Example #1
0
    def read_from_text(cls, path, delimiter, nrows, verbose):
        """
        Load RDD from a text file
        """
        # TODO handle nrows, verbose
        cls._entry(path=path, delimiter=delimiter, nrows=nrows)
        sc = CommonSparkContext.spark_context()
        if delimiter is None:
            rdd = sc.textFile(path)
            res = rdd.map(lambda line: line.encode('utf-8'))
        else:
            conf = {'textinputformat.record.delimiter': delimiter}
            rdd = sc.newAPIHadoopFile(
                path,
                "org.apache.hadoop.mapreduce.lib.input.TextInputFormat",
                "org.apache.hadoop.io.Text",
                "org.apache.hadoop.io.Text",
                conf=conf)

            def fixup_line(line):
                return str(line).replace('\n', ' ').strip()

            res = rdd.values().map(lambda line: fixup_line(line))
        lineage = Lineage.init_array_lineage(path)
        return XArrayImpl(res, str, lineage)
Example #2
0
 def _rv_frame(rdd, col_names=None, col_types=None, lineage=None):
     """
     Return a new XFrameImpl containing the rdd, column names, and element types
     """
     # noinspection PyUnresolvedReferences
     lineage = lineage or Lineage.init_frame_lineage(Lineage.RDD, col_names)
     return xframes.xframe_impl.XFrameImpl(rdd, col_names, col_types, lineage)
Example #3
0
 def load_from_const(cls, value, size):
     """
     Load RDD from const value.
     """
     cls._entry(value=value, size=size)
     values = [value for _ in xrange(0, size)]
     sc = CommonSparkContext.spark_context()
     return cls(XRdd(sc.parallelize(values)), type(value), Lineage.init_array_lineage(Lineage.CONST))
Example #4
0
 def _rv_frame(rdd, col_names=None, col_types=None, lineage=None):
     """
     Return a new XFrameImpl containing the rdd, column names, and element types
     """
     # noinspection PyUnresolvedReferences
     lineage = lineage or Lineage.init_frame_lineage(Lineage.RDD, col_names)
     return xframes.xframe_impl.XFrameImpl(rdd, col_names, col_types,
                                           lineage)
Example #5
0
 def load_from_const(cls, value, size):
     """
     Load RDD from const value.
     """
     cls._entry(value=value, size=size)
     values = [value for _ in xrange(0, size)]
     sc = CommonSparkContext.spark_context()
     return cls(XRdd(sc.parallelize(values)), type(value),
                Lineage.init_array_lineage(Lineage.CONST))
Example #6
0
    def load_from_iterable(cls, values, dtype, ignore_cast_failure):
        """
        Load RDD from values given by iterable.

        Note
        ----
        Values must not only be iterable, but also it must support len and __getitem__

        Modifies the existing RDD: does not return a new XArray.
        """
        cls._entry(dtype=dtype, ignore_cast_failure=ignore_cast_failure)
        dtype = dtype or None
        sc = CommonSparkContext.spark_context()
        try:
            if len(values) == 0:
                dtype = dtype or infer_type_of_list(values[0:100])
                return XArrayImpl(XRdd(sc.parallelize([])), dtype)
        except TypeError:
            # get here if values does not support len or __getitem
            pass

        if dtype is None:
            # try iterating and see if we get something
            cpy = copy.copy(values)
            for val in cpy:
                dtype = infer_type_of_list([val])
                break

        if dtype is None:
            raise TypeError('Cannot determine types.')

        # noinspection PyShadowingNames
        def do_cast(x, dtype, ignore_cast_failure):
            if is_missing(x):
                return x
            if isinstance(x, str) and dtype is datetime.datetime:
                return date_parser.parse(x)
            if isinstance(x, dtype):
                return x
            try:
                return dtype(x)
            except (ValueError, TypeError):
                # TODO: this does not seem to catch as it should
                return None if ignore_cast_failure else ValueError

        raw_rdd = XRdd(sc.parallelize(values))
        rdd = raw_rdd.map(lambda x: do_cast(x, dtype, ignore_cast_failure))
        if not ignore_cast_failure:
            errs = len(rdd.filter(lambda x: x is ValueError).take(1)) == 1
            if errs:
                raise ValueError

        return cls(rdd, dtype, Lineage.init_array_lineage(Lineage.PROGRAM))
Example #7
0
    def load_from_iterable(cls, values, dtype, ignore_cast_failure):
        """
        Load RDD from values given by iterable.

