Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/*
ngs-sra Mapping for SRA submission XSDs.
Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.gnu.org/licenses/lgpl.html
*/
package org.nmdp.ngs.sra;
import static com.google.common.base.Preconditions.checkNotNull;
import java.net.URL;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
import javax.xml.XMLConstants;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import javax.xml.transform.stream.StreamSource;
import javax.xml.validation.Schema;
import javax.xml.validation.SchemaFactory;
import com.google.common.base.Charsets;
import com.google.common.io.Resources;
import org.nmdp.ngs.sra.jaxb.analysis.Analysis;
import org.nmdp.ngs.sra.jaxb.experiment.Experiment;
import org.nmdp.ngs.sra.jaxb.run.RunSet;
import org.nmdp.ngs.sra.jaxb.sample.Sample;
import org.nmdp.ngs.sra.jaxb.study.Study;
import org.nmdp.ngs.sra.jaxb.submission.Submission;
import org.xml.sax.SAXException;
/**
* Reader for SRA xml.
*/
public final class SraReader {
/**
* Read an analysis from the specified reader.
*
* @param reader reader, must not be null
* @return an analysis read from the specified reader
* @throws IOException if an I/O error occurs
*/
public static Analysis readAnalysis(final Reader reader) throws IOException {
checkNotNull(reader);
try {
JAXBContext context = JAXBContext.newInstance(Analysis.class);
Unmarshaller unmarshaller = context.createUnmarshaller();
SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
URL commonSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.common.xsd");
URL analysisSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.analysis.xsd");
Schema schema = schemaFactory.newSchema(new StreamSource[] { new StreamSource(commonSchemaURL.toString()), new StreamSource(analysisSchemaURL.toString()) });
unmarshaller.setSchema(schema);
return (Analysis) unmarshaller.unmarshal(reader);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not unmarshal Analysis", e);
}
}
/**
* Read an analysis from the specified file.
*
* @param file file, must not be null
* @return an analysis read from the specified file
* @throws IOException if an I/O error occurs
*/
public static Analysis readAnalysis(final File file) throws IOException {
checkNotNull(file);
try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
return readAnalysis(reader);
}
}
/**
* Read an analysis from the specified URL.
*
* @param url URL, must not be null
* @return an analysis read from the specified URL
* @throws IOException if an I/O error occurs
*/
public static Analysis readAnalysis(final URL url) throws IOException {
checkNotNull(url);
try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) {
return readAnalysis(reader);
}
}
/**
* Read an analysis from the specified input stream.
*
* @param inputStream input stream, must not be null
* @return an analysis read from the specified input stream
* @throws IOException if an I/O error occurs
*/
public static Analysis readAnalysis(final InputStream inputStream) throws IOException {
checkNotNull(inputStream);
try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
return readAnalysis(reader);
}
}
/**
* Read an experiment from the specified reader.
*
* @param reader reader, must not be null
* @return an experiment read from the specified reader
* @throws IOException if an I/O error occurs
*/
public static Experiment readExperiment(final Reader reader) throws IOException {
checkNotNull(reader);
try {
JAXBContext context = JAXBContext.newInstance(Experiment.class);
Unmarshaller unmarshaller = context.createUnmarshaller();
SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
URL commonSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.common.xsd");
URL experimentSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.experiment.xsd");
Schema schema = schemaFactory.newSchema(new StreamSource[] { new StreamSource(commonSchemaURL.toString()), new StreamSource(experimentSchemaURL.toString()) });
unmarshaller.setSchema(schema);
return (Experiment) unmarshaller.unmarshal(reader);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not unmarshal Experiment", e);
}
}
/**
* Read an experiment from the specified file.
*
* @param file file, must not be null
* @return an experiment read from the specified file
* @throws IOException if an I/O error occurs
*/
public static Experiment readExperiment(final File file) throws IOException {
checkNotNull(file);
try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
return readExperiment(reader);
}
}
/**
* Read an experiment from the specified URL.
*
* @param url URL, must not be null
* @return an experiment read from the specified URL
* @throws IOException if an I/O error occurs
*/
public static Experiment readExperiment(final URL url) throws IOException {
checkNotNull(url);
try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) {
return readExperiment(reader);
}
}
/**
* Read an experiment from the specified input stream.
*
* @param inputStream input stream, must not be null
* @return an experiment read from the specified input stream
* @throws IOException if an I/O error occurs
*/
public static Experiment readExperiment(final InputStream inputStream) throws IOException {
checkNotNull(inputStream);
try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
return readExperiment(reader);
}
}
/**
* Read a run set from the specified reader.
*
* @param reader reader, must not be null
* @return a run set read from the specified reader
* @throws IOException if an I/O error occurs
*/
public static RunSet readRunSet(final Reader reader) throws IOException {
checkNotNull(reader);
try {
JAXBContext context = JAXBContext.newInstance(RunSet.class);
Unmarshaller unmarshaller = context.createUnmarshaller();
SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
URL commonSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.common.xsd");
URL runSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.run.xsd");
Schema schema = schemaFactory.newSchema(new StreamSource[] { new StreamSource(commonSchemaURL.toString()), new StreamSource(runSchemaURL.toString()) });
unmarshaller.setSchema(schema);
return (RunSet) unmarshaller.unmarshal(reader);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not unmarshal RunSet", e);
}
}
/**
* Read a run set from the specified file.
*
* @param file file, must not be null
* @return a run set read from the specified file
* @throws IOException if an I/O error occurs
*/
public static RunSet readRunSet(final File file) throws IOException {
checkNotNull(file);
try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
return readRunSet(reader);
}
}
/**
* Read a run set from the specified URL.
