craftbeerpi4-pione/venv/lib/python3.8/site-packages/pandas/io/sas/sas7bdat.py

"""
Read SAS7BDAT files

Based on code written by Jared Hobbs:
  https://bitbucket.org/jaredhobbs/sas7bdat

See also:
  https://github.com/BioStatMatt/sas7bdat

Partial documentation of the file format:
  https://cran.r-project.org/package=sas7bdat/vignettes/sas7bdat.pdf

Reference for binary data compression:
  http://collaboration.cmc.ec.gc.ca/science/rpn/biblio/ddj/Website/articles/CUJ/1992/9210/ross/ross.htm
"""
from collections import abc
from datetime import datetime, timedelta
import struct
from typing import IO, Any, Union, cast

import numpy as np

from pandas.errors import EmptyDataError, OutOfBoundsDatetime

import pandas as pd

from pandas.io.common import get_handle
from pandas.io.sas._sas import Parser
import pandas.io.sas.sas_constants as const
from pandas.io.sas.sasreader import ReaderBase


def _convert_datetimes(sas_datetimes: pd.Series, unit: str) -> pd.Series:
    """
    Convert to Timestamp if possible, otherwise to datetime.datetime.
    SAS float64 lacks precision for more than ms resolution so the fit
    to datetime.datetime is ok.

    Parameters
    ----------
    sas_datetimes : {Series, Sequence[float]}
       Dates or datetimes in SAS
    unit : {str}
       "d" if the floats represent dates, "s" for datetimes

    Returns
    -------
    Series
       Series of datetime64 dtype or datetime.datetime.
    """
    try:
        return pd.to_datetime(sas_datetimes, unit=unit, origin="1960-01-01")
    except OutOfBoundsDatetime:
        if unit == "s":
            return sas_datetimes.apply(
                lambda sas_float: datetime(1960, 1, 1) + timedelta(seconds=sas_float)
            )
        elif unit == "d":
            return sas_datetimes.apply(
                lambda sas_float: datetime(1960, 1, 1) + timedelta(days=sas_float)
            )
        else:
            raise ValueError("unit must be 'd' or 's'")


class _SubheaderPointer:
    offset: int
    length: int
    compression: int
    ptype: int

    def __init__(self, offset: int, length: int, compression: int, ptype: int):
        self.offset = offset
        self.length = length
        self.compression = compression
        self.ptype = ptype


class _Column:
    col_id: int
    name: Union[str, bytes]
    label: Union[str, bytes]
    format: Union[str, bytes]  # TODO: i think allowing bytes is from py2 days
    ctype: bytes
    length: int

    def __init__(
        self,
        col_id: int,
        name: Union[str, bytes],
        label: Union[str, bytes],
        format: Union[str, bytes],
        ctype: bytes,
        length: int,
    ):
        self.col_id = col_id
        self.name = name
        self.label = label
        self.format = format
        self.ctype = ctype
        self.length = length


# SAS7BDAT represents a SAS data file in SAS7BDAT format.
class SAS7BDATReader(ReaderBase, abc.Iterator):
    """
    Read SAS files in SAS7BDAT format.

    Parameters
    ----------
    path_or_buf : path name or buffer
        Name of SAS file or file-like object pointing to SAS file
        contents.
    index : column identifier, defaults to None
        Column to use as index.
    convert_dates : boolean, defaults to True
        Attempt to convert dates to Pandas datetime values.  Note that
        some rarely used SAS date formats may be unsupported.
    blank_missing : boolean, defaults to True
        Convert empty strings to missing values (SAS uses blanks to
        indicate missing character variables).
    chunksize : int, defaults to None
        Return SAS7BDATReader object for iterations, returns chunks
        with given number of lines.
    encoding : string, defaults to None
        String encoding.
    convert_text : bool, defaults to True
        If False, text variables are left as raw bytes.
    convert_header_text : bool, defaults to True
        If False, header text, including column names, are left as raw
        bytes.
    """

    def __init__(
        self,
        path_or_buf,
        index=None,
        convert_dates=True,
        blank_missing=True,
        chunksize=None,
        encoding=None,
        convert_text=True,
        convert_header_text=True,
    ):

        self.index = index
        self.convert_dates = convert_dates
        self.blank_missing = blank_missing
        self.chunksize = chunksize
        self.encoding = encoding
        self.convert_text = convert_text
        self.convert_header_text = convert_header_text

