Пример #1
0
def test_resource():
    with tmpfile('json') as fn:
        assert isinstance(resource('jsonlines://' + fn), JSONLines)
        assert isinstance(resource('json://' + fn), JSON)

        assert isinstance(
            resource(fn, expected_dshape=dshape('var * {a: int}')), JSONLines)
Пример #2
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def tmp_db_uri():
    """Create a temporary postgres database to run the tests against.
    """
    db_name = '_warp_prism_test_' + uuid4().hex
    root = 'postgresql://localhost/'
    uri = root + db_name
    with disposable_engine(root + 'postgres') as e, e.connect() as root_conn:
        root_conn.execute('COMMIT')
        root_conn.execute('CREATE DATABASE %s' % db_name)
        try:
            yield uri
        finally:
            resource(uri).dispose()
            try:
                _dropdb(root_conn, db_name)
            except sa.exc.OperationalError:
                # We couldn't drop the db. The most likely cause is that there
                # are active queries. Even more likely is that these are
                # rollbacks because there was an exception somewhere inside the
                # tests. We will cancel all the running queries and try to drop
                # the database again.
                pid = _pg_stat_activity.c.pid
                root_conn.execute(
                    sa.select((sa.func.pg_terminate_backend(pid), ), ).where(
                        pid != sa.func.pg_backend_pid(), ))
                try:
                    _dropdb(root_conn, db_name)
                except sa.exc.OperationalError:  # pragma: no cover
                    # The database STILL wasn't cleaned up. Just tell the user
                    # to deal with this manually.
                    warnings.warn(
                        "leaking database '%s', please manually delete this" %
                        db_name, )
Пример #3
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def test_foreign_keys_as_compound_primary_key():
    with tmpfile('db') as fn:
        suppliers = resource(
            'sqlite:///%s::suppliers' % fn,
            dshape='var * {id: int64, name: string}',
            primary_key=['id']
        )
        parts = resource(
            'sqlite:///%s::parts' % fn,
            dshape='var * {id: int64, name: string, region: string}',
            primary_key=['id']
        )
        suppart = resource(
            'sqlite:///%s::suppart' % fn,
            dshape='var * {supp_id: map[int64, T], part_id: map[int64, U]}',
            foreign_keys={
                'supp_id': suppliers.c.id,
                'part_id': parts.c.id
            },
            primary_key=['supp_id', 'part_id']
        )
        expected = dshape("""
            var * {
                supp_id: map[int64, {id: int64, name: string}],
                part_id: map[int64, {id: int64, name: string, region: string}]
            }
        """)
        result = discover(suppart)
        assert result == expected
Пример #4
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def test_compound_primary_key_with_single_reference():
    with tmpfile('db') as fn:
        products = resource('sqlite:///%s::products' % fn,
                            dshape="""
                                var * {
                                    product_no: int32,
                                    product_sku: string,
                                    name: ?string,
                                    price: ?float64
                                }
                            """, primary_key=['product_no', 'product_sku'])
        # TODO: should this fail everywhere? e.g., this fails in postgres, but
        # not in sqlite because postgres doesn't allow partial foreign keys
        # might be best to let the backend handle this
        ds = dshape("""var * {
                          order_id: int32,
                          product_no: map[int32, T],
                          quantity: ?int32
                        }""")
        orders = resource('sqlite:///%s::orders' % fn, dshape=ds,
                          foreign_keys=dict(product_no=products.c.product_no),
                          primary_key=['order_id'])
        assert discover(orders) == dshape(
            """var * {
                order_id: int32,
                product_no: map[int32, {product_no: int32, product_sku: string, name: ?string, price: ?float64}],
                quantity: ?int32
            }
            """
        )
Пример #5
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def test_discover_foreign_keys():
    with tmpfile('db') as fn:
        products = resource('sqlite:///%s::products' % fn,
                            dshape="""
                                var * {
                                    product_no: int32,
                                    name: ?string,
                                    price: ?float64
                                }
                            """,
                            primary_key=['product_no'])
        expected = dshape("""var * {
                          order_id: int32,
                          product_no: map[int32, {
                            product_no: int32,
                            name: ?string,
                            price: ?float64
                          }],
                          quantity: ?int32
                        }""")
        orders = resource('sqlite:///%s::orders' % fn,
                          dshape=expected,
                          foreign_keys=dict(product_no=products.c.product_no))
        result = discover(orders)
        assert result == expected
Пример #6
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def test_compound_primary_key_with_fkey():
    with tmpfile('db') as fn:
        products = resource('sqlite:///%s::products' % fn,
                            dshape="""
                                var * {
                                    product_no: int32,
                                    product_sku: string,
                                    name: ?string,
                                    price: ?float64
                                }
                            """,
                            primary_key=['product_no', 'product_sku'])
        ds = dshape("""var * {
                          order_id: int32,
                          product_no: map[int32, T],
                          product_sku: map[int32, U],
                          quantity: ?int32
                        }""")
        orders = resource('sqlite:///%s::orders' % fn, dshape=ds,
                          primary_key=['order_id'],
                          foreign_keys={
                              'product_no': products.c.product_no,
                              'product_sku': products.c.product_sku
                          })
        assert discover(orders) == dshape(
            """var * {
                order_id: int32,
                product_no: map[int32, {product_no: int32, product_sku: string, name: ?string, price: ?float64}],
                product_sku: map[int32, {product_no: int32, product_sku: string, name: ?string, price: ?float64}],
                quantity: ?int32
            }
            """
        )
Пример #7
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def test_resource():
    with tmpfile('json') as fn:
        assert isinstance(resource('jsonlines://' + fn), JSONLines)
        assert isinstance(resource('json://' + fn), JSON)

