List of usage examples for java.util Map keySet
Set<K> keySet();
From source file:com.act.lcms.v2.MZCollisionCounter.java
public static void main(String[] args) throws Exception { CLIUtil cliUtil = new CLIUtil(MassChargeCalculator.class, HELP_MESSAGE, OPTION_BUILDERS); CommandLine cl = cliUtil.parseCommandLine(args); File inputFile = new File(cl.getOptionValue(OPTION_INPUT_INCHI_LIST)); if (!inputFile.exists()) { cliUtil.failWithMessage("Input file at does not exist at %s", inputFile.getAbsolutePath()); }/*from w w w. ja va2s . co m*/ List<MassChargeCalculator.MZSource> sources = new ArrayList<>(); try (BufferedReader reader = new BufferedReader(new FileReader(inputFile))) { String line; while ((line = reader.readLine()) != null) { line = line.trim(); sources.add(new MassChargeCalculator.MZSource(line)); if (sources.size() % 1000 == 0) { LOGGER.info("Loaded %d sources from input file", sources.size()); } } } Set<String> considerIons = Collections.emptySet(); if (cl.hasOption(OPTION_ONLY_CONSIDER_IONS)) { List<String> ions = Arrays.asList(cl.getOptionValues(OPTION_ONLY_CONSIDER_IONS)); LOGGER.info("Only considering ions for m/z calculation: %s", StringUtils.join(ions, ", ")); considerIons = new HashSet<>(ions); } TSVWriter<String, Long> tsvWriter = new TSVWriter<>(Arrays.asList("collisions", "count")); tsvWriter.open(new File(cl.getOptionValue(OPTION_OUTPUT_FILE))); try { LOGGER.info("Loaded %d sources in total from input file", sources.size()); MassChargeCalculator.MassChargeMap mzMap = MassChargeCalculator.makeMassChargeMap(sources, considerIons); if (!cl.hasOption(OPTION_COUNT_WINDOW_INTERSECTIONS)) { // Do an exact analysis of the m/z collisions if windowing is not specified. LOGGER.info("Computing precise collision histogram."); Iterable<Double> mzs = mzMap.ionMZIter(); Map<Integer, Long> collisionHistogram = histogram( StreamSupport.stream(mzs.spliterator(), false).map(mz -> { // See comment about Iterable below. try { return mzMap.ionMZToMZSources(mz).size(); } catch (NoSuchElementException e) { LOGGER.error("Caught no such element exception for mz %f: %s", mz, e.getMessage()); throw e; } })); List<Integer> sortedCollisions = new ArrayList<>(collisionHistogram.keySet()); Collections.sort(sortedCollisions); for (Integer collision : sortedCollisions) { tsvWriter.append(new HashMap<String, Long>() { { put("collisions", collision.longValue()); put("count", collisionHistogram.get(collision)); } }); } } else { /* After some deliberation (thanks Gil!), the windowed variant of this calculation counts the number of * structures whose 0.01 Da m/z windows (for some set of ions) overlap with each other. * * For example, let's assume we have five total input structures, and are only searching for one ion. Let's * also assume that three of those structures have m/z A and the remaining two have m/z B. The windows might * look like this in the m/z domain: * |----A----| * |----B----| * Because A represents three structures and overlaps with B, which represents two, we assign A a count of 5-- * this is the number of structures we believe could fall into the range of A given our current peak calling * approach. Similarly, B is assigned a count of 5, as the possibility for collision/confusion is symmetric. * * Note that this is an over-approximation of collisions, as we could more precisely only consider intersections * when the exact m/z of B falls within the window around A and vice versa. However, because we have observed * cases where the MS sensor doesn't report structures at exactly the m/z we predict, we employ this weaker * definition of intersection to give a slightly pessimistic view of what confusions might be possible. */ // Compute windows for every m/z. We don't care about the original mz values since we just want the count. List<Double> mzs = mzMap.ionMZsSorted(); final Double windowHalfWidth; if (cl.hasOption(OPTION_WINDOW_HALFWIDTH)) { // Don't use get with default for this option, as we want the exact FP value of the default tolerance. windowHalfWidth = Double.valueOf(cl.getOptionValue(OPTION_WINDOW_HALFWIDTH)); } else { windowHalfWidth = DEFAULT_WINDOW_TOLERANCE; } /* Window = (lower bound, upper bound), counter of represented m/z's that collide with this window, and number * of representative structures (which will be used in counting collisions). */ LinkedList<CollisionWindow> allWindows = new LinkedList<CollisionWindow>() { { for (Double mz : mzs) { // CPU for memory trade-off: don't re-compute the window bounds over and over and over and over and over. try { add(new CollisionWindow(mz, windowHalfWidth, mzMap.ionMZToMZSources(mz).size())); } catch (NoSuchElementException e) { LOGGER.error("Caught no such element exception for mz %f: %s", mz, e.getMessage()); throw e; } } } }; // Sweep line time! The window ranges are the interesting points. We just accumulate overlap counts as we