From 01596a3eb24ac2eb68d05d6c2ee8d75a83f14d50 Mon Sep 17 00:00:00 2001
From: Kelvin Sarink <k.sarink@uni-muenster.de>
Date: Tue, 10 Jan 2023 16:16:23 +0100
Subject: [PATCH] allow setting path to where spm is mounted

---
 .../java/de/wwu/trap/SpmLauncher/App.java     | 20 +------------------
 .../de/wwu/trap/SpmLauncher/OSHandler.java    | 19 +++++++++++++-----
 2 files changed, 15 insertions(+), 24 deletions(-)

diff --git a/src/main/java/de/wwu/trap/SpmLauncher/App.java b/src/main/java/de/wwu/trap/SpmLauncher/App.java
index d08fc96..98b78dc 100644
--- a/src/main/java/de/wwu/trap/SpmLauncher/App.java
+++ b/src/main/java/de/wwu/trap/SpmLauncher/App.java
@@ -43,14 +43,10 @@ public static String getManagedSoftwareDir() {
 	 * the tmp-mount script!
 	 */
 	public static String getMountDir() {
-		if (App.mountDir != null)
-			return App.mountDir;
-		else
-			return App.mountDirDefault;
+		return App.mountDir;
 	}
 
 	private static String mountDir = null;
-	private static final String mountDirDefault = "/tmp/SPMLauncher";
 
 	/**
 	 * The mount script which can be called with sudo without having to enter a
@@ -111,8 +107,6 @@ public static void main(String[] args) {
 		Option optionMountdir = new Option("md", "mount-dir", true,
 				"Path to the directory where the temporary spm dirs are mounted");
 		options.addOption(optionMountdir);
-		Option optionMountscript = new Option("ms", "mount-script", true, "Path to the mount script tmp-mount");
-		options.addOption(optionMountscript);
 
 		// parsing
 		CommandLineParser parser = new DefaultParser();
@@ -134,18 +128,6 @@ public static void main(String[] args) {
 		 */
 		App.managedSoftwareDir = line.getOptionValue(optionMansofdir);
 		App.mountDir = line.getOptionValue(optionMountdir);
-		App.mountScript = line.getOptionValue(optionMountscript);
-		
-		/*
-		 * Create mount dir with correct permissions for multiuser environments
-		 */
-		File mountDir = new File(App.getMountDir());
-		if (!mountDir.exists()) {
-			mountDir.mkdirs();
-			mountDir.setReadable(true, false);
-			mountDir.setWritable(true, false);
-			mountDir.setExecutable(true, false);
-		}
 
 		if (line != null && line.hasOption(optionNc)) {
 			try {
diff --git a/src/main/java/de/wwu/trap/SpmLauncher/OSHandler.java b/src/main/java/de/wwu/trap/SpmLauncher/OSHandler.java
index 0c033b0..85cfa4f 100644
--- a/src/main/java/de/wwu/trap/SpmLauncher/OSHandler.java
+++ b/src/main/java/de/wwu/trap/SpmLauncher/OSHandler.java
@@ -251,7 +251,13 @@ public static void buildLaunchCmdStartAndWait(File matlabDir, File spmDir, List<
 		System.out.println(matlabDir.getAbsolutePath());
 		System.out.println("Starting " + spmDir.getName());
 
-		HashMap<String, String> toolboxBinds = generateToolboxBinds(spmDir, activatedToolboxes);
+		String tmpSpmDirStr = App.getMountDir();
+		File tmpSpmDir = spmDir;
+		if (tmpSpmDirStr != null)
+			tmpSpmDir = new File(tmpSpmDirStr);
+
+
+		HashMap<String, String> toolboxBinds = generateToolboxBinds(tmpSpmDir, activatedToolboxes);
 		LinkedList<String> toolboxBindParameters = generateToolboxBindsParameters(toolboxBinds);
 
 		LinkedList<String> launchCommand = new LinkedList<>();
@@ -265,13 +271,16 @@ public static void buildLaunchCmdStartAndWait(File matlabDir, File spmDir, List<
 		launchCommand.add("--dev-bind");
 		launchCommand.add("/dev");
 		launchCommand.add("/dev");
-//		launchCommand.add("--bind");
-//		launchCommand.add(spmDir.getAbsolutePath());
-//		launchCommand.add(tmpSpmDir.getAbsolutePath());
+		if (tmpSpmDir != spmDir) {
+			launchCommand.add("--bind");
+			launchCommand.add(spmDir.getAbsolutePath());
+			launchCommand.add(tmpSpmDir.getAbsolutePath());
+		}
 		launchCommand.addAll(toolboxBindParameters);
 		launchCommand.add(matlabDir.getAbsolutePath() + "/bin/matlab"); // absolute path to matlab binary
 		launchCommand.add("-r");
-		String matlabCommands = generateMatlabPathCommand(spmDir, activatedToolboxes, toolboxBinds) + "cd('/spm-data');"
+		String matlabCommands = generateMatlabPathCommand(tmpSpmDir, activatedToolboxes, toolboxBinds)
+				+ "cd('/spm-data');"
 				+ "spm fmri;"
 //				+ "quit"
 		;