        assert isinstance(resource(fn, expected_dshape=dshape('var * {a: int}')),
                          JSONLines)
Пример #8
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def test_foreign_keys_auto_construct():
    with tmpfile('db') as fn:
        products = resource('sqlite:///%s::products' % fn,
                            dshape="""
                                var * {
                                    product_no: int32,
                                    name: ?string,
                                    price: ?float64
                                }
                            """,
                            primary_key=['product_no'])
        ds = dshape("""var * {
                          order_id: int32,
                          product_no: map[int32, T],
                          quantity: ?int32
                        }""")
        orders = resource('sqlite:///%s::orders' % fn, dshape=ds,
                          foreign_keys=dict(product_no=products.c.product_no),
                          primary_key=['order_id'])
        assert discover(orders) == dshape("""
            var * {
                order_id: int32,
                product_no: map[int32, {
                                    product_no: int32,
                                    name: ?string,
                                    price: ?float64
                                }],
                quantity: ?int32
            }
        """)
Пример #9
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def test_resource_gzip():
    with tmpfile('json.gz') as fn:
        assert isinstance(resource(fn), (JSON, JSONLines))
        assert isinstance(resource('json://' + fn), (JSON, JSONLines))
        assert isinstance(resource('jsonlines://' + fn), (JSON, JSONLines))

    with tmpfile('jsonlines.gz'):
        assert isinstance(resource('jsonlines://' + fn), (JSON, JSONLines))
Пример #10
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def test_small_chunk_size():
    normal = convert(Temp(CSV), resource(iris_url))
    small_chunk = convert(Temp(CSV), resource(iris_url, chunk_size=1))
    with open(normal.path, 'rb') as fn:
        normal_data = fn.read()
    with open(small_chunk.path, 'rb') as fn:
        small_chunk_data = fn.read()
    assert normal_data == small_chunk_data
Пример #11
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def test_small_chunk_size():
    normal = convert(Temp(CSV), resource(iris_url))
    small_chunk = convert(Temp(CSV), resource(iris_url, chunk_size=1))
    with open(normal.path, 'rb') as fn:
        normal_data = fn.read()
    with open(small_chunk.path, 'rb') as fn:
        small_chunk_data = fn.read()
    assert normal_data == small_chunk_data
Пример #12
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def test_engine_metadata_caching():
    with tmpfile('db') as fn:
        engine = resource('sqlite:///' + fn)
        a = resource('sqlite:///' + fn + '::a', dshape=dshape('var * {x: int}'))
        b = resource('sqlite:///' + fn + '::b', dshape=dshape('var * {y: int}'))

        assert a.metadata is b.metadata
        assert engine is a.bind is b.bind
Пример #13
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def test_sample_different_line_counts():
    with sample(resource(iris_url), lines=10) as fn:
        with open(fn, 'r') as f:
            assert len(list(f)) == 10

