Making some doc and lint fixes (1903dc6f) · Commits · NDIP / Nova Packages / nova-galaxy

docs/api_reference.rst

+0 −18

Original line number	Diff line number	Diff line
		@@ -5,21 +5,3 @@ API Reference

		.. automodule:: nova.galaxy
		:members:

		.. automodule:: nova.galaxy.data_store
		:members:

		.. automodule:: nova.galaxy.dataset
		:members:

		.. automodule:: nova.galaxy.parameters
		:members:

		.. automodule:: nova.galaxy.outputs
		:members:

		.. automodule:: nova.galaxy.tool
		:members:

		.. automodule:: nova.galaxy.tool_runner
		:members:

src/nova/galaxy/workflow.py

+103 −82

Original line number	Diff line number	Diff line
		"""Contains classes to run workflows in Galaxy via Connection."""

		import time
		from threading import Lock, Thread
		from typing import TYPE_CHECKING, Dict, List, Optional, Union

		from bioblend import galaxy
		from typing import TYPE_CHECKING, Dict, List, Optional

		if TYPE_CHECKING:
		from .data_store import Datastore
		from .dataset import AbstractData
		from .job import Job

		from .dataset import AbstractData, Dataset, DatasetCollection
		from nova.common.job import WorkState

		from .dataset import Dataset, DatasetCollection
		from .outputs import Outputs
		from .parameters import Parameters
		from .tool import AbstractWork
		from nova.common.job import WorkState


		class InvocationStatus:
		@@ -24,7 +21,7 @@ class InvocationStatus:
		def __init__(self) -> None:
		self.lock = Lock()
		self._state = WorkState.NOT_STARTED
		self._details = "" # Consolidated error_msg here
		self._details = ""

		@property
		def state(self) -> WorkState:
		@@ -69,11 +66,9 @@ class Invocation:
		"error": WorkState.ERROR,
		"paused": WorkState.QUEUED,
		"canceled": WorkState.CANCELED,

		# Invocation-specific states
		"scheduled": WorkState.QUEUED,
		"failed": WorkState.ERROR,

		# Job-specific states
		"upload": WorkState.UPLOADING_DATA,
		"waiting": WorkState.QUEUED,
		@@ -85,13 +80,13 @@ class Invocation:
		def _extract_error_details_from_invocation(self, invocation_details: Dict) -> str:
		"""Parses invocation details to extract a detailed error message."""
		error_list = [f"Invocation failed. Overall State: {invocation_details.get('state', 'Unknown')}."]
		if 'steps' in invocation_details and isinstance(invocation_details['steps'], list):
		for step in invocation_details['steps']:
		step_galaxy_state = step.get('state')
		if "steps" in invocation_details and isinstance(invocation_details["steps"], list):
		for step in invocation_details["steps"]:
		step_galaxy_state = step.get("state")
		if self._map_galaxy_state_to_workstate(step_galaxy_state) == WorkState.ERROR:
		step_label = step.get('workflow_step_label', f"Step ID {step.get('id', 'Unknown')}")
		step_label = step.get("workflow_step_label", f"Step ID {step.get('id', 'Unknown')}")
		error_list.append(f" - Step '{step_label}' failed with state: {step_galaxy_state}.")
		# TODO: Future enhancement: Extract more specific error messages from step['messages'] or job details if available.
		# TODO: Future enhancement: Extract more specific error messages from step['messages']
		return "\n".join(error_list)

		def _run_and_wait(self, params: Optional[Parameters]) -> None:
		@@ -101,7 +96,7 @@ class Invocation:
		if self.invocation_id:
		self.wait_for_results()
		invocation_details = self.galaxy_instance.invocations.show_invocation(self.invocation_id)
		self.status.state = self._map_galaxy_state_to_workstate(invocation_details['state'])
		self.status.state = self._map_galaxy_state_to_workstate(invocation_details["state"])
		if self.status.state == WorkState.ERROR:
		self.status.details = self._extract_error_details_from_invocation(invocation_details)
		elif self.status.state == WorkState.FINISHED:
		@@ -114,7 +109,6 @@ class Invocation:
		self.status.state = WorkState.ERROR
		self.status.details = f"Error during workflow execution or waiting: {str(e)}"


		def run(self, params: Optional[Parameters], wait: bool) -> Optional[Outputs]:
		"""Runs the workflow invocation."""
		if self.status.state in [WorkState.NOT_STARTED, WorkState.FINISHED, WorkState.ERROR, WorkState.CANCELED]:
		@@ -130,8 +124,10 @@ class Invocation:
		return self.get_results()
		return None
		else:
		raise Exception(f"Workflow {self.workflow_id} (invocation: {self.invocation_id}) is already running or in an intermediate state ({self.status.state}). Cannot start a new run.")

