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Source code for galaxy.workflow.refactor.execute
import logging
from typing import (
Any,
Dict,
)
from galaxy.exceptions import RequestParameterInvalidException
from galaxy.tools.parameters import visit_input_values
from galaxy.tools.parameters.basic import (
ConnectedValue,
contains_workflow_parameter,
runtime_to_json,
)
from .schema import (
AddInputAction,
AddStepAction,
ConnectAction,
DisconnectAction,
ExtractInputAction,
ExtractUntypedParameter,
FileDefaultsAction,
FillStepDefaultsAction,
InputReferenceByOrderIndex,
OutputReferenceByOrderIndex,
RefactorActionExecution,
RefactorActionExecutionMessage,
RefactorActionExecutionMessageTypeEnum,
RefactorActions,
RemoveUnlabeledWorkflowOutputs,
step_reference_union,
StepReferenceByLabel,
UpdateAnnotationAction,
UpdateCreatorAction,
UpdateLicenseAction,
UpdateNameAction,
UpdateOutputLabelAction,
UpdateReportAction,
UpdateStepLabelAction,
UpdateStepPositionAction,
UpgradeAllStepsAction,
UpgradeSubworkflowAction,
UpgradeToolAction,
)
from ..modules import (
InputParameterModule,
NO_REPLACEMENT,
)
log = logging.getLogger(__name__)
[docs]class WorkflowRefactorExecutor:
[docs] def __init__(self, raw_workflow_description, workflow, module_injector):
# we mostly use the ga representation, but there may be cases where the
# models/modules of existing workflow are more usable.
self.raw_workflow_description = raw_workflow_description
self.workflow = workflow
self.module_injector = module_injector
self.module_injector.inject_all(workflow, ignore_tool_missing_exception=True)
[docs] def refactor(self, refactor_request: RefactorActions):
action_executions = []
for action in refactor_request.actions:
# TODO: we need to regenerate a detached workflow from as_dict after
# after each iteration here. Otherwise one set of changes might render
# the workflow state out of sync. It is fine if you're just executing one
# action at a time or just performing actions that use raw_workflow_description.
action_type = action.action_type
refactor_method_name = f"_apply_{action_type}"
refactor_method = getattr(self, refactor_method_name, None)
if refactor_method is None:
raise RequestParameterInvalidException(f"Unknown workflow editing action encountered [{action_type}]")
execution = RefactorActionExecution(
action=action.dict(),
messages=[],
)
refactor_method(action, execution)
action_executions.append(execution)
return action_executions
def _apply_update_step_label(self, action: UpdateStepLabelAction, execution: RefactorActionExecution):
step = self._find_step_for_action(action)
step["label"] = action.label
def _apply_update_step_position(self, action: UpdateStepPositionAction, execution: RefactorActionExecution):
step = self._find_step_for_action(action)
position_update = action.position_shift.to_dict()
step["position"]["left"] = step["position"].get("left", 0) + position_update["left"]
step["position"]["top"] = step["position"].get("top", 0) + position_update["top"]
def _apply_update_output_label(self, action: UpdateOutputLabelAction, execution: RefactorActionExecution):
output_reference = action.output
output_step_dict = self._find_step(output_reference)
output_name = output_reference.output_name
for workflow_output_def in output_step_dict.get("workflow_outputs", []):
if workflow_output_def["output_name"] == output_name:
workflow_output_def["label"] = action.output_label
def _apply_update_name(self, action: UpdateNameAction, execution: RefactorActionExecution):
self._as_dict["name"] = action.name
def _apply_update_annotation(self, action: UpdateAnnotationAction, execution: RefactorActionExecution):
self._as_dict["annotation"] = action.annotation
def _apply_update_license(self, action: UpdateLicenseAction, execution: RefactorActionExecution):
self._as_dict["license"] = action.license
def _apply_update_creator(self, action: UpdateCreatorAction, execution: RefactorActionExecution):
self._as_dict["creator"] = action.creator
def _apply_update_report(self, action: UpdateReportAction, execution: RefactorActionExecution):
self._as_dict["report"] = {"markdown": action.report.markdown}
def _apply_add_step(self, action: AddStepAction, execution: RefactorActionExecution):
steps = self._as_dict["steps"]
order_index = len(steps)
step_dict = {
"order_index": order_index,
"id": "new_%d" % order_index,
"type": action.type,
}
if action.tool_state:
step_dict["tool_state"] = action.tool_state
if action.label:
step_dict["label"] = action.label
if action.position:
step_dict["position"] = action.position.to_dict()
steps[order_index] = step_dict
def _apply_add_input(self, action: AddInputAction, execution: RefactorActionExecution):
input_type = action.type
module_type = None
tool_state: Dict[str, Any] = {}
if input_type in ["data", "dataset"]:
module_type = "data_input"
elif input_type in ["data_collection", "dataset_collection"]:
module_type = "data_collection_input"
tool_state["collection_type"] = action.collection_type
else:
if input_type not in InputParameterModule.POSSIBLE_PARAMETER_TYPES:
raise RequestParameterInvalidException(f"Invalid input type {input_type} encountered")
module_type = "parameter_input"
tool_state["parameter_type"] = input_type
for action_key in ["restrictions", "suggestions", "optional", "default"]:
value = getattr(action, action_key, None)
if value is not None:
tool_state[action_key] = value
if action.restrict_on_connections is not None:
tool_state["restrictOnConnections"] = action.restrict_on_connections
add_step_kwds = {}
if action.label:
add_step_kwds["label"] = action.label
add_step_action = AddStepAction(
action_type="add_step", type=module_type, tool_state=tool_state, position=action.position, **add_step_kwds
)
self._apply_add_step(add_step_action, execution)
def _apply_disconnect(self, action: DisconnectAction, execution: RefactorActionExecution):
input_step_dict, input_name, output_step_dict, output_name = self._connection(action)
output_order_index = output_step_dict["id"] # wish this was order_index...
# default name is name used for input's output terminal - following
# format2 convention of allowing this be absent for clean references
# to workflow inputs.
all_input_connections = input_step_dict.get("input_connections")
self.normalize_input_connections_to_list(all_input_connections, input_name)
input_connections = all_input_connections[input_name]
# multiple outputs attached to this inputs, just detach
# that specific one.
delete_index = None
for connection_index, output in enumerate(input_connections):
if output["id"] == output_order_index and output["output_name"] == output_name:
delete_index = connection_index
break
if delete_index is None:
raise RequestParameterInvalidException("Failed to locate connection to disconnect")
del input_connections[delete_index]
def _apply_connect(self, action: ConnectAction, execution: RefactorActionExecution):
input_step_dict, input_name, output_step_dict, output_name = self._connection(action)
output_order_index = output_step_dict["id"] # wish this was order_index...
all_input_connections = input_step_dict.get("input_connections")
self.normalize_input_connections_to_list(all_input_connections, input_name, add_if_missing=True)
input_connections = all_input_connections[input_name]
input_connections.append(
{
"id": output_order_index,
"output_name": output_name,
}
)
def _apply_fill_defaults(self, action: FileDefaultsAction, execution: RefactorActionExecution):
for _, step in self._iterate_over_step_pairs(execution):
module = step.module
if module.type != "tool":
continue
self._as_dict["steps"][step.order_index]["tool_state"] = step.module.get_tool_state()
def _apply_fill_step_defaults(self, action: FillStepDefaultsAction, execution: RefactorActionExecution):
step = self._find_step_with_module_for_action(action, execution)
self._as_dict["steps"][step.order_index]["tool_state"] = step.module.get_tool_state()
def _apply_extract_input(self, action: ExtractInputAction, execution: RefactorActionExecution):
input_step_dict, input_name = self._input_from_action(action)
step = self._step_with_module(input_step_dict["id"], execution)
module = step.module
inputs = module.get_all_inputs()
input_def = None
found_input_names = []
for input in inputs:
found_input_name = input["name"]
found_input_names.append(found_input_name)
if found_input_name == input_name:
input_def = input
break
if input_def is None:
raise RequestParameterInvalidException(
f"Failed to find input with name {input_name} on step {input_step_dict['id']} - input names found {found_input_names}"
)
if input_def.get("multiple", False):
raise RequestParameterInvalidException("Cannot extract input for multi-input inputs")
module_input_type = input_def.get("input_type")
# convert dataset, dataset_collection => data, data_collection for refactor API
input_type = {
"dataset": "data",
"dataset_collection": "data_collection",
}.get(module_input_type, module_input_type)
input_action = AddInputAction(
action_type="add_input",
optional=input_def.get("optional"),
type=input_type,
label=action.label,
position=action.position,
)
new_input_order_index = self._add_input_get_order_index(input_action, execution)
connect_action = ConnectAction(
action_type="connect",
input=action.input,
output=OutputReferenceByOrderIndex(order_index=new_input_order_index),
)
self._apply_connect(connect_action, execution)
def _apply_extract_untyped_parameter(self, action: ExtractUntypedParameter, execution: RefactorActionExecution):
untyped_parameter_name = action.name
new_label = action.label or untyped_parameter_name
target_value = "${%s}" % untyped_parameter_name
target_tool_inputs = []
rename_pjas = []
for step_def, step in self._iterate_over_step_pairs(execution):
module = step.module
if module.type != "tool":
