List of usage examples for java.util TreeMap keySet
public Set<K> keySet()
From source file:com.sfs.whichdoctor.dao.PersonDAOImpl.java
/** * Load a list of people this person has supervised in the past. * * @param guid the guid/*from w w w . j av a2 s .c o m*/ * @param allRotations the all rotations * @return the collection */ private HashMap<String, ArrayList<PersonBean>> loadSupervisedPeople(final int guid, final boolean allRotations) { HashMap<String, ArrayList<PersonBean>> supervisedPeople = new HashMap<String, ArrayList<PersonBean>>(); // Create new SearchBean of with default values SearchBean searchRotations = this.getSearchDAO().initiate("rotation", null); searchRotations.setLimit(0); RotationBean rotationParam = (RotationBean) searchRotations.getSearchCriteria(); SupervisorBean supervisor = new SupervisorBean(); supervisor.setPersonGUID(guid); rotationParam.addSupervisor(supervisor); BuilderBean loadDetails = new BuilderBean(); loadDetails.setParameter("ASSESSMENTS", true); loadDetails.setParameter("SUPERVISORS", true); searchRotations.setSearchCriteria(rotationParam); searchRotations.setOrderColumn("rotation.StartDate"); searchRotations.setOrderColumn2("people.LastName"); searchRotations.setOrderAscending(false); SearchResultsBean studentsSupervised = new SearchResultsBean(); try { studentsSupervised = this.getSearchDAO().search(searchRotations, loadDetails); } catch (Exception e) { dataLogger.error("Error searching for supervised people: " + e.getMessage()); } final Calendar currentDate = Calendar.getInstance(); final TreeMap<String, ArrayList<RotationBean>> currentlySupervising = new TreeMap<String, ArrayList<RotationBean>>(); final TreeMap<String, ArrayList<RotationBean>> previouslySupervised = new TreeMap<String, ArrayList<RotationBean>>(); final HashMap<String, PersonBean> personMap = new HashMap<String, PersonBean>(); for (Object rotationObj : studentsSupervised.getSearchResults()) { final RotationBean rotation = (RotationBean) rotationObj; boolean currentlyTakingPlace = false; if (rotation.getStartDate().before(currentDate.getTime()) && rotation.getEndDate().after(currentDate.getTime())) { currentlyTakingPlace = true; } if (rotation.getPerson() != null) { final PersonBean person = rotation.getPerson(); final String index = person.getLastName() + " " + person.getPreferredName() + " " + person.getPersonIdentifier(); boolean processed = false; if (currentlySupervising.containsKey(index)) { // The person exists in the currently supervising list. ArrayList<RotationBean> tneRots = currentlySupervising.get(index); if (allRotations || currentlyTakingPlace) { tneRots.add(rotation); } currentlySupervising.put(index, tneRots); processed = true; } if (previouslySupervised.containsKey(index)) { // The person exists in the previously supervised list ArrayList<RotationBean> tneRots = previouslySupervised.get(index); if (allRotations || currentlyTakingPlace) { tneRots.add(rotation); } if (currentlyTakingPlace) { // This is a current rotation, remove from the previously // supervised list and add to currently supervising. previouslySupervised.remove(index); currentlySupervising.put(index, tneRots); } else { previouslySupervised.put(index, tneRots); } processed = true; } if (!processed) { // This person has not been encountered yet. personMap.put(index, person); ArrayList<RotationBean> tneRots = new ArrayList<RotationBean>(); if (allRotations || currentlyTakingPlace) { tneRots.add(rotation); } if (currentlyTakingPlace) { currentlySupervising.put(index, tneRots); } else { previouslySupervised.put(index, tneRots); } } } } final ArrayList<PersonBean> currentPeople = new ArrayList<PersonBean>(); final ArrayList<PersonBean> previousPeople = new ArrayList<PersonBean>(); for (String index : currentlySupervising.keySet()) { final PersonBean person = personMap.get(index); final ArrayList<RotationBean> tneRots = currentlySupervising.get(index); person.setRotations(tneRots); currentPeople.add(person); } for (String index : previouslySupervised.keySet()) { final PersonBean person = personMap.get(index); final ArrayList<RotationBean> tneRots = previouslySupervised.get(index); person.setRotations(tneRots); previousPeople.add(person); } supervisedPeople.put("current", currentPeople); supervisedPeople.put("previous", previousPeople); return supervisedPeople; }
From source file:net.spfbl.spf.SPF.java
public static TreeSet<String> clear(String token) { TreeSet<String> clearSet = new TreeSet<String>(); TreeMap<String, Distribution> distribuitonMap = CacheDistribution.getAll(token); for (String key : distribuitonMap.keySet()) { Distribution distribution = distribuitonMap.get(key); if (distribution != null) { if (distribution.clear()) { clearSet.add(key);/*from www .j a v a 2s .c o m*/ distribution.getStatus(token); Peer.sendToAll(key, distribution); } } if (Block.dropExact(key)) { clearSet.add(key); } } for (String key : Block.getAllTokens(token)) { if (Block.dropExact(key)) { clearSet.add(key); } } // for (String key : Peer.clearAllReputation(token)) { // clearSet.add(key); // } return clearSet; }
From source file:org.apache.coyote.tomcat5.CoyoteRequest.java
