/* 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. 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Contributor(s): Portions Copyrighted 2011 Gephi Consortium. */ package org.gephi.io.importer.plugin.file; import java.io.Reader; import java.util.HashMap; import javax.xml.stream.Location; import javax.xml.stream.XMLInputFactory; import javax.xml.stream.XMLReporter; import javax.xml.stream.XMLStreamException; import javax.xml.stream.XMLStreamReader; import javax.xml.stream.events.XMLEvent; import org.gephi.data.attributes.api.AttributeColumn; import org.gephi.data.attributes.api.AttributeOrigin; import org.gephi.data.attributes.api.AttributeType; import org.gephi.io.importer.api.ContainerLoader; import org.gephi.io.importer.api.EdgeDefault; import org.gephi.io.importer.api.EdgeDraft; import org.gephi.io.importer.api.Issue; import org.gephi.io.importer.api.NodeDraft; import org.gephi.io.importer.api.PropertiesAssociations; import org.gephi.io.importer.api.PropertiesAssociations.EdgeProperties; import org.gephi.io.importer.api.PropertiesAssociations.NodeProperties; 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 ImporterGraphML implements FileImporter, LongTask { //GEXF private static final String GRAPHML = "graphml"; private static final String GRAPH = "graph"; private static final String GRAPH_DEFAULT_EDGETYPE = "edgedefault"; private static final String GRAPH_ID = "id"; private static final String NODE = "node"; private static final String NODE_ID = "id"; private static final String EDGE = "edge"; private static final String EDGE_ID = "id"; private static final String EDGE_SOURCE = "source"; private static final String EDGE_TARGET = "target"; private static final String EDGE_DIRECTED = "directed"; private static final String ATTRIBUTE = "key"; private static final String ATTRIBUTE_ID = "id"; private static final String ATTRIBUTE_TITLE = "attr.name"; private static final String ATTRIBUTE_TYPE = "attr.type"; private static final String ATTRIBUTE_DEFAULT = "default"; private static final String ATTRIBUTE_FOR = "for"; private static final String ATTVALUE = "data"; private static final String ATTVALUE_FOR = "key"; //Architecture private Reader reader; private ContainerLoader container; private boolean cancel; private Report report; private ProgressTicket progress; private XMLStreamReader xmlReader; private PropertiesAssociations properties = new PropertiesAssociations(); private HashMap<String, NodeProperties> nodePropertiesAttributes = new HashMap<String, NodeProperties>(); private HashMap<String, EdgeProperties> edgePropertiesAttributes = new HashMap<String, EdgeProperties>(); public ImporterGraphML() { //Default node associations properties.addNodePropertyAssociation(NodeProperties.LABEL, "label"); properties.addNodePropertyAssociation(NodeProperties.LABEL, "d3"); // Default node label used by yEd from yworks.com. properties.addNodePropertyAssociation(NodeProperties.X, "x"); properties.addNodePropertyAssociation(NodeProperties.Y, "y"); properties.addNodePropertyAssociation(NodeProperties.X, "xpos"); properties.addNodePropertyAssociation(NodeProperties.Y, "ypos"); properties.addNodePropertyAssociation(NodeProperties.Z, "z"); properties.addNodePropertyAssociation(NodeProperties.SIZE, "size"); properties.addNodePropertyAssociation(NodeProperties.R, "r"); properties.addNodePropertyAssociation(NodeProperties.G, "g"); properties.addNodePropertyAssociation(NodeProperties.B, "b"); //Default edge associations properties.addEdgePropertyAssociation(EdgeProperties.LABEL, "label"); properties.addEdgePropertyAssociation(EdgeProperties.LABEL, "edgelabel"); properties.addEdgePropertyAssociation(EdgeProperties.LABEL, "d7"); // Default edge label used by yEd from yworks.com. properties.addEdgePropertyAssociation(EdgeProperties.WEIGHT, "weight"); properties.addEdgePropertyAssociation(EdgeProperties.WEIGHT, "Edge