        self.default_encoding = "latin-1"
        self.compression = b""
        self.column_names_strings = []
        self.column_names = []
        self.column_formats = []
        self.columns = []

        self._current_page_data_subheader_pointers = []
        self._cached_page = None
        self._column_data_lengths = []
        self._column_data_offsets = []
        self._column_types = []

        self._current_row_in_file_index = 0
        self._current_row_on_page_index = 0
        self._current_row_in_file_index = 0

        self.handles = get_handle(path_or_buf, "rb", is_text=False)

        self._path_or_buf = cast(IO[Any], self.handles.handle)

        try:
            self._get_properties()
            self._parse_metadata()
        except Exception:
            self.close()
            raise

    def column_data_lengths(self):
        """Return a numpy int64 array of the column data lengths"""
        return np.asarray(self._column_data_lengths, dtype=np.int64)

    def column_data_offsets(self):
        """Return a numpy int64 array of the column offsets"""
        return np.asarray(self._column_data_offsets, dtype=np.int64)

    def column_types(self):
        """
        Returns a numpy character array of the column types:
           s (string) or d (double)
        """
        return np.asarray(self._column_types, dtype=np.dtype("S1"))

    def close(self):
        self.handles.close()

    def _get_properties(self):

        # Check magic number
        self._path_or_buf.seek(0)
        self._cached_page = self._path_or_buf.read(288)
        if self._cached_page[0 : len(const.magic)] != const.magic:
            raise ValueError("magic number mismatch (not a SAS file?)")

        # Get alignment information
        align1, align2 = 0, 0
        buf = self._read_bytes(const.align_1_offset, const.align_1_length)
        if buf == const.u64_byte_checker_value:
            align2 = const.align_2_value
            self.U64 = True
            self._int_length = 8
            self._page_bit_offset = const.page_bit_offset_x64
            self._subheader_pointer_length = const.subheader_pointer_length_x64
        else:
            self.U64 = False
            self._page_bit_offset = const.page_bit_offset_x86
            self._subheader_pointer_length = const.subheader_pointer_length_x86
            self._int_length = 4
        buf = self._read_bytes(const.align_2_offset, const.align_2_length)
        if buf == const.align_1_checker_value:
            align1 = const.align_2_value
        total_align = align1 + align2

        # Get endianness information
        buf = self._read_bytes(const.endianness_offset, const.endianness_length)
        if buf == b"\x01":
            self.byte_order = "<"
        else:
            self.byte_order = ">"

        # Get encoding information
        buf = self._read_bytes(const.encoding_offset, const.encoding_length)[0]
        if buf in const.encoding_names:
            self.file_encoding = const.encoding_names[buf]
        else:
            self.file_encoding = f"unknown (code={buf})"

        # Get platform information
        buf = self._read_bytes(const.platform_offset, const.platform_length)
        if buf == b"1":
            self.platform = "unix"
        elif buf == b"2":
            self.platform = "windows"
        else:
            self.platform = "unknown"

        buf = self._read_bytes(const.dataset_offset, const.dataset_length)
        self.name = buf.rstrip(b"\x00 ")
        if self.convert_header_text:
            self.name = self.name.decode(self.encoding or self.default_encoding)

        buf = self._read_bytes(const.file_type_offset, const.file_type_length)
        self.file_type = buf.rstrip(b"\x00 ")
        if self.convert_header_text:
            self.file_type = self.file_type.decode(
                self.encoding or self.default_encoding
            )

        # Timestamp is epoch 01/01/1960
        epoch = datetime(1960, 1, 1)
        x = self._read_float(
            const.date_created_offset + align1, const.date_created_length
        )
        self.date_created = epoch + pd.to_timedelta(x, unit="s")
        x = self._read_float(
            const.date_modified_offset + align1, const.date_modified_length
        )
        self.date_modified = epoch + pd.to_timedelta(x, unit="s")

        self.header_length = self._read_int(
            const.header_size_offset + align1, const.header_size_length
        )

        # Read the rest of the header into cached_page.
        buf = self._path_or_buf.read(self.header_length - 288)
        self._cached_page += buf
        if len(self._cached_page) != self.header_length:
            raise ValueError("The SAS7BDAT file appears to be truncated.")

