def get_enzyme_data(query):
seq_fields = [
'id', 'enzyme_type', 'enzyme_name', 'sequence', 'sequence_unavailable',
'accession', 'pdb', 'mutant_of', 'notes', 'papers', 'owner',
'other_names'
]
enzyme_data = list(
Sequence.objects(query).only(
*seq_fields).order_by('enzyme_type').as_pymongo())
owners_dict = {}
for i, data in enumerate(enzyme_data):
enzyme_data[i]['_id'] = str(enzyme_data[i]['_id'])
enzyme_data[i]['sequence_unavailable'] = str(
enzyme_data[i]['sequence_unavailable']).replace('False', '')
if 'papers' not in enzyme_data[i]:
enzyme_data[i]['papers'] = 0
else:
enzyme_data[i]['papers'] = len(enzyme_data[i]['papers'])
if 'owner' in enzyme_data[i]:
owner_id = str(enzyme_data[i]['owner'])
if owner_id not in owners_dict:
owner = User.objects(id=enzyme_data[i]['owner'])[0]
owners_dict[owner_id] = f"{owner.first_name} {owner.last_name}"
enzyme_data[i]['owner'] = owners_dict[owner_id]
else:
enzyme_data[i]['owner'] = ''
if 'sequence' in enzyme_data[i]:
if len(enzyme_data[i]['sequence']) > 50:
enzyme_data[i][
'sequence'] = enzyme_data[i]['sequence'][0:50] + "..."
return enzyme_data
def enzyme_teams():
teams = []
team_info = {}
contributor_role = Role.objects(name='contributor')[0]
contributors = User.objects(roles=contributor_role).select_related()
for user in contributors:
user_string = f"{user.first_name} {user.last_name}"
affiliation_string = f"{user.affiliation}"
for enzyme_type in user.enzyme_teams:
if enzyme_type.enzyme_type not in teams:
teams.append(enzyme_type.enzyme_type)
team_info[enzyme_type.enzyme_type] = {'full_name': enzyme_type.full_name,
'enzyme_champions': [],
'team_members': [],
'progress': calculate_paper_progress.get_enzyme_paper_progress(enzyme_type)}
if enzyme_type in user.enzyme_champion:
team_info[enzyme_type.enzyme_type]['enzyme_champions'].append([user_string, affiliation_string])
else:
team_info[enzyme_type.enzyme_type]['team_members'].append([user_string, affiliation_string])
teams.sort()
return render_template('enzyme_teams.html', teams=teams, team_info=team_info)
def inject_login_mode():
inject_dict = {}
inject_dict['login_mode'] = app.config['USE_EMAIL_CONFIRMATION']
if current_user.is_authenticated:
user = User.objects(id=current_user.id).select_related()[0]
if user.has_role('enzyme_teams') and user.enzyme_teams is not None:
inject_dict['enzyme_teams'] = [enz_type_obj.enzyme_type for enz_type_obj in user.enzyme_teams]
if user.has_role('enzyme_champion') and user.enzyme_champion is not None:
inject_dict['enzyme_champion'] = [enz_type_obj.enzyme_type for enz_type_obj in user.enzyme_champion]
if user.has_role('contributor'):
inject_dict['user_papers_need_data'] = len(Paper.objects(Q(owner=user) & (Q(status='Data required') | Q(status='Enzymes need protein sequences') | Q(status='Issues need to be resolved'))))
inject_dict['user_seqs_need_data'] = len(Sequence.objects(Q(owner=user) & ((Q(sequence=None)|Q(sequence='')) & (Q(sequence_unavailable__ne=True)))))
inject_dict['total_team_notifications'] = 0
inject_dict['team_notifications'] = {}
inject_dict['champ_seq_notifications'] = {}
inject_dict['champ_notifications'] = {}
if 'enzyme_teams' in inject_dict:
for enz_type in inject_dict['enzyme_teams']:
num_papers = len(Paper.objects(Q(tags=enz_type) & Q(owner=None) & (Q(status='Data required') | Q(status='Enzymes need protein sequences'))))
inject_dict['team_notifications'][enz_type] = num_papers
inject_dict['total_team_notifications'] += num_papers
if 'enzyme_champion' in inject_dict:
for enz_type in inject_dict['enzyme_champion']:
num_papers = len(Paper.objects(Q(tags=enz_type) & Q(status='Complete - Awaiting review')))
num_seqs = len(Sequence.objects(Q(enzyme_type=enz_type) & ((Q(sequence=None)|Q(sequence='')) & (Q(sequence_unavailable__ne=True)))))
inject_dict['champ_notifications'][enz_type] = num_papers
inject_dict['champ_seq_notifications'][enz_type] = num_seqs
inject_dict['total_team_notifications'] += num_papers + num_seqs
return inject_dict
def get_usernames(user):
usernames = []
if len(User.objects(
last_name=user.last_name)) == 1 and len(user.last_name) > 2:
usernames.append(str(user.last_name).lower())
if len(User.objects(
first_name=user.first_name)) == 1 and len(user.first_name) > 2:
usernames.append(str(user.first_name).lower())
