try:
# framework is running
from .startup_choice import *
except ImportError as _excp:
# class is imported by itself
if (
'attempted relative import with no known parent package' in str(_excp)
or 'No module named \'omfit_classes\'' in str(_excp)
or "No module named '__main__.startup_choice'" in str(_excp)
):
from startup_choice import *
else:
raise
from omfit_classes.omfit_ascii import *
from omfit_classes.omfit_weblink import OMFITwebLink
import numpy as np
__all__ = ['OMFITbibtex', 'searchdoi']
try:
import bibtexparser
except Exception as _excp:
bibtexparser = None
printe('WARNING! Compromised omfit_bibtex support due to failure to import bibtexparser!')
[docs]class OMFITbibtex(OMFITascii, SortedDict):
r"""
Class used to parse bibtex files
The class should be saved as a dictionary or dictionaries (one dictionary for each bibtex entry)
Each bibtex entry must have defined the keys: `ENTRYTYPE` and `ID`
:param filename: filename of the .bib file to parse
:param \**kw: keyword dictionary passed to OMFITascii class
To generate list of own publications:
1. Export all of your citations from https://scholar.google.com to a `citation.bib` bibtex file
2. OMFIT['bib']=OMFITbibtex('.bib') # load citations as OMFITbibtex
3. OMFIT['bib'].doi(deleteNoDOI=True) # remove entries which do not have a DOI (ie.conferences)
4. OMFIT['bib'].sanitize() # fix entries where needed
4. OMFIT['bib'].update_ID(as_author='Meneghini') # Sort entries and distinguish between first author or contributed
5. print('\n\n'.join(OMFIT['bib'].write_format())) # write to whatever format desired
"""
def __init__(self, filename, **kw):
OMFITascii.__init__(self, filename, **kw)
SortedDict.__init__(self, caseInsensitive=True)
if filename is None:
from datetime import date
self[0] = {'ID': os.environ['USER'] + str(date.today().year), 'ENTRYTYPE': 'article'}
else:
self.dynaLoad = True
[docs] @dynaLoad
def load(self):
with open(self.filename, 'r') as f:
bibtex_str = f.read()
bib_database = bibtexparser.loads(bibtex_str)
for k, item in enumerate(bib_database.get_entry_list()):
label0 = label = item['ID']
k = 0
while label in self:
k += 1
label = label0 + '_%d' % k
self[label] = item
[docs] @dynaSave
def save(self):
tmp = bibtexparser.bibdatabase.BibDatabase()
tmp.entries = list(self.values())
writer = bibtexparser.bwriter.BibTexWriter()
bibtex_str = encode_ascii_ignore(bibtexparser.dumps(tmp))
if self.filename is not None:
with open(self.filename, 'w') as f:
f.write(bibtex_str)
else:
return bibtex_str
[docs] def doi(self, deleteNoDOI=False):
"""
method for adding DOI information to bibtex
:param deleteNoDOI: delete entries without DOI
"""
for item in list(self.keys()):
# only articles
if (
'doi' in self[item]
or np.any([k not in self[item] for k in ['ENTRYTYPE', 'author', 'title', 'journal']])
or self[item]['journal'].lower() in [x.lower() for x in _noDOIjournals]
or self[item]['ENTRYTYPE'].lower() != 'article'
):
printi('%s: %s' % (encode_ascii_ignore(item), self[item].get('doi', '')))
continue
# search for this paper
tmp = searchdoi(self[item]['title'], self[item]['author'])
self[item]['__doi__'] = tmp
self[item]['doi'] = tmp[0]['DOI']
self[item]['doi_score'] = tmp[0]['score']
if self[item]['title'].lower() != tmp[0]['title'][0].lower():
# if the title does not match exactly this is a bad sign
printw('%s: %s' % (encode_ascii_ignore(item), self[item]['doi']))
else:
if np.all([k in tmp[0] for k in ['container-title', 'issue', 'page', 'publisher']]):
# trust the info from crossref.org
self[item]['journal'] = tmp[0]['container-title'][0]
self[item]['number'] = tmp[0]['issue']
self[item]['pages'] = tmp[0]['page']
self[item]['publisher'] = tmp[0]['publisher']
self[item]['author'] = ' and '.join(
[', '.join([_f for _f in [x.get('family', 'others'), x.get('given', '')] if _f]) for x in tmp[0]['author']]
)
printi('%s: %s' % (encode_ascii_ignore(item), self[item]['doi']))
# create URL entry based on DOI
for item in list(self.keys()):
if 'doi' in self[item]:
self[item]['url'] = OMFITwebLink('doi.org/' + self[item]['doi'])