    with sample(resource(iris_url), lines=5) as fn:
        with open(fn, 'r') as f:
            assert len(list(f)) == 5
Пример #14
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def test_resource_gzip():
    with tmpfile('json.gz') as fn:
        assert isinstance(resource(fn), (JSON, JSONLines))
        assert isinstance(resource('json://' + fn), (JSON, JSONLines))
        assert isinstance(resource('jsonlines://' + fn), (JSON, JSONLines))

    with tmpfile('jsonlines.gz'):
        assert isinstance(resource('jsonlines://' + fn), (JSON, JSONLines))
Пример #15
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def test_engine_metadata_caching():
    with tmpfile("db") as fn:
        engine = resource("sqlite:///" + fn)
        a = resource("sqlite:///" + fn + "::a", dshape=dshape("var * {x: int}"))
        b = resource("sqlite:///" + fn + "::b", dshape=dshape("var * {y: int}"))

        assert a.metadata is b.metadata
        assert engine is a.bind is b.bind
Пример #16
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def test_resource_on_file():
    with tmpfile(".db") as fn:
        uri = "sqlite:///" + fn
        sql = resource(uri, "foo", dshape="var * {x: int, y: int}")
        assert isinstance(sql, sa.Table)

    with tmpfile(".db") as fn:
        uri = "sqlite:///" + fn
        sql = resource(uri + "::" + "foo", dshape="var * {x: int, y: int}")
        assert isinstance(sql, sa.Table)
Пример #17
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def test_foreign_keys_bad_field():
    with tmpfile('db') as fn:
        expected = dshape("""var * {
                          order_id: int32,
                          product_no: int64,
                          quantity: ?int32
                        }""")
        with pytest.raises(TypeError):
            resource('sqlite:///%s::orders' % fn, dshape=expected,
                     foreign_keys=dict(foo='products.product_no'))
Пример #18
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def test_engine_metadata_caching():
    with tmpfile('db') as fn:
        engine = resource('sqlite:///' + fn)
        a = resource(
            'sqlite:///' + fn + '::a', dshape=dshape('var * {x: int}'))
        b = resource(
            'sqlite:///' + fn + '::b', dshape=dshape('var * {y: int}'))

        assert a.metadata is b.metadata
        assert engine is a.bind is b.bind
Пример #19
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def test_drop_reflects_database_state(url):
    data = list(zip(range(5), range(1, 6)))

    t = odo(data, url, dshape='var * {A: int64, B: int64}')
    assert t.exists()
    assert resource(url).exists()

    drop(url)
    with pytest.raises(ValueError):
        resource(url)  # Table doesn't exist and no dshape
Пример #20
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def test_resource_on_file():
    with tmpfile('.db') as fn:
        uri = 'sqlite:///' + fn
        sql = resource(uri, 'foo', dshape='var * {x: int, y: int}')
        assert isinstance(sql, sa.Table)

    with tmpfile('.db') as fn:
        uri = 'sqlite:///' + fn
        sql = resource(uri + '::' + 'foo', dshape='var * {x: int, y: int}')
        assert isinstance(sql, sa.Table)
Пример #21
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def test_invalid_foreign_keys():
    with tmpfile('db') as fn:
        expected = dshape("""var * {
                          order_id: int32,
                          product_no: map[int32, {
                            product_no: int32,
                            name: ?string,
                            price: ?float64
                          }],
                          quantity: ?int32
                        }""")
        with pytest.raises(TypeError):
            resource('sqlite:///%s::orders' % fn, dshape=expected)
Пример #22
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def sql_two_tables(url):
    dshape = 'var * {a: int32}'
    try:
        t = resource(url % next(names), dshape=dshape)
        u = resource(url % next(names), dshape=dshape)
    except sa.exc.OperationalError as e:
        pytest.skip(str(e))
    else:
        try:
            yield u, t
        finally:
            drop(t)
            drop(u)
def test_join_count():
    ds = datashape.dshape('{t1: var * {x: int, y: int}, t2: var * {a: int, b: int}}')
    engine = resource('sqlite:///:memory:', dshape=ds)
    db = symbol('db', ds)

    expr = join(db.t1[db.t1.x > -1], db.t2, 'x', 'a').count()

    result = compute(expr, {db: engine}, post_compute=False)

