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Fixes for Windows failures after FileLike refactor #7190

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Merged
labkey-jeckels merged 1 commit into from
Nov 9, 2025
Merged

Fixes for Windows failures after FileLike refactor #7190

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1 change: 1 addition & 0 deletions api/src/org/labkey/api/exp/AbstractFileXarSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,7 @@ public boolean shouldIgnoreDataFiles()
@Override
public String canonicalizeDataFileURL(String dataFileURL)
{
dataFileURL = dataFileURL.replace("\\", "/");
Path xarDirectory = getRootPath();
URI uri = FileUtil.createUri(dataFileURL);
if (!uri.isAbsolute())
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45 changes: 22 additions & 23 deletions assay/src/org/labkey/assay/actions/ImportRunApiAction.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,17 +36,13 @@
import org.labkey.api.assay.AssayRunUploadContext;
import org.labkey.api.assay.AssayUrls;
import org.labkey.api.assay.DefaultAssayRunCreator;
import org.labkey.api.audit.AuditLogService;
import org.labkey.api.audit.TransactionAuditProvider;
import org.labkey.api.audit.provider.FileSystemAuditProvider;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.TSVMapWriter;
import org.labkey.api.dataiterator.MapDataIterator;
import org.labkey.api.exp.ExperimentException;
import org.labkey.api.exp.api.AssayJSONConverter;
import org.labkey.api.exp.api.DataType;
import org.labkey.api.exp.api.ExpData;
import org.labkey.api.exp.api.ExpExperiment;
import org.labkey.api.exp.api.ExpProtocol;
import org.labkey.api.exp.api.ExpRun;
Expand All @@ -66,15 +62,13 @@
import org.labkey.api.security.RequiresPermission;
import org.labkey.api.security.permissions.InsertPermission;
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.JsonUtil;
import org.labkey.api.util.NetworkDrive;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Pair;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.NotFoundException;
import org.labkey.api.view.UnauthorizedException;
import org.labkey.assay.FileBasedModuleDataHandler;
import org.labkey.vfs.FileLike;
import org.labkey.vfs.FileSystemLike;
import org.springframework.beans.MutablePropertyValues;
Expand All @@ -84,19 +78,16 @@
import org.springframework.web.multipart.MultipartFile;

import java.io.File;
import java.io.IOException;
import java.nio.file.InvalidPathException;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;

import static java.util.Collections.emptyMap;
import static org.labkey.api.assay.AssayDataCollector.PRIMARY_FILE;
import static org.labkey.api.assay.AssayFileWriter.createFile;
import static org.labkey.api.util.FileUtil.toFileForWrite;

@ActionNames("importRun")
@RequiresPermission(InsertPermission.class)
Expand Down Expand Up @@ -236,23 +227,31 @@ public ApiResponse execute(ImportRunApiForm form, BindException errors) throws E
}
else
{
// Resolve file under pipeline root
PipeRoot root = PipelineService.get().findPipelineRoot(getContainer());
if (root == null)
throw new NotFoundException("Pipeline root not configured");
try
{
// Resolve file under pipeline root
PipeRoot root = PipelineService.get().findPipelineRoot(getContainer());
if (root == null)
throw new NotFoundException("Pipeline root not configured");

if (!root.hasPermission(getContainer(), getUser(), ReadPermission.class))
throw new UnauthorizedException();
if (!root.hasPermission(getContainer(), getUser(), ReadPermission.class))
throw new UnauthorizedException();

// Attempt absolute path first, then relative path from pipeline root
File f = new File(runFilePath);
if (!root.isUnderRoot(f))
f = root.resolvePath(runFilePath);
// Attempt absolute path first, then relative path from pipeline root
File f = new File(runFilePath);
if (!root.isUnderRoot(f))
f = root.resolvePath(runFilePath);

if (!NetworkDrive.exists(f) || !root.isUnderRoot(f))
throw new NotFoundException("File not found: " + runFilePath);
if (!NetworkDrive.exists(f) || !root.isUnderRoot(f))
throw new NotFoundException("File not found: " + runFilePath);

file = f;
file = f;
}
catch (InvalidPathException e)
{
LOG.info("Invalid path: " + runFilePath, e);
throw new NotFoundException("File not found: " + runFilePath);
}
}
}

Expand Down