org.jgrapht.nio.csv.CSVEventDrivenImporter Maven / Gradle / Ivy
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/*
* (C) Copyright 2016-2023, by Dimitrios Michail and Contributors.
*
* JGraphT : a free Java graph-theory library
*
* See the CONTRIBUTORS.md file distributed with this work for additional
* information regarding copyright ownership.
*
* This program and the accompanying materials are made available under the
* terms of the Eclipse Public License 2.0 which is available at
* http://www.eclipse.org/legal/epl-2.0, or the
* GNU Lesser General Public License v2.1 or later
* which is available at
* http://www.gnu.org/licenses/old-licenses/lgpl-2.1-standalone.html.
*
* SPDX-License-Identifier: EPL-2.0 OR LGPL-2.1-or-later
*/
package org.jgrapht.nio.csv;
import org.antlr.v4.runtime.*;
import org.antlr.v4.runtime.misc.*;
import org.antlr.v4.runtime.tree.*;
import org.jgrapht.alg.util.Triple;
import org.jgrapht.nio.*;
import java.io.*;
import java.util.*;
/**
* Imports a graph from a CSV Format or any other Delimiter-separated value format.
*
*
* The importer supports various different formats which can be adjusted using the
* {@link #setFormat(CSVFormat) setFormat} method. The supported formats are the same CSV formats
* used by Gephi. For some
* of the formats, the behavior of the importer can be adjusted using the
* {@link #setParameter(org.jgrapht.nio.csv.CSVFormat.Parameter, boolean) setParameter} method. See
* {@link CSVFormat} for a description of the formats.
*
*
*
* The importer respects rfc4180. The caller can
* also adjust the separator to something like semicolon or pipe instead of comma. In such a case,
* all fields are unescaped using the new separator. See
* Delimiter-separated values
* for more information.
*
*
*
* This importer does not distinguish between {@link CSVFormat#EDGE_LIST} and
* {@link CSVFormat#ADJACENCY_LIST}. In both cases it assumes the format is
* {@link CSVFormat#ADJACENCY_LIST}.
*
*
* @see CSVFormat
*
* @author Dimitrios Michail
*/
public class CSVEventDrivenImporter
extends BaseEventDrivenImporter>
implements EventDrivenImporter>
{
private static final char DEFAULT_DELIMITER = ',';
private CSVFormat format;
private char delimiter;
private final Set parameters;
/**
* Constructs a new importer using the {@link CSVFormat#ADJACENCY_LIST} format as default.
*/
public CSVEventDrivenImporter()
{
this(CSVFormat.ADJACENCY_LIST, DEFAULT_DELIMITER);
}
/**
* Constructs a new importer.
*
* @param format format to use out of the supported ones
*/
public CSVEventDrivenImporter(CSVFormat format)
{
this(format, DEFAULT_DELIMITER);
}
/**
* Constructs a new importer.
*
* @param format format to use out of the supported ones
* @param delimiter delimiter to use (comma, semicolon, pipe, etc.)
*/
public CSVEventDrivenImporter(CSVFormat format, char delimiter)
{
this.format = format;
if (!DSVUtils.isValidDelimiter(delimiter)) {
throw new IllegalArgumentException("Character cannot be used as a delimiter");
}
this.delimiter = delimiter;
this.parameters = new HashSet<>();
}
/**
* Get the format that the importer is using.
*
* @return the input format
*/
public CSVFormat getFormat()
{
return format;
}
/**
* Set the format of the importer
*
* @param format the format to use
*/
public void setFormat(CSVFormat format)
{
this.format = format;
}
/**
* Get the delimiter (comma, semicolon, pipe, etc).
*
* @return the delimiter
*/
public char getDelimiter()
{
return delimiter;
}
/**
* Set the delimiter (comma, semicolon, pipe, etc).