    expected1 = """
    SELECT count(alias.x) as count
    FROM (SELECT t1.x AS x, t1.y AS y, t2.b AS b
          FROM t1 JOIN t2 ON t1.x = t2.a
          WHERE t1.x > ?) as alias
          """
    expected2 = """
    SELECT count(alias2.x) AS __count
    FROM (SELECT alias1.x AS x, alias1.y AS y, t2.b AS b
          FROM (SELECT t1.x AS x, t1.y AS y
                FROM t1
                WHERE t1.x > ?) AS alias1
          JOIN t2 ON alias1.x = t2.a) AS alias2"""


    assert (normalize(str(result)) == normalize(expected1) or
            normalize(str(result)) == normalize(expected2))
Пример #24
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def test_resource_no_info():
    with tmpfile('.hdf5') as fn:
        r = resource('hdfstore://' + fn)
        try:
            assert isinstance(r, pd.HDFStore)
        finally:
            r.close()
Пример #25
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def test_fixed_shape():
    with tmpfile('.hdf5') as fn:
        df.to_hdf(fn, 'foo')
        r = resource('hdfstore://' + fn + '::/foo')
        assert isinstance(r.shape, list)
        assert discover(r).shape == (len(df), )
        r.parent.close()
Пример #26
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def test_resource():
    res = resource('cql://test-host:9042/keyspace::table')
    assert isinstance(res, Cassandra)
    assert res.host == 'test-host'
    assert res.port == '9042'
    assert res.keyspace == 'keyspace'
    assert res.table == 'table'
Пример #27
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def test_simple_into(tbl):
    csv = CSV(file_name)
    sql = resource(url, tbl, dshape=ds)

    into(sql, csv, dshape=ds)

    assert into(list, sql) == data
Пример #28
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    def from_uri(
        cls,
        uri: str,
        index_col: bool = False,
        source: Optional[DataObject] = None,
        **kwargs
    ) -> "JsonFileDataset":
        resource = odo.resource(uri)
        methods = [
            lambda: JsonFileDataset._read_normalized(uri, **kwargs),
            lambda: JsonFileDataset._read_normalized_lines(uri, **kwargs),
            lambda: pd.read_json(uri, lines=True, **kwargs),
            lambda: odo.odo(uri, pd.DataFrame, index_col=index_col, **kwargs),
        ]

        result = None
        for method in methods:
            try:
                data = method()
                result = cls(inner_data=data, uri=uri, source=source, **kwargs)
                break
            except:
                pass

        if result:
            if not result.name:
                result.inner_data.name = os.path.splitext(os.path.basename(uri))[0]
            return result
        raise RuntimeError("No JSON reading method understands the file.")
Пример #29
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def test_resource():
    sql = resource('sqlite:///:memory:::mytable',
                   dshape='var * {x: int, y: int}')
    assert isinstance(sql, sa.Table)
    assert sql.name == 'mytable'
    assert isinstance(sql.bind, sa.engine.base.Engine)
    assert set(c.name for c in sql.c) == set(['x', 'y'])
Пример #30
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	def correct_commodities():
	src_dir = path.join(data_dir, 'agmarknet/by_commodity')
	init_dir = os.getcwd()
	os.chdir(src_dir)
	folders = glob.glob('*')
	csv_dir = os.getcwd()
	for folder in folders:
		os.chdir(path.join(csv_dir, folder))
		files = glob.glob('*_all.csv')
		for file in files:
			csvr = odo.resource(path.join(csv_dir, folder, file))  # Have to use resource to discover URIs
			num_col = len(odo.discover(csvr)[1].types)	
			ds = None
			if num_col == 9:
				ds = bz.dshape("var * {date: datetime, state: ?string, market: ?string, commodity: ?string, variety: ?string, arrival: ?string, min: ?string, max: ?string, modal: ?string}")
			elif num_col == 10:	
				ds = bz.dshape("var * {date: datetime, state: ?string, market: ?string, commodity: ?string, variety: ?string, arrival: ?string, grade: ?string, min: ?string, max: ?string, modal: ?string}")
			else:
				ds = odo.discover(csvr)

			d = bz.Data(path.join(csv_dir, folder, file), dshape=ds)
			if num_col == 10:
				d = bz.transform(d, grade=d.grade.map(lambda x: x.strip(), 'string'))