elif deleteNoDOI:
del self[item]
# finar clearnup
for item in list(self.keys()):
if '__doi__' in self[item]:
del self[item]['__doi__']
if 'doi_score' in self[item]:
del self[item]['doi_score']
[docs] def sanitize(self):
"""
Sanitizes the database entries:
1. Fix all-caps author names
2. Fix unicodes
"""
for item in self:
# Fix all-caps author names
authors = self[item]['author'].split()
for k, a in enumerate(authors):
if '.' in a or len(a) > 2:
authors[k] = a.title()
self[item]['author'] = ' '.join(authors)
# Fix unicodes
for sub in list(self[item].keys()):
self[item][sub] = encode_ascii_ignore(self[item][sub])
[docs] def filter(self, conditions):
"""
filter database given a set of conditions
:param conditions: list of strings (eg. ['int(year)>2012']
:return: filtered OMFITbibtex object
"""
conditions = tolist(conditions)
self = copy.deepcopy(self)
for condition in conditions:
for item in list(self.keys()):
try:
if not eval(condition, {}, self[item]):
del self[item]
except Exception:
del self[item]
return self
[docs] def update_ID(self, fmt=['year_1stAuthor_jrnl', 'lower1stAuthor_year'][1], separator=':', as_author=False):
"""
set bibtex ID
:param fmt: string with format 'year_1stAuthor_jrnl'
:param separator: string with separator for fmt
:param as_author: only keep entries that have `as_author` as author
"""
for item in list(self.keys()):
tmp = self[item]
del self[item]
try:
tmp['1stAuthor'] = tmp['author'].split()[0].strip(',')
tmp['lower1stAuthor'] = tmp['1stAuthor'].lower()
except Exception:
pass
try:
tmp['jrnl'] = ''.join([x[0] for x in tmp['journal'].split()])
tmp['lowerjrnl'] = tmp['jrnl'].lower()
except Exception:
pass
label0 = label = separator.join([str(tmp[k]) for k in fmt.split('_')])
if as_author:
if as_author.lower() not in tmp['author'].lower():
continue
if tmp['author'].split()[0].strip(',').lower() == as_author.lower():
label = label0 = '_' + label
k = 0
while label in self:
k += 1
label = label0 + '%s' % chr(k + ord('a'))
for item in ['1stAuthor', 'jrnl', 'lower1stAuthor', 'lowerjrnl']:
if item in tmp:
del tmp[item]
self[label] = tmp
self[label]['ID'] = label
self.sort()
return self
[docs]def searchdoi(title, author):
"""
This function returns a list of dictionaries containing the best matching papers
for the title and authors according to the crossref.org website
:param title: string with the title
:param author: string with the authors
:return: list of dictionaries with info about the papers found
"""
data = {"query.author": author.encode('utf-8'), "query.title": title.encode('utf-8')}
url = "http://api.crossref.org/works?"
import requests
import json
response = requests.get(url, data, verify=False)
try:
response.raise_for_status()
return json.loads(response.text)['message']['items']
except Exception:
raise
_noDOIjournals = ['Bulletin of the American Physical Society', 'Bull. Am. Phys. Soc.']
############################################
if __name__ == '__main__':
test_classes_main_header()
import requests
bibtex_text = '''
@article{meneghini2013integrated,
title={Integrated modeling of tokamak experiments with OMFIT},
author={Meneghini, Orso and Lao, Lang},
journal={Plasma and Fusion Research},
volume={8},
pages={2403009--2403009},
year={2013},
publisher={The Japan Society of Plasma Science and Nuclear Fusion Research}
}
@article{meneghini2015integrated,
title={Integrated modeling applications for tokamak experiments with OMFIT},
author={Meneghini, O and Smith, SP and Lao, LL and Izacard, O and Ren, Q and Park, JM and Candy, J and Wang, Z and Luna, CJ and Izzo, VA and others},
journal={Nuclear Fusion},
volume={55},
number={8},
pages={083008},
year={2015},
publisher={IOP Publishing}
}
'''
bib = OMFITbibtex('OMFIT_bibtex', fromString=bibtex_text)
# filter
filtered_bib = bib.filter(['int(year)>2014'])
# sanitize
filtered_bib.sanitize()
# get the DOI (can take some time, and is thus best done after filtering)
try:
bib.doi()
except requests.exceptions.HTTPError:
pass
pprint(filtered_bib)
