Merge pull request #162 from artic-network/background_curation

Background curation

Author: aineniamh

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)

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):