			d = bz.transform(d, commodity=d.commodity.map(lambda x: x.strip(), 'string'))
			d = bz.transform(d, commodity=d.commodity.map(lambda x: commodity_corrections[x] if x in commodity_corrections else x, 'string'))
			d = bz.transform(d, state=d.state.map(lambda x: x.strip(), 'string'))
			d = bz.transform(d, state=d.state.map(lambda x: state_corrections[x] if x in state_corrections else x, 'string'))
			d = bz.transform(d, market=d.market.map(lambda x: x.strip(), 'string'))

	return
Пример #31
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def test_transaction():
    with tmpfile('.db') as fn:
        rsc = resource('sqlite:///%s::table' % fn, dshape='var * {a: int}')

    data = [(1,), (2,), (3,)]

    conn_1 = rsc.bind.connect()
    conn_2 = rsc.bind.connect()

    trans_1 = conn_1.begin()
    conn_2.begin()

    odo(data, rsc, bind=conn_1)

    # inside the transaction the write should be there
    assert odo(rsc, list, bind=conn_1) == data

    # outside of a transaction or in a different transaction the write is not
    # there
    assert odo(rsc, list) == odo(rsc, list, bind=conn_2) == []

    trans_1.commit()

    # now the data should appear outside the transaction
    assert odo(rsc, list) == odo(rsc, list, bind=conn_2) == data
Пример #32
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def test_transaction():
    with tmpfile('.db') as fn:
        rsc = resource('sqlite:///%s::table' % fn, dshape='var * {a: int}')

    data = [(1,), (2,), (3,)]

    conn_1 = rsc.bind.connect()
    conn_2 = rsc.bind.connect()

    trans_1 = conn_1.begin()
    conn_2.begin()

    odo(data, rsc, bind=conn_1)

    # inside the transaction the write should be there
    assert odo(rsc, list, bind=conn_1) == data

    # outside of a transaction or in a different transaction the write is not
    # there
    assert odo(rsc, list) == odo(rsc, list, bind=conn_2) == []

    trans_1.commit()

    # now the data should appear outside the transaction
    assert odo(rsc, list) == odo(rsc, list, bind=conn_2) == data
Пример #33
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def test_resource_collection(mongo_host_port):
    host, port = mongo_host_port
    coll = resource('mongodb://{}:{}/db::mycoll'.format(*mongo_host_port))
    assert coll.name == 'mycoll'
    assert coll.database.name == 'db'
    assert coll.database.connection.host == host
    assert coll.database.connection.port == port
Пример #34
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def s3_bucket(extension):
    with conn():
        b = 's3://%s/%s%s' % (test_bucket_name, next(_tmps), extension)
        try:
            yield b
        finally:
            drop(resource(b))
Пример #35
0
def test_numeric_create():
    tbl = resource('sqlite:///:memory:::test',
                   dshape='var * {a: ?decimal[11, 2], b: decimal[10, 6]}')
    assert tbl.c.a.nullable
    assert not tbl.c.b.nullable
    assert isinstance(tbl.c.a.type, sa.NUMERIC)
    assert isinstance(tbl.c.b.type, sa.NUMERIC)
Пример #36
0
    def from_uri(cls, uri: str, index_col=False, source: Optional[DataObject] = None, **kwargs) -> "CSVFile":
        resource = odo.resource(uri)
        if hasattr(resource, "dialect"):
            kwargs.update(resource.dialect)

        methods = [
            lambda: pd.read_csv(uri, index_col=index_col, **kwargs),
            lambda: pd.read_csv(uri, index_col=index_col, engine="python", sep=None, **kwargs),
            lambda: odo.odo(uri, pd.DataFrame, index_col=index_col, **kwargs),
            lambda: cls._fallback_read(uri, **kwargs),
        ]
        result = None
        for method in methods:
            try:
                data = method()
                result = cls(inner_data=data, uri=uri, source=source, **kwargs)
                break
            except:
                pass
        if result:
            if not result.name:
                import os

