private void intializeMetadataPages() {
metadataWizardPages =
new MetadataWizardPageGroup(
getMetadataWizardPageFactory(),
getLocations(),
CONSTANTS.runWizardType(),
CONSTANTS.runWizardBatchType());
}
ProteomicsRunWizardCommand(final Collection<TreeItem> locations) {
super(locations);
final ArrayList<WizardPage> pages = Lists.newArrayListWithCapacity(8);
intializeMetadataPages();
pages.add(sourcePage);
pages.addAll(metadataWizardPages.asList());
final ServiceSelectionComponent<QueueGridService> thermoSelectionComponent =
serviceSelectionComponentSupplier.get();
thermoSelectionComponent.setServicesType("rawExtract");
thermoServicesSelectionPage =
new ServiceWizardPageImpl<QueueGridService>(thermoSelectionComponent);
final ServiceSelectionComponent<QueueGridService> proteomicsConvertSelectionComponent =
serviceSelectionComponentSupplier.get();
proteomicsConvertSelectionComponent.setServicesType("proteomicsConvert");
proteomicsConvertServicesSelectionPage =
new ServiceWizardPageImpl<QueueGridService>(proteomicsConvertSelectionComponent);
pages.add(thermoServicesSelectionPage);
pages.add(proteomicsConvertServicesSelectionPage);
pages.add(uploadWizardPage);
final WizardOptions options = new WizardOptions();
options.setTitle(CONSTANTS.runWizardTitle());
setupSourceTypeListeners();
updateSourceType();
setWidget(
WizardFactoryImpl.getInstance()
.getWizard(
pages,
options,
new WizardCompletionHandler() {
public void onCompletion(final Window wizard) {
uploadComponent.startUpload();
}
}));
}
private void init(final ListGridRecord sampleRecord, final boolean add) {
final Form form = new Form(nameItem, mudpitItem, categoryItem);
form.setWrapItemTitles(false);
nameItem.setValue(sampleRecord.getAttributeAsString("Name"));
nameItem.addChangedHandler(
new ChangedHandler() {
public void onChanged(final ChangedEvent event) {
checkOk();
}
});
mudpitItem.setValue(sampleRecord.getAttributeAsBoolean("Mudpit"));
categoryItem.setValue(sampleRecord.getAttributeAsString("Category"));
final Label label = new Label(CONSTANTS.scaffoldWizardSampleSearchLabel());
label.setWidth100();
label.setHeight(12);
final TreeOptions treeOptions = new TreeOptions();
treeOptions.setInitialItems(
locationFactory.getTropixObjectSourceRootItems(TropixObjectTreeItemExpanders.get(types)));
treeOptions.setShowPredicate(getShowItemPredicate());
treeOptions.setSelectionPredicate(LocationPredicates.getTropixObjectNotFolderPredicate());
treeOptions.setSelectionType(SelectionType.MULTIPlE);
@SuppressWarnings("unchecked")
final Collection<TreeItem> selectedItems =
(Collection<TreeItem>) sampleRecord.getAttributeAsObject("Selection");
treeOptions.setExpandIds(Locations.getAncestorIds(selectedItems));
treeOptions.setSelectedItems(selectedItems);
final TreeComponent tree = treeComponentFactory.get(treeOptions);
tree.addMultiSelectionListener(this);
final TreeGrid treeGrid = tree.get();
treeGrid.setTooltip("Hold the control key to select multiple items.");
final VLayout layout = new VLayout();
layout.addMember(form);
layout.addMember(label);
layout.addMember(treeGrid);
layout.setSize("500px", "500px");
okButton =
SmartUtils.getButton(
add ? "Add" : "Update",
null,
new Command() {
public void execute() {
sampleRecord.setAttribute("Name", (String) nameItem.getValue());
sampleRecord.setAttribute("Category", (String) categoryItem.getValue());
sampleRecord.setAttribute("Mudpit", (Boolean) mudpitItem.getValue());
sampleRecord.setAttribute("Selection", selection);
if (add) {
dataSource.addData(sampleRecord);
records.add(sampleRecord);
}
listGrid.markForRedraw();
get().markForDestroy();
checkValid();
}
});
final Button cancelButton = SmartUtils.getCancelButton(this);
final Layout opsLayout = new CanvasWithOpsLayout<VLayout>(layout, okButton, cancelButton);
