/*
Copyright 2008-2010 Gephi
Authors : Mathieu Bastian <mathieu.bastian@gephi.org>,
Sebastien Heymann <sebastien.heymann@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.BufferedReader;
import java.io.LineNumberReader;
import java.io.Reader;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.gephi.data.attributes.api.AttributeTable;
import org.gephi.data.attributes.api.AttributeColumn;
import org.gephi.data.attributes.api.AttributeType;
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
* @author Sebastien Heymann
*/
public class ImporterGDF implements FileImporter, LongTask {
//Architecture
private Reader reader;
private ContainerLoader container;
private Report report;
private ProgressTicket progressTicket;
private boolean cancel = false;
//Extract
private List<String> nodeLines = new ArrayList<String>();
private List<String> edgeLines = new ArrayList<String>();
//Matcher
private String[] nodeLineStart;
private String[] edgeLineStart;
//Columns
private GDFColumn[] nodeColumns;
private GDFColumn[] edgeColumns;
public ImporterGDF() {
nodeLineStart = new String[]{"nodedef>name", "nodedef> name", "Nodedef>name", "Nodedef> name", "nodedef>\"name", "nodedef> \"name", "Nodedef>\"name", "Nodedef> \"name"};
edgeLineStart = new String[]{"edgedef>", "Edgedef>"};
}
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
//Verify a node line exists and puts nodes and edges lines in arrays
walkFile(reader);
Progress.switchToDeterminate(progressTicket, nodeLines.size() + edgeLines.size()); //Progress
//Magix regex
Pattern pattern = Pattern.compile("(?<=(?:,|^)\")(.*?)(?=(?<=(?:[^\\\\]))\",|\"$)|(?<=(?:,|^)')(.*?)(?=(?<=(?:[^\\\\]))',|'$)|(?<=(?:,|^))(?=[^'\"])(.*?)(?=(?:,|$))|(?<=,)($)");
//Nodes
for (String nodeLine : nodeLines) {
if (cancel) {
return;
}
//Create Node
NodeDraft node = container.factory().newNodeDraft();
Matcher m = pattern.matcher(nodeLine);
int count = 0;
String id = "";
while (m.find()) {
int start = m.start();
int end = m.end();
if (start != end) {
String data = nodeLine.substring(start, end);
data = data.trim();
if (!data.isEmpty() && !data.toLowerCase().equals("null")) {
if (count == 0) {
//Id
id = data;
node.setId(data);
} else if (count - 1 < nodeColumns.length) {
if (nodeColumns[count - 1] != null) {
setNodeData(node, nodeColumns[count - 1], data);
}
} else {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat7", id), Issue.Level.SEVERE));
}
}
}
count++;
}
container.addNode(node);
Progress.progress(progressTicket); //Progress
}
//Edges
for (String edgeLine : edgeLines) {
if (cancel) {
return;
}
//Create Edge
EdgeDraft edge = container.factory().newEdgeDraft();
Matcher m = pattern.matcher(edgeLine);
int count = 0;
String id = "";
while (m.find()) {
int start = m.start();
int end = m.end();
if (start != end) {
String data = edgeLine.substring(start, end);
data = data.trim();
if (!data.isEmpty() && !data.toLowerCase().equals("null")) {
if (count == 0) {
NodeDraft nodeSource = container.getNode(data);
edge.setSource(nodeSource);
id = data;
} else if (count == 1) {
NodeDraft nodeTarget = container.getNode(data);
edge.setTarget(nodeTarget);
id += "," + data;
} else if (count - 2 < edgeColumns.length) {
if (edgeColumns[count - 2] != null) {
setEdgeData(edge, edgeColumns[count - 2], data);
}
} else {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat7", id), Issue.Level.SEVERE));
}
}
}
count++;
}
container.addEdge(edge);
Progress.progress(progressTicket); //Progress
}
}
private void walkFile(BufferedReader reader) throws Exception {
if (reader.ready()) {
String firstLine = reader.readLine();
if (isNodeFirstLine(firstLine)) {
findNodeColumns(firstLine);
boolean edgesWalking = false;
while (reader.ready() && !cancel) {
String line = reader.readLine();
if (isEdgeFirstLine(line)) {
edgesWalking = true;
findEdgeColumns(line);
} else {
if (!edgesWalking) {
//Nodes
nodeLines.add(line);
} else {
//Edges
edgeLines.add(line);
}
}
}
} else {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat1"), Issue.Level.CRITICAL));
}
} else {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat1"), Issue.Level.CRITICAL));
}
}
private void findNodeColumns(String line) throws Exception {
String[] columns = line.split(",");
nodeColumns = new GDFColumn[columns.length - 1];
for (int i = 1; i < columns.length; i++) {
String columnString = columns[i];
String typeString = "";
String columnName = "";
AttributeType type = AttributeType.STRING;
try {
typeString = columnString.substring(columnString.lastIndexOf(" ")).trim().toLowerCase();
} catch (IndexOutOfBoundsException e) {
}
try {
int end = columnString.lastIndexOf(" ");
if (end != -1) {
columnName = columnString.substring(0, end).trim().toLowerCase();
} else {
columnName = columnString.trim().toLowerCase();
}
} catch (IndexOutOfBoundsException e) {
