def cite_it(bot, chat_id, doi):
"""Returns citation for given DOI"""
# headers = {"content-type":"application/x-bibtex"}
# resp = requests.get("https://doi.org/" + DOI, headers=headers)
# return resp.content
works = Works()
if not works.agency(doi):
bot.send_message(
chat_id=chat_id,
text="Этот документ не входит в базу цитирования CrossRef...")
return SEARCH_RESULTLS
else:
record = works.doi(doi)
found, meta_bib = get_bib(doi)
if not found:
bot.send_message(chat_id=chat_id, text="Документ не найден...")
return SEARCH_RESULTLS
bot.send_message(chat_id=chat_id, text="Цитирование по CrossRef:")
filename = doi.replace('/', '-')
with open(os.path.join('downloads', filename + '.bib'),
'w+') as downloaded_file:
downloaded_file.write(meta_bib)
bot.send_document(
chat_id=chat_id,
document=open(os.path.join('downloads', filename + '.bib'), 'rb'),
)
return SEARCH_RESULTLS
def post(self, request, *args, **kwargs):
unique_id = request.POST.get('unique_id')
project_pk = self.kwargs.get('project_pk')
project_obj = get_object_or_404(Project, pk=project_pk)
matching_source_obj = None
for source in PublicationSource.objects.all():
if source.name == 'doi':
try:
status, bib_str = crossref.get_bib(unique_id)
bp = BibTexParser(interpolate_strings=False)
bib_database = bp.parse(bib_str)
bib_json = bib_database.entries[0]
matching_source_obj = source
break
except:
continue
elif source.name == 'adsabs':
try:
url = 'http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode={}&data_type=BIBTEX'.format(
unique_id)
r = requests.get(url, timeout=5)
bp = BibTexParser(interpolate_strings=False)
bib_database = bp.parse(r.text)
bib_json = bib_database.entries[0]
matching_source_obj = source
break
except:
continue
if not matching_source_obj:
return render(request, self.template_name, {})
year = as_text(bib_json['year'])
author = as_text(bib_json['author']).replace(
'{\\textquotesingle}', "'").replace('{\\textendash}', '-').replace(
'{\\textemdash}',
'-').replace('{\\textasciigrave}',
' ').replace('{\\textdaggerdbl}',
' ').replace('{\\textdagger}', ' ')
title = as_text(bib_json['title']).replace(
'{\\textquotesingle}', "'").replace('{\\textendash}', '-').replace(
'{\\textemdash}',
'-').replace('{\\textasciigrave}',
' ').replace('{\\textdaggerdbl}',
' ').replace('{\\textdagger}', ' ')
author = re.sub("{|}", "", author)
title = re.sub("{|}", "", title)
context = {}
context['author'] = author
context['year'] = year
context['title'] = title
context['unique_id'] = unique_id
context['source'] = matching_source_obj
context['project_pk'] = project_obj.pk
return render(request, self.template_name, context)
def _search_id(self, unique_id):
matching_source_obj = None
for source in PublicationSource.objects.all():
if source.name == 'doi':
try:
status, bib_str = crossref.get_bib(unique_id)
bp = BibTexParser(interpolate_strings=False)
bib_database = bp.parse(bib_str)
bib_json = bib_database.entries[0]
matching_source_obj = source
break
except:
continue
elif source.name == 'adsabs':
try:
url = 'http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode={}&data_type=BIBTEX'.format(
unique_id)
r = requests.get(url, timeout=5)
bp = BibTexParser(interpolate_strings=False)
bib_database = bp.parse(r.text)
bib_json = bib_database.entries[0]
matching_source_obj = source
break
except:
continue
if not matching_source_obj:
return False
year = as_text(bib_json['year'])
author = as_text(bib_json['author']).replace('{\\textquotesingle}', "'").replace('{\\textendash}', '-').replace(
'{\\textemdash}', '-').replace('{\\textasciigrave}', ' ').replace('{\\textdaggerdbl}', ' ').replace('{\\textdagger}', ' ')
title = as_text(bib_json['title']).replace('{\\textquotesingle}', "'").replace('{\\textendash}', '-').replace(
'{\\textemdash}', '-').replace('{\\textasciigrave}', ' ').replace('{\\textdaggerdbl}', ' ').replace('{\\textdagger}', ' ')
author = re.sub("{|}", "", author)
title = re.sub("{|}", "", title)
# not all bibtex entries will have a journal field
if 'journal' in bib_json:
journal = as_text(bib_json['journal']).replace('{\\textquotesingle}', "'").replace('{\\textendash}', '-').replace(
'{\\textemdash}', '-').replace('{\\textasciigrave}', ' ').replace('{\\textdaggerdbl}', ' ').replace('{\\textdagger}', ' ')
journal = re.sub("{|}", "", journal)
else:
# fallback: clearly indicate that data was absent
source_name = matching_source_obj.name
journal = '[no journal info from {}]'.format(source_name.upper())
pub_dict = {}
pub_dict['author'] = author
pub_dict['year'] = year
pub_dict['title'] = title
pub_dict['journal'] = journal
pub_dict['unique_id'] = unique_id
pub_dict['source_pk'] = matching_source_obj.pk
return pub_dict
def post(self, request, *args, **kwargs):
project_obj = get_object_or_404(Project,
pk=self.kwargs.get('project_pk'))
publications_do_export = self.get_publications_to_export(project_obj)
context = {}
formset = formset_factory(PublicationExportForm,
max_num=len(publications_do_export))
formset = formset(request.POST,
initial=publications_do_export,
prefix='publicationform')
publications_deleted_count = 0
bib_text = ''
if formset.is_valid():
for form in formset:
publication_form_data = form.cleaned_data
if publication_form_data['selected']:
publication_obj = Publication.objects.get(
project=project_obj,
title=publication_form_data.get('title'),
year=publication_form_data.get('year'),
unique_id=publication_form_data.get('unique_id'),
)
print("id is" + publication_obj.display_uid())
temp_id = publication_obj.display_uid()
status, bib_str = crossref.get_bib(
publication_obj.display_uid())
bp = BibTexParser(interpolate_strings=False)
bib_database = bp.parse(bib_str)
bib_text += bib_str
response = HttpResponse(content_type='text/plain')
response['Content-Disposition'] = 'attachment; filename=refs.bib'
buffer = io.StringIO()
buffer.write(bib_text)
output = buffer.getvalue()
buffer.close()
response.write(output)
return response
else:
for error in formset.errors:
messages.error(request, error)
return HttpResponseRedirect(
reverse('project-detail', kwargs={'pk': project_obj.pk}))
def make_literature_entry():
"""Read a literature entry, with bibtex."""