                result.inner_data.name = os.path.splitext(os.path.basename(uri))[0]
            return result
        raise RuntimeError(
            "No CSV reading method understands the file: {0}".format(uri)
        )
Пример #37
0
def s3_bucket(extension):
    with conn():
        b = 's3://%s/%s%s' % (test_bucket_name, next(_tmps), extension)
        try:
            yield b
        finally:
            drop(resource(b))
Пример #38
0
def test_fixed_shape():
    with tmpfile('.hdf5') as fn:
        df.to_hdf(fn, 'foo')
        r = resource('hdfstore://'+fn+'::/foo')
        assert isinstance(r.shape, list)
        assert discover(r).shape == (len(df),)
        r.parent.close()
Пример #39
0
def test_s3_to_sqlite():
    with tmpfile('.db') as fn:
        tb = into('sqlite:///%s::tips' % fn,
                  tips_uri,
                  dshape=discover(resource(tips_uri)))
        lhs = into(list, tb)
        assert lhs == into(list, tips_uri)
Пример #40
0
def test_resource_no_info():
    with tmpfile('.hdf5') as fn:
        r = resource('hdfstore://' + fn)
        try:
            assert isinstance(r, pd.HDFStore)
        finally:
            r.close()
Пример #41
0
def test_no_header_no_columns(tbl):
    csv = CSV(file_name)
    sql = resource(url, tbl, dshape=ds)

    into(sql, csv, dshape=ds)

    assert into(list, sql) == data
Пример #42
0
def test_join_count():
    ds = datashape.dshape(
        '{t1: var * {x: int, y: int}, t2: var * {a: int, b: int}}')
    engine = resource('sqlite:///:memory:', dshape=ds)
    db = symbol('db', ds)

    expr = join(db.t1[db.t1.x > -1], db.t2, 'x', 'a').count()

    result = compute(expr, {db: engine}, post_compute=False)

    expected1 = """
    SELECT count(alias.x) as count
    FROM (SELECT t1.x AS x, t1.y AS y, t2.b AS b
          FROM t1 JOIN t2 ON t1.x = t2.a
          WHERE t1.x > ?) as alias
          """
    expected2 = """
    SELECT count(alias2.x) AS count
    FROM (SELECT alias1.x AS x, alias1.y AS y, t2.b AS b
          FROM (SELECT t1.x AS x, t1.y AS y
                FROM t1
                WHERE t1.x > ?) AS alias1
          JOIN t2 ON alias1.x = t2.a) AS alias2"""

    assert (normalize(str(result)) == normalize(expected1)
            or normalize(str(result)) == normalize(expected2))
Пример #43
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def test_s3_jsonlines_discover():
    json_dshape = discover(resource('s3://nyqpug/tips.json'))
    names = list(map(str, sorted(json_dshape.measure.names)))
    assert names == ['day', 'sex', 'size', 'smoker', 'time', 'tip',
                     'total_bill']
    types = [json_dshape.measure[name] for name in names]
    assert types == [string, string, int64, string, string, float64, float64]
Пример #44
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def test_resource_collection(mongo_host_port):
    host, port = mongo_host_port
    coll = resource('mongodb://{}:{}/db::mycoll'.format(*mongo_host_port))
    assert coll.name == 'mycoll'
    assert coll.database.name == 'db'
    assert coll.database.connection.host == host
    assert coll.database.connection.port == port
Пример #45
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def sql(url):
    try:
        t = resource(url, dshape='var * {a: int32, b: int32}')
    except sa.exc.OperationalError as e:
        pytest.skip(str(e))
    else:
        yield t
        drop(t)
Пример #46
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def csv_to_db(csv_file, table_name, db_con='subway.db'):
    dshape = discover(resource(csv_file))
    uri = 'sqlite:///' + db_con + '::' + table_name
    try:
        odo(csv_file, uri, dshape=dshape)
        print "Data loaded"
    except:
        print "Problems loading data"
Пример #47
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def fsql(engine, fcsv, name):
    try:
        t = resource('%s::%s' % (url, name), dshape=discover(fcsv))
    except sqlalchemy.exc.OperationalError as e:
        pytest.skip(str(e))
    else:
        yield t
        drop(t)
Пример #48
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def test_numeric_append():
    tbl = resource('sqlite:///:memory:::test',
                   dshape='var * {a: decimal[11, 2], b: ?decimal[10, 6]}')
    data = [(1.0, 2.0), (2.0, 3.0)]
    tbl = odo(data, tbl)
    assert odo(tbl, list) == list(
        map(lambda row: tuple(map(Decimal, row)),
            tbl.select().execute().fetchall()))