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Source code for galaxy.tool_util.cwl.representation

""" This module is responsible for converting between Galaxy's tool
input description and the CWL description for a job json. """

import json
import logging
import os
from enum import Enum
from typing import Any, NamedTuple, Optional

from galaxy.exceptions import RequestParameterInvalidException
from galaxy.util import safe_makedirs, string_as_bool
from .util import set_basename_and_derived_properties

log = logging.getLogger(__name__)

NOT_PRESENT = object()

NO_GALAXY_INPUT = object()

[docs]class INPUT_TYPE(str, Enum): DATA = "data" INTEGER = "integer" FLOAT = "float" TEXT = "text" BOOLEAN = "boolean" SELECT = "select" FIELD = "field" CONDITIONAL = "conditional" DATA_COLLECTON = "data_collection"
# There are two approaches to mapping CWL tool state to Galaxy tool state # one is to map CWL types to compound Galaxy tool parameters combinations # with conditionals and the other is to use a new Galaxy parameter type that # allows unions, optional specifications, etc.... The problem with the former # is that it doesn't work with the workflow parameters for instance and is # very complex on the backend. The problem with the latter is that the GUI # for this parameter type is undefined curently. USE_FIELD_TYPES = True # There are two approaches to mapping CWL workflow inputs to Galaxy workflow # steps. The first is to simply map everything to expressions and stick them into # files and use data inputs - the second is to use parameter_input steps with # fields types. We are dispatching on USE_FIELD_TYPES for now - to choose but # may diverge later? # There are open issues with each approach: # - Mapping everything to files makes the GUI harder to imagine but the backend # easier to manage in someways. USE_STEP_PARAMETERS = USE_FIELD_TYPES
[docs]class TypeRepresentation(NamedTuple): name: str galaxy_param_type: Any label: str collection_type: Optional[str] @property def uses_param(self): return self.galaxy_param_type is not NO_GALAXY_INPUT
TYPE_REPRESENTATIONS = [ TypeRepresentation("null", NO_GALAXY_INPUT, "no input", None), TypeRepresentation("integer", INPUT_TYPE.INTEGER, "an integer", None), TypeRepresentation("float", INPUT_TYPE.FLOAT, "a decimal number", None), TypeRepresentation("double", INPUT_TYPE.FLOAT, "a decimal number", None), TypeRepresentation("file", INPUT_TYPE.DATA, "a dataset", None), TypeRepresentation("directory", INPUT_TYPE.DATA, "a directory", None), TypeRepresentation("boolean", INPUT_TYPE.BOOLEAN, "a boolean", None), TypeRepresentation("text", INPUT_TYPE.TEXT, "a simple text field", None), TypeRepresentation("record", INPUT_TYPE.DATA_COLLECTON, "record as a dataset collection", "record"), TypeRepresentation("json", INPUT_TYPE.TEXT, "arbitrary JSON structure", None), TypeRepresentation("array", INPUT_TYPE.DATA_COLLECTON, "as a dataset list", "list"), TypeRepresentation("enum", INPUT_TYPE.TEXT, "enum value", None), # TODO: make this a select... TypeRepresentation("field", INPUT_TYPE.FIELD, "arbitrary JSON structure", None), ] FIELD_TYPE_REPRESENTATION = TYPE_REPRESENTATIONS[-1] if not USE_FIELD_TYPES: CWL_TYPE_TO_REPRESENTATIONS = { "Any": ["integer", "float", "file", "boolean", "text", "record", "json"], "org.w3id.cwl.salad.Any": ["integer", "float", "file", "boolean", "text", "record", "json"], "array": ["array"], "string": ["text"], "boolean": ["boolean"], "int": ["integer"], "float": ["float"], "File": ["file"], "org.w3id.cwl.cwl.File": ["file"], "Directory": ["directory"], "org.w3id.cwl.cwl.Directory": ["directory"], "null": ["null"], "record": ["record"], } else: CWL_TYPE_TO_REPRESENTATIONS = { "Any": ["field"], "org.w3id.cwl.salad.Any": ["field"], "array": ["array"], "string": ["text"], "boolean": ["boolean"], "int": ["integer"], "float": ["float"], "File": ["file"], "org.w3id.cwl.cwl.File": ["file"], "Directory": ["directory"], "org.w3id.cwl.cwl.Directory": ["directory"], "null": ["null"], "record": ["record"], "enum": ["enum"], "double": ["double"], }
