diff --git a/civet/command.py b/civet/command.py index 34d3974..6aea819 100644 --- a/civet/command.py +++ b/civet/command.py @@ -274,7 +274,7 @@ def main(sysargs = sys.argv[1:]): # Define what's going to go in the report and sort global report options # stored under config = { "report_content": [1, 2, 3, 4], "reports": [1,2,3,4],[1,2]} - name_dict = report_arg_parsing.parse_global_report_options(args.report_content,args.report_preset, args.input_display_column, args.anonymise, args.input_date_column, args.background_date_column,args.date_format, args.background_location_column, config) + name_dict = report_arg_parsing.parse_global_report_options(args.report_title,args.report_content,args.report_preset, args.global_snipit,args.input_display_column, args.anonymise, args.input_date_column, args.background_date_column,args.date_format, args.background_location_column, config) report_arg_parsing.parse_optional_report_content(args.query_table_content,args.mutations, args.timeline_dates, args.timeline_group_column, args.colour_theme, args.colour_map, config) report_arg_parsing.parse_map_options(args.background_map_date_range, args.background_map_column, args.background_map_file, args.centroid_file, args.background_map_location, args.query_map_file, args.longitude_column, args.latitude_column, found_in_background_data, args.background_map_colours, args.background_map_other_colours,config) report_arg_parsing.parse_tree_options(args.tree_annotations,args.max_tree_size, config) diff --git a/civet/input_parsing/report_arg_parsing.py b/civet/input_parsing/report_arg_parsing.py index 9bf59d5..abed701 100644 --- a/civet/input_parsing/report_arg_parsing.py +++ b/civet/input_parsing/report_arg_parsing.py @@ -84,7 +84,7 @@ def qc_report_content(config): #then at some point we need to update the treefile with these display names using jclusterfunk -def parse_global_report_options(report_content,report_preset,report_column, anonymise,date_column, background_date_column,date_format,location_column, config): +def parse_global_report_options(report_title,report_content,report_preset,global_snipit,report_column, anonymise,date_column, background_date_column,date_format,location_column, config): """ parses the report group arguments --report-content (Default 1,2,3) @@ -94,8 +94,9 @@ def parse_global_report_options(report_content,report_preset,report_column, anon --background-date-column (default: sample_date if present, False if not) --timeline-dates """ - + # if command line arg, overwrite config value + misc.add_arg_to_config(KEY_REPORT_TITLE,report_title,config) misc.add_arg_to_config(KEY_REPORT_CONTENT,report_content,config) misc.add_arg_to_config(KEY_REPORT_PRESET,report_preset,config) if config[KEY_REPORT_PRESET]: @@ -107,6 +108,8 @@ def parse_global_report_options(report_content,report_preset,report_column, anon global_report_functions.parse_date_args(date_column, background_date_column, date_format, config) global_report_functions.parse_location(location_column, config) + misc.add_arg_to_config(KEY_GLOBAL_SNIPIT,global_snipit,config) + return name_output def parse_tree_options(tree_annotations,max_tree_size, config):