go. LinkedList<CollisionWindow> workingSet = new LinkedList<>(); List<CollisionWindow> finished = new LinkedList<>(); while (allWindows.size() > 0) { CollisionWindow thisWindow = allWindows.pop(); // Remove any windows from the working set that don't overlap with the next window. while (workingSet.size() > 0 && workingSet.peekFirst().getMaxMZ() < thisWindow.getMinMZ()) { finished.add(workingSet.pop()); } for (CollisionWindow w : workingSet) { /* Add the size of the new overlapping window's structure count to each of the windows in the working set, * which represents the number of possible confused structures that fall within the overlapping region. * We exclude the window itself as it should already have counted the colliding structures it represents. */ w.getAccumulator().add(thisWindow.getStructureCount()); /* Reciprocally, add the structure counts of all windows with which the current window overlaps to it. */ thisWindow.getAccumulator().add(w.getStructureCount()); } // Now that accumulation is complete, we can safely add the current window. workingSet.add(thisWindow); } // All the interesting events are done, so drop the remaining windows into the finished set. finished.addAll(workingSet); Map<Long, Long> collisionHistogram = histogram( finished.stream().map(w -> w.getAccumulator().longValue())); List<Long> sortedCollisions = new ArrayList<>(collisionHistogram.keySet()); Collections.sort(sortedCollisions); for (Long collision : sortedCollisions) { tsvWriter.append(new HashMap<String, Long>() { { put("collisions", collision); put("count", collisionHistogram.get(collision)); } }); } } } finally { if (tsvWriter != null) { tsvWriter.close(); } } }
From source file:com.act.lcms.db.analysis.IonDetectionAnalysis.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());//from w w w . ja va 2 s .c o m } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s", e.getMessage()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } File lcmsDir = new File(cl.getOptionValue(OPTION_LCMS_FILE_DIRECTORY)); if (!lcmsDir.isDirectory()) { System.err.format("File at %s is not a directory", lcmsDir.getAbsolutePath()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } String plottingDirectory = cl.getOptionValue(OPTION_PLOTTING_DIR); // Get include and excluse ions from command line Set<String> includeIons; if (cl.hasOption(OPTION_INCLUDE_IONS)) { includeIons = new HashSet<>(Arrays.asList(cl.getOptionValues(OPTION_INCLUDE_IONS))); LOGGER.info("Including ions in search: %s", StringUtils.join(includeIons, ", ")); } else { includeIons = new HashSet<>(); includeIons.add(DEFAULT_ION); } try (DB db = DB.openDBFromCLI(cl)) { ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir); File inputPredictionCorpus = new File(cl.getOptionValue(OPTION_INPUT_PREDICTION_CORPUS)); Map<Double, Set<Pair<String, String>>> massChargeToChemicalAndIon = constructMassChargeToChemicalIonsFromInputFile( inputPredictionCorpus, includeIons, cl.hasOption(OPTION_LIST_OF_INCHIS_INPUT_FILE)); Pair<Set<Pair<String, Double>>, Map<String, Double>> values = constructFakeNameToMassChargeAndSetOfMassChargePairs( massChargeToChemicalAndIon.keySet()); Set<Pair<String, Double>> searchMZs = values.getLeft(); Map<String, Double> chemIDToMassCharge = values.getRight(); LOGGER.info("The number of mass charges are: %d", searchMZs.size()); Map<ScanData.KIND, List<LCMSWell>> wellTypeToLCMSWells = readInputExperimentalSetup(db, new File(cl.getOptionValue(OPTION_INPUT_POSITIVE_AND_NEGATIVE_CONTROL_WELLS_FILE))); // Get experimental setup ie. positive and negative wells from config file List<LCMSWell> positiveWells = wellTypeToLCMSWells.get(ScanData.KIND.POS_SAMPLE); List<LCMSWell> negativeWells = wellTypeToLCMSWells.get(ScanData.KIND.NEG_CONTROL); LOGGER.info("Number of positive wells is: %d", positiveWells.size()); LOGGER.info("Number of negative wells is: %d", negativeWells.size()); HashMap<Integer, Plate> plateCache = new HashMap<>(); String outputPrefix = cl.getOptionValue(OPTION_OUTPUT_PREFIX); IonDetectionAnalysis<LCMSWell> ionDetectionAnalysis = new IonDetectionAnalysis<LCMSWell>(lcmsDir, positiveWells, negativeWells, plottingDirectory, plateCache, searchMZs, db); ionDetectionAnalysis.runLCMSMiningAnalysisAndPlotResults(chemIDToMassCharge, massChargeToChemicalAndIon, outputPrefix, cl.hasOption(OPTION_NON_REPLICATE_ANALYSIS)); } }
From source file:com.genentech.chemistry.tool.mm.SDFMMMinimize.java
