Add outputs class to hold tool outputs (3224cfb9) · Commits · NDIP / Nova Packages / nova-galaxy

src/nova/galaxy/dataset.py

+6 −3

Original line number	Diff line number	Diff line
		@@ -6,7 +6,8 @@ as well as output data from Galaxy tools.

		from abc import ABC, abstractmethod
		from enum import Enum
		from typing import Any, Dict, Union
		from pathlib import Path
		from typing import Any, Dict, Optional, Union

		from bioblend.galaxy.dataset_collections import DatasetCollectionClient
		from bioblend.galaxy.datasets import DatasetClient
		@@ -62,8 +63,9 @@ class AbstractData(ABC):
		class Dataset(AbstractData):
		"""Singular file that can be uploaded and used in a Galaxy tool."""

		def __init__(self, path: str):
		def __init__(self, path: str, name: Optional[str] = None):
		self.path = path
		self.name = name or Path(path).name
		self.id: str
		self.store: Datastore

		@@ -88,8 +90,9 @@ class Dataset(AbstractData):
		class DatasetCollection(AbstractData):
		"""A group of files that can be uploaded as a collection and collectively be used in a Galaxy tool."""

		def __init__(self, path: str):
		def __init__(self, path: str, name: Optional[str] = None):
		self.path = path
		self.name = name or Path(path).name
		self.id: str
		self.store: Datastore

src/nova/galaxy/outputs.py

0 → 100644

+34 −0

Original line number	Diff line number	Diff line
		"""Encapsulates the output datasets and collections for a Tool."""

		from typing import Any, List

		from .dataset import AbstractData, Dataset, DatasetCollection


		class Outputs:
		"""Contains the output datasets and collections for a Tool."""

		def __init__(self) -> None:
		self.data: List[AbstractData] = []

		def __iter__(self) -> Any:
		"""Iterator."""
		self._iterator = 0
		return self

		def __next__(self) -> AbstractData:
		"""Get next element for iterator."""
		if self._iterator >= len(self.data):
		raise StopIteration
		d = self.data[self._iterator]
		self._iterator += 1
		return d

		def add_output(self, data: AbstractData) -> None:
		self.data.append(data)

		def get_dataset(self, name: str) -> AbstractData:
		return next(filter(lambda x: isinstance(x, Dataset) and x.name == name, self.data))

		def get_collection(self, name: str) -> AbstractData:
		return next(filter(lambda x: isinstance(x, DatasetCollection) and x.name == name, self.data))

src/nova/galaxy/tool.py

+8 −7

Original line number	Diff line number	Diff line
		"""Contains classes to run tools in Galaxy via Nova."""

		from typing import Any, Dict, List
		from typing import List, Union

		from bioblend import galaxy

		from .data_store import Datastore
		from .dataset import AbstractData, Dataset, DatasetCollection, upload_datasets
		from .outputs import Outputs
		from .parameters import Parameters


		@@ -21,8 +22,8 @@ class AbstractWork:
		def get_inputs(self) -> List[Parameters]:
		return []

		def run(self, data_store: Datastore, params: Parameters) -> Dict[str, AbstractData]:
		return {}
		def run(self, data_store: Datastore, params: Parameters) -> Union[Outputs, None]:
		return None


		class Tool(AbstractWork):
		@@ -31,9 +32,9 @@ class Tool(AbstractWork):
		def __init__(self, id: str):
		super().__init__(id)

		def run(self, data_store: Datastore, params: Parameters) -> Dict[Any, AbstractData]:
		def run(self, data_store: Datastore, params: Parameters) -> Outputs:
		"""Runs this tool in a blocking manner and returns a map of the output datasets and collections."""
		outputs: Dict[Any, AbstractData] = {}
		outputs = Outputs()
		galaxy_instance = data_store.nova.galaxy_instance
		datasets_to_upload = {}

		@@ -65,12 +66,12 @@ class Tool(AbstractWork):
		d = Dataset(dataset["output_name"])
		d.id = dataset["id"]
		d.store = data_store
		outputs[dataset["output_name"]] = d
		outputs.add_output(d)
		if result_collections:
		for collection in result_collections:
		dc = DatasetCollection(collection["output_name"])
		dc.id = collection["id"]
		dc.store = data_store
		outputs[collection["output_name"]] = dc
		outputs.add_output(dc)

		return outputs