# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Define the Enhanced Character-Separated-Values (ECSV) which allows for reading and
writing all the meta data associated with an astropy Table object.
"""
import re
from collections import OrderedDict
import contextlib
import warnings
from . import core, basic
from astropy.table import meta, serialize
from astropy.utils.data_info import serialize_context_as
from astropy.utils.exceptions import AstropyWarning
__doctest_requires__ = {'Ecsv': ['yaml']}
ECSV_VERSION = '0.9'
DELIMITERS = (' ', ',')
class EcsvHeader(basic.BasicHeader):
"""Header class for which the column definition line starts with the
comment character. See the :class:`CommentedHeader` class for an example.
"""
def process_lines(self, lines):
"""Return only non-blank lines that start with the comment regexp. For these
lines strip out the matching characters and leading/trailing whitespace."""
re_comment = re.compile(self.comment)
for line in lines:
line = line.strip()
if not line:
continue
match = re_comment.match(line)
if match:
out = line[match.end():]
if out:
yield out
else:
# Stop iterating on first failed match for a non-blank line
return
def write(self, lines):
"""
Write header information in the ECSV ASCII format. This format
starts with a delimiter separated list of the column names in order
to make this format readable by humans and simple csv-type readers.
It then encodes the full table meta and column attributes and meta
as YAML and pretty-prints this in the header. Finally the delimited
column names are repeated again, for humans and readers that look
for the *last* comment line as defining the column names.
"""
if self.splitter.delimiter not in DELIMITERS:
raise ValueError('only space and comma are allowed for delimiter in ECSV format')
for col in self.cols:
if len(getattr(col, 'shape', ())) > 1:
raise ValueError("ECSV format does not support multidimensional column '{0}'"
.format(col.info.name))
# Now assemble the header dict that will be serialized by the YAML dumper
header = {'cols': self.cols, 'schema': 'astropy-2.0'}
if self.table_meta:
header['meta'] = self.table_meta
# Set the delimiter only for the non-default option(s)
if self.splitter.delimiter != ' ':
header['delimiter'] = self.splitter.delimiter
header_yaml_lines = (['%ECSV {0}'.format(ECSV_VERSION),
'---']
+ meta.get_yaml_from_header(header))
lines.extend([self.write_comment + line for line in header_yaml_lines])
lines.append(self.splitter.join([x.info.name for x in self.cols]))
def write_comments(self, lines, meta):
"""
Override the default write_comments to do nothing since this is handled
in the custom write method.
"""
pass
def update_meta(self, lines, meta):
"""
Override the default update_meta to do nothing. This process is done
in get_cols() for this reader.
"""
pass
def get_cols(self, lines):
"""
Initialize the header Column objects from the table ``lines``.
Parameters
----------
lines : list
List of table lines
"""
# Cache a copy of the original input lines before processing below
raw_lines = lines
# Extract non-blank comment (header) lines with comment character stripped
lines = list(self.process_lines(lines))
# Validate that this is a ECSV file
ecsv_header_re = r"""%ECSV [ ]
(?P<major> \d+)
\. (?P<minor> \d+)
\.? (?P<bugfix> \d+)? $"""
no_header_msg = ('ECSV header line like "# %ECSV <version>" not found as first line.'
' This is required for a ECSV file.')
if not lines:
raise core.InconsistentTableError(no_header_msg)
match = re.match(ecsv_header_re, lines[0].strip(), re.VERBOSE)
if not match:
raise core.InconsistentTableError(no_header_msg)
# ecsv_version could be constructed here, but it is not currently used.
try:
header = meta.get_header_from_yaml(lines)
except ImportError as exc:
if 'PyYAML package is required' in str(exc):
warnings.warn("file looks like ECSV format but PyYAML is not installed "
"so it cannot be parsed as ECSV",
AstropyWarning)
raise core.InconsistentTableError('unable to parse yaml in meta header'
' (PyYAML package is required)')
except meta.YamlParseError:
raise core.InconsistentTableError('unable to parse yaml in meta header')
if 'meta' in header:
self.table_meta = header['meta']
if 'delimiter' in header:
delimiter = header['delimiter']
if delimiter not in DELIMITERS:
raise ValueError('only space and comma are allowed for delimiter in ECSV format')
self.splitter.delimiter = delimiter
self.data.splitter.delimiter = delimiter
# Create the list of io.ascii column objects from `header`
header_cols = OrderedDict((x['name'], x) for x in header['datatype'])
self.names = [x['name'] for x in header['datatype']]