final Window window =
PopOutWindowBuilder.titled((add ? "Add" : "Update") + " Sample")
.withContents(opsLayout)
.autoSized()
.get();
setWidget(window);
checkOk();
get().draw();
}
protected void print(Printer out, List<EventInterface> events) throws IOException {
out.printHeader(
/* 0 */ MESSAGES.colName(),
/* 1 */ MESSAGES.colSection(),
/* 2 */ MESSAGES.colType(),
/* 3 */ MESSAGES.colTitle(),
/* 4 */ MESSAGES.colNote(),
/* 5 */ MESSAGES.colDayOfWeek(),
/* 6 */ MESSAGES.colFirstDate(),
/* 7 */ MESSAGES.colLastDate(),
/* 8 */ MESSAGES.colPublishedStartTime(),
/* 9 */ MESSAGES.colPublishedEndTime(),
/* 10 */ MESSAGES.colAllocatedStartTime(),
/* 11 */ MESSAGES.colAllocatedEndTime(),
/* 12 */ MESSAGES.colSetupTimeShort(),
/* 13 */ MESSAGES.colTeardownTimeShort(),
/* 14 */ MESSAGES.colLocation(),
/* 15 */ MESSAGES.colCapacity(),
/* 16 */ MESSAGES.colEnrollment(),
/* 17 */ MESSAGES.colLimit(),
/* 18 */ MESSAGES.colSponsorOrInstructor(),
/* 19 */ MESSAGES.colEmail(),
/* 20 */ MESSAGES.colMainContact(),
/* 21 */ MESSAGES.colEmail(),
/* 22 */ MESSAGES.colApproval(),
/* 23 */ MESSAGES.colLastChange());
Formats.Format<Date> df = Formats.getDateFormat(Formats.Pattern.DATE_EVENT);
for (EventInterface event : events) {
for (MultiMeetingInterface multi :
EventInterface.getMultiMeetings(event.getMeetings(), false)) {
MeetingInterface meeting = multi.getMeetings().first();
out.printLine(
getName(event),
getSection(event),
event.hasInstruction()
? event.getInstruction()
: event.getType().getAbbreviation(CONSTANTS),
getTitle(event),
event.hasEventNote() ? event.getEventNote("\n").replace("<br>", "\n") : "",
multi.getDays(CONSTANTS.shortDays(), CONSTANTS.shortDays(), CONSTANTS.daily()),
multi.getFirstMeetingDate() == null ? "" : df.format(multi.getFirstMeetingDate()),
multi.getLastMeetingDate() == null
? ""
: multi.getNrMeetings() == 1 ? null : df.format(multi.getLastMeetingDate()),
meeting.isArrangeHours() ? "" : meeting.getStartTime(CONSTANTS, true),
meeting.isArrangeHours() ? "" : meeting.getEndTime(CONSTANTS, true),
meeting.isArrangeHours() ? "" : meeting.getStartTime(CONSTANTS, false),
meeting.isArrangeHours() ? "" : meeting.getEndTime(CONSTANTS, false),
meeting.isArrangeHours() ? "" : String.valueOf(meeting.getStartOffset()),
meeting.isArrangeHours() ? "" : String.valueOf(-meeting.getEndOffset()),
meeting.getLocationName(),
meeting.hasLocation() && meeting.getLocation().hasSize()
? meeting.getLocation().getSize().toString()
: null,
event.hasEnrollment() ? event.getEnrollment().toString() : null,
event.hasMaxCapacity() ? event.getMaxCapacity().toString() : null,
event.hasInstructors()
? event.getInstructorNames("\n", MESSAGES)
: event.hasSponsor() ? event.getSponsor().getName() : null,
event.hasInstructors()
? event.getInstructorEmails("\n")
: event.hasSponsor() ? event.getSponsor().getEmail() : null,
event.hasContact() ? event.getContact().getName(MESSAGES) : null,
event.hasContact() ? event.getContact().getEmail() : null,
event.getType() == EventType.Unavailabile
? ""
: multi.getApprovalStatus() == ApprovalStatus.Approved
? df.format(multi.getApprovalDate())
: multi.getApprovalStatus() == ApprovalStatus.Cancelled
? MESSAGES.approvalCancelled()
: multi.getApprovalStatus() == ApprovalStatus.Rejected
? MESSAGES.approvalRejected()
: multi.getApprovalStatus() == ApprovalStatus.Deleted
? MESSAGES.approvalDeleted()
: multi.isPast()
? MESSAGES.approvalNotApprovedPast()
: event.getExpirationDate() != null
? MESSAGES.approvalExpire(
df.format(event.getExpirationDate()))
: MESSAGES.approvalNotApproved(),
event.getLastNote() != null
? df.format(event.getLastNote().getDate())
+ " "
+ event.getLastNote().getType().getName()
: null);
}
out.flush();