continue
# TODO: require a clean tool state for all tools to do this.
tool = module.tool
tool_inputs = module.state
replace_tool_state = False
def callback(input, prefixed_name, context, value=None, **kwargs):
nonlocal replace_tool_state
# data parameters cannot have untyped parameter values
if input.type in ["data", "data_collection"]:
return NO_REPLACEMENT
if not contains_workflow_parameter(value):
return NO_REPLACEMENT
if value == target_value:
target_tool_inputs.append((step.order_index, input, prefixed_name)) # noqa: B023
replace_tool_state = True
return runtime_to_json(ConnectedValue())
else:
return NO_REPLACEMENT
visit_input_values(tool.inputs, tool_inputs.inputs, callback, no_replacement_value=NO_REPLACEMENT)
if replace_tool_state:
step_def["tool_state"] = step.module.get_tool_state()
for post_job_action in self._iterate_over_rename_pjas():
newname = post_job_action.get("action_arguments", {}).get("newname")
if target_value in newname:
rename_pjas.append(post_job_action)
if len(target_tool_inputs) == 0 and len(rename_pjas) == 0:
raise RequestParameterInvalidException(
f"Failed to find {target_value} in the tool state or any workflow steps."
)
as_parameter_type = {
"text": "text",
"integer": "integer",
"float": "float",
"select": "text",
"genomebuild": "text",
}
target_parameter_types = set()
for _, tool_input, _ in target_tool_inputs:
tool_input_type = tool_input.type
if tool_input_type not in as_parameter_type:
raise RequestParameterInvalidException(
"Extracting inputs for parameters on tool inputs of type {tool_input_type} is unsupported"
)
target_parameter_type = as_parameter_type[tool_input_type]
target_parameter_types.add(target_parameter_type)
if len(target_parameter_types) > 1:
raise RequestParameterInvalidException(
"Extracting inputs for parameters on conflicting tool input types (e.g. numeric and non-numeric) input types is unsupported"
)
if len(target_parameter_types) == 1:
(target_parameter_type,) = target_parameter_types
else:
# only used in PJA, hence only used a string
target_parameter_type = "text"
for rename_pja in rename_pjas:
# if name != label, got to rewrite this rename with new label.
if untyped_parameter_name != new_label:
action_arguments = rename_pja.get("action_arguments")
old_newname = action_arguments["newname"]
new_newname = old_newname.replace(target_value, "${%s}" % new_label)
action_arguments["newname"] = new_newname
optional = False
input_action = AddInputAction(
action_type="add_input",
optional=optional,
type=target_parameter_type,
label=new_label,
position=action.position,
)
new_input_order_index = self._add_input_get_order_index(input_action, execution)
for order_index, _tool_input, prefixed_name in target_tool_inputs:
connect_input = InputReferenceByOrderIndex(order_index=order_index, input_name=prefixed_name)
connect_action = ConnectAction(
action_type="connect",
input=connect_input,
output=OutputReferenceByOrderIndex(order_index=new_input_order_index),
)
self._apply_connect(connect_action, execution)
def _apply_remove_unlabeled_workflow_outputs(
self, action: RemoveUnlabeledWorkflowOutputs, execution: RefactorActionExecution
):
for step in self._as_dict["steps"].values():
new_outputs = []
for workflow_output in step.get("workflow_outputs", []):
if workflow_output.get("label") is None:
continue
new_outputs.append(workflow_output)
step["workflow_outputs"] = new_outputs
def _apply_upgrade_subworkflow(self, action: UpgradeSubworkflowAction, execution: RefactorActionExecution):
step_def = self._find_step(action.step)
assert step_def["content_id"] is not None
trans = self.module_injector.trans
content_id = action.content_id
if content_id is None:
old_workflow = trans.app.workflow_manager.get_owned_workflow(trans, step_def["content_id"])
stored_workflow = old_workflow.stored_workflow
content_id = trans.security.encode_id(stored_workflow.latest_workflow.id)
step_def["content_id"] = content_id
step = self.workflow.steps[step_def["id"]]
new_workflow = trans.app.workflow_manager.get_owned_workflow(trans, content_id)
step.subworkflow = new_workflow
self._inject_for_updated_step(step, execution)
self._patch_step(execution, step, step_def)
def _apply_upgrade_tool(self, action: UpgradeToolAction, execution: RefactorActionExecution):
step_def = self._find_step(action.step)
tool_id = step_def["content_id"]
trans = self.module_injector.trans
tool_version = action.tool_version
if tool_version is None:
latest_tool = trans.app.toolbox.get_tool(tool_id, get_all_versions=True)[-1]
tool_version = latest_tool.version
tool_id = latest_tool.id
step = self.workflow.steps[step_def["id"]]
step.tool_id = tool_id
step.tool_version = tool_version
self._inject_for_updated_step(step, execution)
step_def["tool_version"] = tool_version
step_def["tool_state"] = step.module.get_tool_state()
if step_def.get("tool_id"):
step_def["tool_id"] = step.module.get_content_id()
if step_def.get("content_id"):
step_def["content_id"] = step.module.get_content_id()
self._patch_step(execution, step, step_def)
def _apply_upgrade_all_steps(self, action: UpgradeAllStepsAction, execution: RefactorActionExecution):
for step_order_index, step in self._as_dict["steps"].items():
if step.get("type") == "subworkflow":
step_action_s = UpgradeSubworkflowAction(
action_type="upgrade_subworkflow", step={"order_index": step_order_index}
)
self._apply_upgrade_subworkflow(step_action_s, execution)
elif step.get("type") == "tool":
step_action_t = UpgradeToolAction(action_type="upgrade_tool", step={"order_index": step_order_index})
self._apply_upgrade_tool(step_action_t, execution)
def _find_step(self, step_reference: step_reference_union):
order_index = None
if isinstance(step_reference, StepReferenceByLabel):
label = step_reference.label
if not label:
raise RequestParameterInvalidException("Empty label provided.")
for step_order_index, step in self._as_dict["steps"].items():
if step["label"] == label:
order_index = step_order_index
break
else:
order_index = step_reference.order_index
if order_index is None:
raise RequestParameterInvalidException(f"Failed to resolve step_reference {step_reference}")
if len(self._as_dict["steps"]) <= order_index:
raise RequestParameterInvalidException(f"Failed to resolve step_reference {step_reference}")
return self._as_dict["steps"][order_index]
def _find_step_for_action(self, action):
step_reference = action.step
return self._find_step(step_reference)
def _find_step_with_module_for_action(self, action, execution):
step_reference = action.step
step_def = self._find_step(step_reference)
step = self.workflow.steps[step_def["id"]]
return self._inject(step, execution)
def _step_with_module(self, order_index, execution):
step = self.workflow.steps[order_index]
return self._inject(step, execution)
def _iterate_over_step_pairs(self, execution):
# walk over both the dict-ified steps and the model steps (ensuring)
# module is attached.
for order_index, step_def in self._as_dict["steps"].items():
if order_index >= len(self.workflow.steps):