/** * Main function for running on the command line * @param args/* w ww . j a v a2 s. c o m*/ */ public static void main(String... args) throws IOException { // Get the available options from the programs Map<String, List<String>> allowedProgramsAndForceFields = getAllowedProgramsAndForceFields(); Map<String, List<String>> allowedProgramsAndSolvents = getAllowedProgramsAndSolvents(); // create command line Options object Options options = new Options(); Option opt = new Option(OPT_INFILE, true, "input file oe-supported Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); StringBuilder programOptions = new StringBuilder("Program to use for minimization. Choices are\n"); for (String program : allowedProgramsAndForceFields.keySet()) { programOptions.append("\n*** -program " + program + " ***\n"); String forcefields = ""; for (String option : allowedProgramsAndForceFields.get(program)) { forcefields += option + " "; } programOptions.append("-forcefield " + forcefields + "\n"); String solvents = ""; for (String option : allowedProgramsAndSolvents.get(program)) { solvents += option + " "; } programOptions.append("-solvent " + solvents + "\n"); } opt = new Option(OPT_PROGRAM, true, programOptions.toString()); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_FORCEFIELD, true, "Forcefield options. See -program for choices"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_SOLVENT, true, "Solvent options. See -program for choices"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_FIXED_ATOM_TAG, true, "SD tag name which contains the atom numbers to be held fixed."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_FIX_TORSION, true, "true/false. if true, the atoms in fixedAtomTag contains 4 indices of atoms defining a torsion angle to be held fixed"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_WORKING_DIR, true, "Working directory to put files."); opt.setRequired(false); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); if (args.length != 0) { System.err.println("Unknown arguments" + args); exitWithHelp(options); } if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String inFile = cmd.getOptionValue(OPT_INFILE); String outFile = cmd.getOptionValue(OPT_OUTFILE); String fixedAtomTag = cmd.getOptionValue(OPT_FIXED_ATOM_TAG); boolean fixTorsion = (cmd.getOptionValue(OPT_FIX_TORSION) != null && cmd.getOptionValue(OPT_FIX_TORSION).equalsIgnoreCase("true")); String programName = cmd.getOptionValue(OPT_PROGRAM); String forcefield = cmd.getOptionValue(OPT_FORCEFIELD); String solvent = cmd.getOptionValue(OPT_SOLVENT); String workDir = cmd.getOptionValue(OPT_WORKING_DIR); if (workDir == null || workDir.trim().length() == 0) workDir = "."; // Create a minimizer SDFMMMinimize minimizer = new SDFMMMinimize(); minimizer.setMethod(programName, forcefield, solvent); minimizer.run(inFile, outFile, fixedAtomTag, fixTorsion, workDir); minimizer.close(); System.err.println("Minimization complete."); }
From source file:net.ontopia.topicmaps.cmdlineutils.rdbms.RDBMSIndexTool.java
public static void main(String[] argv) throws Exception { // Initialize logging CmdlineUtils.initializeLogging();//from ww w . java2 s. c o m // Register logging options CmdlineOptions options = new CmdlineOptions("RDBMSIndexTool", argv); CmdlineUtils.registerLoggingOptions(options); // Parse command line options try { options.parse(); } catch (CmdlineOptions.OptionsException e) { System.err.println("Error: " + e.getMessage()); System.exit(1); } // Get command line arguments String[] args = options.getArguments(); if (args.length != 1) { usage(); System.exit(3); } // load database schema project ClassLoader cloader = RDBMSIndexTool.class.getClassLoader(); InputStream istream = cloader.getResourceAsStream("net/ontopia/topicmaps/impl/rdbms/config/schema.xml"); Project dbp = DatabaseProjectReader.loadProject(istream); // open database connection String propfile = args[0]; ConnectionFactoryIF cf = new DefaultConnectionFactory(PropertyUtils.loadProperties(new File(propfile)), true); Connection conn = cf.requestConnection(); try { DatabaseMetaData dbm = conn.getMetaData(); boolean downcase = dbm.storesLowerCaseIdentifiers(); Map extra_indexes = new TreeMap(); Map missing_indexes = new TreeMap(); Iterator tables = dbp.getTables().iterator(); while (tables.hasNext()) { Table table = (Table) tables.next(); String table_name = (downcase ? table.getName().toLowerCase() : table.getName()); //! System.out.println("T :" + table_name); // get primary keys from database Map pkeys = getPrimaryKeys(table_name, dbm); // get indexes from database Map indexes = getIndexes(table_name, dbm); Map dindexes = new HashMap(); if (table.getPrimaryKeys() != null) { String pkey = table_name + '(' + StringUtils.join(table.getPrimaryKeys(), ',') + ')'; if (!pkeys.containsKey(pkey)) System.out.println("PKM: " + pkey); } Iterator iter = table.getIndexes().iterator(); while (iter.hasNext()) { Index index = (Index) iter.next(); String i = table_name + '(' + StringUtils.join(index.getColumns(), ',') + ')'; String index_name = (downcase ? index.getName().toLowerCase() : index.getName()); dindexes.put(i, index_name); } Set extra = new HashSet(indexes.keySet()); extra.removeAll(dindexes.keySet()); extra.removeAll(pkeys.keySet()); if (!extra.isEmpty()) { Iterator i = extra.iterator(); while (i.hasNext()) { Object k = i.next(); extra_indexes.put(k, indexes.get(k)); } } Set