def mutate_and_get_payload(cls, root, info, **input):
# проверяет токен
token = input.get('token', None)
if token != '******************':
return "Invalid token"
publication = Publication(
title=input.get('title'),
preview_text=input.get('preview_text', ''),
detail_text=input.get('detail_text', ''),
image=input.get('image', ''),
rating=input.get('rating', 0),
user_id=input.get('user_id', 5227),
date_create=input.get('date_create'),
show_counter=input.get('show_counter'),
)
if input.get('pk'):
publication.pk = input.get('pk')
if input.get('age'):
publication.age = input.get('age', 0)
publication.save()
if input.get('author'):
publication.author.set(input.get('author'))
publication.save()
if input.get('book'):
try:
publication.book.set(input.get('book'))
publication.save()
except Exception as e:
pass
return AddPublication(publication=publication)
def post(self, request):
"""
Procesa el formulario
:param request: objeto HttpRequest
:return: HttpResponse con la respuesta
"""
publication = Publication()
publication.publisher = request.user
form = PublicationForm(request.POST,
request.FILES,
instance=publication)
if form.is_valid():
# Guardar el anuncio
new_publication = form.save()
# Limpiar el formulario
form = PublicationForm()
# Devolvemos un mensaje de OK
messages.success(request, 'Publicación creada correctamente')
context = {'form': form, 'navbar': "publication-form"}
return render(request, 'publications/publication_form.html', context)
def vue_publication_save(request):
to_template = {}
if request.user.is_authenticated:
image = request.FILES.get('image')
data = request.POST.get('data')
data = json.loads(data)
id = data.get('id', None)
title = data.get('title')
text = data.get('text')
books = data.get('books', None)
authors = data.get('authors', None)
series = data.get('series', None)
if id:
# Сохраняет изменения
publication = Publication.objects.get(pk=id, user=request.user)
publication.title = title
publication.preview_text = Truncator(strip_tags(text)).words(33)
publication.detail_text = text
publication.user = request.user
publication.series_id = series
publication.save()
publication.book.set(books)
publication.author.set(authors)
publication.series.set(series)
else:
# Создает новую коллекцию
publication = Publication(title=title,
user=request.user,
preview_text=Truncator(
strip_tags(text)).words(33),
detail_text=text)
publication.save()
if books:
publication.book.set(books)
if authors:
publication.author.set(authors)
if series:
publication.series.set(series)
if image:
publication.image.save(image.name, image)
to_template['image'] = publication.image.url
to_template['id'] = publication.id
return JsonResponse(to_template)
def add_association(acc, article, is_associated=False):
"""
Adding association between `Publication` and `Experiment` objects in the Django models which is used by
curators to approve or reject linkage between an article and a study.
:param acc: ArrayExpress accession. e.g. ``E-MTAB-xxxx``
:type acc: str
:param article: Json object as collected from Europe BMC.
