From 2dce0f690f586058fc784678ef2d4661c47c045e Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Thu, 27 May 2021 11:39:08 +0200
Subject: [PATCH] remove useless performed_by param
---
constants.py | 1 -
examples/citrus_sinensis.yml | 1 -
speciesData.py | 5 +----
templates/organisms.yml.j2 | 1 -
4 files changed, 1 insertion(+), 7 deletions(-)
diff --git a/constants.py b/constants.py
index 0eada7f..ca78c4a 100644
--- a/constants.py
+++ b/constants.py
@@ -20,7 +20,6 @@ ORG_PARAM_DATA_BLASTP_PATH = "blastp_path"
ORG_PARAM_DATA_BLASTX_PATH = "blastx_path"
ORG_PARAM_DATA_GENOME_VERSION = "genome_version"
ORG_PARAM_DATA_OGS_VERSION = "ogs_version"
-ORG_PARAM_DATA_PERFORMED_BY = "performed_by"
ORG_PARAM_SERVICES = "services"
ORG_PARAM_SERVICES_BLAST = "blast"
ORG_PARAM_SERVICES_GO = "go"
diff --git a/examples/citrus_sinensis.yml b/examples/citrus_sinensis.yml
index 38087bb..7229c3b 100644
--- a/examples/citrus_sinensis.yml
+++ b/examples/citrus_sinensis.yml
@@ -31,7 +31,6 @@
genome_version: 1.0
# Same as genome version, but for the OGS analysis
ogs_version: 1.0
- performed_by:
services:
# List the optional services/resources to add
blast: 0 # "1" to add links to blast form, "some/url" to specify, multiple urls as "Name1=url1&Name2=url2", "0" to disable it. Default: "0"
diff --git a/speciesData.py b/speciesData.py
index 2c16840..c012a46 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -66,11 +66,10 @@ class SpeciesData:
self.genus = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_GENUS])
self.strain = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_STRAIN])
self.sex = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_SEX])
- self.common = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_COMMON_NAME])
+ self.common_name = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_COMMON_NAME])
self.date = datetime.today().strftime("%Y-%m-%d")
self.origin = parameters_dictionary_description[constants.ORG_PARAM_DESC_ORIGIN]
- self.performed = parameters_dictionary_data[constants.ORG_PARAM_DATA_PERFORMED_BY]
if parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_VERSION] == "":
self.genome_version = "1.0"
@@ -100,10 +99,8 @@ class SpeciesData:
self.genus_uppercase = self.genus[0].upper() + self.genus_lowercase[1:]
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"])
self.full_name_lowercase = self.full_name.lower()
- 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_lowercase, self.strain.lower(),
diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2
index 019fce0..2a127ad 100644
--- a/templates/organisms.yml.j2
+++ b/templates/organisms.yml.j2
@@ -21,7 +21,6 @@
{{ org_param_data_blastx_path }}: {{ org_param_data_blastx_path_value }}
{{ org_param_data_genome_version }}: {{ org_param_data_genome_version_value }}
{{ org_param_data_ogs_version }}: {{ org_param_data_ogs_version_value }}
- {{ org_param_data_performed_by }}: {{ org_param_data_performed_by_value }}
{{ org_param_services }}:
{{ org_param_services_blast }}: {{ org_param_services_blast_value }}
{{ org_param_services_go }}: {{ org_param_services_go_value }}
\ No newline at end of file
--
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