missing = new HashSet(dindexes.keySet()); missing.addAll(pkeys.keySet()); missing.removeAll(indexes.keySet()); if (!missing.isEmpty()) { Iterator i = missing.iterator(); while (i.hasNext()) { Object k = i.next(); missing_indexes.put(k, dindexes.get(k)); } } } if (!extra_indexes.isEmpty()) System.out.println("/* --- Extra indexes ----------------------------------------- */"); Iterator eiter = extra_indexes.keySet().iterator(); while (eiter.hasNext()) { Object k = eiter.next(); System.out.println("drop index " + extra_indexes.get(k) + "; /* " + k + " */"); } if (!missing_indexes.isEmpty()) System.out.println("/* --- Missing indexes---------------------------------------- */"); Iterator miter = missing_indexes.keySet().iterator(); while (miter.hasNext()) { Object k = miter.next(); System.out.println("create index " + missing_indexes.get(k) + " on " + k + ";"); } } finally { conn.rollback(); conn.close(); } }
From source file:br.com.autonomiccs.cloudTraces.main.CloudTracesSimulator.java
public static void main(String[] args) { validateInputFile(args);/*w w w.jav a 2 s . c o m*/ String cloudTracesFile = args[0]; Collection<VirtualMachine> virtualMachines = getAllVirtualMachinesFromCloudTraces(cloudTracesFile); logger.info(String.format("#VirtualMachines [%d] found on [%s].", virtualMachines.size(), cloudTracesFile)); Map<Integer, List<VirtualMachine>> mapVirtualMachinesTaskExecutionByTime = createMapVirtualMachinesTaskExecutionByTime( virtualMachines); logger.info(String.format("#Times [%d] that have tasks being executed by VMs ", mapVirtualMachinesTaskExecutionByTime.size())); Cloud cloud = createCloudEnvirtonmentToStartsimulation(); logger.info("Cloud configuration: " + cloud); List<Integer> timesToExecuteTasks = new ArrayList<>(mapVirtualMachinesTaskExecutionByTime.keySet()); Collections.sort(timesToExecuteTasks); Integer firstTimeInTimeUnitOfUsedCloudData = timesToExecuteTasks.get(0); Integer lastTimeInTimeUnitOfUserCloudData = timesToExecuteTasks.get(timesToExecuteTasks.size() - 1); logger.info("First time: " + firstTimeInTimeUnitOfUsedCloudData); logger.info("Last time: " + lastTimeInTimeUnitOfUserCloudData); double timeUnitPerLoopIteration = getTimeUnitPerLoopIteration(firstTimeInTimeUnitOfUsedCloudData, lastTimeInTimeUnitOfUserCloudData); logger.info("The time unit converted to trace time: " + timeUnitPerLoopIteration); double currentTime = firstTimeInTimeUnitOfUsedCloudData; long highetResourceAllocation = Long.MIN_VALUE; String cloudStateHighestMemoryAllocation = ""; while (currentTime < lastTimeInTimeUnitOfUserCloudData + 2 * timeUnitPerLoopIteration) { logger.debug("Current time of iteration: " + currentTime); if (cloud.getMemoryAllocatedInBytes() > highetResourceAllocation) { highetResourceAllocation = cloud.getMemoryAllocatedInBytes(); cloudStateHighestMemoryAllocation = cloud.toString(); } applyLoadOnCloudForCurrentTime(mapVirtualMachinesTaskExecutionByTime, cloud, currentTime); destroyVirtualMachinesIfNeeded(cloud, currentTime); logger.info(String.format("Time [%.3f], cloud state [%s] ", currentTime, cloud)); executeManagement(cloud, currentTime); logClustersConfigurationsAndStdAtTime(cloud.getClusters(), currentTime); currentTime += timeUnitPerLoopIteration; } logger.info("Cloud configuration after simulation: " + cloud); logger.info("Cloud highestResourceUsage: " + cloudStateHighestMemoryAllocation); }
From source file:net.dontdrinkandroot.lastfm.api.CheckImplementationStatus.java
public static void main(final String[] args) throws DocumentException, IOException { CheckImplementationStatus.xmlReader = new Parser(); CheckImplementationStatus.saxReader = new SAXReader(CheckImplementationStatus.xmlReader); final String packagePrefix = "net.dontdrinkandroot.lastfm.api.model."; final Map<String, Map<String, URL>> packages = CheckImplementationStatus.parseOverview(); final StringBuffer html = new StringBuffer(); html.append("<html>\n"); html.append("<head>\n"); html.append("<title>Implementation Status</title>\n"); html.append("</head>\n"); html.append("<body>\n"); html.append("<h1>Implementation Status</h1>\n"); final StringBuffer wiki = new StringBuffer(); int numImplemented = 0; int numTested = 0; int numMethods = 0; final List<String> packageList = new ArrayList<String>(packages.keySet()); Collections.sort(packageList); for (final String pkg : packageList) { System.out.println("Parsing " + pkg); html.append("<h2>" + pkg + "</h2>\n"); wiki.append("\n===== " + pkg + " =====\n\n"); Class<?> modelClass = null; final String className = packagePrefix + pkg; try {/*from w w w. jav a2 s.c o m*/ modelClass = Class.forName(className); System.out.println("\tClass " + modelClass.getName() + " exists"); } catch (final ClassNotFoundException e) { // e.printStackTrace(); System.out.println("\t" + className + ": DOES NOT exist"); } Class<?