--- a/env/lib/python3.7/site-packages/planemo/galaxy/workflows.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,127 +0,0 @@
-"""Utilities for Galaxy workflows."""
-import json
-import os
-from collections import namedtuple
-
-import yaml
-from bioblend.galaxy.client import Client
-from ephemeris import generate_tool_list_from_ga_workflow_files
-from ephemeris import shed_tools
-from gxformat2.converter import python_to_workflow
-from gxformat2.interface import BioBlendImporterGalaxyInterface
-from gxformat2.interface import ImporterGalaxyInterface
-
-from planemo.io import warn
-
-FAILED_REPOSITORIES_MESSAGE = "Failed to install one or more repositories."
-
-
-def load_shed_repos(runnable):
-    if runnable.type.name != "galaxy_workflow":
-        return []
-
-    path = runnable.path
-    if path.endswith(".ga"):
-        generate_tool_list_from_ga_workflow_files.generate_tool_list_from_workflow([path], "Tools from workflows", "tools.yml")
-        with open("tools.yml", "r") as f:
-            tools = yaml.safe_load(f)["tools"]
-
-    else:
-        # It'd be better to just infer this from the tool shed ID somehow than
-        # require explicit annotation like this... I think?
-        with open(path, "r") as f:
-            workflow = yaml.safe_load(f)
-
-        tools = workflow.get("tools", [])
-
-    return tools
-
-
-def install_shed_repos(runnable, admin_gi, ignore_dependency_problems):
-    tools_info = load_shed_repos(runnable)
-    if tools_info:
-        install_tool_manager = shed_tools.InstallRepositoryManager(admin_gi)
-        install_results = install_tool_manager.install_repositories(tools_info)
-        if install_results.errored_repositories:
-            if ignore_dependency_problems:
-                warn(FAILED_REPOSITORIES_MESSAGE)
-            else:
-                raise Exception(FAILED_REPOSITORIES_MESSAGE)
-
-
-def import_workflow(path, admin_gi, user_gi, from_path=False):
-    """Import a workflow path to specified Galaxy instance."""
-    if not from_path:
-        importer = BioBlendImporterGalaxyInterface(
-            admin_gi=admin_gi,
-            user_gi=user_gi
-        )
-        workflow = _raw_dict(path, importer)
-        return importer.import_workflow(workflow)
-    else:
-        # TODO: Update bioblend to allow from_path.
-        path = os.path.abspath(path)
-        payload = dict(
-            from_path=path
-        )
-        workflows_url = user_gi._make_url(user_gi.workflows)
-        workflow = Client._post(user_gi.workflows, payload, url=workflows_url)
-        return workflow
-
-
-def _raw_dict(path, importer=None):
-    if path.endswith(".ga"):
-        with open(path, "r") as f:
-            workflow = json.load(f)
-    else:
-        if importer is None:
-            importer = DummyImporterGalaxyInterface()
-
-        workflow_directory = os.path.dirname(path)
-        workflow_directory = os.path.abspath(workflow_directory)
-        with open(path, "r") as f:
-            workflow = yaml.safe_load(f)
-            workflow = python_to_workflow(workflow, importer, workflow_directory)
-
-    return workflow
-
-
-def find_tool_ids(path):
-    tool_ids = []
-    workflow = _raw_dict(path)
-    for (order_index, step) in workflow["steps"].items():
-        tool_id = step.get("tool_id")
-        tool_ids.append(tool_id)
-
-    return tool_ids
-
-
-WorkflowOutput = namedtuple("WorkflowOutput", ["order_index", "output_name", "label"])
-
-
-def describe_outputs(path):
-    """Return a list of :class:`WorkflowOutput` objects for target workflow."""
-    workflow = _raw_dict(path)
-    outputs = []
-    for (order_index, step) in workflow["steps"].items():
-        step_outputs = step.get("workflow_outputs", [])
-        for step_output in step_outputs:
-            output = WorkflowOutput(
-                int(order_index),
-                step_output["output_name"],
-                step_output["label"],
-            )
-            outputs.append(output)
-    return outputs
-
-
-class DummyImporterGalaxyInterface(ImporterGalaxyInterface):
-
-    def import_workflow(self, workflow, **kwds):
-        return None
-
-
-__all__ = (
-    "import_workflow",
-    "describe_outputs",
-)