org.bridgedb.bio.DataSourceTxt Maven / Gradle / Ivy
// BridgeDb,
// An abstraction layer for identifier mapping services, both local and online.
// Copyright 2006-2009 BridgeDb developers
// Copyright 2012-2013 Christian Brenninkmeijer
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
package org.bridgedb.bio;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.SortedSet;
import java.util.TreeSet;
import java.util.regex.Pattern;
import org.bridgedb.DataSource;
import org.bridgedb.DataSourcePatterns;
public class DataSourceTxt
{
/** Call this to initialize the DataSourcs from org/bridgedb/bio/datasources.tsv
* You should call this before using any of these constants,
* or they may be undefined.
*/
public static void init()
{
try{
InputStream is = DataSourceTxt.class.getClassLoader().getResourceAsStream("org/bridgedb/bio/datasources.tsv");
new DataSourceTxt().loadAnInputStream(is);
}
catch (IOException ex)
{
throw new Error(ex);
}
}
public static String datasourcesTxt = "";
public static void loadInputStream(InputStream is) throws IOException{
new DataSourceTxt().loadAnInputStream(is);
}
protected void loadAnInputStream(InputStream is) throws IOException {
BufferedReader reader = new BufferedReader (
new InputStreamReader (is));
String line;
while ((line = reader.readLine()) != null) {
datasourcesTxt = datasourcesTxt + line + "\n";
String[] fields = line.split ("\\t");
loadLine(fields);
}
}
protected void loadLine(String[] fields) throws IOException
{
DataSource.Builder builder = DataSource.register
(fields[1], // system code
fields[0]); // gpml name
if (fields.length > 2 && fields[2].length() > 0) {
builder.mainUrl(fields[2]);
}
if (fields.length > 3 && fields[3].length() > 0) {
builder.urlPattern(fields[3]);
}
if (fields.length > 4 && fields[4].length() > 0) {
builder.idExample(fields[4]);
}
if (fields.length > 5 && fields[5].length() > 0) {
builder.type(fields[5]);
}
if (fields.length > 6 && fields[6].length() > 0) {
builder.organism(Organism.fromLatinName(fields[6]));
}
if (fields.length > 7 && fields[7].length() > 0) {
builder.primary (fields[7].equals ("1"));
}
if (fields.length > 8) {
builder.urnBase(fields[8]);
}
if (fields.length > 9) {
String patternString = fields[9];
try {
Pattern pattern = Pattern.compile(patternString);
DataSourcePatterns.registerPattern(builder.asDataSource(), pattern);
} catch (Exception ex){
throw new IllegalArgumentException("Unable to parse pattern " + patternString + " for " + builder.asDataSource(), ex);
}
}
if (fields.length > 10) builder.alternative(fields[10]);
// field 11 = Wikidata property
if (fields.length > 12) {
builder.bioregistryPrefix(fields[12]);
}
if (fields.length > 13) {
builder.categories(fields[13]);
}
}
/**
* Writes all currently loaded DataSources to a writer
*
*
*
* @param writer
* @throws IOException
* See org.bridgedb.bio.DataSourceTxtTest#testWriteRead for a working example
*/
public static void writeToBuffer(BufferedWriter writer) throws IOException {
TreeSet sorted = new TreeSet(new DataSourceComparator());
sorted.addAll(DataSource.getDataSources());
writeToBuffer(writer, sorted);
}
public static void writeToBuffer(BufferedWriter writer, SortedSet dataSources) throws IOException
{
for (DataSource dataSource:dataSources){
//Ignore invalid test DataSources
if (dataSource.getSystemCode() != null && dataSource.getFullName() != null){
writer.write(dataSource.getFullName());//[0]
writer.write("\t");
writer.write(dataSource.getSystemCode());//[1]
writer.write("\t");
if (dataSource.getMainUrl() != null){
writer.write(dataSource.getMainUrl());//[2]
}
writer.write("\t");
if (dataSource.getKnownUrl("$id") != null){
writer.write(dataSource.getKnownUrl("$id"));//[3]
}
writer.write("\t");
if (dataSource.getExample().getId() != null){
writer.write(dataSource.getExample().getId());//[4]
}
writer.write("\t");
if (dataSource.getType() != null){
writer.write(dataSource.getType());//[5]
}
writer.write("\t");
if (dataSource.getOrganism() instanceof Organism){
writer.write(((Organism)dataSource.getOrganism()).latinName());//[6]
}
writer.write("\t");
if (dataSource.isPrimary()){
writer.write("1");//[7]
} else {
writer.write("0");//[7]
}
writer.write("\t");
String base = dataSource.getMiriamURN("");
if (base != null){
writer.write(base.substring(0, base.length()-1));//[8]
}
writer.write("\t");
if (DataSourcePatterns.getPatterns().containsKey(dataSource)){
writer.write(DataSourcePatterns.getPatterns().get(dataSource).pattern());//[9]
}
writer.write("\t");
if (dataSource.getAlternative() != null){
writer.write(dataSource.getAlternative());//[10]
}
writer.write("\t");
if (dataSource.getBioregistryPrefix() != null){
writer.write(dataSource.getBioregistryPrefix());//[11]
}
writer.newLine();
}
}
writer.flush();
writer.close();
}
}
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