		raise Exception(
		f"Workflow {self.workflow_id} (invocation: {self.invocation_id}) is already running or in an"
		f"intermediate state ({self.status.state}). Cannot start a new run."
		)

		def submit(self, params: Optional[Parameters]) -> None:
		"""Handles input preparation and submits the workflow invocation."""
		@@ -140,35 +136,57 @@ class Invocation:

		try:
		workflow_details = self.galaxy_instance.workflows.show_workflow(self.workflow_id)
		label_to_input_id = {v['label']: k for k, v in workflow_details.get('inputs', {}).items() if v.get('label')}
		label_to_step_id = {step['label']: str(step['id']) for step in workflow_details.get('steps', {}).values() if step.get('label')}
		label_to_input_id = {v["label"]: k for k, v in workflow_details.get("inputs", {}).items() if v.get("label")}
		label_to_step_id = {
		step["label"]: str(step["id"])
		for step in workflow_details.get("steps", {}).values()
		if step.get("label")
		}

		if params:
		for label, value in params.inputs.items():
		if isinstance(value, Dataset):
		input_id = label_to_input_id.get(label)
		if not input_id:
		raise ValueError(f"Workflow input label '{label}' not found in workflow '{self.workflow_id}'. Available input labels: {list(label_to_input_id.keys())}")
		raise ValueError(
		f"Input label '{label}' not found in workflow '{self.workflow_id}'."
		f" Available input labels: {list(label_to_input_id.keys())}"
		)
		if not value.id:
		raise ValueError(f"Input dataset '{label}' must have an ID (must exist in Galaxy history). Upload it first if necessary.")
		bioblend_inputs[input_id] = {'src': 'hda', 'id': value.id}
		raise ValueError(
		f"Input dataset '{label}' must have an ID (must exist"
		" in Galaxy history). Upload it first if necessary."
		)
		bioblend_inputs[input_id] = {"src": "hda", "id": value.id}
		elif isinstance(value, DatasetCollection):
		input_id = label_to_input_id.get(label)
		if not input_id:
		raise ValueError(f"Workflow input label '{label}' not found in workflow '{self.workflow_id}'. Available input labels: {list(label_to_input_id.keys())}")
		raise ValueError(
		f"Input label '{label}' not found in workflow '{self.workflow_id}'."
		f" Available input labels: {list(label_to_input_id.keys())}"
		)
		if not value.id:
		raise ValueError(f"Input dataset collection '{label}' must have an ID (must exist in Galaxy history).")
		bioblend_inputs[input_id] = {'src': 'hdca', 'id': value.id}
		raise ValueError(
		f"Input dataset collection '{label}' must have an ID (must exist in Galaxy history)."
		)
		bioblend_inputs[input_id] = {"src": "hdca", "id": value.id}
		elif isinstance(value, dict):
		step_id = label_to_step_id.get(label)
		if not step_id:
		raise ValueError(f"Workflow step label '{label}' not found in workflow '{self.workflow_id}' for setting parameters. Available step labels: {list(label_to_step_id.keys())}")
		raise ValueError(
		f"Step label '{label}' not found in workflow "
		"'{self.workflow_id}' for setting parameters. Available "
		f"step labels: {list(label_to_step_id.keys())}"
		)
		bioblend_params[step_id] = value
		else:
		input_id = label_to_input_id.get(label)
		step_id = label_to_step_id.get(label)
		if not input_id and not step_id:
		print(f"Warning: Parameter '{label}' is not a Dataset, DatasetCollection, or a dictionary associated with a known step label. It will be ignored.")
		print(
		f"Warning: Parameter '{label}' is not a Dataset, DatasetCollection, "
		"or dictionary associated with a known step label. It will be ignored."
		)
		else:
		if input_id:
		bioblend_inputs[input_id] = value
		@@ -181,23 +199,21 @@ class Invocation:
		inputs=bioblend_inputs,
		params=bioblend_params,
		history_id=self.store.history_id,
		parameters_normalized=False
		parameters_normalized=False,
		)
		self.invocation_id = invocation_info['id']
		self.status.state = self._map_galaxy_state_to_workstate(invocation_info['state'])
		self.invocation_id = invocation_info["id"]
		self.status.state = self._map_galaxy_state_to_workstate(invocation_info["state"])
		except Exception as e:
		self.status.state = WorkState.ERROR
		self.status.details = f"Failed to prepare or submit workflow invocation: {str(e)}"
		self.invocation_id = None


