use of org.akaza.openclinica.bean.extract.odm.MetaDataReportBean in project OpenClinica by OpenClinica.
the class OdmFileCreation method createODMFile.
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, boolean zipped, boolean saveToDB, boolean deleteOld, String odmType, UserAccountBean userBean) {
Integer ssNumber = getStudySubjectNumber(studySubjectNumber);
MetaDataCollector mdc = new MetaDataCollector(dataSource, datasetBean, currentStudy, ruleSetRuleDao);
AdminDataCollector adc = new AdminDataCollector(dataSource, datasetBean, currentStudy);
ClinicalDataCollector cdc = new ClinicalDataCollector(dataSource, datasetBean, currentStudy);
MetaDataCollector.setTextLength(200);
if (deleteOld) {
File file = new File(generalFileDir);
if (file.isDirectory()) {
files = file.listFiles();
oldFiles = Arrays.asList(files);
}
}
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\"");
xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/odm_ext_v121/v3.1\"");
xmlnsList.add("xmlns:OpenClinicaRules=\"http://www.openclinica.org/ns/rules/v3.1\"");
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");
odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0-OC3-0.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");
odmb.setOdmType(odmType);
mdc.setODMBean(odmb);
adc.setOdmbean(odmb);
cdc.setODMBean(odmb);
}
}
//////////////////////////////////////////
////////// MetaData Extraction //////////
mdc.collectFileData();
MetaDataReportBean metaReport = new MetaDataReportBean(mdc.getOdmStudyMap(), coreResources);
metaReport.setODMVersion(odmVersion);
metaReport.setOdmBean(mdc.getODMBean());
metaReport.createChunkedOdmXml(Boolean.TRUE);
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
String ODMXMLFileName = mdc.getODMBean().getFileOID() + ".xml";
int fId = createFileK(ODMXMLFileName, generalFileDir, metaReport.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
if (!"".equals(generalFileDirCopy)) {
int fId2 = createFileK(ODMXMLFileName, generalFileDirCopy, metaReport.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
}
//////////////////////////////////////////
////////// 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 = createFileK(ODMXMLFileName, generalFileDir, adminReport.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
if (!"".equals(generalFileDirCopy)) {
int fId2 = createFileK(ODMXMLFileName, generalFileDirCopy, adminReport.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
}
//////////////////////////////////////////
////////// ClinicalData Extraction ///////
DatasetDAO dsdao = new DatasetDAO(dataSource);
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()) {
JobTerminationMonitor.check();
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()) {
JobTerminationMonitor.check();
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(dataSource, 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 = createFileK(ODMXMLFileName, generalFileDir, report.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
if (!"".equals(generalFileDirCopy)) {
int fId2 = createFileK(ODMXMLFileName, generalFileDirCopy, report.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
}
}
}
sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
fId = createFileK(ODMXMLFileName, generalFileDir, "</ODM>", datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, saveToDB, zipped, deleteOld, userBean);
if (!"".equals(generalFileDirCopy)) {
int fId2 = createFileK(ODMXMLFileName, generalFileDirCopy, "</ODM>", datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
}
//////////////////////////////////////////
////////// 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);
* }
*/
HashMap answerMap = new HashMap<String, Integer>();
// JN: Zipped in the next stage as thats where the ODM file is named and copied over in default categories.
// if(zipped)
// { try {
// zipFile(ODMXMLFileName,generalFileDir);
//
// } catch (IOException e) {
// // TODO Auto-generated catch block
// logger.error(e.getMessage());
// e.printStackTrace();
// }
//
// } // return ODMXMLFileName;
answerMap.put(ODMXMLFileName, new Integer(fId));
return answerMap;
}
use of org.akaza.openclinica.bean.extract.odm.MetaDataReportBean in project OpenClinica by OpenClinica.
the class RuleController method studyMetadata.
@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-OC3-0.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;
}
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