/** * Parse accept-language header value.//from www .jav a 2s. com */ protected void parseLocalesHeader(String value) { // Store the accumulated languages that have been requested in // a local collection, sorted by the quality value (so we can // add Locales in descending order). The values will be ArrayLists // containing the corresponding Locales to be added TreeMap locales = new TreeMap(); // Preprocess the value to remove all whitespace int white = value.indexOf(' '); if (white < 0) white = value.indexOf('\t'); if (white >= 0) { StringBuffer sb = new StringBuffer(); int len = value.length(); for (int i = 0; i < len; i++) { char ch = value.charAt(i); if ((ch != ' ') && (ch != '\t')) sb.append(ch); } value = sb.toString(); } // Process each comma-delimited language specification parser.setString(value); // ASSERT: parser is available to us int length = parser.getLength(); while (true) { // Extract the next comma-delimited entry int start = parser.getIndex(); if (start >= length) break; int end = parser.findChar(','); String entry = parser.extract(start, end).trim(); parser.advance(); // For the following entry // Extract the quality factor for this entry double quality = 1.0; int semi = entry.indexOf(";q="); if (semi >= 0) { try { quality = Double.parseDouble(entry.substring(semi + 3)); } catch (NumberFormatException e) { quality = 0.0; } entry = entry.substring(0, semi); } // Skip entries we are not going to keep track of if (quality < 0.00005) continue; // Zero (or effectively zero) quality factors if ("*".equals(entry)) continue; // FIXME - "*" entries are not handled // Extract the language and country for this entry String language = null; String country = null; String variant = null; int dash = entry.indexOf('-'); if (dash < 0) { language = entry; country = ""; variant = ""; } else { language = entry.substring(0, dash); country = entry.substring(dash + 1); int vDash = country.indexOf('-'); if (vDash > 0) { String cTemp = country.substring(0, vDash); variant = country.substring(vDash + 1); country = cTemp; } else { variant = ""; } } // Add a new Locale to the list of Locales for this quality level Locale locale = new Locale(language, country, variant); Double key = new Double(-quality); // Reverse the order ArrayList values = (ArrayList) locales.get(key); if (values == null) { values = new ArrayList(); locales.put(key, values); } values.add(locale); } // Process the quality values in highest->lowest order (due to // negating the Double value when creating the key) Iterator keys = locales.keySet().iterator(); while (keys.hasNext()) { Double key = (Double) keys.next(); ArrayList list = (ArrayList) locales.get(key); Iterator values = list.iterator(); while (values.hasNext()) { Locale locale = (Locale) values.next(); addLocale(locale); } } }
From source file:fr.cirad.mgdb.exporting.individualoriented.DARwinExportHandler.java
@Override public void exportData(OutputStream outputStream, String sModule, Collection<File> individualExportFiles, boolean fDeleteSampleExportFilesOnExit, ProgressIndicator progress, DBCursor markerCursor, Map<Comparable, Comparable> markerSynonyms, Map<String, InputStream> readyToExportFiles) throws Exception { MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule); GenotypingProject aProject = mongoTemplate.findOne( new Query(Criteria.where(GenotypingProject.FIELDNAME_PLOIDY_LEVEL).exists(true)), GenotypingProject.class); if (aProject == null) LOG.warn("Unable to find a project containing ploidy level information! Assuming ploidy level is 2."); int ploidy = aProject == null ? 2 : aProject.getPloidyLevel(); File warningFile = File.createTempFile("export_warnings_", ""); FileWriter warningFileWriter = new FileWriter(warningFile); int markerCount = markerCursor.count(); ZipOutputStream zos = new ZipOutputStream(outputStream); if (readyToExportFiles != null) for (String readyToExportFile : readyToExportFiles.keySet()) { zos.putNextEntry(new ZipEntry(readyToExportFile)); InputStream inputStream = readyToExportFiles.get(readyToExportFile); byte[] dataBlock = new byte[1024]; int count = inputStream.read(dataBlock, 0, 1024); while (count != -1) { zos.write(dataBlock, 0, count); count = inputStream.read(dataBlock, 0, 1024); }/*from ww w. j a va 2 s . com*/ } String exportName = sModule + "_" + markerCount + "variants_" + individualExportFiles.size() + "individuals"; StringBuffer donFileContents = new StringBuffer( "@DARwin 5.0 - DON -" + LINE_SEPARATOR + individualExportFiles.size() + "\t" + 1 + LINE_SEPARATOR + "N" + "\t" + "individual" + LINE_SEPARATOR); int count = 0; String missingGenotype = ""; for (int j = 0; j < ploidy; j++) missingGenotype += "\tN"; zos.putNextEntry(new ZipEntry(exportName + ".var")); zos.write(("@DARwin 5.0 - ALLELIC - " + ploidy + LINE_SEPARATOR + individualExportFiles.size() + "\t" + markerCount * ploidy + LINE_SEPARATOR + "N").getBytes()); DBCursor markerCursorCopy = markerCursor.copy(); // dunno how expensive this is, but seems safer than keeping all IDs in memory at any time short nProgress = 0, nPreviousProgress = 0; int avgObjSize = (Integer) mongoTemplate .getCollection(mongoTemplate.getCollectionName(VariantRunData.class)).getStats().get("avgObjSize"); int nChunkSize = nMaxChunkSizeInMb * 1024 * 1024 / avgObjSize; markerCursorCopy.batchSize(nChunkSize); int nMarkerIndex = 0; while (markerCursorCopy.hasNext()) { DBObject exportVariant = markerCursorCopy.next(); Comparable markerId = (Comparable) exportVariant.get("_id"); if (markerSynonyms != null) { Comparable syn = markerSynonyms.get(markerId); if (syn != null) markerId = syn; } for (int j = 0; j < ploidy; j++) zos.write(("\t" + markerId).getBytes()); } TreeMap<Integer, Comparable> problematicMarkerIndexToNameMap = new TreeMap<Integer, Comparable>(); ArrayList<String> distinctAlleles = new ArrayList<String>(); // the index of each allele will be used as its code int i = 0; for (File f : individualExportFiles) { BufferedReader in = new BufferedReader(new FileReader(f)); try { String individualId, line = in.readLine(); // read sample id if (line != null) individualId = line; else throw new Exception("Unable to read first line of temp export file " + f.getName()); donFileContents.append(++count + "\t" + individualId + LINE_SEPARATOR); zos.write((LINE_SEPARATOR + count).getBytes()); nMarkerIndex = 0; while ((line = in.readLine()) != null) { List<String> genotypes = MgdbDao.split(line, "|"); HashMap<Object, Integer> genotypeCounts = new HashMap<Object, Integer>(); // will help us to keep track of missing genotypes int highestGenotypeCount = 0; String mostFrequentGenotype = null; for (String genotype : genotypes) { if (genotype.length() == 0) continue; /* skip missing genotypes */ int gtCount = 1 + MgdbDao.getCountForKey(genotypeCounts, genotype); if (gtCount > highestGenotypeCount) { highestGenotypeCount = gtCount; mostFrequentGenotype = genotype; } genotypeCounts.put(genotype, gtCount); } if (genotypeCounts.size() > 1) { warningFileWriter.write("- Dissimilar genotypes found for variant __" + nMarkerIndex + "__, individual " + individualId + ". Exporting most frequent: " + mostFrequentGenotype + "\n"); problematicMarkerIndexToNameMap.put(nMarkerIndex, ""); } String codedGenotype = ""; if (mostFrequentGenotype != null) for (String allele : mostFrequentGenotype.split(" ")) { if (!distinctAlleles.contains(allele)) distinctAlleles.add(allele); codedGenotype += "\t" + distinctAlleles.indexOf(allele); } else codedGenotype = missingGenotype.replaceAll("N", "-1"); // missing data is coded as -1 zos.write(codedGenotype.getBytes()); nMarkerIndex++; } } catch (Exception e) { LOG.error("Error exporting data", e); progress.setError("Error exporting data: " + e.getClass().getSimpleName() + (e.getMessage() != null ? " - " + e.getMessage() : "")); return; } finally { in.close(); } if (progress.hasAborted()) return; nProgress = (short) (++i * 100 / individualExportFiles.size()); if (nProgress > nPreviousProgress) { // LOG.debug("============= doDARwinExport (" + i + "): " + nProgress + "% ============="); progress.setCurrentStepProgress(nProgress); nPreviousProgress = nProgress; } if (!f.delete()) { f.deleteOnExit(); LOG.info("Unable to delete tmp export file " + f.getAbsolutePath()); } } zos.putNextEntry(new ZipEntry(exportName + ".don")); zos.write(donFileContents.toString().getBytes()); // now read variant names for those that induced warnings nMarkerIndex = 0; markerCursor.batchSize(nChunkSize); while (markerCursor.hasNext()) { DBObject exportVariant = markerCursor.next(); if (problematicMarkerIndexToNameMap.containsKey(nMarkerIndex)) { Comparable markerId = (Comparable) exportVariant.get("_id"); if (markerSynonyms != null) { Comparable syn = markerSynonyms.get(markerId); if (syn != null) markerId = syn; } for (int j = 0; j < ploidy; j++) zos.write(("\t" + markerId).getBytes()); problematicMarkerIndexToNameMap.put(nMarkerIndex, markerId); } } warningFileWriter.close(); if (warningFile.length() > 0) { zos.putNextEntry(new ZipEntry(exportName + "-REMARKS.txt")); int nWarningCount = 0; BufferedReader in = new BufferedReader(new FileReader(warningFile)); String sLine; while ((sLine = in.readLine()) != null) { for (Integer aMarkerIndex : problematicMarkerIndexToNameMap.keySet()) sLine = sLine.replaceAll("__" + aMarkerIndex + "__", problematicMarkerIndexToNameMap.get(aMarkerIndex).toString()); zos.write((sLine + "\n").getBytes()); in.readLine(); nWarningCount++; } LOG.info("Number of Warnings for export (" + exportName + "): " + nWarningCount); in.close(); } warningFile.delete(); zos.close(); progress.setCurrentStepProgress((short) 100); }
From source file:org.apache.catalina.core.StandardContext.java
/** * Load and initialize all servlets marked "load on startup" in the * web application deployment descriptor. * * @param children Array of wrappers for all currently defined * servlets (including those not declared load on startup) *//*from ww w . j ava 2s . c om*/ public void loadOnStartup(Container children[]) { // Collect "load on startup" servlets that need to be initialized TreeMap map = new TreeMap(); for (int i = 0; i < children.length; i++) { Wrapper wrapper = (Wrapper) children[i]; int loadOnStartup = wrapper.getLoadOnStartup(); if (loadOnStartup < 0) continue; if (loadOnStartup == 0) // Arbitrarily put them last loadOnStartup = Integer.MAX_VALUE; Integer key = new Integer(loadOnStartup); ArrayList list = (ArrayList) map.get(key); if (list == null) { list = new ArrayList(); map.put(key, list); } list.add(wrapper); } // Load the collected "load on startup" servlets Iterator keys = map.keySet().iterator(); while (keys.hasNext()) { Integer key = (Integer) keys.next(); ArrayList list = (ArrayList) map.get(key); Iterator wrappers = list.iterator(); while (wrappers.hasNext()) { Wrapper wrapper = (Wrapper) wrappers.next(); try { wrapper.load(); } catch (ServletException e) { getServletContext().log(sm.getString("standardWrapper.loadException", getName()), e); // NOTE: load errors (including a servlet that throws // UnavailableException from tht init() method) are NOT // fatal to application startup } } } }
From source file:uk.ac.leeds.ccg.andyt.projects.moses.process.RegressionReport_UK1.java
public void writeAggregateStatisticsForOptimisationConstraints_ISARHP_ISARCEP(String a_OutputDir_String) throws Exception { HashMap a_ID_RecordID_HashMap = _ISARDataHandler.get_ID_RecordID_HashMap(); File optimisationConstraints_SARs = new File(a_OutputDir_String, "OptimisationConstraints_SARs.csv"); FileOutputStream a_FileOutputStream = new FileOutputStream(optimisationConstraints_SARs); OutputDataHandler_OptimisationConstraints.writeHSARHP_ISARCEPHeader(a_FileOutputStream); a_FileOutputStream.flush();//from w ww .j a va 2s . c om Object[] fitnessCounts; HashMap<String, Integer> a_SARCounts = null; TreeSet<String> a_LADCodes_TreeSet = _CASDataHandler.getLADCodes_TreeSet(); String s2; String s1; Iterator<String> a_Iterator_String = a_LADCodes_TreeSet.iterator(); while (a_Iterator_String.hasNext()) { // Need to reorder data for each LAD as OAs not necessarily returned // in any order and an ordered result is wanted TreeMap<String, HashMap<String, Integer>> resultsForLAD = new TreeMap<String, HashMap<String, Integer>>(); boolean