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Merged
XingY merged 3 commits into from
Sep 20, 2025
Merged

Consolidate more XML parsing, FileLike usages #929

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09a1f75
Arbitrary file access during archive extraction ("Zip Slip")
XingY Sep 18, 2025
332d21f
XML parsing
XingY Sep 18, 2025
932c507
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XingY Sep 20, 2025
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15 changes: 9 additions & 6 deletions flow/enginesrc/org/labkey/flow/Main.java
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@
import org.labkey.flow.persist.AnalysisSerializer;
import org.labkey.flow.persist.AttributeSet;
import org.labkey.flow.persist.ObjectType;
import org.labkey.vfs.FileLike;
import org.w3c.dom.Document;

import javax.xml.transform.OutputKeys;
Expand All @@ -51,6 +52,7 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintStream;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Collection;
import java.util.EnumSet;
Expand Down Expand Up @@ -383,7 +385,7 @@ private static ExternalAnalysis readTsvAnalysisResults(File analysisResultsFile,
if (analysisResultsFile.getName().endsWith(".zip"))
{
// NOTE: Duplicated code in AnalysisScriptController
File statisticsFile;
FileLike statisticsFile;
java.util.zip.ZipFile zipFile;
try
{
Expand All @@ -409,12 +411,13 @@ private static ExternalAnalysis readTsvAnalysisResults(File analysisResultsFile,
// UNDONE: instead of unzipping into temp dir, make zip VirtualFile impl readable.
try
{
File tmpDir = FileUtil.createTempDirectory("flow").toFile();
tmpDir.deleteOnExit();
FileLike tmpDirFileLike = FileUtil.createTempDirectoryFileLike("flow");
Path tmpDirFilePath = tmpDirFileLike.toNioPathForWrite();
tmpDirFilePath.toFile().deleteOnExit();

ZipUtil.unzipToDirectory(analysisResultsFile, tmpDir);
statisticsFile = new File(tmpDir, zipEntry.getName());
rootDir = new FileSystemFile(statisticsFile.getParentFile());
ZipUtil.unzipToDirectory(analysisResultsFile.toPath(), tmpDirFilePath);
statisticsFile = tmpDirFileLike.resolveChild(zipEntry.getName());
rootDir = new FileSystemFile(statisticsFile.getParent().toNioPathForRead());
}
catch (IOException ioe)
{
Expand Down
8 changes: 3 additions & 5 deletions flow/enginesrc/org/labkey/flow/analysis/model/CompensationMatrix.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
import org.labkey.api.util.DateUtil;
import org.labkey.api.util.JunitUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.XmlBeansUtil;
import org.labkey.flow.analysis.data.NumberArray;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
Expand All @@ -32,7 +33,6 @@

import javax.xml.namespace.QName;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
Expand Down Expand Up @@ -131,9 +131,7 @@ public CompensationMatrix(InputStream is) throws Exception
public CompensationMatrix(String name, String str) throws Exception
{
this(name);
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
dbf.setFeature(Constants.SAX_FEATURE_PREFIX + Constants.NAMESPACES_FEATURE, true);
DocumentBuilder db = dbf.newDocumentBuilder();
DocumentBuilder db = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder();
try (var rdr = new StringReader(str))
{
Document doc = db.parse(new InputSource(rdr));
Expand Down Expand Up @@ -556,7 +554,7 @@ public Document toXML()
Document doc;
try
{
doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
doc = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder().newDocument();
}
catch (ParserConfigurationException e)
{
Expand Down
16 changes: 9 additions & 7 deletions flow/enginesrc/org/labkey/flow/persist/AnalysisSerializer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@
import org.labkey.flow.analysis.web.GraphSpec;
import org.labkey.flow.analysis.web.StatisticSpec;
import org.labkey.flow.analysis.web.SubsetSpec;
import org.labkey.vfs.FileLike;

import java.io.File;
import java.io.IOException;
Expand Down Expand Up @@ -253,7 +254,7 @@ public void error(String msg, Throwable t)
}
}

public static File extractArchive(File file, File tempDir)
public static File extractArchive(File file, FileLike tempDir)
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Copilot AI Sep 19, 2025

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The method signature is inconsistent - it accepts a File parameter but returns a File while using FileLike for tempDir. Consider updating the return type to FileLike or the input parameter to FileLike for API consistency.

