--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/RetrieveInitHeaders.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,150 @@
+#! /usr/bin/env python
+
+# 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.
+
+from optparse import OptionParser
+from commons.core.sql.DbMySql import DbMySql
+
+class RetrieveInitHeaders(object):
+
+    def __init__(self, inTableName = "", linkFileName = "", outTableName = "", isQueryHeaders = True, clean = False, verbose = 0):
+        self._inTableName = inTableName
+        self._linkFileName = linkFileName
+        if outTableName == "":
+            self._outTableName = self._inTableName
+        else:
+            self._outTableName = outTableName
+        self._isQueryHeaders = isQueryHeaders
+        self._clean = clean
+        self._verbose = verbose
+        self._iDb = None
+        self._tmpTableName = "%s_tmp" % self._inTableName
+
+    #TODO: can handle config file
+    #TODO: description, help...
+    def setAttributesFromCmdLine(self):
+        description = ""
+        parser = OptionParser(description = description)
+        parser.add_option("-i", "--input", dest = "inTableName", type = "string", help = "", default = "")
+        parser.add_option("-l", "--link", dest = "linkFileName", type = "string", help = "", default = "")
+        parser.add_option("-o", "--output", dest = "outTableName", type = "string", help = "(default = input table name)", default = "")
+        parser.add_option("-s", "--subject", dest = "isQueryHeaders", action = "store_false", help = "change subject name and not query name", default = True)
+        parser.add_option("-c", "--clean", dest = "clean", action = "store_true", help = "drop input table", default = False)
+        parser.add_option("-v", "--verbose", dest = "verbose", type = "int", help = "0 or 1", default = 0)
+        options, args = parser.parse_args()
+        self.setAttributesFromOptions(options)
+        
+    def setAttributesFromOptions(self, options):
+        self.setInTableName(options.inTableName)
+        self.setLinkFileName(options.linkFileName)
+        self.setOutTableName(options.outTableName)
+        self.setIsQueryHeaders(options.isQueryHeaders)
+        self.setClean(options.clean)
+        self.setVerbose(options.verbose)
+        
+    def setInTableName(self, inTableName):
+        self._inTableName = inTableName
+        self._tmpTableName = "%s_tmp" % self._inTableName
+        
+    def setLinkFileName(self, linkFileName):
+        self._linkFileName = linkFileName
+        
+    def setOutTableName(self, outTableName):
+        if outTableName == "":
+            self._outTableName = self._inTableName
+        else:
+            self._outTableName = outTableName
+        
+    def setIsQueryHeaders(self, isQueryHeaders):
+        self._isQueryHeaders = isQueryHeaders
+        
+    def setClean(self, clean):
+        self._clean = clean
+        
+    def setVerbose(self, verbose):
+        self._verbose = verbose
+        
+    #TODO: checkOptions
+    def checkOptions(self):
+        pass    
+    
+    def run(self):
+        if self._verbose > 0:
+            print "START RetrieveInitHeaders.py"
+        self.checkOptions()
+        
+        if self._verbose > 0:
+            print "copy '%s' table to '%s' table" % (self._inTableName, self._tmpTableName)
+        self._iDb = DbMySql()
+        self._iDb.copyTable(self._inTableName, self._tmpTableName)
+        
+        if self._verbose > 0:
+            print "read '%s' file" % self._linkFileName
+        f = open(self._linkFileName)
+        line = f.readline()
+        count = 0
+        while line:
+            oldHeader = line.split()[0]
+            newHeader = line.split()[1]
+            if self._isQueryHeaders:
+                self._updateQueryName(oldHeader, newHeader)
+            else:
+                self._updateSubjectName(oldHeader, newHeader)
+            count += 1
+            line = f.readline()
+        f.close()
+        
+        if self._verbose > 0:
+            print "nb of relationships: %i" % count
+        if self._clean:
+            self._iDb.dropTable(self._inTableName)
+            if self._verbose > 0:
+                print "drop '%s' table" % self._inTableName
+        if self._verbose > 0:
+            print "rename '%s' table to '%s' table" % (self._tmpTableName, self._outTableName)
+        self._iDb.renameTable(self._tmpTableName, self._outTableName)
+        self._iDb.close()
+        if self._verbose > 0:
+            print "END RetrieveInitHeaders.py"
+        
+    #TODO: methods must be in TablePathAdaptator ?
+    def _updateQueryName(self, oldH, newH):
+        sqlCmd = "UPDATE %s SET query_name = '%s' WHERE query_name = '%s'" % (self._tmpTableName, newH, oldH)
+        self._iDb.execute(sqlCmd)
+        
+    def _updateSubjectName(self, oldH, newH):
+        sqlCmd = "UPDATE %s SET subject_name = '%s' WHERE subject_name = '%s'" % (self._tmpTableName, newH, oldH)
+        self._iDb.execute(sqlCmd)
+    
+if __name__ == "__main__":
+    iRIH = RetrieveInitHeaders()
+    iRIH.setAttributesFromCmdLine()
+    iRIH.run()
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