def parse():
src_bib = parse_file(CACHE, 'bibtex')
bib = parse_file(DST, 'bibtex')
for entry in src_bib.entries.values():
if entry.key in IGNORE:
continue
elif entry.type != 'article':
continue
journal = entry.fields['journal'].lower()
if journal == 'biorxiv' and entry.fields['pages'] in BIORXIV_OBSOLETE:
continue
elif entry.key in bib.entries:
if journal == bib.entries[entry.key].fields['journal'].lower():
continue
# fix title
for repl in ACRONYMS:
entry.fields['title'] = re.sub(repl, '{' + repl + '}',
entry.fields['title'])
# URL is redundant with DOI
if 'doi' in entry.fields:
entry.fields.pop('url', None)
key = entry.key
for c in ascii_lowercase:
if key in bib.entries:
key = f'{entry.key}_{c}'
else:
break
bib.add_entry(key, entry)
DST.write_bytes(bib.to_bytes('bibtex').replace(br'\\&', br'\&'))
def dupcheck(fin):
"""
Check INPUT for duplicate entries.
"""
db = parse_file(fin, "bibtex").lower()
tx_key_titles = defaultdict(list)
for key, e in db.entries.items():
if "title" not in e.fields:
continue
title = e.fields["title"]
tx = title.lower()
tx = "".join(c for c in tx if c.isalnum() or c.isspace())
tx = " ".join(tx.split())
tx_key_titles[tx].append((key, title))
bold_wrap_len = len(click.style(" ", bold=True)) - 1
for tx, key_titles in tx_key_titles.items():
if len(key_titles) > 1:
max_keylen = max(len(i) for i, _ in key_titles)
fmt = " (%%-%ds) |- %%s" % (max_keylen + bold_wrap_len)
code = click.style("Duplicate title", fg="red")
tx = click.style(tx, fg="yellow")
click.echo("%s: %s" % (code, tx))
for key, title in key_titles:
key = click.style(key, bold=True)
click.echo(fmt % (key, title))
def check(disable_good_key_check, fin):
"""
Check INPUT for inconsistancies.
"""
db = parse_file(fin, "bibtex").lower()
for key, e in db.entries.items():
if not is_good_key(key) and disable_good_key_check is False:
code = click.style("Bad key", fg="red")
key = click.style(key, bold=True)
msg = "%s: %s" % (code, key)
click.echo(msg)
if not is_good_pages(e):
code = click.style("Bad pages", fg="yellow")
key = click.style(key, bold=True)
msg = "%s for %s: %s" % (code, key, e.fields["pages"])
click.echo(msg)
empty = empty_fields(e)
if empty:
code = click.style("Empty fields", fg="blue")
key = click.style(key, bold=True)
msg = "%s for %s: %s" % (code, key, " ".join(empty))
click.echo(msg)
missing = missing_fields(e)
missing = missing_acceptable(missing, e)
if missing:
code = click.style("Missing fields", fg="magenta")
key = click.style(key, bold=True)
typ = click.style(e.type, fg="green")
msg = "%s for %s: %s | %s" % (code, key, " ".join(missing), typ)
click.echo(msg)
def gather_candidates(self, context):
bib_filepath = '~/.pandoc/library.bib'
bib_file = database.parse_file(bib_filepath, bib_format='bibtex')
bib_entries = bib_file.entries
citation_keys = bib_entries.keys()
titles = [bib_entries[k].fields['title'][1:-1] for k in citation_keys]
absts = [
bib_entries[k].fields['abstract']
if 'abstract' in bib_entries[k].fields else ""
for k in citation_keys
]
kind = []
for k in citation_keys:
if 'year' in bib_entries[k].fields:
tmp = "(" + bib_entries[k].fields['year'] + ") "
if 'journal' in bib_entries[k].fields:
tmp += bib_entries[k].fields['journal']
kind.append(tmp)
citation = []
for k, t, a, j in zip(citation_keys, titles, absts, kind):
citation.append({
'word': k,
'abbr': k + ": " + t,
'info': a,
'kind': j
})
return citation
def format_database(
from_filename, to_filename,
bib_format=None, output_backend=None,
input_encoding=None, output_encoding=None,
parser_options=None,
min_crossrefs=2,
style=None,
**kwargs
):
if parser_options is None:
parser_options = {}
output_backend = find_plugin('pybtex.backends', output_backend, filename=to_filename)
bib_data = database.parse_file(
from_filename,
encoding=input_encoding, bib_format=bib_format,
**parser_options
)
style_cls = find_plugin('pybtex.style.formatting', style)
style = style_cls(
label_style=kwargs.get('label_style'),
name_style=kwargs.get('name_style'),
sorting_style=kwargs.get('sorting_style'),
abbreviate_names=kwargs.get('abbreviate_names'),
min_crossrefs=min_crossrefs,
)
formatted_bibliography = style.format_bibliography(bib_data)
output_backend(output_encoding).write_to_file(formatted_bibliography, to_filename)
def preExecute(self):
duplicates = self.get('duplicates', list())
self.__database = BibliographyData()
bib_files = []
for node in self.translator.getPages():
if node.source.endswith('.bib'):
bib_files.append(node.source)
for bfile in bib_files:
try:
db = parse_file(bfile)
except UndefinedMacro as e:
msg = "The BibTeX file %s has an undefined macro:\n%s"
LOG.warning(msg, bfile, e)
#TODO: https://bitbucket.org/pybtex-devs/pybtex/issues/93/
# databaseadd_entries-method-not-considering
warn = self.get('duplicate_warning')
for key in db.entries:
duplicate_key = key in self.__database.entries
duplicate_key_allowed = key in duplicates
if duplicate_key and (not duplicate_key_allowed):
if warn:
msg = "The BibTeX entry '%s' defined in %s already exists."