[docs]def type_representation_from_name(type_representation_name): for type_representation in TYPE_REPRESENTATIONS: if type_representation.name == type_representation_name: return type_representation else: raise ValueError(f"No type representation for {type_representation_name}")
[docs]def type_descriptions_for_field_types(field_types): type_representation_names = set() for field_type in field_types: if isinstance(field_type, dict) and field_type.get("type"): field_type = field_type.get("type") try: type_representation_names_for_field_type = CWL_TYPE_TO_REPRESENTATIONS.get(field_type) except TypeError: raise Exception(f"Failed to convert field_type {field_type}") if type_representation_names_for_field_type is None: raise Exception(f"Failed to convert type {field_type}") type_representation_names.update(type_representation_names_for_field_type) type_representations = [] for type_representation in TYPE_REPRESENTATIONS: if type_representation.name in type_representation_names: type_representations.append(type_representation) return type_representations
[docs]def dataset_wrapper_to_file_json(inputs_dir, dataset_wrapper): if dataset_wrapper.ext == "expression.json": with open(dataset_wrapper.file_name) as f: return json.load(f) if dataset_wrapper.ext == "directory": return dataset_wrapper_to_directory_json(inputs_dir, dataset_wrapper) extra_files_path = dataset_wrapper.extra_files_path secondary_files_path = os.path.join(extra_files_path, "__secondary_files__") path = str(dataset_wrapper) raw_file_object = {"class": "File"} if os.path.exists(secondary_files_path): safe_makedirs(inputs_dir) name = os.path.basename(path) new_input_path = os.path.join(inputs_dir, name) os.symlink(path, new_input_path) secondary_files = [] for secondary_file_name in os.listdir(secondary_files_path): secondary_file_path = os.path.join(secondary_files_path, secondary_file_name) target = os.path.join(inputs_dir, secondary_file_name) log.info(f"linking [{secondary_file_path}] to [{target}]") os.symlink(secondary_file_path, target) is_dir = os.path.isdir(os.path.realpath(secondary_file_path)) secondary_files.append({"class": "File" if not is_dir else "Directory", "location": target}) raw_file_object["secondaryFiles"] = secondary_files path = new_input_path raw_file_object["location"] = path # Verify it isn't a NoneDataset if dataset_wrapper.unsanitized: raw_file_object["size"] = int(dataset_wrapper.get_size()) set_basename_and_derived_properties(raw_file_object, str(dataset_wrapper.created_from_basename or dataset_wrapper.name)) return raw_file_object
[docs]def dataset_wrapper_to_directory_json(inputs_dir, dataset_wrapper): assert dataset_wrapper.ext == "directory" # get directory name archive_name = str(dataset_wrapper.created_from_basename or dataset_wrapper.name) nameroot, nameext = os.path.splitext(archive_name) directory_name = nameroot # assume archive file name contains the directory name # get archive location try: archive_location = dataset_wrapper.unsanitized.file_name except Exception: archive_location = None directory_json = {"location": dataset_wrapper.extra_files_path, "class": "Directory", "name": directory_name, "archive_location": archive_location, "archive_nameext": nameext, "archive_nameroot": nameroot} return directory_json
[docs]def collection_wrapper_to_array(inputs_dir, wrapped_value): rval = [] for value in wrapped_value: rval.append(dataset_wrapper_to_file_json(inputs_dir, value)) return rval
[docs]def collection_wrapper_to_record(inputs_dir, wrapped_value): rval = {} for key, value in wrapped_value.items(): rval[key] = dataset_wrapper_to_file_json(inputs_dir, value) return rval
