def AbstractPool(request, review_name_slug):
review = Review.objects.get(user=request.user, slug=review_name_slug)
if request.method == "POST":
if request.POST.get('results') == None:
q = request.POST.get('queryField')
s = request.POST.get('sortType')
n = request.POST.get('noResults')
abstractList = search.main(q, s, n)
for document in abstractList:
documentURL = document.get("url")
if Paper.objects.filter(paper_url=documentURL,
review=review).exists():
abstractList.remove(document)
else:
abstractList = eval(request.POST.get('results'))
q = request.POST.get('queryField')
relevant = "Unchecked"
if request.POST.get("relevanceField") == "relevant":
relevant = "Relevant"
else:
if request.POST.get("relevanceField") == "irrelevant":
relevant = "Not Relevant"
if relevant != "Unchecked":
print "traceA"
compareCount_value = int(request.POST.get("hiddenCompareCount"))
for s in abstractList:
if s.get('compareCount') == compareCount_value:
currentDoc = s
paper = Paper(review=review,
title=currentDoc["title"],
paper_url=currentDoc["url"],
full_text=currentDoc['fullText'],
abstract=currentDoc["abstract"],
authors=currentDoc["author"],
abstract_relevance=relevant)
paper.save()
if len(abstractList) > 1:
for abstract in abstractList:
if int(abstract.get(
'compareCount')) > compareCount_value - 1:
abstract['compareCount'] -= 1
del abstractList[compareCount_value - 1]
else:
abstractList = []
#for abstract in abstractList:
#if int(abstract.get('compareCount')) > compareCount_value:
#abstract['compareCount'] -= 1
#del abstractList[compareCount_value]
return render(
request, 'ultimatereview/AbstractPool.html', {
"Abstracts": abstractList,
'query': q,
'review': review.title,
'slug': review_name_slug
})
def createTestPaper():
for i in range(3):
paper = Paper(name="paper" + str(i), description="paper" + str(i) + "...", state='A')
paper.save()
userpaper = UserPaper(user=testUser, paper=paper, finish_state="finished")
userpaper.save()
for i in range(4, 7):
paper = Paper(name="paper" + str(i), description="paper" + str(i) + "...", state='A')
paper.save()
userpaper = UserPaper(user=testUser, paper=paper, finish_state="unfinished")
userpaper.save()
def dbSavePapersAndAuthors(papers, latestMailing=True):
"""Saves an array of paper information into the database. Returns numbers of new papers and authors added.
If the latestMailing argument is true, then sets the paper dates to either today or tomorrow,
regardless of the date from the arXiv. It sets to today if the function is run before 8pm ET, and to
tomorrow otherwise. The idea is that this function should be run regularly every day, the night that the
mailing goes out. If run late in the day before midnight, then the mailing has tomorrow's date. If run
early in the day, e.g., if for some reason it didn't run when it should have, then the mailing was sent out
yesterday and is for today.
"""
if latestMailing:
latestMailingDate = datetime.date.today()
now = datetime.datetime.now(pytz.timezone('US/Eastern'))
cutoff = now.replace(hour=20,minute=0,second=0,microsecond=0)
if now > cutoff:
latestMailingDate += datetime.timedelta(days=+1) # note: The official mailing date is the day the email goes out, a few hours after the paper was made available
numNewPapersAdded = numNewAuthorsAdded = 0
for paper in papers:
authors = []
for author in paper['authors']:
authorsWithSameName = Author.objects.filter(name=author)
if authorsWithSameName: # author with same name already exists in database---don't add a duplicate
a = authorsWithSameName[0] # there might be duplicates --- take the first (maybe fix later)
else:
a = Author(name=author)
a.save()
numNewAuthorsAdded += 1
authors.append(a)
if Paper.objects.filter(arxivId=paper['arxivId']): continue # NOTE: If we make a mistake adding the paper the first time, this line will keep the code below from ever running to fix it
if latestMailing:
mailing_date = latestMailingDate
else:
mailing_date = mailingDate(paper['datePublished'])
p = Paper(
arxivId = paper['arxivId'],
title = paper['title'],
abstract = paper['abstract'],
date_published = paper['datePublished'],
date_mailed = mailing_date,
#authors = authors, # ManyToManyField is set up later
category = paper['category'],
categories = paper['categories'],
version = paper['version'],
linkAbsPage = paper['linkAbsPage'],
linkPdf = paper['linkPdf']
)
p.save() # need to save before setting up the ManyToMany field of authors
for author in authors: # alternatively, to clear a ManyToMany field, use p.authors.clear()
p.authors.add(author)
p.save()
numNewPapersAdded += 1
print "%d new papers, %d new authors added" % (numNewPapersAdded, numNewAuthorsAdded)
return numNewPapersAdded, numNewAuthorsAdded
def api_create_paper(request, *, name, brief, tag):
check_admin(request)
if not name or not name.strip():
raise APIValueError('name', 'name cannot be empty.')