:type article: dict
:param is_associated: Flag indicating whether the publication is already associated with the study in the
AE database or not
:type is_associated: bool
"""
experiment = retrieve_study_by_acc(acc)[0]
exp = Experiment.objects.filter(
Q(accession=acc) | Q(title=experiment.title)
| Q(description=experiment.description)).first()
# print exp, exp_created
if not exp:
exp = Experiment(accession=acc,
title=experiment.title,
description=experiment.description)
exp.save()
pub = Publication.objects.filter(
Q(pubmed=article.get('pmid', -1)) | Q(pmc_id=article.get('pmcid'))
| Q(doi=article.get('doi', 'ANY THING ELSE'))
| Q(title=article['title'])).first()
if not pub:
pub = Publication(pubmed=article.get('pmid', None),
pmc_id=article.get('pmcid'),
doi=article.get('doi', None),
title=article['title'],
whole_article=json.dumps(article))
pub.save()
else:
pub.whole_article = json.dumps(article)
pub.save()
ass, ass_created = Association.objects.get_or_create(experiment=exp,
publication=pub)
if ass_created:
ass.is_associated = is_associated
ass.save()
def add_publications(self, number):
if number > 0:
random = Random()
users = User.objects.all()
charts = string.lowercase + " "
if len(users) > 0:
for i in range(number):
content = "".join([random.choice(charts) for a in range(random.randint(40, 100))])
publication_title = "".join(
[random.choice(string.lowercase) for a in range(random.randint(15, 30))]).title()
author = random.choice(users)
publication_type = random.choice(publication_types)
publication = Publication(author=author, title=publication_title, content=content,
publication_type=publication_type)
publication.save()
self.stdout.write("%i publications was added to database" % number)
else:
self.stdout.write("No user to add publication")
else:
self.stdout.write("Invalid number of publications to add was set. Nothing done")
def import_bibtex(request):
if request.method == 'POST':
# try to parse BibTex
bib = parse(request.POST['bibliography'])
# container for error messages
errors = {}
# publication types
types = Type.objects.all()
# check for errors
if not bib:
if not request.POST['bibliography']:
errors['bibliography'] = 'This field is required.'
if not errors:
publications = []
# try adding publications
for entry in bib:
if entry.has_key('title') and \
entry.has_key('author') and \
entry.has_key('year'):
# parse authors
authors = split(entry['author'], ' and ')
for i in range(len(authors)):
author = split(authors[i], ',')
author = [author[-1]] + author[:-1]
authors[i] = join(author, ' ')
authors = join(authors, ', ')
# add missing keys
keys = [
'journal', 'booktitle', 'publisher', 'url', 'doi',
'keywords', 'note', 'abstract', 'month'
]
for key in keys:
if not entry.has_key(key):
entry[key] = ''
# map integer fields to integers
entry['month'] = MONTHS.get(entry['month'].lower(), 0)
entry['volume'] = entry.get('volume', None)
entry['number'] = entry.get('number', None)
# determine type
type_id = None
for t in types:
if entry['type'] in t.bibtex_type_list:
type_id = t.id
break
if type_id is None:
errors['bibliography'] = 'Type "' + entry[
'type'] + '" unknown.'
break
# add publication
publications.append(
Publication(type_id=type_id,
citekey=entry['key'],
title=entry['title'],
authors=authors,
year=entry['year'],
month=entry['month'],
journal=entry['journal'],
book_title=entry['booktitle'],
publisher=entry['publisher'],
volume=entry['volume'],
number=entry['number'],
note=entry['note'],
url=entry['url'],
doi=entry['doi'],
abstract=entry['abstract'],
keywords=entry['keywords']))
else:
errors[
'bibliography'] = 'Make sure that the keys title, author and year are present.'
break
if not errors and not publications:
errors['bibliography'] = 'No valid BibTex entries found.'
if errors:
# some error occurred
return render_to_response(
'admin/publications/import_bibtex.html', {
'errors': errors,
'title': 'Import BibTex',
'types': Type.objects.all(),
'request': request
}, RequestContext(request))
else:
try:
# save publications
for publication in publications:
publication.save()
except:
msg = 'Some error occured during saving of publications.'
else:
if len(publications) > 1:
msg = 'Successfully added ' + str(
len(publications)) + ' publications.'
else:
msg = 'Successfully added ' + str(
len(publications)) + ' publication.'
