Update to wf_v7: sync in wf

gga_init.py

@@ -89,6 +89,7 @@ class DeploySpeciesStack(species_data.SpeciesData):
                     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)
+                    logging.info("Add picture %s" % self.picture_path)
                 else:
                     logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(self.picture_path))
             else:

utilities.py

@@ -142,13 +142,21 @@ def get_sp_picture(sp_dict_list):
     sp_picture_dict = {}
 
     for sp in sp_dict_list:
-        gspecies = get_gspecies_string_from_sp_dict(sp)
-        if gspecies not in sp_picture_dict.keys() or ( constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys() and
-                                                           sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ):
-            sp_picture_dict[gspecies] = ""
+
+        genus_species = get_gspecies_string_from_sp_dict(sp)
+
+        if genus_species not in sp_picture_dict.keys() \
+            or (genus_species not in sp_picture_dict.keys()
+                and sp_picture_dict[genus_species] != "") \
+            or (constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys()
+                 and sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ) :
+
             if constants.ORG_PARAM_DESC_PICTURE_PATH in sp[constants.ORG_PARAM_DESC].keys() and \
                     sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH] != "":
-                sp_picture_dict[gspecies] = sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH]
+                sp_picture_dict[genus_species] = sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH]
+            else:
+                sp_picture_dict[genus_species] = ""
+
     return sp_picture_dict
 
 def get_sp_jbrowse_links(org_list):