if not tag or not tag.strip():
raise APIValueError('tag', 'tag cannot be empty.')
paper = Paper(name=name.strip(), brief=brief.strip(), tag=tag.strip(), munber=0, total=0)
yield from paper.save()
return paper
def createTestPaper():
for i in range(3):
paper = Paper(name="paper" + str(i),
description="paper" + str(i) + "...",
state='A')
paper.save()
userpaper = UserPaper(user=testUser,
paper=paper,
finish_state="finished")
userpaper.save()
for i in range(4, 7):
paper = Paper(name="paper" + str(i),
description="paper" + str(i) + "...",
state='A')
paper.save()
userpaper = UserPaper(user=testUser,
paper=paper,
finish_state="unfinished")
userpaper.save()
def ingest_csv(csv_file_name, index_name):
with open(csv_file_name, "r") as csv_file:
reader = csv.reader(csv_file)
headers = next(reader)
# Normalize header titles to become valid attribute names
headers = [(re.sub(r'\W+', '',
h.strip().replace(' ', '_'))).lower()
for h in headers]
for row in reader:
paper = Paper(meta={'id': row[0], 'index': index_name})
for ind, header in enumerate(headers):
setattr(paper, header, row[ind])
try:
paper.save(refresh=True)
paper._index.refresh()
except ValidationException as e:
# There are a few blank publish_time values. Didn't find time to make optional
print(f"Unable to save record with id {row[0]}")
print(e)
def AbstractPool(request, review_name_slug):
review = Review.objects.get(user=request.user, slug=review_name_slug)
if request.method == "POST":
if request.POST.get('results') == None:
q = request.POST.get('queryField')
s = request.POST.get('sortType')
n = request.POST.get('noResults')
abstractList = search.main(q,s, n)
for document in abstractList:
documentURL = document.get("url")
if Paper.objects.filter(paper_url= documentURL, review= review).exists():
abstractList.remove(document)
else:
abstractList = eval(request.POST.get('results'))
q = request.POST.get('queryField')
relevant="Unchecked"
if request.POST.get("relevanceField") == "relevant":
relevant="Relevant"
else:
if request.POST.get("relevanceField") == "irrelevant":
relevant="Not Relevant"
if relevant!="Unchecked":
print "traceA"
compareCount_value = int(request.POST.get("hiddenCompareCount"))
for s in abstractList:
if s.get('compareCount') == compareCount_value:
currentDoc = s
paper = Paper(review=review, title=currentDoc["title"], paper_url=currentDoc["url"], full_text=currentDoc['fullText'], abstract=currentDoc["abstract"], authors=currentDoc["author"], abstract_relevance=relevant)
paper.save()
if len(abstractList)>1:
for abstract in abstractList:
if int(abstract.get('compareCount')) > compareCount_value-1:
abstract['compareCount'] -= 1
del abstractList[compareCount_value-1]
else:
abstractList = []
#for abstract in abstractList:
#if int(abstract.get('compareCount')) > compareCount_value:
#abstract['compareCount'] -= 1
#del abstractList[compareCount_value]
return render(request, 'ultimatereview/AbstractPool.html', {"Abstracts": abstractList, 'query': q, 'review':review.title,'slug': review_name_slug})
def _paperAdd(requestData, user):
'''
新增一个问卷的具体处理过程
'''
# 获取Paper模型中的所有属性
keys = requestData.keys()
data = {}
# fields = zip(*Paper._meta.get_fields_with_model())[0]
for field in getModelFields(Paper):
# 跳过系统自动增加的字段
if field.auto_created:
continue
# 读取request数据
value = requestData.get(field.name, None)
# 特殊处理json的Boolean型的变量
if type(field) == BooleanField:
value = jsonBoolean2Python(value)
# 对创建人和修改人的信息进行特殊处理
if field.name in [USER_CREATE_BY_FIELD_NAME, USER_MODIFY_BY_FIELD_NAME]:
value = user
# 如果调用者没有显示执行字段值为空，则不增加到data中去，让模型的默认值发挥作用
# 字段代码不能早于对createBy和modifyBy的处理
if value is None and field.name not in keys:
continue
# 将校验的数据添加到data，准备为创建数据库用
data[field.name] = value
paper = Paper(**data)
# 校验数据
try:
paper.full_clean()
except ValidationError as exception:
return packageResult(
RESULT_CODE.ERROR, RESULT_MESSAGE.VALIDATION_ERROR, {'validationMessage': exception.message_dict})
# 保存到数据库
paper.save()
return packageResult(RESULT_CODE.SUCCESS, RESULT_MESSAGE.SUCCESS, {'paperId': paper.id})
def write_db(self):
print "len of entry list " + str(len(self.entry_list))
for entry in self.entry_list:
paper = Paper()
if entry.has_key("id"):
paper.id = entry["id"]
if entry.has_key("type"):
paper.type = entry["type"]
if entry.has_key("title"):
paper.title = entry["title"]
if entry.has_key("author"):
paper.authors = entry["author"]
if entry.has_key("year"):
paper.year = int(entry["year"])
if entry.has_key("journal"):
paper.journal = entry["journal"]
if entry.has_key("booktitle"):
paper.book_title = entry["booktitle"]
if entry.has_key("publisher"):
paper.publisher = entry["publisher"]
if entry.has_key("institution"):
paper.institution = entry["institution"]
if entry.has_key("volume"):
paper.volume = int(entry["volume"])
if entry.has_key("number"):
paper.number = int(entry["number"])
if entry.has_key("pages"):
paper.pages = entry["pages"]
if entry.has_key("url"):
paper.url = entry["url"]
if entry.has_key("doi"):
paper.doi = entry["doi"]
if entry.has_key("isbn"):
paper.isbn = entry["isbn"]
paper.save()
def upload(request):
if request.method =='POST':
#form = UploaderForm(request.POST,request.FILES)
#if form.is_valid():
paper_title=request.FILES['ups'].name
uploaded=request.FILES['ups']
print uploaded
print uploaded.size
username = get_user_fromcookie(request)
data = {'title': paper_title,'paper_file':uploaded}
form = UploadForm(data)
obj = Paper(title=paper_title,paper_file=uploaded,user=username)
obj.save()
#form.save()
'''
if form.is_valid():
form.save()
else:
print form.errors
'''
#return HttpResponse("errros")
return HttpResponse('Research Paper uploaded')
def upload(request):
if request.method == 'POST':
t = []
#form = UploaderForm(request.POST,request.FILES)
#if form.is_valid():
paper_title = request.FILES['ups'].name
uploaded = request.FILES['ups']
tags = request.POST['tags']
t = tags.split(',')
print t
p = []
for i in range(len(t) - 1):
l = Topic.objects.get(subject=t[i].encode('ascii', 'replace'))
p.append(l.id)
#print uploaded
print p
#print uploaded.size
username = get_user_fromcookie(request)
data = {'title': paper_title, 'paper_file': uploaded}
form = UploadForm(data)
obj = Paper(title=paper_title, paper_file=uploaded, user=username)
obj.save()
pap = Paper.objects.get(title=paper_title)
for i in p:
pap.tags.add(int(i))
convert(paper_title)
#form.save()
'''
if form.is_valid():
form.save()
else:
print form.errors
'''
#return HttpResponse("errros")
return render(request, 'thanks.html',
{'message': 'Research Paper Uploaded'})
def upload(request):
if request.method =='POST':
t = []
#form = UploaderForm(request.POST,request.FILES)
#if form.is_valid():
paper_title=request.FILES['ups'].name
uploaded=request.FILES['ups']
