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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 #3891

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2 changes: 1 addition & 1 deletion api/src/org/labkey/api/assay/TsvDataHandler.java
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Expand Up @@ -156,7 +156,7 @@ public void exportFile(ExpData data, Path dataFile, User user, OutputStream out)
if (results.getSize() == 0)
return;

File tempFile = File.createTempFile(FileUtil.getBaseName(FileUtil.getFileName(dataFile)), ".tsv");
File tempFile = FileUtil.createTempFile(FileUtil.getBaseName(FileUtil.getFileName(dataFile)), ".tsv");

// Figure out the subset of columns to actually export in the TSV, see issue 36746
Set<FieldKey> ignored = Set.of(FieldKey.fromParts("Run"), FieldKey.fromParts("RowId"), FieldKey.fromParts("DataId"), FieldKey.fromParts("Folder"));
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3 changes: 2 additions & 1 deletion api/src/org/labkey/api/dataiterator/DiskCachingDataIterator.java
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Expand Up @@ -9,6 +9,7 @@
import org.junit.Test;
import org.labkey.api.arrays.IntegerArray;
import org.labkey.api.query.BatchValidationException;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.GUID;
import org.labkey.api.util.UnexpectedException;

Expand Down Expand Up @@ -105,7 +106,7 @@ private void writeToDisk()
{
try
{
_tempFile = File.createTempFile("buffer", "dat");
_tempFile = FileUtil.createTempFile("buffer", "dat");
_tempFile.deleteOnExit();
_randomAccessFile = new RandomAccessFile(_tempFile, "rw");
_buffer = _randomAccessFile.getChannel().map(FileChannel.MapMode.READ_WRITE, 0, 128 * 1024);
Expand Down
2 changes: 1 addition & 1 deletion api/src/org/labkey/api/module/ModuleDependencySorter.java
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Expand Up @@ -146,7 +146,7 @@ private void graphModuleDependencies(List<Pair<Module, Set<String>>> dependencie
{
File dir = FileUtil.getTempDirectory();
String dot = buildDigraph(dependencies);
File svgFile = File.createTempFile("modules", ".svg", dir);
File svgFile = FileUtil.createTempFile("modules", ".svg", dir);
DotRunner runner = new DotRunner(dir, dot);
runner.addSvgOutput(svgFile);
runner.execute();
Expand Down
3 changes: 2 additions & 1 deletion api/src/org/labkey/api/query/AbstractQueryImportAction.java
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Expand Up @@ -53,6 +53,7 @@
import org.labkey.api.security.permissions.UpdatePermission;
import org.labkey.api.util.CPUTimer;
import org.labkey.api.util.FileStream;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.NetworkDrive;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Pair;
Expand Down Expand Up @@ -470,7 +471,7 @@ else if (getViewContext().getRequest() instanceof MultipartHttpServletRequest)
hasPostData = true;
originalName = multipartfile.getOriginalFilename();
// can't read the multipart file twice so create temp file (12800)
dataFile = File.createTempFile("~upload", multipartfile.getOriginalFilename());
dataFile = FileUtil.createTempFile("~upload", multipartfile.getOriginalFilename());
PipeRoot root = PipelineService.get().findPipelineRoot(getContainer());
if (null != root && (Boolean.parseBoolean(saveToPipeline) || _useAsync))
{
Expand Down
3 changes: 2 additions & 1 deletion api/src/org/labkey/api/reader/FastaDataLoader.java
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Expand Up @@ -20,6 +20,7 @@
import org.labkey.api.data.Container;
import org.labkey.api.iterator.CloseableIterator;
import org.labkey.api.util.FileType;
import org.labkey.api.util.FileUtil;

import java.io.File;
import java.io.FileOutputStream;
Expand Down Expand Up @@ -57,7 +58,7 @@ public DataLoader createLoader(File file, boolean hasColumnHeaders, Container mv
@NotNull @Override
public DataLoader createLoader(InputStream is, boolean hasColumnHeaders, Container mvIndicatorContainer) throws IOException
{
File f = File.createTempFile("import", ".fasta");
File f = FileUtil.createTempFile("import", ".fasta");
f.deleteOnExit();
IOUtils.copy(is, new FileOutputStream(f));