setPrevious_OA_String = true; s1 = a_Iterator_String.next(); s2 = s1.substring(0, 3); File resultsFile = new File(a_OutputDir_String + s2 + "/" + s1 + "/population.csv"); // A few results are missing if (resultsFile.exists()) { System.out.println(resultsFile.toString() + " exists"); String previous_OA_String = ""; BufferedReader aBufferedReader = new BufferedReader( new InputStreamReader(new FileInputStream(resultsFile))); StreamTokenizer aStreamTokenizer = new StreamTokenizer(aBufferedReader); Generic_StaticIO.setStreamTokenizerSyntax1(aStreamTokenizer); String line = ""; int tokenType = aStreamTokenizer.nextToken(); while (tokenType != StreamTokenizer.TT_EOF) { switch (tokenType) { case StreamTokenizer.TT_EOL: //System.out.println(line); String[] lineFields = line.split(","); String a_OA_String = lineFields[0]; if (previous_OA_String.equalsIgnoreCase(a_OA_String)) { if (lineFields[1].equalsIgnoreCase("HP")) { //System.out.println("HP"); long a_ISARRecordID = (Long) a_ID_RecordID_HashMap.get(new Long(lineFields[2])); ISARDataRecord a_ISARDataRecord = _ISARDataHandler .getISARDataRecord(a_ISARRecordID); GeneticAlgorithm_ISARHP_ISARCEP.addToCountsHP(a_ISARDataRecord, a_SARCounts, _Random); //System.out.println(a_HSARDataRecord.toString()); } else { //System.out.println("CEP"); // From the id of the ISARDataRecord get the // ISARRecordID. long a_ISARRecordID = (Long) a_ID_RecordID_HashMap.get(new Long(lineFields[2])); ISARDataRecord a_ISARDataRecord = _ISARDataHandler .getISARDataRecord(a_ISARRecordID); GeneticAlgorithm_ISARHP_ISARCEP.addToCountsCEP(a_ISARDataRecord, a_SARCounts, _Random); } } else { // Store result if (setPrevious_OA_String) { previous_OA_String = a_OA_String; setPrevious_OA_String = false; } else { // Store resultsForLAD.put(previous_OA_String, a_SARCounts); } // Initialise/Re-initialise CASDataRecord a_CASDataRecord = (CASDataRecord) _CASDataHandler .getDataRecord(a_OA_String); fitnessCounts = GeneticAlgorithm_ISARHP_ISARCEP.getFitnessCounts(a_CASDataRecord); a_SARCounts = (HashMap<String, Integer>) fitnessCounts[1]; // Start a new aggregation if (lineFields[1].equalsIgnoreCase("HP")) { //System.out.println("HP"); long a_ISARRecordID = (Long) a_ID_RecordID_HashMap.get(new Long(lineFields[2])); ISARDataRecord a_ISARDataRecord = _ISARDataHandler .getISARDataRecord(a_ISARRecordID); GeneticAlgorithm_ISARHP_ISARCEP.addToCountsHP(a_ISARDataRecord, a_SARCounts, _Random); //System.out.println(a_HSARDataRecord.toString()); } else { //System.out.println("CEP"); // From the id of the ISARDataRecord get the // ISARRecordID. long a_ISARRecordID = (Long) a_ID_RecordID_HashMap.get(new Long(lineFields[2])); ISARDataRecord a_ISARDataRecord = _ISARDataHandler .getISARDataRecord(a_ISARRecordID); GeneticAlgorithm_ISARHP_ISARCEP.addToCountsCEP(a_ISARDataRecord, a_SARCounts, _Random); //System.out.println(a_ISARDataRecord.toString()); } //a_OA_String = lineFields[0]; } previous_OA_String = a_OA_String; break; case StreamTokenizer.TT_WORD: line = aStreamTokenizer.sval; break; } tokenType = aStreamTokenizer.nextToken(); } } else { System.out.println(resultsFile.toString() + " !exists"); } Iterator<String> string_Iterator = resultsForLAD.keySet().iterator(); while (string_Iterator.hasNext()) { String oa_Code = string_Iterator.next(); a_SARCounts = resultsForLAD.get(oa_Code); //GeneticAlgorithm_ISARHP_ISARCEP.addToCountsCEP(null, a_ID_RecordID_HashMap, _Random) OutputDataHandler_OptimisationConstraints.writeISARHP_ISARCEP(a_SARCounts, oa_Code, a_FileOutputStream); } } a_FileOutputStream.close(); }
From source file:edu.hawaii.soest.kilonalu.adam.AdamSource.java
/** * A method that processes the data ByteBuffer passed in for the given IP * address of the ADAM sensor, parses the binary ADAM data, and flushes the * data to the DataTurbine given the sensor properties in the XMLConfiguration * passed in./*from w w w .j av a 2s . com*/ * * @param datagramAddress - the IP address of the datagram of this packet of data * @param xmlConfig - the XMLConfiguration object containing the list of * sensor properties * @param sampleBuffer - the binary data sample as a ByteBuffer */ protected boolean process(String datagramAddress, XMLConfiguration xmlConfig, ByteBuffer sampleBuffer) { logger.debug("AdamSource.process() called."); // do not execute the stream if there is no connection if (!isConnected()) return false; boolean failed = false; try { // add channels of data that will be pushed to the server. // Each sample will be sent to the Data Turbine as an rbnb frame. Information // on each channel is found in the XMLConfiguration file (sensors.properties.xml) // and the AdamParser object (to get the actual voltages for each ADAM channel) ChannelMap rbnbChannelMap = new ChannelMap(); // used to flush channels ChannelMap registerChannelMap = new ChannelMap(); // used to register channels int channelIndex = 0; this.adamParser = new AdamParser(sampleBuffer); logger.debug("\n" + "channelZero : " + this.adamParser.getChannelZero() + "\n" + "channelOne : " + this.adamParser.getChannelOne() + "\n" + "channelTwo : " + this.adamParser.getChannelTwo() + "\n" + "channelThree : " + this.adamParser.getChannelThree() + "\n" + "channelFour : " + this.adamParser.getChannelFour() + "\n" + "channelFive : " + this.adamParser.getChannelFive() + "\n" + "channelSix : " + this.adamParser.getChannelSix() + "\n" + "channelSeven : " + this.adamParser.getChannelSeven() + "\n" + "channelAverage : " + this.adamParser.getChannelAverage() + "\n" + "channelZeroMax : " + this.adamParser.getChannelZeroMax() + "\n" + "channelOneMax : " + this.adamParser.getChannelOneMax() + "\n" + "channelTwoMax : " + this.adamParser.getChannelTwoMax() + "\n" + "channelThreeMax : " + this.adamParser.getChannelThreeMax() + "\n" + "channelFourMax : " + this.adamParser.getChannelFourMax() + "\n" + "channelFiveMax : " + this.adamParser.getChannelFiveMax() + "\n" + "channelSixMax : " + this.adamParser.getChannelSixMax() + "\n" + "channelSevenMax : " + this.adamParser.getChannelSevenMax() + "\n" + "channelAverageMax : " + this.adamParser.getChannelAverageMax() + "\n" + "channelZeroMin : " + this.adamParser.getChannelZeroMin() + "\n" + "channelOneMin : " + this.adamParser.getChannelOneMin() + "\n" + "channelTwoMin : " + this.adamParser.getChannelTwoMin() + "\n" + "channelThreeMin : " + this.adamParser.getChannelThreeMin() + "\n" + "channelFourMin : " + this.adamParser.getChannelFourMin() + "\n" + "channelFiveMin : " + this.adamParser.getChannelFiveMin() + "\n" + "channelSixMin : " + this.adamParser.getChannelSixMin() + "\n" + "channelSevenMin : " + this.adamParser.getChannelSevenMin() + "\n" + "channelAverageMin : " + this.adamParser.getChannelAverageMin() + "\n" ); // create a TreeMap to hold the voltageChannel and its associated // RBNB ChannelMap channel string. When the RBNB ChannelMap is // populated, this TreeMap will be consulted TreeMap<Integer, String> voltageChannelTreeMap = new TreeMap<Integer, String>(); // create a character string to store characters from the voltage values StringBuilder decimalASCIISampleData = new StringBuilder(); // Create a list of sensors from the properties file, and iterate through // the list, matching the datagram IP address to the address in the // xml configuration file. If there is a match, find the correct voltage // channel to measurement mappings, create a corresponding RBNB channel // map, and flush the data to the DataTurbine. List sensorList = xmlConfig.getList("sensor.address"); // declare the properties that will be pulled from the // sensor.properties.xml file String address = ""; String sourceName = ""; String description = ""; String type = ""; String cacheSize = ""; String archiveSize = ""; String archiveChannel = ""; String portNumber = ""; String voltageChannel = ""; String measurement = ""; // evaluate each sensor listed in the sensor.properties.xml file for (Iterator sIterator = sensorList.iterator(); sIterator.hasNext();) { // get each property value of the sensor int index = sensorList.indexOf(sIterator.next()); address = (String) xmlConfig.getProperty("sensor(" + index + ").address"); sourceName = (String) xmlConfig.getProperty("sensor(" + index + ").name"); description = (String) xmlConfig.getProperty("sensor(" + index + ").description"); type = (String) xmlConfig.getProperty("sensor(" + index + ").type"); logger.debug("Sensor details:" + "\n\t\t\t\t\t\t\t\t\t\taddress : " + address + "\n\t\t\t\t\t\t\t\t\t\tname : " + sourceName + "\n\t\t\t\t\t\t\t\t\t\tdescription : " + description + "\n\t\t\t\t\t\t\t\t\t\ttype : " + type); // move to the next sensor if this doesn't match the RBNB source name if (!sourceName.equals(getRBNBClientName())) { continue; } List portList = xmlConfig.getList("sensor(" + index + ").ports.port[@number]"); // get each port of the sensor, along with the port properties for (Iterator pIterator = portList.iterator(); pIterator.hasNext();) { int pindex = portList.indexOf(pIterator.next()); // get the port number value portNumber = (String) xmlConfig .getProperty("sensor(" + index + ").ports.port(" + pindex + ")[@number]"); logger.debug("\tport " + portNumber + " details:"); List measurementList = xmlConfig .getList("sensor(" + index + ").ports.port(" + pindex + ").measurement[@label]"); // get each measurement and voltageChannel for the given port for (Iterator mIterator = measurementList.iterator(); mIterator.hasNext();) { int mindex = measurementList.indexOf(mIterator.next()); // build the property paths into the config file String voltagePath = "sensor(" + index + ").ports.port(" + pindex + ").measurement(" + mindex + ").voltageChannel"; String measurementPath = "sensor(" + index + ").ports.port(" + pindex + ").measurement(" + mindex + ")[@label]"; // get the voltageChannel and measurement label values voltageChannel = (String) xmlConfig.getProperty(voltagePath); measurement = (String) xmlConfig.getProperty(measurementPath); logger.debug("\t\t" + "voltageChannel: " + voltageChannel + "\n\t\t\t\t\t\t\t\t\t\t\t" + "measurement label: " + measurement); // Match the datagram address with the address in the xmlConfig file if (datagramAddress.equals(address)) { // and only add channel data for this class instance RBNB Source name if (sourceName.equals(getRBNBClientName())) { // create an Integer out of the voltageChannel Integer voltageChannelInt = new Integer(voltageChannel); // build the RBNB channel path string String channelPath = "port" + "/" + portNumber + "/" + measurement; voltageChannelTreeMap.put(voltageChannelInt, channelPath); } else { logger.debug("\t\tSource names don't match: " + sourceName + " != " + getRBNBClientName()); } // end sourceName if() statement } else { logger.debug("\t\tNo IP address match. " + datagramAddress + " != " + address); } //end IP address if() statement } // end for each channel } // end for each port // now that we've found the correct sensor, exit the sensor loop break; } // end for each sensor // Build the RBNB channel map from the entries in the tree map // by doing a lookup of the ADAM voltage channel values based // on the voltage channel number in the treemap. Also add the voltages // to the DecimalASCIISampleData string (and then channel) for (Iterator vcIterator = voltageChannelTreeMap.keySet().iterator(); vcIterator.hasNext();) { int voltageChannelFromMap = ((Integer) vcIterator.next()).intValue(); String channelPathFromMap = voltageChannelTreeMap.get(voltageChannelFromMap); float voltageValue = -9999.0f; // look up the voltage value from the AdamParser object based // on the voltage channel set in the xmlConfig file (via the treemap) switch (voltageChannelFromMap) { case 0: voltageValue = this.adamParser.getChannelZero(); break; case 1: voltageValue = this.adamParser.getChannelOne(); break; case 2: voltageValue = this.adamParser.getChannelTwo(); break; case 3: voltageValue = this.adamParser.getChannelThree(); break; case 4: voltageValue = this.adamParser.getChannelFour(); break; case 5: voltageValue = this.adamParser.getChannelFive(); break; case 6: voltageValue = this.adamParser.getChannelSix(); break; case 7: voltageValue = this.adamParser.getChannelSeven(); break; } // now add the channel and the voltage value to the RBNB channel maps channelIndex = registerChannelMap.Add(channelPathFromMap); registerChannelMap.PutUserInfo(channelIndex, "units=volts"); registerChannelMap.PutUserInfo(channelIndex, "description=" + description); logger.debug("Voltage Channel Tree Map: " + voltageChannelTreeMap.toString()); // then the channel and voltage channelIndex = rbnbChannelMap.Add(channelPathFromMap); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat32(channelIndex, new float[] { voltageValue }); decimalASCIISampleData.append(String.format("%05.3f", (Object) voltageValue) + ", "); } // and only flush data for this class instance RBNB Source name if (sourceName.equals(getRBNBClientName()) && datagramAddress.equals(address)) { // add the timestamp to the rbnb channel map registerChannelMap.PutTimeAuto("server"); rbnbChannelMap.PutTimeAuto("server"); // then add a timestamp to the end of the ASCII version of the sample DATE_FORMAT.setTimeZone(TZ); String sampleDateAsString = DATE_FORMAT.format(new Date()).toString(); decimalASCIISampleData.append(sampleDateAsString); decimalASCIISampleData.append("\n"); // add the DecimalASCIISampleData channel to the channelMap channelIndex = registerChannelMap.Add(getRBNBChannelName()); channelIndex = rbnbChannelMap.Add(getRBNBChannelName()); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, decimalASCIISampleData.toString()); // Now register the RBNB channels, and flush the rbnbChannelMap to the // DataTurbine getSource().Register(registerChannelMap); getSource().Flush(rbnbChannelMap); logger.info(getRBNBClientName() + " Sample sent to the DataTurbine: " + decimalASCIISampleData.toString()); registerChannelMap.Clear(); rbnbChannelMap.Clear(); sampleBuffer.clear(); } else { logger.debug("\t\tSource names don't match: " + sourceName + " != " + getRBNBClientName()); registerChannelMap.Clear(); rbnbChannelMap.Clear(); sampleBuffer.clear(); } } catch (SAPIException sapie) { // In the event of an RBNB communication exception, log the exception, // and allow execute() to return false, which will prompt a retry. failed = true; sapie.printStackTrace(); return !failed; } return !failed; }
From source file:org.opendatakit.services.database.utlities.ODKDatabaseImplUtils.java
/** * If the caller specified a complex json value for a structured type, flush * the value through to the individual columns. * * @param orderedColumns//from w ww. j ava 2 s . c o m * @param values */ private void cleanUpValuesMap(OrderedColumns orderedColumns, Map<String, Object> values) { TreeMap<String, String> toBeResolved = new TreeMap<String, String>(); for (String key : values.keySet()) { if (DataTableColumns.CONFLICT_TYPE.equals(key)) { continue; } else if (DataTableColumns.FILTER_TYPE.equals(key)) { continue; } else if (DataTableColumns.FILTER_VALUE.equals(key)) { continue; } else if (DataTableColumns.FORM_ID.equals(key)) { continue; } else if (DataTableColumns.ID.equals(key)) { continue; } else if (DataTableColumns.LOCALE.equals(key)) { continue; } else if (DataTableColumns.ROW_ETAG.equals(key)) { continue; } else if (DataTableColumns.SAVEPOINT_CREATOR.equals(key)) { continue; } else if (DataTableColumns.SAVEPOINT_TIMESTAMP.equals(key)) { continue; } else if (DataTableColumns.SAVEPOINT_TYPE.equals(key)) { continue; } else if (DataTableColumns.SYNC_STATE.equals(key)) { continue; } else if (DataTableColumns._ID.equals(key)) { continue; } // OK it is one of the data columns ColumnDefinition cp = orderedColumns.find(key); if (!cp.isUnitOfRetention()) { toBeResolved.put(key, (String) values.get(key)); } } // remove these non-retained values from the values set... for (String key : toBeResolved.keySet()) { values.remove(key); } while (!toBeResolved.isEmpty()) { TreeMap<String, String> moreToResolve = new TreeMap<String, String>(); for (TreeMap.Entry<String, String> entry : toBeResolved.entrySet()) { String key = entry.getKey(); String json = entry.getValue(); if (json == null) { // don't need to do anything // since the value is null continue; } ColumnDefinition cp = orderedColumns.find(key); try { TypeReference<Map<String, Object>> reference = new TypeReference<Map<String, Object>>() { }; Map<String, Object> struct = ODKFileUtils.mapper.readValue(json, reference); for (ColumnDefinition child : cp.getChildren()) { String subkey = child.getElementKey(); ColumnDefinition subcp = orderedColumns.find(subkey); if (subcp.isUnitOfRetention()) { ElementType subtype = subcp.getType(); ElementDataType type = subtype.getDataType(); if (type == ElementDataType.integer) { values.put(subkey, (Integer) struct.get(subcp.getElementName())); } else if (type == ElementDataType.number) { values.put(subkey, (Double) struct.get(subcp.getElementName())); } else if (type == ElementDataType.bool) { values.put(subkey, ((Boolean) struct.get(subcp.getElementName())) ? 1 : 0); } else { values.put(subkey, (String) struct.get(subcp.getElementName())); } } else { // this must be a javascript structure... re-JSON it and save (for // next round). moreToResolve.put(subkey, ODKFileUtils.mapper.writeValueAsString(struct.get(subcp.getElementName()))); } } } catch (JsonParseException e) { e.printStackTrace(); throw new IllegalStateException("should not be happening"); } catch (JsonMappingException e) { e.printStackTrace(); throw new IllegalStateException("should not be happening"); } catch (IOException e) { e.printStackTrace(); throw new IllegalStateException("should not be happening"); } } toBeResolved = moreToResolve; } }
