From 8c1e24f2c20bc132de40bad009ee5701ac2decb8 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Thu, 20 May 2021 15:55:26 +0200
Subject: [PATCH] Fix site name
---
gga_init.py | 8 ++++----
speciesData.py | 22 ++++++++++++----------
templates/gspecies_compose.yml.j2 | 14 +++++++-------
3 files changed, 23 insertions(+), 21 deletions(-)
diff --git a/gga_init.py b/gga_init.py
index 5249cb3..6c2f702 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -127,10 +127,10 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# Create input file vars dict
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}
+ "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()),
+ "blast": self.blast, "picture_path": self.picture_path}
if (len(self.config.keys()) == 0):
logging.error("Empty config dictionary")
# Merge the two dicts
diff --git a/speciesData.py b/speciesData.py
index 49ffed5..34c817f 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -93,20 +93,25 @@ class SpeciesData:
else:
self.picture_path = None
- self.genus_lowercase = self.genus[0].lower() + self.genus[1:]
- self.genus_uppercase = self.genus[0].upper() + self.genus[1:]
+ self.genus_lowercase = self.genus.lower()
+ self.species_lower = 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.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.genus_species = "{0}_{1}".format(self.genus.lower(), self.species.lower())
+
+ self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items(
+ [self.genus_lowercase, self.species_lower(), 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_lower + "_" + self.sex[0].lower()
else:
- self.dataset_prefix = self.genus[0].lower() + "_" + self.species.lower()
+ self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lower
# Bioblend/Chado IDs for an organism analyses/organisms/datasets/history/library
self.org_id = None
@@ -131,6 +136,3 @@ class SpeciesData:
self.api_key = None # API key used to communicate with the galaxy instance. Cannot be used to do user-tied actions
self.datasets = dict()
self.config = None # Custom config used to set environment variables inside containers
- self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items(
- [self.genus_lowercase.lower(), self.species.lower(), self.strain.lower(),
- self.sex.lower()])["not_empty"])
diff --git a/templates/gspecies_compose.yml.j2 b/templates/gspecies_compose.yml.j2
index 9b8c3f6..97dbb00 100644
--- a/templates/gspecies_compose.yml.j2
+++ b/templates/gspecies_compose.yml.j2
@@ -38,18 +38,18 @@ services:
- ./docker_data/galaxy/:/export/:ro
- ./src_data/:/project_data/:ro
- ./src_data:/data:ro
- {% if 'tripal_banner_path' is defined %}
+ {% if 'tripal_banner_path' is defined %}
- ./banner.png:/var/www/html/banner.png:ro
- {% endif %}
+ {% endif %}
#- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/...
- {% if 'picture_path' is defined %}
- {% if 'png' in picture_path %}
+ {% if 'picture_path' is defined %}
+ {% if 'png' in picture_path %}
- ./species.png:/var/www/html/species.png:ro
- {% endif %}
- {% if 'jpg' in picture_path %}
+ {% endif %}
+ {% if 'jpg' in picture_path %}
- ./species.jpg:/var/www/html/species.jpg:ro
+ {% endif %}
{% endif %}
- {% endif %}
environment:
DB_HOST: tripal-db.{{ genus_species }}
BASE_URL_PATH: /sp/{{ genus_species }}
--
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