--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/checker/test/Test_ConfigChecker.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,569 @@
+from commons.core.checker.ConfigChecker import ConfigChecker 
+from commons.core.checker.ConfigChecker import ConfigRules
+from commons.core.checker.RepetException import RepetException
+import os
+import unittest
+
+class Test_ConfigChecker(unittest.TestCase):
+    
+    def setUp(self):
+        self._configFileName = "testConfigChecker.cfg"
+        self._iMock = MockConfig()
+     
+    def test_checkIfExistsConfigFile_file_exist(self):
+        f=open(self._configFileName, "w")
+        f.close()
+        
+        doesFileExists = True
+        iConfigRules = ConfigRules()
+        try:
+            iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+            iConfigChecker.checkIfExistsConfigFile()
+        except RepetException:
+            doesFileExists = False
+        os.remove(self._configFileName)        
+        self.assertTrue(doesFileExists)
+        
+    def test_checkIfExistsConfigFile_file_not_exist(self):
+        iConfigRules = ConfigRules()
+        expMsg ="CONFIG FILE not found - '%s'" %self._configFileName
+        doesFileExists = True
+        try:
+            iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)   
+            iConfigChecker.checkIfExistsConfigFile()     
+        except RepetException, re:
+            doesFileExists = False
+        self.assertFalse(doesFileExists)
+        self.assertEqual(expMsg, re.getMessage())
+        
+    def test_readConfigFile(self):
+        self._iMock.write_config(self._configFileName)
+        iConfigRules = ConfigRules()
+        expDictRawConfigValues = {"dir_name" : {"work_dir":"toto"},
+                                  "organism" : {"abbreviation":"T.aestivum",
+                                                "genus":"triticum",
+                                                "species":"aestivum",
+                                                "common_name":"wheat",
+                                                "comment":""},
+                                  'analysis1': {'description': '',
+                                                'gff_name': 'BLASTX.gff2',
+                                                'name': 'BLASTXWheat2',
+                                                'program': 'BLASTX2',
+                                                'programversion': '3.32',
+                                                'sourcename': 'dummyDesc_BLASTX2'}
+                                 }
+        isNoExceptionRaised = True
+        try: 
+            iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+            iConfig = iConfigChecker.readConfigFile()
+            iConfigChecker.setRawConfig(iConfig)
+            obsDictRawConfigValues = iConfigChecker._iRawConfig.dOptionsValues4Sections
+        except RepetException:
+            isNoExceptionRaised = False
+        os.remove(self._configFileName)
+        self.assertTrue(isNoExceptionRaised)
+        self.assertEquals(obsDictRawConfigValues, expDictRawConfigValues)
+        
+    def test_readConfigFile_section_define_twice(self):
+        self._iMock.write_case_section_define_twice(self._configFileName)
+        iConfigRules = ConfigRules()
+        expMsg = "Duplicate section exist in config file %s"  %self._configFileName
+        expDictRawConfigValues = {"dir_name": {"work_dir":"toto"},
+                                  "analysis1" : {"name": "BLASTXWheat2",
+                                                 "program" : "BLASTX2",
+                                                 "programversion" : "3.32",
+                                                 "sourcename" :"dummyDesc_BLASTX2",
+                                                 "description" : "",
+                                                 "gff_name" :"BLASTX.gff2"}
+                                 }
+        doesNoExceptionRaised = True
+        try:
+            iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+            iConfig = iConfigChecker.readConfigFile()
+            iConfigChecker.setRawConfig(iConfig)
+            obsDictRawConfigValues = iConfigChecker._iRawConfig.dOptionsValues4Sections
+        except RepetException, re:
+            doesNoExceptionRaised = False
+        os.remove(self._configFileName)
+#       self.assertFalse(doesNoExceptionRaised)
+#       self.assertEqual(expMsg, re.getMessage())
+#
+        self.assertTrue(doesNoExceptionRaised)
+        self.assertEquals(obsDictRawConfigValues, expDictRawConfigValues)
+
+    def test_readConfigFile_option_define_twice(self):
+        self._iMock.write_case_option_define_twice(self._configFileName)
+        iConfigRules = ConfigRules()
+        doesNoExceptionRaised = True
+        expDictRawConfigValues = {"dir_name": {"work_dir":"toto"},
+                                  "analysis1" : {"name": "BLASTXWheat",
+                                       "program" : "BLASTX2",
+                                       "programversion" : "3.3",
+                                       "sourcename" :"dummyDesc_BLASTX",
+                                       "description" : "",
+                                       "gff_name" :"BLASTX.gff"}
+                    }
+        try:
+            iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+            iConfig = iConfigChecker.readConfigFile()
