""" 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