LOG.warning(msg, key, bfile)
elif not duplicate_key:
self.__database.add_entry(key, db.entries[key])
def bib_reader(filename):
"A generator which yields pbtex.database.Entry instances"
try:
return iter(parse_file(filename).entries.values())
except Exception as e:
print("Error reading bibtex file {}: {}".format(filename, e))
return []
def custom_parse_file(file_bib):
print(file_bib, " " * 30)
loop = True
while loop:
loop = False
try:
bib_data = parse_file(file_bib)
return bib_data
except BibliographyDataError as ex:
repeated_key = ex.args[0].replace(
"repeated bibliograhpy entry: ", "")
if not os.path.isfile(file_bib + ".bkp"):
shutil.copyfile(file_bib, file_bib + ".bkp")
if repeated_key:
with open(file_bib, "r") as file:
file_data = file.read()
while file_data.find(repeated_key + ",") > -1:
new_key = repeated_key + "_" + str(random.randint(1, 101))
file_data = file_data.replace(
repeated_key + ",", new_key + ",", 1)
print(
file_bib + ": repeatedKey", repeated_key, "replaced by", new_key
)
with open(file_bib, "w+") as file:
file.write(file_data)
loop = True
def upload_file():
if request.method == 'POST':
#Check for file selection and appropriate file type
if 'file' not in request.files:
return redirect(url_for('upload', message='Please select a file.'))
file = request.files['file']
if file.filename == '':
return redirect(
url_for('upload', message='Please select a file with a name.'))
if not allowed_file(file.filename):
return redirect(
url_for('upload', message='Please select a .bib file.'))
#if everything looks good, upload the selected file
else:
file.save(
os.path.join(app.config['UPLOAD_FOLDER'],
secure_filename(file.filename)))
collection = request.form['collection']
bib_data = parse_file(
os.path.join(app.config['UPLOAD_FOLDER'],
secure_filename(
file.filename))) #parse the .bib file
fill(bib_data, collection) #populate the database
return redirect(url_for('upload', message='Upload successful!'))
def process_bibtex(corpus_path):
import pybtex
from pybtex.database import parse_file
from topicexplorer.lib.util import overwrite_prompt, safe_symlink
print "Loading BibTeX from", corpus_path
bib = parse_file(corpus_path)
target_dir = os.path.basename(corpus_path).replace('.bib','')
if not os.path.exists(target_dir):
os.makedirs(target_dir)
elif overwrite_prompt(target_dir):
shutil.rmtree(target_dir)
os.makedirs(target_dir)
else:
raise IOError("Path exits: {}".format(target_dir))
for entry in bib.entries:
if bib.entries[entry].fields.get('file', None):
filename = '/' + bib.entries[entry].fields['file'].replace(':pdf','')[1:]
if 'C$\\backslash$:' in filename:
filename = filename.replace('C$\\backslash$:', '')
filename = filename[1:]
filename = os.path.normpath(filename)
filename = os.path.abspath(filename)
if not os.path.exists(filename):
print "Invalid 'file' field for BibTeX entry {}:\n\t({})".format(entry, filename)
else:
new_path = os.path.join(target_dir, os.path.basename(filename))
safe_symlink(filename, new_path)
else:
print "No 'file' field for BibTeX entry: {}".format(entry)
return target_dir
def preExecute(self, content):
self.__database = BibliographyData()
bib_files = []
for node in content:
if node.source.endswith('.bib'):
bib_files.append(node.source)
for bfile in bib_files:
try:
db = parse_file(bfile)
except UndefinedMacro as e:
msg = "The BibTeX file %s has an undefined macro:\n%s"
LOG.warning(msg, bfile, e.message)
#TODO: https://bitbucket.org/pybtex-devs/pybtex/issues/93/
# databaseadd_entries-method-not-considering
warn = self.get('duplicate_warning')
for key in db.entries:
if key in self.__database.entries:
if warn:
msg = "The BibTeX entry '%s' defined in %s already exists."
