# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""An extensible ASCII table reader and writer.
ui.py:
Provides the main user functions for reading and writing tables.
:Copyright: Smithsonian Astrophysical Observatory (2010)
:Author: Tom Aldcroft (aldcroft@head.cfa.harvard.edu)
"""
from __future__ import absolute_import, division, print_function
import re
import os
import sys
from . import core
from . import basic
from . import cds
from . import daophot
from . import ecsv
from . import sextractor
from . import ipac
from . import latex
from . import html
from . import fastbasic
from . import cparser
from . import fixedwidth
from ...table import Table
from ...utils.data import get_readable_fileobj
from ...extern import six
try:
import yaml
HAS_YAML = True
except ImportError:
HAS_YAML = False
# Default setting for guess parameter in read()
_GUESS = True
def _probably_html(table, maxchars=100000):
"""
Determine if ``table`` probably contains HTML content. See PR #3693 and issue
#3691 for context.
"""
if not isinstance(table, six.string_types):
try:
# If table is an iterable (list of strings) then take the first
# maxchars of these. Make sure this is something with random
# access to exclude a file-like object
table[0]
table[:1]
size = 0
for i, line in enumerate(table):
size += len(line)
if size > maxchars:
break
table = os.linesep.join(table[:i+1])
except:
pass
if isinstance(table, six.string_types):
# Look for signs of an HTML table in the first maxchars characters
table = table[:maxchars]
# URL ending in .htm or .html
if re.match(r'( http[s]? | ftp | file ) :// .+ \.htm[l]?$', table,
re.IGNORECASE | re.VERBOSE):
return True
# Filename ending in .htm or .html which exists
if re.search(r'\.htm[l]?$', table[-5:], re.IGNORECASE) and os.path.exists(table):
return True
# Table starts with HTML document type declaration
if re.match(r'\s* <! \s* DOCTYPE \s* HTML', table, re.IGNORECASE | re.VERBOSE):
return True
# Look for <TABLE .. >, <TR .. >, <TD .. > tag openers.
if all(re.search(r'< \s* {0} [^>]* >'.format(element), table, re.IGNORECASE | re.VERBOSE)
for element in ('table', 'tr', 'td')):
return True
return False
[docs]def set_guess(guess):
"""
Set the default value of the ``guess`` parameter for read()
Parameters
----------
guess : bool
New default ``guess`` value (e.g., True or False)
"""
global _GUESS
_GUESS = guess
[docs]def get_reader(Reader=None, Inputter=None, Outputter=None, **kwargs):
"""
Initialize a table reader allowing for common customizations. Most of the
default behavior for various parameters is determined by the Reader class.
Parameters
----------
Reader : `~astropy.io.ascii.BaseReader`
Reader class (DEPRECATED) (default= :class:`Basic`)
Inputter : `~astropy.io.ascii.BaseInputter`
Inputter class
Outputter : `~astropy.io.ascii.BaseOutputter`
Outputter class
delimiter : str
Column delimiter string
comment : str
Regular expression defining a comment line in table
quotechar : str
One-character string to quote fields containing special characters
header_start : int
Line index for the header line not counting comment lines
data_start : int
Line index for the start of data not counting comment lines
data_end : int
Line index for the end of data (can be negative to count from end)
converters : dict
Dictionary of converters
data_Splitter : `~astropy.io.ascii.BaseSplitter`
Splitter class to split data columns
header_Splitter : `~astropy.io.ascii.BaseSplitter`
Splitter class to split header columns
names : list
List of names corresponding to each data column
include_names : list
List of names to include in output (default= ``None`` selects all names)
exclude_names : list
List of names to exclude from output (applied after ``include_names``)
fill_values : dict
specification of fill values for bad or missing table values
fill_include_names : list
List of names to include in fill_values (default= ``None`` selects all names)
fill_exclude_names : list
List of names to exclude from fill_values (applied after ``fill_include_names``)
"""
# This function is a light wrapper around core._get_reader to provide a public interface
# with a default Reader.
if Reader is None:
Reader = basic.Basic
reader = core._get_reader(Reader, Inputter=Inputter, Outputter=Outputter, **kwargs)
return reader
def _get_format_class(format, ReaderWriter, label):
if format is not None and ReaderWriter is not None:
raise ValueError('Cannot supply both format and {0} keywords'.format(label))
if format is not None:
if format in core.FORMAT_CLASSES:
ReaderWriter = core.FORMAT_CLASSES[format]
else:
raise ValueError('ASCII format {0!r} not in allowed list {1}'
.format(format, sorted(core.FORMAT_CLASSES)))
return ReaderWriter
[docs]def read(table, guess=None, **kwargs):
"""
Read the input ``table`` and return the table. Most of
the default behavior for various parameters is determined by the Reader
class.
