replace call() with run(). Factorize run_command() and...

replace call() with run(). Factorize run_command() and run_docker_stack_deploy(service, working_dir)

gga_init.py

@@ -113,6 +113,8 @@ class DeploySpeciesStack(speciesData.SpeciesData):
                       "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:]}
+        if (len(self.config.keys()) == 0):
+            logging.error("Empty config dictionary")
         # Merge the two dicts
         render_vars = {**self.config, **input_vars}
 
@@ -131,6 +133,8 @@ class DeploySpeciesStack(speciesData.SpeciesData):
                 logging.debug("Writing the galaxy_nginx.conf file for %s" % self.genus_species)
                 galaxy_nginx_conf_file.truncate(0)
                 galaxy_nginx_conf_file.write(galaxy_nginx_conf_output)
+        else:
+            logging.debug("galaxy_nginx.conf alredy exists")
 
         # Create the volumes (directory) of the species docker-compose file
         create_mounts(working_dir=".", main_dir=self.main_dir)
@@ -364,6 +368,8 @@ if __name__ == "__main__":
     else:
         config_file = os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])), constants.DEFAULT_CONFIG)
     config = utilities.parse_config(config_file)
+    if (len(config.keys()) == 0):
+        logging.error("Empty config dictionary")
 
     main_dir = None
     if not args.main_directory:

templates/gspecies_compose.yml.j2

@@ -53,10 +53,10 @@ services:
             SITE_NAME: "{{ Genus_species }}"
             ELASTICSEARCH_HOST: elasticsearch.{{ genus_species }}
             ENABLE_JBROWSE: /jbrowse/?data=data/{{ genus_species_strain_sex }}
-            ENABLE_APOLLO: {{ apollo }}
+            ENABLE_APOLLO: 0
             ENABLE_BLAST: {{ blast }}
-            ENABLE_DOWNLOAD: {{ download }}
-            ENABLE_WIKI: {{ wiki }}
+            ENABLE_DOWNLOAD: 1
+            ENABLE_WIKI: 0
             ENABLE_GO: 0
             ENABLE_ORTHOLOGY: 0
             ENABLE_ORTHOLOGY_LINKS: 0