Example usage for org.apache.commons.collections15.map ListOrderedMap ListOrderedMap

List of usage examples for org.apache.commons.collections15.map ListOrderedMap ListOrderedMap

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Introduction

In this page you can find the example usage for org.apache.commons.collections15.map ListOrderedMap ListOrderedMap.

Prototype

public ListOrderedMap()

Source Link

Document

Constructs a new empty ListOrderedMap that decorates a HashMap.

Usage

From source file:edu.brown.hstore.PartitionExecutor.java

/**
 * Execute the given fragment tasks on this site's underlying EE
 * /*from  w  w w  .  j ava2s  .  c o m*/
 * @param ts
 * @param undoToken
 * @param batchSize
 * @param fragmentIds
 * @param parameterSets
 * @param output_depIds
 * @param input_depIds
 * @return
 */
private DependencySet executePlanFragments(AbstractTransaction ts, long undoToken, int batchSize,
        long fragmentIds[], ParameterSet parameterSets[], int output_depIds[], int input_depIds[],
        Map<Integer, List<VoltTable>> input_deps) {
    assert (this.ee != null) : "The EE object is null. This is bad!";
    Long txn_id = ts.getTransactionId();

    // *********************************** DEBUG
    // ***********************************
    if (d) {
        StringBuilder sb = new StringBuilder();
        sb.append(String.format("%s - Executing %d fragments [lastTxnId=%d, undoToken=%d]", ts, batchSize,
                this.lastCommittedTxnId, undoToken));
        if (t) {
            Map<String, Object> m = new ListOrderedMap<String, Object>();
            m.put("Fragments", Arrays.toString(fragmentIds));

            Map<Integer, Object> inner = new ListOrderedMap<Integer, Object>();
            for (int i = 0; i < batchSize; i++)
                inner.put(i, parameterSets[i].toString());
            m.put("Parameters", inner);

            if (batchSize > 0 && input_depIds[0] != HStoreConstants.NULL_DEPENDENCY_ID) {
                inner = new ListOrderedMap<Integer, Object>();
                for (int i = 0; i < batchSize; i++) {
                    List<VoltTable> deps = input_deps.get(input_depIds[i]);
                    inner.put(input_depIds[i], (deps != null ? StringUtil.join("\n", deps) : "???"));
                } // FOR
                m.put("Input Dependencies", inner);
            }
            m.put("Output Dependencies", Arrays.toString(output_depIds));
            sb.append("\n" + StringUtil.formatMaps(m));
        }
        LOG.debug(sb.toString());
    }
    // *********************************** DEBUG
    // ***********************************

    // pass attached dependencies to the EE (for non-sysproc work).
    if (input_deps != null && input_deps.isEmpty() == false) {
        if (d)
            LOG.debug(String.format("%s - Stashing %d InputDependencies at partition %d", ts, input_deps.size(),
                    this.partitionId));
        ee.stashWorkUnitDependencies(input_deps);
    }

    // Check whether this fragments are read-only
    if (ts.isExecReadOnly(this.partitionId)) {

        boolean readonly = PlanFragmentIdGenerator.areFragmentsReadOnly(this.database, fragmentIds, batchSize);

        if (readonly == false) {
            if (d)
                LOG.debug(String.format("%s - Marking txn as not read-only %s", ts,
                        Arrays.toString(fragmentIds)));
            ts.markExecNotReadOnly(this.partitionId);
        }

        // We can do this here because the only way that we're not read-only
        // is if
        // we actually modify data at this partition
        ts.setSubmittedEE(this.partitionId);
    }

    DependencySet result = null;
    boolean needs_profiling = (hstore_conf.site.txn_profiling && ts.isExecLocal(this.partitionId));
    if (needs_profiling)
        ((LocalTransaction) ts).profiler.startExecEE();
    Throwable error = null;
    try {
        if (d)
            LOG.debug(String.format("%s - Executing fragments %s at partition %d", ts,
                    Arrays.toString(fragmentIds), this.partitionId));

        result = this.ee.executeQueryPlanFragmentsAndGetDependencySet(fragmentIds, batchSize, input_depIds,
                output_depIds, parameterSets, batchSize, txn_id.longValue(), this.lastCommittedTxnId,
                undoToken);

    } catch (SerializableException ex) {
        if (d)
            LOG.error(String.format("%s - Unexpected error in the ExecutionEngine on partition %d", ts,
                    this.partitionId), ex);
        error = ex;
        throw ex;
    } catch (Throwable ex) {
        error = ex;
        new ServerFaultException(
                String.format("%s - Failed to execute PlanFragments: %s", ts, Arrays.toString(fragmentIds)),
                ex);
    } finally {
        if (needs_profiling)
            ((LocalTransaction) ts).profiler.stopExecEE();
        if (error == null && result == null) {
            LOG.warn(String.format(
                    "%s - Finished executing fragments but got back null results [fragmentIds=%s]", ts,
                    Arrays.toString(fragmentIds)));
        }
    }

