Fix site name

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

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"])

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 }}