--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/convCoord/test/Test_PathChunkConnector.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,121 @@
+import unittest
+import time
+import os
+from commons.core.sql.TablePathAdaptator import TablePathAdaptator
+from commons.pyRepetUnit.convCoord.PathChunkConnector import PathChunkConnector
+from commons.core.sql.DbMySql import DbMySql
+
+
+class Test_PathChunkConnector( unittest.TestCase ):
+    
+    def setUp(self):
+        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
+        self._configFileName = "dummyConfigFile_%s" % ( self._uniqId )
+        configF = open(self._configFileName, "w" )
+        configF.write( "[repet_env]\n" )
+        configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
+        configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
+        configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
+        configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
+        configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
+        configF.close()
+        self._db = DbMySql( cfgFileName=self._configFileName )
+        self._table = "dummyPathTable_%s" % ( self._uniqId )
+        self._tpA = TablePathAdaptator( self._db, self._table )
+        self._mapDict = {'chunk1': ('dmel_chr4', 1, 100000),'chunk2': ('dmel_chr4', 90001, 190000),'chunk3': ('dmel_chr4', 180001, 280000), }
+        self._mapFileName = "map_file.map"
+        
+    def tearDown(self):
+        self._db.close()
+        
+    def testTwoQueryOverlapsOnPlusStrand (self):
+        lines = [
+                 "1\tdmel_chr4\t95535\t95570\tsbj2\t125423\t125467\t7e-15\t82\t97.78\n",
+                 "2\tdmel_chr4\t95545\t95576\tsbj2\t125457\t133465\t2e-38\t83\t65\n"
+                ]
+        
+        expectedList =[("dmel_chr4", 95535, 95576, "sbj2", 125423, 133465, 2e-38, 83,97.78)]
+        self._templateTest(lines, expectedList)
+        
+    def testTwoQueryOverlapsOnReverseStrand (self):
+        lines = [
+                 "1\tdmel_chr4\t95535\t95570\tsbj2\t125467\t125423\t7e-15\t82\t97.78\n",
+                 "2\tdmel_chr4\t95545\t95576\tsbj2\t133465\t125457\t2e-38\t83\t65\n"
+                ]
+
+        expectedList =[("dmel_chr4", 95535, 95576, "sbj2", 133465, 125423, 2e-38, 83,97.78)]
+        self._templateTest(lines, expectedList)
+        
+    def testTwoQueryOverlapsOnDifferentStrands (self):
+        lines = [                   
+                 "1\tdmel_chr4\t95535\t95570\tsbj2\t125423\t125467\t7e-15\t82\t97.78\n",
+                 "2\tdmel_chr4\t95545\t95576\tsbj2\t133465\t125457\t2e-38\t83\t65\n"
+                ]
+        expectedList =[
+                       ("dmel_chr4", 95535, 95570, "sbj2", 125423, 125467, 7e-15, 82,97.78),
+                       ("dmel_chr4", 95545, 95576, "sbj2", 133465, 125457, 2e-38, 83,65)
+                       ]
+        self._templateTest(lines, expectedList)
+        
+    def _templateTest(self, datas2TestList, expectedList ):
+        pathFileName = "dummyPathFile_%s" % ( self._uniqId )
+        _MockPathFile(pathFileName, datas2TestList)
+        
+
+        self._db.createTable( self._table, "path", pathFileName )
+
+        _MockMapFile(self._mapFileName)
+        chunkConnector = PathChunkConnector(self._mapFileName, self._db, self._table, 0)
+        chunkConnector.run()
+       
+        sql_cmd = 'select * from %s' % (self._table)
+        self._db.execute(sql_cmd)
+        res = self._db.fetchall()
+        
+        for i in xrange(len(expectedList)):
+            resultTuple = res[i]
+            expectedTuple = expectedList[i]
+            self._assertExpectedTupleEqualsObsTuple(expectedTuple, resultTuple)
+        
+        self._db.dropTable( self._table )
+        os.remove(pathFileName)
+        os.remove(self._mapFileName)
+        
+    def _assertExpectedTupleEqualsObsTuple(self, expectedTuple, resultTuple):
+        self.assertEquals(expectedTuple[0], resultTuple[1])
+        self.assertEquals(expectedTuple[1], resultTuple[2])
+        self.assertEquals(expectedTuple[2], resultTuple[3])
+        self.assertEquals(expectedTuple[3], resultTuple[4])
+        self.assertEquals(expectedTuple[4], resultTuple[5])
+        self.assertEquals(expectedTuple[5], resultTuple[6])
+        self.assertEquals(expectedTuple[6], resultTuple[7])
+        self.assertEquals(expectedTuple[7], resultTuple[8])
+        self.assertEquals(expectedTuple[8], resultTuple[9])
+        
+
+class _MockPathFile:
+    
+    def __init__(self, fileName, lines):
+        path = open(fileName, "w");
+        for line in lines:
+            path.write(line)
+        path.close
+        
+        
+class _MockMapFile:
+    
+    def __init__ (self, fileName):
+        map = open(fileName, "w")
+        line1 = "chunk1" + '\t'   + "dmel_chr4" + '\t' +   "1" + '\t'+   "100000" + "\n"
+        line2 = "chunk2" + '\t'   + "dmel_chr4" + '\t' +   "90001" + '\t'+   "190000" + "\n"
+        line3 = "chunk3" + '\t'   + "dmel_chr4" + '\t' +   "180001" + '\t' + "280000" + "\n"  
+        map.write(line1)
+        map.write(line2)
+        map.write(line3)
+        map.close
+        
+        
+test_suite = unittest.TestSuite()
+test_suite.addTest( unittest.makeSuite( Test_PathChunkConnector ) )
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run( test_suite )