def load_sql_settings():
global config
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# Get SQL settings
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
if is_sql_connection_defined():
script_dir = os.path.dirname(__file__)
rel_path = "preferences/sql_connection.cnf"
abs_file_path = os.path.join(script_dir, rel_path)
with open(abs_file_path, 'r') as document:
config = {}
for line in document:
line = line.split()
if not line:
continue
try:
config[line[0]] = line[1:][0]
except:
config[line[0]] = ''
if 'user' not in list(config):
config['user'] = ''
config['password'] = ''
else:
config = {
'host': 'localhost',
'dbname': 'dvh',
'port': '5432',
'user': '',
'password': ''
}
def test_import_sql_cnx_definitions():
if not is_import_settings_defined() and not is_sql_connection_defined():
print("ERROR: Import and SQL settings are not yet defined.",
"Please run:\n",
" $ dvh settings_simple",
sep='')
elif not is_import_settings_defined():
print("ERROR: Import settings are not yet defined.",
"Please run:\n",
" $ dvh settings_simple --dir",
sep='')
elif not is_sql_connection_defined():
print("ERROR: Invalid or empty SQL settings.",
"Please run:\n",
" $ dvh settings_simple --sql",
sep='')
else:
return True
return False
def load_sql_settings():
global config
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# Get SQL settings
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
if is_sql_connection_defined():
config = parse_settings_file(get_settings('sql'))
if 'user' not in list(config):
config['user'] = ''
config['password'] = ''
if 'password' not in list(config):
config['password'] = ''
else:
config = {'host': 'localhost',
'dbname': 'dvh',
'port': '5432',
'user': '',
'password': ''}
from __future__ import print_function
from dicom_to_sql import dicom_to_sql
from utilities import Temp_DICOM_FileSet
from sql_connector import DVH_SQL
from analysis_tools import DVH
from utilities import is_import_settings_defined, is_sql_connection_defined,\
write_import_settings, write_sql_connection_settings, validate_import_settings, validate_sql_connection
import os
from getpass import getpass
import argparse
from subprocess import call
script_dir = os.path.dirname(__file__)
if is_sql_connection_defined():
try:
DVH_SQL().initialize_database()
except:
print("Warning: could not initialize SQL database")
def settings(**kwargs):
if not kwargs:
set_import_settings()
set_sql_connection_parameters()
else:
if 'dir' in kwargs and kwargs['dir']:
set_import_settings()
if 'sql' in kwargs and kwargs['sql']:
set_sql_connection_parameters()
def test_dvh_code():
if not is_import_settings_defined() and not is_sql_connection_defined():
print("ERROR: Import and SQL settings are not yet defined.",
"Please run:\n",
" $ dvh settings_simple",
sep='')
elif not is_import_settings_defined():
print("ERROR: Import settings are not yet defined.",
"Please run:\n",
" $ dvh settings_simple --dir",
sep='')
elif not is_sql_connection_defined():
print("ERROR: Invalid or empty SQL settings.",
"Please run:\n",
" $ dvh settings_simple --sql",
sep='')
else:
is_import_valid = validate_import_settings()
is_sql_connection_valid = validate_sql_connection()
if not is_import_valid and not is_sql_connection_valid:
print(
"ERROR: Create the directories listed above or input valid directories.\n",
"ERROR: Cannot connect to SQL.\n",
"Please run:\n $ dvh settings",
sep='')
elif not is_import_valid:
print(
"ERROR: Create the directories listed above or input valid directories by running:\n",
" $ dvh settings --dir",
sep='')
elif not is_sql_connection_valid:
print(
"ERROR: Cannot connect to SQL.\n",
"Verify database is active and/or update SQL connection information with:\n",
" $ dvh settings --sql",
sep='')
else:
print("Importing test files")
dicom_to_sql(start_path="test_files/",
organize_files=False,
move_files=False,
force_update=False)
print("Reading data from SQL DB with analysis_tools.py")
test = DVH()
print(
"Reading dicom information from test files with utilities.py (for plan review module)"
)
test_files = Temp_DICOM_FileSet(start_path="test_files/")
print("Deleting test data from SQL database")
for i in range(0, test_files.count):
cond_str = "mrn = '" + test_files.mrn[i]
cond_str += "' and study_instance_uid = '" + test_files.study_instance_uid[
i] + "'"
DVH_SQL().delete_rows(cond_str)
print("Tests successful!")