diff --git a/gga_init.py b/gga_init.py
index e630db1238f396cdd0e294c8d38d02058bb77561..6c2f7029bf9f7898deaf172f2303565406cfb9c3 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -38,7 +38,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
"""
- def make_directory_tree(self):
+ def make_directory_tree(self, picture_path):
"""
Generate the directory tree for an organism
@@ -76,19 +76,19 @@ class DeploySpeciesStack(speciesData.SpeciesData):
logging.debug("Using default banner for Tripal pages")
self.config.pop(constants.CONF_TRIPAL_BANNER_PATH, None)
- # Copy the organism picture for tripal if one was specified in the input species
- if self.picture_path is not None:
- if os.path.isfile(self.picture_path):
- picture_path_basename = os.path.basename(self.picture_path)
+ # Copy the organism picture for tripal
+ if picture_path is not None:
+ if os.path.isfile(picture_path):
+ picture_path_basename = os.path.basename(picture_path)
picture_path_filename, picture_path_extension = os.path.splitext(picture_path_basename)
if picture_path_extension == ".png" or picture_path_extension == ".jpg":
picture_dest_name = "species%s" % picture_path_extension
picture_dest_path = os.path.join(self.species_dir, picture_dest_name)
- shutil.copy(self.picture_path, picture_dest_path)
+ shutil.copy(picture_path, picture_dest_path)
else:
- logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(self.picture_path))
+ logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(picture_path))
else:
- logging.error("Specified organism picture not found {0} for {1}".format(self.picture_path, self.genus_uppercase + " " + self.species))
+ logging.error("Specified organism picture not found {0} for {1}".format(picture_path, self.genus_uppercase + " " + self.species))
# Create nginx dirs and write/re-write nginx conf
make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
@@ -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
@@ -402,6 +402,7 @@ if __name__ == "__main__":
make_traefik_compose_files(config=config, main_dir=main_dir)
unique_sp_dict_list = utilities.get_unique_species_dict_list(sp_dict_list=sp_dict_list)
+ sp_picture_dict = utilities.get_sp_picture(sp_dict_list=sp_dict_list)
logging.info("Deploying stacks for organisms in input file %s" % args.input)
for sp_dict in unique_sp_dict_list:
@@ -422,7 +423,8 @@ if __name__ == "__main__":
logging.info("gga_init.py called for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
# Make/update directory tree
- deploy_stack_for_current_organism.make_directory_tree()
+ picture_path = sp_picture_dict[deploy_stack_for_current_organism.genus_species]
+ deploy_stack_for_current_organism.make_directory_tree(picture_path)
logging.info("Successfully generated the directory tree for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
# Make compose files
diff --git a/speciesData.py b/speciesData.py
index 49ffed5416ede69e0f49fd295608ebd20cc735e7..34c817fd23e93710c086b1534d0207730fcfc83f 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 9b8c3f60f5f6532312a707f2d6d7c090fa6e0b02..97dbb0000bcf779a9f6667d5376d24f888c096be 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 }}
diff --git a/utilities.py b/utilities.py
index bae4e0241df54ecf4340fba978044f608b4ac992..f08c11b25b25d1e4a65eeb2685acc68f987c01f1 100755
--- a/utilities.py
+++ b/utilities.py
@@ -162,14 +162,28 @@ def get_unique_species_dict_list(sp_dict_list):
if gspecies not in unique_species_dict.keys() or ( constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys() and
sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ) :
unique_species_dict[gspecies] = sp
- else:
- continue
for k, v in unique_species_dict.items():
unique_species_list_of_dict.append(v)
return unique_species_list_of_dict
+def get_sp_picture(sp_dict_list):
+ """
+ Get the picture for each species: the picture of the main strain if exists, other strain if not
+ """
+
+ sp_picture_dict = {}
+
+ for sp in sp_dict_list:
+ gspecies = get_gspecies_string_from_sp_dict(sp)
+ if gspecies not in sp_picture_dict.keys() or ( constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys() and
+ sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ):
+ if sp[constants.ORG_PARAM_DESC_PICTURE_PATH] != "":
+ sp_picture_dict[gspecies] = sp[constants.ORG_PARAM_DESC_PICTURE_PATH]
+
+ return sp_picture_dict
+
def run_tool(instance, tool_id, history_id, tool_inputs):
output_dict = None
@@ -223,4 +237,4 @@ def create_org_param_dict_from_constants():
org_param_dict["org_param_services"] = constants.ORG_PARAM_SERVICES
org_param_dict["org_param_services_blast"] = constants.ORG_PARAM_SERVICES_BLAST
- return org_param_dict
\ No newline at end of file
+ return org_param_dict