Expand Down
2 changes: 1 addition & 1 deletion api/src/org/labkey/api/reader/TabLoader.java
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Expand Up @@ -744,7 +744,7 @@ public static class TabLoaderTestCase extends Assert

private File _createTempFile(String data, String ext) throws IOException
{
File f = File.createTempFile("junit", ext);
File f = FileUtil.createTempFile("junit", ext);
f.deleteOnExit();

try (Writer w = PrintWriters.getPrintWriter(f))
Expand Down
2 changes: 1 addition & 1 deletion api/src/org/labkey/api/reports/report/RReportJob.java
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Expand Up @@ -316,7 +316,7 @@ protected void processOutputs(RReport report, List<ParamReplacement> outputSubst
// report.log == getLogFile(), copy it and update the path (this is the RReportJob case)
if (LOG_FILE_NAME.equalsIgnoreCase(getJob().getLogFile().getName()))
{
newFile = File.createTempFile(LOG_FILE_PREFIX, ".log", parentDir);
newFile = FileUtil.createTempFile(LOG_FILE_PREFIX, ".log", parentDir);
getJob().setLogFile(newFile);
FileUtils.copyFile(file, newFile);
}
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5 changes: 3 additions & 2 deletions api/src/org/labkey/api/reports/report/r/view/ConsoleOutput.java
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Expand Up @@ -20,6 +20,7 @@
import org.labkey.api.reports.report.RReport;
import org.labkey.api.reports.report.ScriptOutput;
import org.labkey.api.reports.report.r.AbstractParamReplacement;
import org.labkey.api.util.FileUtil;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;

Expand Down Expand Up @@ -50,9 +51,9 @@ protected File getSubstitution(File directory) throws Exception
{
File file;
if (directory != null)
file = File.createTempFile(RReport.FILE_PREFIX, "Result.txt", directory);
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.txt", directory);
else
file = File.createTempFile(RReport.FILE_PREFIX, "Result.txt");
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.txt");

addFile(file);
return file;
Expand Down
5 changes: 3 additions & 2 deletions api/src/org/labkey/api/reports/report/r/view/HtmlOutput.java
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Expand Up @@ -20,6 +20,7 @@
import org.labkey.api.reports.report.ScriptOutput;
import org.labkey.api.reports.report.r.AbstractParamReplacement;
import org.labkey.api.reports.report.r.ParamReplacement;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;
Expand Down Expand Up @@ -50,9 +51,9 @@ protected File getSubstitution(File directory) throws Exception
{
File file;
if (directory != null)
file = File.createTempFile(RReport.FILE_PREFIX, "Result.html", directory);
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.html", directory);
else
file = File.createTempFile(RReport.FILE_PREFIX, "Result.html");
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.html");

addFile(file);
return file;
Expand Down
5 changes: 3 additions & 2 deletions api/src/org/labkey/api/reports/report/r/view/ImageOutput.java
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Expand Up @@ -26,6 +26,7 @@
import org.labkey.api.reports.report.r.AbstractParamReplacement;
import org.labkey.api.reports.report.r.ParamReplacement;
import org.labkey.api.thumbnail.Thumbnail;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.GUID;
import org.labkey.api.util.ImageUtil;
import org.labkey.api.util.PageFlowUtil;
Expand Down Expand Up @@ -66,9 +67,9 @@ protected File getSubstitution(File directory) throws Exception
{
File file;
if (directory != null)
file = File.createTempFile(RReport.FILE_PREFIX, "Result." + getExtension(), directory);
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result." + getExtension(), directory);
else
file = File.createTempFile(RReport.FILE_PREFIX, "Result." + getExtension());
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result." + getExtension());