}
out.close();
}
public static GwtRpcResponseList<ClassAssignmentInterface.Enrollment> convert(
Collection<StudentClassEnrollment> enrollments,
Map<Long, List<Meeting>> conflicts,
boolean canShowExtId,
boolean canRegister,
boolean canUseAssistant) {
GwtRpcResponseList<ClassAssignmentInterface.Enrollment> converted =
new GwtRpcResponseList<ClassAssignmentInterface.Enrollment>();
Map<String, String> approvedBy2name = new Hashtable<String, String>();
Hashtable<Long, ClassAssignmentInterface.Enrollment> student2enrollment =
new Hashtable<Long, ClassAssignmentInterface.Enrollment>();
for (StudentClassEnrollment enrollment : enrollments) {
ClassAssignmentInterface.Enrollment enrl =
student2enrollment.get(enrollment.getStudent().getUniqueId());
if (enrl == null) {
ClassAssignmentInterface.Student st = new ClassAssignmentInterface.Student();
st.setId(enrollment.getStudent().getUniqueId());
st.setExternalId(enrollment.getStudent().getExternalUniqueId());
st.setCanShowExternalId(canShowExtId);
st.setCanRegister(canRegister);
st.setCanUseAssistant(canUseAssistant);
st.setName(
enrollment
.getStudent()
.getName(ApplicationProperty.OnlineSchedulingStudentNameFormat.value()));
for (AcademicAreaClassification ac :
enrollment.getStudent().getAcademicAreaClassifications()) {
st.addArea(ac.getAcademicArea().getAcademicAreaAbbreviation());
st.addClassification(ac.getAcademicClassification().getCode());
}
for (PosMajor m : enrollment.getStudent().getPosMajors()) {
st.addMajor(m.getCode());
}
for (StudentGroup g : enrollment.getStudent().getGroups()) {
st.addGroup(g.getGroupAbbreviation());
}
for (StudentAccomodation a : enrollment.getStudent().getAccomodations()) {
st.addAccommodation(a.getAbbreviation());
}
enrl = new ClassAssignmentInterface.Enrollment();
enrl.setStudent(st);
enrl.setEnrolledDate(enrollment.getTimestamp());
CourseAssignment c = new CourseAssignment();
c.setCourseId(enrollment.getCourseOffering().getUniqueId());
c.setSubject(enrollment.getCourseOffering().getSubjectAreaAbbv());
c.setCourseNbr(enrollment.getCourseOffering().getCourseNbr());
enrl.setCourse(c);
student2enrollment.put(enrollment.getStudent().getUniqueId(), enrl);
if (enrollment.getCourseRequest() != null) {
enrl.setPriority(1 + enrollment.getCourseRequest().getCourseDemand().getPriority());
if (enrollment.getCourseRequest().getCourseDemand().getCourseRequests().size() > 1) {
CourseRequest first = null;
for (CourseRequest r :
enrollment.getCourseRequest().getCourseDemand().getCourseRequests()) {
if (first == null || r.getOrder().compareTo(first.getOrder()) < 0) first = r;
}
if (!first.equals(enrollment.getCourseRequest()))
enrl.setAlternative(first.getCourseOffering().getCourseName());
}
if (enrollment.getCourseRequest().getCourseDemand().isAlternative()) {
CourseDemand first = enrollment.getCourseRequest().getCourseDemand();
demands:
for (CourseDemand cd : enrollment.getStudent().getCourseDemands()) {
if (!cd.isAlternative()
&& cd.getPriority().compareTo(first.getPriority()) < 0
&& !cd.getCourseRequests().isEmpty()) {
for (CourseRequest cr : cd.getCourseRequests())
if (cr.getClassEnrollments().isEmpty()) continue demands;
first = cd;
}
}
CourseRequest alt = null;
for (CourseRequest r : first.getCourseRequests()) {
if (alt == null || r.getOrder().compareTo(alt.getOrder()) < 0) alt = r;
}
enrl.setAlternative(alt.getCourseOffering().getCourseName());
}
enrl.setRequestedDate(enrollment.getCourseRequest().getCourseDemand().getTimestamp());
enrl.setApprovedDate(enrollment.getApprovedDate());
if (enrollment.getApprovedBy() != null) {
String name = approvedBy2name.get(enrollment.getApprovedBy());
if (name == null) {
TimetableManager mgr =
(TimetableManager)
EventDAO.getInstance()
.getSession()
