debug

gga_init.py

@@ -128,8 +128,8 @@ class DeploySpeciesStack(speciesData.SpeciesData):
 
         input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species,
                         "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name,
-                        "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species_lower, self.sex),
-                        "strain": self.strain, "sex": self.sex, "Genus_species": "{0} {1}".format(self.genus_uppercase, self.species_lower),
+                        "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species_lowercase, self.sex),
+                        "strain": self.strain, "sex": self.sex, "Genus_species": "{0} {1}".format(self.genus_uppercase, self.species_lowercase),
                         "blast": self.blast, "go": self.go, "picture_path": self.picture_path}
         if (len(self.config.keys()) == 0):
             logging.error("Empty config dictionary")

speciesData.py

@@ -94,9 +94,9 @@ class SpeciesData:
         self.go = self.set_service_attribute(constants.ORG_PARAM_SERVICES_GO, parameters_dictionary)
 
         self.genus_lowercase = self.genus.lower()
-        self.species_lower = self.species.lower()
+        self.species_lowercase = self.species.lower()
         self.genus_uppercase = self.genus[0].upper() + self.genus_lowercase[1:]
-        self.genus_species = "{0}_{1}".format(self.genus_lowercase, self.species_lower)
+        self.genus_species = "{0}_{1}".format(self.genus_lowercase, self.species_lowercase)
 
         self.chado_species_name = "{0} {1}".format(self.species, self.sex)
         self.full_name = ' '.join(utilities.filter_empty_not_empty_items([self.genus_uppercase, self.species, self.strain, self.sex])["not_empty"])
@@ -104,14 +104,14 @@ class SpeciesData:
         self.abbreviation = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase[0], self.species, self.strain, self.sex])["not_empty"])
 
         self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items(
-            [self.genus_lowercase, self.species_lower, self.strain.lower(),
+            [self.genus_lowercase, self.species_lowercase, self.strain.lower(),
              self.sex.lower()])["not_empty"])
 
         self.dataset_prefix = None
         if self.sex is not None or self.sex != "":
-            self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lower + "_" + self.sex[0].lower()
+            self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lowercase + "_" + self.sex[0].lower()
         else:
-            self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lower
+            self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lowercase
 
         # Bioblend/Chado IDs for an organism analyses/organisms/datasets/history/library
         self.org_id = None

utilities.py

@@ -183,7 +183,7 @@ def get_sp_picture(sp_dict_list):
             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]
-
+    print(sp_picture_dict)
     return sp_picture_dict
 
 def run_tool(instance, tool_id, history_id, tool_inputs):