/usr/lib/python3/dist-packages/duecredit/io.py is in python3-duecredit 0.4.5.3-1.
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# ex: set sts=4 ts=4 sw=4 noet:
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the duecredit package for the
# copyright and license terms.
#
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
# Just for testing of robust operation
import os
if 'DUECREDIT_TEST_EARLY_IMPORT_ERROR' in os.environ.keys():
raise ImportError("DUECREDIT_TEST_EARLY_IMPORT_ERROR")
import time
from collections import defaultdict, Iterator
import copy
from os.path import dirname, exists
import pickle
import requests
import tempfile
from six import PY2, itervalues, iteritems
import warnings
from .config import CACHE_DIR, DUECREDIT_FILE
from .entries import BibTeX, Doi
from .log import lgr
def get_doi_cache_file(doi):
return os.path.join(CACHE_DIR, doi)
def import_doi(doi):
cached = get_doi_cache_file(doi)
if exists(cached):
with open(cached) as f:
doi = f.read()
if PY2:
return doi.decode('utf-8')
return doi
# else -- fetch it
headers = {'Accept': 'text/bibliography; style=bibtex'}
url = 'http://dx.doi.org/' + doi
retries = 10
while retries > 0:
r = requests.get(url, headers=headers)
r.encoding = 'UTF-8'
bibtex = r.text.strip()
if bibtex.startswith('@'):
# no more retries necessary
break
lgr.warning("Failed to obtain bibtex from doi.org, retrying...")
time.sleep(0.5) # give some time to the server
retries -= 1
status_code = r.status_code
if not bibtex.startswith('@'):
raise ValueError('Query %(url)s for BibTeX for a DOI %(doi)s (wrong doi?) has failed. '
'Response code %(status_code)d. '
#'BibTeX response was: %(bibtex)s'
% locals())
if not exists(cached):
cache_dir = dirname(cached)
if not exists(cache_dir):
os.makedirs(cache_dir)
with open(cached, 'w') as f:
if PY2:
f.write(bibtex.encode('utf-8'))
else:
f.write(bibtex)
return bibtex
class EnumeratedEntries(Iterator):
"""A container of entries enumerated referenced by their entry_key"""
def __init__(self):
self._keys2refnr = {}
self._refnr2keys = {}
self._refnr = 1
def add(self, entry_key):
"""Add entry_key and update refnr"""
if entry_key not in self._keys2refnr:
self._keys2refnr[entry_key] = self._refnr
self._refnr2keys[self._refnr] = entry_key
self._refnr += 1
def __getitem__(self, item):
if item not in self._keys2refnr:
raise KeyError('{0} not present'.format(item))
return self._keys2refnr[item]
def fromrefnr(self, refnr):
if refnr not in self._refnr2keys:
raise KeyError('{0} not present'.format(refnr))
return self._refnr2keys[refnr]
def __iter__(self):
return iteritems(self._keys2refnr)
# Python 3
def __next__(self):
return self.next()
def next(self):
yield next(self.__iter__())
def __len__(self):
return len(self._keys2refnr)
class TextOutput(object): # TODO some parent class to do what...?
def __init__(self, fd, collector, style=None):
self.fd = fd
self.collector = collector
# TODO: check that CLS style actually exists
self.style = style
if 'DUECREDIT_STYLE' in os.environ.keys():
self.style = os.environ['DUECREDIT_STYLE']
else:
self.style = 'harvard1'
# TODO: refactor name to sth more intuitive
def _model_citations(self, tags=None):
if not tags:
tags = os.environ.get('DUECREDIT_REPORT_TAGS', 'reference-implementation,implementation').split(',')
tags = set(tags)
citations = self.collector.citations
if tags != {'*'}:
# Filter out citations
citations = dict((k, c)
for k, c in iteritems(citations)
if tags.intersection(c.tags))
packages = {}
modules = {}
objects = {}
for key in ('citations', 'entry_keys'):
packages[key] = defaultdict(list)
modules[key] = defaultdict(list)
objects[key] = defaultdict(list)
# for each path store both a list of entry keys and of citations
for (path, entry_key), citation in iteritems(citations):
if ':' in path:
target_dict = objects
elif '.' in path:
target_dict = modules
else:
target_dict = packages
target_dict['citations'][path].append(citation)
target_dict['entry_keys'][path].append(entry_key)
return packages, modules, objects
def dump(self, tags=None):
# get 'model' of citations
packages, modules, objects = self._model_citations(tags)
# mapping key -> refnr
enum_entries = EnumeratedEntries()
citations_ordered = []
# set up view
# package level
sublevels = [modules, objects]
for package in sorted(packages['entry_keys']):
for entry_key in packages['entry_keys'][package]:
enum_entries.add(entry_key)
citations_ordered.append(package)
# sublevels
for sublevel in sublevels:
for obj in sorted(filter(lambda x: package in x, sublevel['entry_keys'])):
for entry_key_obj in sublevel['entry_keys'][obj]:
enum_entries.add(entry_key_obj)
