예제 #1
0
파일: views.py 프로젝트: danielfranca/Tintz
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),
    )
예제 #2
0
파일: views.py 프로젝트: Feduch/libsreview
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")
예제 #6
0
파일: schema.py 프로젝트: Feduch/libsreview
    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)
예제 #7
0
파일: install.py 프로젝트: PeterisP/aiweb6
				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)
예제 #8
0
파일: utils.py 프로젝트: xueyanmu/tribe
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!!')