def update_sqlite(self, skip=[], goto_reaction=None, key_names='all'):
for key_values in self.read(skip=skip, goto_reaction=goto_reaction):
with CathubSQLite(self.cathub_db) as db:
id = db.check(key_values['reaction_energy'])
#print('Allready in reaction db with row id = {}'.format(id))
if id is not None:
db.update(id, key_values, key_names)
def write(self, skip=[], goto_reaction=None):
for key_values in self.read(skip=skip, goto_reaction=goto_reaction):
with CathubSQLite(self.cathub_db) as db:
id = db.check(key_values['chemical_composition'], key_values['reaction_energy'])
#print('Allready in reaction db with row id = {}'.format(id))
if id is None:
id = db.write(key_values)
print('Written to reaction db row id = {}'.format(id))
elif self.update:
db.update(id, key_values)
print('Updated reaction db row id = {}'.format(id))
else:
print('Allready in reaction db with row id = {}'.format(id))
def get_reactions(columns='all', n_results=20, write_db=False, **kwargs):
"""
Get reactions from server
Give key value strings as arguments
"""
if write_db or columns == 'all':
columns = all_columns['reactions']
queries = {}
for key, value in kwargs.items():
key = map_column_names(key)
if key == 'distinct':
if value in [True, 'True', 'true']:
queries.update({key: True})
continue
if isinstance(value, int) or isinstance(value, float):
queries.update({key: value})
else:
queries.update({key: '{0}'.format(value)})
subtables = []
if write_db:
subtables = ['reactionSystems', 'publication']
else:
subtables = []
data = query(table='reactions',
subtables=subtables,
columns=columns,
n_results=n_results,
queries=queries)
if not write_db:
return data
print('Writing result to Reactions.db')
unique_ids = []
for row in data['reactions']['edges']:
with CathubSQLite('Reactions.db') as db:
row = row['node']
key_values = {}
for key in all_columns['reactions']:
v = row[key]
# if isinstance(v, unicode):
# v = v.encode('utf-8')
try:
v = json.loads(v)
except BaseException:
pass
key_values[convert(key)] = v
ase_ids = {}
energy_corrections = {}
for row_rs in row['reactionSystems']:
if row_rs['name'] == 'N/A':
continue
ase_ids[row_rs['name']] = row_rs['aseId']
energy_corrections[row_rs['name']] = row_rs['energyCorrection']
if not ase_ids:
ase_ids = None
energy_corrections = None
else:
unique_ids += ase_ids.values()
key_values['ase_ids'] = ase_ids
key_values['energy_corrections'] = ase_ids
# publications
pub_key_values = {}
row_p = row['publication']
for key in all_columns['publications']:
pub_key_values[convert(key)] = row_p[key]
db.write_publication(pub_key_values)
# reactions and reaction_systems
id = db.check(key_values['chemical_composition'],
key_values['reaction_energy'])
if id is None:
id = db.write(key_values)
else:
db.update(id, key_values)
if ase_ids is not None:
# Ase structures
with ase.db.connect('Reactions.db') as ase_db:
con = ase_db.connection
cur = con.cursor()
cur.execute('SELECT unique_id from systems;')
unique_ids0 = cur.fetchall()
unique_ids0 = [un[0] for un in unique_ids0]
unique_ids = [un for un in unique_ids if un not in unique_ids0]
for unique_id in list(set(unique_ids)):
# if ase_db.count('unique_id={}'.format(unique_id)) == 0:
atomsrow = get_atomsrow_by_id(unique_id)
ase_db.write(atomsrow)
print('Writing complete!')
return data
def get_reactions(n_results=20, write_db=False, **kwargs):
queries = {}
for key, value in kwargs.items():
key = map_column_names(key)
if key == 'distinct':
if value in ['True', 'true']:
# WARNING: undefined variable name 'query_dict'
query_dict.update({key: True})
continue
try:
value = int(value)
queries.update({key: value})
except BaseException:
queries.update({key: '{0}'.format(value)})
subtables = []
# if write_local:
subtables = ['reactionSystems', 'publication']
data = query(table='reactions',
subtables=subtables,
columns=all_columns['reactions'],
n_results=n_results,
queries=queries)
if not write_db:
return data
for row in data['data']['reactions']['edges']:
with CathubSQLite('Reactions.db') as db:
row = row['node']
key_values = {}
for key in all_columns['reactions']:
v = row[key]
# if isinstance(v, unicode):
# v = v.encode('utf-8')
try:
v = json.loads(v)
except BaseException:
pass
key_values[convert(key)] = v
ase_ids = {}
energy_corrections = {}
for row_rs in row['reactionSystems']:
if row_rs['name'] == 'N/A':
continue
ase_ids[row_rs['name']] = row_rs['aseId']
energy_corrections[row_rs['name']] = row_rs['energyCorrection']
if not ase_ids:
ase_ids = None
energy_corrections = None
key_values['ase_ids'] = ase_ids
key_values['energy_corrections'] = ase_ids
# publications
pub_key_values = {}
row_p = row['publication']
for key in all_columns['publications']:
pub_key_values[convert(key)] = row_p[key]
db.write_publication(pub_key_values)
# reactions and reaction_systems
id = db.check(key_values['chemical_composition'],
key_values['reaction_energy'])
if id is None:
id = db.write(key_values)
else:
db.update(id, key_values)
if ase_ids is not None:
# Ase structures
with ase.db.connect('Reactions.db') as ase_db:
for unique_id in ase_ids.values():
if ase_db.count('unique_id={}'.format(unique_id)) == 0:
atomsrow = get_atomsrow_by_id(unique_id)
ase_db.write(atomsrow)
return data