citations_ordered.append(obj)
# Now we can "render" different views of our "model"
# Here for now just text BUT that is where we can "split" the logic and provide
# different renderings given the model -- text, rest, md, tex+latex, whatever
self.fd.write('\nDueCredit Report:\n')
for path in citations_ordered:
if ':' in path:
self.fd.write(' ')
target_dict = objects
elif '.' in path:
self.fd.write(' ')
target_dict = modules
else:
target_dict = packages
# TODO: absorb common logic into a common function
citations = target_dict['citations'][path]
entry_keys = target_dict['entry_keys'][path]
descriptions = sorted(map(str, set(str(r.description) for r in citations)))
versions = sorted(map(str, set(str(r.version) for r in citations)))
refnrs = sorted([str(enum_entries[entry_key]) for entry_key in entry_keys])
self.fd.write('- {0} / {1} (v {2}) [{3}]\n'.format(
", ".join(descriptions), path, ', '.join(versions), ', '.join(refnrs)))
# Print out some stats
obj_names = ('packages', 'modules', 'functions')
n_citations = map(len, (packages['citations'], modules['citations'], objects['citations']))
for citation_type, n in zip(obj_names, n_citations):
self.fd.write('\n{0} {1} cited'.format(n, citation_type))
if enum_entries:
citations_fromentrykey = self.collector._citations_fromentrykey()
self.fd.write('\n\nReferences\n' + '-' * 10 + '\n')
# collect all the entries used
refnr_key = [(nr, enum_entries.fromrefnr(nr)) for nr in range(1, len(enum_entries)+1)]
for nr, key in refnr_key:
self.fd.write('\n[{0}] '.format(nr))
self.fd.write(get_text_rendering(citations_fromentrykey[key], style=self.style))
self.fd.write('\n')
def get_text_rendering(citation, style='harvard1'):
from .collector import Citation
entry = citation.entry
if isinstance(entry, Doi):
bibtex_rendering = get_bibtex_rendering(entry)
bibtex_citation = copy.copy(citation)
bibtex_citation.set_entry(bibtex_rendering)
return get_text_rendering(bibtex_citation)
elif isinstance(entry, BibTeX):
return format_bibtex(entry, style=style)
else:
return str(entry)
def get_bibtex_rendering(entry):
if isinstance(entry, Doi):
return BibTeX(import_doi(entry.doi))
elif isinstance(entry, BibTeX):
return entry
else:
raise ValueError("Have no clue how to get bibtex out of %s" % entry)
def format_bibtex(bibtex_entry, style='harvard1'):
try:
from citeproc.source.bibtex import BibTeX as cpBibTeX
import citeproc as cp
except ImportError as e:
raise RuntimeError(
"For formatted output we need citeproc and all of its dependencies "
"(such as lxml) but there is a problem while importing citeproc: %s"
% str(e))
key = bibtex_entry.get_key()
# need to save it temporarily to use citeproc-py
fname = tempfile.mktemp(suffix='.bib')
try:
with open(fname, 'wt') as f:
bibtex = bibtex_entry.rawentry
bibtex = bibtex.replace(u'\u2013', '--') + "\n"
# TODO: manage to save/use UTF-8
if PY2:
bibtex = bibtex.encode('ascii', 'ignore')
f.write(bibtex)
# We need to avoid cpBibTex spitting out warnings
old_filters = warnings.filters[:] # store a copy of filters
warnings.simplefilter('ignore', UserWarning)
try:
bib_source = cpBibTeX(fname)
except Exception as e:
lgr.error("Failed to process BibTeX file %s: %s" % (fname, e))
return "ERRORED: %s" % str(e)
finally:
# return warnings back
warnings.filters = old_filters
bib_style = cp.CitationStylesStyle(style, validate=False)
# TODO: specify which tags of formatter we want
bibliography = cp.CitationStylesBibliography(bib_style, bib_source,
cp.formatter.plain)
citation = cp.Citation([cp.CitationItem(key)])
bibliography.register(citation)
finally:
if not os.environ.get("DUECREDIT_KEEPTEMP"):
os.unlink(fname)
biblio_out = bibliography.bibliography()
assert(len(biblio_out) == 1)
biblio_out = ''.join(biblio_out[0])
return biblio_out # if biblio_out else str(bibtex_entry)
# TODO: harmonize order of arguments
class PickleOutput(object):
def __init__(self, collector, fn=DUECREDIT_FILE):
self.collector = collector
self.fn = fn
def dump(self):
with open(self.fn, 'wb') as f:
pickle.dump(self.collector, f)
@classmethod
def load(cls, filename=DUECREDIT_FILE):
with open(filename, 'rb') as f:
return pickle.load(f)
class BibTeXOutput(object): # TODO some parent class to do what...?
def __init__(self, fd, collector):
self.fd = fd
self.collector = collector
def dump(self):
for citation in self.collector.citations.values():
try:
bibtex = get_bibtex_rendering(citation.entry)
except:
lgr.warning("Failed to generate bibtex for %s" % citation.entry)
continue
self.fd.write(bibtex.rawentry + "\n")
def load_due(filename):
return PickleOutput.load(filename)
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