# show message
messages.info(request, msg)
# redirect to publication listing
return HttpResponseRedirect('../')
else:
return render_to_response(
'admin/publications/import_bibtex.html', {
'title': 'Import BibTex',
'types': Type.objects.all(),
'request': request
}, RequestContext(request))
def import_bibtex(request):
if request.method == 'POST':
# try to parse BibTex
bib = parse(request.POST['bibliography'])
# container for error messages
errors = {}
# publication types
types = Type.objects.all()
# check for errors
if not bib:
if not request.POST['bibliography']:
errors['bibliography'] = 'This field is required.'
if not errors:
publications = []
# try adding publications
for entry in bib:
if 'title' in entry and \
'author' in entry and \
'year' in entry:
# parse authors
authors = entry['author'].split(' and ')
for i in range(len(authors)):
author = authors[i].split(',')
author = [author[-1]] + author[:-1]
authors[i] = ' '.join(author)
authors = ', '.join(authors)
# add missing keys
keys = [
'journal', 'booktitle', 'publisher', 'institution',
'url', 'doi', 'isbn', 'keywords', 'pages', 'note',
'abstract', 'month'
]
for key in keys:
if not key in entry:
entry[key] = ''
# map integer fields to integers
entry['month'] = MONTHS.get(entry['month'].lower(), 0)
entry['volume'] = entry.get('volume', None)
entry['number'] = entry.get('number', None)
if isinstance(entry['volume'], six.text_type):
entry['volume'] = int(
re.sub('[^0-9]', '', entry['volume']))
if isinstance(entry['number'], six.text_type):
entry['number'] = int(
re.sub('[^0-9]', '', entry['number']))
# remove whitespace characters (likely due to line breaks)
entry['url'] = re.sub(r'\s', '', entry['url'])
# determine type
type_id = None
for t in types:
if entry['type'] in t.bibtex_type_list:
type_id = t.id
break
if type_id is None:
errors['bibliography'] = 'Type "' + entry[
'type'] + '" unknown.'
break
# add publication
publications.append(
Publication(type_id=type_id,
citekey=entry['key'],
title=entry['title'],
authors=authors,
year=entry['year'],
month=entry['month'],
journal=entry['journal'],
book_title=entry['booktitle'],
publisher=entry['publisher'],
institution=entry['institution'],
volume=entry['volume'],
number=entry['number'],
pages=entry['pages'],
note=entry['note'],
url=entry['url'],
doi=entry['doi'],
isbn=entry['isbn'],
external=False,
abstract=entry['abstract'],
keywords=entry['keywords']))
else:
errors[
'bibliography'] = 'Make sure that the keys title, author and year are present.'
break
if not errors and not publications:
errors['bibliography'] = 'No valid BibTex entries found.'
if errors:
# some error occurred
return render(
request, 'admin/publications/import_bibtex.html', {
'errors': errors,
'title': 'Import BibTex',
'types': Type.objects.all(),
'request': request
})
else:
try:
# save publications
for publication in publications:
publication.save()
except:
msg = 'Some error occured during saving of publications.'
else:
if len(publications) > 1:
msg = 'Successfully added ' + str(
len(publications)) + ' publications.'
else:
msg = 'Successfully added ' + str(
len(publications)) + ' publication.'
# show message
messages.info(request, msg)
# redirect to publication listing
if len(publications) == 1:
return HttpResponseRedirect('../%s/change/' %
publications[0].id)
else:
return HttpResponseRedirect('../')
else:
return render(
request, 'admin/publications/import_bibtex.html', {
'title': 'Import BibTex',
'types': Type.objects.all(),
'request': request
})
def import_bibtex(request):
if request.method == 'POST':
# try to parse BibTex
the_bibtex_file_content = ''
creators = request.POST.getlist('creators')
productions = request.POST.getlist('productions')
work_records = request.POST.getlist('work_records')
the_bibtex_file = request.FILES.get('bibtex_file', '')
if the_bibtex_file:
if the_bibtex_file.multiple_chunks():
the_bibtex_file_content = ''.join(
chunk for chunk in the_bibtex_file.chunks())
else:
the_bibtex_file_content = the_bibtex_file.read()
bib = parse(the_bibtex_file_content)
if not bib:
bib = parse(request.POST['bibliography'])
# container for error messages
errors = {}
# publication types
types = Type.objects.all()
# check for errors
if not bib:
if not request.POST['bibliography']:
errors[
'bibliography'] = 'Please populate Bibliography or click browse to upload a Bibtex format file.'