[docs]def to_cwl_job(tool, param_dict, local_working_directory): """ tool is Galaxy's representation of the tool and param_dict is the parameter dictionary with wrapped values. """ tool_proxy = tool._cwl_tool_proxy input_fields = tool_proxy.input_fields() inputs = tool.inputs input_json = {} inputs_dir = os.path.join(local_working_directory, "_inputs") def simple_value(input, param_dict_value, type_representation_name=None): type_representation = type_representation_from_name(type_representation_name) # Hmm... cwl_type isn't really the cwl type in every case, # like in the case of json for instance. if type_representation.galaxy_param_type == NO_GALAXY_INPUT: assert param_dict_value is None return None if type_representation.name == "file": dataset_wrapper = param_dict_value return dataset_wrapper_to_file_json(inputs_dir, dataset_wrapper) elif type_representation.name == "directory": dataset_wrapper = param_dict_value return dataset_wrapper_to_directory_json(inputs_dir, dataset_wrapper) elif type_representation.name == "integer": return int(str(param_dict_value)) elif type_representation.name == "long": return int(str(param_dict_value)) elif type_representation.name in ["float", "double"]: return float(str(param_dict_value)) elif type_representation.name == "boolean": return string_as_bool(param_dict_value) elif type_representation.name == "text": return str(param_dict_value) elif type_representation.name == "enum": return str(param_dict_value) elif type_representation.name == "json": raw_value = param_dict_value.value return json.loads(raw_value) elif type_representation.name == "field": if param_dict_value is None: return None if hasattr(param_dict_value, "value"): # Is InputValueWrapper rval = param_dict_value.value if isinstance(rval, dict) and "src" in rval and rval["src"] == "json": # needed for wf_step_connect_undeclared_param, so non-file defaults? return rval["value"] return rval elif not param_dict_value.is_collection: # Is DatasetFilenameWrapper return dataset_wrapper_to_file_json(inputs_dir, param_dict_value) else: # Is DatasetCollectionWrapper hdca_wrapper = param_dict_value if hdca_wrapper.collection_type == "list": # TODO: generalize to lists of lists and lists of non-files... return collection_wrapper_to_array(inputs_dir, hdca_wrapper) elif hdca_wrapper.collection_type.collection_type == "record": return collection_wrapper_to_record(inputs_dir, hdca_wrapper) elif type_representation.name == "array": # TODO: generalize to lists of lists and lists of non-files... return collection_wrapper_to_array(inputs_dir, param_dict_value) elif type_representation.name == "record": return collection_wrapper_to_record(inputs_dir, param_dict_value) else: return str(param_dict_value) for input_name, input in inputs.items(): if input.type == "repeat": only_input = next(iter(input.inputs.values())) array_value = [] for instance in param_dict[input_name]: array_value.append(simple_value(only_input, instance[input_name[:-len("_repeat")]])) input_json[input_name[:-len("_repeat")]] = array_value elif input.type == "conditional": assert input_name in param_dict, f"No value for {input_name} in {param_dict}" current_case = param_dict[input_name]["_cwl__type_"] if str(current_case) != "null": # str because it is a wrapped... case_index = input.get_current_case(current_case) case_input = input.cases[case_index].inputs["_cwl__value_"] case_value = param_dict[input_name]["_cwl__value_"] input_json[input_name] = simple_value(case_input, case_value, current_case) else: matched_field = None for field in input_fields: if field["name"] == input_name: matched_field = field field_type = field_to_field_type(matched_field) if isinstance(field_type, list): assert USE_FIELD_TYPES type_descriptions = [FIELD_TYPE_REPRESENTATION] else: type_descriptions = type_descriptions_for_field_types([field_type]) assert len(type_descriptions) == 1 type_description_name = type_descriptions[0].name input_json[input_name] = simple_value(input, param_dict[input_name], type_description_name) log.debug(f"Galaxy Tool State is CWL State is {input_json}") return input_json
