#! /usr/bin/env python
# -*- coding: utf-8 -*-
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
BibTeX interface.
"""
import re
import textwrap
from dendropy.utility.container import OrderedCaselessDict
from dendropy.utility import deprecate
# default order of fields
BIBTEX_FIELDS = [
'author',
'year',
'title',
'journal',
'volume',
'number',
'editor',
'booktitle',
'series',
'chapter',
'pages',
'publisher',
'institution',
'address',
'annote',
'edition',
'howpublished',
'key',
'month',
'organization',
'school',
'note',
'abstract',
'keywords',
'localfile',
]
def _clean_parsed_text(text):
"""
Strips outer quotes, curly braces, etc.; remove multiple
consecutive whitespaces, etc.
"""
if text.startswith('{') and text.endswith('}'):
text = text[1:-1]
elif text.startswith('"') and text.endswith('"'):
text = text[1:-1]
text = re.sub(r"[\s]+", " ", text).strip()
return text
def _format_bibtex_value(text, col_start=1, wrap=True, width=78):
"""
Formats text of a BibTeX field.
"""
ftext = re.sub(r"[\s]+", " ", text).strip()
col_indent = " " * col_start
if not ftext[0].isdigit():
if wrap:
initial_indent = '{'
subsequent_indent = ' '
else:
ftext = '{' + ftext
ftext = ftext + '}'
else:
initial_indent = ''
subsequent_indent = ''
if wrap:
wrapped = textwrap.wrap(ftext,
width=width,
initial_indent=initial_indent,
subsequent_indent=subsequent_indent)
for index, line in enumerate(wrapped[1:]):
wrapped[index+1] = (" " * col_start) + wrapped[index+1]
return '\n'.join(wrapped)
else:
return ftext
[docs]
class BibTexEntry(object):
"""
Tracks a single BibTeX entry.
"""
decompose_pattern = re.compile(r'^@(\w*)\s*{\s*([\w|\:|\-]*),(.*)}')
# works, but misses last field
field_pattern = re.compile(r'\s*([\w|\-]*?)\s*=\s*(.*?),(?=\s*[\w|\-]*\s*\=)')
# get the last field
last_field_pattern = re.compile(r'\s*([\w|\-]*?)\s*=\s*(.*?)\s*[,]*\s*$')
def __init__(self, citation=None):
"""
Sets up internal dictionary of BibTeX fields, and initializes
if argument is given.
"""
deprecate.dendropy_deprecation_warning(
message=(
"BibTexEntry is deprecated as of DendroPy 5.0 and will be removed in a future release ."
"It no longer maintaned, and known to be broken. "
"If this functionality is needed, please open an issue on GitHub."
),
)
self.bibtype = None
self.citekey = None
if isinstance(citation, BibTexEntry):
self._entry_dict = OrderedCaselessDict(citation._entry_dict)
elif isinstance(citation, dict):
self._entry_dict = OrderedCaselessDict()
for k, v in citation.items():
self._entry_dict[k.lower()] = v
self.bibtype = self._entry_dict.get("bibtype", None)
self.citekey = self._entry_dict.get("citekey", None)
else:
self._entry_dict = OrderedCaselessDict()
self.parse_text(citation)
[docs]
def __getattr__(self, name):
"""
Allows bibtex fields (and any additional ones) to be treated
like object attributes.
"""
entry_dict = self._get_entry_dict()
if name == '_entry_dict' or name == '_BibTexEntry_entry_dict':
return entry_dict
elif name == '__dict__':
return object.__getattribute__(self, '__dict__')
elif name == 'bibtype' and hasattr(self, 'bibtype'):
return object.__getattribute__(self, '__dict__')['bibtype']
elif name == 'citekey' and hasattr(self, 'citekey'):
return object.__getattribute__(self, '__dict__')['citekey']
elif name in entry_dict:
return entry_dict[name]
elif name in BIBTEX_FIELDS:
return ""
else:
raise AttributeError(name)
[docs]
def __setattr__(self, name, value):
"""
Allows bibtex fields (and any additional ones) to be treated
like object attributes.
"""
entry_dict = self._get_entry_dict()
if name == '_entry_dict' or name == '_BibTexEntry_entry_dict':
entry_dict = value
elif name == 'bibtype' or name == 'citekey':
object.__setattr__(self, name, value)
else:
self._entry_dict[name] = value
[docs]
def __delattr__(self, name):
"""
Allows bibtex fields (and any additional ones) to be treated
like object attributes.