# newly added step during refactoring, don't iterate over it...
continue
else:
step = self._step_with_module(order_index, execution)
yield step_def, step
def _inject_for_updated_step(self, step, execution):
step.clear_module_extras()
return self._inject(step, execution)
def _inject(self, step, execution):
# compute runtime state, capture upgrade messages that result
if not hasattr(step, "module"):
self.module_injector.inject(step)
self.module_injector.compute_runtime_state(step)
if getattr(step, "upgrade_messages", None):
for key, value in step.upgrade_messages.items():
message = RefactorActionExecutionMessage(
message=value,
message_type=RefactorActionExecutionMessageTypeEnum.tool_state_adjustment,
input_name=key,
step_label=step.label,
order_index=step.order_index,
)
execution.messages.append(message)
if getattr(step.module, "version_changes", None):
for version_change in step.module.version_changes:
message = RefactorActionExecutionMessage(
message=version_change,
message_type=RefactorActionExecutionMessageTypeEnum.tool_version_change,
step_label=step.label,
order_index=step.order_index,
)
execution.messages.append(message)
return step
def _iterate_over_rename_pjas(self):
for _, step_def in self._as_dict["steps"].items():
if step_def["type"] != "tool":
continue
post_job_actions = step_def.get("post_job_actions", [])
for post_job_action in post_job_actions.values():
if post_job_action["action_type"] == "RenameDatasetAction":
yield post_job_action
def _add_input_get_order_index(self, input_action: AddInputAction, execution: RefactorActionExecution):
self._apply_add_input(input_action, execution)
return len(self._as_dict["steps"]) - 1
def _input_from_action(self, action):
input_reference = action.input
input_step_dict = self._find_step(input_reference)
input_name = input_reference.input_name
return input_step_dict, input_name
def _connection(self, action):
input_step_dict, input_name = self._input_from_action(action)
output_reference = action.output
output_step_dict = self._find_step(output_reference)
output_name = output_reference.output_name
return input_step_dict, input_name, output_step_dict, output_name
def _patch_step(self, execution, step, step_def):
"""
patch a workflow step after upgrading the tool / subworkflow
"""
# TODO: find workflow outputs that need to be dropped and report them
upgrade_inputs = step.module.get_all_inputs()
upgrade_outputs = step.module.get_all_outputs()
upgrade_output_names = {u["name"] for u in upgrade_outputs}
upgrade_order_index = step_def["id"]
upgrade_label = step_def.get("label")
all_input_connections = step_def.get("input_connections")
inputs_to_delete = []
for input_name, input_connections in all_input_connections.items():
# try and find an input connection for each input
matching_input = None
for upgrade_input in upgrade_inputs:
if upgrade_input["name"] == input_name:
matching_input = upgrade_input
break
# In the future check parameter type, format, mapping status...
if matching_input is None:
inputs_to_delete.append(input_name)
for input_connection in _listify_connections(input_connections):
message_text = (
f"Tool or subworkflow input '{input_name}' no longer available, dropping connection to it."
)
from_order_index = input_connection["id"]
from_step_label = self._as_dict["steps"].get(from_order_index, {}).get("label")
message = RefactorActionExecutionMessage(
message=message_text,
message_type=RefactorActionExecutionMessageTypeEnum.connection_drop_forced,
input_name=input_name,
step_label=upgrade_label,
order_index=upgrade_order_index,
output_name=input_connection["output_name"],
from_order_index=from_order_index,
from_step_label=from_step_label,
)
execution.messages.append(message)
for input_name in inputs_to_delete:
del all_input_connections[input_name]
for _, step in self._as_dict["steps"].items():
all_input_connections = step.get("input_connections")
for input_name, input_connections in all_input_connections.items():
rebuilt_valid_connections = []
for input_connection in _listify_connections(input_connections):
include = False
if input_connection["id"] != upgrade_order_index:
include = True
else:
output_name = input_connection["output_name"]
if output_name in upgrade_output_names:
include = True
else:
# dropped outputs
message_text = f"Tool or subworkflow output '{output_name}' no longer available, dropping connection from it."
message = RefactorActionExecutionMessage(
message=message_text,
message_type=RefactorActionExecutionMessageTypeEnum.connection_drop_forced,
input_name=input_name,
step_label=step.get("label"),
order_index=step["id"],
output_name=output_name,
from_step_label=upgrade_label,
from_order_index=upgrade_order_index,
)
execution.messages.append(message)
if include:
rebuilt_valid_connections.append(input_connection)
all_input_connections[input_name] = rebuilt_valid_connections
workflow_outputs_to_delete = []
for workflow_output in step_def.get("workflow_outputs", []):
output_label = workflow_output.get("label")
output_name = workflow_output["output_name"]
if not output_label:
continue
if output_name not in upgrade_output_names:
workflow_outputs_to_delete.append(workflow_output)
message_text = f"Subworkflow output '{output_name}' no longer available, dropping corresponding workflow output label {output_label}."
message = RefactorActionExecutionMessage(
message=message_text,
message_type=RefactorActionExecutionMessageTypeEnum.workflow_output_drop_forced,
step_label=upgrade_label,
order_index=upgrade_order_index,
output_name=workflow_output.get("output_name"),
output_label=output_label,
)
execution.messages.append(message)
[docs] @staticmethod
def normalize_input_connections_to_list(all_input_connections, input_name, add_if_missing=False):
if add_if_missing and input_name not in all_input_connections:
all_input_connections[input_name] = []
input_connections = all_input_connections[input_name]
all_input_connections[input_name] = _listify_connections(input_connections)
@property
def _as_dict(self):
return self.raw_workflow_description.as_dict
def _listify_connections(input_connections):
if not isinstance(input_connections, list):
return [input_connections]
return input_connections