diff smart_toolShed/SMART/Java/PythonProgramFinder.java @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/PythonProgramFinder.java	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,92 @@
+/**
+ *
+ * Copyright INRA-URGI 2009-2010
+ * 
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ * 
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ * 
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+import java.io.*;
+import java.util.*;
+
+public class PythonProgramFinder {
+
+  String             dirName;
+  Vector < Program > programs;
+
+  public PythonProgramFinder(String dirName) {
+    this.dirName = dirName;  
+  }
+
+  public String findPrograms() {
+    java.io.File directory = new java.io.File(this.dirName);
+    String[] files         = directory.list(new FilenameFilter() {public boolean accept(java.io.File dir, String name) {return ((! name.startsWith(".")) && (! name.startsWith("test")) && ((new java.io.File(dir, name)).isFile()) && (name.endsWith(".py")) && (name.compareToIgnoreCase("__init__.py") != 0));}});
+    this.programs          = new Vector < Program > ();
+
+    for (int i = 0; i < files.length; i++) {
+      String[] commandList  = {Global.pythonCommand, "Python" + java.io.File.separator + files[i], "-h"};
+      String command = "";
+      for (int j = 0; j < commandList.length; j++) {
+        command += commandList[j] + " ";
+      }
+      ProcessBuilder pb = new ProcessBuilder(commandList);
+      pb = pb.redirectErrorStream(true);
+      Map<String, String> env = pb.environment();
+      env.put("PYTHONPATH", System.getProperty("user.dir") + java.io.File.separator + "Python");
+      env.put("SMARTPATH", System.getProperty("user.dir") + java.io.File.separator + "Python");
+      env.put("SMARTMYSQLPATH", Global.mysqlCommand);
+      env.put("SMARTRPATH", Global.rCommand);
+
+      PythonHelperReader helperReader = new PythonHelperReader(files[i]);
+      try {
+        final Process process = pb.start();
+        InputStream is        = process.getInputStream();
+        InputStreamReader isr = new InputStreamReader(is);
+        BufferedReader br     = new BufferedReader(isr);
+        helperReader.setReader(br);
+        helperReader.run();
+      }
+      catch (IOException e) {
+        final Writer result = new StringWriter();
+        final PrintWriter printWriter = new PrintWriter(result);
+        e.printStackTrace(printWriter);
+        return "Command '" + command + "' failed (I/O error)...\n" + result.toString();
+      }
+      String comments = helperReader.getMessage();
+      if (comments != null) return comments;
+      Program program = helperReader.getProgram();
+      if (("Personnal".compareToIgnoreCase(program.getSection()) != 0) && ("Personal".compareToIgnoreCase(program.getSection()) != 0)) {
+        this.programs.add(program);
+      }
+    }
+    return null;
+  }
+
+  public Vector <Program> getPrograms () {
+    return this.programs;
+  }
+}
+