def uploadpublication(request, form_class=PublicationUploadForm, template_name="publications/upload.html"):
"""
upload form for publications
"""
publication = Publication()
publication.author = request.user
publication_form = form_class()
if request.method == "POST":
if request.POST.get("action") == "upload":
publication_form = form_class(request.user, request.POST, request.FILES, instance=publication)
if publication_form.is_valid():
if not is_valid_format(request.FILES["file_name"].name, request.FILES["file_name"].content_type):
request.user.message_set.create(
message=u"Tipo de arquivo inválido (Somente arquivos PDF/CBR/CBZ ou Imagem: JPG/GIF/PNG) ou nome do arquivo muito longo"
)
else:
publication = publication_form.save(commit=False)
publication.date_added = datetime.datetime.now()
publication.status = 0
publication.nr_pages = 0
publication.save()
request.user.message_set.create(message=_(u"Publicação feita com sucesso '%s'") % publication.title)
return HttpResponseRedirect(reverse("publications", args=(publication.author,)))
calc_age(request.user.get_profile())
return render_to_response(
template_name,
{"form": publication_form, "is_me": True, "other_user": request.user},
context_instance=RequestContext(request),
)
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 get_publication(unique_name, pmid):
#check if publication exist, if so return, if not create new
try:
result = get_esummary_pmid(pmid)
tmp_date = datetime.strptime(result["result"][pmid]["sortpubdate"], '%Y/%m/%d %H:%M')
publication = Publication(title=result["result"][pmid]["title"],
volume=result["result"][pmid]["volume"],
issue=result["result"][pmid]["issue"],
publication_year=tmp_date.strftime('%Y-%m-%d'),
pages=result["result"][pmid]["pages"],
unique_name=pmid+'-'+result["result"][pmid]["title"],
publisher=result["result"][pmid]["fulljournalname"])
publication.validate_unique()
publication.save()
db = Db.objects.get(name='Pubmed')
dbxref = Dbxref(accession=pmid, version='1', db=db)
dbxref.validate_unique()
dbxref.save()
publication_dbxref = PublicationDbxref(publication=publication, dbxref=dbxref)
publication_dbxref.validate_unique()
publication_dbxref.save()
rank = 1
tmp_list = result["result"][pmid]["authors"]
for tmp in tmp_list:
author = get_author(tmp["name"])
publication_author = PublicationAuthor(rank=rank, publication=publication, author=author)
publication_author.validate_unique()
publication_author.save()
rank+=1
except ValidationError as e:
publication = Publication.objects.get(unique_name=pmid+'-'+result["result"][pmid]["title"])
return publication
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 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)
volume = int(volume.split('(')[0])
if not volume:
volume = None
year = pub['year']
if not year:
year = None # tukšo string aizstājam ar none
publication = Publication(
type_id=2,
title=bibtex, # excelī tajā vietā bija raksta nosaukums
authors=pub.get('authors'),
year=year,
journal=pub['journal'],
publisher=pub['publisher'],
volume=volume,
external=False)
publication.save()
for author in publication.authors_list:
person = findPerson(author.strip())
if person:
person.publications.add(publication)
# --- beigas tam, ja jāveido publikācija pašam jo nav bibtex
if pub['indexed']:
publication.indexed = pub['indexed']
publication.save()
if pub['project_name']:
for name in pub['project_name'].split(';'):
for project in Project.objects.all():
if project.title == name.strip():
project.publications.add(publication)
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!!')
