ODMXMLFileName,
generalFileDirCopy,
adminReport.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
}
//////////////////////////////////////////
////////// ClinicalData Extraction ///////
DatasetDAO dsdao = new DatasetDAO(ds);
String sql = eb.getDataset().getSQLStatement();
String st_sed_in = dsdao.parseSQLDataset(sql, true, true);
String st_itemid_in = dsdao.parseSQLDataset(sql, false, true);
int datasetItemStatusId = eb.getDataset().getDatasetItemStatus().getId();
String ecStatusConstraint = dsdao.getECStatusConstraint(datasetItemStatusId);
String itStatusConstraint = dsdao.getItemDataStatusConstraint(datasetItemStatusId);
Iterator<OdmStudyBase> it = cdc.getStudyBaseMap().values().iterator();
while (it.hasNext()) {
OdmStudyBase u = it.next();
ArrayList newRows =
dsdao.selectStudySubjects(
u.getStudy().getId(),
0,
st_sed_in,
st_itemid_in,
dsdao.genDatabaseDateConstraint(eb),
ecStatusConstraint,
itStatusConstraint);
///////////////
int fromIndex = 0;
boolean firstIteration = true;
while (fromIndex < newRows.size()) {
int toIndex =
fromIndex + ssNumber < newRows.size() ? fromIndex + ssNumber : newRows.size() - 1;
List x = newRows.subList(fromIndex, toIndex + 1);
fromIndex = toIndex + 1;
String studySubjectIds = "";
for (int i = 0; i < x.size(); i++) {
StudySubjectBean sub = new StudySubjectBean();
sub = (StudySubjectBean) x.get(i);
studySubjectIds += "," + sub.getId();
} // for
studySubjectIds = studySubjectIds.replaceFirst(",", "");
ClinicalDataUnit cdata =
new ClinicalDataUnit(
ds,
datasetBean,
cdc.getOdmbean(),
u.getStudy(),
cdc.getCategory(),
studySubjectIds);
cdata.setCategory(cdc.getCategory());
cdata.collectOdmClinicalData();
FullReportBean report = new FullReportBean();
report.setClinicalData(cdata.getOdmClinicalData());
report.setOdmStudyMap(mdc.getOdmStudyMap());
report.setODMVersion(odmVersion);
// report.setOdmStudy(mdc.getOdmStudy());
report.setOdmBean(mdc.getODMBean());
if (firstIteration && fromIndex >= newRows.size()) {
report.createChunkedOdmXml(Boolean.TRUE, true, true);
firstIteration = false;
} else if (firstIteration) {
report.createChunkedOdmXml(Boolean.TRUE, true, false);
firstIteration = false;
} else if (fromIndex >= newRows.size()) {
report.createChunkedOdmXml(Boolean.TRUE, false, true);
} else {
report.createChunkedOdmXml(Boolean.TRUE, false, false);
}
fId =
this.createFileK(
ODMXMLFileName,
generalFileDir,
report.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFileK(
ODMXMLFileName,
generalFileDirCopy,
report.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
}
}
}
sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
fId =
this.createFileK(
ODMXMLFileName,
generalFileDir,
"</ODM>",
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
true);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFileK(
ODMXMLFileName,
generalFileDirCopy,
"</ODM>",
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
}
//////////////////////////////////////////
////////// pre pagination extraction /////
/*
mdc.collectFileData();
adc.collectOdmAdminDataMap();
cdc.collectOdmClinicalDataMap();
FullReportBean report = new FullReportBean();
report.setClinicalDataMap(cdc.getOdmClinicalDataMap());
report.setAdminDataMap(adc.getOdmAdminDataMap());
report.setOdmStudyMap(mdc.getOdmStudyMap());
report.setOdmBean(mdc.getODMBean());
report.setODMVersion(odmVersion);
report.createOdmXml(Boolean.TRUE);
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
String ODMXMLFileName = mdc.getODMBean().getFileOID() + ".xml";
int fId = this.createFile(ODMXMLFileName, generalFileDir, report.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, true);
if (!"".equals(generalFileDirCopy)) {
int fId2 = this.createFile(ODMXMLFileName, generalFileDirCopy, report.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false);
} */
// return ODMXMLFileName;
HashMap answerMap = new HashMap<String, Integer>();
answerMap.put(ODMXMLFileName, new Integer(fId));
return answerMap;
}
@RequestMapping(value = "/studies/{study}/metadata", method = RequestMethod.GET)
public ModelAndView studyMetadata(
Model model,
HttpSession session,
@PathVariable("study") String studyOid,
HttpServletResponse response)
throws Exception {
ResourceBundleProvider.updateLocale(new Locale("en_US"));
StudyBean currentStudy = (StudyBean) session.getAttribute("study");
UserAccountBean userAccount = (UserAccountBean) session.getAttribute("userBean");
UserAccountDAO userAccountDao = new UserAccountDAO(dataSource);
userAccount = (UserAccountBean) userAccountDao.findByUserName("root");
StudyDAO studyDao = new StudyDAO(dataSource);
currentStudy = studyDao.findByOid(studyOid);
MetaDataCollector mdc = new MetaDataCollector(dataSource, currentStudy, getRuleSetRuleDao());
AdminDataCollector adc = new AdminDataCollector(dataSource, currentStudy);
// RulesDataCollector rdc = new RulesDataCollector(sm.getDataSource(),
// currentStudy,getRuleSetRuleDao());
MetaDataCollector.setTextLength(200);
ODMBean odmb = mdc.getODMBean();
odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0-OC2-0.xsd");
ArrayList<String> xmlnsList = new ArrayList<String>();
xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
// xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.3\"");
xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/odm_ext_v130/v3.1\"");
xmlnsList.add("xmlns:OpenClinicaRules=\"http://www.openclinica.org/ns/rules/v3.1\"");
odmb.setXmlnsList(xmlnsList);
odmb.setODMVersion("oc1.3");
mdc.setODMBean(odmb);
adc.setOdmbean(odmb);
// rdc.setOdmbean(odmb);
mdc.collectFileData();
MetaDataReportBean metaReport = new MetaDataReportBean(mdc.getOdmStudyMap(), coreResources);
metaReport.setODMVersion("oc1.3");
metaReport.setOdmBean(mdc.getODMBean());
metaReport.createChunkedOdmXml(Boolean.FALSE);
adc.collectFileData();
AdminDataReportBean adminReport = new AdminDataReportBean(adc.getOdmAdminDataMap());
adminReport.setODMVersion("oc1.3");
adminReport.setOdmBean(mdc.getODMBean());
adminReport.createChunkedOdmXml(Boolean.FALSE);
// rdc.collectFileData();
// RulesDataReportBean rulesReport = new
// RulesDataReportBean(rdc.getOdmRulesDataMap(),getCoreResources());
// rulesReport.setODMVersion("oc1.3");
// rulesReport.setOdmBean(mdc.getODMBean());
// rulesReport.createChunkedOdmXml(Boolean.FALSE);
FullReportBean report = new FullReportBean();
report.setAdminDataMap(adc.getOdmAdminDataMap());
report.setOdmStudyMap(mdc.getOdmStudyMap());
report.setCoreResources(coreResources);
// report.setRulesDataMap(rdc.getOdmRulesDataMap());
report.setOdmBean(mdc.getODMBean());
report.setODMVersion("oc1.3");
report.createStudyMetaOdmXml(Boolean.FALSE);
response.setContentType("application/xml");
PrintWriter out = response.getWriter();
out.print(report.getXmlOutput().toString().trim());
return null;
}
