/** createTabFile, added by tbh, 01/2009 */
public HashMap<String, Integer> createTabFile(
ExtractBean eb,
long sysTimeBegin,
String generalFileDir,
DatasetBean datasetBean,
int activeStudyId,
int parentStudyId,
String generalFileDirCopy) {
TabReportBean answer = new TabReportBean();
DatasetDAO dsdao = new DatasetDAO(ds);
// create the extract bean here, tbh
eb = dsdao.getDatasetData(eb, activeStudyId, parentStudyId);
eb.getMetadata();
eb.computeReport(answer);
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
String TXTFileName = datasetBean.getName() + "_tab.xls";
int fId =
this.createFile(
TXTFileName,
generalFileDir,
answer.toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.TXTFILE,
true);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFile(
TXTFileName,
generalFileDirCopy,
answer.toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.TXTFILE,
false);
}
logger.info("created txt file");
// return TXTFileName;
HashMap answerMap = new HashMap<String, Integer>();
answerMap.put(TXTFileName, new Integer(fId));
return answerMap;
}
public ExtractBean generateExtractBean(
DatasetBean dsetBean, StudyBean currentStudy, StudyBean parentStudy) {
ExtractBean eb = new ExtractBean(ds);
eb.setDataset(dsetBean);
eb.setShowUniqueId(CoreResources.getField("show_unique_id"));
eb.setStudy(currentStudy);
eb.setParentStudy(parentStudy);
eb.setDateCreated(new java.util.Date());
return eb;
}
/**
* createSPSSFile, added by tbh, 01/2009
*
* @param db
* @param eb
* @param currentstudyid
* @param parentstudy
* @return
*/
public HashMap<String, Integer> createSPSSFile(
DatasetBean db,
ExtractBean eb2,
StudyBean currentStudy,
StudyBean parentStudy,
long sysTimeBegin,
String generalFileDir,
SPSSReportBean answer,
String generalFileDirCopy) {
setUpResourceBundles();
String SPSSFileName = db.getName() + "_data_spss.dat";
String DDLFileName = db.getName() + "_ddl_spss.sps";
String ZIPFileName = db.getName() + "_spss";
SPSSVariableNameValidationBean svnvbean = new SPSSVariableNameValidationBean();
answer.setDatFileName(SPSSFileName);
// DatasetDAO dsdao = new DatasetDAO(ds);
// create the extract bean here, tbh
// ExtractBean eb = this.generateExtractBean(db, currentStudy,
// parentStudy);
// eb = dsdao.getDatasetData(eb, currentStudy.getId(),
// parentStudy.getId());
// eb.getMetadata();
// eb.computeReport(answer);
answer.setItems(eb2.getItemNames()); // set up items here to get
// itemMetadata
// set up response sets for each item here
ItemDAO itemdao = new ItemDAO(ds);
ItemFormMetadataDAO imfdao = new ItemFormMetadataDAO(ds);
ArrayList items = answer.getItems();
for (int i = 0; i < items.size(); i++) {
DisplayItemHeaderBean dih = (DisplayItemHeaderBean) items.get(i);
ItemBean item = dih.getItem();
ArrayList metas = imfdao.findAllByItemId(item.getId());
// for (int h = 0; h < metas.size(); h++) {
// ItemFormMetadataBean ifmb = (ItemFormMetadataBean)
// metas.get(h);
// logger.info("group name found:
// "+ifmb.getGroupLabel());
// }
// logger.info("crf versionname" +
// meta.getCrfVersionName());
item.setItemMetas(metas);
}
HashMap eventDescs = new HashMap<String, String>();
eventDescs = eb2.getEventDescriptions();
eventDescs.put("SubjID", resword.getString("study_subject_ID"));
eventDescs.put("ProtocolID", resword.getString("protocol_ID_site_ID"));
eventDescs.put("DOB", resword.getString("date_of_birth"));
eventDescs.put("YOB", resword.getString("year_of_birth"));
eventDescs.put("Gender", resword.getString("gender"));
answer.setDescriptions(eventDescs);
ArrayList generatedReports = new ArrayList<String>();
try {
// YW <<
generatedReports.add(answer.getMetadataFile(svnvbean, eb2).toString());
generatedReports.add(answer.getDataFile().toString());
// YW >>
} catch (IndexOutOfBoundsException i) {
generatedReports.add(answer.getMetadataFile(svnvbean, eb2).toString());
logger.debug("throw the error here");
}
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
ArrayList titles = new ArrayList();
// YW <<
titles.add(DDLFileName);
titles.add(SPSSFileName);
// YW >>
// create new createFile method that accepts array lists to
// put into zip files
int fId =
this.createFile(
ZIPFileName,
titles,
generalFileDir,
generatedReports,
db,
sysTimeEnd,
ExportFormatBean.TXTFILE,
true);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFile(
ZIPFileName,
titles,
generalFileDirCopy,
generatedReports,
db,
sysTimeEnd,
ExportFormatBean.TXTFILE,
false);
}
// return DDLFileName;
HashMap answerMap = new HashMap<String, Integer>();
answerMap.put(DDLFileName, new Integer(fId));
return answerMap;
}
/** 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;
}