Weight"); properties.addEdgePropertyAssociation(EdgeProperties.ID, "id"); properties.addEdgePropertyAssociation(EdgeProperties.ID, "edgeid"); properties.addEdgePropertyAssociation(EdgeProperties.R, "r"); properties.addEdgePropertyAssociation(EdgeProperties.G, "g"); properties.addEdgePropertyAssociation(EdgeProperties.B, "b"); } public boolean execute(ContainerLoader container) { this.container = container; this.report = new Report(); Progress.start(progress); try { XMLInputFactory inputFactory = XMLInputFactory.newInstance(); if (inputFactory.isPropertySupported("javax.xml.stream.isValidating")) { inputFactory.setProperty("javax.xml.stream.isValidating", Boolean.FALSE); } inputFactory.setXMLReporter(new XMLReporter() { @Override public void report(String message, String errorType, Object relatedInformation, Location location) throws XMLStreamException { System.out.println("Error:" + errorType + ", message : " + message); } }); xmlReader = inputFactory.createXMLStreamReader(reader); while (xmlReader.hasNext()) { Integer eventType = xmlReader.next(); if (eventType.equals(XMLEvent.START_ELEMENT)) { String name = xmlReader.getLocalName(); if (GRAPHML.equalsIgnoreCase(name)) { } else if (GRAPH.equalsIgnoreCase(name)) { readGraph(xmlReader); } else if (NODE.equalsIgnoreCase(name)) { readNode(xmlReader, null); } else if (EDGE.equalsIgnoreCase(name)) { readEdge(xmlReader); } else if (ATTRIBUTE.equalsIgnoreCase(name)) { readAttribute(xmlReader); } } else if (eventType.equals(XMLStreamReader.END_ELEMENT)) { String name = xmlReader.getLocalName(); if (NODE.equalsIgnoreCase(name)) { } } } xmlReader.close(); } catch (Exception e) { if (e instanceof RuntimeException) { throw (RuntimeException) e; } throw new RuntimeException(e); } Progress.finish(progress); return !cancel; } private void readGraph(XMLStreamReader reader) throws Exception { String id = ""; String defaultEdgeType = ""; //Attributes for (int i = 0; i < reader.getAttributeCount(); i++) { String attName = reader.getAttributeName(i).getLocalPart(); if (GRAPH_DEFAULT_EDGETYPE.equalsIgnoreCase(attName)) { defaultEdgeType = reader.getAttributeValue(i); } else if (GRAPH_ID.equalsIgnoreCase(attName)) { id = reader.getAttributeValue(i); } } //Edge Type if (!defaultEdgeType.isEmpty()) { if (defaultEdgeType.equalsIgnoreCase("undirected")) { container.setEdgeDefault(EdgeDefault.UNDIRECTED); } else if (defaultEdgeType.equalsIgnoreCase("directed")) { container.setEdgeDefault(EdgeDefault.DIRECTED); } else { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_defaultedgetype", defaultEdgeType), Issue.Level.SEVERE)); } } } private void readNode(XMLStreamReader reader, NodeDraft parent) throws Exception { String id = ""; //Attributes for (int i = 0; i < reader.getAttributeCount(); i++) { String attName = reader.getAttributeName(i).getLocalPart(); if (NODE_ID.equalsIgnoreCase(attName)) { id = reader.getAttributeValue(i); } } if (id.isEmpty()) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_nodeid"), Issue.Level.SEVERE)); return; } NodeDraft node = null; if (container.nodeExists(id)) { node = container.getNode(id); } else { node = container.factory().newNodeDraft(); } node.setId(id); //Parent if (parent != null) { node.setParent(parent); } if (!container.nodeExists(id)) { container.addNode(node); } boolean end = false; while (reader.hasNext() && !end) { int type = reader.next(); switch (type) { case XMLStreamReader.START_ELEMENT: String name = xmlReader.getLocalName(); if (ATTVALUE.equalsIgnoreCase(xmlReader.getLocalName())) { readNodeAttValue(reader, node); } else if (NODE.equalsIgnoreCase(name)) { readNode(reader, node); } break; case XMLStreamReader.END_ELEMENT: if (NODE.equalsIgnoreCase(xmlReader.getLocalName())) { end = true; } break; } } } private void readNodeAttValue(XMLStreamReader reader, NodeDraft node) throws Exception { String fore = ""; String value = ""; for (int i = 0; i < reader.getAttributeCount(); i++) { String attName = reader.getAttributeName(i).getLocalPart(); if (ATTVALUE_FOR.equalsIgnoreCase(attName)) { fore = reader.getAttributeValue(i); } } if (fore.isEmpty()) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_datakey", node), Issue.Level.SEVERE)); return; } boolean