title = input("Title: ")
authors = get_authors()
found, bibtex = crossref.get_bib(input("DOI: "))
print('-' * 40)
msg = FORMAT.format(title=title, authors=authors, bibtex=bibtex)
print(msg)
pyperclip.copy(msg)
print('-' * 40)
print('...copied entry to clipboard.')
print('-' * 40)
print('Hit <Enter> to copy filename to clipboard')
filename = title.lower().replace(' ', '-') + ".pdf"
print('Filename:', filename)
input()
pyperclip.copy(filename)
print('...copied filename to clipboard')
def get_data(self, output=False):
url = 'http://satellite.mpic.de/spectral_atlas/' + self.spurl
r = requests.get(url)
html = r.text
ind1 = html.find('Data Sets:')
ind2 = html[ind1:].find('</table>') + ind1
parsed = BeautifulSoup(html[ind1:ind2], "html.parser")
i = 0
files = []
papers = []
yr = []
temp = []
for i in range(1, len(parsed.table.find_all('tr'))):
details = parsed.table.find_all('tr')[i].find_all('td')
# only consider data that is a function of wavelength
if details[3].text.find('-')<0 and \
details[-1].text.find('-')>0:
try:
tempp = float(details[3].text[:-1])
except ValueError:
tempp = 300
if tempp > self.T_low and tempp < self.T_high:
try:
paper = parsed.table.find_all('tr')[i].find_all(
'td')[2].text
yr.append(
float(paper[paper.find('(') + 1:paper.find(')')]))
files.append(
parsed.table.find_all('tr')[i].td.a['href'])
papers.append(paper)
temp.append(tempp)
except:
yr = yr[:len(temp)]
files = files[:len(temp)]
papers = papers[:len(temp)]
pass
pre = 'http://joseba.mpch-mainz.mpg.de/spectral_atlas_data/'
yr1 = []
files1 = []
papers1 = []
refs = []
temp1 = []
wv = []
xs = []
for i in range(len(files)):
if self.verbose:
print(i, ' files parsed', end='\r')
r = requests.get(pre + files[i])
data1 = r.text.replace('\t', ' ').replace('\r', '').split('\n')
wvv1 = []
xss1 = []
for dat in data1:
try:
wvv, xss = [float(a) for a in dat.split()]
wvv1.append(wvv)
xss1.append(xss)
except:
pass
if len(wvv1) == 0 or np.min(xss1) <= 0:
pass
else:
wv.append(wvv1)
xs.append(xss1)
yr1.append(yr[i])
files1.append(files[i])
papers1.append(papers[i])
temp1.append(temp[i])
# get a bibtex citation
try:
pre_details = 'http://satellite.mpic.de/spectral_atlas/'
rr = requests.get(pre_details + files[i])
ind1 = [m.start() for m in re.finditer('DOI', rr.text)][1]
ind2 = rr.text[ind1:].find('</a>') + ind1 + 4
soup = BeautifulSoup(rr.text[ind1:ind2], "html.parser")
out = get_bib(soup.a['href'])
refs.append(out[1])
except:
refs.append('Resource not found.')
if len(wv) > self.max_studies:
break
# build dict
out = {}
out['wavelength'] = wv
out['cross section'] = xs
out['temperature'] = temp1
out['year'] = yr1
out['papers'] = papers1
out['bibtex'] = refs
self.all_data = out
# flatten data
self.all_wv = np.array([item for w in wv for item in w])
self.all_xs = np.array([item for w in xs for item in w])
temps = np.array([])
for i in range(len(temp1)):
temps = np.append(temps, np.ones(len(wv[i])) * temp1[i])
self.all_temps = temps
if output:
return out