		def wait_for_results(self) -> None:
		"""Waits for the workflow invocation to complete."""
		if not self.invocation_id:
		raise Exception("Cannot wait for results, invocation ID is not set.")
		self.galaxy_instance.invocations.wait_for_invocation(self.invocation_id)


		def get_state(self) -> InvocationStatus:
		"""Returns the current state of the workflow invocation."""
		if not self.invocation_id or self.status.state in [WorkState.FINISHED, WorkState.ERROR, WorkState.CANCELED]:
		@@ -205,7 +221,7 @@ class Invocation:

		try:
		invocation_details = self.galaxy_instance.invocations.show_invocation(self.invocation_id)
		self.status.state = self._map_galaxy_state_to_workstate(invocation_details['state'])
		self.status.state = self._map_galaxy_state_to_workstate(invocation_details["state"])
		if self.status.state == WorkState.ERROR and not self.status.details: # Check details
		self.status.details = self._extract_error_details_from_invocation(invocation_details)
		if self.status.state == WorkState.FINISHED:
		@@ -216,7 +232,6 @@ class Invocation:

		return self.status


		def get_results(self) -> Optional[Outputs]:
		"""Returns the results (outputs) from a completed workflow invocation."""
		current_status = self.get_state()
		@@ -227,33 +242,38 @@ class Invocation:

		if not self.outputs_data:
		try:
		assert isinstance(self.invocation_id, str)
		self.outputs_data = self.galaxy_instance.invocations.show_invocation(self.invocation_id)
		except Exception as e:
		raise Exception(f"Failed to fetch invocation details for results processing: {e}")
		raise Exception(f"Failed to fetch invocation details for results processing: {e}") from e

		outputs = Outputs()
		try:
		if 'outputs' in self.outputs_data:
		for output_name, dataset_info in self.outputs_data['outputs'].items():
		if dataset_info and 'id' in dataset_info and 'src' in dataset_info and dataset_info['src'] == 'hda':
		if "outputs" in self.outputs_data:
		for output_name, dataset_info in self.outputs_data["outputs"].items():
		if dataset_info and "id" in dataset_info and "src" in dataset_info and dataset_info["src"] == "hda":
		d = Dataset(output_name)
		d.id = dataset_info['id']
		d.id = dataset_info["id"]
		d.store = self.store
		outputs.add_output(d)

		if 'output_collections' in self.outputs_data:
		for output_name, collection_info in self.outputs_data['output_collections'].items():
		if collection_info and 'id' in collection_info and 'src' in collection_info and collection_info['src'] == 'hdca':
		if "output_collections" in self.outputs_data:
		for output_name, collection_info in self.outputs_data["output_collections"].items():
		if (
		collection_info
		and "id" in collection_info
		and "src" in collection_info
		and collection_info["src"] == "hdca"
		):
		dc = DatasetCollection(output_name)
		dc.id = collection_info['id']
		dc.id = collection_info["id"]
		dc.store = self.store
		outputs.add_output(dc)

		return outputs

		except Exception as e:
		raise Exception(f"Error processing invocation results: {e}")

		raise Exception(f"Error processing invocation results: {e}") from e

		def cancel(self) -> bool:
		"""Cancels the workflow invocation."""
		@@ -265,7 +285,7 @@ class Invocation:
		if success:
		self.status.state = WorkState.CANCELED
		self.status.details = "Invocation canceled by user."
		return success
		return True
		except Exception as e:
		print(f"Error cancelling invocation {self.invocation_id}: {e}")
		return False
		@@ -286,13 +306,13 @@ class Invocation:
		step_jobs = []

		for job_info in jobs_summary:
		if job_info.get('id') and job_info.get('tool_id'):
		if job_info.get("id") and job_info.get("tool_id"):
		# Create a Job instance for this step
		job = Job(job_info['tool_id'], self.store)
		job.id = job_info['id']
		job = Job(job_info["tool_id"], self.store)
		job.id = job_info["id"]

