Sync in wf

utilities.py

@@ -142,13 +142,35 @@ 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] = ""
-            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]
+
+        genus_species = get_gspecies_string_from_sp_dict(sp)
+        # logging.debug("picture path for {0} {1}: {2}".format(genus_species,
+        #                                                      sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_STRAIN],
+        #                                                      sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH]))
+
+        # no picture stored yet for this genus_species
+        if genus_species not in sp_picture_dict.keys() \
+            or (genus_species in sp_picture_dict.keys()
+                and sp_picture_dict[genus_species] == None):
+
+            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] != None \
+                and 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] = None
+
+        # overwrite stored picture if a picture exists for the main strain
+        if (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 )\
+            and (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] != None
+                and 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]
+
+    # logging.debug("picture dict: %s" % sp_picture_dict)
+
     return sp_picture_dict
 
 def get_sp_jbrowse_links(org_list):