fix empty strain/sex

species_data.py

@@ -70,7 +70,11 @@ class SpeciesData:
         self.species = clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_SPECIES])
         self.genus = clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_GENUS])
         self.strain = clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_STRAIN])
+        if self.strain is None:
+            self.strain = ""
         self.sex = clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_SEX])
+        if self.sex is None:
+            self.sex = ""
         self.common_name = clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_COMMON_NAME])
 
         self.date = datetime.today().strftime("%Y-%m-%d")
@@ -102,8 +106,14 @@ class SpeciesData:
 
         self.genus_lowercase = self.genus.lower()
         self.species_lowercase = self.species.lower()
-        self.strain_lowercase = self.strain.lower()
-        self.sex_lowercase = self.sex.lower()
+        try:
+            self.strain_lowercase = self.strain.lower()
+        except AttributeError as exc:
+            self.strain_lowercase = None
+        try:
+            self.sex_lowercase = self.sex.lower()
+        except AttributeError as exc:
+            self.sex_lowercase = None
 
         self.genus_uppercase = self.genus[0].upper() + self.genus_lowercase[1:]
         self.genus_species = "{0}_{1}".format(self.genus_lowercase, self.species_lowercase)
@@ -113,10 +123,15 @@ class SpeciesData:
         self.full_name_lowercase = self.full_name.lower()
 
         self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items(
-            [self.genus_lowercase, self.species_lowercase, self.strain.lower(),
-             self.sex.lower()])["not_empty"])
+            [self.genus_lowercase,
+             self.species_lowercase,
+             self.strain_lowercase,
+             self.sex_lowercase])["not_empty"])
 
         self.dataset_prefix = self.strain_sex
+        # If both strain and sex are empty attributes, change the dataset prefix to nothing instead of "_"
+        if self.dataset_prefix == "_":
+            self.dataset_prefix = ""
 
         self.genome_filename = "{0}_v{1}.fasta".format(self.dataset_prefix, self.genome_version)
         self.gff_filename = "{0}_OGS{1}_{2}.gff".format(self.dataset_prefix, self.ogs_version, constants.DATA_DATE.replace("-",""))