		# Map Galaxy job state to WorkState
		galaxy_state = job_info.get('state', 'unknown')
		galaxy_state = job_info.get("state", "unknown")
		job.status.state = self._map_galaxy_state_to_workstate(galaxy_state)

		step_jobs.append(job)
		@@ -302,6 +322,7 @@ class Invocation:
		print(f"Warning: Could not fetch invocation step jobs for {self.invocation_id}: {e}")
		return []


		class Workflow(AbstractWork):
		"""Represents a Galaxy workflow that can be invoked (run).

		@@ -417,11 +438,11 @@ class Workflow(AbstractWork):

		def stop(self) -> bool:
		"""Stops (cancels) the currently running workflow invocation.

		Alias for cancel().
		"""
		return self.cancel()


		def get_invocation_id(self) -> Optional[str]:
		"""Gets the Galaxy invocation ID for the last run.

tests/test_workflow.py

+14 −13

Original line number	Diff line number	Diff line
		"""Integration tests for Workflow functionality."""

		import os
		import time

		import pytest

		from nova.common.job import WorkState
		from nova.galaxy.connection import Connection
		from nova.galaxy.data_store import Datastore
		from nova.galaxy.parameters import Parameters
		from nova.galaxy.workflow import Workflow

		@@ -18,15 +14,17 @@ GALAXY_API_KEY = os.environ.get("NOVA_GALAXY_TEST_GALAXY_KEY", "")
		WORKFLOW_NAME = "Simple_test_workflow"
		TEST_HISTORY_NAME_WF = "nova_galaxy_workflow_test_history"

		def test_workflow_lifecycle_with_placeholder_id(nova_instance: Connection):

		def test_workflow_lifecycle_with_placeholder_id(nova_instance: Connection) -> None:
		"""
		Tests the Workflow class lifecycle methods when using a placeholder workflow ID.

		This test expects failures when trying to run the workflow, as the ID is a placeholder.
		"""
		with nova_instance.connect() as connection:
		ds = connection.get_data_store(name=TEST_HISTORY_NAME_WF)
		workflows = connection.galaxy_instance.workflows.get_workflows(name=WORKFLOW_NAME, published=True)
		workflow_id = workflows[0]['id']
		workflow_id = workflows[0]["id"]
		params = Parameters()

		workflow = Workflow(id=workflow_id)
		@@ -42,8 +40,9 @@ def test_workflow_lifecycle_with_placeholder_id(nova_instance: Connection):
		print(f"Invocation ID after run(wait=True): {invocation_id}")
		print(f"Full status details: {full_status.details if full_status else 'N/A'}")

		assert status in [WorkState.ERROR, WorkState.QUEUED], \
		assert status in [WorkState.ERROR, WorkState.QUEUED], (
		f"Expected ERROR or QUEUED state after run(wait=False), got {status}"
		)

		if status == WorkState.ERROR:
		assert full_status is not None
		@@ -65,10 +64,12 @@ def test_workflow_lifecycle_with_placeholder_id(nova_instance: Connection):
		assert len(step_jobs) == 0, "Expected no step jobs for a placeholder/failed workflow"

		final_status = workflow.get_status()
		assert final_status in [WorkState.ERROR, WorkState.CANCELED, WorkState.QUEUED], \
		assert final_status in [WorkState.ERROR, WorkState.CANCELED, WorkState.QUEUED], (
		f"Unexpected final state: {final_status}"
		)


		def test_workflow_initial_state():
		def test_workflow_initial_state() -> None:
		"""Tests the initial state of a Workflow object before any run."""
		workflow = Workflow(id="another_placeholder_id")
		assert workflow.id == "another_placeholder_id"