Debug cellranger/symlinks

bbimber · bbimber · commit d75cf73f468f · 2025-11-26T16:57:26.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java
@@ -52,6 +52,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -643,8 +644,13 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException
             {
                 try
                 {
-                    exe = Files.readSymbolicLink(exe.toPath()).resolve(exe.getParentFile().toPath()).toFile();
-                    logger.debug("cellranger symlink target: " + exe.getPath());
+                    Path exePath = Files.readSymbolicLink(exe.toPath());
+                    logger.debug("cellranger symlink target: " + exePath.toString());
+                    logger.debug("cellranger symlink absolute path: " + exePath.toAbsolutePath());
+                    logger.debug("cellranger symlink realpath path: " + exePath.toRealPath());
+
+                    exe = exePath.toFile();
+                    logger.debug("cellranger resolved symlink target: " + exe.getPath());
                 }
                 catch (IOException e)
                 {

Original file line number	Diff line number	Diff line change
`@@ -52,6 +52,7 @@`
`52`	`52`	`import java.io.File;`
`53`	`53`	`import java.io.IOException;`
`54`	`54`	`import java.nio.file.Files;`
	`55`	`+import java.nio.file.Path;`
`55`	`56`	`import java.util.ArrayList;`
`56`	`57`	`import java.util.Arrays;`
`57`	`58`	`import java.util.Collection;`
`@@ -643,8 +644,13 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException`
`643`	`644`	`{`
`644`	`645`	`try`
`645`	`646`	`{`
`646`		`- exe = Files.readSymbolicLink(exe.toPath()).resolve(exe.getParentFile().toPath()).toFile();`
`647`		`- logger.debug("cellranger symlink target: " + exe.getPath());`
	`647`	`+ Path exePath = Files.readSymbolicLink(exe.toPath());`
	`648`	`+ logger.debug("cellranger symlink target: " + exePath.toString());`
	`649`	`+ logger.debug("cellranger symlink absolute path: " + exePath.toAbsolutePath());`
	`650`	`+ logger.debug("cellranger symlink realpath path: " + exePath.toRealPath());`
	`651`	`+`
	`652`	`+ exe = exePath.toFile();`
	`653`	`+ logger.debug("cellranger resolved symlink target: " + exe.getPath());`
`648`	`654`	`}`
`649`	`655`	`catch (IOException e)`
`650`	`656`	`{`