--- a/env/lib/python3.7/site-packages/gxformat2/lint.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,180 +0,0 @@
-"""Workflow linting entry point - main script."""
-import argparse
-import os
-import sys
-
-from gxformat2._scripts import ensure_format2
-from gxformat2._yaml import ordered_load
-from gxformat2.linting import LintContext
-from gxformat2.markdown_parse import validate_galaxy_markdown
-
-EXIT_CODE_SUCCESS = 0
-EXIT_CODE_LINT_FAILED = 1
-EXIT_CODE_FORMAT_ERROR = 2
-EXIT_CODE_FILE_PARSE_FAILED = 3
-
-LINT_FAILED_NO_OUTPUTS = "Workflow contained no outputs"
-LINT_FAILED_OUTPUT_NO_LABEL = "Workflow contained output without a label"
-
-
-def ensure_key(lint_context, has_keys, key, has_class=None, has_value=None):
-    if key not in has_keys:
-        lint_context.error("expected to find key [{key}] but absent", key=key)
-        return None
-
-    value = has_keys[key]
-    return ensure_key_has_value(lint_context, has_keys, key, value, has_class=has_class, has_value=has_value)
-
-
-def ensure_key_if_present(lint_context, has_keys, key, default=None, has_class=None):
-    if key not in has_keys:
-        return default
-
-    value = has_keys[key]
-    return ensure_key_has_value(lint_context, has_keys, key, value, has_class=has_class, has_value=None)
-
-
-def ensure_key_has_value(lint_context, has_keys, key, value, has_class=None, has_value=None):
-    if has_class is not None and not isinstance(value, has_class):
-        lint_context.error("expected value [{value}] with key [{key}] to be of class {clazz}", key=key, value=value, clazz=has_class)
-    if has_value is not None and value != has_value:
-        lint_context.error("expected value [{value}] with key [{key}] to be {expected_value}", key=key, value=value, expected_value=has_value)
-    return value
-
-
-def _lint_step_errors(lint_context, step):
-    step_errors = step.get("errors")
-    if step_errors is not None:
-        lint_context.warn("tool step contains error indicated during Galaxy export - %s" % step_errors)
-
-
-def lint_ga(lint_context, workflow_dict, path=None):
-    """Lint a native/legacy style Galaxy workflow and populate the corresponding LintContext."""
-    ensure_key(lint_context, workflow_dict, "format-version", has_value="0.1")
-    ensure_key(lint_context, workflow_dict, "a_galaxy_workflow", has_value="true")
-
-    native_steps = ensure_key(lint_context, workflow_dict, "steps", has_class=dict) or {}
-
-    found_outputs = False
-    found_output_without_label = False
-    for order_index_str, step in native_steps.items():
-        if not order_index_str.isdigit():
-            lint_context.error("expected step_key to be integer not [{value}]", value=order_index_str)
-
-        workflow_outputs = ensure_key_if_present(lint_context, step, "workflow_outputs", default=[], has_class=list)
-        for workflow_output in workflow_outputs:
-            found_outputs = True
-
-            if not workflow_output.get("label"):
-                found_output_without_label = True
-
-        step_type = step.get("type")
-        if step_type == "subworkflow":
-            subworkflow = ensure_key(lint_context, step, "subworkflow", has_class=dict)
-            lint_ga(lint_context, subworkflow)
-
-        _lint_step_errors(lint_context, step)
-        _lint_tool_if_present(lint_context, step)
-
-    _validate_report(lint_context, workflow_dict)
-    if not found_outputs:
-        lint_context.warn(LINT_FAILED_NO_OUTPUTS)
-
-    if found_output_without_label:
-        lint_context.warn(LINT_FAILED_OUTPUT_NO_LABEL)
-
-    _lint_training(lint_context, workflow_dict)
-
-
-def lint_format2(lint_context, workflow_dict, path=None):
-    """Lint a Format 2 Galaxy workflow and populate the corresponding LintContext."""
-    from gxformat2.schema.v19_09 import load_document
-    from schema_salad.exceptions import SchemaSaladException
-    try:
-        load_document("file://" + os.path.normpath(path))
-    except SchemaSaladException as e:
-        lint_context.error("Validation failed " + str(e))
-
-    steps = ensure_key_if_present(lint_context, workflow_dict, 'steps', default={}, has_class=dict)
-    for key, step in steps.items():
-        _lint_step_errors(lint_context, step)
-        _lint_tool_if_present(lint_context, step)
-
-    _validate_report(lint_context, workflow_dict)
-    _lint_training(lint_context, workflow_dict)
-
-
-def _lint_tool_if_present(lint_context, step_dict):
-    tool_id = step_dict.get('tool_id')
-    if tool_id and 'testtoolshed' in tool_id:
-        lint_context.warn('Step references a tool from the test tool shed, this should be replaced with a production tool')
-
-
-def _validate_report(lint_context, workflow_dict):
-    report_dict = ensure_key_if_present(lint_context, workflow_dict, "report", default=None, has_class=dict)
-    if report_dict is not None:
-        markdown = ensure_key(lint_context, report_dict, "markdown", has_class=str)
-        if isinstance(markdown, str):
-            try:
-                validate_galaxy_markdown(markdown)
-            except ValueError as e:
-                lint_context.error("Report markdown validation failed [%s]" % e)
-
-
-def _lint_training(lint_context, workflow_dict):
-    if lint_context.training_topic is None:
-        return
-
-    if "tags" not in workflow_dict:
-        lint_context.warn("Missing tag(s).")
-    else:
-        tags = workflow_dict["tags"]
-        if lint_context.training_topic not in tags:
-            lint_context.warn("Missing expected training topic (%s) as workflow tag." % lint_context.training_topic)
-    # Move up into individual lints - all workflows should have docs.
-    format2_dict = ensure_format2(workflow_dict)
-    if "doc" not in format2_dict:
-        lint_context.warn("Missing workflow documentation (annotation or doc element)")
-    elif not format2_dict["doc"]:
-        lint_context.warn("Empty workflow documentation (annotation or doc element)")
-
-
-def main(argv=None):
-    """Script entry point for linting workflows."""
-    if argv is None:
-        argv = sys.argv
-    args = _parser().parse_args(argv[1:])
-    path = args.path
-    with open(path, "r") as f:
-        try:
-            workflow_dict = ordered_load(f)
-        except Exception:
-            return EXIT_CODE_FILE_PARSE_FAILED
-    workflow_class = workflow_dict.get("class")
-    lint_func = lint_format2 if workflow_class == "GalaxyWorkflow" else lint_ga
-    lint_context = LintContext(training_topic=args.training_topic)
-    lint_func(lint_context, workflow_dict, path=path)
-    lint_context.print_messages()
-    if lint_context.found_errors:
-        return EXIT_CODE_FORMAT_ERROR
-    elif lint_context.found_warns:
-        return EXIT_CODE_LINT_FAILED
-    else:
-        return EXIT_CODE_SUCCESS
-
-
-def _parser():
-    parser = argparse.ArgumentParser()
-    parser.add_argument("--training-topic",
-                        required=False,
-                        help='If this is a training workflow, specify a training topic.')
-    parser.add_argument('path', metavar='PATH', type=str,
-                        help='workflow path')
-    return parser
-
-
-if __name__ == "__main__":
-    sys.exit(main())
-
-
-__all__ = ('main', 'lint_format2', 'lint_ga')