LOG.warning(msg, key, bfile)
else:
self.__database.add_entry(key, db.entries[key])
def parse_refs(bibtexf, verbose=False):
"""
Parse the references and return some data structure
:param bibtexf: the bibtex file
:param verbose: more output
:return: the BibliographyData object and a dictionary linking lower case titles to entry keys
"""
if verbose:
message(f"Parsing {bibtexf}", "GREEN")
bib = parse_file(bibtexf, 'bibtex')
titles = {}
for e in bib.entries:
try:
if 'title' in bib.entries[e].fields:
# sys.stderr.write(f"{bcolors.BLUE}{bib.entries[e].fields['title'].lower()}{bcolors.ENDC}\n")
t = bib.entries[e].fields['title'].lower()
t = t.replace('{', '')
t = t.replace('}', '')
titles[t.lower()] = e
except Exception as ex:
sys.stderr.write(f"Error parsing entry: {e}\n")
print(ex)
if verbose:
message(f"Found {len(titles)} references", "BLUE")
return bib, titles
def main():
if len(sys.argv) != 3:
print('Filters BibTeX file preserving order and limiting to last 5 years')
print('usage: %s <original-bib> <output-bib>' % \
os.path.basename(sys.argv[0]))
print('example: %s publications.bib filtered.bib')
sys.exit(1)
original = sys.argv[1]
minyear = datetime.date.today().year - 5
output = sys.argv[2]
from pybtex.database import parse_file, BibliographyData
bib_data = parse_file(original)
filtered = BibliographyData()
for key in bib_data.entries:
entry = bib_data.entries[key]
year = int(entry.fields['year'])
if year > minyear:
print('Selecting @%s[%s] from %s' % (entry.type, key, year))
filtered.entries[key] = entry
print('Saving to %s...' % output)
s = filtered.to_string('bibtex')
for f, t in FIX_STRINGS: s = s = s.replace(f, t)
with open(output, 'wt') as f: f.write(s)
def init(viewer, config, args):
global metadata
try:
filename = args.bibtex or config.get('bibtex', 'path')
except ConfigParser.Error:
model_path = config.get('main','path')
filename = os.path.join(model_path, 'library.bib')
print "Loading Bibtex metadata from", filename
bib = parse_file(filename)
metadata = dict()
for entry in bib.entries:
key = '/' + bib.entries[entry].fields.get('file','').replace(':pdf','')[1:]
if 'C$\\backslash$:' in key:
key = key.replace('C$\\backslash$:', '')
key = key[1:]
key = os.path.normpath(key)
key = os.path.basename(key)
try:
citation = pybtex.format_from_file(
filename, style='plain', output_backend='text', citations=[entry])[3:]
metadata[key] = citation
except PybtexError:
metadata[key] = filename
def build_bib_dict():
pybtex_style = pybtex.plugin.find_plugin('pybtex.style.formatting',
'plain')()
pybtex_html_backend = pybtex.plugin.find_plugin('pybtex.backends',
'html')()
pybtex_parser = pybtex.database.input.bibtex.Parser()
bib_dict = {}
bib_files = [bib for bib in listdir('bib') if bib[-4:] == '.bib']
for bib_file in bib_files:
full_path = join('bib', bib_file)
print(full_path)
data = parse_file(full_path)
data_formatted = pybtex_style.format_entries(
six.itervalues(data.entries))
output = io.StringIO()
pybtex_html_backend.write_to_stream(data_formatted, output)
html = output.getvalue()
output.close()
html = html.split("<dd>")[1]
html = html.split("</dd>")[0]
for old_string, new_string in replace_strings:
html = html.replace(old_string, new_string)
key = next(iter(data.entries))
bib_dict[key] = html
return bib_dict
def preExecute(self, content):
duplicates = self.get('duplicates', list())
self.__database = BibliographyData()
bib_files = []
for node in content:
if node.source.endswith('.bib'):
bib_files.append(node.source)
for bfile in bib_files:
try:
db = parse_file(bfile)
except UndefinedMacro as e:
msg = "The BibTeX file %s has an undefined macro:\n%s"
LOG.warning(msg, bfile, e.message)
#TODO: https://bitbucket.org/pybtex-devs/pybtex/issues/93/
# databaseadd_entries-method-not-considering
warn = self.get('duplicate_warning')
for key in db.entries:
duplicate_key = key in self.__database.entries
duplicate_key_allowed = key in duplicates
if duplicate_key and (not duplicate_key_allowed):
if warn:
msg = "The BibTeX entry '%s' defined in %s already exists."
