def fetch_and_update(self, bibtex=True, latex_format='EU', append_bbl=False):
existing_keys = self.bib().entries.keys() if bibtex else self.bbl_keys()
existing_keys = [k.lower() for k in existing_keys]
replace_keys = ODict()
new_entries = ODict()
type_name = 'BibTeX' if bibtex else 'LaTeX({})'.format(latex_format)
for ref in self.references.values():
if ref.key.lower() in existing_keys:
if DEBUG:
print('skip existing: {}'.format(ref.key))
continue
if Key.is_unknown(ref.key):
print('WARNING: skip non-existing but unknown-type key {}'.format(ref.key))
continue
try:
print('fetching', type_name, 'from inspire:', ref.key, end=' ')
if bibtex:
ref.fetch_bibtex()
else:
ref.fetch_latex(latex_format)
sys.stdout.flush()
time.sleep(0.3)
except RecordNotFound or MultipleRecordsFound as e:
print('\nERROR: {}'.format(e))
continue
if ref.new_key:
replace_keys[ref.old_key] = ref
print('->', ref.new_key, end=' ')
sys.stdout.flush()
time.sleep(0.3)
if ref.key.lower() not in existing_keys:
existing_keys.append(ref.key.lower())
new_entries[ref.key] = ref
print('[new entry]', end='')
print('')
replacements = list()
for ref in replace_keys.values():
for appearance in ref.positions:
replacements.append((appearance, ref.old_key, ref.new_key))
self.replace_text(replacements)
self.write_tex()
new_ref_contents = '\n'.join(r.content for r in new_entries.values())
if bibtex:
self.append_and_update_bib(new_ref_contents)
else:
self.modify_and_write_bbl(new_ref_contents, append_bbl)
class TeX(object):
CITE_REGEX = re.compile(r'(?P<pre>(\\cite(\[.*?\])?{))(?P<body>.*?)}', re.DOTALL)
CITE_BIB_IN_TEX = re.compile(r'\\bibliography{(.*?)}', re.DOTALL)
CITE_BIB_IN_BBL = re.compile(r'\\bibitem{(.*?)}', re.DOTALL)
COMMENTS_REGEX = re.compile(r'((?:^|[^\\])(?:\\\\)*)%.*$', re.MULTILINE)
@classmethod
def strip_comment(cls, string):
return cls.COMMENTS_REGEX.sub(r'\1', string)
def __init__(self, filename):
self.text = None
errors = []
possible_paths = [filename, filename + '.tex']
for path in possible_paths:
try:
with open(path, mode='r') as file:
self.text_original = file.read()
self.text = self.text_original
self.filename = path
self.stem = os.path.splitext(path)[0]
break
except IOError as e:
errors.append(e)
pass
if self.text is None:
raise FileLookupFailedError(errors=errors, paths=possible_paths)
self._bib_name = None
self._bib = None
self._bbl = None
# generate references
text_uncommented = self.strip_comment(self.text)
self.references = ODict() # Order is important!
for cite in self.CITE_REGEX.finditer(text_uncommented):
pos = Position(str=text_uncommented[:cite.start()])
pos.shift(cite.group('pre'))
for key_raw in re.split(r',', cite.group('body')):
stripping = re.match(r'^(\s*)(\S+)(\s*)$', key_raw)
pos.shift(stripping.group(1))
key = stripping.group(2)
if key not in self.references:
self.references[key] = Ref(key, position=pos.copy())
else:
self.references[key].positions.append(pos.copy())
pos.shift(stripping.group(2)).shift(stripping.group(3))
pos.shift(',')
def write_tex(self):
with open(self.filename, mode='w') as file:
file.write(self.text)
def bbl_name(self):
return self.stem + '.bbl'
def bbl(self):
if self._bbl is None:
if self.bbl_name() and os.path.exists(self.bbl_name()):
try:
with open(self.bbl_name(), mode='r') as file:
self._bbl = file.read()
except:
pass
self._bbl = self._bbl or ""
return self._bbl
def modify_and_write_bbl(self, new_content, append=True):
begin = '\\begin{thebibliography}{99}'
end = '\\end{thebibliography}'
if append:
sep = re.split(r'\\end\s*{\s*thebibliography\s*}', self.bbl(), maxsplit=1)
(bbl, footer) = sep if len(sep) == 2 else (sep[0], "")
self._bbl = '\n'.join([bbl, new_content, end + footer])
else:
self._bbl = '\n\n'.join([begin, new_content, end])
with open(self.bbl_name(), mode='w') as file:
file.write(self.bbl())
def bib_name(self):
if self._bib_name is None:
bib_keys = self.CITE_BIB_IN_TEX.findall(self.strip_comment(self.text))
stem = None
for bib_key in bib_keys:
for bib in re.split(r'\s*,\s*', bib_key):
if stem is None:
stem = bib
elif stem != bib:
raise MultipleBibError
if stem is None:
self._bib_name = False # for "not found"
else:
self._bib_name = os.path.join(os.path.dirname(self.filename), stem + '.bib')
return self._bib_name
def bib(self):
if self._bib is None:
if self.bib_name() and os.path.exists(self.bib_name()):
try:
self._bib = pybtex.database.parse_file(self.bib_name(), bib_format='bibtex')
except:
pass
self._bib = self._bib or pybtex.database.BibliographyData()
