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Fix SAS 0x40 control byte handling and column name parsing #47113

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Merged
merged 10 commits into from
Jun 24, 2022
+64 −65
Merged

Fix SAS 0x40 control byte handling and column name parsing #47113

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7669f6e
Fix reading SAS7BDAT files with zero rows (#47116)
jonashaag May 31, 2022
93db2f3
Review feedback
jonashaag Jun 9, 2022
f9f98e8
Add back untested .rstrip
jonashaag Jun 9, 2022
dda849e
Fix lint
jonashaag Jun 9, 2022
25fac4b
Add tests
jonashaag Jun 10, 2022
e379917
Fix rebase
jonashaag Jun 10, 2022
7e5cd63
Merge branch 'main' into issue-31243
jonashaag Jun 12, 2022
e0cd625
Merge branch 'main' into issue-31243
jonashaag Jun 12, 2022
064d394
Merge branch 'main' into issue-31243
jonashaag Jun 15, 2022
0cd96bf
Merge branch 'main' into issue-31243
jonashaag Jun 15, 2022
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3 changes: 3 additions & 0 deletions doc/source/whatsnew/v1.5.0.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -844,6 +844,9 @@ I/O
- :meth:`to_html` now excludes the ``border`` attribute from ``<table>`` elements when ``border`` keyword is set to ``False``.
- Bug in :func:`read_sas` returned ``None`` rather than an empty DataFrame for SAS7BDAT files with zero rows (:issue:`18198`)
- Bug in :class:`StataWriter` where value labels were always written with default encoding (:issue:`46750`)
- Bug in :func:`read_sas` with RLE-compressed SAS7BDAT files that contain 0x40 control bytes (:issue:`31243`)
- Bug in :func:`read_sas` that scrambled column names (:issue:`31243`)
-

Period
^^^^^^
Expand Down
112 changes: 49 additions & 63 deletions pandas/io/sas/sas7bdat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -180,9 +180,9 @@ def __init__(

self.default_encoding = "latin-1"
self.compression = b""
self.column_names_strings: list[str] = []
self.column_names: list[str] = []
self.column_formats: list[str] = []
self.column_names_raw: list[bytes] = []
self.column_names: list[str | bytes] = []
self.column_formats: list[str | bytes] = []
self.columns: list[_Column] = []

self._current_page_data_subheader_pointers: list[_SubheaderPointer] = []
Expand Down Expand Up @@ -274,17 +274,13 @@ def _get_properties(self) -> None:
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)
self.name = self._read_and_convert_header_text(
const.dataset_offset, const.dataset_length
)

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
)
self.file_type = self._read_and_convert_header_text(
const.file_type_offset, const.file_type_length
)

# Timestamp is epoch 01/01/1960
epoch = datetime(1960, 1, 1)
Expand Down Expand Up @@ -316,46 +312,25 @@ def _get_properties(self) -> None:
const.page_count_offset + align1, const.page_count_length
)

buf = self._read_bytes(
self.sas_release_offset = self._read_and_convert_header_text(
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(
self.server_type = self._read_and_convert_header_text(
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(
self.os_version = self._read_and_convert_header_text(
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(
self.os_name = self._read_and_convert_header_text(
const.os_name_offset + total_align, const.os_name_length
)
if not self.os_name:
self.os_name = self._read_and_convert_header_text(
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)
Expand Down Expand Up @@ -398,6 +373,11 @@ def _read_bytes(self, offset: int, length: int):
raise ValueError("The cached page is too small.")
return self._cached_page[offset : offset + length]

def _read_and_convert_header_text(self, offset: int, length: int) -> str | bytes:
return self._convert_header_text(
self._read_bytes(offset, length).rstrip(b"\x00 ")
)

def _parse_metadata(self) -> None:
done = False
while not done:
Expand Down Expand Up @@ -570,12 +550,9 @@ def _process_columntext_subheader(self, offset: int, length: int) -> None:

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)
self.column_names_raw.append(cname_raw)

if len(self.column_names_strings) == 1:
if len(self.column_names_raw) == 1:
compression_literal = b""
for cl in const.compression_literals:
if cl in cname_raw:
Expand Down Expand Up @@ -609,11 +586,8 @@ def _process_columntext_subheader(self, offset: int, length: int) -> None:
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
)
if hasattr(self, "creator_proc"):
self.creator_proc = self._convert_header_text(self.creator_proc)

def _process_columnname_subheader(self, offset: int, length: int) -> None:
int_len = self._int_length
Expand Down Expand Up @@ -644,8 +618,9 @@ def _process_columnname_subheader(self, offset: int, length: int) -> None:
)
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])
name_raw = self.column_names_raw[idx]
cname = name_raw[col_offset : col_offset + col_len]
self.column_names.append(self._convert_header_text(cname))

def _process_columnattributes_subheader(self, offset: int, length: int) -> None:
int_len = self._int_length
Expand Down Expand Up @@ -693,7 +668,7 @@ def _process_format_subheader(self, offset: int, length: int) -> None:
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_idx = min(x, len(self.column_names_raw) - 1)

format_start = self._read_int(
col_format_offset, const.column_format_offset_length
Expand All @@ -703,15 +678,19 @@ def _process_format_subheader(self, offset: int, length: int) -> None:
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_idx = min(label_idx, len(self.column_names_raw) - 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]
label_names = self.column_names_raw[label_idx]
column_label = self._convert_header_text(
label_names[label_start : label_start + label_len]
)
format_names = self.column_names_raw[format_idx]
column_format = self._convert_header_text(
format_names[format_start : format_start + format_len]
)
current_column_number = len(self.columns)

col = _Column(
Expand Down Expand Up @@ -809,9 +788,7 @@ def _chunk_to_dataframe(self) -> DataFrame:
elif self._column_types[j] == b"s":
rslt[name] = pd.Series(self._string_chunk[js, :], index=ix)
if self.convert_text and (self.encoding is not None):
rslt[name] = rslt[name].str.decode(
self.encoding or self.default_encoding
)
rslt[name] = self._decode_string(rslt[name].str)
if self.blank_missing:
ii = rslt[name].str.len() == 0
rslt[name][ii] = np.nan
Expand All @@ -822,3 +799,12 @@ def _chunk_to_dataframe(self) -> DataFrame:

df = DataFrame(rslt, columns=self.column_names, index=ix, copy=False)
return df

def _decode_string(self, b):
return b.decode(self.encoding or self.default_encoding)

def _convert_header_text(self, b: bytes) -> str | bytes:
if self.convert_header_text:
return self._decode_string(b)
else:
return b