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Route all temp file creation through FileUtil for consistency #545

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Merged
labkey-adam merged 1 commit into from
Dec 2, 2022
Merged

Route all temp file creation through FileUtil for consistency #545

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3 changes: 2 additions & 1 deletion elispotassay/src/org/labkey/elispot/pipeline/BackgroundSubtractionJob.java
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Expand Up @@ -39,6 +39,7 @@
import org.labkey.api.assay.plate.PlateBasedAssayProvider;
import org.labkey.api.assay.plate.PlateReader;
import org.labkey.api.util.DateUtil;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.URLHelper;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.elispot.ElispotAssayProvider;
Expand Down Expand Up @@ -71,7 +72,7 @@ public BackgroundSubtractionJob(String provider, ViewBackgroundInfo info, PipeRo
{
super(provider, info, root);

File logFile = File.createTempFile("backgroundSubtractionJob", ".log", root.getLogDirectory());
File logFile = FileUtil.createTempFile("backgroundSubtractionJob", ".log", root.getLogDirectory());
setLogFile(logFile);

_runs = runs;
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3 changes: 2 additions & 1 deletion flow/src/org/labkey/flow/FlowSettings.java
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Expand Up @@ -20,6 +20,7 @@
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.util.FileUtil;

import java.io.File;
import java.io.IOException;
Expand All @@ -39,7 +40,7 @@ static private File getTempAnalysisDirectory()
File file;
try
{
file = File.createTempFile("FlowAnalysis", "tmp");
file = FileUtil.createTempFile("FlowAnalysis", "tmp");
}
catch (IOException e)
{
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3 changes: 2 additions & 1 deletion flow/src/org/labkey/flow/script/WorkspaceJob.java
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Expand Up @@ -33,6 +33,7 @@
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.security.User;
import org.labkey.api.util.FileUtil;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.flow.FlowSettings;
import org.labkey.flow.analysis.model.Analysis;
Expand Down Expand Up @@ -123,7 +124,7 @@ public WorkspaceJob(ViewBackgroundInfo info,
if (name == null)
name = "workspace";
_workspaceName = name;
_workspaceFile = File.createTempFile(_workspaceName, null, FlowSettings.getWorkingDirectory());
_workspaceFile = FileUtil.createTempFile(_workspaceName, null, FlowSettings.getWorkingDirectory());

ObjectOutputStream oos = new ObjectOutputStream(new FileOutputStream(_workspaceFile));
oos.writeObject(workspaceData.getWorkspaceObject());
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3 changes: 2 additions & 1 deletion ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java
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Expand Up @@ -21,6 +21,7 @@
import org.junit.Test;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.exp.Lsid;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.UnexpectedException;
import org.labkey.api.view.ViewContext;
Expand Down Expand Up @@ -72,7 +73,7 @@ public BibliospecSpectrumRenderer(ViewContext context)
public void render(SpectrumIterator iter) throws IOException
{
String shortName = _context.getContainer().getName() + "SpectraLibrary";
File tempFile = File.createTempFile(shortName, ".blib");
File tempFile = FileUtil.createTempFile(shortName, ".blib");
try
{
Class.forName("org.sqlite.JDBC");
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3 changes: 2 additions & 1 deletion ms2/src/org/labkey/ms2/pipeline/ImportScanCountsUpgradeJob.java
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Expand Up @@ -24,6 +24,7 @@
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.DateUtil;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.URLHelper;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.ms2.MS2Fraction;
Expand Down Expand Up @@ -52,7 +53,7 @@ public ImportScanCountsUpgradeJob(ViewBackgroundInfo info, PipeRoot root) throws
{
super(null, info, root);

File logFile = File.createTempFile("importScanCounts", ".log", root.ensureSystemDirectory());
File logFile = FileUtil.createTempFile("importScanCounts", ".log", root.ensureSystemDirectory());
setLogFile(logFile);
}

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3 changes: 2 additions & 1 deletion ms2/src/org/labkey/ms2/pipeline/MSPictureUpgradeJob.java
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Expand Up @@ -27,6 +27,7 @@
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.query.ValidationException;
import org.labkey.api.util.DateUtil;
import org.labkey.api.util.FileUtil;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.ms2.MS2Module;
Expand Down Expand Up @@ -63,7 +64,7 @@ public MSPictureUpgradeJob(ViewBackgroundInfo info, PipeRoot root) throws IOExce
{
super(null, info, root);

File logFile = File.createTempFile("attachMSPicture", ".log", root.ensureSystemDirectory());
File logFile = FileUtil.createTempFile("attachMSPicture", ".log", root.ensureSystemDirectory());
setLogFile(logFile);
}

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3 changes: 2 additions & 1 deletion ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java
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Expand Up @@ -36,6 +36,7 @@
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.pipeline.PipelineJobService;
import org.labkey.api.settings.AppProps;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.HelpTopic;
import org.labkey.api.view.ActionURL;
import org.labkey.ms2.pipeline.AbstractMS2SearchProtocolFactory;
Expand Down Expand Up @@ -1543,7 +1544,7 @@ public void testMockMascotServer() throws IOException
if (!new File(paramFile).exists())
{
InputStream is = getClass().getClassLoader().getResourceAsStream(mascotDefaultsPath);
File file = File.createTempFile("MascotDefaults", ".xml");
File file = FileUtil.createTempFile("MascotDefaults", ".xml");
file.deleteOnExit();
FileUtils.copyInputStreamToFile(is, file);
paramFile = file.getAbsolutePath();
Expand Down
3 changes: 2 additions & 1 deletion ms2/src/org/labkey/ms2/protein/FastaReloaderJob.java
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Expand Up @@ -19,6 +19,7 @@
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.settings.AppProps;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.URLHelper;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.ms2.protein.fasta.FastaFile;
Expand All @@ -41,7 +42,7 @@ public FastaReloaderJob(int[] fastaIds, ViewBackgroundInfo info, PipeRoot root)
{
super(ProteinAnnotationPipelineProvider.NAME, info, root);
_fastaIds = fastaIds;
setLogFile(File.createTempFile("FastaReload", ".log", AppProps.getInstance().getFileSystemRoot()));
setLogFile(FileUtil.createTempFile("FastaReload", ".log", AppProps.getInstance().getFileSystemRoot()));
}

@Override
Expand Down