tags = request.POST['tags']
t = tags.split(',')
print t
p = []
for i in range(len(t)-1):
l = Topic.objects.get(subject=t[i].encode('ascii','replace'))
p.append(l.id)
#print uploaded
print p
#print uploaded.size
username = get_user_fromcookie(request)
data = {'title': paper_title,'paper_file':uploaded}
form = UploadForm(data)
obj = Paper(title=paper_title,paper_file=uploaded,user=username)
obj.save()
pap = Paper.objects.get(title=paper_title)
for i in p:
pap.tags.add(int(i))
convert(paper_title)
#form.save()
'''
if form.is_valid():
form.save()
else:
print form.errors
'''
#return HttpResponse("errros")
return render(request,'thanks.html',{'message': 'Research Paper Uploaded'})
def save(self, user):
d = self.cleaned_data
authors = [user]
if 'coauthor1' in d:
authors.append(d['coauthor1'])
if 'coauthor2' in d:
authors.append(d['coauthor2'])
if 'coauthor3' in d:
authors.append(d['coauthor3'])
paper = Paper()
paper.save()
paper.authors.add(user)
for coauthor in d['coauthors']:
paper.authors.add(coauthor)
paper.save()
d['contents'].name = '%030x' % random.randrange(16**30) + ".pdf"
paper_version = PaperVersion(
paper = paper,
title = d['title'],
abstract = d['abstract'],
contents = d['contents'],
)
paper_version.save()
# need to save paper twice since paper and paper_version point to each other...
paper.latest_version = paper_version
paper.save()
for conflict_username in d['conflicts']:
ra = ReviewAssignment()
ra.user = User.objects.get(username=conflict_username)
ra.paper = paper
ra.type = 'conflict'
ra.save()
return paper
def add(search_query, author, title):
fl = [
'id', 'author', 'first_author', 'bibcode', 'id', 'year', 'title',
'abstract', 'doi', 'pubdate', "pub", "keyword", "doctype",
"identifier", "links_data"
]
if author:
search_query += "author:" + author
if title:
search_query += "title:" + title
papers = list(ads.SearchQuery(q=search_query, fl=fl))
if len(papers) == 0:
selection = ads.search.Article
exit()
elif len(papers) == 1:
selection = papers[0] # type:ads.search.Article
else:
# first_ten = itertools.islice(papers, 10)
first_ten = papers[:10]
single_paper: ads.search.Article
for index, single_paper in enumerate(first_ten):
print(index, single_paper.title[0], single_paper.first_author)
selected_index = click.prompt('select paper', type=int)
selection = papers[selected_index] # type:ads.search.Article
assert len(selection.doi) == 1
doi = selection.doi[0]
try:
paper = Paper.get(Paper.doi == doi)
print("this paper has already been added")
exit(1)
except peewee.DoesNotExist:
pass
print("fetching bibcode")
q = ads.ExportQuery([selection.bibcode])
bibtex = q.execute()
print("saving in db")
paper = Paper()
assert len(selection.title) == 1
paper.doi = doi
paper.title = selection.title[0]
paper.abstract = selection.abstract
paper.bibcode = selection.bibcode
paper.year = selection.year
paper.pubdate = selection.pubdate
paper.pdf_downloaded = False
paper.first_author = Author.get_or_create(name=selection.first_author)[0]
paper.publication = Publication.get_or_create(name=selection.pub)[0]
paper.doctype = Doctype.get_or_create(name=selection.doctype)[0]
paper.arxiv_identifier = [
ident for ident in selection.identifier if "arXiv:" in ident
][0].split("arXiv:")[-1]
paper.bibtex = bibtex
links = [json.loads(string) for string in selection.links_data]
print(links)
paper.save()
