From 9ac2c7dd86c4e19bd4a4e0a3e160680d3f78918c Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Thu, 20 May 2021 22:25:02 +0200
Subject: [PATCH] debug
---
gga_init.py | 4 ++--
speciesData.py | 10 +++++-----
utilities.py | 2 +-
3 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/gga_init.py b/gga_init.py
index 5eb6f24..e91ea41 100755
--- a/gga_init.py
+++ b/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")
diff --git a/speciesData.py b/speciesData.py
index b0d6190..4826663 100755
--- a/speciesData.py
+++ b/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
diff --git a/utilities.py b/utilities.py
index 18d2623..68a4513 100755
--- a/utilities.py
+++ b/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):
--
GitLab