    // *********************************** DEBUG
    // ***********************************
    if (d) {
        if (result != null) {
            LOG.debug(String.format("%s - Finished executing fragments and got back %d results", ts,
                    result.depIds.length));
        } else {
            LOG.warn(String.format(
                    "%s - Finished executing fragments but got back null results? That seems bad...", ts));
        }
    }
    // *********************************** DEBUG
    // ***********************************
    return (result);
}

From source file:org.isatools.gui.datamanager.exportisa.ExportISAGUI.java

private void processStudies(Collection<Study> studies) {
    availableStudies = new ListOrderedMap<String, List<String>>();
    for (Study study : studies) {
        //         System.out.println("study investigation is : " + study.getInvestigations().size());
        if (study.getInvestigations().size() > 0) {
            for (Investigation inv : study.getInvestigations()) {
                if (!availableStudies.containsKey(inv.getAcc())) {
                    availableStudies.put(inv.getAcc(), new ArrayList<String>());
                }/* ww  w.ja v  a2s  . c  o m*/
                availableStudies.get(inv.getAcc()).add(study.getAcc());
            }
        } else {

            availableStudies.put(study.getAcc(), null);
        }
    }
}

From source file:org.isatools.gui.datamanager.studyaccess.StudyAccessionGUI.java

private void processStudies(Collection<Study> studies) {
    availableStudies = new ListOrderedMap<String, List<String>>();
    for (Study study : studies) {
        if (study.getInvestigations().size() > 0) {
            for (Investigation inv : study.getInvestigations()) {
                if (!availableStudies.containsKey(inv.getAcc())) {
                    availableStudies.put(inv.getAcc(), new ArrayList<String>());
                }//from  w w w .ja v  a  2  s .  co m
                availableStudies.get(inv.getAcc()).add(study.getAcc());
            }
        } else {

            availableStudies.put(study.getAcc(), null);
        }
    }
}

From source file:org.isatools.gui.optionselector.OptionGroup.java

/**
 * OptionGroup contains a number of items which you can either select one or many of depending on the single selection parameter
 *
 * @param alignment       - e.g. OptionGroup.HORIZONTAL_ALIGNMENT to align the options in a horizontal arrangement.
 * @param singleSelection - whether or not this group should allow singular selection (true) or multiple option selection (false)
 *//* w w  w .  j  ava 2 s. c  o  m*/
public OptionGroup(int alignment, boolean singleSelection) {
    this.singleSelection = singleSelection;
    this.alignment = alignment;

    availableOptions = new ListOrderedMap<T, OptionItem>();

    setLayout(
            new BoxLayout(this, alignment == HORIZONTAL_ALIGNMENT ? BoxLayout.LINE_AXIS : BoxLayout.PAGE_AXIS));
    setOpaque(false);
}

From source file:org.isatools.isacreator.api.utils.SpreadsheetUtils.java

/**
 * @param targetSheet - Spreadsheet to 'look at' for extraction of desired column names
 * @param toIgnore    - Set<String> containing the columns to be ignored.
 * @return Map containing all the desired columns along with their index.
 *//*from  www .  j a  v a 2s  . c  o m*/
public static Map<String, Integer> getColumnNames(Spreadsheet targetSheet, Set<String> toIgnore) {

    Map<String, Integer> columnNamesToIndex = new ListOrderedMap<String, Integer>();

    Map<Integer, String> columnIndexToName = getColumns(targetSheet, toIgnore);

    for (Integer columnIndex : columnIndexToName.keySet()) {
        columnNamesToIndex.put(columnIndexToName.get(columnIndex), columnIndex);
    }

    return columnNamesToIndex;
}

From source file:org.isatools.isacreator.api.utils.SpreadsheetUtils.java

public static Map<Integer, String> getColumns(Spreadsheet targetSheet, Set<String> toIgnore) {
    int columnCount = targetSheet.getTable().getColumnCount();

    Map<Integer, String> columnNames = new ListOrderedMap<Integer, String>();

    for (int column = 1; column < columnCount; column++) {
        String colName = targetSheet.getTable().getColumnName(column);

        if (toIgnore != null) {

            boolean isIgnored = false;

            for (String ignoredFields : toIgnore) {
                if (colName.contains(ignoredFields)) {
                    isIgnored = true;/*from  w ww .  j a  va2 s .co  m*/
                    break;
                }
            }

            if (!isIgnored) {
                columnNames.put(column, colName);
            }

        } else {
            columnNames.put(column, colName);
        }
    }
    return columnNames;
}

From source file:org.isatools.isacreator.api.utils.SpreadsheetUtils.java

/**
 * Pulls out all values of a particular column and associates the other metadata with it as well
 *
 * @param primaryColumnName - e.g. Sample Name to pull out all the unique sample names available.
 * @param targetSheet       - Spreadsheet to 'look at' for extraction of desired column names
 * @return Map<String, Map<String, String>> -> primary Column values mapped to the key/value pairs describing the particular group
 *///  ww w.  j  ava 2  s.  c  om
public static Map<String, SampleInformation> getGroupInformation(String primaryColumnName,
        Spreadsheet targetSheet) {

