--- a/env/lib/python3.7/site-packages/gxformat2/export.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,245 +0,0 @@
-"""Functionality for converting a standard Galaxy workflow into a format 2 workflow."""
-
-import json
-from collections import OrderedDict
-
-from ._labels import Labels
-from ._yaml import ordered_dump
-
-
-def _copy_common_properties(from_native_step, to_format2_step):
-    annotation = from_native_step.get("annotation", "")
-    if annotation:
-        to_format2_step["doc"] = annotation
-    position = from_native_step.get("position", None)
-    if position:
-        to_format2_step["position"] = position
-
-
-def from_galaxy_native(native_workflow_dict, tool_interface=None, json_wrapper=False):
-    """Convert native .ga workflow definition to a format2 workflow.
-
-    This is highly experimental and currently broken.
-    """
-    data = OrderedDict()
-    data['class'] = 'GalaxyWorkflow'
-    _copy_common_properties(native_workflow_dict, data)
-    if "name" in native_workflow_dict:
-        data["label"] = native_workflow_dict.pop("name")
-    for top_level_key in ['tags', 'uuid', 'report']:
-        value = native_workflow_dict.get(top_level_key)
-        if value:
-            data[top_level_key] = value
-
-    native_steps = native_workflow_dict.get("steps")
-
-    label_map = {}
-    all_labeled = True
-    for key, step in native_steps.items():
-        label = step.get("label")
-        if not label:
-            all_labeled = False
-        label_map[str(key)] = label
-
-    inputs = OrderedDict()
-    outputs = OrderedDict()
-    steps = []
-
-    labels = Labels()
-
-    # For each step, rebuild the form and encode the state
-    for step in native_steps.values():
-        for workflow_output in step.get("workflow_outputs", []):
-            source = _to_source(workflow_output, label_map, output_id=step["id"])
-            output_id = labels.ensure_new_output_label(workflow_output.get("label"))
-            outputs[output_id] = {"outputSource": source}
-
-        module_type = step.get("type")
-        if module_type in ['data_input', 'data_collection_input', 'parameter_input']:
-            step_id = step["label"]  # TODO: auto-label
-            input_dict = {}
-            if module_type == 'data_collection_input':
-                input_dict['type'] = 'collection'
-            elif module_type == 'data_input':
-                input_dict['type'] = 'data'
-            elif module_type == "parameter_input":
-                tool_state = _tool_state(step)
-                input_dict['type'] = tool_state.get("parameter_type")
-            # TODO: handle parameter_input types
-            _copy_common_properties(step, input_dict)
-            # If we are only copying property - use the CWL-style short-hand
-            if len(input_dict) == 1:
-                inputs[step_id] = input_dict["type"]
-            else:
-                inputs[step_id] = input_dict
-            continue
-
-        if module_type == "pause":
-            step_dict = OrderedDict()
-            optional_props = ['label']
-            _copy_common_properties(step, step_dict)
-            _copy_properties(step, step_dict, optional_props=optional_props)
-            _convert_input_connections(step, step_dict, label_map)
-            step_dict["type"] = "pause"
-            steps.append(step_dict)
-            continue
-
-        if module_type == 'subworkflow':
-            step_dict = OrderedDict()
-            optional_props = ['label']
-            _copy_common_properties(step, step_dict)
-            _copy_properties(step, step_dict, optional_props=optional_props)
-            _convert_input_connections(step, step_dict, label_map)
-            _convert_post_job_actions(step, step_dict)
-            subworkflow_native_dict = step["subworkflow"]
-            subworkflow = from_galaxy_native(subworkflow_native_dict, tool_interface=tool_interface, json_wrapper=False)
-            step_dict["run"] = subworkflow
-            steps.append(step_dict)
-            continue
-
-        if module_type != 'tool':
-            raise NotImplementedError("Unhandled module type %s" % module_type)
-
-        step_dict = OrderedDict()
-        optional_props = ['label', 'tool_shed_repository']
-        required_props = ['tool_id', 'tool_version']
-        _copy_properties(step, step_dict, optional_props, required_props)
-        _copy_common_properties(step, step_dict)
-
-        tool_state = _tool_state(step)
-        tool_state.pop("__page__", None)
-        tool_state.pop("__rerun_remap_job_id__", None)
-        step_dict['tool_state'] = tool_state
-
-        _convert_input_connections(step, step_dict, label_map)
-        _convert_post_job_actions(step, step_dict)
-        steps.append(step_dict)
-