end = false; while (reader.hasNext() && !end) { int xmltype = reader.next(); switch (xmltype) { case XMLStreamReader.CHARACTERS: if (!xmlReader.isWhiteSpace()) { value += xmlReader.getText(); } break; case XMLStreamReader.END_ELEMENT: if (ATTVALUE.equalsIgnoreCase(xmlReader.getLocalName())) { end = true; } break; } } if (!value.isEmpty()) { //Property NodeProperties prop = nodePropertiesAttributes.get(fore); if (prop != null) { try { switch (prop) { case X: node.setX(parseFloat(value)); break; case Y: node.setY(parseFloat(value)); break; case Z: node.setZ(parseFloat(value)); break; case SIZE: node.setSize(parseFloat(value)); break; case LABEL: node.setLabel(value); break; case R: if (node.getColor() == null) { node.setColor(Integer.parseInt(value), 0, 0); } else { node.setColor(Integer.parseInt(value), node.getColor().getGreen(), node.getColor().getBlue()); } break; case G: if (node.getColor() == null) { node.setColor(0, Integer.parseInt(value), 0); } else { node.setColor(node.getColor().getRed(), Integer.parseInt(value), node.getColor().getBlue()); } break; case B: if (node.getColor() == null) { node.setColor(0, 0, Integer.parseInt(value)); } else { node.setColor(node.getColor().getRed(), node.getColor().getGreen(), Integer.parseInt(value)); } break; } } catch (Exception e) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_datavalue", fore, node, prop.toString()), Issue.Level.SEVERE)); } return; } //Data attribute value AttributeColumn column = container.getAttributeModel().getNodeTable().getColumn(fore); if (column != null) { try { Object val = column.getType().parse(value); node.addAttributeValue(column, val); } catch (Exception e) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_datavalue", fore, node, column.getTitle()), Issue.Level.SEVERE)); } } } } private void readEdge(XMLStreamReader reader) throws Exception { String id = ""; String source = ""; String target = ""; String directed = ""; //Attributes for (int i = 0; i < reader.getAttributeCount(); i++) { String attName = reader.getAttributeName(i).getLocalPart(); if (EDGE_SOURCE.equalsIgnoreCase(attName)) { source = reader.getAttributeValue(i); } else if (EDGE_TARGET.equalsIgnoreCase(attName)) { target = reader.getAttributeValue(i); } else if (EDGE_ID.equalsIgnoreCase(attName)) { id = reader.getAttributeValue(i); } else if (EDGE_DIRECTED.equalsIgnoreCase(attName)) { directed = reader.getAttributeValue(i); } } EdgeDraft edge = container.factory().newEdgeDraft(); NodeDraft nodeSource = container.getNode(source); NodeDraft nodeTarget = container.getNode(target); edge.setSource(nodeSource); edge.setTarget(nodeTarget); //Type if (!directed.isEmpty()) { if (directed.equalsIgnoreCase("true")) { edge.setType(EdgeDraft.EdgeType.DIRECTED); } else if (directed.equalsIgnoreCase("false")) { edge.setType(EdgeDraft.EdgeType.UNDIRECTED); } else { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_edgetype", directed, edge), Issue.Level.SEVERE)); } } //Id if (!id.isEmpty()) { edge.setId(id); } boolean end = false; while (reader.hasNext() && !end) { int type = reader.next(); switch (type) { case XMLStreamReader.START_ELEMENT: if (ATTVALUE.equalsIgnoreCase(xmlReader.getLocalName())) { readEdgeAttValue(reader, edge); } break; case XMLStreamReader.END_ELEMENT: if (EDGE.equalsIgnoreCase(xmlReader.getLocalName())) { end = true; } break; } } container.addEdge(edge); } private void readEdgeAttValue(XMLStreamReader reader, EdgeDraft edge) throws Exception { String fore = ""; String value = ""; for (int i = 0; i < reader.getAttributeCount(); i++) { String attName = reader.getAttributeName(i).getLocalPart(); if (ATTVALUE_FOR.equalsIgnoreCase(attName)) { fore = reader.getAttributeValue(i); } } if (fore.isEmpty()) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_datakey", edge), Issue.Level.SEVERE)); return; } boolean end = false; while (reader.hasNext() && !end) { int xmltype = reader.next(); switch (xmltype) { case XMLStreamReader.CHARACTERS: if (!xmlReader.isWhiteSpace()) { value += xmlReader.getText(); } break; case XMLStreamReader.END_ELEMENT: if (ATTVALUE.equalsIgnoreCase(xmlReader.getLocalName())) { end = true; } break; } } if (!value.isEmpty()) { EdgeProperties prop = edgePropertiesAttributes.get(fore); if (prop != null) { try { switch (prop) { case WEIGHT: edge.setWeight(parseFloat(value)); break; case LABEL: edge.setLabel(value); break; case ID: edge.setId(value); break; case R: if (edge.getColor() == null) { edge.setColor(Integer.parseInt(value), 0, 0); } else { edge.setColor(Integer.parseInt(value), edge.getColor().getGreen(), edge.getColor().getBlue()); } break; case G: if (edge.getColor() == null) { edge.setColor(0, Integer.parseInt(value), 0); } else { edge.setColor(edge.getColor().getRed(), Integer.parseInt(value), edge.getColor().getBlue()); } break; case B: if (edge.getColor() == null) { edge.setColor(0, 0, Integer.parseInt(value)); } else { edge.setColor(edge.getColor().getRed(), edge.getColor().getGreen(), Integer.parseInt(value)); } break; } } catch (Exception e) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_datavalue", fore, edge, prop.toString()), Issue.Level.SEVERE)); } return; } //Data attribute value AttributeColumn column = container.getAttributeModel().getEdgeTable().getColumn(fore); if (column != null) { try { Object val = column.getType().parse(value); edge.addAttributeValue(column, val); } catch (Exception e) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_datavalue", fore, edge, column.getTitle()), Issue.Level.SEVERE)); } } } } private void readAttribute(XMLStreamReader reader) throws Exception { String id = ""; String type = ""; String title = ""; String defaultStr = ""; String forStr = ""; for (int i = 0; i < reader.getAttributeCount(); i++) { String attName = reader.getAttributeName(i).getLocalPart(); if (ATTRIBUTE_ID.equalsIgnoreCase(attName)) { id = reader.getAttributeValue(i); } else if (ATTRIBUTE_TYPE.equalsIgnoreCase(attName)) { type = reader.getAttributeValue(i); } else if (ATTRIBUTE_TITLE.equalsIgnoreCase(attName)) { title = reader.getAttributeValue(i); } else if (ATTRIBUTE_FOR.equalsIgnoreCase(attName)) { forStr = reader.getAttributeValue(i); } } if (title.isEmpty()) { title = id; } boolean property = false; if (!id.isEmpty()) { //Properties if (forStr.equalsIgnoreCase("node")) { NodeProperties prop = properties.getNodeProperty(id) == null ? properties.getNodeProperty(title) : properties.getNodeProperty(id); if (prop != null) { nodePropertiesAttributes.put(id, prop); report.log(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_log_nodeproperty", title)); property = true; } } else if (forStr.equalsIgnoreCase("edge")) { EdgeProperties prop = properties.getEdgeProperty(id) == null ? properties.getEdgeProperty(title) : properties.getEdgeProperty(id); if (prop != null) { edgePropertiesAttributes.put(id, prop); report.log(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_log_edgeproperty", title)); property = true; } } if (property) { return; } } else { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_attributeempty", title), Issue.Level.SEVERE)); return; } if (!property && type.isEmpty()) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_attributetype1", title), Issue.Level.SEVERE)); type = "string"; } if (!property) { //Class type if (forStr.isEmpty() || !(forStr.equalsIgnoreCase("node") || forStr.equalsIgnoreCase("edge") || forStr.equalsIgnoreCase("all"))) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_attributeclass", title), Issue.Level.SEVERE)); return; } //Default? boolean end = false; boolean defaultFlag = false; while (reader.hasNext() && !end) { int xmltype = reader.next(); switch (xmltype) { case XMLStreamReader.START_ELEMENT: if (ATTRIBUTE_DEFAULT.equalsIgnoreCase(xmlReader.getLocalName())) { defaultFlag = true; } break; case XMLStreamReader.CHARACTERS: if (defaultFlag && !xmlReader.isWhiteSpace()) { defaultStr = xmlReader.getText(); } break; case XMLStreamReader.END_ELEMENT: if (ATTRIBUTE.equalsIgnoreCase(xmlReader.getLocalName())) { end = true; } break; } } //Type