def update_paper_molecule():
paper_id = request.form['paper_id']
id = request.form['id']
smi = request.form['smi']
name = request.form['name']
paper_query = Paper.objects(id=paper_id).select_related()
if len(paper_query) != 0:
paper = paper_query[0]
if check_permission.check_paper_permission(current_user.id, paper):
act_mol = ActivityMol.objects(id=id)[0]
if smi != act_mol.smi:
try:
mol = Chem.MolFromSmiles(smi)
svg = moltosvg(mol)
except:
svg = ""
act_mol.svg = svg
act_mol.smi = smi
act_mol.name = name
act_mol.save()
result = {'status': 'success',
'msg': 'Molecule saved',
'issues': []}
return jsonify(result=result)
result = {'status': 'danger',
'msg': 'Could not delete molecule',
'issues': []}
return jsonify(result=result)
def duplicate_paper_molecule():
id = request.form['id']
paper_id = request.form['paper_id']
paper_query = Paper.objects(id=paper_id).select_related()
if len(paper_query) != 0:
paper = paper_query[0]
if check_permission.check_paper_permission(current_user.id, paper):
mols = ActivityMol.objects(db.Q(id=id))
if len(mols) != 0:
mol = mols[0]
num_paper_mols = ActivityMol.objects(paper=paper).count()
new_mol = ActivityMol(name=f"{num_paper_mols+1}",
smi=mol.smi,
svg=mol.svg,
paper=paper)
new_mol.save()
mol_list = [(new_mol.name, new_mol.smi, new_mol.svg, str(new_mol.id))]
result = {'status': 'success',
'msg': 'Molecule deleted',
'issues': [],
'mol_list': mol_list}
return jsonify(result=result)
result = {'status': 'danger',
'msg': 'Could not delete molecule',
'issues': []}
return jsonify(result=result)
def submission_main_page(paper_id):
user = user_datastore.get_user(current_user.id)
paper_query = Paper.objects(id=paper_id).select_related()
if len(paper_query) == 0:
flash('Paper has not been added yet, please add to the database first', 'fail')
return redirect(url_for("biocatdb.launch_add_paper"))
paper = paper_query[0]
if not check_permission.check_paper_permission(current_user.id, paper):
flash('No access to edit this entry', 'fail')
return redirect(url_for("biocatdb.launch_add_paper"))
paper_data = get_paper_data(paper, user)
activity_data = get_activity_data(paper)
reactions = list(Reaction.objects().distinct('name'))
enzyme_names = list(Sequence.objects(papers=paper).distinct('enzyme_name'))
enzyme_types = list(EnzymeType.objects().distinct('enzyme_type'))
enzyme_data = sequence_table.get_enzyme_data(db.Q(papers=paper))
enzyme_types_in_paper = list(Sequence.objects(papers=paper).distinct('enzyme_type'))
reactions_in_paper = list(Reaction.objects(enzyme_types__in=enzyme_types_in_paper).distinct('name'))
reactions_in_activity = list(Activity.objects(paper=paper).distinct('reaction'))
status_dict = get_status(paper, user)
comments = get_comments(paper, user)
paper_molecules = get_paper_molecules(paper)
admin_panel = False
admin_dict = {}
if current_user.has_role('admin'):
admin_panel = True
admin_dict = get_admin_dict(paper)
reactions_ordered = reactions_in_activity + [r for r in reactions_in_paper if r not in reactions_in_activity]
reactions_ordered += [r for r in reactions_in_paper if r not in reactions_ordered]
reactions_ordered += [r for r in reactions if r not in reactions_ordered]
return render_template('data_submission/submission_main_page.html',
paper=paper_data,
activity_data=activity_data,
seq_data=enzyme_data, seq_button_columns=['edit', 'remove', 'papers'],
status=status_dict,
seq_table_height='60vh', enzyme_types=enzyme_types, show_header_filters=False, include_owner=True, lock_enz_type='false',
reactions=reactions_ordered, enzyme_names=enzyme_names+['Chemical'],
doi=paper.doi,
comments=comments,
paper_molecules=paper_molecules,
