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Graph I/O library which can be used to load and store graphs
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/*
* Copyright or © or Copr. Ecole des Mines d'Alès (2012-2014)
*
* This software is a computer program whose purpose is to provide
* several functionalities for the processing of semantic data
* sources such as ontologies or text corpora.
*
* This software is governed by the CeCILL license under French law and
* abiding by the rules of distribution of free software. You can use,
* modify and/ or redistribute the software under the terms of the CeCILL
* license as circulated by CEA, CNRS and INRIA at the following URL
* "http://www.cecill.info".
*
* As a counterpart to the access to the source code and rights to copy,
* modify and redistribute granted by the license, users are provided only
* with a limited warranty and the software's author, the holder of the
* economic rights, and the successive licensors have only limited
* liability.
* In this respect, the user's attention is drawn to the risks associated
* with loading, using, modifying and/or developing or reproducing the
* software by the user in light of its specific status of free software,
* that may mean that it is complicated to manipulate, and that also
* therefore means that it is reserved for developers and experienced
* professionals having in-depth computer knowledge. Users are therefore
* encouraged to load and test the software's suitability as regards their
* requirements in conditions enabling the security of their systems and/or
* data to be ensured and, more generally, to use and operate it in the
* same conditions as regards security.
*
* The fact that you are presently reading this means that you have had
* knowledge of the CeCILL license and that you accept its terms.
*/
package slib.graph.io.loader.annot;
import au.com.bytecode.opencsv.CSVReader;
import java.io.FileReader;
import java.util.regex.Pattern;
import org.openrdf.model.URI;
import org.openrdf.model.vocabulary.RDF;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import slib.graph.io.conf.GDataConf;
import slib.graph.io.loader.GraphLoader;
import slib.graph.model.graph.G;
import slib.graph.model.graph.elements.E;
import slib.graph.model.impl.repo.URIFactoryMemory;
import slib.graph.model.impl.graph.elements.Edge;
import slib.utils.ex.SLIB_Ex_Critic;
import slib.utils.ex.SLIB_Exception;
import slib.utils.impl.Util;
/**
* Class used to load annotation file:
* XXXX1[TAB]c1;c2;c3
* XXXX2[TAB]c2;c3
* ...
*
*
* To each line is associated an entry defining a key and a set of annotations
* separated by ';'. As an example the first line XXXX1[TAB]c1;c2;c3 will lead
* to the creation of three statements: XXXXX1 RDF.TYPE c1
* XXXXX1 RDF.TYPE c2
* XXXXX1 RDF.TYPE c3
* By default the semantic relationship is RDF.TYPE. Prefixes can also be
* defined for the subjects and the objects of the statements created.
*
* @author Sébastien Harispe
*/
public class GraphLoader_TSVannot implements GraphLoader {
public final static String PARAM_HEADER = "header";
public final static String PARAM_PREFIX_SUBJECT = "prefixSubject";
public final static String PARAM_PREFIX_OBJECT = "prefixObject";
public final static String PARAM_PREDICATE = "predicate";
boolean skipHeader = false;
URIFactoryMemory uriRepo = URIFactoryMemory.getSingleton();
Character pattern = '\t'; // the one used
G g;
Logger logger = LoggerFactory.getLogger(this.getClass());
URI predicate = RDF.TYPE;
String prefixSubject = null;
String prefixObject = null;
Pattern colon = Pattern.compile(":");
@Override
public void populate(GDataConf conf, G g) throws SLIB_Exception {
logger.info("-------------------------------------");
logger.info("Loading Annotations using TSV loader.");
logger.info("-------------------------------------");
this.g = g;
loadConf(conf);
loadTSV(conf.getLoc());
logger.info("TSV specification loaded.");
logger.info("-------------------------------------");
}
private void loadConf(GDataConf conf) throws SLIB_Ex_Critic {
String header = (String) conf.getParameter(PARAM_HEADER);
String prefixSubjectParam = (String) conf.getParameter(PARAM_PREFIX_SUBJECT);
String prefixObjectParam = (String) conf.getParameter(PARAM_PREFIX_OBJECT);
String predicateParam = (String) conf.getParameter(PARAM_PREDICATE);
if (header == null || Util.stringToBoolean(header) == true) {
skipHeader = true;
}
if (predicateParam != null) {
try {
predicate = uriRepo.getURI(predicateParam);
} catch (IllegalArgumentException e) {
throw new SLIB_Ex_Critic("Error in data loader, parameter " + PARAM_PREDICATE + ", cannot create an URI from " + predicateParam + "\n" + e.getMessage());
}
}
if (prefixSubjectParam != null) {
prefixSubject = prefixSubjectParam;
}
if (prefixObjectParam != null) {
prefixObject = prefixObjectParam;
}
logger.info("file " + conf.getLoc());
logger.info("Skipping header " + skipHeader);
logger.info("predicate '" + predicate + "'");
if (prefixSubject != null) {
logger.info("prefix subject '" + prefixSubject + "'");
}
if (prefixObject != null) {
logger.info("prefix object '" + prefixObject + "'");
}
}
public void loadTSV(String fileLoc) throws SLIB_Ex_Critic {
try {
CSVReader csvReader = new CSVReader(new FileReader(fileLoc), '\t');
String[] row;
String subjectLocalName;
String[] data;
URI s, o;
int skipped = 0;
int statementsLoaded = 0;
int processed = 0;
while ((row = csvReader.readNext()) != null) {
if (skipHeader) {
skipHeader = false;
} else if (row.length == 2) {
subjectLocalName = row[0];
data = row[1].split(";");
if (prefixSubject == null) {
s = uriRepo.getURI(subjectLocalName);
} else {
s = uriRepo.getURI(prefixSubject + subjectLocalName);
}
for (String os : data) {
if (prefixObject == null) {
o = uriRepo.getURI(buildURIString(os));
} else {
o = uriRepo.getURI(prefixObject + os);
}
E edge = new Edge(s, predicate, o);
g.addE(edge);
statementsLoaded++;
}
processed++;
} else {
skipped++;
}
}
csvReader.close();
logger.info("Number of lines skipped " + skipped);
logger.info("Number of lines processed " + processed);
logger.info("Number of statements loaded " + statementsLoaded);
} catch (Exception e) {
throw new SLIB_Ex_Critic("Error processing file " + fileLoc + "\n" + e.getMessage());
}
}
private String buildURIString(String value) throws SLIB_Ex_Critic {
String info[] = getDataColonSplit(value);
if (info != null && info.length == 2) {
String ns = uriRepo.getNamespace(info[0]);
if (ns == null) {
throw new SLIB_Ex_Critic("No namespace associated to prefix " + info[0] + ". Cannot load " + value + ", please load required namespace prefix");
}
return ns + info[1];
} else {
return value;
}
}
private String[] getDataColonSplit(String value) {
String data[] = colon.split(value);
data[0] = data[0].trim();
if (data.length > 1) {
data[1] = data[1].trim();
}
return data;
}
}
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