        Note
        ----
        Values must not only be iterable, but also it must support len and __getitem__

        Modifies the existing RDD: does not return a new XArray.
        """
        cls._entry(dtype=dtype, ignore_cast_failure=ignore_cast_failure)
        dtype = dtype or None
        sc = CommonSparkContext.spark_context()
        try:
            if len(values) == 0:
                dtype = dtype or infer_type_of_list(values[0:100])
                return XArrayImpl(XRdd(sc.parallelize([])), dtype)
        except TypeError:
            # get here if values does not support len or __getitem
            pass

        if dtype is None:
            # try iterating and see if we get something
            cpy = copy.copy(values)
            for val in cpy:
                dtype = infer_type_of_list([val])
                break

        if dtype is None:
            raise TypeError('Cannot determine types.')

        # noinspection PyShadowingNames
        def do_cast(x, dtype, ignore_cast_failure):
            if is_missing(x):
                return x
            if isinstance(x, str) and dtype is datetime.datetime:
                return date_parser.parse(x)
            if isinstance(x, dtype):
                return x
            try:
                return dtype(x)
            except (ValueError, TypeError):
                # TODO: this does not seem to catch as it should
                return None if ignore_cast_failure else ValueError

        raw_rdd = XRdd(sc.parallelize(values))
        rdd = raw_rdd.map(lambda x: do_cast(x, dtype, ignore_cast_failure))
        if not ignore_cast_failure:
            errs = len(rdd.filter(lambda x: x is ValueError).take(1)) == 1
            if errs:
                raise ValueError

        return cls(rdd, dtype, Lineage.init_array_lineage(Lineage.PROGRAM))
Example #8
0
 def create_sequential_xarray(size, start, reverse):
     """
     Create RDD with sequential integer values of given size and starting pos.
     """
     if not reverse:
         stop = start + size
         step = 1
     else:
         stop = start - size
         step = -1
     sc = CommonSparkContext.spark_context()
     rdd = XRdd(sc.parallelize(range(start, stop, step)))
     return XArrayImpl(rdd, int, Lineage.init_array_lineage(Lineage.RANGE))
Example #9
0
 def create_sequential_xarray(size, start, reverse):
     """
     Create RDD with sequential integer values of given size and starting pos.
     """
     if not reverse:
         stop = start + size
         step = 1
     else:
         stop = start - size
         step = -1
     sc = CommonSparkContext.spark_context()
     rdd = XRdd(sc.parallelize(range(start, stop, step)))
     return XArrayImpl(rdd, int, Lineage.init_array_lineage(Lineage.RANGE))
Example #10
0
 def __init__(self, rdd=None, elem_type=None, lineage=None):
     # The RDD holds all the data for the XArray.
     # The rows must be of a single type.
     # Types permitted include int, long, float, string, list, and dict.
     # We record the element type here.
     self._entry(elem_type=elem_type)
     if rdd is None:
         sc = CommonSparkContext.spark_context()
         rdd = XRdd(sc.parallelize([]))
     super(XArrayImpl, self).__init__(rdd)
     self.elem_type = elem_type
     self.lineage = lineage or Lineage.init_array_lineage(Lineage.EMPTY)
     self.materialized = False
     self.iter_pos = 0
Example #11
0
 def __init__(self, rdd=None, elem_type=None, lineage=None):
     # The RDD holds all the data for the XArray.
     # The rows must be of a single type.
     # Types permitted include int, long, float, string, list, and dict.
     # We record the element type here.
     self._entry(elem_type=elem_type)
     if rdd is None:
         sc = CommonSparkContext.spark_context()
         rdd = XRdd(sc.parallelize([]))
     super(XArrayImpl, self).__init__(rdd)
     self.elem_type = elem_type
     self.lineage = lineage or Lineage.init_array_lineage(Lineage.EMPTY)
     self.materialized = False
     self.iter_pos = 0
Example #12
0
    def load_autodetect(cls, path, dtype):
        """
        Load from the given path.

        This can be anything that spark will read from: local file or HDFS file.
        It can also be a directory, and spark will read and concatenate them all.
        """
        # Read the file as string
        # Examine the first 100 lines, and cast if necessary to int, float, or datetime
        cls._entry(path=path, dtype=dtype)
        # If the path is a directory, then look for sarray-data file in the directory.
        # If the path is a file, look for that file
        # Use type inference to determine the element type.
        # Passed-in dtype is always str and is ignored.
        lineage = Lineage.init_array_lineage(path)
        sc = CommonSparkContext.spark_context()
        if os.path.isdir(path):
            res = XRdd(sc.pickleFile(path))
            metadata_path = os.path.join(path, '_metadata')
            with fileio.open_file(metadata_path) as f:
                dtype = pickle.load(f)
            lineage_path = os.path.join(path, '_lineage')
            if fileio.exists(lineage_path):
                lineage = Lineage.load(lineage_path)
        else:
            res = XRdd(sc.textFile(path, use_unicode=False))
            dtype = infer_type(res)

        if dtype != str:
            if dtype in (list, dict):
                res = res.map(lambda x: ast.literal_eval(x))
            elif dtype is datetime.datetime:
                res = res.map(lambda x: date_parser.parse(x))
            else:
                res = res.map(lambda x: dtype(x))
        return cls(res, dtype, lineage)
Example #13
0
    def load_autodetect(cls, path, dtype):
        """
        Load from the given path.