usernames.append(f"{user.first_name} {user.last_name}".lower())
usernames.append(
f"{user.first_name} {user.last_name}, {user.affiliation}".lower())
for name in usernames:
if len(name) > 3:
usernames.remove(name)
return usernames
def check_paper_permission(user_id, paper):
user = User.objects(id=user_id).select_related()[0]
if user.has_role('super_contributor'):
return True
if paper.owner == user:
return True
if user.has_role('enzyme_champion'):
champ_types = [e.enzyme_type for e in user.enzyme_champion]
if any(i in champ_types for i in paper.tags):
return True
return False
def check_seq_permissions(user_id, seq):
user = User.objects(id=user_id).select_related()[0]
if user.has_role('super_contributor'):
return True
if seq.owner == user:
return True
if user.has_role('enzyme_champion'):
champ_types = [e.enzyme_type for e in user.enzyme_champion]
if seq.enzyme_type in champ_types:
return True
return False
def admin_set_owner():
paper = Paper.objects(id=request.form['paper_id'])[0]
new_owner_id = request.form['new_owner_id']
print(new_owner_id)
new_owner = User.objects(id=new_owner_id)[0]
paper.owner = new_owner
paper.save()
result = {'status': 'success', 'msg': 'Paper owner updated', 'issues': []}
return jsonify(result=result)
def get_admin_dict(paper):
admin_dict = {}
contributor_choices = [(f"{c.first_name} {c.last_name}", str(c.id)) for c in User.contributors()]
admin_dict['contributors'] = [('Unassigned', '')] + contributor_choices
if paper.owner != None:
admin_dict['owner'] = str(paper.owner.id)
else:
admin_dict['owner'] = ''
return admin_dict
def task_add_sequence_data(df):
users = User.objects()
for i, row in df.iterrows():
seq_query = Sequence.objects(enzyme_name=row['enzyme_name'])
if len(seq_query) != 0:
seq = seq_query[0]
if row['sequence'] != '' and row['sequence'] is not None:
seq.sequence = str(row['sequence'])
for user in users:
usernames = get_usernames(user)
if does_username_match(usernames, row['added_by']):
seq.added_by = user
seq.owner = user
seq.save()
def process_papers_dict(papers_data, show_owner=True):
owners_dict = {}
for i, data in enumerate(papers_data):
papers_data[i]['_id'] = str(papers_data[i]['_id'])
if show_owner == False:
if 'owner' in papers_data[i]:
papers_data[i].pop('owner')
else:
if 'owner' in papers_data[i]:
owner_id = str(papers_data[i]['owner'])
if owner_id not in owners_dict:
owner = User.objects(id=papers_data[i]['owner'])[0]
owners_dict[
owner_id] = f"{owner.first_name} {owner.last_name}"
papers_data[i]['owner'] = owners_dict[owner_id]
else:
papers_data[i]['owner'] = '-'
return papers_data
def task_assign_papers():
users = User.objects()
papers = Paper.objects()
for paper in papers:
paper_status.update_status(paper)
for user in users:
usernames = get_usernames(user)
for paper in papers:
if paper.added_by is None or paper.added_by == '':
activities = Activity.objects(paper=paper)
for activity in activities:
if does_username_match(usernames,
activity.added_by_string):
activity.added_by = user
activity.save()
if paper.added_by is None or paper.added_by == '':
paper.added_by = user
paper.owner = user
paper.save()
def leaderboard():
contributor_role = Role.objects(name='contributor')[0]
contributors = User.objects(roles=contributor_role)
papers_dict = {}
sequence_dict = {}
activity_dict = {}
for user in contributors:
username = f"{user.first_name} {user.last_name}, {user.affiliation}"
num_papers = len(Paper.objects(owner=user))
num_sequences = len(Sequence.objects(owner=user))
papers_dict[username] = num_papers
sequence_dict[username] = num_sequences
papers_dict = {k: v for k, v in sorted(papers_dict.items(), key=lambda item: item[1], reverse=True)}
papers_dict = {k: v for k, v in papers_dict.items() if v != 0}
sequence_dict = {k: v for k, v in sorted(sequence_dict.items(), key=lambda item: item[1], reverse=True)}
sequence_dict = {k: v for k, v in sequence_dict.items() if v != 0}
return render_template('leaderboard.html',
top_papers=papers_dict,
top_sequences=sequence_dict)
def make_added_by_user_dict():
added_by_dict = {}
users = User.objects()
for user in users:
added_by_dict[f"{user.first_name} {user.last_name}"] = user
return added_by_dict
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"))