def transfer_file(data_file):
"""Transfer contents of soakdb.sqlite file to xcdb into separate
(crystal, lab, refinement, dimple and data_processing tables.
:param data_file: File-path(?) pointing towards a soakdb.sqlite file
:type data_file: str
:return: Function should not return anything but will write to a database.
:rtype: None
"""
maint_exists = db_functions.check_table_sqlite(data_file, 'mainTable')
if maint_exists == 1:
db_functions.transfer_table(translate_dict=db_functions.crystal_translations(), filename=data_file,
model=Crystal)
db_functions.transfer_table(translate_dict=db_functions.lab_translations(), filename=data_file,
model=Lab)
db_functions.transfer_table(translate_dict=db_functions.refinement_translations(), filename=data_file,
model=Refinement)
db_functions.transfer_table(translate_dict=db_functions.dimple_translations(), filename=data_file,
model=Dimple)
db_functions.transfer_table(translate_dict=db_functions.data_processing_translations(),
filename=data_file, model=DataProcessing)
soakdb_query = SoakdbFiles.objects.get(filename=data_file)
soakdb_query.status = 2
soakdb_query.save()
def transfer_file(data_file):
maint_exists = db_functions.check_table_sqlite(data_file, 'mainTable')
if maint_exists == 1:
db_functions.transfer_table(
translate_dict=db_functions.crystal_translations(),
filename=data_file,
model=Crystal)
db_functions.transfer_table(
translate_dict=db_functions.lab_translations(),
filename=data_file,
model=Lab)
db_functions.transfer_table(
translate_dict=db_functions.refinement_translations(),
filename=data_file,
model=Refinement)
db_functions.transfer_table(
translate_dict=db_functions.dimple_translations(),
filename=data_file,
model=Dimple)
db_functions.transfer_table(
translate_dict=db_functions.data_processing_translations(),
filename=data_file,
model=DataProcessing)
soakdb_query = SoakdbFiles.objects.get(filename=data_file)
soakdb_query.status = 2
soakdb_query.save()
def run(self):
out_err_file = os.path.join(DirectoriesConfig().log_directory,
str(str(self.filename.split('/')[3]) +
'_' + str(self.filename.split('/')[4]) +
'_' + str(self.filename.split('/')[5]) + '_' +
str(misc_functions.get_mod_date(self.filename)) +
str(self.model).replace("<class '", '').replace("'>", '') + '.txt'))
print(out_err_file)
results = db_functions.soakdb_query(self.filename)
try:
print('Number of rows from file = ' + str(len(results)))
proteins = list(set([protein for protein in [protein['ProteinName'] for protein in results]]))
print('Unique targets in soakdb file: ' + str(proteins))
translations = {Lab: db_functions.lab_translations(),
Refinement: db_functions.refinement_translations(),
DataProcessing: db_functions.data_processing_translations(),
Dimple: db_functions.dimple_translations()}
translation = translations[self.model]
error_dict = {
'crystal': [],
'soakdb_field': [],
'model_field': [],
'soakdb_value': [],
'model_value': []
}
for row in results:
lab_object = self.model.objects.filter(crystal_name__crystal_name=row['CrystalName'],
crystal_name__visit__filename=str(self.filename),
crystal_name__compound__smiles=row['CompoundSMILES'])
if len(lab_object) > 1:
raise Exception('Multiple Crystals!')
if len(lab_object) == 0:
if self.model == Dimple and not row['DimplePathToPDB'] and not row['DimplePathToMTZ']:
pass
else:
raise Exception('No entry for ' + str(row['CrystalName'] + ' ' + row['DimplePathToPDB'] + ' '
+ row['DimplePathToMTZ']))
for key in translation.keys():
test_xchem_val = eval(str('lab_object[0].' + key))
soakdb_val = row[translation[key]]
if key == 'outcome':
pattern = re.compile('-?\d+')
try:
soakdb_val = int(pattern.findall(str(soakdb_val))[0])
except:
continue
if translation[key] == 'CrystalName':
test_xchem_val = lab_object[0].crystal_name.crystal_name
if translation[key] == 'DimpleReferencePDB' and soakdb_val:
test_xchem_val = lab_object[0].reference
if test_xchem_val is not None:
test_xchem_val = lab_object[0].reference.reference_pdb
if soakdb_val == '' or soakdb_val == 'None' or not soakdb_val:
continue
if isinstance(test_xchem_val, float):
if float(test_xchem_val) == float(soakdb_val):
continue
if isinstance(test_xchem_val, int):
if int(soakdb_val) == int(test_xchem_val):
continue
if test_xchem_val != soakdb_val:
if soakdb_val in [None, 'None', '', '-', 'n/a', 'null', 'pending', 'NULL', '#NAME?', '#NOM?',
'None\t',
'Analysis Pending', 'in-situ']:
continue
else:
error_dict['crystal'].append(str(lab_object[0].crystal_name.crystal_name))
error_dict['soakdb_field'].append(translation[key])
error_dict['model_field'].append(key)
error_dict['soakdb_value'].append(soakdb_val)
error_dict['model_value'].append(test_xchem_val)
if error_dict['crystal']:
pd.DataFrame.from_dict(error_dict).to_csv(out_err_file)
except IndexError:
if 'No item with that key' in traceback.format_exc():
pass
else:
with open(out_err_file, 'w') as f:
f.write(traceback.format_exc())
with open(out_err_file, 'a') as f:
f.write('\n' + str(key))
except AttributeError:
with open(out_err_file, 'w') as f:
f.write(traceback.format_exc())
with open(out_err_file, 'a') as f:
f.write('\n' + str(lab_object))
except:
with open(out_err_file, 'w') as f:
f.write(traceback.format_exc())
with self.output().open('w') as f:
f.write('')
def check_file_upload(filename, model, log_directory = DirectoriesConfig().log_directory):
"""Check if a soakdb file has been uploaded to a given django model
:param filename: filename to check, :class:`transfer_soakdb.CheckFileUpload` self.filename
:type filename: str
:param model: model to check if file had uploaded correctly to, :class:`transfer_soakdb.CheckFileUpload` self.model
:type model: str or model class, not sure tbh, I didn't write the code!