addFile(file);
return file;
Expand Down
5 changes: 3 additions & 2 deletions api/src/org/labkey/api/reports/report/r/view/JsonOutput.java
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Expand Up @@ -20,6 +20,7 @@
import org.labkey.api.reports.report.ScriptOutput;
import org.labkey.api.reports.report.r.AbstractParamReplacement;
import org.labkey.api.reports.report.r.ParamReplacement;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;
Expand All @@ -45,9 +46,9 @@ protected File getSubstitution(File directory) throws Exception
{
File file;
if (directory != null)
file = File.createTempFile(RReport.FILE_PREFIX, "Result.json", directory);
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.json", directory);
else
file = File.createTempFile(RReport.FILE_PREFIX, "Result.json");
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.json");

addFile(file);
return file;
Expand Down
5 changes: 3 additions & 2 deletions api/src/org/labkey/api/reports/report/r/view/TextOutput.java
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Expand Up @@ -20,6 +20,7 @@
import org.labkey.api.reports.report.ScriptOutput;
import org.labkey.api.reports.report.r.AbstractParamReplacement;
import org.labkey.api.reports.report.r.ParamReplacement;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;
Expand All @@ -45,9 +46,9 @@ protected File getSubstitution(File directory) throws Exception
{
File file;
if (directory != null)
file = File.createTempFile(RReport.FILE_PREFIX, "Result.txt", directory);
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.txt", directory);
else
file = File.createTempFile(RReport.FILE_PREFIX, "Result.txt");
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.txt");

addFile(file);
return file;
Expand Down
5 changes: 3 additions & 2 deletions api/src/org/labkey/api/reports/report/r/view/TsvOutput.java
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Expand Up @@ -23,6 +23,7 @@
import org.labkey.api.reports.report.ScriptOutput;
import org.labkey.api.reports.report.r.AbstractParamReplacement;
import org.labkey.api.reports.report.r.ParamReplacement;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;
Expand Down Expand Up @@ -52,9 +53,9 @@ protected File getSubstitution(File directory) throws Exception
{
File file;
if (directory != null)
file = File.createTempFile(RReport.FILE_PREFIX, "Result.tsv", directory);
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.tsv", directory);
else
file = File.createTempFile(RReport.FILE_PREFIX, "Result.tsv");
file = FileUtil.createTempFile(RReport.FILE_PREFIX, "Result.tsv");

addFile(file);
return file;
Expand Down
20 changes: 13 additions & 7 deletions api/src/org/labkey/api/util/FileUtil.java
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Expand Up @@ -1170,7 +1170,7 @@ else if (!".".equals(file.getName()))
return new File(resolveFile(parent), file.getName());
}

public static Path createTempDirectory(String prefix) throws IOException
public static Path createTempDirectory(@Nullable String prefix) throws IOException
{
return Files.createTempDirectory(prefix);
}
Expand All @@ -1184,7 +1184,7 @@ public static File getTempDirectory()
{
try
{
File temp = File.createTempFile("deleteme", null);
File temp = createTempFile("deleteme", null);
_tempDir = temp.getParentFile();
temp.delete();
}
Expand All @@ -1197,18 +1197,24 @@ public static File getTempDirectory()
return _tempDir;
}

// Use this instead of File.createTempFile() (see Issue #46794)
public static File createTempFile(@Nullable String prefix, @Nullable String suffix, File directory) throws IOException
{
return Files.createTempFile(directory.toPath(), prefix, suffix).toFile();
}

public static File createTempFile(String prefix, String suffix) throws IOException
// Use this instead of File.createTempFile() (see Issue #46794)
public static File createTempFile(@Nullable String prefix, @Nullable String suffix) throws IOException
{
return createTempFile(prefix, suffix, false);
}

public static File createTempFile(String prefix, String suffix, boolean threadLocal) throws IOException
public static File createTempFile(@Nullable String prefix, @Nullable String suffix, boolean threadLocal) throws IOException
{
var ret = File.createTempFile(prefix, suffix);
var path = Files.createTempFile(prefix, suffix);
if (threadLocal)
tempPaths.get().add(ret.toPath());
return ret;
tempPaths.get().add(path);
return path.toFile();
}

public static void deleteTempFile(File f)
Expand Down
4 changes: 2 additions & 2 deletions assay/src/org/labkey/assay/AssayIntegrationTestCase.jsp
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Expand Up @@ -215,7 +215,7 @@
final var materialName = material.getName();