LOG.warning(msg, key, bfile)
elif not duplicate_key:
self.__database.add_entry(key, db.entries[key])
def read_wmt_bib() -> List[Paper]:
result = []
with open("downloads/2020.wmt-1.0.bib") as f:
bib = database.parse_file(f)
for i, entry in enumerate(bib.entries.values()):
if entry.type == "book":
continue
title = LatexNodes2Text().latex_to_text(entry.fields["title"])
url = entry.fields["url"]
abstract = LatexNodes2Text().latex_to_text(
entry.fields["abstract"])
author = "|".join([
" ".join(reversed(str(e).split(", ")))
for e in entry.persons["author"]
])
uid = url.replace("https://www.aclweb.org/anthology/", "")
url = "https://www.statmt.org/wmt20/pdf/" + uid + ".pdf"
paper = Paper(
uid=f"WS-2.{uid}",
ws_id="WS-2",
title=title,
authors=author,
abstract=abstract,
track="WS-2",
kind="workshop",
link=url,
)
result.append(paper)
return result
def _add_file(fname, force_redownload, db, per_file_progress_bar):
"""
Return #added, #skipped, file_skipped
"""
if fname.startswith('http'):
if not force_redownload and db.file_has_been_downloaded(fname):
return 0, 0, True
try:
new_entries = pybtex.parse_string(download_file(fname),
bib_format="bibtex").entries
except urllib.error.URLError as e:
raise AddFileError("Error downloading '%s' [%s]" % (fname, str(e)))
except pybtex.PybtexError:
raise AddFileError("Error parsing file %s" % fname)
db.register_file_downloaded(fname)
else:
new_entries = pybtex.parse_file(fname, bib_format="bibtex").entries
added = 0
skipped = 0
if per_file_progress_bar:
iterable = tqdm(
new_entries.values(),
ncols=80,
bar_format="{l_bar}{bar}| [Elapsed: {elapsed} ETA: {remaining}]")
else:
iterable = new_entries.values()
for entry in iterable:
if db.add(entry):
added += 1
else:
skipped += 1
return added, skipped, False
def run(self, lines):
"""
Create a bibliography from cite commands.
"""
# Join the content to enable regex searches throughout entire text
content = '\n'.join(lines)
# Build the database of bibtex data
bibfiles = []
match = re.search(self.RE_BIBLIOGRAPHY, content)
if match:
bib_string = match.group(0)
for bfile in match.group(1).split(','):
try:
bibfiles.append(os.path.join(self._root, bfile))
data = parse_file(bibfiles[-1])
except:
log.error('Failed to parse bibtex file: {}'.format(bfile))
return lines
self._bibtex.add_entries(data.entries.iteritems())
else:
return lines
# Determine the style
match = re.search(self.RE_STYLE, content)
if match:
content = content.replace(match.group(0), '')
try:
style = find_plugin('pybtex.style.formatting', match.group(1))
except:
log.error('Unknown bibliography style "{}"'.format(match.group(1)))
return lines
else:
style = find_plugin('pybtex.style.formatting', 'plain')
# Replace citations with author date, as an anchor
content = re.sub(self.RE_CITE, self.authors, content)
# Create html bibliography
if self._citations:
# Generate formatted html using pybtex
formatted_bibliography = style().format_bibliography(self._bibtex, self._citations)
backend = find_plugin('pybtex.backends', 'html')
stream = io.StringIO()
backend().write_to_stream(formatted_bibliography, stream)
# Strip the bib items from the formatted html
html = re.findall(r'\<dd\>(.*?)\</dd\>', stream.getvalue(), flags=re.MULTILINE|re.DOTALL)
# Produces an ordered list with anchors to the citations
output = u'<ol class="moose-bibliography" data-moose-bibfiles="{}">\n'.format(str(bibfiles))
for i, item in enumerate(html):
output += u'<li name="{}">{}</li>\n'.format(self._citations[i], item)
output += u'</ol>\n'
content = re.sub(self.RE_BIBLIOGRAPHY, output, content)
return content.split('\n')
def _harvest(ds, **kw):
for bib in ds.cldf_dir.glob('*.bib'):