> testClass = null; final String testClassName = packagePrefix + pkg + "Test"; try { testClass = Class.forName(testClassName); System.out.println("\tTestClass " + testClass.getName() + " exists"); } catch (final ClassNotFoundException e) { // e.printStackTrace(); System.out.println("\t" + testClassName + ": TestClass for DOES NOT exist"); } final List<String> methods = new ArrayList<String>(packages.get(pkg).keySet()); Collections.sort(methods); final Method[] classMethods = modelClass.getMethods(); final Method[] testMethods = testClass.getMethods(); html.append("<table>\n"); html.append("<tr><th>Method</th><th>Implemented</th><th>Tested</th></tr>\n"); wiki.append("^ Method ^ Implemented ^ Tested ^\n"); numMethods += methods.size(); for (final String method : methods) { System.out.println("\t\t parsing " + method); html.append("<tr>\n"); html.append("<td>" + method + "</td>\n"); wiki.append("| " + method + " "); boolean classMethodFound = false; for (final Method classMethod : classMethods) { if (classMethod.getName().equals(method)) { classMethodFound = true; break; } } if (classMethodFound) { System.out.println("\t\t\tMethod " + method + " found"); html.append("<td style=\"background-color: green\">true</td>\n"); wiki.append("| yes "); numImplemented++; } else { System.out.println("\t\t\t" + method + " NOT found"); html.append("<td style=\"background-color: red\">false</td>\n"); wiki.append("| **no** "); } boolean testMethodFound = false; final String testMethodName = "test" + StringUtils.capitalize(method); for (final Method testMethod : testMethods) { if (testMethod.getName().equals(testMethodName)) { testMethodFound = true; break; } } if (testMethodFound) { System.out.println("\t\t\tTestMethod " + method + " found"); html.append("<td style=\"background-color: green\">true</td>\n"); wiki.append("| yes |\n"); numTested++; } else { System.out.println("\t\t\t" + testMethodName + " NOT found"); html.append("<td style=\"background-color: red\">false</td>\n"); wiki.append("| **no** |\n"); } html.append("</tr>\n"); } html.append("</table>\n"); // for (String methodName : methods) { // URL url = pkg.getValue().get(methodName); // System.out.println("PARSING: " + pkg.getKey() + "." + methodName + ": " + url); // String html = loadIntoString(url); // String description = null; // Matcher descMatcher = descriptionPattern.matcher(html); // if (descMatcher.find()) { // description = descMatcher.group(1).trim(); // } // boolean post = false; // Matcher postMatcher = postPattern.matcher(html); // if (postMatcher.find()) { // post = true; // } // Matcher paramsMatcher = paramsPattern.matcher(html); // List<String[]> params = new ArrayList<String[]>(); // boolean authenticated = false; // if (paramsMatcher.find()) { // String paramsString = paramsMatcher.group(1); // Matcher paramMatcher = paramPattern.matcher(paramsString); // while (paramMatcher.find()) { // String[] param = new String[3]; // param[0] = paramMatcher.group(1); // param[1] = paramMatcher.group(3); // param[2] = paramMatcher.group(5); // // System.out.println(paramMatcher.group(1) + "|" + paramMatcher.group(3) + "|" + // paramMatcher.group(5)); // if (param[0].equals("")) { // /* DO NOTHING */ // } else if (param[0].equals("api_key")) { // /* DO NOTHING */ // } else if (param[0].equals("api_sig")) { // authenticated = true; // } else { // params.add(param); // } // } // } // } // count++; // } html.append("<hr />"); html.append("<p>" + numImplemented + "/" + numMethods + " implemented (" + numImplemented * 100 / numMethods + "%)</p>"); html.append("<p>" + numTested + "/" + numMethods + " tested (" + numTested * 100 / numMethods + "%)</p>"); html.append("</body>\n"); html.append("</html>\n"); FileOutputStream out = new FileOutputStream(new File(FileUtils.getTempDirectory(), "apistatus.html")); IOUtils.write(html, out); IOUtils.closeQuietly(out); out = new FileOutputStream(new File(FileUtils.getTempDirectory(), "apistatus.wiki.txt")); IOUtils.write(wiki, out); IOUtils.closeQuietly(out); }
From source file:MyMap.java
public static void main(String[] argv) { // Construct and load the hash. This simulates loading a // database or reading from a file, or wherever the data is. Map map = new MyMap(); // The hash maps from company name to address. // In real life this might map to an Address object... map.put("Adobe", "Mountain View, CA"); map.put("Learning Tree", "Los Angeles, CA"); map.put("IBM", "White Plains, NY"); map.put("Netscape", "Mountain View, CA"); map.put("Microsoft", "Redmond, WA"); map.put("Sun", "Mountain View, CA"); map.put("O'Reilly", "Sebastopol, CA"); // Two versions of the "retrieval" phase. // Version 1: get one pair's value given its key // (presumably the key would really come from user input): String queryString = "O'Reilly"; System.out.println("You asked about " + queryString + "."); String resultString = (String) map.get(queryString); System.out.println("They are located in: " + resultString); System.out.println();/*from ww w .j a v a 2s .c om*/ // Version 2: get ALL the keys and pairs // (maybe to print a report, or to save to disk) Iterator k = map.keySet().iterator(); while (k.hasNext()) { String key = (String) k.next(); System.out.println("Key " + key + "; Value " + (String) map.get(key)); } // Step 3 - try out the entrySet() method. Set es = map.entrySet(); System.out.println("entrySet() returns " + es.size() + " Map.Entry's"); }
