From 6c86b6f97fdba6178e46fa849210d7a4c69260f3 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 30 May 2021 19:45:30 +0200
Subject: [PATCH] Rename methods
---
gga_run_workflow_phaeo_jbrowse.py | 8 ++++----
utilities_bioblend.py | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/gga_run_workflow_phaeo_jbrowse.py b/gga_run_workflow_phaeo_jbrowse.py
index 89a0718..96f141e 100644
--- a/gga_run_workflow_phaeo_jbrowse.py
+++ b/gga_run_workflow_phaeo_jbrowse.py
@@ -82,7 +82,7 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
self.transcripts_hda_id = None
self.proteins_hda_id = None
- def install_changesets_revisions_for_individual_tools(self):
+ def install_individual_tools(self):
"""
This function is used to verify that installed tools called outside workflows have the correct versions and changesets
If it finds versions don't match, will install the correct version + changeset in the instance
@@ -273,7 +273,7 @@ def prepare_history_and_get_wf_param(sp_dict_list, main_dir, config):
run_workflow_for_current_organism.set_galaxy_instance(config)
run_workflow_for_current_organism.set_history()
- run_workflow_for_current_organism.install_changesets_revisions_for_individual_tools()
+ run_workflow_for_current_organism.install_individual_tools()
run_workflow_for_current_organism.import_datasets_into_history()
analyses_dict_list = run_workflow_for_current_organism.get_analyses()
@@ -391,7 +391,7 @@ if __name__ == "__main__":
workflow_path = os.path.join(os.path.abspath(script_dir), constants_phaeo.WORKFLOWS_PATH, constants_phaeo.WF_LOAD_GFF_JB_1_ORG_FILE)
# Check if the versions of tools specified in the workflow are installed in galaxy
- utilities_bioblend.install_changesets_revisions_from_workflow(workflow_path=workflow_path, instance=org_wf_param.instance)
+ utilities_bioblend.install_workflow_tools(workflow_path=workflow_path, instance=org_wf_param.instance)
# Set the workflow parameters (individual tools runtime parameters in the workflow)
workflow_parameters = {}
@@ -484,7 +484,7 @@ if __name__ == "__main__":
workflow_path = os.path.join(os.path.abspath(script_dir), constants_phaeo.WORKFLOWS_PATH, constants_phaeo.WF_LOAD_GFF_JB_2_ORG_FILE)
# Check if the versions of tools specified in the workflow are installed in galaxy
- utilities_bioblend.install_changesets_revisions_from_workflow(workflow_path=workflow_path, instance=sp_wf_param_org1.instance)
+ utilities_bioblend.install_workflow_tools(workflow_path=workflow_path, instance=sp_wf_param_org1.instance)
# Set the workflow parameters (individual tools runtime parameters in the workflow)
workflow_parameters = {}
diff --git a/utilities_bioblend.py b/utilities_bioblend.py
index dc19d0e..3cfcc48 100644
--- a/utilities_bioblend.py
+++ b/utilities_bioblend.py
@@ -139,7 +139,7 @@ def install_repository_revision(instance, tool_id, version, changeset_revision):
install_repository_dependencies=False,
install_resolver_dependencies=True)
-def install_changesets_revisions_from_workflow(instance, workflow_path):
+def install_workflow_tools(instance, workflow_path):
"""
Read a .ga file to extract the information about the different tools called.
Check if every tool is installed via a "show_tool".
--
GitLab