Copilot uses AI. Check for mistakes.
throws IOException
{
File statisticsFile = null;
Expand All @@ -271,13 +272,13 @@ else if (file.getName().endsWith(".zip"))

ZipFile zipFile = new ZipFile(file);

File importDir;
FileLike importDir;
String zipBaseName = FileUtil.getBaseName(file);
ZipEntry zipEntry = zipFile.getEntry(AnalysisSerializer.STATISTICS_FILENAME);
if (zipEntry != null)
{
// Create extra directory under tempDir to extract into.
importDir = new File(tempDir, zipBaseName);
importDir = tempDir.resolveChild(zipBaseName);
}
else
{
Expand All @@ -288,12 +289,13 @@ else if (file.getName().endsWith(".zip"))
if (zipEntry == null)
throw new IOException("Couldn't find '" + AnalysisSerializer.STATISTICS_FILENAME + "' or '" + zipBaseName + "/" + AnalysisSerializer.STATISTICS_FILENAME + "' in the zip archive.");

//File importDir = File.createTempFile(zipBaseName, null, tempDir);
if (importDir.exists() && !FileUtil.deleteDir(importDir))
if (importDir.exists() && !FileUtil.deleteDir(importDir.toNioPathForWrite()))
throw new IOException("Could not delete the directory \"" + importDir + "\"");

ZipUtil.unzipToDirectory(file, importDir);
statisticsFile = new File(importDir, zipEntry.getName());
ZipUtil.unzipToDirectory(file.toPath(), importDir.toNioPathForWrite());
FileLike statisticsFileLike = importDir.resolveChild(zipEntry.getName());
if (statisticsFileLike.exists())
statisticsFile = statisticsFileLike.toNioPathForRead().toFile();
}

if (statisticsFile == null)
Expand Down
5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/WorkspaceData.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@
import org.labkey.flow.data.FlowProtocol;
import org.labkey.flow.persist.AnalysisSerializer;
import org.labkey.flow.persist.AttributeCache;
import org.labkey.vfs.FileLike;
import org.springframework.validation.Errors;

import java.io.File;
Expand Down Expand Up @@ -206,8 +207,8 @@ public void validate(User user, Container container, Errors errors) throws Excep
else if (path.endsWith(".zip"))
{
// Extract external analysis zip into pipeline
File tempDir = pipeRoot.resolvePath(PipelineService.UNZIP_DIR);
if (tempDir.exists() && !FileUtil.deleteDir(tempDir))
FileLike tempDir = pipeRoot.resolvePathToFileLike(PipelineService.UNZIP_DIR);
if (tempDir != null && tempDir.exists() && !FileUtil.deleteDir(tempDir.toNioPathForWrite()))
throw new IOException("Failed to delete temp directory");

String originalPath = path;
Expand Down
6 changes: 2 additions & 4 deletions protein/src/org/labkey/protein/ProteinServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@
import org.labkey.api.security.User;
import org.labkey.api.util.DeadlockPreventingException;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.XmlBeansUtil;
import org.labkey.api.util.logging.LogHelper;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.JspView;
Expand All @@ -60,7 +61,6 @@
import org.xml.sax.SAXException;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import java.io.BufferedReader;
import java.io.IOException;
Expand Down Expand Up @@ -314,9 +314,7 @@ public List<ProteinFeature> load(@NotNull String accession, @Nullable Object arg
}
}

DocumentBuilderFactory dbf =
DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
DocumentBuilder db = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder();
InputSource is = new InputSource();
is.setCharacterStream(new StringReader(response.toString()));

Expand Down