}
//Check error
if (columnName.isEmpty()) {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat2"), Issue.Level.SEVERE));
columnName = "default" + i;
}
if (typeString.isEmpty()) {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat6", columnName), Issue.Level.INFO));
typeString = "varchar";
}
//Clean parenthesis
typeString = typeString.replaceAll("\\([0-9]*\\)", "");
if (typeString.equals("varchar")) {
type = AttributeType.STRING;
} else if (typeString.equals("bool")) {
type = AttributeType.BOOLEAN;
} else if (typeString.equals("boolean")) {
type = AttributeType.BOOLEAN;
} else if (typeString.equals("integer")) {
type = AttributeType.INT;
} else if (typeString.equals("tinyint")) {
type = AttributeType.INT;
} else if (typeString.equals("int")) {
type = AttributeType.INT;
} else if (typeString.equals("double")) {
type = AttributeType.DOUBLE;
} else if (typeString.equals("float")) {
type = AttributeType.FLOAT;
} else {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat5", typeString), Issue.Level.WARNING));
}
if (columnName.equals("x")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.X);
report.log("Node property found: x");
} else if (columnName.equals("y")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.Y);
report.log("Node property found: y");
} else if (columnName.equals("visible")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.VISIBLE);
report.log("Node property found: visible");
} else if (columnName.equals("color")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.COLOR);
report.log("Node property found: color");
} else if (columnName.equals("fixed")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.FIXED);
report.log("Node property found: fixed");
} else if (columnName.equals("style")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.STYLE);
report.log("Node property found: style");
} else if (columnName.equals("width")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.WIDTH);
report.log("Node property found: width");
} else if (columnName.equals("height")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.HEIGHT);
report.log("Node property found: height");
} else if (columnName.equals("label")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.LABEL);
report.log("Node property found: label");
} else if (columnName.equals("labelvisible")) {
nodeColumns[i - 1] = new GDFColumn(GDFColumn.NodeGuessColumn.LABELVISIBLE);
report.log("Node property found: labelvisible");
} else {
AttributeTable nodeClass = container.getAttributeModel().getNodeTable();
if (!nodeClass.hasColumn(columnName)) {
AttributeColumn newColumn = nodeClass.addColumn(columnName, type);
nodeColumns[i - 1] = new GDFColumn(newColumn);
report.log("Node attribute " + columnName + " (" + type.getTypeString() + ")");
} else {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat8", columnName), Issue.Level.SEVERE));
}
}
}
}
private void findEdgeColumns(String line) throws Exception {
String[] columns = line.split(",");
edgeColumns = new GDFColumn[columns.length - 2];
for (int i = 2; i < columns.length; i++) {
String columnString = columns[i];
String typeString = "";
String columnName = "";
AttributeType type = AttributeType.STRING;
try {
typeString = columnString.substring(columnString.lastIndexOf(" ")).trim().toLowerCase();
} catch (IndexOutOfBoundsException e) {
}
try {
int end = columnString.lastIndexOf(" ");
if (end != -1) {
columnName = columnString.substring(0, end).trim().toLowerCase();
} else {
columnName = columnString.trim().toLowerCase();
}
} catch (IndexOutOfBoundsException e) {
}
//Check error
if (columnName.isEmpty()) {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat2"), Issue.Level.SEVERE));
columnName = "default" + i;
}
if (typeString.isEmpty()) {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat6", columnName), Issue.Level.INFO));
typeString = "varchar";
}
//Clean parenthesis
typeString = typeString.replaceAll("\\([0-9]*\\)", "");
if (typeString.equals("varchar")) {
type = AttributeType.STRING;
} else if (typeString.equals("bool")) {
type = AttributeType.BOOLEAN;
} else if (typeString.equals("boolean")) {
type = AttributeType.BOOLEAN;
} else if (typeString.equals("integer")) {
type = AttributeType.INT;
} else if (typeString.equals("tinyint")) {
type = AttributeType.INT;
} else if (typeString.equals("int")) {
type = AttributeType.INT;
} else if (typeString.equals("double")) {
type = AttributeType.DOUBLE;
} else if (typeString.equals("float")) {
type = AttributeType.FLOAT;
} else {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat5", typeString), Issue.Level.WARNING));
}
if (columnName.equals("color")) {
edgeColumns[i - 2] = new GDFColumn(GDFColumn.EdgeGuessColumn.COLOR);
report.log("Edge property found: color");
} else if (columnName.equals("visible")) {