AttributeType attributeType = AttributeType.STRING; if (type.equalsIgnoreCase("boolean") || type.equalsIgnoreCase("bool")) { attributeType = AttributeType.BOOLEAN; } else if (type.equalsIgnoreCase("integer") || type.equalsIgnoreCase("int")) { attributeType = AttributeType.INT; } else if (type.equalsIgnoreCase("long")) { attributeType = AttributeType.LONG; } else if (type.equalsIgnoreCase("float")) { attributeType = AttributeType.FLOAT; } else if (type.equalsIgnoreCase("double")) { attributeType = AttributeType.DOUBLE; } else if (type.equalsIgnoreCase("string")) { attributeType = AttributeType.STRING; } else if (type.equalsIgnoreCase("bigdecimal")) { attributeType = AttributeType.BIGDECIMAL; } else if (type.equalsIgnoreCase("biginteger")) { attributeType = AttributeType.BIGINTEGER; } else if (type.equalsIgnoreCase("byte")) { attributeType = AttributeType.BYTE; } else if (type.equalsIgnoreCase("char")) { attributeType = AttributeType.CHAR; } else if (type.equalsIgnoreCase("short")) { attributeType = AttributeType.SHORT; } else if (type.equalsIgnoreCase("listboolean")) { attributeType = AttributeType.LIST_BOOLEAN; } else if (type.equalsIgnoreCase("listint")) { attributeType = AttributeType.LIST_INTEGER; } else if (type.equalsIgnoreCase("listlong")) { attributeType = AttributeType.LIST_LONG; } else if (type.equalsIgnoreCase("listfloat")) { attributeType = AttributeType.LIST_FLOAT; } else if (type.equalsIgnoreCase("listdouble")) { attributeType = AttributeType.LIST_DOUBLE; } else if (type.equalsIgnoreCase("liststring")) { attributeType = AttributeType.LIST_STRING; } else if (type.equalsIgnoreCase("listbigdecimal")) { attributeType = AttributeType.LIST_BIGDECIMAL; } else if (type.equalsIgnoreCase("listbiginteger")) { attributeType = AttributeType.LIST_BIGINTEGER; } else if (type.equalsIgnoreCase("listbyte")) { attributeType = AttributeType.LIST_BYTE; } else if (type.equalsIgnoreCase("listchar")) { attributeType = AttributeType.LIST_CHARACTER; } else if (type.equalsIgnoreCase("listshort")) { attributeType = AttributeType.LIST_SHORT; } else { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_attributetype2", type), Issue.Level.SEVERE)); return; } //Default Object Object defaultValue = null; if (!defaultStr.isEmpty()) { try { defaultValue = attributeType.parse(defaultStr); report.log(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_log_default", defaultStr, title)); } catch (Exception e) { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_attributedefault", title, attributeType.getTypeString()), Issue.Level.SEVERE)); } } //Add to model if ("node".equalsIgnoreCase(forStr) || "all".equalsIgnoreCase(forStr)) { if (container.getAttributeModel().getNodeTable().hasColumn(id) || container.getAttributeModel().getNodeTable().hasColumn(title)) { report.log(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_attributecolumn_exist", id)); return; } container.getAttributeModel().getNodeTable().addColumn(id, title, attributeType, AttributeOrigin.DATA, defaultValue); report.log(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_log_nodeattribute", title, attributeType.getTypeString())); } else if ("edge".equalsIgnoreCase(forStr) || "all".equalsIgnoreCase(forStr)) { if (container.getAttributeModel().getEdgeTable().hasColumn(id) || container.getAttributeModel().getEdgeTable().hasColumn(title)) { report.log(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_attributecolumn_exist", id)); return; } container.getAttributeModel().getEdgeTable().addColumn(id, title, attributeType, AttributeOrigin.DATA, defaultValue); report.log(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_log_edgeattribute", title, attributeType.getTypeString())); } } else { report.logIssue(new Issue(NbBundle.getMessage(ImporterGraphML.class, "importerGraphML_error_attributeempty", title), Issue.Level.SEVERE)); } } private float parseFloat(String str) { str = str.replace(',', '.'); return Float.parseFloat(str); } 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.progress = progressTicket; } }