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())
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())
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())
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())
def load_schema(db): schema_str = StringIO(db.attrs['schema']) return Schema.load(schema_str)
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)
def load_schema(db): schema_str = StringIO(db.attrs['schema']) return Schema.load(schema_str)
def load(self): with open(self.path) as f: return Schema.load(f)
def load(self): with open(self.path) as f: return Schema.load(f)