From 9c994e9886fcaa74978639772e6c50b855f746bc Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Thu, 1 Dec 2022 15:28:58 -0800 Subject: [PATCH] Route all temp file creation through FileUtil for consistency --- .../org/labkey/elispot/pipeline/BackgroundSubtractionJob.java | 3 ++- flow/src/org/labkey/flow/FlowSettings.java | 3 ++- flow/src/org/labkey/flow/script/WorkspaceJob.java | 3 ++- ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java | 3 ++- .../org/labkey/ms2/pipeline/ImportScanCountsUpgradeJob.java | 3 ++- ms2/src/org/labkey/ms2/pipeline/MSPictureUpgradeJob.java | 3 ++- ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java | 3 ++- ms2/src/org/labkey/ms2/protein/FastaReloaderJob.java | 3 ++- 8 files changed, 16 insertions(+), 8 deletions(-) diff --git a/elispotassay/src/org/labkey/elispot/pipeline/BackgroundSubtractionJob.java b/elispotassay/src/org/labkey/elispot/pipeline/BackgroundSubtractionJob.java index 7e73134a98..28fa2b9879 100644 --- a/elispotassay/src/org/labkey/elispot/pipeline/BackgroundSubtractionJob.java +++ b/elispotassay/src/org/labkey/elispot/pipeline/BackgroundSubtractionJob.java @@ -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; @@ -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; diff --git a/flow/src/org/labkey/flow/FlowSettings.java b/flow/src/org/labkey/flow/FlowSettings.java index 6b75a8c656..ee16b04dae 100644 --- a/flow/src/org/labkey/flow/FlowSettings.java +++ b/flow/src/org/labkey/flow/FlowSettings.java @@ -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; @@ -39,7 +40,7 @@ static private File getTempAnalysisDirectory() File file; try { - file = File.createTempFile("FlowAnalysis", "tmp"); + file = FileUtil.createTempFile("FlowAnalysis", "tmp"); } catch (IOException e) { diff --git a/flow/src/org/labkey/flow/script/WorkspaceJob.java b/flow/src/org/labkey/flow/script/WorkspaceJob.java index d365148259..136ea778b8 100644 --- a/flow/src/org/labkey/flow/script/WorkspaceJob.java +++ b/flow/src/org/labkey/flow/script/WorkspaceJob.java @@ -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; @@ -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()); diff --git a/ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java b/ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java index 110f1cd478..d1a4f56a69 100644 --- a/ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java +++ b/ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java @@ -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; @@ -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"); diff --git a/ms2/src/org/labkey/ms2/pipeline/ImportScanCountsUpgradeJob.java b/ms2/src/org/labkey/ms2/pipeline/ImportScanCountsUpgradeJob.java index aa5b54c599..e6e8714759 100644 --- a/ms2/src/org/labkey/ms2/pipeline/ImportScanCountsUpgradeJob.java +++ b/ms2/src/org/labkey/ms2/pipeline/ImportScanCountsUpgradeJob.java @@ -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; @@ -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); } diff --git a/ms2/src/org/labkey/ms2/pipeline/MSPictureUpgradeJob.java b/ms2/src/org/labkey/ms2/pipeline/MSPictureUpgradeJob.java index c1e71cda8f..6afb6e0522 100644 --- a/ms2/src/org/labkey/ms2/pipeline/MSPictureUpgradeJob.java +++ b/ms2/src/org/labkey/ms2/pipeline/MSPictureUpgradeJob.java @@ -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; @@ -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); } diff --git a/ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java b/ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java index 5d991cdefa..6a7b517a31 100644 --- a/ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java +++ b/ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java @@ -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; @@ -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(); diff --git a/ms2/src/org/labkey/ms2/protein/FastaReloaderJob.java b/ms2/src/org/labkey/ms2/protein/FastaReloaderJob.java index f10d651dc7..ab6da997d1 100644 --- a/ms2/src/org/labkey/ms2/protein/FastaReloaderJob.java +++ b/ms2/src/org/labkey/ms2/protein/FastaReloaderJob.java @@ -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; @@ -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