public static SearchType forName(String name) {
for (SearchType type : values()) {
if (type.name().equalsIgnoreCase(name)) {
return type;
}
}
return COMMIT;
}
public void testDeepScrollingDoesNotBlowUp() throws Exception {
client()
.prepareIndex("index", "type", "1")
.setSource("field", "value")
.setRefresh(true)
.execute()
.get();
for (SearchType searchType : SearchType.values()) {
SearchRequestBuilder builder =
client()
.prepareSearch("index")
.setSearchType(searchType)
.setQuery(QueryBuilders.matchAllQuery())
.setSize(Integer.MAX_VALUE)
.setScroll("1m");
SearchResponse response = builder.execute().actionGet();
try {
ElasticsearchAssertions.assertHitCount(response, 1l);
} finally {
String scrollId = response.getScrollId();
if (scrollId != null) {
clearScroll(scrollId);
}
}
}
}
@SuppressWarnings("unchecked")
public static SearchFilter getSearchFilter(HttpServletRequest request) {
SearchFilter searchFilter = new SearchFilter();
Enumeration<String> enumeration = request.getParameterNames();
while (enumeration.hasMoreElements()) {
String string = enumeration.nextElement();
if (!string.startsWith(SearchFilter.STARTPREFIX)) continue;
String[] split = string.split(SearchFilter.SPLITTAG);
if (split.length != 3) continue;
SearchType searchType = SearchType.parseString(split[1]);
String fieldName = split[2];
String fieldValue = request.getParameter(string);
SearchOperator searchOperator = new SearchOperator(fieldName, fieldValue, searchType);
searchFilter.getSearchOperatorList().add(searchOperator);
}
return searchFilter;
}
/**
* Marshalls the additional parameters and returns them as a string.
*
* @return A string holding the marshalled parameters
*/
private String marshallAdditionalParameters() {
String parameters = "";
if (accessions != null && accessions.size() > 0) {
parameters += "ACCESSION=";
for (int i = 0; i < accessions.size(); i++)
parameters += ((i > 0) ? "," : "") + "\"" + accessions.get(i) + "\"";
parameters += "\n";
}
if (charge != null) parameters += "CHARGE=" + charge + "\n";
if (enzyme != null) parameters += "CLE=" + enzyme + "\n";
if (searchTitle != null) parameters += "COM=" + searchTitle + "\n";
if (precursorRemoval != null) parameters += "CUTOUT=" + precursorRemoval + "\n";
if (database != null) parameters += "DB=" + database + "\n";
if (performDecoySearch != null)
parameters += "DECOY=" + ((performDecoySearch) ? "1" : "0") + "\n";
if (isErrorTolerant != null)
parameters += "ERRORTOLERANT=" + ((isErrorTolerant) ? "1" : "0") + "\n";
if (format != null) parameters += "FORMAT=" + format + "\n";
if (frames != null && frames.size() > 0) {
parameters += "FRAMES=";
for (int i = 0; i < frames.size(); i++)
parameters += ((i > 0) ? "," : "") + frames.get(i).toString();
parameters += "\n";
}
if (instrument != null) parameters += "INSTRUMENT=" + instrument + "\n";
if (variableModifications != null) parameters += "IT_MODS=" + variableModifications + "\n";
if (fragmentIonTolerance != null)
parameters += "ITOL=" + fragmentIonTolerance.toString() + "\n";
if (fragmentIonToleranceUnit != null)
parameters +=
"ITOLU="
+ ((fragmentIonToleranceUnit == FragmentToleranceUnits.MMU) ? "mmu" : "Da")
+ "\n";
if (massType != null)
parameters += "MASS=" + ((massType == MassType.AVERAGE) ? "Average" : "Monoisotopic") + "\n";
if (fixedMofications != null) parameters += "MODS=" + fixedMofications + "\n";
if (peptideIsotopeError != null)
parameters += "PEP_ISOTOPE_ERROR=" + peptideIsotopeError.toString() + "\n";
if (partials != null) parameters += "PFA=" + partials.toString() + "\n";
if (precursor != null) parameters += "PRECURSOR=" + precursor.toString() + "\n";
if (quantitation != null) parameters += "QUANTITATION=" + quantitation + "\n";
if (maxHitsToReport != null) parameters += "REPORT=" + maxHitsToReport + "\n";
if (reportType != null) parameters += "REPTYPE=" + reportType.toString() + "\n";
if (searchType != null) parameters += "SEARCH=" + searchType.toString() + "\n";
if (proteinMass != null) parameters += "SEG=" + proteinMass + "\n";
if (taxonomy != null) parameters += "TAXONOMY=" + taxonomy + "\n";
if (peptideMassTolerance != null) parameters += "TOL=" + peptideMassTolerance.toString() + "\n";
if (peptideMassToleranceUnit != null)
parameters += "TOLU=" + peptideMassToleranceUnit.toString() + "\n";
if (userMail != null) parameters += "USEREMAIL=" + userMail + "\n";
if (userName != null) parameters += "USERNAME="******"\n";
if (userParameter != null) {
for (Integer i = 0; i < userParameter.size(); i++) {
parameters +=
"USER" + ((i < 10) ? "0" : "") + i.toString() + "=" + userParameter.get(i) + "\n";
}
}
return parameters;
}
/** 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();
}
