From ef94ba2cf4b383cdad0089b1c84d1d6235c03c1e Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Thu, 3 Jun 2021 11:14:36 +0200
Subject: [PATCH] fix empty strain/sex
---
species_data.py | 20 ++++++++++++++++----
1 file changed, 16 insertions(+), 4 deletions(-)
diff --git a/species_data.py b/species_data.py
index 308478e..0882881 100644
--- a/species_data.py
+++ b/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)
@@ -113,8 +123,10 @@ 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
--
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