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Merged
github-actions merged 1 commit into from
Jan 19, 2026
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[bot] Fast-forward for 24.11.17 #1164

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7 changes: 7 additions & 0 deletions src/org/labkey/targetedms/TargetedMSModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@
import org.labkey.api.security.permissions.AdminPermission;
import org.labkey.api.security.permissions.ApplicationAdminPermission;
import org.labkey.api.settings.AdminConsole;
import org.labkey.api.settings.OptionalFeatureService;
import org.labkey.api.targetedms.TargetedMSService;
import org.labkey.api.usageMetrics.UsageMetricsService;
import org.labkey.api.util.PageFlowUtil;
Expand Down Expand Up @@ -127,6 +128,8 @@ public class TargetedMSModule extends SpringModule implements ProteomicsModule
public static final String PROTEIN_TAB_NAME = "Proteins";
public static final String MOLECULE_TAB_NAME = "Molecules";

public static final String USE_TEMP_DIR_FOR_SKYD_IMPORT = "UseTempDirForSkydImport";

public static final String[] EXPERIMENT_FOLDER_WEB_PARTS = new String[] {MSSearchWebpart.NAME,
TARGETED_MS_RUNS_WEBPART_NAME};

Expand Down Expand Up @@ -214,6 +217,10 @@ public TargetedMSModule()
MAX_PRECURSORS_PROPERTY.setShowDescriptionInline(true);
addModuleProperty(MAX_PRECURSORS_PROPERTY);

AdminConsole.addOptionalFeatureFlag(new AdminConsole.OptionalFeatureFlag(USE_TEMP_DIR_FOR_SKYD_IMPORT,
"Stage SKYD files to a temporary local file for import purposes",
"When using a non-local file system, the latency for random access requests can be significantly slower than first copying to local storage",
false, false, OptionalFeatureService.FeatureType.Optional));
}

@Override
Expand Down
38 changes: 32 additions & 6 deletions src/org/labkey/targetedms/parser/SkylineBinaryParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,9 @@
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.exp.api.DataType;
import org.labkey.api.settings.OptionalFeatureService;
import org.labkey.api.util.FileUtil;
import org.labkey.targetedms.TargetedMSModule;
import org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass;
import org.labkey.targetedms.parser.skyd.CacheFormat;
import org.labkey.targetedms.parser.skyd.CacheFormatVersion;
Expand All @@ -44,15 +47,12 @@

/**
* Parses the .skyd binary file format, for chromatogram data.
*
* Based on ChromatogramCache.cs and ChromHeaderInfo.cs from Skyline
*
* User: jeckels
* Date: Apr 13, 2012
*/
public class SkylineBinaryParser
{
private final File _file;
private final boolean _deleteFileOnClose;
private final Logger _log;
private FileChannel _channel;
private RandomAccessFile _randomAccessFile;
Expand All @@ -71,10 +71,24 @@ public class SkylineBinaryParser

private CachedFile[] _cacheFiles;

public SkylineBinaryParser(File file, Logger log)
public SkylineBinaryParser(File file, Logger log) throws IOException
{
_file = file;
_log = log;

if (OptionalFeatureService.get().isFeatureEnabled(TargetedMSModule.USE_TEMP_DIR_FOR_SKYD_IMPORT))
{
_deleteFileOnClose = true;
_file = FileUtil.createTempFile(file.getName(), ".skyd");
_file.deleteOnExit();
_log.info("Copying SKYD to temp directory for import purposes");
FileUtil.copyFile(file, _file);
_log.info("Copying complete");
}
else
{
_file = file;
_deleteFileOnClose = false;
}
}

public ChromGroupHeaderInfo[] getChromatograms()
Expand All @@ -97,6 +111,18 @@ public void close()
// using a FileChannel there is a known Java issue on Windows that prevents the mapped file from being deleted,
// http://bugs.java.com/bugdatabase/view_bug.do?bug_id=4715154 and http://bugs.java.com/bugdatabase/view_bug.do?bug_id=4469299
System.gc();

if (_deleteFileOnClose && _file != null)
{
if (!_file.delete())
{
_log.warn("Failed to delete temp copy of SKYD file: " + _file.getAbsolutePath());
}
else
{
_log.info("Deleted temp copy of SKYD file");
}
}
}

public void parse() throws IOException
Expand Down