:return: Should check if file is uploaded correctly
:rtype: None
"""
out_err_file = os.path.join(log_directory,
str(str(filename.split('/')[3]) +
'_' + str(filename.split('/')[4]) +
'_' + str(filename.split('/')[5]) + '_' +
str(misc_functions.get_mod_date(filename)) +
str(model).replace("<class '", '').replace("'>", '') + '.txt'))
print(out_err_file)
results = db_functions.soakdb_query(filename)
try:
print(f"Number of rows from file = {len(results)}")
translations = {Lab: db_functions.lab_translations(),
Refinement: db_functions.refinement_translations(),
DataProcessing: db_functions.data_processing_translations(),
Dimple: db_functions.dimple_translations()}
translation = translations[model]
# different from what is in class...
error_dict = dict(crystal=[], soakdb_field=[], model_field=[], soakdb_value=[], model_value=[])
for row in results:
lab_object = model.objects.filter(crystal_name__crystal_name=row['CrystalName'],
crystal_name__visit__filename=str(filename),
crystal_name__compound__smiles=row['CompoundSMILES'])
if len(lab_object) > 1:
raise Exception('Multiple Crystals!')
if len(lab_object) == 0:
if model == Dimple and not row['DimplePathToPDB'] and not row['DimplePathToMTZ']:
pass
else:
raise Exception(
f"No entry for {row['CrystalName']}, {row['DimplePathToPDB']}, {row['DimplePathToMTZ']}")
for key in translation.keys():
test_xchem_val = eval(f"lab_objects[0].{key}")
soakdb_val = row[translation[key]]
if key == 'outcome':
pattern = re.compile('-?\d+')
try:
soakdb_val = int(pattern.findall(str(soakdb_val))[0])
except:
continue
if translation[key] == 'CrystalName':
test_xchem_val = lab_object[0].crystal_name.crystal_name
if translation[key] == 'DimpleReferencePDB' and soakdb_val:
test_xchem_val = lab_object[0].reference
if test_xchem_val is not None:
test_xchem_val = lab_object[0].reference.reference_pdb
if soakdb_val == '' or soakdb_val == 'None' or not soakdb_val:
continue
if isinstance(test_xchem_val, float):
if float(test_xchem_val) == float(soakdb_val):
continue
if isinstance(test_xchem_val, int):
if int(soakdb_val) == int(test_xchem_val):
continue
if test_xchem_val != soakdb_val:
if soakdb_val in [None, 'None', '', '-', 'n/a', 'null', 'pending', 'NULL', '#NAME?', '#NOM?',
'None\t',
'Analysis Pending', 'in-situ']:
continue
else:
error_dict['crystal'].append(str(lab_object[0].crystal_name.crystal_name))
error_dict['soakdb_field'].append(translation[key])
error_dict['model_field'].append(key)
error_dict['soakdb_value'].append(soakdb_val)
error_dict['model_value'].append(test_xchem_val)
if error_dict['crystal']:
pd.DataFrame.from_dict(error_dict).to_csv(out_err_file)
except IndexError:
if 'No item with that key' in traceback.format_exc():
pass
else:
with open(out_err_file, 'w') as f:
f.write(traceback.format_exc())
with open(out_err_file, 'a') as f:
f.write('\n' + str(key))
except AttributeError:
with open(out_err_file, 'w') as f:
f.write(traceback.format_exc())
with open(out_err_file, 'a') as f:
f.write('\n' + str(lab_object))
except:
with open(out_err_file, 'w') as f:
f.write(traceback.format_exc())