        self._page_length = self._read_int(
            const.page_size_offset + align1, const.page_size_length
        )
        self._page_count = self._read_int(
            const.page_count_offset + align1, const.page_count_length
        )

        buf = self._read_bytes(
            const.sas_release_offset + total_align, const.sas_release_length
        )
        self.sas_release = buf.rstrip(b"\x00 ")
        if self.convert_header_text:
            self.sas_release = self.sas_release.decode(
                self.encoding or self.default_encoding
            )

        buf = self._read_bytes(
            const.sas_server_type_offset + total_align, const.sas_server_type_length
        )
        self.server_type = buf.rstrip(b"\x00 ")
        if self.convert_header_text:
            self.server_type = self.server_type.decode(
                self.encoding or self.default_encoding
            )

        buf = self._read_bytes(
            const.os_version_number_offset + total_align, const.os_version_number_length
        )
        self.os_version = buf.rstrip(b"\x00 ")
        if self.convert_header_text:
            self.os_version = self.os_version.decode(
                self.encoding or self.default_encoding
            )

        buf = self._read_bytes(const.os_name_offset + total_align, const.os_name_length)
        buf = buf.rstrip(b"\x00 ")
        if len(buf) > 0:
            self.os_name = buf.decode(self.encoding or self.default_encoding)
        else:
            buf = self._read_bytes(
                const.os_maker_offset + total_align, const.os_maker_length
            )
            self.os_name = buf.rstrip(b"\x00 ")
            if self.convert_header_text:
                self.os_name = self.os_name.decode(
                    self.encoding or self.default_encoding
                )

    def __next__(self):
        da = self.read(nrows=self.chunksize or 1)
        if da is None:
            self.close()
            raise StopIteration
        return da

    # Read a single float of the given width (4 or 8).
    def _read_float(self, offset, width):
        if width not in (4, 8):
            self.close()
            raise ValueError("invalid float width")
        buf = self._read_bytes(offset, width)
        fd = "f" if width == 4 else "d"
        return struct.unpack(self.byte_order + fd, buf)[0]

    # Read a single signed integer of the given width (1, 2, 4 or 8).
    def _read_int(self, offset: int, width: int) -> int:
        if width not in (1, 2, 4, 8):
            self.close()
            raise ValueError("invalid int width")
        buf = self._read_bytes(offset, width)
        it = {1: "b", 2: "h", 4: "l", 8: "q"}[width]
        iv = struct.unpack(self.byte_order + it, buf)[0]
        return iv

    def _read_bytes(self, offset: int, length: int):
        if self._cached_page is None:
            self._path_or_buf.seek(offset)
            buf = self._path_or_buf.read(length)
            if len(buf) < length:
                self.close()
                msg = f"Unable to read {length:d} bytes from file position {offset:d}."
                raise ValueError(msg)
            return buf
        else:
            if offset + length > len(self._cached_page):
                self.close()
                raise ValueError("The cached page is too small.")
            return self._cached_page[offset : offset + length]

    def _parse_metadata(self):
        done = False
        while not done:
            self._cached_page = self._path_or_buf.read(self._page_length)
            if len(self._cached_page) <= 0:
                break
            if len(self._cached_page) != self._page_length:
                raise ValueError("Failed to read a meta data page from the SAS file.")
            done = self._process_page_meta()

    def _process_page_meta(self):
        self._read_page_header()
        pt = [const.page_meta_type, const.page_amd_type] + const.page_mix_types
        if self._current_page_type in pt:
            self._process_page_metadata()
        is_data_page = self._current_page_type & const.page_data_type
        is_mix_page = self._current_page_type in const.page_mix_types
        return (
            is_data_page
            or is_mix_page
            or self._current_page_data_subheader_pointers != []
        )

    def _read_page_header(self):
        bit_offset = self._page_bit_offset
        tx = const.page_type_offset + bit_offset
        self._current_page_type = self._read_int(tx, const.page_type_length)
        tx = const.block_count_offset + bit_offset
        self._current_page_block_count = self._read_int(tx, const.block_count_length)
        tx = const.subheader_count_offset + bit_offset
        self._current_page_subheaders_count = self._read_int(
            tx, const.subheader_count_length
        )