// create a file in the pipeline root to import
var file = File.createTempFile(getClass().getSimpleName(), ".tsv", pipeRoot.getRootPath());
var file = FileUtil.createTempFile(getClass().getSimpleName(), ".tsv", pipeRoot.getRootPath());
Files.writeString(file.toPath(), "SampleLookup\n" + materialName + "\n", Charsets.UTF_8);

// import the file
Expand Down Expand Up @@ -316,7 +316,7 @@
final var materialName = material.getName();

// create a file in the pipeline root to import
var file = File.createTempFile(getClass().getSimpleName(), ".tsv", pipeRoot.getRootPath());
var file = FileUtil.createTempFile(getClass().getSimpleName(), ".tsv", pipeRoot.getRootPath());
Files.writeString(file.toPath(), "SampleLookup\n" + materialName + "\n", Charsets.UTF_8);

var firstData = ExperimentService.get().createData(c, UPLOADED_FILE, file.getName());
Expand Down
3 changes: 2 additions & 1 deletion core/src/org/labkey/core/admin/ValidateDomainsPipelineJob.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.util.DateUtil;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.URLHelper;
import org.labkey.api.util.UnexpectedException;
import org.labkey.api.view.ViewBackgroundInfo;
Expand All @@ -42,7 +43,7 @@ public ValidateDomainsPipelineJob(ViewBackgroundInfo info, PipeRoot root)

try
{
File logFile = File.createTempFile("validateDomains", ".log", root.ensureSystemDirectory());
File logFile = FileUtil.createTempFile("validateDomains", ".log", root.ensureSystemDirectory());
setLogFile(logFile);
}
catch (IOException e)
Expand Down
2 changes: 1 addition & 1 deletion core/src/org/labkey/core/portal/UtilController.java
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Expand Up @@ -81,7 +81,7 @@ public ModelAndView getView(DotForm form, BindException errors) throws Exception
File svgFile = null;
try
{
svgFile = File.createTempFile("groups", ".svg", dir);
svgFile = FileUtil.createTempFile("groups", ".svg", dir);
svgFile.deleteOnExit();
DotRunner runner = new DotRunner(dir, dot);
runner.addSvgOutput(svgFile);
Expand Down
2 changes: 1 addition & 1 deletion core/src/org/labkey/core/security/SecurityController.java
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Expand Up @@ -1894,7 +1894,7 @@ public ApiResponse execute(GroupDiagramForm form, BindException errors) throws E