bib = parse_file(str(bib))
for id_, entry in bib.entries.items():
id_ = '{0}:{1}'.format(ds.id, id_)
if id_ not in gbib.entries:
gbib.add_entry(id_, entry)
def init(app, config_file):
global metadata
config = topicexplorer.config.read(config_file)
try:
filename = config.get('bibtex', 'path')
except ConfigParserError:
model_path = config.get('main', 'path')
filename = os.path.join(model_path, 'library.bib')
print("Loading Bibtex metadata from", filename)
bib = parse_file(filename)
metadata = dict()
for entry in bib.entries:
key = '/' + bib.entries[entry].fields.get('file', '').replace(
':pdf', '')[1:]
if 'C$\\backslash$:' in key:
key = key.replace('C$\\backslash$:', '')
key = key[1:]
key = os.path.normpath(key)
key = os.path.basename(key)
try:
citation = pybtex.format_from_file(filename,
style='plain',
output_backend='text',
citations=[entry])[3:]
metadata[key] = citation
except PybtexError:
metadata[key] = filename
def init(self, translator):
command.CommandExtension.init(self, translator)
bib_files = []
for node in anytree.PreOrderIter(self.translator.root):
if node.source.endswith('.bib'):
bib_files.append(node.source)
for bfile in bib_files:
try:
db = parse_file(bfile)
except UndefinedMacro as e:
msg = "The BibTeX file %s has an undefined macro:\n%s"
LOG.warning(msg, bfile, e.message)
#TODO: https://bitbucket.org/pybtex-devs/pybtex/issues/93/
# databaseadd_entries-method-not-considering
warn = self.get('duplicate_warning')
for key in db.entries:
if key in self.__database.entries:
if warn:
msg = "The BibTeX entry '%s' defined in %s already exists."
LOG.warning(msg, key, bfile)
else:
self.__database.add_entry(key, db.entries[key])
def preExecute(self):
set_strict_mode(
False) # allow incorrectly formatted author/editor names
# If this is invoked during a live serve, we need to recompile the list of '.bib' files and
# read them again, otherwise there's no way to distinguish existing entries from duplicates
self.__bib_files = []
for node in self.translator.findPages(
lambda p: p.source.endswith('.bib')):
self.__bib_files.append(node.source)
self.__database = BibliographyData()
for bfile in self.__bib_files:
try:
db = parse_file(bfile)
self.__bib_file_database[bfile] = db
except UndefinedMacro as e:
msg = "The BibTeX file %s has an undefined macro:\n%s"
LOG.warning(msg, bfile, e)
#TODO: https://bitbucket.org/pybtex-devs/pybtex/issues/93/
# databaseadd_entries-method-not-considering
for key in db.entries:
if key in self.__database.entries:
if self.get('duplicate_warning') and (
key not in self.get('duplicates')):
msg = "The BibTeX entry '%s' defined in %s already exists."
LOG.warning(msg, key, bfile)
else:
self.__database.add_entry(key, db.entries[key])
def main():
args = get_args()
print("Parsing %s file..." % args.input_file)
bib_data = parse_file(args.input_file)
print('Generating %i citations...' % len(bib_data.entries))
citations = generate_citations(bib_data)
print("Saving %s file..." % args.output_file)
save(args.output_file, sort_citations(citations))
def test_on_page_markdown(self):
self.plugin.on_config(self.plugin.config)
test_data = parse_file(os.path.join(test_files_dir, "single.bib"))
test_markdown = "This is a citation. [@test]\n\n \\bibliography"
self.assertIn(
"[^1]: First Author and Second Author\. Test title\. *Testing Journal*, 2019\.",
self.plugin.on_page_markdown(test_markdown, None, None, None),
)
def fmt(fin, fout):
"""
Clean up the INPUT bibtex file and write to OUTPUT
"""
bib_data = parse_file(fin, "bibtex")
writer = Writer()
writer.write_stream(bib_data, fout)
def __init__(self, db_file, key):
"""Immediately read in citations and references, if files exist."""