Parameters
----------
table : str, file-like, list
Input table as a file name, file-like object, list of strings, or
single newline-separated string.
guess : bool
Try to guess the table format (default= ``True``)
format : str, `~astropy.io.ascii.BaseReader`
Input table format
Inputter : `~astropy.io.ascii.BaseInputter`
Inputter class
Outputter : `~astropy.io.ascii.BaseOutputter`
Outputter class
delimiter : str
Column delimiter string
comment : str
Regular expression defining a comment line in table
quotechar : str
One-character string to quote fields containing special characters
header_start : int
Line index for the header line not counting comment lines
data_start : int
Line index for the start of data not counting comment lines
data_end : int
Line index for the end of data (can be negative to count from end)
converters : dict
Dictionary of converters
data_Splitter : `~astropy.io.ascii.BaseSplitter`
Splitter class to split data columns
header_Splitter : `~astropy.io.ascii.BaseSplitter`
Splitter class to split header columns
names : list
List of names corresponding to each data column
include_names : list
List of names to include in output (default= ``None`` selects all names)
exclude_names : list
List of names to exclude from output (applied after ``include_names``)
fill_values : dict
specification of fill values for bad or missing table values
fill_include_names : list
List of names to include in fill_values (default= ``None`` selects all names)
fill_exclude_names : list
List of names to exclude from fill_values (applied after ``fill_include_names``)
fast_reader : bool
Whether to use the C engine, can also be a dict with options which default to ``False``
(default= ``True``)
Reader : `~astropy.io.ascii.BaseReader`
Reader class (DEPRECATED) (default= :class:`Basic`).
"""
if 'fill_values' not in kwargs:
kwargs['fill_values'] = [('', '0')]
# If an Outputter is supplied in kwargs that will take precedence.
new_kwargs = {}
fast_reader_param = kwargs.get('fast_reader', True)
if 'Outputter' in kwargs: # user specified Outputter, not supported for fast reading
fast_reader_param = False
format = kwargs.get('format')
new_kwargs.update(kwargs)
# Get the Reader class based on possible format and Reader kwarg inputs.
Reader = _get_format_class(format, kwargs.get('Reader'), 'Reader')
if Reader is not None:
new_kwargs['Reader'] = Reader
format = Reader._format_name
# Remove format keyword if there, this is only allowed in read() not get_reader()
if 'format' in new_kwargs:
del new_kwargs['format']
if guess is None:
guess = _GUESS
if guess:
# If ``table`` is probably an HTML file then tell guess function to add
# the HTML reader at the top of the guess list. This is in response to
# issue #3691 (and others) where libxml can segfault on a long non-HTML
# file, thus prompting removal of the HTML reader from the default
# guess list.
new_kwargs['guess_html'] = _probably_html(table)
dat = _guess(table, new_kwargs, format, fast_reader_param)
else:
reader = get_reader(**new_kwargs)
# Try the fast reader first if applicable
if fast_reader_param and format is not None and 'fast_{0}'.format(format) \
in core.FAST_CLASSES:
new_kwargs['Reader'] = core.FAST_CLASSES['fast_{0}'.format(format)]
fast_reader = get_reader(**new_kwargs)
try:
return fast_reader.read(table)
except (core.ParameterError, cparser.CParserError) as e:
# special testing value to avoid falling back on the slow reader
if fast_reader_param == 'force':
raise e
# If the fast reader doesn't work, try the slow version
dat = reader.read(table)
else:
dat = reader.read(table)
return dat
def _guess(table, read_kwargs, format, fast_reader):
"""Try to read the table using various sets of keyword args. First try the
original args supplied in the read() call. Then try the standard guess
keyword args. For each key/val pair specified explicitly in the read()
call make sure that if there is a corresponding definition in the guess
then it must have the same val. If not then skip this guess."""