try
{
svgFile = File.createTempFile("groups", ".svg", dir);
svgFile = FileUtil.createTempFile("groups", ".svg", dir);
svgFile.deleteOnExit();
DotRunner runner = new DotRunner(dir, dot);
runner.addSvgOutput(svgFile);
Expand Down
2 changes: 1 addition & 1 deletion experiment/src/org/labkey/experiment/ExperimentRunGraph.java
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Expand Up @@ -81,7 +81,7 @@ public synchronized static File getBaseDirectory() throws IOException
{
if (baseDirectory == null)
{
File tempFile = File.createTempFile("Exp", ".dir");
File tempFile = FileUtil.createTempFile("Exp", ".dir");
tempFile.delete();
File tempDir = new File(tempFile.getParentFile(), "ExperimentRunGraphs");
if (tempDir.exists())
Expand Down
2 changes: 1 addition & 1 deletion experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
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Expand Up @@ -2319,7 +2319,7 @@ public Object execute(ParseForm form, BindException errors) throws Exception
File tempFile = null;
try
{
tempFile = File.createTempFile("parse", formFile.getOriginalFilename());
tempFile = FileUtil.createTempFile("parse", formFile.getOriginalFilename());
FileUtil.copyData(formFile.getInputStream(), tempFile);
streamToJSON(tempFile, form.getFormat(), form.getMaxRows(), formFile.getOriginalFilename());
}
Expand Down
5 changes: 3 additions & 2 deletions experiment/src/org/labkey/experiment/controllers/property/PropertyController.java
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Expand Up @@ -87,6 +87,7 @@
import org.labkey.api.security.permissions.AdminPermission;
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.util.ExceptionUtil;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.JsonUtil;
import org.labkey.api.util.JunitUtil;
import org.labkey.api.util.Pair;
Expand Down Expand Up @@ -1233,7 +1234,7 @@ protected File getTargetFile(String filename) throws IOException
// File.createTempFile() requires that the prefix be at least three characters long
prefix = "prefix-" + prefix;
}
File tempFile = File.createTempFile(prefix, suffix);
File tempFile = FileUtil.createTempFile(prefix, suffix);
tempFile.deleteOnExit();
return tempFile;
}
Expand Down Expand Up @@ -1339,7 +1340,7 @@ private String getDataFromFile(Writer writer) throws IOException
String suffix = filename.substring(dotIndex).toLowerCase();
String prefix = filename.substring(0, dotIndex);

File tempFile = File.createTempFile(prefix, suffix);
File tempFile = FileUtil.createTempFile(prefix, suffix);
tempFile.deleteOnExit();

try
Expand Down
2 changes: 1 addition & 1 deletion experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java
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Expand Up @@ -172,7 +172,7 @@ public MoveRunsXarSource(String xml, Path root, MoveRunsPipelineJob job) throws
{
try
{
_logFileDir = File.createTempFile("xarupload", "");
_logFileDir = FileUtil.createTempFile("xarupload", "");
}
catch (IOException e)
{
Expand Down
2 changes: 1 addition & 1 deletion internal/src/org/labkey/api/util/FTPUtil.java
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Expand Up @@ -80,7 +80,7 @@ public static File downloadFile(String user, String password, String url, String
{
ftp = getConnectedClient(user, password, url, directory);
ftp.setFileType(FTPClient.BINARY_FILE_TYPE);
File outputFile = File.createTempFile(filename, null);
File outputFile = FileUtil.createTempFile(filename, null);
fos = new FileOutputStream(outputFile);
ftp.retrieveFile(filename, fos);
return outputFile;
Expand Down
2 changes: 1 addition & 1 deletion pipeline/src/org/labkey/pipeline/analysis/AnalysisController.java
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Expand Up @@ -710,7 +710,7 @@ private DOM.Renderable generateGraph(@Nullable TaskPipeline pipeline)
{
File dir = FileUtil.getTempDirectory();
String dot = buildDigraph(pipeline);
svgFile = File.createTempFile("pipeline", ".svg", dir);
svgFile = FileUtil.createTempFile("pipeline", ".svg", dir);
DotRunner runner = new DotRunner(dir, dot);
runner.addSvgOutput(svgFile);
runner.execute();
Expand Down
4 changes: 2 additions & 2 deletions pipeline/src/org/labkey/pipeline/api/WorkDirectoryRemote.java
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Expand Up @@ -129,7 +129,7 @@ public WorkDirectory createWorkDirectory(String jobId, FileAnalysisJobSupport su
}
else
{
dirParent = File.createTempFile(jobId, "", dirParent);
dirParent = FileUtil.createTempFile(jobId, "", dirParent);
tempDirBase = dirParent;
}

Expand Down Expand Up @@ -164,7 +164,7 @@ else if (name.length() < 3)
}
else
{
tempDir = File.createTempFile(name, WORK_DIR_SUFFIX, dirParent);
tempDir = FileUtil.createTempFile(name, WORK_DIR_SUFFIX, dirParent);
}

if (_allowReuseExistingTempDirectory && tempDir.exists())
Expand Down
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