self.db_file = db_file
self.key = key
if os.path.isfile(
os.path.join('bib_files', f'{self.key}_citations.bib')):
self.citations = parse_file(
os.path.join('bib_files', f'{self.key}_citations.bib'))
else:
self.citations = None
if os.path.isfile(
os.path.join('bib_files', f'{self.key}_references.bib')):
self.references = parse_file(
os.path.join('bib_files', f'{self.key}_references.bib'))
else:
self.references = None
self._citations()
self._text_data()
def test_full_bibliography(self):
test_data = parse_file(os.path.join(test_files_dir, "single.bib"))
self.plugin.csl_file = None
self.plugin.format_citations(test_data.entries.items())
self.assertIn("First Author and Second Author", self.plugin.full_bibliography)
self.plugin.csl_file = os.path.join(test_files_dir, "nature.csl")
self.plugin.format_citations(test_data.entries.items())
self.assertIn("Author, F. & Author, S", self.plugin.full_bibliography)
def readBib(fileName):
"""
Read the BibTeX entry contained in the given file.
:param fileName: The name of the file.
:return: The BibTeX entry.
"""
return parse_file(fileName) # This is a BibliographyData object
def create_bib():
"""Read bibtex file and create publications page."""
bib_data = parse_file('local.bib')
# Maps to which section add each entry, based on its type
TYPE2SEC = {
'article' : 'Articles',
'mastersthesis' : 'Theses',
'misc' : 'Theses',
'other' : 'Talks',
'phdthesis' : 'Theses',
'proceedings' : 'Articles',
}
# add the headings for type of publications, automatically extracting
# from the values above in alphabetical order
bib_entries = {}
headings = sorted(set(TYPE2SEC.values()))
for heading in headings:
bib_entries[heading] = []
# Fill categories with entries by year
for entry_key in bib_data.entries:
year = int(bib_data.entries[entry_key].fields['Year'])
entry_type = bib_data.entries[entry_key].type
bib_entry = bib_data.entries[entry_key].fields
bib_entry['Author'] = '; '.join([str(p) for p in bib_data.entries[entry_key].persons['Author']])
bib_entries[TYPE2SEC[entry_type]].append(bib_data.entries[entry_key].fields)
# handler for the file
pub_handler = open('publications.md', 'w')
pub_handler.write("---\n")
pub_handler.write("title: Publications\n")
pub_handler.write("author: Tiago Tresoldi\n")
pub_handler.write("---\n")
pub_handler.write("Here is a list of my main publications. The BibTex reference (from where it is generated), can be downloaded [here](local.bib).\n")
# Fill the output
for heading in headings:
pub_handler.write('\n## %s\n\n' % heading)
# Negative Year so we can sort correctly: by year descending, by title
# ascending
sorted_entries = sorted(
bib_entries[heading],
key = lambda x: (-int(x['Year']), x['Title']))
for entry in sorted_entries:
pub_handler.write('- %s\n' % bibtex2md(entry))
# close the handler
pub_handler.close()
def parseBibtexFile(self, bibfile):
"""
Returns parsed bibtex file. If "macro_files" are supplied in the configuration
file, then a temporary file will be made that contains the supplied macros
above the original bib file. This temporary combined file can then be
parsed by pybtex.
"""
if self._macro_files:
t_bib_path = os.path.join(MooseDocs.ROOT_DIR, "tBib.bib")
with open(t_bib_path, "wb") as t_bib:
for t_file in self._macro_files:
with open(os.path.join(MooseDocs.ROOT_DIR, t_file.strip()), "rb") as in_file:
shutil.copyfileobj(in_file, t_bib)
with open(bibfile, "rb") as in_file:
shutil.copyfileobj(in_file, t_bib)
data = parse_file(t_bib_path)
if os.path.isfile(t_bib_path):
os.remove(t_bib_path)
else:
data = parse_file(bibfile)
return data
def gen_refs(bibfile):
target = os.path.splitext(os.path.split(bibfile)[1])[0] + '.yml'
call_citeproc(bibfile, target)
bib = ptd.parse_file(bibfile)
ybib = yaml.safe_load(open(target, encoding='utf-8'))
for yitem in ybib['references']:
bitem = bib.entries.get(yitem['id'])
yitem = merge(bitem, yitem)
yaml.dump(ybib, open('publications.yml', 'w', encoding="utf-8"))
return ybib
def parseBibtexFile(self, bibfile):
"""
Returns parsed bibtex file. If "macro_files" are supplied in the configuration
file, then a temporary file will be made that contains the supplied macros
above the original bib file. This temporary combined file can then be
parsed by pybtex.