[docs]def to_galaxy_parameters(tool, as_dict): """ Tool is Galaxy's representation of the tool and as_dict is a Galaxified representation of the input json (no paths, HDA references for instance). """ inputs = tool.inputs galaxy_request = {} def from_simple_value(input, param_dict_value, type_representation_name=None): if type_representation_name == "json": return json.dumps(param_dict_value) else: return param_dict_value for input_name, input in inputs.items(): as_dict_value = as_dict.get(input_name, NOT_PRESENT) galaxy_input_type = input.type if galaxy_input_type == "repeat": if input_name not in as_dict: continue only_input = next(iter(input.inputs.values())) for value in as_dict_value: key = f"{input_name}_repeat_0|{only_input.name}" galaxy_value = from_simple_value(only_input, value) galaxy_request[key] = galaxy_value elif galaxy_input_type == "conditional": case_strings = input.case_strings # TODO: less crazy handling of defaults... if (as_dict_value is NOT_PRESENT or as_dict_value is None) and "null" in case_strings: type_representation_name = "null" elif (as_dict_value is NOT_PRESENT or as_dict_value is None): raise RequestParameterInvalidException( "Cannot translate CWL datatype - value [{}] of type [{}] with case_strings [{}]. Non-null property must be set.".format( as_dict_value, type(as_dict_value), case_strings ) ) elif isinstance(as_dict_value, bool) and "boolean" in case_strings: type_representation_name = "boolean" elif isinstance(as_dict_value, int) and "integer" in case_strings: type_representation_name = "integer" elif isinstance(as_dict_value, int) and "long" in case_strings: type_representation_name = "long" elif isinstance(as_dict_value, (int, float)) and "float" in case_strings: type_representation_name = "float" elif isinstance(as_dict_value, (int, float)) and "double" in case_strings: type_representation_name = "double" elif isinstance(as_dict_value, str) and "string" in case_strings: type_representation_name = "string" elif isinstance(as_dict_value, dict) and "src" in as_dict_value and "id" in as_dict_value and "file" in case_strings: type_representation_name = "file" elif isinstance(as_dict_value, dict) and "src" in as_dict_value and "id" in as_dict_value and "directory" in case_strings: # TODO: can't disambiuate with above if both are available... type_representation_name = "directory" elif "field" in case_strings: type_representation_name = "field" elif "json" in case_strings and as_dict_value is not None: type_representation_name = "json" else: raise RequestParameterInvalidException( "Cannot translate CWL datatype - value [{}] of type [{}] with case_strings [{}].".format( as_dict_value, type(as_dict_value), case_strings ) ) galaxy_request[f"{input_name}|_cwl__type_"] = type_representation_name if type_representation_name != "null": current_case_index = input.get_current_case(type_representation_name) current_case_inputs = input.cases[current_case_index].inputs current_case_input = current_case_inputs["_cwl__value_"] galaxy_value = from_simple_value(current_case_input, as_dict_value, type_representation_name) galaxy_request[f"{input_name}|_cwl__value_"] = galaxy_value elif as_dict_value is NOT_PRESENT: continue else: galaxy_value = from_simple_value(input, as_dict_value) galaxy_request[input_name] = galaxy_value log.info(f"Converted galaxy_request is {galaxy_request}") return galaxy_request
[docs]def field_to_field_type(field): field_type = field["type"] if isinstance(field_type, dict): field_type = field_type["type"] if isinstance(field_type, list): field_type_length = len(field_type) if field_type_length == 0: raise Exception("Zero-length type list encountered, invalid CWL?") elif len(field_type) == 1: field_type = field_type[0] return field_type