authors = [Author.get_or_create(name=name)[0] for name in selection.author]
for author in db.batch_commit(authors, 100):
PaperAuthors.create(author=author, paper=paper)
keywords = [
Keyword.get_or_create(keyword=keyword)[0]
for keyword in selection.keyword
]
for keyword in db.batch_commit(keywords, 100):
PaperKeywords.create(keyword=keyword, paper=paper)
print("fetching PDF")
arxiv_url = "https://arxiv.org/pdf/{id}".format(id=paper.arxiv_identifier)
r = requests.get(arxiv_url, stream=True)
print(arxiv_url)
with open('library/{filename}.pdf'.format(filename=paper.id), 'wb') as f:
chunk_size = 1024 # bytes
file_size = int(r.headers.get('content-length', 0))
progress_length = math.ceil(file_size // chunk_size)
with click.progressbar(r.iter_content(chunk_size=20),
length=progress_length) as progress_chunks:
for chunk in progress_chunks:
f.write(chunk)
paper.pdf_downloaded = True
paper.save()
def post(self, request):
param = QueryDict(request.body)
uuid = param.get('uuid')
title = param.get('title')
time = param.get('time')
origin = param.get('origin')
_authors = param.getlist('authors')
link = param.get('link')
_tags = param.getlist('tags')
content = param.get('content')
refer_to = param.getlist('reference')
score = param.get('score')
try:
year, month = time.split('-')
year, month = int(year), int(month)
publish_time = datetime.date(year, month, 1)
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '提供的日期{}有误'.format(time)}, status=500)
for _tag in _tags:
try:
_tag = int(_tag)
_ = ResearchTag.objects.get(research_tag_id=_tag)
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '错误的标签{}'.format(_tag)},
status=500)
tags = ResearchTag.objects.filter(
research_tag_id__in=[int(_t) for _t in _tags])
author_ids = []
for _author in _authors:
if _author.isdigit():
author_ids.append(int(_author))
elif Author.objects.filter(name=_author).exists():
a = Author.objects.get(name=_author).author_id
author_ids.append(a)
else:
a = Author(name=_author)
a.save()
author_ids.append(a.author_id)
authors = Author.objects.filter(author_id__in=author_ids)
try:
score = int(score)
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '错误的评分分数格式'}, status=500)
if not Paper.objects.filter(paper_uuid=uuid).exists():
# 新建的场合
try:
comment = PaperComment(content=content)
comment.save()
paper = Paper(paper_uuid=uuid,
title=title,
publish_origin=origin,
publish_time=publish_time,
author=authors,
link=link,
tag=tags,
comment=comment,
self_score=score)
paper.save()
redis.set(self.LATEST_KEY, str(uuid_gen.uuid4()))
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '保存失败'}, status=500)
else:
return JsonResponse({
'next':
reverse('paperdb.detail',
kwargs={'paper_uuid': paper.paper_uuid})
})
try:
# 编辑的场合
paper = Paper.objects.get(paper_uuid=uuid)
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '错误的uuid/未找到相关论文记录'}, status=404)
else:
paper.title = title
paper.publish_time = publish_time
paper.publish_origin = origin
paper.author = authors
paper.link = paper.link
paper.tag = tags
paper.self_score = score
try:
paper.save()
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '保存失败'}, status=500)
if paper.comment is None:
if content != '':
comment = PaperComment(content=content)
comment.save()
paper.comment = comment
paper.save()
elif content != paper.comment.content.replace(
'\r\n', '\n'): # traditional下的换行符出入
paper.comment.content = content
