From 785c4b02c06f4547fc8cc505f329aeb75e394cd8 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 12 Dec 2025 09:57:18 -0800
Subject: [PATCH] Do not relativize ExpData URIs when making the LSID unless
 under file root

---
 .../experiment/api/ExperimentServiceImpl.java   | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
index f3d51bf42b7..705e05c82d6 100644
--- a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
@@ -230,13 +230,13 @@
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.SubstitutionFormat;
 import org.labkey.api.util.TestContext;
+import org.labkey.api.util.URIUtil;
 import org.labkey.api.util.UnexpectedException;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspTemplate;
 import org.labkey.api.view.JspView;
-import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.UnauthorizedException;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.api.view.ViewContext;
@@ -244,7 +244,6 @@
 import org.labkey.experiment.FileLinkFileListener;
 import org.labkey.experiment.MissingFilesCheckInfo;
 import org.labkey.experiment.XarExportType;
-import org.labkey.experiment.XarExporter;
 import org.labkey.experiment.XarReader;
 import org.labkey.experiment.api.property.DomainPropertyManager;
 import org.labkey.experiment.controllers.exp.ExperimentController;
@@ -253,13 +252,11 @@
 import org.labkey.experiment.pipeline.ExperimentPipelineJob;
 import org.labkey.experiment.pipeline.MoveRunsPipelineJob;
 import org.labkey.experiment.xar.AutoFileLSIDReplacer;
-import org.labkey.experiment.xar.XarExportSelection;
 import org.labkey.vfs.FileLike;
 import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.dao.PessimisticLockingFailureException;
 
 import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.UncheckedIOException;
 import java.net.MalformedURLException;
@@ -778,7 +775,17 @@ public ExpDataImpl createData(URI uri, XarSource source) throws XarFormatExcepti
                 {
                     path = FileUtil.stringToPath(source.getXarContext().getContainer(),
                             source.getCanonicalDataFileURL(FileUtil.pathToString(path)));
-                    pathStr = FileUtil.relativizeUnix(source.getRootPath(), path, false);
+
+                    // Only convert to a relative path if this is a descendant of the root:
+                    path = path.normalize();
+                    if (URIUtil.isDescendant(source.getRootPath().toUri(), path.toUri()))
+                    {
+                        pathStr = FileUtil.relativizeUnix(source.getRootPath(), path, false);
+                    }
+                    else
+                    {
+                        pathStr = FileUtil.pathToString(path);
+                    }
                 }
                 catch (IOException e)
                 {