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Route all temp file creation through FileUtil for consistency #191

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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 #191

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2 changes: 1 addition & 1 deletion SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -258,7 +258,7 @@ public static void logModuleVersions(Logger log)
log.debug("java.io.tmpDir: " + System.getProperty("java.io.tmpdir"));
try
{
File tmp = File.createTempFile("sa-tmp", "tmp");
File tmp = FileUtil.createTempFile("sa-tmp", "tmp");
log.debug("temp file location: " + tmp.getParent());
tmp.delete();
}
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3 changes: 2 additions & 1 deletion SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java
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Expand Up @@ -8,6 +8,7 @@
import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
import org.labkey.api.util.FileUtil;
import org.labkey.sequenceanalysis.util.SequenceUtil;

import java.io.File;
Expand All @@ -34,7 +35,7 @@ public File sortGxf(File gxf, @Nullable File output) throws PipelineJobException
if (output == null)
{
getLogger().debug("file will sort sorted in place");
outputFile = File.createTempFile("gffread", ".txt");
outputFile = FileUtil.createTempFile("gffread", ".txt");
}
else
{
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2 changes: 1 addition & 1 deletion SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java
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Expand Up @@ -554,7 +554,7 @@ public void setUp()
try
{
//create input data
_input = File.createTempFile("barcodeTest", ".fastq");
_input = FileUtil.createTempFile("barcodeTest", ".fastq");
if (_input.exists())
_input.delete();

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2 changes: 1 addition & 1 deletion SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java
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Expand Up @@ -541,7 +541,7 @@ public static Set<String> getContigsInVcf(File vcf) throws PipelineJobException
{
try
{
File script = File.createTempFile("script", "sh");
File script = FileUtil.createTempFile("script", "sh");
try (PrintWriter writer = PrintWriters.getPrintWriter(script))
{
writer.println("#!/bin/bash");
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5 changes: 3 additions & 2 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/visualization/VariationChart.java
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Expand Up @@ -23,6 +23,7 @@
import org.jfree.ui.RectangleEdge;
import org.jfree.ui.TextAnchor;
import org.json.old.JSONObject;
import org.labkey.api.util.FileUtil;
import org.labkey.api.writer.PrintWriters;
import org.w3c.dom.DOMImplementation;
import org.w3c.dom.Document;
Expand Down Expand Up @@ -311,7 +312,7 @@ private FeatureList readGff(String gff) throws IOException
if (gff == null)
return new FeatureList();

File f = File.createTempFile("variationChart", ".gff");
File f = FileUtil.createTempFile("variationChart", ".gff");
try (PrintWriter writer = PrintWriters.getPrintWriter(f))
{
writer.write(gff);
Expand Down Expand Up @@ -354,7 +355,7 @@ public Map<String, Object> toSVG(List<JFreeChart> charts, int width, int height)
i++;
}

File output = File.createTempFile("sequenceGraph", ".svg");
File output = FileUtil.createTempFile("sequenceGraph", ".svg");
try (BufferedWriter writer = new BufferedWriter(new FileWriter(output)))
{
generator.stream(writer);
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2 changes: 1 addition & 1 deletion singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunCellHashing.java
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Expand Up @@ -184,7 +184,7 @@ protected List<Chunk> addAdditionalChunks(SequenceOutputHandler.JobContext ctx,
//Add one more indentation to headers:
try
{
File updated = File.createTempFile("headerUpdate", ".md");
File updated = FileUtil.createTempFile("headerUpdate", ".md");
try (PrintWriter writer = PrintWriters.getPrintWriter(updated); BufferedReader reader = Readers.getReader(markdown))
{
String line;
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