ImporterDL.java

/*
Copyright 2008-2010 Gephi
Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
Website : http://www.gephi.org

This file is part of Gephi.

DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.

Copyright 2011 Gephi Consortium. All rights reserved.

The contents of this file are subject to the terms of either the GNU
General Public License Version 3 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with the
License. You can obtain a copy of the License at
http://gephi.org/about/legal/license-notice/
or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
specific language governing permissions and limitations under the
License.  When distributing the software, include this License Header
Notice in each file and include the License files at
/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
License Header, with the fields enclosed by brackets [] replaced by
your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"

If you wish your version of this file to be governed by only the CDDL
or only the GPL Version 3, indicate your decision by adding
"[Contributor] elects to include this software in this distribution
under the [CDDL or GPL Version 3] license." If you do not indicate a
single choice of license, a recipient has the option to distribute
your version of this file under either the CDDL, the GPL Version 3 or
to extend the choice of license to its licensees as provided above.
However, if you add GPL Version 3 code and therefore, elected the GPL
Version 3 license, then the option applies only if the new code is
made subject to such option by the copyright holder.

Contributor(s):

Portions Copyrighted 2011 Gephi Consortium.
 */
package org.gephi.io.importer.plugin.file;

import java.io.LineNumberReader;
import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;
import org.gephi.io.importer.api.ContainerLoader;
import org.gephi.io.importer.api.EdgeDraft;
import org.gephi.io.importer.api.ImportUtils;
import org.gephi.io.importer.api.Issue;
import org.gephi.io.importer.api.NodeDraft;
import org.gephi.io.importer.api.Report;
import org.gephi.io.importer.spi.FileImporter;
import org.gephi.utils.longtask.spi.LongTask;
import org.gephi.utils.progress.Progress;
import org.gephi.utils.progress.ProgressTicket;
import org.openide.util.NbBundle;

/**
 *
 * @author Mathieu Bastian
 */
public class ImporterDL implements FileImporter, LongTask {

    //enum
    private enum Format {

        FULLMATRIX, EDGELIST1
    };
    //Architecture
    private Reader reader;
    private ContainerLoader container;
    private Report report;
    private ProgressTicket progressTicket;
    private boolean cancel = false;
    //Data
    private Format format = Format.FULLMATRIX;
    private Map<String, String> headerMap;
    private int numNodes;
    private int numMatricies;
    private int dataLineStartDelta = -1;

    public boolean execute(ContainerLoader container) {
        this.container = container;
        this.report = new Report();
        LineNumberReader lineReader = ImportUtils.getTextReader(reader);
        try {
            importData(lineReader);
        } catch (Exception e) {
            throw new RuntimeException(e);
        }
        return !cancel;
    }

    private void importData(LineNumberReader reader) throws Exception {
        Progress.start(progressTicket);        //Progress

        List<String> lines = new ArrayList<String>();
        for (; reader.ready();) {
            String line = reader.readLine();
            if (line != null && !line.isEmpty()) {
                lines.add(line);
            }
        }

        if (lines.isEmpty() || (!lines.get(0).startsWith("DL") && !lines.get(0).startsWith("dl"))) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_firstline"), Issue.Level.CRITICAL));
        }

        headerMap = new HashMap<String, String>();
        readHeaderLine(lines.get(0).substring(2));

        int i = 1;
        for (; i < lines.size(); i++) {
            String line = lines.get(i).toLowerCase();
            if (line.trim().endsWith("data:") || line.trim().endsWith("labels:")) {
                break;
            } else {
                readHeaderLine(line);
            }
        }

        computeHeaders();

        if (lines.get(i).toLowerCase().trim().endsWith("labels:") && lines.size() > i + 1) {
            readLabels(lines.get(++i));
        }

        int dataLineStart = -1;
        for (; i < lines.size(); i++) {
            String line = lines.get(i).toLowerCase();
            if (line.trim().endsWith("data:")) {
                dataLineStart = i + 1;
                break;
            }
        }
        if (dataLineStart == -1) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_nodata"), Issue.Level.SEVERE));
        } else if (lines.size() > dataLineStart) {
            dataLineStartDelta = dataLineStart + 1;
            lines = lines.subList(dataLineStart, lines.size());

            if (format.equals(Format.FULLMATRIX)) {
                readeMatrixBlock(lines);
            } else if (format.equals(Format.EDGELIST1)) {
                readEdgelistBlock(lines);
            }
        }
    }

    private void readHeaderLine(String line) {
        line = line.replaceAll(" = ", "=");
        StringTokenizer firstLineTokenizer = new StringTokenizer(line, " ,;");
        while (firstLineTokenizer.hasMoreTokens()) {
            String tag = firstLineTokenizer.nextToken().toLowerCase();
            if (tag.indexOf("=") != -1) {
                headerMap.put(tag.substring(0, tag.indexOf("=")).trim(), tag.substring(tag.indexOf("=") + 1).trim());
            } else {
                //report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_unknowntag", tag), Issue.Level.WARNING));
            }
        }
    }

    private void computeHeaders() {
        //read format
        String form = (String) headerMap.get("format");
        if (form == null) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_formatmissing"), Issue.Level.INFO));
        } else if (!form.equals("edgelist1") && !form.equals("fullmatrix")) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_badformat", form), Issue.Level.SEVERE));
        } else if (form.equals("edgelist1")) {
            format = Format.EDGELIST1;
        } else if (form.equals("fullmatrix")) {
            format = Format.FULLMATRIX;
        }