+            iConfigChecker.setRawConfig(iConfig)
+            obsDictRawConfigValues = iConfigChecker._iRawConfig.dOptionsValues4Sections
+        except RepetException, re:
+            doesNoExceptionRaised = False
+        os.remove(self._configFileName)
+##       self.assertFalse(doesNoExceptionRaised)
+##       self.assertEqual(expMsg, re.getMessage())
+
+        self.assertTrue(doesNoExceptionRaised)
+        self.assertEquals(obsDictRawConfigValues, expDictRawConfigValues)
+       
+    def test_checkMandatorySections(self):
+        self._iMock.write_config(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="dir_name", mandatory=True)
+        iConfigRules.addRuleSection(section="organism", mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatorySectionsFound = True
+        try:
+            iConfigChecker.checkMandatorySections()
+        except RepetException:
+            areAllMandatorySectionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatorySectionsFound)
+ 
+    def test_checkMandatorySections_one_missing (self):
+        self._iMock.write_config(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="dir_name", mandatory=True)
+        iConfigRules.addRuleSection(section="target", mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        expMsg = "Error in configuration file %s, following sections are missing:\n - target\n"% self._configFileName
+        areAllMandatorySectionsFound = True
+        try:
+            iConfigChecker.checkMandatorySections()
+        except RepetException, re:
+            areAllMandatorySectionsFound = False
+        os.remove(self._configFileName)
+        self.assertFalse(areAllMandatorySectionsFound)
+        self.assertEquals(expMsg, re.getMessage())
+        
+    def test_checkMandatorySections_mandatory_section_with_pattern_section_is_missing (self):
+        self._iMock.write_config(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="dir_name", mandatory=True)
+        iConfigRules.addRuleSection(section="mandatorySection", mandatory=True, isPattern = True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        expMsg = "Error in configuration file %s, following sections are missing:\n - mandatorySection\n"% self._configFileName 
+        areAllMandatorySectionsFound = True
+        try:
+            iConfigChecker.checkMandatorySections()
+        except RepetException, re:
+            areAllMandatorySectionsFound = False
+        os.remove(self._configFileName)
+        self.assertFalse(areAllMandatorySectionsFound)
+        self.assertEquals(expMsg, re.getMessage())
+
+    def test_checkMandatorySections_mandatory_section_is_pattern (self):
+        self._iMock.write_case_pattern_rule(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="dir_name", mandatory=True)
+        iConfigRules.addRuleSection(section="analysis[0-9]*", mandatory=True, isPattern = True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatorySectionsFound = True
+        try:
+            iConfigChecker.checkMandatorySections()
+        except RepetException:
+            areAllMandatorySectionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatorySectionsFound)
+
+    def test_checkMandatoryOptions_in_mandatory_section (self):
+        self._iMock.write_config(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="organism", mandatory=True)
+        iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatoryOptionsFound)
+
+    def test_checkMandatoryOptions_in_mandatory_section_option_is_missing (self):
+        self._iMock.write_config(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="organism", mandatory=True)
+        iConfigRules.addRuleOption(section="organism", option ="MissingOption", mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        expMsg = "Error in configuration file %s, following options are missing: \n - [organism]: MissingOption\n" % self._configFileName
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException, re:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertFalse(areAllMandatoryOptionsFound)
+        self.assertEquals(expMsg, re.getMessage())
+
+    def test_checkMandatoryOptions_in_non_mandatory_section_and_section_and_option_exist (self):
+        self._iMock.write_config(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatoryOptionsFound)
+        
+    def test_checkMandatoryOptions_in_non_mandatory_section_and_section_exist_option_is_missing (self):
+        self._iMock.write_config(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleOption(section="organism", option ="MissingOption", mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        expMsg = "Error in configuration file %s, following options are missing: \n - [organism]: MissingOption\n" % self._configFileName
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException, re:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertFalse(areAllMandatoryOptionsFound)
+        self.assertEquals(expMsg,re.getMessage())
+        
+    def test_checkMandatoryOptions_in_non_mandatory_section_and_section_does_not_exist (self):
+        self._iMock.write_config(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleOption(section="NonExistingAndNonMandatorySection", option ="genus", mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatoryOptionsFound)
+        
+    def test_checkMandatoryOptions_with_Pattern_rules_in_section  (self):