.createQuery("from TimetableManager where externalUniqueId = :externalId")
.setString("externalId", enrollment.getApprovedBy())
.setMaxResults(1)
.uniqueResult();
if (mgr != null) {
name = mgr.getName();
} else {
DepartmentalInstructor instr =
(DepartmentalInstructor)
EventDAO.getInstance()
.getSession()
.createQuery(
"from DepartmentalInstructor where externalUniqueId = :externalId and department.session.uniqueId = :sessionId")
.setString("externalId", enrollment.getApprovedBy())
.setLong(
"sessionId", enrollment.getStudent().getSession().getUniqueId())
.setMaxResults(1)
.uniqueResult();
if (instr != null) name = instr.nameLastNameFirst();
}
if (name != null) approvedBy2name.put(enrollment.getApprovedBy(), name);
}
enrl.setApprovedBy(name == null ? enrollment.getApprovedBy() : name);
}
} else {
enrl.setPriority(-1);
}
List<Meeting> conf =
(conflicts == null ? null : conflicts.get(enrollment.getStudent().getUniqueId()));
if (conf != null) {
Map<Event, TreeSet<Meeting>> events = new HashMap<Event, TreeSet<Meeting>>();
for (Meeting m : conf) {
TreeSet<Meeting> ms = events.get(m.getEvent());
if (ms == null) {
ms = new TreeSet<Meeting>();
events.put(m.getEvent(), ms);
}
ms.add(m);
}
for (Event confEvent : new TreeSet<Event>(events.keySet())) {
Conflict conflict = new Conflict();
conflict.setName(confEvent.getEventName());
conflict.setType(confEvent.getEventTypeAbbv());
String lastDate = null, lastTime = null, lastRoom = null;
for (MultiMeeting mm : Event.getMultiMeetings(events.get(confEvent))) {
String date =
getDateFormat().format(mm.getMeetings().first().getMeetingDate())
+ (mm.getMeetings().size() == 1
? ""
: " - "
+ getDateFormat().format(mm.getMeetings().last().getMeetingDate()));
if (lastDate == null) {
conflict.setDate(date);
} else if (lastDate.equals(date)) {
conflict.setDate(conflict.getDate() + "<br>");
} else {
conflict.setDate(conflict.getDate() + "<br>" + date);
}
lastDate = date;
String time =
mm.getDays(CONSTANTS.days(), CONSTANTS.shortDays())
+ " "
+ (mm.getMeetings().first().isAllDay()
? "All Day"
: mm.getMeetings().first().startTime()
+ " - "
+ mm.getMeetings().first().stopTime());
if (lastTime == null) {
conflict.setTime(time);
} else if (lastTime.equals(time)) {
conflict.setTime(conflict.getTime() + "<br>");
} else {
conflict.setTime(conflict.getTime() + "<br>" + time);
}
lastTime = time;
String room =
(mm.getMeetings().first().getLocation() == null
? ""
: mm.getMeetings().first().getLocation().getLabel());
if (lastRoom == null) {
conflict.setRoom(room);
} else if (lastRoom.equals(room)) {
conflict.setRoom(conflict.getRoom() + "<br>");
} else {
conflict.setRoom(conflict.getRoom() + "<br>" + room);
}
lastRoom = room;
}
enrl.addConflict(conflict);
}
}
converted.add(enrl);
}
ClassAssignmentInterface.ClassAssignment c = enrl.getCourse().addClassAssignment();
c.setClassId(enrollment.getClazz().getUniqueId());
c.setSection(enrollment.getClazz().getClassSuffix(enrollment.getCourseOffering()));
if (c.getSection() == null) c.setSection(enrollment.getClazz().getSectionNumberString());
c.setClassNumber(enrollment.getClazz().getSectionNumberString());
c.setSubpart(enrollment.getClazz().getSchedulingSubpart().getItypeDesc());
}
return converted;
}
private class ProteomicsRunWizardCommand extends WizardCommand {
private MetadataWizardPageGroup metadataWizardPages;
private final ServiceWizardPageImpl<QueueGridService> thermoServicesSelectionPage;
private final ServiceWizardPageImpl<QueueGridService> proteomicsConvertServicesSelectionPage;
private final UploadComponentOptions uploadOpts =
new UploadComponentOptions(
true,
new AsyncCallbackImpl<List<FileSource>>() {
@Override
public void handleSuccess() {
try {
final PeakListWorkflowBuilder builder = new PeakListWorkflowBuilder(CONSTANTS);
