from planemo.exit_codes import EXIT_CODE_UNKNOWN_FILE_TYPE, ExitCodeException
from planemo.galaxy.workflows import describe_outputs
from planemo.io import error
from planemo.test import check_output
TEST_SUFFIXES = ["-tests", "_tests", "-test", "_test"]
TEST_EXTENSIONS = [".yml", ".yaml", ".json"]
TEST_FILE_NOT_LIST_MESSAGE = ("Invalid test definition file [%s] - file must "
"contain a list of tests")
TEST_FIELD_MISSING_MESSAGE = ("Invalid test definition [test #%d in %s] -"
"defintion must field [%s].")
RunnableType = aenum.Enum(
"RunnableType",
'galaxy_tool galaxy_datamanager galaxy_workflow cwl_tool cwl_workflow directory'
)
@property
def _runnable_type_has_tools(runnable_type):
return runnable_type.name in [
"galaxy_tool", "galaxy_datamanager", "cwl_tool", "directory"
]
@property
def _runnable_type_is_single_artifact(runnable_type):
return runnable_type.name not in ["directory"]
"""Module defines abstractions for configuring Planemo."""
import os
import aenum
import click
import yaml
PLANEMO_CONFIG_ENV_PROP = "PLANEMO_GLOBAL_CONFIG_PATH"
DEFAULT_CONFIG = {}
VALUE_UNSET = object()
OptionSource = aenum.Enum("OptionSource", 'cli profile global_config default')
def _default_callback(
default,
use_global_config=False,
resolve_path=False,
):
def callback(ctx, param, value):
planemo_ctx = ctx.obj
param_name = param.name
if value is not None:
result = value
option_source = OptionSource.cli
else:
result, option_source = _find_default(
planemo_ctx,
param,