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Update MS2 SpectrumImporter to work with Java 25 #967

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Merged
labkey-tchad merged 2 commits into from
Dec 15, 2025
Merged

Update MS2 SpectrumImporter to work with Java 25 #967

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96b3529
Fix FileLike error on Java 25
labkey-tchad Dec 12, 2025
2dbec9d
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labkey-tchad Dec 12, 2025
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19 changes: 6 additions & 13 deletions ms2/src/org/labkey/ms2/PepXmlImporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -226,8 +226,7 @@ protected static String switchSuffix(String filename, String suffix)

protected void processSpectrumFile(PepXmlFraction fraction, Set<Integer> scans, MS2Progress progress, boolean shouldLoadSpectra, boolean shouldLoadRetentionTimes)
{
File mzXmlFile = getMzXMLFile(fraction);
FileLike mzXmlFileLike = null;
FileLike mzXmlFile = FileSystemLike.wrapFile(getMzXMLFile(fraction));
if ((_run.getType().equalsIgnoreCase(MS2RunType.Mascot.name())||_run.getType().equalsIgnoreCase(MS2RunType.Sequest.name())) // TODO: Move this check (perhaps all the code) into the appropriate run classes
&& null == mzXmlFile)
{
Expand All @@ -242,25 +241,19 @@ protected void processSpectrumFile(PepXmlFraction fraction, Set<Integer> scans,
String mzXmlFileName = engineProtocolMzXMLFile.getName();
FileLike engineProtocolDir = engineProtocolMzXMLFile.getParent();
FileLike engineDir = engineProtocolDir.getParent();
FileLike mzXMLFile = engineDir.getParent().resolveFile(Path.parse(mzXmlFileName));
mzXmlFileLike = mzXMLFile;
}
String gzFileName = _path + "/" + _gzFileName;
File gzFile = _context.findFile(gzFileName);
if (gzFile != null)
{
gzFileName = gzFile.toString();
mzXmlFile = engineDir.getParent().resolveFile(Path.parse(mzXmlFileName));
}
FileLike gzFile = FileSystemLike.wrapFile(_context.findFile(_path)).resolveChild(_gzFileName);
//sequest spectra are imported from the tgz but are deleted after they are imported.
if(_run.getType().equalsIgnoreCase("sequest") && mzXmlFile != null) // TODO: Move this check (perhaps all the code) into the appropriate run classes
if(_run.getType().equalsIgnoreCase(MS2RunType.Sequest.name()) && mzXmlFile != null) // TODO: Move this check (perhaps all the code) into the appropriate run classes
{
if (NetworkDrive.exists(mzXmlFile))
{
gzFileName = "";
gzFile = null;
}
}

SpectrumImporter sl = new SpectrumImporter(gzFileName, "", mzXmlFileLike, scans, progress, _fractionId, _log, shouldLoadSpectra, shouldLoadRetentionTimes);
SpectrumImporter sl = new SpectrumImporter(gzFile, "", mzXmlFile, scans, progress, _fractionId, _log, shouldLoadSpectra, shouldLoadRetentionTimes);
sl.upload();
updateFractionSpectrumFileName(sl.getFile() == null ? null : sl.getFile().toNioPathForRead().toFile());
}
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25 changes: 12 additions & 13 deletions ms2/src/org/labkey/ms2/SpectrumImporter.java
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Expand Up @@ -16,17 +16,18 @@

package org.labkey.ms2;

import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.labkey.api.data.DbSchema;
import org.labkey.api.util.NetworkDrive;
import org.labkey.api.util.Pair;
import org.labkey.ms2.reader.*;
import org.labkey.ms2.reader.AbstractMzxmlIterator;
import org.labkey.ms2.reader.SimpleScan;
import org.labkey.ms2.reader.SimpleScanIterator;
import org.labkey.ms2.reader.TarIterator;
import org.labkey.vfs.FileLike;
import org.labkey.vfs.FileSystemLike;

import javax.xml.stream.XMLStreamException;
import java.io.File;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
Expand Down Expand Up @@ -55,7 +56,7 @@ public class SpectrumImporter
private final boolean _shouldImportRetentionTime;


protected SpectrumImporter(String gzFileName, String dtaFileNamePrefix, FileLike mzXmlFile, Set<Integer> scans, MS2Importer.MS2Progress progress, int fractionId, Logger log, boolean shouldImportSpectra, boolean shouldImportRetentionTime)
protected SpectrumImporter(FileLike gzFile, String dtaFileNamePrefix, FileLike mzXmlFile, Set<Integer> scans, MS2Importer.MS2Progress progress, int fractionId, Logger log, boolean shouldImportSpectra, boolean shouldImportRetentionTime)
{
_scans = scans;
_progress = progress;
Expand All @@ -70,22 +71,20 @@ protected SpectrumImporter(String gzFileName, String dtaFileNamePrefix, FileLike
try
{
// Try to access the gz file first... if that fails, try to open the mzXML file
File gz = new File(gzFileName);

if (NetworkDrive.exists(gz))
if (NetworkDrive.exists(gzFile))
{
_file = FileSystemLike.wrapFile(gz);
_scanIterator = new TarIterator(gz, dtaFileNamePrefix);
_file = gzFile;
_scanIterator = new TarIterator(gzFile, dtaFileNamePrefix);
}
else
{
if (null == mzXmlFile)
_log.warn("Spectra were not imported: " + gzFileName + " could not be opened and no mzXML file name was specified.");
_log.warn("Spectra were not imported: " + gzFile + " could not be opened and no mzXML file name was specified.");
else
{
_file = mzXmlFile;
// prefer ProteoWizard's RAMPAdapter interface
// (with JNI bindings via SWIG) as it's actively
// (with JNI bindings via SWIG) as it's actively
// maintained, handles mzML and mzXML, and gzipped
// files natively
_scanIterator = AbstractMzxmlIterator.createParser(_file, 2);
Expand All @@ -99,7 +98,7 @@ protected SpectrumImporter(String gzFileName, String dtaFileNamePrefix, FileLike
catch (XMLStreamException x)
{
throw new RuntimeException(x);
}
}
}

protected void upload()
Expand Down
9 changes: 4 additions & 5 deletions ms2/src/org/labkey/ms2/reader/TarIterator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,15 +17,14 @@

import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.labkey.api.arrays.FloatArray;
import org.labkey.ms2.FloatParser;
import org.labkey.ms2.MS2Importer;
import org.labkey.vfs.FileLike;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.zip.GZIPInputStream;
Expand Down Expand Up @@ -53,13 +52,13 @@ public class TarIterator implements SimpleScanIterator
private byte[] _spectrumData = new byte[BUFFER_SIZE];


public TarIterator(File gzFile, String dtaFileNamePrefix) throws java.io.IOException
public TarIterator(FileLike gzFile, String dtaFileNamePrefix) throws java.io.IOException
{
boolean success = false;
try
{
_dtaFileNamePrefix = dtaFileNamePrefix;
_is = new BufferedInputStream(new FileInputStream(gzFile), STREAM_BUFFER_SIZE);
_is = new BufferedInputStream(gzFile.openInputStream(), STREAM_BUFFER_SIZE);
_gzInputStream = new GZIPInputStream(_is);
_tis = new TarArchiveInputStream(_gzInputStream);
success = true;
Expand Down