admin_panel=admin_panel,
admin_dict=admin_dict,
enzyme_reactions=reactions_in_paper)
def save_paper():
user = user_datastore.get_user(current_user.id)
paper = Paper.objects(id=request.form['paper_id'])[0]
if not check_permission.check_paper_permission(current_user.id, paper):
result = {
'status': 'danger',
'msg': 'No access to edit this paper',
'issues': [],
'redirect': url_for("biocatdb.launch_add_paper")
}
return jsonify(result=result)
paper.short_citation = request.form['short_cit']
paper.doi = request.form['doi'].replace(' ', '')
paper.html = 'https://doi.org/' + request.form['doi']
if request.form['date'] != "":
paper.date = request.form['date']
paper.title = request.form['title']
paper.journal = request.form['journal']
paper.authors = request.form['authors'].split(', ')
paper.tags = request.form['tags'].split(', ')
if user not in paper.edits_by:
paper.edits_by.append(user)
if (paper.owner == user) and (request.form['self_assign'] == 'false'):
paper.owner = None
paper.save()
unassign_seqs_in_paper(user, paper)
if not current_user.has_role('super_contributor'):
result = {
'status': 'warning',
'msg': 'Paper no longer assigned to you',
'issues': [],
'redirect': url_for("biocatdb.launch_add_paper")
}
return jsonify(result=result)
elif request.form['self_assign'] == 'true':
paper.owner = user
paper.save()
papers_functions.tag_paper_with_enzyme_types(paper)
result = {
'status': 'success',
'msg': 'Paper information updated',
'issues': []
}
return jsonify(result=result)
def reorder_paper_molecules():
paper_id = request.form['paper_id']
paper_query = Paper.objects(id=paper_id).select_related()
if len(paper_query) != 0:
paper = paper_query[0]
if check_permission.check_paper_permission(current_user.id, paper):
paper_mols = list(ActivityMol.objects(paper=paper))
paper_mols = natsorted(paper_mols, key=lambda x: x.name)
for i, mol in enumerate(list(paper_mols)):
mol.name = str(i+1)
mol.save()
result = {'status': 'success',
'msg': 'Molecules reordered',
'issues': []}
return jsonify(result=result)
result = {'status': 'danger',
'msg': 'Could not delete molecule',
'issues': []}
return jsonify(result=result)
def delete_paper():
user = user_datastore.get_user(current_user.id)
paper = Paper.objects(id=request.form['paper_id'])[0]
if not check_permission.check_paper_permission(current_user.id, paper):
result = {
'status': 'danger',
'msg': 'You are not the owner of this paper',
'issues': ['Assign this paper to yourself in order to delete it']
}
return jsonify(result=result)
elif len(Sequence.objects(papers=paper)) != 0:
result = {
'status': 'danger',
'msg': 'Paper still contains sequences',
'issues':
['Please remove any sequences from paper before deleting']
}
return jsonify(result=result)
elif len(Activity.objects(paper=paper)) != 0:
result = {
'status':
'danger',
'msg':
'Paper still contains activity data',
'issues':
['Please remove any activity data from paper before deleting']
}
return jsonify(result=result)
else:
paper.delete()
result = {'status': 'success', 'msg': 'Paper deleted', 'issues': []}
return jsonify(result=result)
def delete_paper_molecule():
id = request.form['id']
paper_id = request.form['paper_id']
paper_query = Paper.objects(id=paper_id).select_related()
if len(paper_query) != 0:
paper = paper_query[0]
if check_permission.check_paper_permission(current_user.id, paper):
mols = ActivityMol.objects(db.Q(id=id))
if len(mols) != 0:
mol = mols[0]
mol.delete()
result = {'status': 'success',
'msg': 'Molecule deleted',
'issues': []}
return jsonify(result=result)
result = {'status': 'danger',
'msg': 'Could not delete molecule',
'issues': []}
return jsonify(result=result)