+        self._iMock.write_case_pattern_rule(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="analysis", isPattern=True)
+        iConfigRules.addRuleOption(section="analysis", option ="name", mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatoryOptionsFound)
+
+    def test_checkMandatoryOptions_with_pattern_rules_in_option_section_is_mandatory (self):
+        self._iMock.write_case_pattern_rule(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="section_with_option_pattern", mandatory=True)
+        iConfigRules.addRuleOption(section="section_with_option_pattern", option ="option", isPattern= True, mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatoryOptionsFound)
+
+    def test_checkMandatoryOptions_with_pattern_rules_in_option_in_mandatory_section_option_is_missing (self):
+        self._iMock.write_case_pattern_rule(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="section_with_option_pattern", mandatory=True)
+        iConfigRules.addRuleOption(section="section_with_option_pattern", option ="MissingOption", isPattern= True, mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        expMsg = "Error in configuration file %s, following options are missing: \n - [section_with_option_pattern]: MissingOption\n" % self._configFileName
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException, re:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertFalse(areAllMandatoryOptionsFound)
+        self.assertEquals(expMsg, re.getMessage())
+
+    def test_checkMandatoryOptions_with_pattern_rules_in_non_mandatory_section_and_section_and_option_exist (self):
+        self._iMock.write_case_pattern_rule(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleOption(section="section_with_option_pattern", option ="option", isPattern= True, mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatoryOptionsFound)
+        
+    def test_checkMandatoryOptions_with_pattern_rules_in_non_mandatory_section_and_section_exist_option_is_missing (self):
+        self._iMock.write_case_pattern_rule(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleOption(section="section_with_option_pattern", option ="MissingOption", isPattern= True, mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        expMsg = "Error in configuration file %s, following options are missing: \n - [section_with_option_pattern]: MissingOption\n" % self._configFileName
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException, re:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertFalse(areAllMandatoryOptionsFound)
+        self.assertEquals(expMsg,re.getMessage())
+        
+    def test_checkMandatoryOptions_with_pattern_rules_in_non_mandatory_section_and_section_does_not_exist (self):
+        self._iMock.write_case_pattern_rule(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleOption(section="non_mandatory_section", option ="MissingOption", isPattern= True, mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatoryOptionsFound)
+        
+    def test_checkMandatoryOptions_with_pattern_rules_for_both_section_and_option  (self):
+        self._iMock.write_case_pattern_rule(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section="section_with_option_pattern", isPattern=True)
+        iConfigRules.addRuleOption(section="section_with_option_pattern", option ="option", isPattern= True, mandatory=True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatoryOptionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException:
+            areAllMandatoryOptionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatoryOptionsFound)
+       
+    def test_checkMandatoryOptions_case(self):
+        self._iMock.write_config_case(self._configFileName)
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection("dir_name", True)
+        iConfigRules.addRuleSection("organism", True)
+        iConfigRules.addRuleOption("organism", "min_SSR_coverage", True)
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        iConfig = iConfigChecker.readConfigFile()
+        iConfigChecker.setRawConfig(iConfig)
+        iConfigChecker.extendConfigRulesWithPatternRules()
+        areAllMandatorySectionsFound = True
+        try:
+            iConfigChecker.checkMandatoryOptions()
+        except RepetException:
+            areAllMandatorySectionsFound = False
+        os.remove(self._configFileName)
+        self.assertTrue(areAllMandatorySectionsFound)
+
+#TODO Test de extendConfigRulesWithPatternRules et de applyRuleToRawValue
+# option avec une liste de valeurs possibles dans un ensemble
+# option type=string type="num" type="date"???.
+#option define twice and options use in other
+             
+class MockConfig (object):
+    
+    def write_config(self, configFileName):
+        configF = open(configFileName, "w" )
+        configF.write( "[dir_name]\n")
+        configF.write( "work_dir : toto \n") 
+        configF.write( "\n")
+        configF.write( "[organism]\n")
+        configF.write( "abbreviation: T.aestivum\n")
+        configF.write( "genus: triticum\n")
+        configF.write( "species: aestivum\n")
+        configF.write( "common_name: wheat\n")
+        configF.write( "comment: \n")
+        configF.write( "[analysis1]\n")
+        configF.write( "name: BLASTXWheat2\n")
+        configF.write( "program: BLASTX2\n")
+        configF.write( "programversion: 3.32\n")
+        configF.write( "sourcename: dummyDesc_BLASTX2\n")
+        configF.write( "description: \n")
+        configF.write( "gff_name: BLASTX.gff2\n")
