Ejemplo n.º 1
0
    def test_ignore_columns(self):
    
        names = ["gene_id"] 
        roles = ['feature_id']
        for i in range(8):
            names.append('sample_' + str(i))
            if (i % 2) == 0:
                roles.append('sample')
            else:
                roles.append(None)

        schema = Schema(
            column_names=names,
            column_roles=roles)
        self.assertEquals(len(schema.sample_column_names), 4)


        schema.add_factor('treated', [False, True])

        schema.set_factor('sample_0', 'treated', False)
        schema.set_factor('sample_2', 'treated', False)
        schema.set_factor('sample_4', 'treated', True)
        schema.set_factor('sample_6', 'treated', True)

        with self.assertRaises(Exception):
            schema.set_factor('sample_1' + str(i), 'treated', True)

        self.assertEquals(schema.possible_assignments(['treated']),
                          [OrderedDict([('treated', False)]), 
                           OrderedDict([('treated', True )])])

        self.assertEquals(schema.indexes_with_assignments(
                OrderedDict([('treated', False)])),
                          [0, 1])

        self.assertEquals(schema.indexes_with_assignments(
                OrderedDict([('treated', True)])),
                          [2, 3])

        self.assertEquals(schema.samples_with_assignments(
                OrderedDict([('treated', False)])),
                          ['sample_0', 'sample_2'])

        self.assertEquals(schema.samples_with_assignments(
                OrderedDict([('treated', True)])),
                          ['sample_4', 'sample_6'])
        
        out = StringIO()

        schema.save(out)
        loaded = Schema.load(out.getvalue())

        out2 = StringIO()
        loaded.save(out2)

        self.maxDiff = None
        self.assertEquals(out.getvalue(),
                          out2.getvalue())        
Ejemplo n.º 2
0
    def test_ignore_columns(self):

        names = ["gene_id"]
        roles = ['feature_id']
        for i in range(8):
            names.append('sample_' + str(i))
            if (i % 2) == 0:
                roles.append('sample')
            else:
                roles.append(None)

        schema = Schema(column_names=names, column_roles=roles)
        self.assertEquals(len(schema.sample_column_names), 4)

        schema.add_factor('treated', [False, True])

        schema.set_factor('sample_0', 'treated', False)
        schema.set_factor('sample_2', 'treated', False)
        schema.set_factor('sample_4', 'treated', True)
        schema.set_factor('sample_6', 'treated', True)

        with self.assertRaises(Exception):
            schema.set_factor('sample_1' + str(i), 'treated', True)

        self.assertEquals(schema.possible_assignments(['treated']), [
            OrderedDict([('treated', False)]),
            OrderedDict([('treated', True)])
        ])

        self.assertEquals(
            schema.indexes_with_assignments(OrderedDict([('treated', False)])),
            [0, 1])

        self.assertEquals(
            schema.indexes_with_assignments(OrderedDict([('treated', True)])),
            [2, 3])

        self.assertEquals(
            schema.samples_with_assignments(OrderedDict([('treated', False)])),
            ['sample_0', 'sample_2'])

        self.assertEquals(
            schema.samples_with_assignments(OrderedDict([('treated', True)])),
            ['sample_4', 'sample_6'])

        out = StringIO()

        schema.save(out)
        loaded = Schema.load(out.getvalue())

        out2 = StringIO()
        loaded.save(out2)

        self.maxDiff = None
        self.assertEquals(out.getvalue(), out2.getvalue())
Ejemplo n.º 3
0
    def test_yaml(self):
        self.maxDiff = None
        # Save the schema, load it, and save it again. Compare the two
        # versions to make sure they're the same, so that we know we
        # can round-trip.
        out = StringIO()

        self.schema.save(out)
        loaded = Schema.load(out.getvalue())

        out2 = StringIO()
        loaded.save(out2)

        self.assertEquals(out.getvalue(), out2.getvalue())
Ejemplo n.º 4
0
    def test_yaml(self):
        self.maxDiff = None
        # Save the schema, load it, and save it again. Compare the two
        # versions to make sure they're the same, so that we know we
        # can round-trip.
        out = StringIO()

        self.schema.save(out)
        loaded = Schema.load(out.getvalue())

        out2 = StringIO()
        loaded.save(out2)

        self.assertEquals(out.getvalue(),
                          out2.getvalue())
Ejemplo n.º 5
0
Archivo: tasks.py Proyecto: itmat/pade
def load_schema(db):
    schema_str = StringIO(db.attrs['schema'])
    return Schema.load(schema_str)
Ejemplo n.º 6
0
def load_schema(path):
    try:
        with open(path) as f:
            return Schema.load(f)
    except IOError as e:
        raise UsageException("Couldn't load schema: " + e.filename + ": " + e.strerror)    
Ejemplo n.º 7
0
def load_schema(db):
    schema_str = StringIO(db.attrs['schema'])
    return Schema.load(schema_str)
Ejemplo n.º 8
0
Archivo: metadb.py Proyecto: itmat/pade
 def load(self):
     with open(self.path) as f:
         return Schema.load(f)
Ejemplo n.º 9
0
 def load(self):
     with open(self.path) as f:
         return Schema.load(f)