edgeColumns[i - 2] = new GDFColumn(GDFColumn.EdgeGuessColumn.VISIBLE);
report.log("Edge property found: visible");
} else if (columnName.equals("weight")) {
edgeColumns[i - 2] = new GDFColumn(GDFColumn.EdgeGuessColumn.WEIGHT);
report.log("Edge property found: weight");
} else if (columnName.equals("directed")) {
edgeColumns[i - 2] = new GDFColumn(GDFColumn.EdgeGuessColumn.DIRECTED);
report.log("Edge property found: directed");
} else if (columnName.equals("label")) {
edgeColumns[i - 2] = new GDFColumn(GDFColumn.EdgeGuessColumn.LABEL);
report.log("Edge property found: label");
} else if (columnName.equals("labelvisible")) {
edgeColumns[i - 2] = new GDFColumn(GDFColumn.EdgeGuessColumn.LABELVISIBLE);
report.log("Edge property found: labelvisible");
} else {
AttributeTable edgeClass = container.getAttributeModel().getEdgeTable();
if (!edgeClass.hasColumn(columnName)) {
AttributeColumn newColumn = edgeClass.addColumn(columnName, type);
edgeColumns[i - 2] = new GDFColumn(newColumn);
report.log("Edge attribute " + columnName + " (" + type.getTypeString() + ")");
} else {
report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat9", columnName), Issue.Level.SEVERE));
}
}
}
}
private boolean isNodeFirstLine(String line) {
for (String s : nodeLineStart) {
if (line.contains(s)) {
return true;
}
}
return false;
}
private boolean isEdgeFirstLine(String line) {
for (String s : edgeLineStart) {
if (line.contains(s)) {
return true;
}
}
return false;
}
private void setNodeData(NodeDraft node, GDFColumn column, String data) throws Exception {
if (column.getNodeColumn() != null) {
try {
switch (column.getNodeColumn()) {
case X:
node.setX(Float.parseFloat(data));
break;
case Y:
node.setY(Float.parseFloat(data));
break;
case COLOR:
String[] rgb = data.split(",");
if (rgb.length == 3) {
node.setColor(rgb[0], rgb[1], rgb[2]);
}
break;
case FIXED:
node.setFixed(Boolean.parseBoolean(data));
break;
case HEIGHT:
break;
case WIDTH:
node.setSize(Float.parseFloat(data));
break;
case LABEL:
node.setLabel(data);
break;
case LABELVISIBLE:
node.setLabelVisible(Boolean.parseBoolean(data));
break;
case VISIBLE:
node.setVisible(Boolean.parseBoolean(data));
break;
}
} catch (Exception e) {
String message = NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat3", column.getNodeColumn(), node, data);
report.logIssue(new Issue(message, Issue.Level.WARNING, e));
}
} else if (column.getAttributeColumn() != null) {
try {
node.addAttributeValue(column.getAttributeColumn(), data);
} catch (Exception e) {
String message = NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat4", column.getAttributeColumn().getType(), column.getAttributeColumn().getTitle(), node);
report.logIssue(new Issue(message, Issue.Level.WARNING, e));
}
}
}
private void setEdgeData(EdgeDraft edge, GDFColumn column, String data) throws Exception {
if (column.getEdgeColumn() != null) {
try {
switch (column.getEdgeColumn()) {
case COLOR:
String[] rgb = data.split(",");
if (rgb.length == 3) {
edge.setColor(rgb[0], rgb[1], rgb[2]);
}
break;
case VISIBLE:
edge.setVisible(Boolean.parseBoolean(data));
break;
case WEIGHT:
edge.setWeight(Float.parseFloat(data));
break;
case DIRECTED:
if (Boolean.parseBoolean(data)) {
edge.setType(EdgeDraft.EdgeType.DIRECTED);
} else {
edge.setType(EdgeDraft.EdgeType.UNDIRECTED);
}
break;
case LABEL:
edge.setLabel(data);
break;
case LABELVISIBLE:
edge.setLabelVisible(Boolean.parseBoolean(data));
break;
}
} catch (Exception e) {
String message = NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat3", column.getEdgeColumn(), data);
report.logIssue(new Issue(message, Issue.Level.WARNING, e));
}
} else if (column.getAttributeColumn() != null) {
try {
edge.addAttributeValue(column.getAttributeColumn(), data);
} catch (Exception e) {
String message = NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat4", column.getAttributeColumn().getType(), column.getAttributeColumn().getTitle(), edge);
report.logIssue(new Issue(message, Issue.Level.WARNING, e));
}
}
}
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;
}
private static class GDFColumn {
public enum NodeGuessColumn {
X, Y, VISIBLE, FIXED, STYLE, COLOR, WIDTH, HEIGHT, LABEL, LABELVISIBLE
};
public enum EdgeGuessColumn {
VISIBLE, COLOR, WEIGHT, DIRECTED, LABEL, LABELVISIBLE
};
private AttributeColumn column;
private NodeGuessColumn nodeColumn;
private EdgeGuessColumn edgeColumn;
public GDFColumn(NodeGuessColumn column) {
this.nodeColumn = column;
}
public GDFColumn(EdgeGuessColumn column) {
this.edgeColumn = column;
}
public GDFColumn(AttributeColumn column) {
this.column = column;
}
public NodeGuessColumn getNodeColumn() {
return nodeColumn;
}
public EdgeGuessColumn getEdgeColumn() {
return edgeColumn;
}
public AttributeColumn getAttributeColumn() {
return column;
}
}
}