diff smart_toolShed/commons/core/checker/OldConfigChecker.py @ 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/commons/core/checker/OldConfigChecker.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,101 @@
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# 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 ConfigParser
+from ConfigParser import NoOptionError
+from commons.core.checker.IChecker import IChecker
+from commons.core.checker.ConfigException import ConfigException
+
+
+## A checker for a configuration file
+#
+#
+# A configuration file is formatted as follow:
+#
+# [section1]
+#
+# option_name1: option_value1
+# 
+# option_name2: option_value2
+#
+# option_name3: option_value3
+#
+# [section2]
+# 
+# ...
+#
+# 
+# This class performs 3 checkes on a configuration file: 
+#
+# (i) check if file exists
+#
+# (ii) check if section exists
+#
+# (iii) check if option exists
+#
+class ConfigChecker( IChecker ):
+    
+    ## Constructor A checker for configuration file.
+    #
+    # @param  sectionName name of section to check in configuration file
+    # @param  optionsDict dictionary with option(s) to check as keys and empty strings ("") as values
+    def __init__ (self, sectionName, optionsDict):
+        self._sectionName = sectionName
+        self._optionsDict = optionsDict
+        
+        
+    ## Perform 3 checks : file exists, sections exists, option exists
+    # 
+    # @param configFile configuration file to check
+    # @exception ConfigException with a list of messages
+    def check (self, configFile):
+        config = ConfigParser.ConfigParser()
+        msg = []
+        try:
+            config.readfp( open(configFile) )
+        except IOError, e:
+            msg.append("CONFIG FILE not found - " + e.message)
+            raise ConfigException("", msg) 
+
+        if not (config.has_section(self._sectionName)):
+            msg.append("[" + self._sectionName + "]" + " section not found - ")
+            raise ConfigException("", msg)
+         
+        isExceptionOccured = False        
+        for key in self._optionsDict.keys():
+            try:
+                self._optionsDict[key] = config.get(self._sectionName, key) 
+            except NoOptionError, e:
+                msg.append("[" + self._sectionName + "]" + " - " + e.message)
+                isExceptionOccured = True
+        
+        if (isExceptionOccured):
+            raise ConfigException("", msg)