"""
if self._macro_files:
with open("tBib.bib", "wb") as tBib:
for tFile in self._macro_files:
with open(MooseDocs.abspath(tFile.strip()),
"rb") as inFile:
shutil.copyfileobj(inFile, tBib)
with open(bibfile, "rb") as inFile:
shutil.copyfileobj(inFile, tBib)
data = parse_file("tBib.bib")
os.remove("tBib.bib")
else:
data = parse_file(bibfile)
return data
def convert_bibtex_keys(input_file: str, output_file: str):
"""
Convert keys in a bibtex file to Google Scholar format.
@input_file: string, input file name.
@output_file: string, output file name.
"""
bib_data = parse_file(input_file)
keys, new_keys = obtain_replace_keys(bib_data)
new_entries = OrderedCaseInsensitiveDict()
for key, new_key in zip(keys, new_keys):
new_entries[new_key] = bib_data.entries[key]
bib_data.entries = new_entries
bib_data = update_arxiv_information(bib_data)
with open(output_file, 'w', encoding='utf-8') as ofile:
bib_data.to_file(ofile)
def gen_refs(bibfile):
target = os.path.splitext(os.path.split(bibfile)[1])[0] + '.yml'
call_citeproc(bibfile, target)
bib = ptd.parse_file(bibfile)
ybib = yaml.load(open(target, encoding = 'utf-8'))
for yitem in ybib['references']:
bitem = bib.entries.get(yitem['id'])
yitem = merge(bitem, yitem)
newdic = dict({yitem['id'] : bitem})
output = ptd.BibliographyData(newdic)
output.to_file( os.path.join(BIBTEMPDIRECTORY, yitem['id'] + ".bib"), "bibtex")
yaml.dump(ybib, open('publications.yml', 'w', encoding="utf-8"))
return ybib
def __init__(self, filename='../references.bib'):
logger.info('Reading references from {}'.format(filename))
self.data = parse_file(filename)
logger.info(self.data.entries.keys())
# set up bibliography formatting
self.style = pybtex.plugin.find_plugin('pybtex.style.formatting',
self.style_name)()
self.backend = pybtex.plugin.find_plugin('pybtex.backends', 'html')()
# set up inline reference and doi dictionaries
entries = self.data.entries
self.inline = ({k: self._parse_entry(v) for k, v in entries.items()})
self.doi = ({k: self._get_doi(v) for k, v in entries.items()})
# set up key regex
pattern = '(' + ')|('.join(self.data.entries.keys()) + ')'
self.regex = re.compile(pattern)
def _parse_bib(self, b):
self.M[b] = os.path.getmtime(b)
self.E[b] = {}
try:
bib = parse_file(b)
except Exception as ERR:
nvimr_warn('Error parsing ' + b + ': ' + str(ERR))
return
for k in bib.entries:
self.E[b][k] = {'citekey': k, 'title': '', 'year': '????'}
self.E[b][k]['author'] = self._get_authors(bib.entries[k].persons)
if 'title' in bib.entries[k].fields:
self.E[b][k]['title'] = bib.entries[k].fields['title']
if 'year' in bib.entries[k].fields:
self.E[b][k]['year'] = bib.entries[k].fields['year']
if 'file' in bib.entries[k].fields:
self.E[b][k]['file'] = bib.entries[k].fields['file']
def convert(
from_filename, to_filename,
from_format=None, to_format=None,
input_encoding=None, output_encoding=None,
parser_options=None,
preserve_case=True,
**kwargs
):
if parser_options is None:
parser_options = {}
if from_filename == to_filename:
raise ConvertError('input and output file can not be the same')
bib_data = database.parse_file(
from_filename,
bib_format=from_format, encoding=input_encoding,
**parser_options
)
if not preserve_case:
bib_data = bib_data.lower()
bib_data.to_file(to_filename, bib_format=to_format, encoding=output_encoding)
def init(self, translator):
command.CommandExtension.init(self, translator)
bib_files = []
for node in anytree.PreOrderIter(self.translator.root):
if node.source.endswith('.bib'):
bib_files.append(node.source)
for bfile in bib_files:
try:
db = parse_file(bfile)
except UndefinedMacro as e:
msg = "The BibTeX file %s has an undefined macro:\n%s"
LOG.warning(msg, bfile, e.message)
#TODO: https://bitbucket.org/pybtex-devs/pybtex/issues/93/
# databaseadd_entries-method-not-considering
for key in db.entries:
if key in self.__database.entries:
msg = "The BibTeX entry '%s' defined in %s already exists."