From source file:com.thed.zapi.cloud.sample.FetchExecuteUpdate.java
public static void main(String[] args) throws JSONException, URISyntaxException, ParseException, IOException { final String issueSearchUri = API_SEARCH_ISSUES.replace("{SERVER}", jiraBaseURL); /**//from w ww. j a v a2 s. c o m * Get Test Issues by JQL * */ //Json object for JQL search JSONObject jqlJsonObj = new JSONObject(); jqlJsonObj.put("jql", "project = SUP"); // Replace the value with Valid JQL jqlJsonObj.put("startAt", 0); jqlJsonObj.put("maxResults", 21); // maxResults to be returned by search jqlJsonObj.put("fieldsByKeys", false); String[] IssueIds = getIssuesByJQL(issueSearchUri, userName, password, jqlJsonObj); // System.out.println(ArrayUtils.toString(IssueIds)); /** * Add tests to Cycle * */ final String addTestsUri = API_ADD_TESTS.replace("{SERVER}", zephyrBaseUrl) + cycleId; /** Create JSON object by providing input values */ String[] IssueIds = new String[25]; JSONObject addTestsObj = new JSONObject(); addTestsObj.put("issues", IssueIds); addTestsObj.put("method", "1"); addTestsObj.put("projectId", projectId); addTestsObj.put("versionId", versionId); StringEntity addTestsJSON = null; try { addTestsJSON = new StringEntity(addTestsObj.toString()); } catch (UnsupportedEncodingException e1) { e1.printStackTrace(); } addTestsToCycle(addTestsUri, client, accessKey, addTestsJSON); /** * Get Execution Id's by CycleId and Add them to Ad Hoc cycle of * UnScheduled Version * */ Map<String, String> executionIds = new HashMap<String, String>(); final String getExecutionsUri = API_GET_EXECUTIONS.replace("{SERVER}", zephyrBaseUrl) + cycleId + "?projectId=" + projectId + "&versionId=" + versionId; executionIds = getExecutionsByCycleId(getExecutionsUri, client, accessKey); /** * Bulk Update Executions with Status by Execution Id * */ JSONObject statusObj = new JSONObject(); statusObj.put("id", "1"); JSONObject executeTestsObj = new JSONObject(); executeTestsObj.put("status", statusObj); executeTestsObj.put("cycleId", cycleId); executeTestsObj.put("projectId", projectId); executeTestsObj.put("versionId", versionId); executeTestsObj.put("comment", "Executed by ZAPI Cloud"); for (String key : executionIds.keySet()) { final String updateExecutionUri = API_UPDATE_EXECUTION.replace("{SERVER}", zephyrBaseUrl) + key; // System.out.println(updateExecutionUri); // System.out.println(executionIds.get(key)); executeTestsObj.put("issueId", executionIds.get(key)); // System.out.println(executeTestsObj.toString()); StringEntity executeTestsJSON = null; try { executeTestsJSON = new StringEntity(executeTestsObj.toString()); } catch (UnsupportedEncodingException e1) { e1.printStackTrace(); } updateExecutions(updateExecutionUri, client, accessKey, executeTestsJSON); } }
From source file:com.act.lcms.db.analysis.StandardIonAnalysis.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());/*w ww . ja v a2s .co m*/ } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY)); if (!lcmsDir.isDirectory()) { System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } try (DB db = DB.openDBFromCLI(cl)) { ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir); StandardIonAnalysis analysis = new StandardIonAnalysis(); HashMap<Integer, Plate> plateCache = new HashMap<>(); String plateBarcode = cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE); String inputChemicals = cl.getOptionValue(OPTION_STANDARD_CHEMICAL); String medium = cl.getOptionValue(OPTION_MEDIUM); // If standard chemical is specified, do standard LCMS ion selection analysis if (inputChemicals != null && !inputChemicals.equals("")) { String[] chemicals; if (!inputChemicals.contains(",")) { chemicals = new String[1]; chemicals[0] = inputChemicals; } else { chemicals = inputChemicals.split(","); } String outAnalysis = cl.getOptionValue(OPTION_OUTPUT_PREFIX) + "." + CSV_FORMAT; String plottingDirectory = cl.getOptionValue(OPTION_PLOTTING_DIR); String[] headerStrings = { "Molecule", "Plate Bar Code", "LCMS Detection Results" }; CSVPrinter printer = new CSVPrinter(new FileWriter(outAnalysis), CSVFormat.DEFAULT.withHeader(headerStrings)); for (String inputChemical : chemicals) { List<StandardWell> standardWells; Plate queryPlate = Plate.getPlateByBarcode(db, cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE)); if (plateBarcode != null && medium != null) { standardWells = analysis.getStandardWellsForChemicalInSpecificPlateAndMedium(db, inputChemical, queryPlate.getId(), medium); } else