Merge branch 'check_config_param' into 'dev'

Check required config param are not empty

See merge request !21

constants.py

@@ -54,3 +54,6 @@ DELETE_ORGANISMS_TOOL = "toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_
 
 HOST_DATA_DIR='src_data'
 CONTAINER_DATA_DIR_ROOT='/project_data'
+
+REQUIRED_PARAMETERS = [CONF_ALL_HOSTNAME, CONF_ALL_HTTP_PORT, CONF_GALAXY_DEFAULT_ADMIN_EMAIL, CONF_GALAXY_DEFAULT_ADMIN_USER, 
+					   CONF_GALAXY_DEFAULT_ADMIN_PASSWORD, CONF_TRIPAL_PASSWORD, CONF_GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN]

utilities.py

@@ -36,12 +36,16 @@ def parse_config(config_file):
     """
 
     config_dict = load_yaml(config_file)
-    if isinstance(config_dict, dict):
-        #logging.debug("Config dictionary: {0}".format(config_dict))
-        return config_dict
-    else:
-        logging.critical("Config yaml file is not a dictionary" % config_file)
+    if not isinstance(config_dict, dict):
+        logging.critical("Config yaml file is not a dictionary (%s)" % config_file)
         sys.exit()
+    else:
+        for required_parameter in constants.REQUIRED_PARAMETERS:
+            if not config_dict[required_parameter]:
+                logging.critical("{0} parameter improperly configured in config file {1}".format(required_parameter, config_file))
+                sys.exit()
+
+        return config_dict
 
 def parse_input(input_file):
     """