diff TEisotools-1.1.a/commons/core/checker/CheckerUtils.py @ 13:feef9a0db09d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.1.a/commons/core/checker/CheckerUtils.py	Wed Jul 20 09:04:42 2016 -0400
@@ -0,0 +1,315 @@
+# 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 os
+import sys
+import re
+import glob
+from ConfigParser import NoOptionError
+from ConfigParser import NoSectionError
+from commons.core.checker.CheckerException import CheckerException
+
+
+## A set of static methods used to perform checks.
+#
+#
+class CheckerUtils( object ):
+    
+    ## Check if blastName param is in ["blastn", "blastp", "blastx", "tblastn", "tblastx"]
+    # 
+    # @param blastName name to check
+    # @return True if name is in list False otherwise
+    #
+    def isBlastNameNotInBlastValues( blastName ):
+        blastValuesSet = set( ["blastn", "blastp", "blastx", "tblastn", "tblastx"] )
+        blastNameSet = set( [ blastName ] )
+        return not blastNameSet.issubset( blastValuesSet )
+    
+    isBlastNameNotInBlastValues = staticmethod( isBlastNameNotInBlastValues )
+    
+    
+    ## Check if param is NOT "TRUE" and NOT false "FALSE"
+    #
+    # @param param str to check
+    # @return True if param is not eq to "TRUE" AND not eq to "FALSE", false otherwise 
+    #
+    def isNotTRUEisNotFALSE( param ):
+        return param != "TRUE" and param != "FALSE"
+    
+    isNotTRUEisNotFALSE = staticmethod( isNotTRUEisNotFALSE )
+    
+    
+    ## Check if resource (file or dir) do NOT exists
+    #  
+    # @param resource file or dir to check
+    # @return True if resource exists False otherwise
+    #
+    def isRessourceNotExits( resource ):
+        return not os.path.exists( resource )
+    
+    isRessourceNotExits = staticmethod( isRessourceNotExits )
+    
+    
+    ## Check a specific E-value format: de-dd 
+    #
+    # @param param E-value to check
+    # @return True if format is de-dd False otherwise
+    #
+    def isNotAeValueWithOneDigit2DecimalsAtLeast( param ):
+        # \d\d stands for 2 digits and more ???
+        return not re.match( "\de\-\d\d", param )
+    
+    isNotAeValueWithOneDigit2DecimalsAtLeast = staticmethod( isNotAeValueWithOneDigit2DecimalsAtLeast )
+    
+    
+    ## Check a number format
+    #
+    # @param param value to check
+    # @return True if param is a number (d+) False otherwise
+    #
+    def isNotANumber( param ):
+        return not re.match( "\d+", param )
+    
+    isNotANumber = staticmethod( isNotANumber )
+    
+
+    ## Check if an executable is in the user's PATH
+    #
+    # @param exeName name of the executable
+    # @return True if executable in user's PATH, False otherwise
+    #
+    def isExecutableInUserPath( exeName ):
+        dirPathList = os.environ["PATH"].split(":")
+        for dirPath in dirPathList:
+            if os.path.isdir( dirPath ):
+                try:
+                    binPathList = glob.glob( dirPath + "/*" )
+                except OSError, e:
+                    continue
+                for binPath in binPathList:
+                    bin = os.path.basename( binPath )
+                    if bin == exeName:
+                        return True
+        return False
+    
+    isExecutableInUserPath = staticmethod( isExecutableInUserPath )
+    
+    
+    ## Return the full path of a given executable
+    #
+    def getFullPathFromExecutable( exeName ):
+        lDirFromUserPath = os.environ["PATH"].split(":")
+        for dir in lDirFromUserPath:
+            if os.path.isdir( dir ):
+                try:
+                    lExecutables = glob.glob( "%s/*" % ( dir ) )
+                except OSError, e:
+                    continue
+                for exe in lExecutables:
+                    path, exe = os.path.split( exe )
+                    if exe == exeName:
+                        return path
+        return ""
+    
+    getFullPathFromExecutable = staticmethod( getFullPathFromExecutable )
+    
+    
+    #TODO: to remove ?
