def clear_databases():
EnzymeType.drop_collection()
Sequence.drop_collection()
Paper.drop_collection()
Reaction.drop_collection()
Activity.drop_collection()
Molecule.drop_collection()
def init_db():
form = InitDB()
if form.validate_on_submit() == True:
if form.rxns.data != None:
rxns_data = form.rxns.data
filename = secure_filename(rxns_data.filename)
try:
rxns_data.save(filename)
yaml_dict = rxn_rules_to_db.load_yaml_dict(filename)
Reaction.drop_collection()
current_app.db_queue.enqueue(rxn_rules_to_db.load_into_mongo,
yaml_dict)
flash("Yaml loaded ok, reactions_to_db in queue", 'success')
except:
flash("Failed to load reactions", 'fail')
os.remove(filename)
if form.biocatdb.data != None:
filename = secure_filename(form.biocatdb.data.filename)
form.biocatdb.data.save(filename)
try:
df = biocatdb_excel_to_db.load_df(filename)
Paper.drop_collection()
Activity.drop_collection()
Molecule.drop_collection()
Sequence.drop_collection()
current_app.db_queue.enqueue(biocatdb_excel_to_db.df_to_db, df)
current_app.db_queue.enqueue(make_molecule_db.make_fp_db)
flash("Biocatdb excel loaded ok, added to queue", "success")
except:
flash("Problem loading biocatdb_2 excel", "fail")
os.remove(filename)
if form.sequences.data != None:
filename = secure_filename(form.sequences.data.filename)
form.sequences.data.save(filename)
try:
if '.xlsx' in filename:
df = pd.read_excel(filename)
elif '.csv' in filename:
df = pd.read_csv(filename)
else:
df = None
Exception('File must be .csv or .xlsx')
current_app.db_queue.enqueue(task_add_sequence_data, df)
flash("Sequences excel loaded ok, added to queue", "success")
except Exception as e:
flash(f"Problem loading sequences excel - {e}", "fail")
os.remove(filename)
if form.mongo_dump.data != None:
filename = secure_filename(form.mongo_dump.data.filename)
form.mongo_dump.data.save(filename)
try:
if 'mongo_dump.gz' in filename:
execute_mongo_restore(filename)
else:
Exception('File must be mongo_dump.gz')
flash("mongo dump loaded ok", "success")
except Exception as e:
flash(f"Problem loading mongo dump - {e}", "fail")
return render_template('init_db/init_db.html', form=form)
enzyme_types=enzymes,
cofactors=yaml_dict[rxn_name]['enzymes'],
positive_tests=yaml_dict[rxn_name]['positive_tests'],
negative_tests=yaml_dict[rxn_name]['negative_tests'],
type=yaml_dict[rxn_name]['type'])
if 'experimental' in yaml_dict[rxn_name]:
reaction.experimental = bool(yaml_dict[rxn_name]['experimental'])
if 'two_step' in yaml_dict[rxn_name]:
reaction.two_step = bool(yaml_dict[rxn_name]['two_step'])
reaction.save()
def load_reaction_rules_into_mongo(yaml_file=YAML_PATH):
yaml_dict = load_yaml_dict(yaml_file)
load_into_mongo(yaml_dict)
if __name__ == '__main__':
from retrobiocat_web.mongo.default_connection import make_default_connection
make_default_connection()
Reaction.drop_collection()
load_reaction_rules_into_mongo()
test_reaction = Reaction.objects.get(name='Primary alcohol oxidation')
print(test_reaction.smarts)