*
* @param delimiter the delimiter to use
*/
public void setDelimiter(char delimiter)
{
if (!DSVUtils.isValidDelimiter(delimiter)) {
throw new IllegalArgumentException("Character cannot be used as a delimiter");
}
this.delimiter = delimiter;
}
/**
* Return if a particular parameter of the exporter is enabled
*
* @param p the parameter
* @return {@code true} if the parameter is set, {@code false} otherwise
*/
public boolean isParameter(CSVFormat.Parameter p)
{
return parameters.contains(p);
}
/**
* Set the value of a parameter of the exporter
*
* @param p the parameter
* @param value the value to set
*/
public void setParameter(CSVFormat.Parameter p, boolean value)
{
if (value) {
parameters.add(p);
} else {
parameters.remove(p);
}
}
@Override
public void importInput(Reader input)
throws ImportException
{
notifyImportEvent(ImportEvent.START);
switch (format) {
case EDGE_LIST:
case ADJACENCY_LIST:
read(input, new AdjacencyListCSVListener());
break;
case MATRIX:
read(input, new MatrixCSVListener());
break;
}
notifyImportEvent(ImportEvent.END);
}
private void read(Reader input, CSVBaseListener listener)
throws ImportException
{
try {
ThrowingErrorListener errorListener = new ThrowingErrorListener();
// create lexer
CSVLexer lexer = new CSVLexer(CharStreams.fromReader(input));
lexer.setSep(delimiter);
lexer.removeErrorListeners();
lexer.addErrorListener(errorListener);
// create parser
CSVParser parser = new CSVParser(new CommonTokenStream(lexer));
parser.removeErrorListeners();
parser.addErrorListener(errorListener);
// Specify our entry point
CSVParser.FileContext graphContext = parser.file();
// Walk it and attach our listener
ParseTreeWalker walker = new ParseTreeWalker();
walker.walk(listener, graphContext);
} catch (IOException | ParseCancellationException | IllegalArgumentException e) {
throw new ImportException("Failed to import CSV graph: " + e.getMessage(), e);
}
}
private class ThrowingErrorListener
extends BaseErrorListener
{
@Override
public void syntaxError(
Recognizer recognizer, Object offendingSymbol, int line, int charPositionInLine,
String msg, RecognitionException e)
throws ParseCancellationException
{
throw new ParseCancellationException(
"line " + line + ":" + charPositionInLine + " " + msg);
}
}
// listener for the edge list format
private class AdjacencyListCSVListener
extends RowCSVListener
{
private boolean assumeEdgeWeights;
public AdjacencyListCSVListener()
{
super();
this.assumeEdgeWeights = parameters.contains(CSVFormat.Parameter.EDGE_WEIGHTS);
}
@Override
protected void handleRow()
{
// first is source
String source = row.get(0);
if (source.isEmpty()) {
throw new ParseCancellationException("Source vertex cannot be empty");
}
if (!vertices.contains(source)) {
vertices.add(source);
notifyVertex(source);
}
row.remove(0);
// remaining are targets (if weighted pairs of target-weight)
int step = assumeEdgeWeights ? 2 : 1;
for (int i = 0; i < row.size(); i += step) {
String target = row.get(i);
if (target.isEmpty()) {
throw new ParseCancellationException("Target vertex cannot be empty");
}
if (!vertices.contains(target)) {
vertices.add(target);
notifyVertex(target);
}
Double weight = null;
if (assumeEdgeWeights) {
try {
weight = Double.parseDouble(row.get(i + 1));
} catch (NumberFormatException nfe) {
throw new ParseCancellationException("Failed to parse edge weight");
}
}
notifyEdge(Triple.of(source, target, weight));
}
}
}
// listener for the edge list format
private class MatrixCSVListener
extends RowCSVListener
{
private boolean assumeNodeIds;
private boolean assumeEdgeWeights;
private boolean assumeZeroWhenNoEdge;
private int verticesCount;
private int currentVertex;
private String currentVertexName;
private Map columnIndex;
public MatrixCSVListener()
{
super();
this.assumeNodeIds = parameters.contains(CSVFormat.Parameter.MATRIX_FORMAT_NODEID);