"""
entry_dict = self._get_entry_dict()
if name == '_entry_dict' or name == '_BibTexEntry_entry_dict':
object.__delattr__(self, '_entry_dict')
elif name in entry_dict:
del(entry_dict[name])
elif name in BIBTEX_FIELDS:
pass
elif name in object.__getattribute__(self, '__dict__'):
object.__delattr__(name)
else:
raise AttributeError(name)
[docs]
def __str__(self):
"""
String representation of self.
"""
return self.as_bibtex()
[docs]
def __repr__(self):
"""
Internal representation of self.
"""
repr_dict = {}
repr_dict['bibtype'] = self.bibtype
repr_dict['citekey'] = self.citekey
repr_dict.update(self.fields_as_dict())
return repr_dict
def _get_entry_dict(self):
"""
Returns the internal field dictionary, creating it first if
neccessary.
"""
if not hasattr(self, '_entry_dict'):
object.__setattr__(self, '_entry_dict', {})
return object.__getattribute__(self, '_entry_dict')
def _get_fields(self):
"""
Returns list of populated fields in order (does not include
bibtype and citekey).
"""
fields = []
for field in BIBTEX_FIELDS:
if field in self._entry_dict:
fields.append(field)
for key in self._entry_dict:
if key not in fields:
fields.append(key)
return fields
fields = property(_get_fields)
[docs]
def parse_text(self, text):
"""
Parses a BibTeX text entry.
"""
text = text.replace("\n", "")
self.bibtype = None
self.citekey = None
text = text.strip()
decompose_match = self.decompose_pattern.match(text)
try:
self.bibtype = decompose_match.group(1)
except AttributeError as exception:
raise ValueError("Failed to parse bibtype: {}".format(text))
try:
self.citekey = decompose_match.group(2)
except AttributeError as exception:
raise ValueError("Failed to parse citekey: {}".format(text))
remaining = decompose_match.group(3)
field_match = self.field_pattern.match(remaining)
while field_match:
field_match = self.field_pattern.match(remaining)
if field_match:
field_name = field_match.group(1).lower()
field_value = _clean_parsed_text(field_match.group(2))
self._entry_dict[field_name] = field_value
remaining = remaining.replace(field_match.group(), '')
if remaining:
last_field_match = self.last_field_pattern.match(remaining)
if last_field_match:
field_name = last_field_match.group(1).lower()
field_value = _clean_parsed_text(last_field_match.group(2))
self._entry_dict[field_name] = field_value
[docs]
def fields_as_dict(self):
"""
Returns the fields (i.e., all public attributes except for
bibtype and citekey as a dictionary).
"""
return dict(self._entry_dict)
[docs]
def as_bibtex(self, wrap_width=78):
"""
Composes entry in BibTex format.
"""
entry = []
sep = " = "
entry.append('@{}{{},'.format((self.bibtype, self.citekey)))
fields = self.fields
# maxlen = max([len(field) for field in fields])
maxlen = max([len(field) for field in BIBTEX_FIELDS])
for field in fields:
if field != 'url':
wrap = True
else:
wrap = False
field_header = field.ljust(maxlen)
field_value = _format_bibtex_value(self._entry_dict[field],
wrap=wrap,
width = wrap_width - maxlen - len(sep) + 2,
col_start = maxlen + len(sep) + 2 )
entry.append(" {}{}{},".format((field_header, sep, field_value)))
entry.append('}')
return '\n'.join(entry)
[docs]
def as_compact_bibtex(self):
"""
Composes entry in BibTex format.
"""
entry = []
entry.append('@{}{{{},'.format((self.bibtype, self.citekey)))
fields = self.fields
for field in fields:
field_value = _format_bibtex_value(self._entry_dict[field],
wrap=False,
width=None,
col_start=1)
entry.append("{}={},".format((field, field_value)))
entry.append('}')
return ''.join(entry)
class BibTexDb(object):
"""
A BibTeX database.
"""
def __init__(self, bibfilepath=None):
"""
Initializes database, optionally from file.
"""
deprecate.dendropy_deprecation_warning(
message=(
"BibTexEntry is deprecated as of DendroPy 5.0 and will be removed in a future release ."
"It no longer maintaned, and known to be broken. "
"If this functionality is needed, please open an issue on GitHub."
),
)
self.entries = []
if bibfilepath:
self.add_from_file(bibfilepath)
def add_from_file(self, filepath):
"""
Reads and loads a BibTeX database file.
"""
bibfile = open(filepath, 'r')
self.add_from_text(bibfile.read())
bibfile.close()
def add_from_text(self, text):
"""
Loads from text.
"""
text = text.replace('\n','')
entry_pattern = re.compile(r'@\w*{([^{}]+{[^{}]*({[^{}]*}[^{}]*)*})+}')
for match in entry_pattern.finditer(text):
entry = BibTexEntry(match.group())
self.entries.append(entry)