return self._bib
# pybtex output are a bit buggy and avoided.
# def append_bib(self, entries):
# # self._bib.add_entries(entries) # maybe buggy?
# for k in entries.order:
# self._bib.add_entry(k, entries[k])
# def update_bib(self):
# if self.bib_name():
# self._bib.to_file(self.bib_name(), bib_format='bibtex')
# else:
# raise RuntimeError()
def append_and_update_bib(self, new_text):
with open(self.bib_name(), mode='a') as file:
file.write('\n' + new_text + '\n')
self._bib = None # clear and to be reload
def bbl_keys(self):
try:
with open(self.bbl_name(), mode='r') as file:
return self.CITE_BIB_IN_BBL.findall(self.strip_comment(file.read()))
except IOError:
return []
def fetch_and_update(self, bibtex=True, latex_format='EU', append_bbl=False):
existing_keys = self.bib().entries.keys() if bibtex else self.bbl_keys()
existing_keys = [k.lower() for k in existing_keys]
replace_keys = ODict()
new_entries = ODict()
type_name = 'BibTeX' if bibtex else 'LaTeX({})'.format(latex_format)
for ref in self.references.values():
if ref.key.lower() in existing_keys:
if DEBUG:
print('skip existing: {}'.format(ref.key))
continue
if Key.is_unknown(ref.key):
print('WARNING: skip non-existing but unknown-type key {}'.format(ref.key))
continue
try:
print('fetching', type_name, 'from inspire:', ref.key, end=' ')
if bibtex:
ref.fetch_bibtex()
else:
ref.fetch_latex(latex_format)
sys.stdout.flush()
time.sleep(0.3)
except RecordNotFound or MultipleRecordsFound as e:
print('\nERROR: {}'.format(e))
continue
if ref.new_key:
replace_keys[ref.old_key] = ref
print('->', ref.new_key, end=' ')
sys.stdout.flush()
time.sleep(0.3)
if ref.key.lower() not in existing_keys:
existing_keys.append(ref.key.lower())
new_entries[ref.key] = ref
print('[new entry]', end='')
print('')
replacements = list()
for ref in replace_keys.values():
for appearance in ref.positions:
replacements.append((appearance, ref.old_key, ref.new_key))
self.replace_text(replacements)
self.write_tex()
new_ref_contents = '\n'.join(r.content for r in new_entries.values())
if bibtex:
self.append_and_update_bib(new_ref_contents)
else:
self.modify_and_write_bbl(new_ref_contents, append_bbl)
def replace_text(self, replacement_rules):
# replace from the end to the beginning not to break the positions
replacement_rules = sorted(replacement_rules, key=lambda x: x[0], reverse=True)
lines = Position.LINESEP_REGEX.split(self.text)
for pos, old, new in replacement_rules:
if lines[pos.l][pos.c:pos.c + len(old)] == old:
lines[pos.l] = lines[pos.l][:pos.c] + new + lines[pos.l][pos.c + len(old):]
else:
raise ReplacementError(pos.l, pos.c, old, new, lines[pos.l][pos.c:pos.c + len(old)])
self.text = '\n'.join(lines)