    def _process_page_metadata(self):
        bit_offset = self._page_bit_offset

        for i in range(self._current_page_subheaders_count):
            pointer = self._process_subheader_pointers(
                const.subheader_pointers_offset + bit_offset, i
            )
            if pointer.length == 0:
                continue
            if pointer.compression == const.truncated_subheader_id:
                continue
            subheader_signature = self._read_subheader_signature(pointer.offset)
            subheader_index = self._get_subheader_index(
                subheader_signature, pointer.compression, pointer.ptype
            )
            self._process_subheader(subheader_index, pointer)

    def _get_subheader_index(self, signature, compression, ptype):
        index = const.subheader_signature_to_index.get(signature)
        if index is None:
            f1 = (compression == const.compressed_subheader_id) or (compression == 0)
            f2 = ptype == const.compressed_subheader_type
            if (self.compression != b"") and f1 and f2:
                index = const.SASIndex.data_subheader_index
            else:
                self.close()
                raise ValueError("Unknown subheader signature")
        return index

    def _process_subheader_pointers(self, offset: int, subheader_pointer_index: int):

        subheader_pointer_length = self._subheader_pointer_length
        total_offset = offset + subheader_pointer_length * subheader_pointer_index

        subheader_offset = self._read_int(total_offset, self._int_length)
        total_offset += self._int_length

        subheader_length = self._read_int(total_offset, self._int_length)
        total_offset += self._int_length

        subheader_compression = self._read_int(total_offset, 1)
        total_offset += 1

        subheader_type = self._read_int(total_offset, 1)

        x = _SubheaderPointer(
            subheader_offset, subheader_length, subheader_compression, subheader_type
        )

        return x

    def _read_subheader_signature(self, offset):
        subheader_signature = self._read_bytes(offset, self._int_length)
        return subheader_signature

    def _process_subheader(self, subheader_index, pointer):
        offset = pointer.offset
        length = pointer.length

        if subheader_index == const.SASIndex.row_size_index:
            processor = self._process_rowsize_subheader
        elif subheader_index == const.SASIndex.column_size_index:
            processor = self._process_columnsize_subheader
        elif subheader_index == const.SASIndex.column_text_index:
            processor = self._process_columntext_subheader
        elif subheader_index == const.SASIndex.column_name_index:
            processor = self._process_columnname_subheader
        elif subheader_index == const.SASIndex.column_attributes_index:
            processor = self._process_columnattributes_subheader
        elif subheader_index == const.SASIndex.format_and_label_index:
            processor = self._process_format_subheader
        elif subheader_index == const.SASIndex.column_list_index:
            processor = self._process_columnlist_subheader
        elif subheader_index == const.SASIndex.subheader_counts_index:
            processor = self._process_subheader_counts
        elif subheader_index == const.SASIndex.data_subheader_index:
            self._current_page_data_subheader_pointers.append(pointer)
            return
        else:
            raise ValueError("unknown subheader index")

        processor(offset, length)

    def _process_rowsize_subheader(self, offset, length):

        int_len = self._int_length
        lcs_offset = offset
        lcp_offset = offset
        if self.U64:
            lcs_offset += 682
            lcp_offset += 706
        else:
            lcs_offset += 354
            lcp_offset += 378

        self.row_length = self._read_int(
            offset + const.row_length_offset_multiplier * int_len, int_len
        )
        self.row_count = self._read_int(
            offset + const.row_count_offset_multiplier * int_len, int_len
        )
        self.col_count_p1 = self._read_int(
            offset + const.col_count_p1_multiplier * int_len, int_len
        )
        self.col_count_p2 = self._read_int(
            offset + const.col_count_p2_multiplier * int_len, int_len
        )
        mx = const.row_count_on_mix_page_offset_multiplier * int_len
        self._mix_page_row_count = self._read_int(offset + mx, int_len)
        self._lcs = self._read_int(lcs_offset, 2)
        self._lcp = self._read_int(lcp_offset, 2)

    def _process_columnsize_subheader(self, offset, length):
        int_len = self._int_length
        offset += int_len
        self.column_count = self._read_int(offset, int_len)
        if self.col_count_p1 + self.col_count_p2 != self.column_count:
            print(
                f"Warning: column count mismatch ({self.col_count_p1} + "
                f"{self.col_count_p2} != {self.column_count})\n"
            )

