@Override
public void onClick(final ClickEvent event) {
updateUserMessage();
updateOutputLocation();
final String titleText = title.getText();
if (titleText == null) {
Window.alert("No title specified");
title.setFocus(true);
return;
}
if (!titleText.matches(TITLE_ALLOWED)) {
Window.alert(
"The search title "
+ titleText
+ " is invalid. Please use only letters, numbers, - + . _ ( ) [ ] { } = # and a space.");
title.setFocus(true);
return;
}
final String effectiveOutputPath = outputPathUserSpecified ? output.getText() : outputPath;
final String user = users.getValue(users.getSelectedIndex());
final List<ClientFileSearch> fileSearches = getFileSearches();
if (fileSearches == null || fileSearches.isEmpty()) {
Window.alert("No files added to the search");
return;
}
if (effectiveOutputPath == null || "".equals(effectiveOutputPath)) {
Window.alert("The output folder not specified");
return;
}
if ("".equals(user) || user.equals(SELECT_USER_STRING)) {
Window.alert("No user selected");
users.setFocus(true);
return;
}
// The user will likely create a broken output on Windows
if (effectiveOutputPath.length()
+ "/scaffold/".length()
+ titleText.length()
+ ".sf3".length()
> 220) {
Window.alert("The output folder path is too long.");
title.setFocus(true);
return;
}
final ProgressDialogBox dialog = new ProgressDialogBox();
dialog.setProgressMessage("Submitting search...");
dialog.setRelativeSize(0.25, 0.25);
dialog.setMinimumSize(200, 200);
dialog.showModal();
try {
final List<ClientFileSearch> entries = files.getData();
final ClientSpectrumQa clientSpectrumQa;
if (spectrumQaSetupPanel != null) {
clientSpectrumQa = spectrumQaSetupPanel.getParameters();
} else {
clientSpectrumQa = new ClientSpectrumQa();
}
final ClientSwiftSearchDefinition def =
new ClientSwiftSearchDefinition(
getTitleText(),
userInfo.get(users.getValue(users.getSelectedIndex())),
effectiveOutputPath,
paramsEditor.getSelectedParamSet(),
entries,
clientSpectrumQa,
reportSetupPanel == null
? new ClientPeptideReport(false)
: reportSetupPanel.getParameters(),
additionalSettingsPanel.isPublicMgfs(),
additionalSettingsPanel.isPublicMzxmls(),
additionalSettingsPanel.isPublicSearchFiles(),
getSearchMetadata(),
previousSearchRunId);
def.setFromScratch(additionalSettingsPanel.isFromScratch());
def.setLowPriority(additionalSettingsPanel.isLowPriority());
if (additionalSettingsPanel.isMzIdentMl()) {
def.getMetadata().put("mzIdentMl", "1");
}
if (!"".equals(additionalSettingsPanel.getComment())) {
def.getMetadata().put("comment", additionalSettingsPanel.getComment());
} else {
def.getMetadata().remove("comment");
}
ServiceConnection.instance()
.startSearch(
def,
new AsyncCallback<Void>() {
@Override
public void onFailure(final Throwable throwable) {
dialog.hide();
ErrorDialog.handleGlobalError(throwable);
}
@Override
public void onSuccess(final Void o) {
dialog.hide();
redirect("/report/");
}
});
} catch (Exception e) {
dialog.hide();
ErrorDialog.handleGlobalError(e);
}
}
/** Check query string to see if the user wants to load previous search data into the forms. */
private void loadPreviousSearch(final ClientLoadedSearch result) {
if (result == null) {
return;
}
final ClientSwiftSearchDefinition definition = result.getDefinition();
displayMessage("Loaded previous search " + definition.getSearchTitle());
if (result.getClientParamSetList() != null) {
// We transfered a new parameter set list together with search definition
// Update the parameter editor.
paramsEditor.setParamSetList(result.getClientParamSetList());
}
paramsEditor.setSelectedParamSet(result.getDefinition().getParamSet());
// Determine search type
SearchType searchType = null;
for (final ClientFileSearch clientFileSearch : definition.getInputFiles()) {
final String fileNamefileNameWithoutExtension =
FilePathWidget.getFileNameWithoutExtension(clientFileSearch.getPath());
final SearchType newSearchType =
SearchTypeList.getSearchTypeFromSetup(
definition.getSearchTitle(),
fileNamefileNameWithoutExtension,
clientFileSearch.getExperiment(),
clientFileSearch.getBiologicalSample());
if (searchType == null) {
searchType = newSearchType;
} else {
if (!searchType.equals(newSearchType)) {
searchType = SearchType.Custom;
break;
}
}
}
final String title = definition.getSearchTitle();
setTitleText(title);
if (spectrumQaSetupPanel != null) {
spectrumQaSetupPanel.setParameters(definition.getSpectrumQa());
}
if (reportSetupPanel != null) {
reportSetupPanel.setParameters(definition.getPeptideReport());
}
final List<ClientFileSearch> inputFiles = definition.getInputFiles();
files.setFiles(inputFiles, searchType);
selectUser(definition.getUser().getEmail());
final String filePath = getOutputPathFromFileTable(inputFiles);
// If the loaded path differs from what the file table would produce, it is user-specified
// .. set the proper flags
if (definition.getOutputFolder() == null || !definition.getOutputFolder().equals(filePath)) {
outputPathUserSpecified = true;
}
outputPath = definition.getOutputFolder();
output.setText(outputPath);
updateOutputLocation();
additionalSettingsPanel.setDefinition(definition);
showPageContentsAfterLoad();
}