From 978fc06c002800c339d005436eaeae62d47144a7 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Thu, 20 May 2021 12:23:31 +0200
Subject: [PATCH] remove useless diff for picture_path
---
gga_init.py | 10 +---------
templates/organisms.yml.j2 | 2 --
2 files changed, 1 insertion(+), 11 deletions(-)
diff --git a/gga_init.py b/gga_init.py
index d5fc63f..e630db1 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -126,19 +126,11 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# To do so we need both input file vars and config vars
# Create input file vars dict
- input_vars = {}
- if self.picture_path is not None:
- input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species,
+ 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": self.genus_species[0].upper() + self.genus_species[1:],
"blast": self.blast, "picture_path": self.picture_path}
- else:
- 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": self.genus_species[0].upper() + self.genus_species[1:],
- "blast": self.blast}
if (len(self.config.keys()) == 0):
logging.error("Empty config dictionary")
# Merge the two dicts
diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2
index 22e8c29..9a05ccf 100644
--- a/templates/organisms.yml.j2
+++ b/templates/organisms.yml.j2
@@ -6,9 +6,7 @@
{{ org_param_desc_strain }}: {{ org_param_desc_strain_value }}
{{ org_param_desc_common_name }}: {{ org_param_desc_common_name_value }}
{{ org_param_desc_origin }}: {{ org_param_desc_origin_value }}
- {% if org_param_desc_picture_path_value is defined %}
{{ org_param_desc_picture_path }}: {{ org_param_desc_picture_path_value }}
- {% endif %}
{% if org_param_desc_main_species_value is defined and org_param_desc_main_species_value is sameas true %}
{{ org_param_desc_main_species }}: yes
{% endif %}
--
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