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org.nmdp.ngs.sra.SraWriter Maven / Gradle / Ivy
/*
ngs-sra Mapping for SRA submission XSDs.
Copyright (c) 2014 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.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;
import javax.xml.XMLConstants;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.validation.Schema;
import javax.xml.validation.SchemaFactory;
import javax.xml.transform.stream.StreamSource;
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;
/**
* Writer for SRA xml.
*/
public final class SraWriter {
/**
* Private no-arg constructor.
*/
private SraWriter() {
// empty
}
public static void writeAnalysis(final Analysis analysis, final Writer writer) throws IOException {
checkNotNull(analysis);
checkNotNull(writer);
try {
JAXBContext context = JAXBContext.newInstance(Analysis.class);
Marshaller marshaller = context.createMarshaller();
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()) });
marshaller.setSchema(schema);
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
marshaller.marshal(analysis, writer);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not marshal Analysis", e);
}
}
public static void writeAnalysis(final Analysis analysis, final File file) throws IOException {
checkNotNull(analysis);
checkNotNull(file);
try (BufferedWriter writer = new BufferedWriter(new FileWriter(file))) {
writeAnalysis(analysis, writer);
}
}
public static void writeAnalysis(final Analysis analysis, final OutputStream outputStream) throws IOException {
checkNotNull(analysis);
checkNotNull(outputStream);
try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(outputStream))) {
writeAnalysis(analysis, writer);
}
}
public static void writeExperiment(final Experiment experiment, final Writer writer) throws IOException {
checkNotNull(experiment);
checkNotNull(writer);
try {
JAXBContext context = JAXBContext.newInstance(Experiment.class);
Marshaller marshaller = context.createMarshaller();
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()) });
marshaller.setSchema(schema);
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
marshaller.marshal(experiment, writer);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not marshal Experiment", e);
}
}
public static void writeExperiment(final Experiment experiment, final File file) throws IOException {
checkNotNull(experiment);
checkNotNull(file);
try (BufferedWriter writer = new BufferedWriter(new FileWriter(file))) {
writeExperiment(experiment, writer);
}
}
public static void writeExperiment(final Experiment experiment, final OutputStream outputStream) throws IOException {
checkNotNull(experiment);
checkNotNull(outputStream);
try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(outputStream))) {
writeExperiment(experiment, writer);
}
}
public static void writeRunSet(final RunSet runSet, final Writer writer) throws IOException {
checkNotNull(runSet);
checkNotNull(writer);
try {
JAXBContext context = JAXBContext.newInstance(RunSet.class);
Marshaller marshaller = context.createMarshaller();
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()) });
marshaller.setSchema(schema);
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
marshaller.marshal(runSet, writer);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not marshal RunSet", e);
}
}
public static void writeRunSet(final RunSet runSet, final File file) throws IOException {
checkNotNull(runSet);
checkNotNull(file);
try (BufferedWriter writer = new BufferedWriter(new FileWriter(file))) {
writeRunSet(runSet, writer);
}
}
public static void writeRunSet(final RunSet runSet, final OutputStream outputStream) throws IOException {
checkNotNull(runSet);
checkNotNull(outputStream);
try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(outputStream))) {
writeRunSet(runSet, writer);
}
}
public static void writeSample(final Sample sample, final Writer writer) throws IOException {
checkNotNull(sample);
checkNotNull(writer);
try {
JAXBContext context = JAXBContext.newInstance(Sample.class);
Marshaller marshaller = context.createMarshaller();
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()) });
marshaller.setSchema(schema);
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
marshaller.marshal(sample, writer);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not marshal Sample", e);
}
}
public static void writeSample(final Sample sample, final File file) throws IOException {
checkNotNull(sample);
checkNotNull(file);
try (BufferedWriter writer = new BufferedWriter(new FileWriter(file))) {
writeSample(sample, writer);
}
}
public static void writeSample(final Sample sample, final OutputStream outputStream) throws IOException {
checkNotNull(sample);
checkNotNull(outputStream);
try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(outputStream))) {
writeSample(sample, writer);
}
}
public static void writeStudy(final Study study, final Writer writer) throws IOException {
checkNotNull(study);
checkNotNull(writer);
try {
JAXBContext context = JAXBContext.newInstance(Study.class);
Marshaller marshaller = context.createMarshaller();
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()) });
marshaller.setSchema(schema);
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
marshaller.marshal(study, writer);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not marshal Study", e);
}
}
public static void writeStudy(final Study study, final File file) throws IOException {
checkNotNull(study);
checkNotNull(file);
try (BufferedWriter writer = new BufferedWriter(new FileWriter(file))) {
writeStudy(study, writer);
}
}
public static void writeStudy(final Study study, final OutputStream outputStream) throws IOException {
checkNotNull(study);
checkNotNull(outputStream);
try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(outputStream))) {
writeStudy(study, writer);
}
}
public static void writeSubmission(final Submission submission, final Writer writer) throws IOException {
checkNotNull(submission);
checkNotNull(writer);
try {
JAXBContext context = JAXBContext.newInstance(Submission.class);
Marshaller marshaller = context.createMarshaller();
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()) });
marshaller.setSchema(schema);
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
marshaller.marshal(submission, writer);
}
catch (JAXBException | SAXException e) {
throw new IOException("could not marshal Submission", e);
}
}
public static void writeSubmission(final Submission submission, final File file) throws IOException {
checkNotNull(submission);
checkNotNull(file);
try (BufferedWriter writer = new BufferedWriter(new FileWriter(file))) {
writeSubmission(submission, writer);
}
}
public static void writeSubmission(final Submission submission, final OutputStream outputStream) throws IOException {
checkNotNull(submission);
checkNotNull(outputStream);
try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(outputStream))) {
writeSubmission(submission, writer);
}
}
}
