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_load_data.py

@@ -69,7 +69,8 @@ class LoadData(speciesData.SpeciesData):
         """
 
         logging.debug("Getting 'Homo sapiens' ID in chado database")
-        get_sapiens_id_job_output_dataset_id = utilities.run_tool_and_get_single_output_dataset_id(self.instance,
+        get_sapiens_id_job_output_dataset_id = utilities.run_tool_and_get_single_output_dataset_id(
+            self.instance,
             tool_id=constants.GET_ORGANISMS_TOOL, # If this version if not found, Galaxy will use the one that is found
             history_id=self.history_id,
             tool_inputs={"genus": "Homo", "species": "sapiens"})
@@ -80,6 +81,7 @@ class LoadData(speciesData.SpeciesData):
             get_sapiens_id_final_output = json.loads(get_sapiens_id_json_output)[0]
             sapiens_id = str(get_sapiens_id_final_output["organism_id"])  # needs to be str to be recognized by the chado tool
             utilities.run_tool(
+                self.instance,
                 tool_id=constants.DELETE_ORGANISMS_TOOL,
                 history_id=self.history_id,
                 tool_inputs={"organism": sapiens_id})