# Read the first non-commented line of table and split to get the CSV
# header column names. This is essentially what the Basic reader does.
header_line = next(super().process_lines(raw_lines))
header_names = next(self.splitter([header_line]))
# Check for consistency of the ECSV vs. CSV header column names
if header_names != self.names:
raise core.InconsistentTableError('column names from ECSV header {} do not '
'match names from header line of CSV data {}'
.format(self.names, header_names))
# BaseHeader method to create self.cols, which is a list of
# io.ascii.core.Column objects (*not* Table Column objects).
self._set_cols_from_names()
# Transfer attributes from the column descriptor stored in the input
# header YAML metadata to the new columns to create this table.
for col in self.cols:
for attr in ('description', 'format', 'unit', 'meta'):
if attr in header_cols[col.name]:
setattr(col, attr, header_cols[col.name][attr])
col.dtype = header_cols[col.name]['datatype']
# ECSV "string" means numpy dtype.kind == 'U' AKA str in Python 3
if col.dtype == 'string':
col.dtype = 'str'
if col.dtype.startswith('complex'):
raise TypeError('ecsv reader does not support complex number types')
class EcsvOutputter(core.TableOutputter):
"""
After reading the input lines and processing, convert the Reader columns
and metadata to an astropy.table.Table object. This overrides the default
converters to be an empty list because there is no "guessing" of the
conversion function.
"""
default_converters = []
def __call__(self, cols, meta):
# Convert to a Table with all plain Column subclass columns
out = super().__call__(cols, meta)
# If mixin columns exist (based on the special '__mixin_columns__'
# key in the table ``meta``), then use that information to construct
# appropriate mixin columns and remove the original data columns.
# If no __mixin_columns__ exists then this function just passes back
# the input table.
out = serialize._construct_mixins_from_columns(out)
return out
class EcsvData(basic.BasicData):
def _set_fill_values(self, cols):
"""Set the fill values of the individual cols based on fill_values of BaseData
For ECSV handle the corner case of data that has been serialized using
the serialize_method='data_mask' option, which writes the full data and
mask directly, AND where that table includes a string column with zero-length
string entries ("") which are valid data.
Normally the super() method will set col.fill_value=('', '0') to replace
blanks with a '0'. But for that corner case subset, instead do not do
any filling.
"""
super()._set_fill_values(cols)
# Get the serialized columns spec. It might not exist and there might
# not even be any table meta, so punt in those cases.
try:
scs = self.header.table_meta['__serialized_columns__']
except (AttributeError, KeyError):
return
# Got some serialized columns, so check for string type and serialized
# as a MaskedColumn. Without 'data_mask', MaskedColumn objects are
# stored to ECSV as normal columns.
for col in cols:
if (col.dtype == 'str' and col.name in scs and
scs[col.name]['__class__'] == 'astropy.table.column.MaskedColumn'):
col.fill_values = {} # No data value replacement
[docs]class Ecsv(basic.Basic):
"""
Read a file which conforms to the ECSV (Enhanced Character Separated
Values) format. This format allows for specification of key table
and column meta-data, in particular the data type and unit. For details
see: https://github.com/astropy/astropy-APEs/blob/master/APE6.rst.
Examples
--------
>>> from astropy.table import Table
>>> ecsv_content = '''# %ECSV 0.9
... # ---
... # datatype:
... # - {name: a, unit: m / s, datatype: int64, format: '%03d'}
... # - {name: b, unit: km, datatype: int64, description: This is column b}
... a b
... 001 2
... 004 3
... '''
>>> Table.read(ecsv_content, format='ascii.ecsv')
<Table length=2>
a b
m / s km
int64 int64
----- -----
001 2
004 3
"""
_format_name = 'ecsv'
_description = 'Enhanced CSV'
_io_registry_suffix = '.ecsv'
header_class = EcsvHeader
data_class = EcsvData
outputter_class = EcsvOutputter
[docs] def update_table_data(self, table):
"""
Update table columns in place if mixin columns are present.
This is a hook to allow updating the table columns after name
filtering but before setting up to write the data. This is currently
only used by ECSV and is otherwise just a pass-through.
Parameters
----------
table : `astropy.table.Table`
Input table for writing
Returns
-------
table : `astropy.table.Table`
Output table for writing
"""
with serialize_context_as('ecsv'):
out = serialize._represent_mixins_as_columns(table)
return out