-    data['inputs'] = inputs
-    data['outputs'] = outputs
-
-    if all_labeled:
-        steps_dict = OrderedDict()
-        for step in steps:
-            label = step.pop("label")
-            steps_dict[label] = step
-        data['steps'] = steps_dict
-    else:
-        data['steps'] = steps
-
-    if json_wrapper:
-        return {
-            "yaml_content": ordered_dump(data)
-        }
-
-    return data
-
-
-def _tool_state(step):
-    tool_state = json.loads(step['tool_state'])
-    return tool_state
-
-
-def _copy_properties(from_native_step, to_format2_step, optional_props=[], required_props=[]):
-    for prop in optional_props:
-        value = from_native_step.get(prop)
-        if value:
-            to_format2_step[prop] = value
-    for prop in required_props:
-        value = from_native_step.get(prop)
-        to_format2_step[prop] = value
-
-
-def _convert_input_connections(from_native_step, to_format2_step, label_map):
-    in_dict = from_native_step.get("in", {}).copy()
-    input_connections = from_native_step['input_connections']
-    for input_name, input_defs in input_connections.items():
-        if not isinstance(input_defs, list):
-            input_defs = [input_defs]
-        for input_def in input_defs:
-            source = _to_source(input_def, label_map)
-            if input_name == "__NO_INPUT_OUTPUT_NAME__":
-                input_name = "$step"
-                assert source.endswith("/__NO_INPUT_OUTPUT_NAME__")
-                source = source[:-len("/__NO_INPUT_OUTPUT_NAME__")]
-            in_dict[input_name] = {
-                "source": source
-            }
-    to_format2_step["in"] = in_dict
-
-
-def _convert_post_job_actions(from_native_step, to_format2_step):
-
-    def _ensure_output_def(key):
-        if "outputs" in to_format2_step:
-            to_format2_step["out"] = to_format2_step.pop("outputs")
-        elif "out" not in to_format2_step:
-            to_format2_step["out"] = {}
-
-        outputs_dict = to_format2_step["out"]
-        if key not in outputs_dict:
-            outputs_dict[key] = {}
-        return outputs_dict[key]
-
-    if "post_job_actions" in from_native_step:
-        post_job_actions = from_native_step["post_job_actions"].copy()
-        to_remove_keys = []
-
-        for post_job_action_key, post_job_action_value in post_job_actions.items():
-            action_type = post_job_action_value["action_type"]
-            output_name = post_job_action_value.get("output_name")
-            action_args = post_job_action_value.get("action_arguments", {})
-
-            handled = True
-            if action_type == "RenameDatasetAction":
-                output_dict = _ensure_output_def(output_name)
-                output_dict["rename"] = action_args["newname"]
-                handled = True
-            elif action_type == "HideDatasetAction":
-                output_dict = _ensure_output_def(output_name)
-                output_dict["hide"] = True
-                handled = True
-            elif action_type == "DeleteIntermediatesAction":
-                output_dict = _ensure_output_def(output_name)
-                output_dict["delete_intermediate_datasets"] = True
-            elif action_type == "ChangeDatatypeAction":
-                output_dict = _ensure_output_def(output_name)
-                output_dict['change_datatype'] = action_args
-                handled = True
-            elif action_type == "TagDatasetAction":
-                output_dict = _ensure_output_def(output_name)
-                output_dict["add_tags"] = action_args["tags"].split(",")
-            elif action_type == "RemoveTagDatasetAction":
-                output_dict = _ensure_output_def(output_name)
-                output_dict["remove_tags"] = action_args["tags"].split(",")
-            elif action_type == "ColumnSetAction":
-                output_dict = _ensure_output_def(output_name)
-                output_dict["set_columns"] = action_args
-            else:
-                handled = False
-
-            if handled:
-                to_remove_keys.append(post_job_action_key)
-
-        for to_remove in to_remove_keys:
-            del post_job_actions[to_remove]
-
-        if post_job_actions:
-            to_format2_step["post_job_actions"] = post_job_actions
-
-
-def _to_source(has_output_name, label_map, output_id=None):
-    output_id = output_id if output_id is not None else has_output_name['id']
-    output_id = str(output_id)
-    output_name = has_output_name['output_name']
-    output_label = label_map.get(output_id) or output_id
-    if output_name == "output":
-        source = output_label
-    else:
-        source = "%s/%s" % (output_label, output_name)
-    return source
-
-
-__all__ = (
-    'from_galaxy_native',
-)