builder.setFileSources(getResult());
builder.setCommonMetadataProvider(
metadataWizardPages.getEnabledWizardPage().getMetadataCanvasSupplier());
builder.setSourcePage(sourcePage);
builder.setThermoServicesSelectionPage(thermoServicesSelectionPage);
builder.setProteomicsConvertServicesSelectionPage(
proteomicsConvertServicesSelectionPage);
JobSubmitService.Util.getInstance()
.submit(builder.build(), new AsyncCallbackImpl<Void>());
} finally {
destroy();
}
}
});
private final DynamicUploadComponent uploadComponent = uploadComponentFactory.get(uploadOpts);
private UploadWizardPageImpl uploadWizardPage =
new UploadWizardPageImpl(
uploadComponent,
CONSTANTS.runWizardSourceTitle(),
CONSTANTS.runWizardSourceDescription());
private final ProteomicsRunSourceTypeWizardPageImpl sourcePage =
new ProteomicsRunSourceTypeWizardPageImpl(false);
private void intializeMetadataPages() {
metadataWizardPages =
new MetadataWizardPageGroup(
getMetadataWizardPageFactory(),
getLocations(),
CONSTANTS.runWizardType(),
CONSTANTS.runWizardBatchType());
}
private final Listener<Object> sourceTypeListener =
new Listener<Object>() {
public void onEvent(final Object event) {
updateSourceType();
}
};
private void updateSourceType() {
final ProteomicsRunSource type = sourcePage.getProteomicsRunSourceProperty().get();
final boolean batch = sourcePage.getBatchProperty().get();
metadataWizardPages.setBatch(batch);
if (type == ProteomicsRunSource.THERMO) {
uploadOpts.setTypes("*.raw;*.RAW");
uploadOpts.setTypesDescription("Thermo Finnigan RAW");
uploadOpts.setExtension(StockFileExtensionEnum.THERMO_RAW.getExtension());
} else if (type == ProteomicsRunSource.MZXML) {
uploadOpts.setTypes("*.mzXML;*.mzxml;*.MZXML;*.MzXML");
uploadOpts.setTypesDescription("MzXML");
uploadOpts.setExtension(null);
} else if (type == ProteomicsRunSource.MGF) {
uploadOpts.setTypes("*.mgf;*.MGF;*.msm;*.MSM");
uploadOpts.setTypesDescription("Mascot Generic Format");
uploadOpts.setExtension(null);
}
uploadOpts.setAllowMultiple(batch);
uploadComponent.update(uploadOpts);
thermoServicesSelectionPage.setEnabled(type == ProteomicsRunSource.THERMO);
proteomicsConvertServicesSelectionPage.setEnabled(type == ProteomicsRunSource.MGF);
}
private void setupSourceTypeListeners() {
sourcePage.getBatchProperty().addListener(sourceTypeListener);
sourcePage.getProteomicsRunSourceProperty().addListener(sourceTypeListener);
}
ProteomicsRunWizardCommand(final Collection<TreeItem> locations) {
super(locations);
final ArrayList<WizardPage> pages = Lists.newArrayListWithCapacity(8);
intializeMetadataPages();
pages.add(sourcePage);
pages.addAll(metadataWizardPages.asList());
final ServiceSelectionComponent<QueueGridService> thermoSelectionComponent =
serviceSelectionComponentSupplier.get();
thermoSelectionComponent.setServicesType("rawExtract");
thermoServicesSelectionPage =
new ServiceWizardPageImpl<QueueGridService>(thermoSelectionComponent);
final ServiceSelectionComponent<QueueGridService> proteomicsConvertSelectionComponent =
serviceSelectionComponentSupplier.get();
proteomicsConvertSelectionComponent.setServicesType("proteomicsConvert");
proteomicsConvertServicesSelectionPage =
new ServiceWizardPageImpl<QueueGridService>(proteomicsConvertSelectionComponent);
pages.add(thermoServicesSelectionPage);
pages.add(proteomicsConvertServicesSelectionPage);
pages.add(uploadWizardPage);
final WizardOptions options = new WizardOptions();
options.setTitle(CONSTANTS.runWizardTitle());
setupSourceTypeListeners();
updateSourceType();
setWidget(
WizardFactoryImpl.getInstance()
.getWizard(
pages,
options,
new WizardCompletionHandler() {
public void onCompletion(final Window wizard) {
uploadComponent.startUpload();
}
}));
}
}