LOG.warning(msg, key, bfile)
else:
self.__database.add_entry(key, db.entries[key])
import os
import pybtex.database as pybib_db
import wordcloud as wc
from PIL import Image
import numpy as np
import matplotlib
matplotlib.use('Qt5Agg')
import matplotlib.pyplot as plt
bib_data = pybib_db.parse_file('weishinn-ku.bib')
bib_data = bib_data.lower()
titles = []
for entry in bib_data.entries.values():
titles.append(entry.fields['title'])
print("Total {0} titles.".format(len(titles)))
text = ' '.join(titles)
text = text.upper()
# "network" appears 22 times
text = text.replace("NETWORK", " ", 16)
text = text.replace("QUERY", "QUERIES")
stopwords = set([
can include it in the webpage.
"""
for key,entry in db.entries.items():
for auth in entry.persons["author"]:
if ("Harrison" not in auth.first_names or
"Chapman" not in auth.last_names):
entry.add_person(auth, "otherauthor")
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(
description="Convert a bibtex file into a yaml file, for "
"intelligent inclusion into Jekyll pages")
parser.add_argument(
"bibfile", type=argparse.FileType("r"),
help="BibTeX file to convert into YAML")
parser.add_argument(
"yamlfile", type=argparse.FileType("w"),
help="YAML file to write, will be overwritten")
args = parser.parse_args()
bibdb = database.parse_file(args.bibfile)
extra_bibparse(bibdb)
writer = Writer()
writer.write_file(bibdb, args.yamlfile)
parser.add_argument('-y', help="Earliest year to report conflict (default={})".format(earlyyear), default=earlyyear, type=int)
args = parser.parse_args()
entries = set()
dupentries=False
with open(args.f, 'r') as bin:
for l in bin:
if l.startswith('@'):
l = l.replace('@misc', '')
l = l.replace('@article', '')
l = l.replace('@inproceedings', '')
if l in entries:
sys.stderr.write("Duplicate entry " + l.replace('{', '').replace(',', ''))
dupentries=True
entries.add(l)
if dupentries:
sys.stderr.write("FATAL: The bibtex file has duplicate entries in it. Please remove them before trying to continue\n")
sys.stderr.write("(It is an issue with Google Scholar, but pybtex breaks with duplicate entries. Sorry)\n")
sys.exit(-1)
bib = parse_file(args.f, 'bibtex')
for e in bib.entries:
if 'year' in bib.entries[e].fields:
if int(bib.entries[e].fields['year']) >= args.y:
bib_data = BibliographyData({e : bib.entries[e]})
print(bib_data.to_string('bibtex'))
from pybtex.database import parse_file
from pybtex.plugin import find_plugin
SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
SITE_ROOT = os.path.dirname(SCRIPT_DIR)
INFILE = os.path.join(SCRIPT_DIR, 'publications.bib')
OUTFILE = os.path.join(SITE_ROOT, '_data', 'publications.json')
# Retrieves the year for a BibTeX entry
def getYear(entry):
return int(entry.fields['year'])
# Read the BibTeX database file
db = parse_file(INFILE)
# Retrieve the Style class for the "plain" style
PlainStyle = find_plugin('pybtex.style.formatting', 'plain')
style = PlainStyle()
# Retrieve the HTML backend
HtmlBackend = find_plugin('pybtex.backends', 'html')
backend = HtmlBackend('utf-8')
# Sort the BibTeX database entries in reverse-chronological order
entries = list(db.entries.values())
entries = list(reversed(sorted(entries, key = getYear)))
# Retrieve the list of years that have publications
years = list([getYear(entry) for entry in entries])
matchintemporal
brodbeck2018transformation
""".split()
ACRONYMS = ['EEG', 'MEG', 'MRI']
querier = ScholarQuerier()
settings = ScholarSettings()
settings.set_citation_format(ScholarSettings.CITFORM_BIBTEX)
querier.apply_settings(settings)
query = SearchScholarQuery()
query.set_phrase("eelbrain")
query.set_timeframe(2012, None)
query.set_include_patents(False)
bib = parse_file(DST, 'bibtex')
start = 0
while True:
querier.send_query(query)
if len(querier.articles) == 0:
break
# extract articles
for article in querier.articles:
querier.get_citation_data(article)
# convert to pybtex entry
data = parse_bytes(article.citation_data, 'bibtex')
assert len(data.entries) == 1
for entry in data.entries.values():
if entry.key in IGNORE:
continue
elif entry.type != 'article':