From source file:fr.cirad.mgdb.exporting.individualoriented.PLinkExportHandler.java
@Override public void exportData(OutputStream outputStream, String sModule, Collection<File> individualExportFiles, boolean fDeleteSampleExportFilesOnExit, ProgressIndicator progress, DBCursor markerCursor, Map<Comparable, Comparable> markerSynonyms, Map<String, InputStream> readyToExportFiles) throws Exception { File warningFile = File.createTempFile("export_warnings_", ""); FileWriter warningFileWriter = new FileWriter(warningFile); ZipOutputStream zos = new ZipOutputStream(outputStream); if (readyToExportFiles != null) for (String readyToExportFile : readyToExportFiles.keySet()) { zos.putNextEntry(new ZipEntry(readyToExportFile)); InputStream inputStream = readyToExportFiles.get(readyToExportFile); byte[] dataBlock = new byte[1024]; int count = inputStream.read(dataBlock, 0, 1024); while (count != -1) { zos.write(dataBlock, 0, count); count = inputStream.read(dataBlock, 0, 1024); }// w w w. j a v a 2 s . c o m } MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule); int markerCount = markerCursor.count(); String exportName = sModule + "_" + markerCount + "variants_" + individualExportFiles.size() + "individuals"; zos.putNextEntry(new ZipEntry(exportName + ".ped")); TreeMap<Integer, Comparable> problematicMarkerIndexToNameMap = new TreeMap<Integer, Comparable>(); short nProgress = 0, nPreviousProgress = 0; int i = 0; for (File f : individualExportFiles) { BufferedReader in = new BufferedReader(new FileReader(f)); try { String individualId, line = in.readLine(); // read sample id if (line != null) { individualId = line; String population = getIndividualPopulation(sModule, line); String individualInfo = (population == null ? "." : population) + " " + individualId; zos.write((individualInfo + " 0 0 0 " + getIndividualGenderCode(sModule, individualId)) .getBytes()); } else throw new Exception("Unable to read first line of temp export file " + f.getName()); int nMarkerIndex = 0; while ((line = in.readLine()) != null) { List<String> genotypes = MgdbDao.split(line, "|"); HashMap<Object, Integer> genotypeCounts = new HashMap<Object, Integer>(); // will help us to keep track of missing genotypes int highestGenotypeCount = 0; String mostFrequentGenotype = null; for (String genotype : genotypes) { if (genotype.length() == 0) continue; /* skip missing genotypes */ int gtCount = 1 + MgdbDao.getCountForKey(genotypeCounts, genotype); if (gtCount > highestGenotypeCount) { highestGenotypeCount = gtCount; mostFrequentGenotype = genotype; } genotypeCounts.put(genotype, gtCount); } if (genotypeCounts.size() > 1) { warningFileWriter.write("- Dissimilar genotypes found for variant " + nMarkerIndex + ", individual " + individualId + ". Exporting most frequent: " + mostFrequentGenotype + "\n"); problematicMarkerIndexToNameMap.put(nMarkerIndex, ""); } String[] alleles = mostFrequentGenotype == null ? new String[0] : mostFrequentGenotype.split(" "); if (alleles.length > 2) { warningFileWriter.write("- More than 2 alleles found for variant " + nMarkerIndex + ", individual " + individualId + ". Exporting only the first 2 alleles.\n"); problematicMarkerIndexToNameMap.put(nMarkerIndex, ""); } String all1 = alleles.length == 0 ? "0" : alleles[0]; String all2 = alleles.length == 0 ? "0" : alleles[alleles.length == 1 ? 0 : 1]; if (all1.length() != 1 || all2.length() != 1) { warningFileWriter .write("- SNP expected, but alleles are not coded on a single char for variant " + nMarkerIndex + ", individual " + individualId + ". Ignoring this genotype.\n"); problematicMarkerIndexToNameMap.put(nMarkerIndex, ""); } else zos.write((" " + all1 + " " + all2).getBytes()); nMarkerIndex++; } } catch (Exception e) { LOG.error("Error exporting data", e); progress.setError("Error exporting data: " + e.getClass().getSimpleName() + (e.getMessage() != null ? " - " + e.getMessage() : "")); return; } finally { in.close(); } if (progress.hasAborted()) return; nProgress = (short) (++i * 100 / individualExportFiles.size()); if (nProgress > nPreviousProgress) { progress.setCurrentStepProgress(nProgress); nPreviousProgress = nProgress; } zos.write('\n'); if (!f.delete()) { f.deleteOnExit(); LOG.info("Unable to delete tmp export file " + f.getAbsolutePath()); } } warningFileWriter.close(); zos.putNextEntry(new ZipEntry(exportName + ".map")); int avgObjSize = (Integer) mongoTemplate .getCollection(mongoTemplate.getCollectionName(VariantRunData.class)).getStats().get("avgObjSize"); int nChunkSize = nMaxChunkSizeInMb * 1024 * 1024 / avgObjSize; markerCursor.batchSize(nChunkSize); int nMarkerIndex = 0; while (markerCursor.hasNext()) { DBObject exportVariant = markerCursor.next(); DBObject refPos = (DBObject) exportVariant.get(VariantData.FIELDNAME_REFERENCE_POSITION); Comparable markerId = (Comparable) exportVariant.get("_id"); String chrom = (String) refPos.get(ReferencePosition.FIELDNAME_SEQUENCE); Long pos = ((Number) refPos.get(ReferencePosition.FIELDNAME_START_SITE)).longValue(); if (chrom == null) LOG.warn("Chromosomal position not found for marker " + markerId); Comparable exportedId = markerSynonyms == null ? markerId : markerSynonyms.get(markerId); zos.write(((chrom == null ? "0" : chrom) + " " + exportedId + " " + 0 + " " + (pos == null ? 0 : pos) + LINE_SEPARATOR).getBytes()); if (problematicMarkerIndexToNameMap.containsKey(nMarkerIndex)) { // we are going to need this marker's name for the warning file Comparable variantName = markerId; if (markerSynonyms != null) { Comparable syn = markerSynonyms.get(markerId); if (syn != null) variantName = syn; } problematicMarkerIndexToNameMap.put(nMarkerIndex, variantName); } nMarkerIndex++; } if (warningFile.length() > 0) { zos.putNextEntry(new ZipEntry(exportName + "-REMARKS.txt")); int nWarningCount = 0; BufferedReader in = new BufferedReader(new FileReader(warningFile)); String sLine; while ((sLine = in.readLine()) != null) { for (Integer aMarkerIndex : problematicMarkerIndexToNameMap.keySet()) sLine = sLine.replaceAll("__" + aMarkerIndex + "__", problematicMarkerIndexToNameMap.get(aMarkerIndex).toString()); zos.write((sLine + "\n").getBytes()); in.readLine(); nWarningCount++; } LOG.info("Number of Warnings for export (" + exportName + "): " + nWarningCount); in.close(); } warningFile.delete(); zos.close(); progress.setCurrentStepProgress((short) 100); }