*
* @param url URL, must not be null
* @return a run set read from the specified URL
* @throws IOException if an I/O error occurs
*/
public static RunSet readRunSet(final URL url) throws IOException {
checkNotNull(url);
try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) {
return readRunSet(reader);
}
}
/**
* Read a run set from the specified input stream.
*
* @param inputStream input stream, must not be null
* @return a run set read from the specified input stream
* @throws IOException if an I/O error occurs
*/
public static RunSet readRunSet(final InputStream inputStream) throws IOException {
checkNotNull(inputStream);
try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
return readRunSet(reader);
}
}
/**
* Read a sample from the specified reader.
*
* @param reader reader, must not be null
* @return a sample read from the specified reader
* @throws IOException if an I/O error occurs
*/
public static Sample readSample(final Reader reader) throws IOException {
checkNotNull(reader);
try {
JAXBContext context = JAXBContext.newInstance(Sample.class);
Unmarshaller unmarshaller = context.createUnmarshaller();
SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
URL commonSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.common.xsd");
URL sampleSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.sample.xsd");
Schema schema = schemaFactory.newSchema(new StreamSource[] { new StreamSource(commonSchemaURL.toString()), new StreamSource(sampleSchemaURL.toString()) });
unmarshaller.setSchema(schema);
return (Sample) unmarshaller.unmarshal(reader);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not unmarshal Sample", e);
}
}
/**
* Read a sample from the specified file.
*
* @param file file, must not be null
* @return a sample read from the specified file
* @throws IOException if an I/O error occurs
*/
public static Sample readSample(final File file) throws IOException {
checkNotNull(file);
try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
return readSample(reader);
}
}
/**
* Read a sample from the specified URL.
*
* @param url URL, must not be null
* @return a sample read from the specified URL
* @throws IOException if an I/O error occurs
*/
public static Sample readSample(final URL url) throws IOException {
checkNotNull(url);
try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) {
return readSample(reader);
}
}
/**
* Read a sample from the specified input stream.
*
* @param inputStream input stream, must not be null
* @return a sample read from the specified input stream
* @throws IOException if an I/O error occurs
*/
public static Sample readSample(final InputStream inputStream) throws IOException {
checkNotNull(inputStream);
try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
return readSample(reader);
}
}
/**
* Read a study from the specified reader.
*
* @param reader reader, must not be null
* @return a study read from the specified reader
* @throws IOException if an I/O error occurs
*/
public static Study readStudy(final Reader reader) throws IOException {
checkNotNull(reader);
try {
JAXBContext context = JAXBContext.newInstance(Study.class);
Unmarshaller unmarshaller = context.createUnmarshaller();
SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
URL commonSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.common.xsd");
URL studySchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.study.xsd");
Schema schema = schemaFactory.newSchema(new StreamSource[] { new StreamSource(commonSchemaURL.toString()), new StreamSource(studySchemaURL.toString()) });
unmarshaller.setSchema(schema);
return (Study) unmarshaller.unmarshal(reader);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not unmarshal Study", e);
}
}
/**
* Read a study from the specified file.
*
* @param file file, must not be null
* @return a study read from the specified file
* @throws IOException if an I/O error occurs
*/
public static Study readStudy(final File file) throws IOException {
checkNotNull(file);
try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
return readStudy(reader);
}
}
/**
* Read a study from the specified URL.
*
* @param url URL, must not be null
* @return a study read from the specified URL
* @throws IOException if an I/O error occurs
*/
public static Study readStudy(final URL url) throws IOException {
checkNotNull(url);
try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) {
return readStudy(reader);
}
}
/**
* Read a study from the specified input stream.
*
* @param inputStream input stream, must not be null
* @return a study read from the specified input stream
* @throws IOException if an I/O error occurs
*/
public static Study readStudy(final InputStream inputStream) throws IOException {
checkNotNull(inputStream);
try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
return readStudy(reader);
}
}
/**
* Read a submission from the specified reader.
*
* @param reader reader, must not be null
* @return a submission read from the specified reader
* @throws IOException if an I/O error occurs
*/
public static Submission readSubmission(final Reader reader) throws IOException {
checkNotNull(reader);
try {
JAXBContext context = JAXBContext.newInstance(Submission.class);
Unmarshaller unmarshaller = context.createUnmarshaller();
SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
URL commonSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.common.xsd");
URL submissionSchemaURL = SraReader.class.getResource("/org/nmdp/ngs/sra/xsd/SRA.submission.xsd");
Schema schema = schemaFactory.newSchema(new StreamSource[] { new StreamSource(commonSchemaURL.toString()), new StreamSource(submissionSchemaURL.toString()) });
unmarshaller.setSchema(schema);
return (Submission) unmarshaller.unmarshal(reader);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not unmarshal Submission", e);
}
}
/**
* Read a submission from the specified file.
*
* @param file file, must not be null
* @return a submission read from the specified file
* @throws IOException if an I/O error occurs
*/
public static Submission readSubmission(final File file) throws IOException {
checkNotNull(file);
try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
return readSubmission(reader);
}
}
/**
* Read a submission from the specified URL.
*
* @param url URL, must not be null
* @return a submission read from the specified URL
* @throws IOException if an I/O error occurs
*/
public static Submission readSubmission(final URL url) throws IOException {
checkNotNull(url);
try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) {
return readSubmission(reader);
}
}
/**
* Read a submission from the specified input stream.
*
* @param inputStream input stream, must not be null
* @return a submission read from the specified input stream
* @throws IOException if an I/O error occurs
*/
public static Submission readSubmission(final InputStream inputStream) throws IOException {
checkNotNull(inputStream);
try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
return readSubmission(reader);
}
}
}