        This can be anything that spark will read from: local file or HDFS file.
        It can also be a directory, and spark will read and concatenate them all.
        """
        # Read the file as string
        # Examine the first 100 lines, and cast if necessary to int, float, or datetime
        cls._entry(path=path, dtype=dtype)
        # If the path is a directory, then look for sarray-data file in the directory.
        # If the path is a file, look for that file
        # Use type inference to determine the element type.
        # Passed-in dtype is always str and is ignored.
        lineage = Lineage.init_array_lineage(path)
        sc = CommonSparkContext.spark_context()
        if os.path.isdir(path):
            res = XRdd(sc.pickleFile(path))
            metadata_path = os.path.join(path, '_metadata')
            with fileio.open_file(metadata_path) as f:
                dtype = pickle.load(f)
            lineage_path = os.path.join(path, '_lineage')
            if fileio.exists(lineage_path):
                lineage = Lineage.load(lineage_path)
        else:
            res = XRdd(sc.textFile(path, use_unicode=False))
            dtype = infer_type(res)

        if dtype != str:
            if dtype in (list, dict):
                res = res.map(lambda x: ast.literal_eval(x))
            elif dtype is datetime.datetime:
                res = res.map(lambda x: date_parser.parse(x))
            else:
                res = res.map(lambda x: dtype(x))
        return cls(res, dtype, lineage)
Example #14
0
    def copy_range(self, start, step, stop):
        """
        Returns an RDD consisting of the values between start and stop, counting by step.
        """
        self._entry(start=start, step=step, stop=stop)

        # noinspection PyShadowingNames
        def select_row(x, start, step, stop):
            if x < start or x >= stop:
                return False
            return (x - start) % step == 0
        pairs = self._rdd.zipWithIndex()
        res = pairs.filter(lambda x: select_row(x[1], start, step, stop)).map(lambda x: x[0])
        lineage = Lineage.init_array_lineage(Lineage.RANGE)
        return self._rv(res, lineage=lineage)
Example #15
0
    def copy_range(self, start, step, stop):
        """
        Returns an RDD consisting of the values between start and stop, counting by step.
        """
        self._entry(start=start, step=step, stop=stop)

        # noinspection PyShadowingNames
        def select_row(x, start, step, stop):
            if x < start or x >= stop:
                return False
            return (x - start) % step == 0

        pairs = self._rdd.zipWithIndex()
        res = pairs.filter(lambda x: select_row(x[1], start, step, stop)).map(
            lambda x: x[0])
        lineage = Lineage.init_array_lineage(Lineage.RANGE)
        return self._rv(res, lineage=lineage)
Example #16
0
    def read_from_text(cls, path, delimiter, nrows, verbose):
        """
        Load RDD from a text file
        """
        # TODO handle nrows, verbose
        cls._entry(path=path, delimiter=delimiter, nrows=nrows)
        sc = CommonSparkContext.spark_context()
        if delimiter is None:
            rdd = sc.textFile(path)
            res = rdd.map(lambda line: line.encode('utf-8'))
        else:
            conf = {'textinputformat.record.delimiter': delimiter}
            rdd = sc.newAPIHadoopFile(path,
                                      "org.apache.hadoop.mapreduce.lib.input.TextInputFormat",
                                      "org.apache.hadoop.io.Text",
                                      "org.apache.hadoop.io.Text",
                                      conf=conf)

            def fixup_line(line):
                return str(line).replace('\n', ' ').strip()
            res = rdd.values().map(lambda line: fixup_line(line))
        lineage = Lineage.init_array_lineage(path)
        return XArrayImpl(res, str, lineage)
Example #17
0
 def from_rdd(cls, rdd, dtype, lineage=None):
     if lineage:
         cls(rdd, dtype, lineage=Lineage.from_dict(lineage))
     return cls(rdd, dtype, Lineage.init_array_lineage(Lineage.RDD))
Example #18
0
 def from_rdd(cls, rdd, dtype, lineage=None):
     if lineage:
         cls(rdd, dtype, lineage=Lineage.from_dict(lineage))
     return cls(rdd, dtype, Lineage.init_array_lineage(Lineage.RDD))