[bot] Merge 25.11 to develop

experiment/src/org/labkey/experiment/DataURLRelativizer.java

@@ -22,6 +22,7 @@
 import org.labkey.api.security.User;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.view.ActionURL;
+import org.labkey.experiment.api.ExperimentServiceImpl;
 import org.labkey.experiment.controllers.exp.ExperimentController;
 
 import java.io.IOException;
@@ -75,21 +76,16 @@ public URLRewriter createURLRewriter()
                 @Override
                 public String rewriteURL(Path path, ExpData data, String roleName, ExpRun expRun, User user, String rootFilePath) throws ExperimentException
                 {
-                    try
-                    {
-                        if (path == null)
-                            return null;
+                    if (path == null)
+                        return null;
 
-                        if (expRun == null || expRun.getFilePathRoot() == null)
-                        {
-                            return FileUtil.pathToString(path);
-                        }
-                        return FileUtil.relativizeUnix(expRun.getFilePathRootPath(), path, false);
-                    }
-                    catch (IOException e)
+                    if (expRun == null || expRun.getFilePathRoot() == null)
                     {
-                        throw new ExperimentException(e);
+                        return FileUtil.pathToString(path);
                     }
+
+                    // NOTE: this will only write a relative path if the file is a direct descendant of the root.
+                    return ExperimentServiceImpl.get().generatePathStringRelativeToRootIfUnderRoot(path, expRun.getFilePathRootPath());
                 }
             };
         }

experiment/src/org/labkey/experiment/ExperimentModule.java

@@ -153,6 +153,7 @@
 import org.labkey.experiment.lineage.ExpLineageServiceImpl;
 import org.labkey.experiment.lineage.LineagePerfTest;
 import org.labkey.experiment.pipeline.ExperimentPipelineProvider;
+import org.labkey.experiment.pipeline.XarTestPipelineJob;
 import org.labkey.experiment.samples.DataClassFolderImporter;
 import org.labkey.experiment.samples.DataClassFolderWriter;
 import org.labkey.experiment.samples.SampleStatusFolderImporter;
@@ -1079,7 +1080,8 @@ public Collection<String> getSummary(Container c)
             SampleTypeServiceImpl.TestCase.class,
             StorageNameGenerator.TestCase.class,
             StorageProvisionerImpl.TestCase.class,
-            UniqueValueCounterTestCase.class
+            UniqueValueCounterTestCase.class,
+            XarTestPipelineJob.TestCase.class
         );
     }
 

experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java

@@ -768,33 +768,10 @@ public ExpDataImpl createData(URI uri, XarSource source) throws XarFormatExcepti
             String[] parts = pathStr.split("/");
             String name = FileUtil.decodeSpaces(parts[parts.length - 1]);
             Path path = FileUtil.getPath(source.getXarContext().getContainer(), uri);
-
             if (path != null)
             {
-                try
-                {
-                    path = FileUtil.stringToPath(source.getXarContext().getContainer(),
-                            source.getCanonicalDataFileURL(FileUtil.pathToString(path)));
-
-                    // 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)
-                {
-                    pathStr = FileUtil.pathToString(path);
-                }
-            }
-            else
-            {
-                pathStr = FileUtil.uriToString(uri);
+                path = FileUtil.stringToPath(source.getXarContext().getContainer(), source.getCanonicalDataFileURL(FileUtil.pathToString(path)));
+                pathStr = generatePathStringRelativeToRootIfUnderRoot(path, source.getRootPath());
             }
 
             Lsid.LsidBuilder lsid = new Lsid.LsidBuilder(LsidUtils.resolveLsidFromTemplate(AutoFileLSIDReplacer.AUTO_FILE_LSID_SUBSTITUTION, source.getXarContext(), "Data", new AutoFileLSIDReplacer(pathStr, source.getXarContext().getContainer(), source)));
@@ -816,6 +793,30 @@ public ExpDataImpl createData(URI uri, XarSource source) throws XarFormatExcepti
         return data;
     }
 
+    public String generatePathStringRelativeToRootIfUnderRoot(@NotNull Path path, @Nullable Path pipeRootPath)
+    {
+        String pathStr;
+        try
+        {
+            // Only convert to a relative path if this is a descendant of the root:
+            path = path.normalize();
+            if (pipeRootPath != null && URIUtil.isDescendant(pipeRootPath.toUri(), path.toUri()))
+            {
+                pathStr = FileUtil.relativizeUnix(pipeRootPath, path, false);
+            }
+            else
+            {
+                pathStr = FileUtil.pathToString(path);
+            }
+        }
+        catch (IOException e)
+        {
+            pathStr = FileUtil.pathToString(path);
+        }
+
+        return pathStr;
+    }
+
     @Override
     public ExpDataImpl createData(Container container, @NotNull DataType type)
     {