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(); }