Mercurial > repos > yufei-luo > s_mart
view smart_toolShed/commons/core/sql/test/Test_TableSetAdaptator.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
---|---|
date | Thu, 17 Jan 2013 10:52:14 -0500 |
parents | |
children |
line wrap: on
line source
# 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.TableSetAdaptator import TableSetAdaptator from commons.core.sql.DbMySql import DbMySql from commons.core.coord.Set import Set class Test_TableSetAdaptator( 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 = "dummySetTable_%s" % ( self._uniqId ) self._tSetA = TableSetAdaptator( self._iDb, self._table ) def tearDown( self ): self._uniqId = None self._iDb.dropTable( self._table ) self._iDb.close() self._table = None self._tSetA = None os.remove( self._configFileName ) self._configFileName = "" def test_insert(self): set2Insert = Set() set2Insert.id = 1 set2Insert.name = "name1" set2Insert.seqname = "name2" set2Insert.start = 1L set2Insert.end = 50L self._iDb.createTable( self._table, "set", "" ) self._tSetA.insert( set2Insert, False ) sqlCmd = "SELECT * FROM %s" % ( self._table ) self._iDb.execute( sqlCmd ) expTsetTuple = ((1, "name1", "name2", 1L, 50L),) obsTsetTuples = self._iDb.cursor.fetchall() self.assertEquals(expTsetTuple, obsTsetTuples ) def test_insertList ( self ): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) lset = [ set1, set2 ] self._tSetA.insertList( lset ) sqlCmd = "SELECT * FROM %s" % ( self._table ) self._iDb.execute( sqlCmd ) expTsetTuple = ((1, "name1", "desc1", 1, 120), (2, "name2", "desc2", 1, 20)) obsTsetTuples = self._iDb.cursor.fetchall() self.assertEqual( expTsetTuple, obsTsetTuples ) def test_getIdList(self): set2Insert = Set() set2Insert.id = 1 set2Insert.name = "name1" set2Insert.seqname = "name2" set2Insert.start = 1 set2Insert.end = 50 self._iDb.createTable( self._table, "set", "" ) self._tSetA.insert( set2Insert ) l = self._tSetA.getIdList() self.assertEquals( set2Insert.id, l[0] ) def test_getSeqNameList(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) set3 = Set() set3.setFromString( "2\tname2\tdesc2\t1\t50\n" ) for m in [ set1, set2, set3 ]: self._tSetA.insert( m ) lExp = ["desc1", "desc2"] lObs = self._tSetA.getSeqNameList() self.assertEqual( lObs, lExp ) def test_getSetListFromSeqName(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) set3 = Set() set3.setFromString( "3\tname2\tdesc2\t1\t50\n" ) for m in [ set1, set2, set3 ]: self._tSetA.insert( m ) explSet = [Set( 2,"name2", "desc2", 1, 20), Set( 3,"name2", "desc2", 1, 50)] obslSet = self._tSetA.getSetListFromSeqName("desc2") self.assertEqual( explSet, obslSet ) def test_getSetListFromId(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) lset = [ set1, set2 ] self._tSetA.insertList( lset ) explSet = [Set( 2,"name2", "desc2", 1, 20)] obslSet = self._tSetA.getSetListFromId(2) self.assertEqual( explSet, obslSet ) def test_getSetListFromIdList(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) lset = [ set1, set2 ] self._tSetA.insertList( lset ) explSet = [Set( 1, "name1", "desc1", 1, 120), Set( 2,"name2", "desc2", 1, 20)] lId = [1, 2] obslSet = self._tSetA.getSetListFromIdList(lId) self.assertEqual( explSet, obslSet ) def test_getSetListFromIdList_emptyList(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) lset = [ set1, set2 ] self._tSetA.insertList( lset ) explSet = [] lId = [] obslSet = self._tSetA.getSetListFromIdList(lId) self.assertEqual( explSet, obslSet ) def test_getSetListOverlappingCoord(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc2\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) lset = [ set1, set2 ] self._tSetA.insertList( lset ) explSet = [Set( 1,"name1", "desc2", 1, 120)] obslSet = self._tSetA.getSetListOverlappingCoord("desc2", 30, 70) self.assertEqual( explSet, obslSet ) def test_deleteFromId(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) set3 = Set() set3.setFromString( "3\tname2\tdesc3\t1\t50\n" ) for m in [ set1, set2, set3 ]: self._tSetA.insert( m ) self._tSetA.deleteFromId(1) expTSetTuples = (( 2,"name2", "desc2", 1, 20), ( 3,"name2", "desc3", 1, 50)) sqlCmd = "SELECT * FROM %s" % ( self._table ) self._iDb.execute( sqlCmd ) obsTsetTuples = self._iDb.cursor.fetchall() self.assertEqual( expTSetTuples, obsTsetTuples ) def test_deleteFromIdList(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) set3 = Set() set3.setFromString( "3\tname2\tdesc3\t1\t50\n" ) for m in [ set1, set2, set3 ]: self._tSetA.insert( m ) lId2del = [1, 2] self._tSetA.deleteFromIdList(lId2del) expTSetTuples = (( 3,"name2", "desc3", 1, 50),) sqlCmd = "SELECT * FROM %s" % ( self._table ) self._iDb.execute( sqlCmd ) obsTsetTuples = self._iDb.cursor.fetchall() self.assertEqual( expTSetTuples, obsTsetTuples ) def test_deleteFromIdListWithEmptyList(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) set3 = Set() set3.setFromString( "3\tname2\tdesc3\t1\t50\n" ) for m in [ set1, set2, set3 ]: self._tSetA.insert( m ) lId2del = [] self._tSetA.deleteFromIdList(lId2del) expTSetTuples = ((1L, 'name1', 'desc1', 1L, 120L), (2L, 'name2', 'desc2', 1L, 20L), (3L, 'name2', 'desc3', 1L, 50L)) sqlCmd = "SELECT * FROM %s" % ( self._table ) self._iDb.execute( sqlCmd ) obsTsetTuples = self._iDb.cursor.fetchall() self.assertEqual( expTSetTuples, obsTsetTuples ) def test_joinTwoSets(self): self._iDb.createTable( self._table, "set", "" ) idSet1 = 5 set1 = Set() set1.setFromString( "5\tname1\tdesc1\t1\t120\n" ) idSet2 = 2 set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) lset = [ set1, set2 ] self._tSetA.insertList( lset ) self._tSetA.joinTwoSets(idSet1, idSet2) sqlCmd = "SELECT * FROM %s" % ( self._table ) self._iDb.execute( sqlCmd ) expTSetTuples = ((2L, "name1", "desc1", 1L, 120L ), (2L, "name2", "desc2", 1L, 20L )) obsTSetTuples = self._iDb.cursor.fetchall() self.assertEqual( expTSetTuples, obsTSetTuples) self._iDb.dropTable(self._table) def test_joinTwoSetsWhereId1InfId2(self): self._iDb.createTable( self._table, "set", "" ) idSet1 = 2 set1 = Set() set1.setFromString( "5\tname1\tdesc1\t1\t120\n" ) idSet2 = 5 set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) lset = [ set1, set2 ] self._tSetA.insertList( lset ) self._tSetA.joinTwoSets(idSet1, idSet2) sqlCmd = "SELECT * FROM %s" % ( self._table ) self._iDb.execute( sqlCmd ) expTSetTuples = ((2L, "name1", "desc1", 1L, 120L ), (2L, "name2", "desc2", 1L, 20L )) obsTSetTuples = self._iDb.cursor.fetchall() self.assertEqual( expTSetTuples, obsTSetTuples) self._iDb.dropTable(self._table) def test_getNewId(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) set2 = Set() set2.setFromString( "2\tname2\tdesc2\t1\t20\n" ) set3 = Set() set3.setFromString( "5\tname1\tdesc1\t1\t120\n" ) set4 = Set() set4.setFromString( "8\tname2\tdesc2\t1\t20\n" ) lset = [ set1, set2, set3, set4 ] self._tSetA.insertList( lset ) expId = 9 obsId = self._tSetA.getNewId() self.assertEqual( expId, obsId) self._iDb.dropTable(self._table) def test_getNewId_set_null(self): self._iDb.createTable( self._table, "set", "" ) set1 = Set() lset = [ set1 ] self._tSetA.insertList( lset ) expId = 1 obsId = self._tSetA.getNewId() self.assertEqual( expId, obsId) self._iDb.dropTable(self._table) def test_getListOfAllSets( self ): self._iDb.createTable( self._table, "set" ) s1 = Set() s1.setFromString( "1\tchr1\tTE3\t1\t10\n" ) s2a = Set() s2a.setFromString( "2\tchr1\tTE2\t2\t9\n" ) s2b = Set() s2b.setFromString( "2\tchr1\tTE2\t12\t19\n" ) lSets = [ s1, s2a, s2b ] self._tSetA.insertList( lSets ) expLSets = [ s1, s2a, s2b ] obsLSets = self._tSetA.getListOfAllSets() self.assertEqual( expLSets, obsLSets ) def test_getListOfAllSets_empty_table( self ): self._iDb.createTable( self._table, "set" ) expList = [] obsList = self._tSetA.getListOfAllSets() self.assertEqual( expList, obsList ) test_suite = unittest.TestSuite() test_suite.addTest( unittest.makeSuite( Test_TableSetAdaptator ) ) if __name__ == "__main__": unittest.TextTestRunner(verbosity=2).run( test_suite )