From source file:uk.ac.leeds.ccg.andyt.projects.moses.process.RegressionReport_UK1.java
public void writeAggregateStatisticsForOptimisationConstraints_HSARHP_ISARCEP(String a_OutputDir_String) throws Exception { HashMap a_HID_HSARDataRecordVector_HashMap = _HSARDataHandler.get_HID_HSARDataRecordVector_HashMap(); HashMap a_ID_RecordID_HashMap = _ISARDataHandler.get_ID_RecordID_HashMap(); File optimisationConstraints_SARs = new File(a_OutputDir_String, "OptimisationConstraints_SARs.csv"); FileOutputStream a_FileOutputStream = new FileOutputStream(optimisationConstraints_SARs); OutputDataHandler_OptimisationConstraints.writeHSARHP_ISARCEPHeader(a_FileOutputStream); a_FileOutputStream.flush();// ww w . ja v a 2 s . c om HashMap<String, Integer> a_SARCounts = null; CASDataRecord a_CASDataRecord; TreeSet<String> a_LADCodes_TreeSet = _CASDataHandler.getLADCodes_TreeSet(); String s2; String s1; Iterator<String> a_Iterator_String = a_LADCodes_TreeSet.iterator(); while (a_Iterator_String.hasNext()) { // Need to reorder data for each LAD as OAs not necessarily returned // in any order and an ordered result is wanted TreeMap<String, HashMap<String, Integer>> resultsForLAD = new TreeMap<String, HashMap<String, Integer>>(); boolean setPrevious_OA_String = true; s1 = a_Iterator_String.next(); s2 = s1.substring(0, 3); File resultsFile = new File(a_OutputDir_String + s2 + "/" + s1 + "/population.csv"); // A few results are missing if (resultsFile.exists()) { System.out.println(resultsFile.toString() + " exists"); String previous_OA_String = ""; BufferedReader aBufferedReader = new BufferedReader( new InputStreamReader(new FileInputStream(resultsFile))); StreamTokenizer aStreamTokenizer = new StreamTokenizer(aBufferedReader); Generic_StaticIO.setStreamTokenizerSyntax1(aStreamTokenizer); String line = ""; int tokenType = aStreamTokenizer.nextToken(); while (tokenType != StreamTokenizer.TT_EOF) { switch (tokenType) { case StreamTokenizer.TT_EOL: //System.out.println(line); String[] lineFields = line.split(","); String a_OA_String = lineFields[0]; if (previous_OA_String.equalsIgnoreCase(a_OA_String)) { if (lineFields[1].equalsIgnoreCase("HP")) { //System.out.println("HP"); // From the id of a household get a Vector // of HSARDataRecords Vector household = (Vector) a_HID_HSARDataRecordVector_HashMap .get(new Integer(lineFields[2])); HSARDataRecord a_HSARDataRecord; for (int i = 0; i < household.size(); i++) { a_HSARDataRecord = (HSARDataRecord) household.elementAt(i); GeneticAlgorithm_HSARHP_ISARCEP.addToCounts(a_HSARDataRecord, a_SARCounts, _Random); } //System.out.println(a_HSARDataRecord.toString()); } else { //System.out.println("CEP"); // From the id of the ISARDataRecord get the // ISARRecordID. long a_ISARRecordID = (Long) a_ID_RecordID_HashMap.get(new Long(lineFields[2])); ISARDataRecord a_ISARDataRecord = _ISARDataHandler .getISARDataRecord(a_ISARRecordID); GeneticAlgorithm_HSARHP_ISARCEP.addToCountsCEP(a_ISARDataRecord, a_SARCounts, _Random); } } else { // Store result if (setPrevious_OA_String) { previous_OA_String = a_OA_String; setPrevious_OA_String = false; } else { // Store resultsForLAD.put(previous_OA_String, a_SARCounts); } // Initialise/Re-initialise a_CASDataRecord = (CASDataRecord) _CASDataHandler.getDataRecord(a_OA_String); Object[] fitnessCounts = GeneticAlgorithm_HSARHP_ISARCEP .getFitnessCounts(a_CASDataRecord); a_SARCounts = (HashMap<String, Integer>) fitnessCounts[1]; // Start a new aggregation if (lineFields[1].equalsIgnoreCase("HP")) { //System.out.println("HP"); // From the id of a household get a Vector // of HSARDataRecords Vector household = (Vector) a_HID_HSARDataRecordVector_HashMap .get(new Integer(lineFields[2])); HSARDataRecord a_HSARDataRecord; for (int i = 0; i < household.size(); i++) { a_HSARDataRecord = (HSARDataRecord) household.elementAt(i); GeneticAlgorithm_HSARHP_ISARCEP.addToCounts(a_HSARDataRecord, a_SARCounts, _Random); } //System.out.println(a_HSARDataRecord.toString()); } else { //System.out.println("CEP"); // From the id of the ISARDataRecord get the // ISARRecordID. long a_ISARRecordID = (Long) a_ID_RecordID_HashMap.get(new Long(lineFields[2])); ISARDataRecord a_ISARDataRecord = _ISARDataHandler .getISARDataRecord(a_ISARRecordID); GeneticAlgorithm_HSARHP_ISARCEP.addToCountsCEP(a_ISARDataRecord, a_SARCounts, _Random); //System.out.println(a_ISARDataRecord.toString()); } //a_OA_String = lineFields[0]; } previous_OA_String = a_OA_String; break; case StreamTokenizer.TT_WORD: line = aStreamTokenizer.sval; break; } tokenType = aStreamTokenizer.nextToken(); } } else { System.out.println(resultsFile.toString() + " !exists"); } Iterator<String> string_Iterator = resultsForLAD.keySet().iterator(); while (string_Iterator.hasNext()) { String oa_Code = string_Iterator.next(); OutputDataHandler_OptimisationConstraints.writeHSARHP_ISARCEP(resultsForLAD.get(oa_Code), oa_Code, a_FileOutputStream); } } a_FileOutputStream.close(); }