org.intermine.bio.dataconversion.DataSourceUpdater Maven / Gradle / Ivy
package org.intermine.bio.dataconversion;
/*
* Copyright (C) 2002-2021 FlyMine
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. See the LICENSE file for more
* information or http://www.gnu.org/copyleft/lesser.html.
*
*/
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Reader;
import java.io.Writer;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
import org.apache.tools.ant.BuildException;
import org.apache.tools.ant.Task;
import org.intermine.objectstore.ObjectStore;
import org.intermine.objectstore.ObjectStoreFactory;
import org.intermine.objectstore.query.Query;
import org.intermine.objectstore.query.QueryClass;
import org.intermine.xml.full.FullRenderer;
import org.intermine.xml.full.Item;
import org.intermine.xml.full.ItemFactory;
import org.intermine.model.bio.DataSource;
/**
* Class to fill in organism information using UniProt.
* @author Julie Sullivan
*/
public class DataSourceUpdater extends Task
{
protected static final Logger LOG = Logger.getLogger(DataSourceUpdater.class);
private String osAlias = null;
private String outputFile = null;
private String dataSourceFile = null;
private Set dataSourceNames = new HashSet();
/**
* Set the ObjectStore alias.
* @param osAlias The ObjectStore alias
*/
public void setOsAlias(String osAlias) {
this.osAlias = osAlias;
}
/**
* Set the output file name
* @param outputFile The output file name
*/
public void setOutputFile(String outputFile) {
this.outputFile = outputFile;
}
/**
* Set the file name for the data file from UniProt
* @param dataSourceFile the name of the data file to process (from uniprot)
*/
public void setDataSourceFile(String dataSourceFile) {
this.dataSourceFile = dataSourceFile;
}
/**
* For each data set in the objectstore, retreive it's details from UniProt data file
* @throws BuildException if an error occurs
*/
@Override
public void execute() {
// Needed so that STAX can find it's implementation classes
ClassLoader cl = Thread.currentThread().getContextClassLoader();
Thread.currentThread().setContextClassLoader(getClass().getClassLoader());
if (osAlias == null) {
throw new BuildException("osAlias attribute is not set");
}
if (outputFile == null) {
throw new BuildException("outputFile attribute is not set");
}
if (dataSourceFile == null) {
throw new BuildException("dataSourceFile attribute is not set");
}
LOG.info("Starting DataSourceUpdater");
Writer writer = null;
try {
writer = new FileWriter(outputFile);
ObjectStore os = ObjectStoreFactory.getObjectStore(osAlias);
// get the data sources already in the database
dataSourceNames = getDataSources(os);
// parse the uniprot data source file
Map allDataSources
= parseDataFile(new FileReader(dataSourceFile));
ItemFactory itemFactory = new ItemFactory(os.getModel(), "-1_");
writer.write(FullRenderer.getHeader() + "\n");
// write the relevant data sources to file
for (DataSourceHolder holder : allDataSources.values()) {
Item datasource = itemFactory.makeItemForClass("DataSource");
datasource.setAttribute("name", holder.name);
if (holder.descr != null) {
datasource.setAttribute("description", holder.descr);
}
if (holder.url != null) {
datasource.setAttribute("url", holder.url);
}
if (holder.pubMedId != null) {
Item publication = itemFactory.makeItemForClass("Publication");
publication.setAttribute("pubMedId", holder.pubMedId);
writer.write(FullRenderer.render(publication));
datasource.addToCollection("publications", publication);
}
writer.write(FullRenderer.render(datasource));
}
writer.write(FullRenderer.getFooter() + "\n");
} catch (Exception e) {
throw new BuildException("exception while retrieving data sets", e);
} finally {
Thread.currentThread().setContextClassLoader(cl);
if (writer != null) {
try {
writer.close();
} catch (Exception e) {
// ignore
}
}
}
}
// AC : DB-0026
// Abbrev: FlyBase
// Name : Drosophila genome database
// Ref : Nucleic Acids Res. 35:D486-D491(2007); PubMed=17099233; DOI=10.1093/nar/gkl827;
// LinkTp: Explicit
// Server: http://flybase.org/
// Db_URL: http://flybase.org/reports/%s.html
// Note : Obsolete abbreviation: DMAP
// Cat : Organism-specific database
private Map parseDataFile(Reader reader) throws IOException {
Map datasources = new HashMap();
BufferedReader br = new BufferedReader(reader);
String line = null;
DataSourceHolder datasource = null;
int labelLength = 8;
while ((line = br.readLine()) != null) {
if (line.length() < 8) {
continue;
}
String value = line.substring(labelLength).trim();
if (line.startsWith("Abbrev: ")) {
if (dataSourceNames.contains(value)) {
datasource = new DataSourceHolder(value);
datasources.put(value, datasource);
} else {
datasource = null;
}
} else if (datasource != null) {
if (line.startsWith("Name")) {
datasource.descr = value;
} else if (line.startsWith("Server: ")) {
datasource.url = value;
} else if (line.startsWith("Ref : ")) {
String pubMedId = parseRefString(value);
if (pubMedId != null) {
datasource.pubMedId = pubMedId;
}
}
}
}
return datasources;
}
private static String parseRefString(String refs) {
for (String ref : refs.split("\\;")) {
String[] refStrings = ref.split("=");
if (refStrings.length == 2) {
String name = refStrings[0].trim();
String id = refStrings[1].trim();
if ("PubMed".equals(name)) {
return id;
}
}
}
return null;
}
/**
* get all the data sources from the database
* @param os objectstore
* @return set of strings representing datasources
*/
protected Set getDataSources(ObjectStore os) {
Query q = new Query();
QueryClass qc = new QueryClass(DataSource.class);
q.addFrom(qc);
q.addToSelect(qc);
List results = os.executeSingleton(q);
Set names = new HashSet();
Iterator resIter = results.iterator();
while (resIter.hasNext()) {
DataSource datasource = (DataSource) resIter.next();
names.add(datasource.getName());
}
return names;
}
private class DataSourceHolder
{
protected String name;
protected String descr;
protected String pubMedId;
protected String url;
public DataSourceHolder(String name) {
this.name = name;
}
}
}