        // read number of nodes
        try {
            String nArg = (String) headerMap.get("n");
            numNodes = Integer.parseInt(nArg);
        } catch (Exception e) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_nmissing"), Issue.Level.SEVERE));
        }

        // read number matricies
        String mats = (String) headerMap.get("nm");
        if (mats != null) {
            try {
                numMatricies = Integer.parseInt(mats);
            } catch (Exception e) {
                report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_mmissing"), Issue.Level.SEVERE));
            }
        } else {
            numMatricies = 1;
        }
    }

    private void readLabels(String labels) {
        StringTokenizer labelkonizer = new StringTokenizer(labels, ",");
        // check that there are the right number of labels
        if (labelkonizer.countTokens() != numNodes) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_labelscount", labelkonizer.countTokens(), numNodes), Issue.Level.SEVERE));
        }
        int nodeCount = 0;
        while (labelkonizer.hasMoreTokens()) {
            String label = labelkonizer.nextToken();
            nodeCount++;
            NodeDraft nodeDraft = container.factory().newNodeDraft();
            nodeDraft.setId("" + nodeCount);
            nodeDraft.setLabel(label);
            container.addNode(nodeDraft);
        }
    }

    private void readeMatrixBlock(List<String> data) {
        int startTime = 0;
        for (int i = 0; i < data.size(); i++) {
            int rowNum = 0;
            for (; i < data.size() && !data.get(i).trim().equals("!"); i++) {
                if (rowNum <= numNodes) {
                    readMatrixRow(data.get(i), i, rowNum, startTime, startTime + 1);
                    rowNum++;
                } else {
                    report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_matrixrowscount", rowNum, numNodes), Issue.Level.SEVERE));
                    break;
                }
            }
            if (rowNum < numNodes) {
                report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_matrixrowscount2", rowNum, numNodes), Issue.Level.SEVERE));
            }
            startTime++;
        }
        if (startTime != numMatricies) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_matriciescount", startTime, numMatricies), Issue.Level.SEVERE));
        }
    }

    private void readMatrixRow(String line, int pointer, int row, int startTime, int endTime) {
        StringTokenizer rowkonizer = new StringTokenizer(line, " ");
        int from = row + 1;
        int to = 1;
        double weight = 0;
        while (rowkonizer.hasMoreTokens()) {
            String toParse = (String) rowkonizer.nextToken();
            if (to > numNodes) {
                report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_matrixentriescount", row, startTime, getLineNumber(pointer)), Issue.Level.SEVERE));
            }
            try {
                weight = Double.parseDouble(toParse);
            } catch (Exception e) {
                report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_weightparseerror", toParse, startTime, getLineNumber(pointer)), Issue.Level.SEVERE));
            }

            if (weight != 0) {
                NodeDraft sourceNode = container.getNode("" + from);
                NodeDraft targetNode = container.getNode("" + to);
                EdgeDraft edgeDraft = null;
                if (container.edgeExists(sourceNode, targetNode)) {
                    edgeDraft = container.getEdge(sourceNode, targetNode);
                    //dynamic
                } else {
                    edgeDraft = container.factory().newEdgeDraft();
                    edgeDraft.setSource(sourceNode);
                    edgeDraft.setTarget(targetNode);
                    edgeDraft.setWeight((float) weight);
                    container.addEdge(edgeDraft);
                }
            }
            to++;
        }
    }

    private void readEdgelistBlock(List<String> data) {
        int startTime = 0;
        for (int i = 0; i < data.size(); i++) {
            for (; i < data.size() && !data.get(i).trim().equals("!"); i++) {
                readEdgelistRow(data.get(i), i, startTime, startTime + 1);
            }
            // increment the time step before starting next matrix
            startTime++;
        }
        if (startTime != numMatricies) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_edgelistssetscount", startTime, numMatricies), Issue.Level.SEVERE));
        }
    }

    private void readEdgelistRow(String row, int pointer, double startTime, double endTime) {
        StringTokenizer rowkonizer = new StringTokenizer(row);
        if (!rowkonizer.hasMoreTokens()) {
            return;
        }
        // should have three entries, int from, int to, weight
        String from = rowkonizer.nextToken();
        if (!rowkonizer.hasMoreTokens()) {
            return;
        }
        String to = rowkonizer.nextToken();
        double weight = 1.0;

        if (rowkonizer.hasMoreTokens()) {
            String weightParse = rowkonizer.nextToken();
            try {
                weight = Double.parseDouble(weightParse);
            } catch (Exception e) {
                report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_edgeparseweight", weightParse, getLineNumber(pointer)), Issue.Level.WARNING));
            }
        }

        NodeDraft sourceNode = container.getNode(from);
        NodeDraft targetNode = container.getNode(to);
        EdgeDraft edgeDraft = null;
        if (container.edgeExists(sourceNode, targetNode)) {
            edgeDraft = container.getEdge(sourceNode, targetNode);
            //dynamic
        } else {
            edgeDraft = container.factory().newEdgeDraft();
            edgeDraft.setSource(sourceNode);
            edgeDraft.setTarget(targetNode);
            edgeDraft.setWeight((float) weight);
            container.addEdge(edgeDraft);
        }
    }

    private int getLineNumber(int pointer) {
        return pointer + dataLineStartDelta;
    }

    public void setReader(Reader reader) {
        this.reader = reader;
    }

    public ContainerLoader getContainer() {
        return container;
    }

    public Report getReport() {
        return report;
    }

    public boolean cancel() {
        cancel = true;
        return true;
    }

    public void setProgressTicket(ProgressTicket progressTicket) {
        this.progressTicket = progressTicket;
    }
}