Workflow v2

gga_load_data.py

@@ -87,37 +87,6 @@ class LoadData(speciesData.SpeciesData):
         get_organism_tool_version = get_organism_tool["version"]
         delete_organism_tool_version = delete_organism_tool["version"]
 
-        # if delete_organism_tool["version"] != "2.3.4+galaxy0":
-        #     toolshed_dict = delete_organism_tool["tool_shed_repository"]
-        #     logging.warning("Changeset for %s is not installed" % toolshed_dict["name"])
-        #     changeset_revision = "b1aa4f9d82fe"
-        #     name = toolshed_dict["name"]
-        #     owner = toolshed_dict["owner"]
-        #     toolshed = "https://" + toolshed_dict["tool_shed"]
-        #     logging.warning("Installing changeset for %s" % toolshed_dict["name"])
-
-        #     self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner, 
-        #                                                        changeset_revision=changeset_revision,
-        #                                                        install_tool_dependencies=True,
-        #                                                        install_repository_dependencies=False,
-        #                                                        install_resolver_dependencies=True)
-
-
-        # if get_organism_tool["version"] != "2.3.4+galaxy0":
-        #     toolshed_dict = get_organism_tool["tool_shed_repository"]
-        #     logging.warning("Changeset for %s is not installed" % toolshed_dict["name"])
-        #     changeset_revision = "831229e6cda2"
-        #     name = toolshed_dict["name"]
-        #     owner = toolshed_dict["owner"]
-        #     toolshed = "https://" + toolshed_dict["tool_shed"]
-        #     logging.warning("Installing changeset for %s" % toolshed_dict["name"])
-
-        #     self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner, 
-        #                                                        changeset_revision=changeset_revision,
-        #                                                        install_tool_dependencies=True,
-        #                                                        install_repository_dependencies=False,
-        #                                                        install_resolver_dependencies=True)
-
         logging.debug("Getting 'Homo sapiens' ID in instance's chado database")
         get_sapiens_id_job = self.instance.tools.run_tool(
             tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/%s" % get_organism_tool_version,