    # Unknown purpose
    def _process_subheader_counts(self, offset, length):
        pass

    def _process_columntext_subheader(self, offset, length):

        offset += self._int_length
        text_block_size = self._read_int(offset, const.text_block_size_length)

        buf = self._read_bytes(offset, text_block_size)
        cname_raw = buf[0:text_block_size].rstrip(b"\x00 ")
        cname = cname_raw
        if self.convert_header_text:
            cname = cname.decode(self.encoding or self.default_encoding)
        self.column_names_strings.append(cname)

        if len(self.column_names_strings) == 1:
            compression_literal = b""
            for cl in const.compression_literals:
                if cl in cname_raw:
                    compression_literal = cl
            self.compression = compression_literal
            offset -= self._int_length

            offset1 = offset + 16
            if self.U64:
                offset1 += 4

            buf = self._read_bytes(offset1, self._lcp)
            compression_literal = buf.rstrip(b"\x00")
            if compression_literal == b"":
                self._lcs = 0
                offset1 = offset + 32
                if self.U64:
                    offset1 += 4
                buf = self._read_bytes(offset1, self._lcp)
                self.creator_proc = buf[0 : self._lcp]
            elif compression_literal == const.rle_compression:
                offset1 = offset + 40
                if self.U64:
                    offset1 += 4
                buf = self._read_bytes(offset1, self._lcp)
                self.creator_proc = buf[0 : self._lcp]
            elif self._lcs > 0:
                self._lcp = 0
                offset1 = offset + 16
                if self.U64:
                    offset1 += 4
                buf = self._read_bytes(offset1, self._lcs)
                self.creator_proc = buf[0 : self._lcp]
            if self.convert_header_text:
                if hasattr(self, "creator_proc"):
                    self.creator_proc = self.creator_proc.decode(
                        self.encoding or self.default_encoding
                    )

    def _process_columnname_subheader(self, offset, length):
        int_len = self._int_length
        offset += int_len
        column_name_pointers_count = (length - 2 * int_len - 12) // 8
        for i in range(column_name_pointers_count):
            text_subheader = (
                offset
                + const.column_name_pointer_length * (i + 1)
                + const.column_name_text_subheader_offset
            )
            col_name_offset = (
                offset
                + const.column_name_pointer_length * (i + 1)
                + const.column_name_offset_offset
            )
            col_name_length = (
                offset
                + const.column_name_pointer_length * (i + 1)
                + const.column_name_length_offset
            )

            idx = self._read_int(
                text_subheader, const.column_name_text_subheader_length
            )
            col_offset = self._read_int(
                col_name_offset, const.column_name_offset_length
            )
            col_len = self._read_int(col_name_length, const.column_name_length_length)

            name_str = self.column_names_strings[idx]
            self.column_names.append(name_str[col_offset : col_offset + col_len])

    def _process_columnattributes_subheader(self, offset, length):
        int_len = self._int_length
        column_attributes_vectors_count = (length - 2 * int_len - 12) // (int_len + 8)
        for i in range(column_attributes_vectors_count):
            col_data_offset = (
                offset + int_len + const.column_data_offset_offset + i * (int_len + 8)
            )
            col_data_len = (
                offset
                + 2 * int_len
                + const.column_data_length_offset
                + i * (int_len + 8)
            )
            col_types = (
                offset + 2 * int_len + const.column_type_offset + i * (int_len + 8)
            )

            x = self._read_int(col_data_offset, int_len)
            self._column_data_offsets.append(x)

            x = self._read_int(col_data_len, const.column_data_length_length)
            self._column_data_lengths.append(x)

            x = self._read_int(col_types, const.column_type_length)
            self._column_types.append(b"d" if x == 1 else b"s")

    def _process_columnlist_subheader(self, offset, length):
        # unknown purpose
        pass

    def _process_format_subheader(self, offset, length):
        int_len = self._int_length
        text_subheader_format = (
            offset + const.column_format_text_subheader_index_offset + 3 * int_len
        )
        col_format_offset = offset + const.column_format_offset_offset + 3 * int_len
        col_format_len = offset + const.column_format_length_offset + 3 * int_len
        text_subheader_label = (
            offset + const.column_label_text_subheader_index_offset + 3 * int_len
        )
        col_label_offset = offset + const.column_label_offset_offset + 3 * int_len
        col_label_len = offset + const.column_label_length_offset + 3 * int_len