    Map<String, SampleInformation> groupInformation = new HashMap<String, SampleInformation>();

    Map<Integer, String> columnIndicesToName = getColumns(targetSheet, new HashSet<String>());

    for (int rowNo = 0; rowNo < targetSheet.getTable().getRowCount(); rowNo++) {

        String primaryColumnValue = "";

        if (!groupInformation.containsKey(primaryColumnName)) {

            Map<String, String> keyValues = new ListOrderedMap<String, String>();
            Map<String, Integer> columnNameToIndex = new HashMap<String, Integer>();

            for (int column = 1; column < targetSheet.getColumnCount(); column++) {
                Object dataVal = targetSheet.getTable().getValueAt(rowNo, column);

                String columnName = columnIndicesToName.get(column);

                if (columnName.equalsIgnoreCase(primaryColumnName)) {
                    primaryColumnValue = dataVal == null ? "" : dataVal.toString();
                } else {
                    keyValues.put(columnName, dataVal == null ? "" : dataVal.toString());
                    columnNameToIndex.put(columnName, column);
                }
            }
            groupInformation.put(primaryColumnValue,
                    new SampleInformation(rowNo, primaryColumnValue, keyValues, columnNameToIndex));
        }
    }

    return groupInformation;
}

From source file:org.isatools.isacreator.common.filterableTree.TreeFilterModel.java

public TreeFilterModel(TreeNode treeNode, FilterableJTree targetJTree) {
    super(treeNode);
    this.targetJTree = targetJTree;
    items = new ListOrderedMap<T, Set<V>>();
    filterItems = new ListOrderedMap<T, Set<V>>();
}

From source file:org.isatools.isacreator.formatmappingutility.loader.CSVFileLoader.java

/**
 * File should be checked to determine whether or not it is a directory. if not, then just load the single file
 *
 * @param f - Either a file or pointer to a directory!
 * @return Map<String, String[]> where key is the file name and the String[] is the list of column names
 *///from   w ww  . j a  va  2 s .co  m
public Map<String, String[]> processFile(File f) {
    Map<String, String[]> result = new ListOrderedMap<String, String[]>();

    try {
        File[] files;
        if (f.isDirectory()) {
            files = f.listFiles();
        } else {
            files = new File[] { f };
        }

        for (File file : files) {

            if (!file.isHidden()) {
                String[] firstLine;

                CSVReader reader = new CSVReader(new FileReader(file), delimiter);

                if (delimiter == FileLoader.COMMA_DELIM) {
                    readerUsed = FileLoader.CSV_READER_CSV;
                } else {
                    readerUsed = FileLoader.CSV_READER_TXT;
                }

                int rowOffSet;
                try {
                    rowOffSet = Integer.parseInt(ISAcreatorProperties.getProperty("isacreator.rowOffset")) - 1;
                } catch (NumberFormatException nfe) {
                    rowOffSet = 0;
                }

                for (int skipCount = 0; skipCount < rowOffSet; skipCount++) {
                    reader.readNext();
                }

                firstLine = reader.readNext();

                // clean up
                for (int i = 0; i < firstLine.length; i++) {
                    firstLine[i] = firstLine[i].trim();
                }

                result.put(file.getPath(), firstLine);
            }
        }

    } catch (FileNotFoundException e) {
        log.error("file not found: " + e.getMessage());
    } catch (IOException e) {
        log.error("io exception occurred " + e.getMessage());
    } catch (Exception e) {
        log.error(
                "problem with incoming file. We were unable to process it for this reason: " + e.getMessage());
    }
    return result;

}

From source file:org.isatools.isacreator.formatmappingutility.loader.ExcelFileLoader.java

public Map<String, String[]> processFile(File f) {
    Map<String, String[]> columnHeaders = new ListOrderedMap<String, String[]>();
    Workbook w;//  w  w  w  .ja  v  a 2 s  . com
    try {
        if (!f.isHidden()) {
            w = Workbook.getWorkbook(f);
            // Get the first sheet
            for (Sheet s : w.getSheets()) {

                int rowStart;
                try {
                    rowStart = Integer.parseInt(ISAcreatorProperties.getProperty("isacreator.rowOffset")) - 1;
                    System.out.println("Row offset is: " + rowStart);
                } catch (NumberFormatException nfe) {
                    System.out.println(nfe.getMessage());
                    rowStart = 0;
                }

                if (s.getRows() > 0) {

                    List<String> headersForSheet = new ArrayList<String>();
                    for (int j = 0; j < s.getColumns(); j++) {

                        String cellContents = s.getCell(j, rowStart).getContents();
                        if (!cellContents.trim().equals("")) {
                            headersForSheet.add(cellContents);
                        }
                    }

                    columnHeaders.put(s.getName(), headersForSheet.toArray(new String[headersForSheet.size()]));
                }
            }
        }

    } catch (BiffException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }

    return columnHeaders;
}