if not errors:
publications = []
# try adding publications
for entry in bib:
if (entry.has_key('title') and entry.has_key('author')
and entry.has_key('year')):
# parse authors
authors = split(entry['author'], ' and ')
for i in range(len(authors)):
author = split(authors[i], ',')
author = [author[-1]] + author[:-1]
authors[i] = join(author, ' ')
authors = join(authors, ', ')
# add missing keys
keys = [
'annote', 'booktitle', 'chapter', 'edition', 'section',
'editor', 'howpublished', 'institution', 'journal',
'key', 'month', 'note', 'number', 'organization',
'pages', 'publisher', 'address', 'school', 'series',
'volume', 'issue', 'url', 'isbn', 'issn', 'lccn',
'abstract', 'keywords', 'price', 'copyright',
'language', 'contents', 'doi'
]
for key in keys:
if not entry.has_key(key):
if key == 'price':
entry[key] = 0
else:
entry[key] = ''
# map integer fields to integers
entry['month'] = MONTHS.get(entry['month'].lower(), 0)
entry['volume'] = entry.get('volume', None)
entry['number'] = entry.get('number', None)
# determine type
type_id = None
for t in types:
if entry['type'] in t.bibtex_type_list:
type_id = t.id
break
if type_id is None:
errors['bibliography'] = 'Type "' + entry[
'type'] + '" unknown.'
break
# add publication
publications.append(
Publication(type_id=type_id,
annote=entry['annote'],
authors=authors,
book_title=entry['booktitle'],
chapter=entry['chapter'],
edition=entry['edition'],
section=entry['section'],
editor=entry['editor'],
how_published=entry['howpublished'],
institution=entry['institution'],
journal=entry['journal'],
citekey=entry['key'],
year=entry['year'],
month=entry['month'],
note=entry['note'],
organization=entry['organization'],
pages=entry['pages'],
publisher=entry['publisher'],
address=entry['address'],
university=entry['school'],
series=entry['series'],
title=entry['title'],
volume=entry['volume'],
number=entry['issue'],
url=entry['url'],
isbn=entry['isbn'],
issn=entry['issn'],
archive_location=entry['lccn'],
abstract=entry['abstract'],
keywords=entry['keywords'],
price=entry['price'],
rights=entry['copyright'],
language=entry['language'],
table_of_content=entry['contents'],
doi=entry['doi']))
else:
errors[
'bibliography'] = 'Make sure that the keys title, author and year are present.'
break
if not errors and not publications:
errors['bibliography'] = 'No valid BibTex entries found.'
if errors:
# some error occurred
return render_to_response(
'admin/publications/import_bibtex.html', {
'errors': errors,
'title': 'Import BibTex',
'types': Type.objects.all(),
'request': request
}, RequestContext(request))
else:
try:
# save publications
for publication in publications:
publication.save()
try:
for creator_id in creators:
creator = Creator.objects.get(pk=creator_id)
creator.primary_publications.add(publication)
except:
pass
try:
for production_id in productions:
production = Production.objects.get(
pk=production_id)
production.primary_publications.add(publication)
except:
pass
try:
for work_record_id in work_records:
work_record = WorkRecord.objects.get(
pk=work_record_id)
work_record.primary_publications.add(publication)
except:
pass
except:
msg = 'Some error occured during saving of publications.'
else:
if len(publications) > 1:
msg = 'Successfully added ' + str(
len(publications)) + ' publications.'
else:
msg = 'Successfully added ' + str(
len(publications)) + ' publication.'