# If `table` is a readable file object then read in the file now. This
# prevents problems in Python 3 with the file object getting closed or
# left at the file end. See #3132, #3013, #3109, #2001. If a `readme`
# arg was passed that implies CDS format, in which case the original
# `table` as the data filename must be left intact.
if 'readme' not in read_kwargs:
try:
with get_readable_fileobj(table) as fileobj:
table = fileobj.read()
except:
pass
# Keep a trace of all failed guesses kwarg
failed_kwargs = []
full_list_guess = _get_guess_kwargs_list(read_kwargs)
if fast_reader and format is not None and 'fast_{0}'.format(format) in \
core.FAST_CLASSES:
# If a fast version of the reader is available, try that before the slow version
fast_kwargs = read_kwargs.copy()
fast_kwargs['Reader'] = core.FAST_CLASSES['fast_{0}'.format(format)]
full_list_guess = [fast_kwargs] + full_list_guess
else:
fast_kwargs = None
# First try guessing
for guess_kwargs in full_list_guess:
guess_kwargs_ok = True # guess_kwargs are consistent with user_kwargs?
for key, val in read_kwargs.items():
# Do guess_kwargs.update(read_kwargs) except that if guess_args has
# a conflicting key/val pair then skip this guess entirely.
if key not in guess_kwargs:
guess_kwargs[key] = val
elif val != guess_kwargs[key] and guess_kwargs != fast_kwargs:
guess_kwargs_ok = False
break
if not guess_kwargs_ok:
# User-supplied kwarg is inconsistent with the guess-supplied kwarg, e.g.
# user supplies delimiter="|" but the guess wants to try delimiter=" ",
# so skip the guess entirely.
continue
try:
# If guessing will try all Readers then use strict req'ts on column names
if 'Reader' not in read_kwargs:
guess_kwargs['strict_names'] = True
reader = get_reader(**guess_kwargs)
reader.guessing = True
return reader.read(table)
except (core.InconsistentTableError, ValueError, TypeError, AttributeError,
core.OptionalTableImportError, core.ParameterError, cparser.CParserError):
failed_kwargs.append(guess_kwargs)
else:
# failed all guesses, try the original read_kwargs without column requirements
try:
reader = get_reader(**read_kwargs)
return reader.read(table)
except (core.InconsistentTableError, ValueError, ImportError,
core.OptionalTableImportError, core.ParameterError, cparser.CParserError):
failed_kwargs.append(read_kwargs)
lines = ['\nERROR: Unable to guess table format with the guesses listed below:']
for kwargs in failed_kwargs:
sorted_keys = sorted([x for x in sorted(kwargs)
if x not in ('Reader', 'Outputter')])
reader_repr = repr(kwargs.get('Reader', basic.Basic))
keys_vals = ['Reader:' + re.search(r"\.(\w+)'>", reader_repr).group(1)]
kwargs_sorted = ((key, kwargs[key]) for key in sorted_keys)
keys_vals.extend(['%s: %s' % (key, repr(val)) for key, val in kwargs_sorted])
lines.append(' '.join(keys_vals))
msg = ['',
'************************************************************************',
'** ERROR: Unable to guess table format with the guesses listed above. **',
'** **',
'** To figure out why the table did not read, use guess=False and **',
'** appropriate arguments to read(). In particular specify the format **',
'** and any known attributes like the delimiter. **',
'************************************************************************']
lines.extend(msg)
raise core.InconsistentTableError('\n'.join(lines))
def _get_guess_kwargs_list(read_kwargs):
guess_kwargs_list = []
# If the table is probably HTML based on some heuristics then start with the
# HTML reader.
if read_kwargs.pop('guess_html', None):
guess_kwargs_list.append(dict(Reader=html.HTML))
# Start with ECSV because an ECSV file will be read by Basic. This format
# has very specific header requirements and fails out quickly.
if HAS_YAML:
guess_kwargs_list.append(dict(Reader=ecsv.Ecsv))