paper.comment.save()
for refer_to_paper in Paper.objects.filter(paper_uuid__in=refer_to):
if not Reference.objects.filter(
reference_src=paper,
reference_trg=refer_to_paper).exists():
reference = Reference(reference_src=paper,
reference_trg=refer_to_paper)
reference.save()
return JsonResponse({
'next':
reverse('paperdb.detail', kwargs={'paper_uuid': paper.paper_uuid})
})
def get_references_citations_by_id(profile_id):
if isinstance(profile_id, dict):
profile_id = profile_id.get('profile_id')
if MONGO:
if data_collection.find({"id": profile_id}).count() > 0:
# 说明这个数据已经被爬取过了
return []
print('func2')
if not profile_id:
return -1
headers = {
'user-agent':
'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/77.0.3865.75 Safari/537.36',
'accept-language': 'zh-CN,zh;q=0.9'
}
session = requests.Session()
while True:
try:
response = session.get(
'https://cn.bing.com/academic/profile?id={}&encoded=0&v=paper_preview&mkt=zh-cn'
.format(profile_id),
headers=headers)
response.raise_for_status()
response.encoding = 'utf-8'
break
except KeyboardInterrupt:
raise KeyboardInterrupt
except Exception as e:
time.sleep(3.0)
print(e)
result = re.search(r'IG:"(.*?)"', response.text)
if result:
ig = result.group(1)
result = re.search(
r'被 引 量</span></span><span class="aca_content"><div>(\d*)</div>',
response.text)
if result:
citation_num = result.group(1)
html = etree.HTML(response.text)
paper = Paper(save2mongo=MONGO)
try:
paper.title = html.xpath('//li[@class="aca_title"]/text()')[0]
paper.id = profile_id
paper.citation_num = citation_num
result = re.search(
r'<span class="aca_label">DOI</span></span><span class="aca_content"><div>(.*?)</div>',
response.text)
if result:
paper.doi = result.group(1)
paper.authors = html.xpath(
'//div[@class="aca_desc b_snippet"]/span//a/text()')
paper.abstract = html.xpath(
'//div[@class="aca_desc b_snippet"]/span[1]//text()')[-1]
result = re.search(
r'<span class="aca_label">发表日期</span></span><span class="aca_content"><div>(\d*)</div>',
response.text)
if result:
paper.publish_year = result.group(1)
base_url = 'https://cn.bing.com/academic/papers?ajax=scroll&infscroll=1&id={id}&encoded=0&v=paper_preview&mkt=zh-cn&first={first}&count={count}&IG={ig}&IID=morepage.{num}&SFX={num}&rt={rt}'
count = 9
citation_links = list()
for i in range(1, int(citation_num) // count):
ajax_url = base_url.format(id=profile_id,
first=i * (count + 1),
count=count + 1,
ig=ig,
num=i,
rt='2')
while True:
try:
response = session.get(ajax_url, headers=headers)
response.raise_for_status()
response.encoding = 'utf-8'
break
except KeyboardInterrupt:
raise KeyboardInterrupt
except Exception as e:
time.sleep(3.0)
print(e)
html = etree.HTML(response.text)
citation_links.extend(html.xpath('//a[@target="_blank"]/@href'))
print('number of citation_links', len(citation_links), 'citation_num',
citation_num)
if len(citation_links) >= 0:
for i, citation_link in enumerate(citation_links):
profile_id = get_profile_id(citation_link)
if profile_id.get('title', False):
paper.citations.append(profile_id)
print('get_profile_id: {}/{}\r'.format(i + 1,
len(citation_links)),
end='')
print('\nnumber of ids:', len(paper.citations))
except KeyboardInterrupt:
raise KeyboardInterrupt
except Exception as e:
print(e)
paper.save()
# for profile_id in paper.citations:
# get_references_citations_by_id(profile_id)
return paper.citations