+    ## Check if a queue Name is valid. Warning: Only with the queue manager SGE
+    #
+    # @param fullQueueName name of the queue to test (with or without parameters)
+    # @return True if queue name is valid, False otherwise
+    #
+    def isQueueNameValid( fullQueueName ):
+        queueName = fullQueueName.split()[0]
+        if queueName == "none":
+            return True
+        queueFile = "queueName.txt"
+        if not CheckerUtils.isExecutableInUserPath( "qconf" ):
+            msg = "executable 'qconf' can't be found"
+            sys.stderr.write( "%s\n" % ( msg ) )
+            return False
+        cmd = "qconf -sql > " + queueFile
+        os.system( cmd )
+        queueFileHandler = open( queueFile, "r" )
+        lQueueNames = queueFileHandler.readlines()
+        queueFileHandler.close()
+        os.remove( queueFile )
+        queueNameValid = False
+        for qName in lQueueNames:
+            qName = qName.strip()
+            if qName == queueName:
+                queueNameValid = True
+                break
+        return queueNameValid
+    
+    isQueueNameValid = staticmethod( isQueueNameValid )
+    
+    
+    ## Check if a string length is lower or equal than 15
+    #
+    # @param strName any string
+    # @return True if string length is <= 15, False otherwise
+    #
+    def isMax15Char( strName ):
+        return (len(strName) <= 15 )
+    
+    isMax15Char = staticmethod( isMax15Char )
+    
+    
+    ## Check if a string is made with only alphanumeric or underscore character
+    #
+    # @param strName any string
+    # @return True if string is with alphanumeric or underscore, False otherwise
+    #
+    def isCharAlphanumOrUnderscore( strName ):
+        # authorized ALPHABET [a-z,A-Z,0-9,_]
+        p = re.compile('\W')
+        errList=p.findall(strName)
+        if len( errList ) > 0 :
+            return False
+        else:
+            return True
+        
+    isCharAlphanumOrUnderscore = staticmethod( isCharAlphanumOrUnderscore )
+    
+    
+    ## Check if sectionName is in the configuration file
+    #
+    # @param config filehandle of configuration file
+    # @param sectionName string of section name to check
+    # @exception NoSectionError: if section not found raise a NoSectionError 
+    # 
+    def checkSectionInConfigFile( config, sectionName ):
+        if not (config.has_section(sectionName)):
+            raise NoSectionError(sectionName)
+        
+    checkSectionInConfigFile = staticmethod( checkSectionInConfigFile )
+    
+    
+    ## Check if an option is in a specified section in the configuration file
+    #
+    # @param config filehandle of configuration file
+    # @param sectionName string of section name
+    # @param optionName string of option name to check
+    # @exception NoOptionError: if option not found raise a NoOptionError
+    #
+    def checkOptionInSectionInConfigFile( config, sectionName, optionName ):
+        config.get( sectionName, optionName )
+    
+    checkOptionInSectionInConfigFile = staticmethod( checkOptionInSectionInConfigFile )
+    
+    
+    ## Check version number coherency between configFile and CHANGELOG
+    #
+    # @param config ConfigParser Instance of configuration file
+    # @param changeLogFileHandle CHANGELOG file handle
+    # @exception NoOptionError: if option not found raise a NoOptionError
+    #
+    def checkConfigVersion( changeLogFileHandle, config ):
+        line = changeLogFileHandle.readline()
+        while not line.startswith("REPET release "):
+            line = changeLogFileHandle.readline()
+        numVersionChangeLog = line.split()[2]
+        
+        numVersionConfig = config.get("repet_env", "repet_version")
+        
+        if not numVersionChangeLog == numVersionConfig:
+            message = "*** Error: wrong config file version. Expected version num is " + numVersionChangeLog + " but actual in config file is " + numVersionConfig
+            raise CheckerException(message)
+    
+    checkConfigVersion = staticmethod( checkConfigVersion )
+    
+    
+    ## Get version number from CHANGELOG
+    #
+    # @param changeLogFile CHANGELOG file name
+    #
+    def getVersionFromChangelogFile(changeLogFileName):
+        with open(changeLogFileName) as changeLogFileHandle:
+            line = changeLogFileHandle.readline()
+            while not line.startswith("REPET release "):
+                line = changeLogFileHandle.readline()
+            numVersionChangeLog = line.split()[2]
+            return numVersionChangeLog
+        
+            
+    getVersionFromChangelogFile = staticmethod( getVersionFromChangelogFile )
+    
+    
+    ## Check if headers of an input file contain only alpha numeric characters and "_ : . -"
+    #
+    # @param fileHandler file handle
+    # @exception CheckerException if bad header raise a CheckerException
+    #
+    def checkHeaders( fileHandler ):
+        lHeaders = CheckerUtils._getHeaderFromFastaFile(fileHandler)
+        p = re.compile('[^a-zA-Z0-9_:\.\-]', re.IGNORECASE)
+        lWrongHeaders = []
+        for header in lHeaders:
+            errList=p.findall(header)
+            if len( errList ) > 0 :
+                lWrongHeaders.append(header)
+        if lWrongHeaders != []:
+            exception = CheckerException()
+            exception.setMessages(lWrongHeaders)
+            raise exception
+        
+    checkHeaders = staticmethod( checkHeaders )  
+    
+    
+    def _getHeaderFromFastaFile( inFile ):
+        lHeaders = []
+        while True:
+            line = inFile.readline()
+            if line == "":
+                break
+            if line[0] == ">":
+                lHeaders.append( line[1:-1] )
+        return lHeaders
+    
+    _getHeaderFromFastaFile = staticmethod( _getHeaderFromFastaFile ) 
+
+
+    ## Return True if an option is in a specified section in the configuration file, False otherwise
+    #
+    # @param config handler of configuration file
+    # @param sectionName string of section name
+    # @param optionName string of option name to check
+    #
+    def isOptionInSectionInConfig( configHandler, section, option ):
+        try:
+            CheckerUtils.checkOptionInSectionInConfigFile( configHandler, section, option ) 
+        except NoOptionError:
+            return False
+        return True
+    
+    isOptionInSectionInConfig = staticmethod( isOptionInSectionInConfig )