private List<FileReadAttributeBean> processFileReadBeans(
String _projectName, String _sampleName, List<FileReadAttributeBean> loadingList)
throws Exception {
List<FileReadAttributeBean> processedList = new ArrayList<FileReadAttributeBean>();
for (FileReadAttributeBean fBean : loadingList) {
if (fBean.getProjectName() == null
|| eventName.equals(Constants.EVENT_PROJECT_REGISTRATION)) {
fBean.setProjectName(_projectName);
}
if (fBean.getSampleName() == null) {
fBean.setSampleName(_sampleName);
}
// handle file uploads
if (fBean.getUpload() != null
&& fBean.getUploadFileName() != null
&& !fBean.getUploadFileName().isEmpty()) {
fileStoragePath =
fileStoragePath + (fileStoragePath.endsWith(File.separator) ? "" : File.separator);
String originalFileName = fBean.getUploadFileName();
String fileDirectoryPathProject = _projectName.replaceAll(" ", "_"); // project folder
String fileDirectoryPathSample =
fileDirectoryPathProject
+ File.separator
+ (_sampleName != null && !_sampleName.isEmpty()
? _sampleName.replaceAll(" ", "_")
: "project"); // sample folder
String fileDirectoryPath =
fileDirectoryPathSample
+ File.separator
+ CommonTool.convertTimestampToDate(new Date()); // date folder
String fileName =
originalFileName.substring(0, originalFileName.indexOf("."))
+ "_"
+ System.currentTimeMillis()
+ originalFileName.substring(
originalFileName.indexOf(
".")); // append "_" + current time in milliseconds to file name
File fileDirectory = new File(fileStoragePath + fileDirectoryPath);
if (!fileDirectory.exists() || !fileDirectory.isDirectory()) {
fileDirectory.mkdirs();
}
File theFile = new File(fileDirectory.getPath() + File.separator + fileName);
FileUtils.copyFile(fBean.getUpload(), theFile);
if (theFile.exists() && theFile.isFile() && theFile.canRead()) {
fBean.getUpload().delete();
fBean.setAttributeValue(fileDirectoryPath + File.separator + fileName);
if (loadedFiles == null) {
loadedFiles = new ArrayList<String>();
}
loadedFiles.add(fBean.getAttributeValue());
}
}
if (!fBean.getAttributeName().equals("0")
&& fBean.getAttributeValue() != null
&& !fBean.getAttributeValue().equals("0")
&& !fBean.getAttributeValue().isEmpty()) {
processedList.add(fBean);
}
}
return processedList;
}
public String execute() {
String rtnVal = SUCCESS;
UserTransaction tx = null;
try {
sampleName = sampleName != null && sampleName.equals("0") ? null : sampleName;
if (jobType != null) {
boolean isProjectRegistration = eventName.equals(Constants.EVENT_PROJECT_REGISTRATION);
boolean isSampleRegistration = eventName.equals(Constants.EVENT_SAMPLE_REGISTRATION);
if (projectName == null
|| projectName.equals("0")
|| eventName == null
|| eventName.equals("0")) throw new Exception("Project or Event type is not selected.");
if (jobType.equals("insert")) { // loads single event
tx = (UserTransaction) new InitialContext().lookup("java:comp/UserTransaction");
tx.begin();
psewt.loadAll(
null,
this.createMultiLoadParameter(projectName, loadingProject, loadingSample, beanList));
this.reset();
} else if (jobType.equals("grid")) { // loads multiple events from grid view
tx = (UserTransaction) new InitialContext().lookup("java:comp/UserTransaction");
tx.begin();
for (GridBean gBean : gridList) {
if (gBean != null) {
if (isProjectRegistration
&& gBean.getProjectName() != null
&& gBean.getProjectPublic() != null) {
loadingProject = new Project();
loadingProject.setProjectName(gBean.getProjectName());
loadingProject.setIsPublic(Integer.valueOf(gBean.getProjectPublic()));
} else if (isSampleRegistration
&& gBean.getSampleName() != null
&& gBean.getSamplePublic() != null) {
loadingSample = new Sample();
loadingSample.setSampleName(gBean.getSampleName());
loadingSample.setParentSampleName(gBean.getParentSampleName());
loadingSample.setIsPublic(Integer.valueOf(gBean.getSamplePublic()));
} else {
if (gBean.getSampleName() != null) {
this.sampleName = gBean.getSampleName();
}
}
List<FileReadAttributeBean> fBeanList = gBean.getBeanList();
if (fBeanList != null && fBeanList.size() > 0) {
psewt.loadAll(
null,
this.createMultiLoadParameter(
