From 451b855060ce8e5c20eb2f0770d535d92fa0b087 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Mon, 22 Mar 2021 10:38:23 +0100
Subject: [PATCH] localhost instance access
---
gga_load_data.py | 9 +--------
run_workflow_phaeoexplorer.py | 10 ++++++----
2 files changed, 7 insertions(+), 12 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index 2d83b83..6eac2bc 100644
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -125,8 +125,6 @@ class LoadData(speciesData.SpeciesData):
Create a "Project Data" library in galaxy, mirroring the "src_data" folder of the current organism
directory tree
- TODO - What about the interproscan, orthofinder and blast results ?
-
:return:
"""
@@ -327,10 +325,6 @@ if __name__ == "__main__":
type=str,
help="Where the stack containers will be located, defaults to working directory")
- parser.add_argument("--load-history",
- help="Load the found files into history, will ask for confirmation if a file with the same name is already found in an history",
- action="store_false")
-
args = parser.parse_args()
if args.verbose:
@@ -370,8 +364,7 @@ if __name__ == "__main__":
load_data_for_current_species.config = utilities.parse_config(args.config)
# Set the instance url attribute -- Does not work with localhost on scratch (ALB)
print(load_data_for_current_species.config["http_port"])
- load_data_for_current_species.instance_url = "http://scratchgmodv1:{0}/sp/{1}_{2}/galaxy/".format(
- load_data_for_current_species.config["http_port"],
+ load_data_for_current_species.instance_url = "http://localhost/sp/{1}_{2}/galaxy/".format(
load_data_for_current_species.genus_lowercase,
load_data_for_current_species.species)
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 4f73193..4125f52 100644
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -157,7 +157,8 @@ class RunWorkflow(speciesData.SpeciesData):
# (If it's not installed, the show_tool version returned will be a default version with the suffix "XXXX+0")
if show_tool["version"] != v["tool_version"]:
# If it doesn't match, proceed to install of the correct changeset revision
- logging.warning("Tool versions don't match for {0} (changeset installed: {1} | changeset required: {2}). Installing changeset revision {3}...".format(v["tool_shed_repository"]["name"], show_tool["changeset_revision"], v["tool_shed_repository"]["changeset_revision"], v["tool_shed_repository"]["changeset_revision"]))
+ print(show_tool)
+ # logging.warning("Tool versions don't match for {0} (changeset installed: {1} | changeset required: {2}). Installing changeset revision {3}...".format(v["tool_shed_repository"]["name"], show_tool["changeset_revision"], v["tool_shed_repository"]["changeset_revision"], v["tool_shed_repository"]["changeset_revision"]))
toolshed = "https://" + v["tool_shed_repository"]["tool_shed"]
name = v["tool_shed_repository"]["name"]
owner = v["tool_shed_repository"]["owner"]
@@ -488,7 +489,7 @@ 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__", "https://{host}:{port}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(host=self.config["host"], port=self.config["https_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__", "https://{hostname}:{port}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(hostname=self.config["hostname"], port=self.config["https_port"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}"))
# The UNIQUE_ID is specific to a combination genus_species_strain_sex so every combination should have its unique workflow
# in galaxy --> define a naming method for these workflows
workflow_dict["steps"]["3"]["tool_state"] = workflow_dict["steps"]["3"]["tool_state"].replace("__FULL_NAME__", self.full_name).replace("__UNIQUE_ID__", self.abbreviation)
@@ -846,8 +847,7 @@ if __name__ == "__main__":
# Parse the config yaml file
run_workflow_for_current_organism.config = utilities.parse_config(args.config)
# Set the instance url attribute --> TODO: the localhost rule in the docker-compose still doesn't work on scratchgmodv1
- run_workflow_for_current_organism.instance_url = "http://scratchgmodv1:{0}/sp/{1}_{2}/galaxy/".format(
- run_workflow_for_current_organism.config["http_port"],
+ run_workflow_for_current_organism.instance_url = "http://localhost/sp/{1}_{2}/galaxy/".format(
run_workflow_for_current_organism.genus_lowercase,
run_workflow_for_current_organism.species)
@@ -977,6 +977,7 @@ if __name__ == "__main__":
run_workflow_for_current_organism.connect_to_instance()
run_workflow_for_current_organism.set_get_history()
+ run_workflow_for_current_organism.install_changesets_revisions_from_workflow(workflow_path=workflow)
# run_workflow_for_current_organism.get_species_history_id()
# Get the attributes of the instance and project data files
@@ -1017,6 +1018,7 @@ if __name__ == "__main__":
run_workflow_for_current_organism.connect_to_instance()
run_workflow_for_current_organism.set_get_history()
+ run_workflow_for_current_organism.install_changesets_revisions_from_workflow(workflow_path=workflow)
# run_workflow_for_current_organism.get_species_history_id()
# Get the attributes of the instance and project data files
--
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