Exemplo n.º 1
0
 def setup(self):
     # test will be skipped if unavailable
     import MySQLdb
     
     createTable = """\
     CREATE TABLE test.sqlsequence_test (primary_id INTEGER PRIMARY KEY AUTO_INCREMENT, sequence TEXT)
     """
     
     try:
         self.db = sqlgraph.SQLTable('test.sqlsequence_test',
                                          dropIfExists=True,
                                          createTable=createTable,
                                          attrAlias=dict(seq='sequence'))
     except MySQLdb.MySQLError:
         tempcurs = sqlgraph.getNameCursor()[1]
         try: # hmm, maybe need to create the test database?
             tempcurs.execute('create database if not exists test')
             self.db = sqlgraph.SQLTable('test.sqlsequence_test',
                                              dropIfExists=True,
                                              createTable=createTable,
                                              attrAlias=dict(seq='sequence'))
         except MySQLdb.MySQLError: # no server, database or privileges?
             print """\
             The MySQL 'test' database doesn't exist and/or can't be
             created or accessed on this account. This test will be skipped.
             """
             raise ImportError #  skip tests.
     
     self.db.cursor.execute("""\
     INSERT INTO test.sqlsequence_test (sequence)
           VALUES ('CACCCTGCCCCATCTCCCCAGCCTGGCCCCTCGTGTCTCAGAACCCTCGGGGGGAGGCACAGAAGCCTTCGGGG')
     """)
     self.db.cursor.execute("""\
     INSERT INTO test.sqlsequence_test (sequence)
           VALUES ('GAAAGAAAGAAAGAAAGAAAGAAAGAGAGAGAGAGAGACAGAAG')
     """)
     
     class DNASeqRow(seqdb.DNASQLSequence):
         def __len__(self): # just speed optimization
             return self._select('length(sequence)') # SQL SELECT expression
     
     self.db.objclass(DNASeqRow) # force the table object to return DNASeqRow objects
     self.row1 = self.db[1]
     self.row2 = self.db[2]
Exemplo n.º 2
0
 def setup(self):
     from pygr import sqlgraph
     import MySQLdb # test will be skipped if unavailable
     createOpts = dict(source_id='int', target_id='int', edge_id='int')
     try:
         self.datagraph = sqlgraph.SQLGraph('test.dumbo_foo_test',
                                            dropIfExists=True,
                                            createTable=createOpts)
     except MySQLdb.MySQLError:
         tempcurs = sqlgraph.getNameCursor()[1]
         try: # hmm, maybe need to create the test database
             tempcurs.execute('create database if not exists test')
             self.datagraph = sqlgraph.SQLGraph('test.dumbo_foo_test',
                                                dropIfExists=True,
                                                createTable=createOpts)
         except MySQLdb.MySQLError: # no server, database or privileges?
             print """The MySQL 'test' database doesn't exist and/or can't be
             created or accessed on this account. This test will be skipped
             """
             raise ImportError #  skip tests.
Exemplo n.º 3
0
    def setup(self):
        # test will be skipped if unavailable
        import MySQLdb
        
        createTable = """\
        CREATE TABLE test.sqltable_test (primary_id INTEGER PRIMARY KEY AUTO_INCREMENT, seq_id TEXT, start INTEGER, stop INTEGER)
        """
        
        try:
            self.db = SQLTable('test.sqltable_test',
                               dropIfExists=True,
                               createTable=createTable)
        except MySQLdb.MySQLError:
            tempcurs = getNameCursor()[1]
            try: # hmm, maybe need to create the test database?
                tempcurs.execute('create database if not exists test')
                self.db = SQLTable('test.sqltable_test',
                                   dropIfExists=True,
                                   createTable=createTable)
            except MySQLdb.MySQLError: # no server, database or privileges?
                print """\
                The MySQL 'test' database doesn't exist and/or can't be
                created or accessed on this account. This test will be skipped.
                """
                raise ImportError #  skip tests.

        self.db.cursor.execute("""\
        INSERT INTO test.sqltable_test (seq_id, start, stop)
              VALUES ('seq1', 0, 10)
        """)
        self.db.cursor.execute("""\
        INSERT INTO test.sqltable_test (seq_id, start, stop)
              VALUES ('seq2', 5, 15)
        """)
        self.sourceDB = SQLTable('test.sqltable_join1',
                                 dropIfExists=True, createTable="""\
        CREATE TABLE test.sqltable_join1 (my_id INTEGER PRIMARY KEY,
              other_id VARCHAR(16))
        """)
        self.targetDB = SQLTable('test.sqltable_join2',
                                 dropIfExists=True, createTable="""\
        CREATE TABLE test.sqltable_join2 (third_id INTEGER PRIMARY KEY,
              other_id VARCHAR(16))
        """)
        self.db.cursor.execute("""\
        INSERT INTO test.sqltable_join1 VALUES (2,'seq2')
        """)
        self.db.cursor.execute("""\
        INSERT INTO test.sqltable_join1 VALUES (3,'seq3')
        """)
        self.db.cursor.execute("""\
        INSERT INTO test.sqltable_join1 VALUES (4,'seq4')
        """)
        self.db.cursor.execute("""\
        INSERT INTO test.sqltable_join2 VALUES (7, 'seq2')
        """)
        self.db.cursor.execute("""\
        INSERT INTO test.sqltable_join2 VALUES (99, 'seq3')
        """)
        self.db.cursor.execute("""\
        INSERT INTO test.sqltable_join2 VALUES (6, 'seq4')
        """)
        self.db.cursor.execute("""\
        INSERT INTO test.sqltable_join2 VALUES (8, 'seq4')
        """)
Exemplo n.º 4
0
Arquivo: testutil.py Projeto: ctb/pygr
    suites = map(loader, tests)
    return unittest.TestSuite(suites)

def mysql_enabled():
    """
    Detects whether mysql is functional on the current system
    """
    try:
        import MySQLdb
    except ImportError, exc:
        msg = 'MySQLdb error: %s' % exc
        warn(msg)
        return False
    try:
        from pygr import sqlgraph
        tempcurs = sqlgraph.getNameCursor()[1]
        # disable some MySQL specific spurious warnings, current scope only
        warnings.simplefilter("ignore") 
        tempcurs.execute('create database if not exists test')
    except Exception, exc:
        msg = 'cannot operate on MySql database: %s' % exc
        warn(msg)
        return False

    return True


def sqlite_enabled():
    """
    Detects whether sqlite3 is functional on the current system
    """