        x = self._read_int(
            text_subheader_format, const.column_format_text_subheader_index_length
        )
        format_idx = min(x, len(self.column_names_strings) - 1)

        format_start = self._read_int(
            col_format_offset, const.column_format_offset_length
        )
        format_len = self._read_int(col_format_len, const.column_format_length_length)

        label_idx = self._read_int(
            text_subheader_label, const.column_label_text_subheader_index_length
        )
        label_idx = min(label_idx, len(self.column_names_strings) - 1)

        label_start = self._read_int(col_label_offset, const.column_label_offset_length)
        label_len = self._read_int(col_label_len, const.column_label_length_length)

        label_names = self.column_names_strings[label_idx]
        column_label = label_names[label_start : label_start + label_len]
        format_names = self.column_names_strings[format_idx]
        column_format = format_names[format_start : format_start + format_len]
        current_column_number = len(self.columns)

        col = _Column(
            current_column_number,
            self.column_names[current_column_number],
            column_label,
            column_format,
            self._column_types[current_column_number],
            self._column_data_lengths[current_column_number],
        )

        self.column_formats.append(column_format)
        self.columns.append(col)

    def read(self, nrows=None):

        if (nrows is None) and (self.chunksize is not None):
            nrows = self.chunksize
        elif nrows is None:
            nrows = self.row_count

        if len(self._column_types) == 0:
            self.close()
            raise EmptyDataError("No columns to parse from file")

        if self._current_row_in_file_index >= self.row_count:
            return None

        m = self.row_count - self._current_row_in_file_index
        if nrows > m:
            nrows = m

        nd = self._column_types.count(b"d")
        ns = self._column_types.count(b"s")

        self._string_chunk = np.empty((ns, nrows), dtype=object)
        self._byte_chunk = np.zeros((nd, 8 * nrows), dtype=np.uint8)

        self._current_row_in_chunk_index = 0
        p = Parser(self)
        p.read(nrows)

        rslt = self._chunk_to_dataframe()
        if self.index is not None:
            rslt = rslt.set_index(self.index)

        return rslt

    def _read_next_page(self):
        self._current_page_data_subheader_pointers = []
        self._cached_page = self._path_or_buf.read(self._page_length)
        if len(self._cached_page) <= 0:
            return True
        elif len(self._cached_page) != self._page_length:
            self.close()
            msg = (
                "failed to read complete page from file (read "
                f"{len(self._cached_page):d} of {self._page_length:d} bytes)"
            )
            raise ValueError(msg)

        self._read_page_header()
        page_type = self._current_page_type
        if page_type == const.page_meta_type:
            self._process_page_metadata()

        is_data_page = page_type & const.page_data_type
        pt = [const.page_meta_type] + const.page_mix_types
        if not is_data_page and self._current_page_type not in pt:
            return self._read_next_page()

        return False

    def _chunk_to_dataframe(self):

        n = self._current_row_in_chunk_index
        m = self._current_row_in_file_index
        ix = range(m - n, m)
        rslt = pd.DataFrame(index=ix)

        js, jb = 0, 0
        for j in range(self.column_count):

            name = self.column_names[j]

            if self._column_types[j] == b"d":
                rslt[name] = self._byte_chunk[jb, :].view(dtype=self.byte_order + "d")
                rslt[name] = np.asarray(rslt[name], dtype=np.float64)
                if self.convert_dates:
                    if self.column_formats[j] in const.sas_date_formats:
                        rslt[name] = _convert_datetimes(rslt[name], "d")
                    elif self.column_formats[j] in const.sas_datetime_formats:
                        rslt[name] = _convert_datetimes(rslt[name], "s")
                jb += 1
            elif self._column_types[j] == b"s":
                rslt[name] = self._string_chunk[js, :]
                if self.convert_text and (self.encoding is not None):
                    rslt[name] = rslt[name].str.decode(
                        self.encoding or self.default_encoding
                    )
                if self.blank_missing:
                    ii = rslt[name].str.len() == 0
                    rslt.loc[ii, name] = np.nan
                js += 1
            else:
                self.close()
                raise ValueError(f"unknown column type {self._column_types[j]}")

        return rslt