/**
* Finds any missing information from the sample object, and fills it in so that DB writeback will
* be complete.
*
* @param sample may or may not have all its data.
* @throws Exception by called methods.
*/
private void prepareSampleForWriteback(
Sample sample, String actorName, Date transactionDate, Session session) throws DAOException {
handleNonNewSample(sample, session);
handleCreationTracking(sample, actorName, transactionDate, session);
handleProjectRelation(sample, sample.getProjectName(), sample.getSampleName(), session);
}
public void update(Sample sample, Date transactionDate, Session session) throws DAOException {
try {
if (sample.getModifiedDate() == null) {
sample.setModifiedDate(transactionDate);
}
session.merge(sample);
} catch (Exception ex) {
throw new DAOException(ex);
}
}
private void handleNonNewSample(Sample sample, Session session) throws DAOException {
// See: any old sample by same name, and in same project? Then throw exception.
Criteria crit = session.createCriteria(Sample.class);
String sampleName = sample.getSampleName();
crit.add(Restrictions.eq("sampleName", sampleName));
crit.add(Restrictions.eq("projectId", sample.getProjectId()));
List results = crit.list();
if (results != null && results.size() > 0) {
throw new DAOException(
"Do not call writeback loop with an existing sample. Sample "
+ sampleName
+ " is in the database.");
}
}
private Sample feedSampleData(Sample sample) throws Exception {
sample.setProjectId(projectId);
sample.setProjectName(projectName);
// set project level by adding 1 to selected parent project's level
if (sample.getParentSampleName() == null || sample.getParentSampleName().equals("0"))
sample.setParentSampleName(null);
String parentSampleName = sample.getParentSampleName();
if (parentSampleName != null && !parentSampleName.isEmpty() && !parentSampleName.equals("0")) {
Sample selectedParentSample = readPersister.getSample(projectId, parentSampleName);
sample.setSampleLevel(selectedParentSample.getSampleLevel() + 1);
} else {
sample.setParentSampleId(null);
sample.setSampleLevel(1);
}
return sample;
}
private MultiLoadParameter createMultiLoadParameter(
String projectName, Project project, Sample sample, List<FileReadAttributeBean> frab)
throws Exception {
MultiLoadParameter loadParameter = new MultiLoadParameter();
boolean isSampleRegistration = false;
boolean isProjectRegistration = false;
if (this.eventName.equals(Constants.EVENT_PROJECT_REGISTRATION)
&& project.getProjectName() != null
&& !project.getProjectName().isEmpty()) {
isProjectRegistration = true;
List<Project> projectList = new ArrayList<Project>();
projectList.add(feedProjectData(project));
loadParameter.addProjects(projectList);
/*
* loads all event meta attributes from the parent
* by hkim 6/11/13
*/
List<EventMetaAttribute> emas =
this.readPersister.getEventMetaAttributes(
projectName, null); // , Constants.EVENT_PROJECT_REGISTRATION);
if (emas != null && emas.size() > 0) {
List<EventMetaAttribute> newEmas = new ArrayList<EventMetaAttribute>(emas.size());
for (EventMetaAttribute ema : emas) {
EventMetaAttribute newEma = new EventMetaAttribute();
newEma.setProjectName(project.getProjectName());
newEma.setEventName(ema.getEventName());
newEma.setEventTypeLookupId(ema.getEventTypeLookupId());
newEma.setAttributeName(ema.getAttributeName());
newEma.setNameLookupId(ema.getNameLookupId());
newEma.setActive(ema.isActive());
newEma.setRequired(ema.isRequired());
newEma.setDesc(ema.getDesc());
newEma.setDataType(ema.getDataType());
newEma.setLabel(ema.getLabel());
newEma.setOntology(ema.getOntology());
newEma.setOptions(ema.getOptions());
newEma.setSampleRequired(ema.isSampleRequired());
newEmas.add(newEma);
}
loadParameter.addEventMetaAttributes(newEmas);
} else {
throw new Exception(
String.format(
"Event Metadata has not been set up for the parent project and the '%s' event type.",
Constants.EVENT_PROJECT_REGISTRATION));
}
List<SampleMetaAttribute> smas = this.readPersister.getSampleMetaAttributes(projectId);
if (smas != null && smas.size() > 0) {
List<SampleMetaAttribute> newSmas = new ArrayList<SampleMetaAttribute>(smas.size());
for (SampleMetaAttribute sma : smas) {
SampleMetaAttribute newSma = new SampleMetaAttribute();
newSma.setProjectName(project.getProjectName());
newSma.setAttributeName(sma.getAttributeName());
newSma.setNameLookupId(sma.getNameLookupId());
newSma.setDataType(sma.getDataType());
newSma.setDesc(sma.getDesc());
newSma.setLabel(sma.getLabel());
newSma.setOntology(sma.getOntology());
newSma.setOptions(sma.getOptions());
newSma.setRequired(sma.isRequired());
newSma.setActive(sma.isActive());
newSmas.add(newSma);
}
loadParameter.addSampleMetaAttributes(newSmas);
}
List<ProjectMetaAttribute> pmas = this.readPersister.getProjectMetaAttributes(projectName);
if (pmas != null && pmas.size() > 0) {
List<ProjectMetaAttribute> newPmas = new ArrayList<ProjectMetaAttribute>(pmas.size());
for (ProjectMetaAttribute pma : pmas) {
ProjectMetaAttribute newPma = new ProjectMetaAttribute();
newPma.setProjectName(project.getProjectName());
newPma.setAttributeName(pma.getAttributeName());
newPma.setDataType(pma.getDataType());
newPma.setDesc(pma.getDesc());
newPma.setLabel(pma.getLabel());
newPma.setNameLookupId(pma.getNameLookupId());
newPma.setOntology(pma.getOntology());
newPma.setOptions(pma.getOptions());
newPma.setRequired(pma.isRequired());
newPma.setActive(pma.isActive());
newPmas.add(newPma);
}
loadParameter.addProjectMetaAttributes(newPmas);
}
} else if (this.eventName.equals(Constants.EVENT_SAMPLE_REGISTRATION)
&& sample.getSampleName() != null
&& !sample.getSampleName().isEmpty()) {
isSampleRegistration = true;
List<Sample> sampleList = new ArrayList<Sample>();
sampleList.add(feedSampleData(sample));
loadParameter.addSamples(sampleList);
}
List<FileReadAttributeBean> loadingList = null;
if (frab != null && frab.size() > 0) {
loadingList =
processFileReadBeans(
isProjectRegistration ? project.getProjectName() : projectName,
isSampleRegistration ? sample.getSampleName() : this.sampleName,
frab);
}
if (loadingList != null && loadingList.size() > 0) {
if (isProjectRegistration) {
loadParameter.addProjectRegistrations(Constants.EVENT_PROJECT_REGISTRATION, loadingList);
} else if (isSampleRegistration) {
loadParameter.addSampleRegistrations(Constants.EVENT_SAMPLE_REGISTRATION, loadingList);
} else {
loadParameter.addEvents(this.eventName, loadingList);
}
}
return loadParameter;
}
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;
}