projectName, loadingProject, loadingSample, fBeanList));
}
}
}
this.reset();
} else if (jobType.equals("file")) { // loads data from a CSV file to grid view
if (!this.uploadFile.canRead()) {
throw new Exception("Error in reading the file.");
} else {
try {
CSVReader reader = new CSVReader(new FileReader(this.uploadFile));
int lineCount = 0;
List<String> columns = new ArrayList<String>();
String currProjectName = null;
gridList = new ArrayList<GridBean>();
boolean hasSampleName = false;
String[] line;
while ((line = reader.readNext()) != null) {
if (lineCount != 1) {
if (lineCount == 0) {
Collections.addAll(columns, line);
hasSampleName = columns.indexOf("SampleName") >= 0;
} else {
int colIndex = 0;
currProjectName = line[colIndex++];
if (!isProjectRegistration && !currProjectName.equals(this.projectName)) {
throw new Exception(MULTIPLE_SUBJECT_IN_FILE_MESSAGE);
}
GridBean gBean = new GridBean();
gBean.setProjectName(currProjectName);
if (hasSampleName) {
gBean.setSampleName(line[(colIndex++)]);
}
if (isProjectRegistration) {
gBean.setProjectName(currProjectName);
gBean.setProjectPublic(line[(colIndex++)]);
} else if (isSampleRegistration) {
gBean.setParentSampleName(line[(colIndex++)]);
gBean.setSamplePublic(line[(colIndex++)]);
}
gBean.setBeanList(new ArrayList<FileReadAttributeBean>());
for (; colIndex < columns.size(); colIndex++) {
FileReadAttributeBean fBean = new FileReadAttributeBean();
fBean.setProjectName(
isProjectRegistration ? currProjectName : this.projectName);
fBean.setAttributeName(columns.get(colIndex));
fBean.setAttributeValue(line[colIndex]);
gBean.getBeanList().add(fBean);
}
this.gridList.add(gBean);
}
}
lineCount++;
}
jobType = "grid";
} catch (Exception ex) {
throw ex;
}
}
} else if (jobType.equals("template")) { // download template
List<EventMetaAttribute> emaList =
readPersister.getEventMetaAttributes(projectName, eventName);
/*
* removing the sanity check on sample requirement since multiple sample support is in action
* by hkim 5/2/13
ModelValidator validator = new ModelValidator();
validator.validateEventTemplateSanity(emaList, projectName, sampleName, eventName);
*/
TemplatePreProcessingUtils cvsUtils = new TemplatePreProcessingUtils();
String templateType = jobType.substring(jobType.indexOf("_") + 1);
downloadStream =
cvsUtils.buildFileContent(templateType, emaList, projectName, sampleName, eventName);
downloadContentType = templateType.equals("c") ? "csv" : "vnd.ms-excel";
rtnVal = Constants.FILE_DOWNLOAD_MSG;
}
}
} catch (Exception ex) {
logger.error("Exception in EventLoader : " + ex.toString());
ex.printStackTrace();
if (ex.getClass() == ForbiddenResourceException.class) {
addActionError(Constants.DENIED_USER_EDIT_MESSAGE);
return Constants.FORBIDDEN_ACTION_RESPONSE;
} else if (ex.getClass() == ForbiddenResourceException.class) {
addActionError(Constants.DENIED_USER_EDIT_MESSAGE);
return LOGIN;
} else if (ex.getClass() == ParseException.class)
addActionError(Constants.INVALID_DATE_MESSAGE);
else {
addActionError(ex.toString());
}
// deletes uploaded files in event of error
if (loadedFiles != null && loadedFiles.size() > 0) {
for (String filePath : loadedFiles) {
File tempFile = new File(fileStoragePath + filePath);
if (tempFile.exists()) tempFile.delete();
}
}
try {
if (tx != null) tx.rollback();
} catch (SystemException se) {
addActionError(se.toString());
}
rtnVal = ERROR;
} finally {
try {
// get project list for the drop down box
List<String> projectNameList = new ArrayList<String>();
if (projectNames == null || projectNames.equals("")) {
projectNameList.add("ALL");
} else if (projectNames.contains(",")) {
projectNameList.addAll(Arrays.asList(projectNames.split(",")));
} else {
projectNameList.add(projectNames);
}
projectList = readPersister.getProjects(projectNameList);
if (tx != null && tx.getStatus() != Status.STATUS_NO_TRANSACTION) {
tx.commit();
}
if (jobType != null && jobType.equals("grid") && this.uploadFile != null) {
this.uploadFile.delete();
}
} catch (Exception ex) {
ex.printStackTrace();
}
}
return rtnVal;
}