def high_importance_papers():
hi_papers = Paper.objects(high_importance=True).select_related()
enzyme_types = EnzymeType.objects()
tags = []
for paper in hi_papers:
for tag in paper.tags:
if tag not in tags:
tags.append(str(tag))
tags = sorted(tags)
data_by_tag = {}
for tag in tags:
hi_q = db.Q(high_importance=True)
tag_q = db.Q(tags=tag)
papers_data = list(
Paper.objects(hi_q & tag_q).only(
*papers_table.PAPERS_TABLE_FIELDS).order_by(
'-status').as_pymongo())
papers_data = papers_table.process_papers_dict(papers_data,
show_owner=False)
data_by_tag[tag] = papers_data
enzyme_full_names = {}
for enz_type in enzyme_types:
enzyme_full_names[enz_type.enzyme_type] = enz_type.full_name
return render_template('edit_tables/high_importance_papers.html',
data_by_tag=data_by_tag,
tags=tags,
enzyme_full_names=enzyme_full_names)
def papers_that_need_data():
user = user_datastore.get_user(current_user.id)
title = "Papers that require curating"
args = request.args.to_dict()
q_no_user = db.Q(owner=None)
q_no_data = db.Q(status__nin=['Complete - Awaiting review', 'Complete'])
if 'enzyme_type' in args:
q_e_type = db.Q(tags=args['enzyme_type'])
title += f" - {args['enzyme_type']}"
else:
q_e_type = db.Q()
papers_data = list(
Paper.objects(q_no_user & q_no_data & q_e_type).only(
*papers_table.PAPERS_TABLE_FIELDS).order_by(
'-status').as_pymongo())
papers_data = papers_table.process_papers_dict(papers_data,
show_owner=False)
return render_template('edit_tables/edit_papers.html',
papers_data=papers_data,
papers_table_height='80vh',
papers_button_columns=['self_assign'],
show_owner=False,
title=title,
row_click_modal=False)
def papers_with_orhpan_sequences():
title = "Papers with orphan sequences"
activity_enzyme_names = list(
set(Activity.objects().distinct('enzyme_name')))
paper_ids = []
for name in activity_enzyme_names:
if len(Sequence.objects(enzyme_name=name)) == 0:
act = Activity.objects(enzyme_name=name)[0]
paper_ids.append(act.paper)
papers_data = list(
Paper.objects(id__in=paper_ids).only(
*papers_table.PAPERS_TABLE_FIELDS).order_by(
'-status').as_pymongo())
papers_data = papers_table.process_papers_dict(papers_data,
show_owner=False)
return render_template('edit_tables/edit_papers.html',
papers_data=papers_data,
papers_table_height='80vh',
papers_button_columns=['delete', 'edit'],
show_owner=True,
title=title,
row_click_modal=False)
def edit_papers():
papers_data = list(Paper.objects().only(*papers_table.PAPERS_TABLE_FIELDS).order_by('-status').as_pymongo())
papers_data = papers_table.process_papers_dict(papers_data)
return render_template('edit_tables/edit_papers.html',
papers_data=papers_data, papers_table_height='80vh',
papers_button_columns=['delete', 'edit', 'link'],
show_owner=True,
title="Super contributor access to all papers",
row_click_modal=False)
def my_papers():
user = user_datastore.get_user(current_user.id)
papers_data = list(Paper.objects(owner=user).only(*papers_table.PAPERS_TABLE_FIELDS).order_by('-status').as_pymongo())
papers_data = papers_table.process_papers_dict(papers_data)
papers_button_columns = ['edit']
if user.has_role('paper_adder'):
papers_button_columns.append('delete')
return render_template('edit_tables/edit_papers.html',
papers_data=papers_data, papers_table_height='80vh',
papers_button_columns=papers_button_columns,
show_owner=True,
title=f"Papers assigned to {user.first_name} {user.last_name}",
row_click_modal=False)
def enzyme_champion_papers(enzyme_type):
user = user_datastore.get_user(current_user.id)
enzyme_type_obj = EnzymeType.objects(enzyme_type=enzyme_type)[0]
if enzyme_type_obj not in user.enzyme_champion:
flash('No access', 'danger')
return redirect(url_for('main_site.home'))
papers_data = list(Paper.objects(tags=enzyme_type).only(*papers_table.PAPERS_TABLE_FIELDS).order_by('-status').as_pymongo())
papers_data = papers_table.process_papers_dict(papers_data)
return render_template('edit_tables/edit_papers.html',
papers_data=papers_data, papers_table_height='80vh',
papers_button_columns=['delete', 'edit'],
show_owner=True,
title=f"Enzyme champion for {enzyme_type} papers",
row_click_modal=False)
def show_papers():
args = request.args.to_dict()
title = "Papers"
if 'reviewed' in args:
revQ = db.Q(reviewed=True)
else:
revQ = db.Q()
status_query = db.Q(status_not='Data required')
if 'enzyme_type' in args:
enzyme_type_query = db.Q(tags=args['enzyme_type'])
title += f" - featuring {args['enzyme_type']} enzymes"
else:
enzyme_type_query = db.Q()
papers = Paper.objects(enzyme_type_query & revQ)
if 'enzyme_name' in args:
papers = filter_papers_by_enzyme_name(papers, args['enzyme_name'])
title += f" - featuring {args['enzyme_name']}"
if 'reaction' in args:
papers = filter_papers_by_reaction(papers, args['reaction'])
title += f" - featuring a {args['reaction']} reaction"
paper_ids = [paper.id for paper in papers]
papers_data = list(
Paper.objects(id__in=paper_ids).only(
*papers_table.PAPERS_TABLE_FIELDS).order_by(
'-status').as_pymongo())
papers_data = papers_table.process_papers_dict(papers_data)
return render_template('edit_tables/edit_papers.html',
papers_data=papers_data,
papers_table_height='80vh',
papers_button_columns=[],
show_owner=True,
title=title,
row_click_modal=True)