# Now try readers that accept the common arguments with the input arguments
# (Unless there are not arguments - we try that in the next step anyway.)
# FixedWidthTwoLine would also be read by Basic, so it needs to come first.
if len(read_kwargs) > 0:
for reader in [fixedwidth.FixedWidthTwoLine,
basic.Basic]:
first_kwargs = read_kwargs.copy()
first_kwargs.update(dict(Reader=reader))
guess_kwargs_list.append(first_kwargs)
# Then try a list of readers with default arguments
guess_kwargs_list.extend([dict(Reader=fixedwidth.FixedWidthTwoLine),
dict(Reader=fastbasic.FastBasic),
dict(Reader=basic.Basic),
dict(Reader=basic.Rdb),
dict(Reader=fastbasic.FastTab),
dict(Reader=basic.Tab),
dict(Reader=cds.Cds),
dict(Reader=daophot.Daophot),
dict(Reader=sextractor.SExtractor),
dict(Reader=ipac.Ipac),
dict(Reader=latex.Latex),
dict(Reader=latex.AASTex)
])
for Reader in (basic.CommentedHeader, fastbasic.FastBasic, basic.Basic,
fastbasic.FastNoHeader, basic.NoHeader):
for delimiter in ("|", ",", " ", "\s"):
for quotechar in ('"', "'"):
guess_kwargs_list.append(dict(
Reader=Reader, delimiter=delimiter, quotechar=quotechar))
return guess_kwargs_list
extra_writer_pars = ('delimiter', 'comment', 'quotechar', 'formats',
'names', 'include_names', 'exclude_names', 'strip_whitespace')
[docs]def get_writer(Writer=None, fast_writer=True, **kwargs):
"""
Initialize a table writer allowing for common customizations. Most of the
default behavior for various parameters is determined by the Writer class.
Parameters
----------
Writer : ``Writer``
Writer class (DEPRECATED) (default= :class:`Basic`)
delimiter : str
Column delimiter string
comment : str
String defining a comment line in table
quotechar : str
One-character string to quote fields containing special characters
formats : dict
Dictionary of format specifiers or formatting functions
strip_whitespace : bool
Strip surrounding whitespace from column values (default= ``True``)
names : list
List of names corresponding to each data column
include_names : list
List of names to include in output (default= ``None`` selects all names)
exclude_names : list
List of names to exclude from output (applied after ``include_names``)
fast_writer : bool
Whether to use the fast Cython writer (default= ``True``)
"""
if Writer is None:
Writer = basic.Basic
if 'strip_whitespace' not in kwargs:
kwargs['strip_whitespace'] = True
writer = core._get_writer(Writer, fast_writer, **kwargs)
# Handle the corner case of wanting to disable writing table comments for the
# commented_header format. This format *requires* a string for `write_comment`
# because that is used for the header column row, so it is not possible to
# set the input `comment` to None. Without adding a new keyword or assuming
# a default comment character, there is no other option but to tell user to
# simply remove the meta['comments'].
if (isinstance(writer, (basic.CommentedHeader, fastbasic.FastCommentedHeader))
and not isinstance(kwargs.get('comment', ''), six.string_types)):
raise ValueError("for the commented_header writer you must supply a string\n"
"value for the `comment` keyword. In order to disable writing\n"
"table comments use `del t.meta['comments']` prior to writing.")
return writer
[docs]def write(table, output=None, format=None, Writer=None, fast_writer=True, **kwargs):
"""Write the input ``table`` to ``filename``. Most of the default behavior
for various parameters is determined by the Writer class.
Parameters
----------
table : `~astropy.io.ascii.BaseReader`, array_like, str, file_like, list
Input table as a Reader object, Numpy struct array, file name,
file-like object, list of strings, or single newline-separated string.
output : str, file_like
Output [filename, file-like object] (default = ``sys.stdout``)
format : str
Output table format (default= ``basic``)
delimiter : str
Column delimiter string
comment : str
String defining a comment line in table
quotechar : str
One-character string to quote fields containing special characters
formats : dict
Dictionary of format specifiers or formatting functions
strip_whitespace : bool
Strip surrounding whitespace from column values (default= ``True``)
names : list
List of names corresponding to each data column
include_names : list
List of names to include in output (default= ``None`` selects all names)
exclude_names : list
List of names to exclude from output (applied after ``include_names``)
fast_writer : bool
Whether to use the fast Cython writer (default= ``True``)
Writer : ``Writer``
Writer class (DEPRECATED) (default= :class:`Basic`)
"""
if output is None:
output = sys.stdout
table = Table(table, names=kwargs.get('names'))
if table.has_mixin_columns:
fast_writer = False
Writer = _get_format_class(format, Writer, 'Writer')
writer = get_writer(Writer=Writer, fast_writer=fast_writer, **kwargs)
if writer._format_name in core.FAST_CLASSES:
writer.write(table, output)
return
lines = writer.write(table)
# Write the lines to output
outstr = os.linesep.join(lines)
if not hasattr(output, 'write'):
output = open(output, 'w')
output.write(outstr)
output.write(os.linesep)
output.close()
else:
output.write(outstr)
output.write(os.linesep)