# show message
messages.info(request, msg)
# redirect to publication listing
return HttpResponseRedirect('../')
else:
Creators_qs = Creator.objects.all()
Productions_qs = Production.objects.all().order_by('title')
WorkRecord_qs = WorkRecord.objects.all().order_by('title')
CREATOR_CHOICES = [] #[("", "-- Select a Creator --")]
CREATOR_CHOICES += [(e.id, e.creator_name) for e in Creators_qs]
PRODUCTION_CHOICES = [] #[("", "-- Select a Production --")]
PRODUCTION_CHOICES += [(e.id, e.title) for e in Productions_qs]
WORKRECORD_CHOICES = [] #[("", "-- Select a Written Work --")]
WORKRECORD_CHOICES += [(e.id, e.title) for e in WorkRecord_qs]
return render_to_response(
'admin/publications/import_bibtex.html', {
'title': 'Import BibTex',
'types': Type.objects.all(),
'creators': CREATOR_CHOICES,
'productions': PRODUCTION_CHOICES,
'work_records': WORKRECORD_CHOICES,
'request': request
}, RequestContext(request))
def load_pmids(pmids, force_update=False):
"""
Loads publications into the database from a list of PubMed IDs passed
as integers into the database when they do not already exist.
"""
pmids = list(set([int(x) for x in pmids]))
logger.debug('Starting to load PMID(S) %s', pmids)
if not force_update:
logger.info('Checking %s PMIDS', len(pmids))
existing_pubs = set(Publication.objects.filter(pmid__in=pmids).values_list('pmid', flat=True))
pmids = set(pmids)
pmids.difference_update(existing_pubs)
logger.info('About to fetch %s new PMIDs.', len(pmids), extra={'data':{'pmids': pmids}})
if not pmids:
logger.debug('pmids are none')
return None
pmids_mia = [str(x) for x in pmids]
for i in xrange(len(pmids_mia) / 5000 + 1): #Efetch Maximum, Batch 5000 per request
query_list = pmids_mia[i * 5000:(i + 1) * 5000]
query_str = ','.join(query_list)
qdict = settings.ETOOLS_CONFIG['query_params']
qdict['id'] = query_str
# Have to use post if data being sent is > 200
r = requests.post(settings.ETOOLS_CONFIG['base_url'], data=qdict)
error_cnt = 0
while r.status_code != 200 and error_cnt < NUM_PUBMED_RETRIES:
error_cnt += 1
time.sleep(0.5)
r = requests.post(settings.ETOOLS_CONFIG['base_url'],
data=qdict)
if r.status_code != 200:
logger.warning('Requests to the PubMed server with data %s failed '
'after %s attempts.', qdict, NUM_PUBMED_RETRIES + 1)
pub_page = r.text
if pub_page:
logger.debug('Request to pubmed server returned pub_page')
xmltree = ET.fromstring(pub_page.encode('utf-8'))
pubs = xmltree.findall('.//DocumentSummary')
# pub_dicts will be a list of publications, where each
# of them is a dictionary
pub_dicts = map(parse_pub, pubs)
for index, pub in enumerate(pub_dicts):
logger.debug('Making new pub %s', pub)
if pub is not None:
new_pub = None
if force_update:
try:
new_pub = Publication.objects.get(pmid=pub['pmid'])
except Publication.DoesNotExist:
new_pub = Publication()
new_pub.pmid = pub['pmid']
new_pub.title = pub['title']
new_pub.authors = pub['authors']
new_pub.date = pub['date']
new_pub.journal = pub['journal']
new_pub.volume = pub['volume']
new_pub.pages = pub['pages']
new_pub.issue = pub['issue']
else:
new_pub = Publication(**pub)
if not new_pub.issue:
logger.info('no issue for %s', new_pub.pmid)
if not new_pub.volume:
logger.info('no volume for %s', new_pub.pmid)
if not new_pub.pages:
logger.info('no pages for %s', new_pub.pmid)
new_pub.save()
logger.debug('Finished saving pub %s', new_pub)
else:
bad_pmid = pubs[index].get('uid')
logger.warning('PMID %s has no publication in pub_page %s',
bad_pmid, pub_page)
else:
logger.warning('There was no page returned from pubmed server!!')
