better handle of makeflow path checking

src/jflow/component.py

@@ -16,12 +16,14 @@
 #
 
 import os
+import sys
 import inspect
 import tempfile
 
 from jflow.workflows_manager import WorkflowsManager
 from jflow.config_reader import JFlowConfigReader
 from jflow.dataset import ArrayList
+from jflow.utils import which
 
 from weaver.util import parse_string_list
 
@@ -131,7 +133,16 @@ class Component(object):
         return self.config_reader.get_resource(resource)
     
     def get_exec_path(self, software):
-        return self.config_reader.get_exec(software)
+        exec_path = self.config_reader.get_exec(software)
+        if exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)):
+            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)
+        elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)):
+            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)
+        if exec_path is None: exec_path = software
+        if which(exec_path) == None:
+            sys.stderr.write("Error: '" + software + "' path connot be retrieved either in the PATH and in the application.properties file!\n")
+            sys.exit(1)
+        return exec_path
     
     def get_nameid(self):
         return self.__class__.__name__ + "." + self.prefix

src/jflow/config_reader.py

@@ -20,7 +20,9 @@ import sys
 import inspect
 
 from ConfigParser import ConfigParser, NoOptionError
-    
+
+from jflow.utils import which
+
 
 class JFlowConfigReader(object):
     """
@@ -34,25 +36,6 @@ class JFlowConfigReader(object):
         self.reader = ConfigParser()
         self.reader.read(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), self.CONFIG_FILE_PATH))
 
-    def __which(self, program):
-        """
-        Return if the asked program exist in the user path
-          @param options : the options asked by the user
-        """
-        import os
-        def is_exe(fpath):
-            return os.path.exists(fpath) and os.access(fpath, os.X_OK)
-        fpath, fname = os.path.split(program)
-        if fpath:
-            if is_exe(program):
-                return program
-        else:
-            for path in os.environ["PATH"].split(os.pathsep):
-                exe_file = os.path.join(path, program)
-                if is_exe(exe_file):
-                    return exe_file
-        return None
-
     def get_tmp_directory(self):
         return self.reader.get("storage", "tmp_directory")
         
@@ -61,18 +44,9 @@ class JFlowConfigReader(object):
     
     def get_exec(self, software):
         try:
-            exec_path = self.reader.get("softwares", software)
+            return self.reader.get("softwares", software)
         except NoOptionError, e:
-            exec_path = None
-        if exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)):
-            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)
-        elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)):
-            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)
-        if exec_path is None: exec_path = software
-        if self.__which(exec_path) == None:
-            sys.stderr.write("Error: '" + software + "' path connot be retrieved either in the PATH and in the application.properties file!\n")
-            sys.exit(1)
-        return exec_path
+            return None
 
     def get_resource(self, resource):
         return self.reader.get("resources", resource)
@@ -93,7 +67,7 @@ class JFlowConfigReader(object):
         except NoOptionError, e:
             exec_path = None
         if exec_path is None: exec_path = software
-        if self.__which(exec_path) == None:
+        if which(exec_path) == None:
             sys.stderr.write("Error: 'makeflow' path connot be retrieved either in the PATH and in the application.properties file!\n")
             sys.exit(1)
         return exec_path

src/jflow/utils.py

@@ -15,6 +15,25 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
+def which(program):
+    """
+    Return if the asked program exist in the user path
+      @param options : the options asked by the user
+    """
+    import os
+    def is_exe(fpath):
+        return os.path.exists(fpath) and os.access(fpath, os.X_OK)
+    fpath, fname = os.path.split(program)
+    if fpath:
+        if is_exe(program):
+            return program
+    else:
+        for path in os.environ["PATH"].split(os.pathsep):
+            exe_file = os.path.join(path, program)
+            if is_exe(exe_file):
+                return exe_file
+    return None
+
 def get_file_base (file):
     """
     Return the file base

src/jflow/workflow.py

@@ -179,7 +179,16 @@ class Workflow(threading.Thread):
         return [parameters, parameters_order]
     
     def get_exec_path(self, software):
-        return self.jflow_config_reader.get_exec(software)
+        exec_path = self.jflow_config_reader.get_exec(software)
+        if exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)):
+            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)
+        elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)):
+            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)
+        if exec_path is None: exec_path = software
+        if utils.which(exec_path) == None:
+            sys.stderr.write("Error: '" + software + "' path connot be retrieved either in the PATH and in the application.properties file!\n")
+            sys.exit(1)
+        return exec_path
     
     def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
         # first build and check if this component is OK