this.assumeEdgeWeights = parameters.contains(CSVFormat.Parameter.EDGE_WEIGHTS);
;
this.assumeZeroWhenNoEdge =
parameters.contains(CSVFormat.Parameter.MATRIX_FORMAT_ZERO_WHEN_NO_EDGE);
this.verticesCount = 0;
this.currentVertex = 1;
this.currentVertexName = null;
this.columnIndex = new HashMap<>();
}
@Override
protected void handleRow()
{
if (assumeNodeIds) {
if (!header) {
currentVertexName = row.get(0);
}
row.remove(0);
} else {
currentVertexName = String.valueOf(currentVertex);
}
if (header) {
if (assumeNodeIds) {
createVerticesFromNodeIds();
} else {
createVertices();
createEdges();
currentVertex++;
}
} else {
createEdges();
currentVertex++;
}
}
private void createVerticesFromNodeIds()
{
// header line contains nodes
verticesCount = row.size();
if (verticesCount < 1) {
throw new ParseCancellationException("Failed to parse header with vertices");
}
int v = 1;
for (String vertexName : row) {
if (vertexName.trim().isEmpty()) {
throw new ParseCancellationException(
"Failed to parse header with vertices (empty name)");
}
if (!vertices.contains(vertexName)) {
vertices.add(vertexName);
notifyVertex(vertexName);
}
columnIndex.put(v, vertexName);
v++;
}
}
private void createVertices()
{
// header line contains nodes
verticesCount = row.size();
if (verticesCount < 1) {
throw new ParseCancellationException("Failed to parse header with vertices");
}
int v = 1;
for (v = 1; v <= verticesCount; v++) {
String vertexName = String.valueOf(v);
if (!vertices.contains(vertexName)) {
vertices.add(vertexName);
notifyVertex(vertexName);
}
columnIndex.put(v, vertexName);
}
}
private void createEdges()
{
if (row.size() != verticesCount) {
throw new ParseCancellationException(
"Row contains fewer than " + verticesCount + " entries");
}
int target = 1;
for (String entry : row) {
// try to parse an integer
try {
Integer entryAsInteger = Integer.parseInt(entry);
if (entryAsInteger == 0) {
if (!assumeZeroWhenNoEdge && assumeEdgeWeights) {
notifyEdge(Triple.of(currentVertexName, columnIndex.get(target), 0d));
}
} else {
if (assumeEdgeWeights) {
notifyEdge(Triple.of(
currentVertexName, columnIndex.get(target),
Double.valueOf(entryAsInteger)));
} else {
notifyEdge(Triple.of(currentVertexName, columnIndex.get(target), null));
}
}
target++;
continue;
} catch (NumberFormatException nfe) {
// nothing
}
// try to parse a double
try {
Double entryAsDouble = Double.parseDouble(entry);
if (assumeEdgeWeights) {
notifyEdge(
Triple.of(currentVertexName, columnIndex.get(target), entryAsDouble));
} else {
throw new ParseCancellationException(
"Double entry found when expecting no weights");
}
} catch (NumberFormatException nfe) {
// nothing
}
target++;
}
}
}
// base listener
private abstract class RowCSVListener
extends CSVBaseListener
{
protected List row;
protected Set vertices;
protected boolean header;
public RowCSVListener()
{
this.row = new ArrayList<>();
this.vertices = new HashSet<>();
this.header = false;
}
@Override
public void enterHeader(CSVParser.HeaderContext ctx)
{
header = true;
}
@Override
public void exitHeader(CSVParser.HeaderContext ctx)
{
header = false;
}
@Override
public void enterRecord(CSVParser.RecordContext ctx)
{
row.clear();
}
@Override
public void exitRecord(CSVParser.RecordContext ctx)
{
if (row.isEmpty()) {
throw new ParseCancellationException("Empty CSV record");
}
handleRow();
}
@Override
public void exitTextField(CSVParser.TextFieldContext ctx)
{
row.add(ctx.TEXT().getText());
}
@Override
public void exitStringField(CSVParser.StringFieldContext ctx)
{
row.add(DSVUtils.unescapeDSV(ctx.STRING().getText(), delimiter));
}
@Override
public void exitEmptyField(CSVParser.EmptyFieldContext ctx)
{
row.add("");
}
protected abstract void handleRow();
}
}
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