+        configF.write( "\n")
+        configF.close()
+        
+    def write_case_section_define_twice(self, configFileName):
+        configF = open(configFileName, "w" )
+        configF.write( "[dir_name]\n")
+        configF.write( "work_dir : toto \n") 
+        configF.write( "\n")
+        configF.write( "[analysis1]\n")
+        configF.write( "name: BLASTXWheat\n")
+        configF.write( "program: BLASTX\n")
+        configF.write( "programversion: 3.3\n")
+        configF.write( "sourcename: dummyDesc_BLASTX\n")
+        configF.write( "description: \n")
+        configF.write( "gff_name: BLASTX.gff\n")
+        configF.write( "\n")
+        configF.write( "[analysis1]\n")
+        configF.write( "name: BLASTXWheat2\n")
+        configF.write( "program: BLASTX2\n")
+        configF.write( "programversion: 3.32\n")
+        configF.write( "sourcename: dummyDesc_BLASTX2\n")
+        configF.write( "description: \n")
+        configF.write( "gff_name: BLASTX.gff2\n")
+        configF.write( "\n")
+        configF.close()
+        
+    def write_case_option_define_twice(self, configFileName):
+        configF = open(configFileName, "w" )
+        configF.write( "[dir_name]\n")
+        configF.write( "work_dir : toto \n") 
+        configF.write( "\n")
+        configF.write( "[analysis1]\n")
+        configF.write( "name: BLASTXWheat\n")
+        configF.write( "program: BLASTX\n")
+        configF.write( "programversion: 3.3\n")
+        configF.write( "sourcename: dummyDesc_BLASTX\n")
+        configF.write( "program: BLASTX2\n")
+        configF.write( "description: \n")
+        configF.write( "gff_name: BLASTX.gff\n")
+        configF.write( "\n")
+        configF.write( "\n")
+        configF.close()
+        
+    #configuration file with section with option depends on presence of other options
+    def write_with_one_option_depends_of_an_other_one(self, configFileName ):
+        configF = open(configFileName, "w" )
+        configF.write( "[dir_name]\n")
+        configF.write( "work_dir : toto\n") 
+        configF.write( "\n")
+        configF.write( "[organism]\n")
+        configF.write( "abbreviation: T.aestivum\n")
+        configF.write( "genus: Triticum\n")
+        configF.write( "species: aestivum\n")
+        configF.write( "common_name: wheat\n")
+        configF.write( "comment: \n")
+        configF.write( "\n")
+        configF.write( "[analysis1]\n")
+        configF.write( "name: BLASTXWheat\n")
+        configF.write( "program: BLASTX\n")
+        configF.write( "programversion: 3.3\n")
+        configF.write( "sourcename: src_BLASTX\n")
+        configF.write( "description: \n")
+        configF.write( "gff_name: BLASTX.gff\n")
+        configF.write( "\n")
+        configF.write( "[analysis2]\n")
+        configF.write( "name: GMHMMWheat\n")
+        configF.write( "program: GMHMM\n")
+        configF.write( "programversion: 4.3\n")
+        configF.write( "sourcename: src_GMHMM\n")
+        configF.write( "description: \n")
+        configF.write( "gff_name: GMHMM.gff\n")
+        configF.write( "\n")
+        configF.write( "[target]\n")
+        configF.write( "target_used: yes\n")
+        configF.write( "target_used_list: target.lst\n")
+        configF.close()
+        
+    def write_case_pattern_rule(self, configFileName ):
+        configF = open(configFileName, "w" )
+        configF.write( "[dir_name]\n")
+        configF.write( "work_dir : toto\n" ) 
+        configF.write( "\n")
+        configF.write( "[organism]\n")
+        configF.write( "abbreviation: T.aestivum\n")
+        configF.write( "genus: Triticum\n")
+        configF.write( "species: aestivum\n")
+        configF.write( "common_name: wheat\n")
+        configF.write( "comment: \n")
+        configF.write( "\n")
+        configF.write( "[analysis1]\n")
+        configF.write( "name: BLASTXWheat\n")
+        configF.write( "program: BLASTX\n")
+        configF.write( "programversion: 3.3\n")
+        configF.write( "sourcename: src_BLASTX\n")
+        configF.write( "description: \n")
+        configF.write( "gff_name: BLASTX.gff\n")
+        configF.write( "\n")
+        configF.write( "[analysis2]\n")
+        configF.write( "name: GMHMMWheat\n")
+        configF.write( "program: GMHMM\n")
+        configF.write( "programversion: 4.3\n")
+        configF.write( "sourcename: src_GMHMM\n")
+        configF.write( "description: \n")
+        configF.write( "gff_name: GMHMM.gff\n")
+        configF.write( "\n")
+        configF.write( "[target]\n")
+        configF.write( "target_used: yes\n")
+        configF.write( "target_used_list: target.lst\n")
+        configF.write( "\n")
+        configF.write( "[section_with_option_pattern]\n")
+        configF.write( "option1: value1\n")
+        configF.write( "option2: value2\n")
+        configF.write( "[second_section_with_option_pattern]\n")
+        configF.write( "option1: value1\n")
+        configF.write( "option2: value2\n")
+        configF.close()
+        
+    def write_config_case(self, configFileName):
+        configF = open(configFileName, "w" )
+        configF.write( "[dir_name]\n")
+        configF.write( "work_dir : toto \n") 
+        configF.write( "\n")
+        configF.write( "[organism]\n")
+        configF.write( "min_SSR_coverage: 0.50\n")
+        configF.write( "\n")
+        configF.close()
+        
+if __name__ == "__main__":
+    unittest.main()
\ No newline at end of file