def get_paper_data(paper, user):
self_assigned = ''
other_user = ''
if paper.owner == user:
self_assigned = 'checked'
elif paper.owner is not None and paper.owner != '':
other_user = '******'
paper_owner_name = 'None'
if paper.owner is not None:
paper_owner_name = f"{paper.owner.first_name} {paper.owner.last_name}, {paper.owner.affiliation}"
paper_dict = {
'short_cit': paper.short_citation,
'doi': paper.doi,
'date': paper.date,
'title': paper.title,
'journal': paper.journal,
'authors': papers_functions.list_to_string(paper.authors),
'tags': papers_functions.list_to_string(paper.tags),
'self_assigned': self_assigned,
'disable_for_other_user': other_user,
'id': paper.id,
'paper_owner_name': paper_owner_name
}
return paper_dict
def query_crossref():
paper = Paper.objects(id=request.form['paper_id'])[0]
doi = str(paper.doi).replace(' ', '')
title, authors_list, journal, date, cite_mini = papers_crossref.get_metadata_from_crossref(
doi)
print(f"{title}, {authors_list}, {journal}, {type(date)}, {cite_mini}")
if cite_mini == '':
result = {
'status': 'danger',
'msg': 'DOI not found in crossref',
'issues': []
}
else:
paper_dict = {
'short_cit': cite_mini,
'doi': doi,
'date': str(date),
'title': title,
'journal': journal,
'authors': papers_functions.list_to_string(authors_list)
}
result = {
'status': 'success',
'msg': 'Fields updated, click save to update the database',
'issues': [],
'paper': paper_dict
}
return jsonify(result=result)
def create_paper():
form = PaperInfo()
if 'doi' in session:
doi = session['doi']
else:
doi = ''
if form.validate_on_submit() == False:
user = User.objects(id=current_user.id)[0]
papers = Paper.objects(doi__iexact=doi)
if len(papers) != 0:
paper = papers[0]
if paper.owner == user or user.has_role('super_contributor'):
flash("Paper already in the database", 'success')
return redirect(
url_for("biocatdb.submission_main_page",
paper_id=paper.id))
elif paper.owner == None:
flash(
'Paper already in database, self-assign the paper to add data',
'warning')
return redirect(url_for("biocatdb.papers_that_need_data"))
elif paper.owner != user and not user.has_role(
'super_contributor'):
flash(
"Paper already in the database and is assigned to another user",
'danger')
else:
flash("error", 'danger')
return redirect(url_for("biocatdb.launch_add_paper"))
else:
title, authors_list, journal, date, cite_mini = papers_crossref.get_metadata_from_crossref(
doi)
if cite_mini == '':
title, authors_list, journal, date, cite_mini = papers_functions.query_pubmed(
doi)
form.title.data = title
form.authors.data = papers_functions.list_to_string(authors_list)
form.journal.data = journal
form.date.data = date
form.short_cit.data = cite_mini
form.doi.data = doi.replace(' ', '').lower()
can_self_assign = papers_functions.can_self_assign(user)
if cite_mini == '':
flash(
"Paper not found in crossref, pubmed or db, please add manually",
'fail')
else:
flash("Paper found, please check information", 'success')
return render_template(
'add_paper_workflow/edit_paper_information.html',
form=form,
can_self_assign=can_self_assign)
else:
user = User.objects(id=current_user.id)[0]
session.pop('doi')
if form.self_assign.data == True:
owner = user
else:
owner = None
new_paper = Paper(doi=form.doi.data.replace(' ', '').lower(),
short_citation=form.short_cit.data,
title=form.title.data,
html='https://doi.org/' + form.doi.data,
journal=form.journal.data,
date=form.date.data,
tags=form.tags.data.split(', '),
authors=form.authors.data.split(', '),
owner=owner,
added_by=user,
status='Data required')
new_paper.save()
flash("Paper saved", 'success')
if owner == user:
return redirect(
url_for("biocatdb.submission_main_page",
paper_id=new_paper.id))
else:
return redirect(url_for("biocatdb.launch_add_paper"))