Release_2.0 next

General

• Move constants to file constants.py
• Set default config file in scripts.
• Update description of scripts in main.
• Update README.md

Input config file

• Change config root to dict and update parse_config().
• Change some config parameters name (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url), update example config file and compose templates.
• Remove apollo config variables (webapollo_user, webapollo_password) in config file and in gspecies compose template, because apollo service not deployed here.

Utilities.py

• Factorize parse_input() et parse_config().
• Get input yml keys from constants (update organisms.yml.j2 and add create_org_param_dict_from_constants())

gspecies_compose.yml

• set ENABLE_WIKI and ENABLE_APOLLO to 0 in gspecies compose template
• fix ENABLE_BLAST value in gspecies compose template

gga_get_data.py

• Remove useless variable datasets_to_get

gga_init.py

• replace subprocess.call() with subprocess.run(). Factorize run_command() and run_docker_stack_deploy()
• fix banner copy

gga_init.py

@@ -236,7 +236,6 @@ def make_traefik_compose_files(config, main_dir):
         # Return to main directory
         os.chdir(main_dir)
 
-
 def create_mounts(working_dir, main_dir):
         """
         Create the folders (volumes) required by a container (to see required volumes, check their compose file)
@@ -287,6 +286,12 @@ def create_mounts(working_dir, main_dir):
             logging.critical("Cannot access %s, exiting" % main_dir)
             sys.exit(exc)
 
+def run_command(command, working_dir):
+    subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=working_dir)
+
+def run_docker_stack_deploy(service, working_dir):
+    run_command(["docker", "stack", "deploy", "-c", "./docker-compose.yml", service], working_dir)
+
 def deploy_stacks(input_list, main_dir, deploy_traefik):
     """
     This function first deploys/redeploys the traefik stack, then deploys/redeploys the organism stack, then redeploys the traefik stack
@@ -296,7 +301,7 @@ def deploy_stacks(input_list, main_dir, deploy_traefik):
     """
 
     main_dir = os.path.abspath(main_dir)
-    os.chdir(main_dir)
+    traefik_dir = os.path.join(main_dir, "traefik")
 
     # Get species for which to deploy the stacks
     # Uses the get_unique_species_list method from utilities to deploy a stack only for the "species" level (i.e genus_species)
@@ -305,31 +310,22 @@ def deploy_stacks(input_list, main_dir, deploy_traefik):
     if deploy_traefik:
         # Create the swarm cluster if needed
         logging.info("Initializing docker swarm (adding node)")
-        subprocess.call(["docker", "swarm", "init"],
-                        stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=main_dir)
+        run_command(["docker", "swarm", "init"], main_dir)
         
         # Deploy traefik stack
         logging.info("Deploying traefik stack")
-        os.chdir("./traefik")
-        subprocess.call(["docker", "stack", "deploy", "-c", "./docker-compose.yml", "traefik"],
-                                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=".")
-        os.chdir(main_dir)
+        run_docker_stack_deploy("traefik", traefik_dir)
 
     # Deploy individual species stacks
     for sp in to_deploy_species_li:
-        os.chdir(sp)
+        sp_dir = os.path.join(main_dir, sp)
         logging.info("Deploying %s stack" % sp)
-        subprocess.call(["docker", "stack", "deploy", "-c", "./docker-compose.yml", "{0}_{1}".format(sp.split("_")[0], sp.split("_")[1])],
-                                           stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=".")
+        run_docker_stack_deploy("{0}_{1}".format(sp.split("_")[0], sp.split("_")[1]), sp_dir)
         logging.info("Deployed %s stack" % sp)
-        os.chdir(main_dir)
 
     # Update traefik stack
     logging.info("Updating traefik stack")
-    os.chdir("./traefik")
-    subprocess.call(["docker", "stack", "deploy", "-c", "./docker-compose.yml", "traefik"],
-                                            stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=".")
-    os.chdir(main_dir)
+    run_docker_stack_deploy("traefik", traefik_dir)
 
 
 if __name__ == "__main__":
@@ -400,7 +396,6 @@ if __name__ == "__main__":
 
         # Starting
         logging.info("gga_init.py called for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
-        logging.debug("Jbrowse url to %s %s %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species, deploy_stack_for_current_organism.sex, deploy_stack_for_current_organism.strain)
 
         # Make/update directory tree
         deploy_stack_for_current_organism.make_directory_tree()