fixes

• Get the picture for each species: the picture of the main strain if exists, other strain if not
• Fix site name

gga_init.py

@@ -38,7 +38,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
 
     """
 
-    def make_directory_tree(self):
+    def make_directory_tree(self, picture_path):
         """
         Generate the directory tree for an organism
 
@@ -76,19 +76,19 @@ class DeploySpeciesStack(speciesData.SpeciesData):
             logging.debug("Using default banner for Tripal pages")
             self.config.pop(constants.CONF_TRIPAL_BANNER_PATH, None)
 
-        # Copy the organism picture for tripal if one was specified in the input species
-        if self.picture_path is not None:
-            if os.path.isfile(self.picture_path):
-                picture_path_basename = os.path.basename(self.picture_path)
+        # Copy the organism picture for tripal
+        if picture_path is not None:
+            if os.path.isfile(picture_path):
+                picture_path_basename = os.path.basename(picture_path)
                 picture_path_filename, picture_path_extension = os.path.splitext(picture_path_basename)
                 if picture_path_extension == ".png" or picture_path_extension == ".jpg":
                     picture_dest_name = "species%s" % picture_path_extension
                     picture_dest_path = os.path.join(self.species_dir, picture_dest_name)
-                    shutil.copy(self.picture_path, picture_dest_path)
+                    shutil.copy(picture_path, picture_dest_path)
                 else:
-                    logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(self.picture_path))
+                    logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(picture_path))
             else:
-                logging.error("Specified organism picture not found {0} for {1}".format(self.picture_path, self.genus_uppercase + " " + self.species))
+                logging.error("Specified organism picture not found {0} for {1}".format(picture_path, self.genus_uppercase + " " + self.species))
                 
         # Create nginx dirs and write/re-write nginx conf
         make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
@@ -402,6 +402,7 @@ if __name__ == "__main__":
         make_traefik_compose_files(config=config, main_dir=main_dir)
 
     unique_sp_dict_list = utilities.get_unique_species_dict_list(sp_dict_list=sp_dict_list)
+    sp_picture_dict = utilities.get_sp_picture(sp_dict_list=sp_dict_list)
 
     logging.info("Deploying stacks for organisms in input file %s" % args.input)
     for sp_dict in unique_sp_dict_list:
@@ -422,7 +423,8 @@ if __name__ == "__main__":
         logging.info("gga_init.py called for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
 
         # Make/update directory tree
-        deploy_stack_for_current_organism.make_directory_tree()
+        picture_path = sp_picture_dict[deploy_stack_for_current_organism.genus_species]
+        deploy_stack_for_current_organism.make_directory_tree(picture_path)
         logging.info("Successfully generated the directory tree for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
 
         # Make compose files