Keep species with best assembly in get_uniq_species_dict_list() (will be main jbrowse url).

gga_init.py

@@ -393,6 +393,7 @@ if __name__ == "__main__":
 
         # Starting
         logging.info("gga_init.py called for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
+        logging.debug("Jbrowse url to %s %s %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species, deploy_stack_for_current_organism.sex, deploy_stack_for_current_organism.strain)
 
         # Make/update directory tree
         deploy_stack_for_current_organism.make_directory_tree()

utilities.py

@@ -123,6 +123,16 @@ def get_species_history_id(instance, full_name):
 
     return [history_id, show_history]
 
+def get_gspecies_string_from_sp_dict(sp_dict):
+
+    gspecies = ""
+    for k, v in sp_dict.items():
+        for k2, v2 in v.items():
+            if k2 == "genus":
+                gspecies = gspecies.lower() + v2
+            elif k2 == "species":
+                gspecies = gspecies.lower() + "_" + v2
+    return gspecies
 
 def get_unique_species_str_list(sp_dict_list):
     """
@@ -165,7 +175,7 @@ def get_unique_species_dict_list(sp_dict_list):
     unique_species_genus_species = get_unique_species_str_list(sp_dict_list=sp_dict_list)
 
     for sp in sp_dict_list:
-        for gspecies in unique_species_genus_species:
+        gspecies = get_gspecies_string_from_sp_dict(sp)
         if gspecies not in unique_species_dict.keys() or sp["description"]["main_species"] == "yes" :
             unique_species_dict[gspecies] = sp
         else: