Rename methods

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 = {}

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".