From 858dc86a224297e44479cd7945123decd2eb4f56 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Thu, 1 Dec 2022 15:28:46 -0800 Subject: [PATCH] Route all temp file creation through FileUtil for consistency --- .../labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java | 2 +- .../org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java | 3 ++- .../src/org/labkey/sequenceanalysis/util/Barcoder.java | 2 +- .../src/org/labkey/sequenceanalysis/util/SequenceUtil.java | 2 +- .../sequenceanalysis/visualization/VariationChart.java | 5 +++-- .../singlecell/pipeline/singlecell/RunCellHashing.java | 2 +- 6 files changed, 9 insertions(+), 7 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java index 9ce9f545f..8c8029bff 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceTaskHelper.java @@ -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(); } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java index e6cf2c291..3d5b5ec25 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GFFReadWrapper.java @@ -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; @@ -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 { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java index 7be2998f3..e0db8b054 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/Barcoder.java @@ -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(); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java index 31ad873d6..d6b87e9b6 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java @@ -541,7 +541,7 @@ public static Set 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"); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/visualization/VariationChart.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/visualization/VariationChart.java index 3f9fa95f7..9a9bd7ee2 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/visualization/VariationChart.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/visualization/VariationChart.java @@ -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; @@ -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); @@ -354,7 +355,7 @@ public Map toSVG(List 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); diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunCellHashing.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunCellHashing.java index 207ed8275..0414b4040 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunCellHashing.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunCellHashing.java @@ -184,7 +184,7 @@ protected List 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;