if (plateBarcode != null) { standardWells = analysis.getStandardWellsForChemicalInSpecificPlate(db, inputChemical, queryPlate.getId()); } else { standardWells = analysis.getStandardWellsForChemical(db, inputChemical); } if (standardWells.size() == 0) { throw new RuntimeException("Found no LCMS wells for " + inputChemical); } // Sort in descending order of media where MeOH and Water related media are promoted to the top and // anything derived from yeast media are demoted. Collections.sort(standardWells, new Comparator<StandardWell>() { @Override public int compare(StandardWell o1, StandardWell o2) { if (StandardWell.doesMediaContainYeastExtract(o1.getMedia()) && !StandardWell.doesMediaContainYeastExtract(o2.getMedia())) { return 1; } else { return 0; } } }); Map<StandardWell, StandardIonResult> wellToIonRanking = StandardIonAnalysis .getBestMetlinIonsForChemical(inputChemical, lcmsDir, db, standardWells, plottingDirectory); if (wellToIonRanking.size() != standardWells.size() && !cl.hasOption(OPTION_OVERRIDE_NO_SCAN_FILE_FOUND)) { throw new Exception("Could not find a scan file associated with one of the standard wells"); } for (StandardWell well : wellToIonRanking.keySet()) { LinkedHashMap<String, XZ> snrResults = wellToIonRanking.get(well).getAnalysisResults(); String snrRankingResults = ""; int numResultsToShow = 0; Plate plateForWellToAnalyze = Plate.getPlateById(db, well.getPlateId()); for (Map.Entry<String, XZ> ionToSnrAndTime : snrResults.entrySet()) { if (numResultsToShow > 3) { break; } String ion = ionToSnrAndTime.getKey(); XZ snrAndTime = ionToSnrAndTime.getValue(); snrRankingResults += String.format(ion + " (%.2f SNR at %.2fs); ", snrAndTime.getIntensity(), snrAndTime.getTime()); numResultsToShow++; } String[] resultSet = { inputChemical, plateForWellToAnalyze.getBarcode() + " " + well.getCoordinatesString() + " " + well.getMedia() + " " + well.getConcentration(), snrRankingResults }; printer.printRecord(resultSet); } } try { printer.flush(); printer.close(); } catch (IOException e) { System.err.println("Error while flushing/closing csv writer."); e.printStackTrace(); } } else { // Get the set of chemicals that includes the construct and all it's intermediates Pair<ConstructEntry, List<ChemicalAssociatedWithPathway>> constructAndPathwayChems = analysis .getChemicalsForConstruct(db, cl.getOptionValue(OPTION_CONSTRUCT)); System.out.format("Construct: %s\n", constructAndPathwayChems.getLeft().getCompositionId()); for (ChemicalAssociatedWithPathway pathwayChem : constructAndPathwayChems.getRight()) { System.out.format(" Pathway chem %s\n", pathwayChem.getChemical()); // Get all the standard wells for the pathway chemicals. These wells contain only the // the chemical added with controlled solutions (ie no organism or other chemicals in the // solution) List<StandardWell> standardWells; if (plateBarcode != null) { Plate queryPlate = Plate.getPlateByBarcode(db, cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE)); standardWells = analysis.getStandardWellsForChemicalInSpecificPlate(db, pathwayChem.getChemical(), queryPlate.getId()); } else { standardWells = analysis.getStandardWellsForChemical(db, pathwayChem.getChemical()); } for (StandardWell wellToAnalyze : standardWells) { List<StandardWell> negativeControls = analysis.getViableNegativeControlsForStandardWell(db, wellToAnalyze); Map<StandardWell, List<ScanFile>> allViableScanFiles = analysis .getViableScanFilesForStandardWells(db, wellToAnalyze, negativeControls); List<String> primaryStandardScanFileNames = new ArrayList<>(); for (ScanFile scanFile : allViableScanFiles.get(wellToAnalyze)) { primaryStandardScanFileNames.add(scanFile.getFilename()); } Plate plate = plateCache.get(wellToAnalyze.getPlateId()); if (plate == null) { plate = Plate.getPlateById(db, wellToAnalyze.getPlateId()); plateCache.put(plate.getId(), plate); } System.out.format(" Standard well: %s @ %s, '%s'%s%s\n", plate.getBarcode(), wellToAnalyze.getCoordinatesString(), wellToAnalyze.getChemical(), wellToAnalyze.getMedia() == null ? "" : String.format(" in %s", wellToAnalyze.getMedia()), wellToAnalyze.getConcentration() == null ? "" : String.format(" @ %s", wellToAnalyze.getConcentration())); System.out.format(" Scan files: %s\n", StringUtils.join(primaryStandardScanFileNames, ", ")); for (StandardWell negCtrlWell : negativeControls) { plate = plateCache.get(negCtrlWell.getPlateId()); if (plate == null) { plate = Plate.getPlateById(db, negCtrlWell.getPlateId()); plateCache.put(plate.getId(), plate); } List<String> negativeControlScanFileNames = new ArrayList<>(); for (ScanFile scanFile : allViableScanFiles.get(negCtrlWell)) { negativeControlScanFileNames.add(scanFile.getFilename()); } System.out.format(" Viable negative: %s @ %s, '%s'%s%s\n", plate.getBarcode(), negCtrlWell.getCoordinatesString(), negCtrlWell.getChemical(), negCtrlWell.getMedia() == null ? "" : String.format(" in %s", negCtrlWell.getMedia()), negCtrlWell.getConcentration() == null ? "" : String.format(" @ %s", negCtrlWell.getConcentration())); System.out.format(" Scan files: %s\n", StringUtils.join(negativeControlScanFileNames, ", ")); // TODO: do something useful with the standard wells and their scan files, and then stop all the printing. } } } } } }
