Mercurial > repos > yufei-luo > s_mart
view commons/core/sql/test/Test_TableMapAdaptator.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
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# 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 unittest import time import os from commons.core.sql.TableMapAdaptator import TableMapAdaptator from commons.core.sql.DbMySql import DbMySql from commons.core.coord.Map import Map from commons.core.coord.Set import Set class Test_TableMapAdaptator( 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._iDb = DbMySql( cfgFileName=self._configFileName ) self._table = "dummyMapTable_%s" % ( self._uniqId ) self._tMapA = TableMapAdaptator( self._iDb, self._table ) def tearDown( self ): self._uniqId = None self._iDb.dropTable( self._table ) self._iDb.close() self._table = None self._tMapA = None os.remove( self._configFileName ) self._configFileName = "" ################################################################################## ################## Tests for methods in ITableMapAdaptator ####################### ################################################################################## def test_getEndFromSeqName(self): self._iDb.createTable( self._table, "map", "" ) map1 = Map() map1.setFromString( "name1\tdesc1\t1\t120\n" ) map2 = Map() map2.setFromString( "name2\tdesc2\t1\t20\n" ) for m in [ map1, map2]: self._tMapA.insert(m) expEnd = 20 obsEnd = self._tMapA.getEndFromSeqName("desc2") self.assertEqual(expEnd, obsEnd) def test_getMapListFromSeqName( self ): self._iDb.createTable( self._table, "map", "" ) map1 = Map() map1.setFromString( "name1\tdesc1\t1\t120\n" ) map2 = Map() map2.setFromString( "name2\tdesc2\t1\t20\n" ) map3 = Map() map3.setFromString( "name2\tdesc2\t1\t50\n" ) for m in [ map1, map2, map3 ]: self._tMapA.insert( m ) lExp = [ map2, map3 ] lObs = self._tMapA.getMapListFromSeqName("name2") self.assertEqual( lObs, lExp ) def test_getMapListFromChr( self ): self._iDb.createTable( self._table, "map", "" ) map1 = Map() map1.setFromString( "name1\tchr1\t1\t120\n" ) map2 = Map() map2.setFromString( "name2\tchr2\t1\t20\n" ) map3 = Map() map3.setFromString( "name2\tchr2\t1\t50\n" ) for m in [ map1, map2, map3 ]: self._tMapA.insert( m ) lExp = [ map2, map3 ] lObs = self._tMapA.getMapListFromChr("chr2") self.assertEqual( lObs, lExp ) def test_getSeqNameList(self): self._iDb.createTable( self._table, "map", "" ) map1 = Map() map1.setFromString( "name1\tdesc1\t1\t120\n" ) map2 = Map() map2.setFromString( "name2\tdesc2\t1\t20\n" ) map3 = Map() map3.setFromString( "name2\tdesc2\t1\t50\n" ) for m in [ map1, map2, map3 ]: self._tMapA.insert( m ) lExp = ["desc1", "desc2"] lObs = self._tMapA.getSeqNameList() self.assertEqual( lObs, lExp ) def test_insert_one_element( self ): map2Insert = Map() map2Insert.name="name1" map2Insert.seqname="name2" map2Insert.start=1L map2Insert.end=50L self._iDb.createTable( self._table, "map", "" ) self._tMapA.insert( map2Insert ) sqlCmd = "SELECT * FROM %s" % ( self._table ) self._iDb.execute( sqlCmd ) expTmapTuple = (('name1', 'name2', 1L, 50L),) obsTmapTuples = self._iDb.cursor.fetchall() self.assertEquals( expTmapTuple, obsTmapTuples ) def test_insert_two_elements( self ): map1 = Map() map1.setFromString( "name1\tdesc1\t1\t120\n" ) map2 = Map() map2.setFromString( "name2\tdesc2\t1\t20\n" ) self._iDb.createTable( self._table, "map", "" ) for m in [ map1, map2 ]: self._tMapA.insert( m ) expTmapTuple = ( ('name1', 'desc1', 1L, 120L), ('name2', 'desc2', 1L, 20L) ) sqlCmd = "SELECT * FROM %s" % ( self._table ) self._iDb.execute( sqlCmd ) obsTmapTuples = self._iDb.cursor.fetchall() self.assertEquals(expTmapTuple, obsTmapTuples ) def test_insertList( self ): self._iDb.createTable( self._table, "map", "" ) map1 = Map() map1.setFromString( "name1\tdesc1\t1\t120\n" ) map2 = Map() map2.setFromString( "name2\tdesc2\t1\t20\n" ) lmap = [ map1, map2 ] self._tMapA.insertList( lmap ) lExp = lmap lObs = self._tMapA.getListOfAllMaps() self.assertEqual( lObs, lExp ) def test_getSetListFromSeqName( self ): self._iDb.createTable( self._table, "map", "" ) map1 = Map() map1.setFromString( "name1\tdesc1\t1\t120\n" ) map2 = Map() map2.setFromString( "name2\tdesc2\t1\t20\n" ) map3 = Map() map3.setFromString( "name2\tdesc2\t1\t50\n" ) for m in [ map1, map2, map3 ]: self._tMapA.insert( m ) explMap = [Set( 1,"name2", "desc2", 1, 20), Set( 2,"name2", "desc2", 1, 50)] obslMap = self._tMapA.getSetListFromSeqName("name2") self.assertEqual( explMap, obslMap ) def test_getMapListOverlappingCoord( self ): self._iDb.createTable( self._table, "map", "" ) map1 = Map() map1.setFromString( "name1\tdesc1\t70\t120\n" ) map2 = Map() map2.setFromString( "name2\tdesc1\t1\t20\n" ) map3 = Map() map3.setFromString( "name3\tdesc1\t1\t50\n" ) for m in [ map1, map2, map3 ]: self._tMapA.insert( m ) explMap = [Map("name2", "desc1", 1, 20), Map("name3", "desc1", 1, 50)] obslMap = self._tMapA.getMapListOverlappingCoord("desc1", 1, 60) self.assertEqual( explMap, obslMap ) def test_getSetListOverlappingCoord( self ): self._iDb.createTable( self._table, "map", "" ) map1 = Map() map1.setFromString( "name1\tdesc1\t70\t120\n" ) map2 = Map() map2.setFromString( "name2\tdesc1\t1\t20\n" ) map3 = Map() map3.setFromString( "name3\tdesc1\t1\t50\n" ) for m in [ map1, map2, map3 ]: self._tMapA.insert( m ) explSet = [Set(1, "name2", "desc1", 1, 20), Set(2, "name3", "desc1", 1, 50)] obslSet = self._tMapA.getSetListOverlappingCoord("desc1", 1, 60) self.assertEqual( explSet, obslSet ) ################################################################################## ########################### Tests for other methods ############################## ################################################################################## def test_getListOfAllMaps( self ): self._iDb.createTable( self._table, "map", "" ) map1 = Map() map1.setFromString( "name1\tdesc1\t1\t120\n" ) map2 = Map() map2.setFromString( "name2\tdesc2\t1\t20\n" ) for m in [ map1, map2 ]: self._tMapA.insert( m ) lExp = [ map1, map2 ] lObs = self._tMapA.getListOfAllMaps() self.assertEqual( lObs, lExp ) def test_getDictPerNameFromMapFile( self ): self._iDb.createTable( self._table, "map", "" ) iMap1 = Map( "chunk1", "chromosome1", 1, 100 ) iMap2 = Map( "chunk2", "chromosome1", 91, 190 ) iMap3 = Map( "chunk3", "chromosome2", 1, 100 ) iMap4 = Map( "chunk1", "chromosome1", 1, 100 ) # redundant with iMap1 for iMap in [ iMap1, iMap2, iMap3, iMap4 ]: self._tMapA.insert( iMap ) dExp = { "chunk1": iMap1, "chunk2": iMap2, "chunk3": iMap3 } dObs = self._tMapA.getDictPerName() self.assertEquals( dExp, dObs ) #TODO: Check getListFromSeqName method: uses name instead of seqname # def test_getMapListFromSeqNameList( self ): # self._iDb.createTable( self._table, "map", "" ) # map1 = Map() # map1.setFromString( "name1\tdesc1\t1\t120\n" ) # map2 = Map() # map2.setFromString( "name2\tdesc2\t1\t20\n" ) # map3 = Map() # map3.setFromString( "name3\tdesc2\t1\t10\n" ) # map4 = Map() # map4.setFromString( "name4\tdesc3\t10\t200\n" ) # for m in [map1, map2, map3, map4]: self._tMapA.insert( m ) # # lMapToRetrieve = ["name1", "desc2"] # lExp = [map1, map2, map3] # lObs = self._tMapA.getMapListFromSeqNameList(lMapToRetrieve) # self.assertEqual( lObs, lExp ) test_suite = unittest.TestSuite() test_suite.addTest( unittest.makeSuite( Test_TableMapAdaptator ) ) if __name__ == "__main__": unittest.TextTestRunner(verbosity=2).run( test_suite )