From ec4a3d743ae0bba44c1ecf820f18b95f0baa9814 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Loraine=20Gu=C3=A9guen?=
<loraine-gueguen@users.noreply.github.com>
Date: Mon, 22 Feb 2021 23:15:46 +0100
Subject: [PATCH] Always connect to galaxy with localhost as hostname
---
run_workflow_phaeoexplorer.py | 14 ++++----------
1 file changed, 4 insertions(+), 10 deletions(-)
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 70f6387..6796816 100644
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -235,7 +235,7 @@ class RunWorkflow(speciesData.SpeciesData):
# In case of the Jbrowse workflow, we unfortunately have to manually edit the parameters instead of setting them
# as runtime values, using runtime parameters makes the tool throw an internal critical error ("replace not found" error)
if workflow_name == "Jbrowse":
- workflow_dict["steps"]["2"]["tool_state"] = workflow_dict["steps"]["2"]["tool_state"].replace("__MENU_URL__", "http://{hostname}:{port}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(hostname=self.config["hostname"], port=self.config["http_port"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}"))
+ workflow_dict["steps"]["2"]["tool_state"] = workflow_dict["steps"]["2"]["tool_state"].replace("__MENU_URL__", "http://localhost:{port}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(port=self.config["http_port"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}"))
workflow_dict["steps"]["3"]["tool_state"] = workflow_dict["steps"]["3"]["tool_state"].replace("__FULL_NAME__", self.full_name).replace("__UNIQUE_ID__", self.abbreviation)
# Import the workflow in galaxy as a dict
@@ -594,15 +594,9 @@ if __name__ == "__main__":
# Parse the config yaml file
run_workflow_for_current_organism.config = utilities.parse_config(args.config)
# Set the instance url attribute
- for env_variable, value in run_workflow_for_current_organism.config.items():
- if env_variable == "hostname":
- run_workflow_for_current_organism.instance_url = "http://{0}:8888/sp/{1}/galaxy/".format(
- value, run_workflow_for_current_organism.genus_species)
- break
- else:
- run_workflow_for_current_organism.instance_url = "http://localhost:8888/sp/{0}_{1}/galaxy/".format(
- run_workflow_for_current_organism.genus_lowercase,
- run_workflow_for_current_organism.species)
+ run_workflow_for_current_organism.instance_url = "http://localhost:8888/sp/{0}_{1}/galaxy/".format(
+ run_workflow_for_current_organism.genus_lowercase,
+ run_workflow_for_current_organism.species)
# If input workflow is Chado_load_Tripal_synchronize.ga
if "Chado_load_Tripal_synchronize" in str(workflow):
--
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