From source file:com.thed.zapi.cloud.sample.CycleExecutionReportByVersion.java
public static void main(String[] args) throws JSONException, URISyntaxException, ParseException, IOException { String API_GET_EXECUTIONS = "{SERVER}/public/rest/api/1.0/executions/search/cycle/"; String API_GET_CYCLES = "{SERVER}/public/rest/api/1.0/cycles/search?"; // Delimiter used in CSV file final String NEW_LINE_SEPARATOR = "\n"; final String fileName = "F:\\cycleExecutionReport.csv"; /** Declare JIRA,Zephyr URL,access and secret Keys */ // JIRA Cloud URL of the instance String jiraBaseURL = "https://demo.atlassian.net"; // Replace zephyr baseurl <ZAPI_Cloud_URL> shared with the user for ZAPI Cloud Installation String zephyrBaseUrl = "<ZAPI_Cloud_URL>"; // zephyr accessKey , we can get from Addons >> zapi section String accessKey = "YjE2MjdjMGEtNzExNy0zYjY1LWFkMzQtNjcwMDM3OTljFkbWluIGFkbWlu"; // zephyr secretKey , we can get from Addons >> zapi section String secretKey = "qufnbimi96Ob2hq3ISF08yZ8Qw4c1eHGeGlk"; /** Declare parameter values here */ String userName = "admin"; String versionId = "-1"; String projectId = "10100"; String projectName = "Support"; String versionName = "Unscheduled"; ZFJCloudRestClient client = ZFJCloudRestClient.restBuilder(zephyrBaseUrl, accessKey, secretKey, userName) .build();/* w ww .ja v a2 s. c om*/ /** * Get List of Cycles by Project and Version */ final String getCyclesUri = API_GET_CYCLES.replace("{SERVER}", zephyrBaseUrl) + "projectId=" + projectId + "&versionId=" + versionId; Map<String, String> cycles = getCyclesByProjectVersion(getCyclesUri, client, accessKey); // System.out.println("cycles :"+ cycles.toString()); /** * Iterating over the Cycles and writing the report to CSV * */ FileWriter fileWriter = null; System.out.println("Writing CSV file....."); try { fileWriter = new FileWriter(fileName); // Write the CSV file header fileWriter.append("Cycle Execution Report By Version and Project"); fileWriter.append(NEW_LINE_SEPARATOR); fileWriter.append("PROJECT:" + "," + projectName); fileWriter.append(NEW_LINE_SEPARATOR); fileWriter.append("VERSION:" + "," + versionName); fileWriter.append(NEW_LINE_SEPARATOR); JSONArray executions; int totalUnexecutedCount = 0; int totalExecutionCount = 0; for (String key : cycles.keySet()) { int executionCount = 0; int unexecutedCount = 0; final String getExecutionsUri = API_GET_EXECUTIONS.replace("{SERVER}", zephyrBaseUrl) + key + "?projectId=" + projectId + "&versionId=" + versionId; fileWriter.append("Cycle:" + "," + cycles.get(key)); fileWriter.append(NEW_LINE_SEPARATOR); executions = getExecutionsByCycleId(getExecutionsUri, client, accessKey); // System.out.println("executions :" + executions.toString()); HashMap<String, Integer> counter = new HashMap<String, Integer>(); String[] statusName = new String[executions.length()]; for (int i = 0; i < executions.length(); i++) { JSONObject executionObj = executions.getJSONObject(i).getJSONObject("execution"); // System.out.println("executionObj // "+executionObj.toString()); JSONObject statusObj = executionObj.getJSONObject("status"); // System.out.println("statusObj :"+statusObj.toString()); statusName[i] = statusObj.getString("name"); } if (statusName.length != 0) { // System.out.println(statusName.toString()); for (String a : statusName) { if (counter.containsKey(a)) { int oldValue = counter.get(a); counter.put(a, oldValue + 1); } else { counter.put(a, 1); } } for (String status : counter.keySet()) { fileWriter.append(" " + "," + " " + "," + status + "," + counter.get(status)); fileWriter.append(NEW_LINE_SEPARATOR); if (status.equalsIgnoreCase("UNEXECUTED")) { unexecutedCount += counter.get(status); } else { executionCount += counter.get(status); } } } totalExecutionCount += executionCount; totalUnexecutedCount += unexecutedCount; fileWriter.append(NEW_LINE_SEPARATOR); } fileWriter.append(NEW_LINE_SEPARATOR); fileWriter.append("TOTAL CYCLES:" + "," + cycles.size()); fileWriter.append(NEW_LINE_SEPARATOR); fileWriter.append("TOTAL EXECUTIONS:" + "," + totalExecutionCount); fileWriter.append(NEW_LINE_SEPARATOR); fileWriter.append("TOTAL ASSIGNED:" + "," + (totalUnexecutedCount + totalExecutionCount)); System.out.println("CSV file was created successfully !!!"); } catch (Exception e) { System.out.println("Error in CsvFileWriter !!!"); e.printStackTrace(); } finally { try { fileWriter.flush(); fileWriter.close(); } catch (IOException e) { System.out.println("Error while flushing/closing fileWriter !!!"); e.printStackTrace(); } } }