Commit c576a345 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Refactor data stores and expose all classes on package level

parent 3f645b05

src/nova/galaxy/__init__.py

+5 −1
Original line number Diff line number Diff line 
import importlib.metadata



from .data_store import Datastore

from .dataset import Dataset, DatasetCollection, upload_datasets

from .nova import Nova

from .parameters import Parameters

from .tool import Tool



__all__ = ["Nova"]

__all__ = ["Nova", "Datastore", "Dataset", "DatasetCollection", "upload_datasets", "Tool", "Parameters"]



__version__ = importlib.metadata.version("nova-galaxy")

src/nova/galaxy/data_store.py

+6 −2
Original line number Diff line number Diff line
@@ -7,8 +7,12 @@ if TYPE_CHECKING: 




class Datastore:

    """Groups tool outputs together."""

    """Groups tool outputs together.



    def __init__(self, name: str, nova_instance: "Nova"):

    The constructor is not intended for external use. Use nova.galaxy.Nova.create_data_store() instead.

    """



    def __init__(self, name: str, nova_instance: "Nova", history_id: str):

        self.name = name

        self.nova = nova_instance

        self.history_id = history_id

src/nova/galaxy/dataset.py

+9 −4
Original line number Diff line number Diff line
@@ -64,6 +64,8 @@ class Dataset(AbstractData): 


    def __init__(self, path: str):

        self.path = path

        self.id: str

        self.store: Datastore



    def upload(self, store: Datastore) -> None:

        galaxy_instance = store.nova.galaxy_instance
@@ -72,7 +74,6 @@ class Dataset(AbstractData): 
        dataset_id = galaxy_instance.tools.upload_file(path=self.path, history_id=history_id)

        self.id = dataset_id["outputs"][0]["id"]

        self.store = store

        if self.id:

        dataset_client.wait_for_dataset(self.id)



    def download(self, local_path: str) -> None:
@@ -80,7 +81,8 @@ class Dataset(AbstractData): 
        if self.store and self.id:

            dataset_client = DatasetClient(self.store.nova.galaxy_instance)

            dataset_client.download_dataset(self.id, use_default_filename=False, file_path=local_path)

            dataset_client.wait_for_dataset(self.id)

        else:

            raise Exception("Dataset is not present in Galaxy.")





class DatasetCollection(AbstractData):
@@ -88,6 +90,8 @@ class DatasetCollection(AbstractData): 


    def __init__(self, path: str):

        self.path = path

        self.id: str

        self.store: Datastore



    def upload(self, store: Datastore) -> None:

        """Will need to handle this differently than single datasets."""
@@ -98,7 +102,8 @@ class DatasetCollection(AbstractData): 
        if self.store and self.id:

            dataset_client = DatasetCollectionClient(self.store.nova.galaxy_instance)

            dataset_client.download_dataset_collection(self.id, file_path=local_path)

            dataset_client.wait_for_dataset_collection(self.id)

        else:

            raise Exception("Dataset collection is not present in Galaxy.")





def upload_datasets(store: Datastore, datasets: Dict[str, AbstractData]) -> Dict[str, str]:

src/nova/galaxy/nova.py

+11 −3
Original line number Diff line number Diff line
@@ -41,10 +41,10 @@ class Nova: 
        Args:

            galaxy_url (Optional[str]): URL of the Galaxy instance.

            galaxy_key (Optional[str]): API key for the Galaxy instance.

            namespace (str): Namespace for Galaxy histories.

        """

        self.galaxy_url = galaxy_url

        self.galaxy_api_key = galaxy_key

        self.galaxy_instance: galaxy.GalaxyInstance



    def connect(self) -> None:

        """
@@ -64,5 +64,13 @@ class Nova: 


    def create_data_store(self, name: str) -> Datastore:

        """Creates a datastore with the given name."""

        self.galaxy_instance.histories.create_history(name=name)["id"]

        return Datastore(name, self)
 
        histories = self.galaxy_instance.histories.get_histories(name=name)

        if len(histories) > 0:

            return Datastore(name, self, histories[0]["id"])

        history_id = self.galaxy_instance.histories.create_history(name=name)["id"]

        return Datastore(name, self, history_id)



    def remove_data_store(self, name: str) -> None:

        """Permanently deletes the data store with the given name."""

        history = self.galaxy_instance.histories.get_histories(name=name)[0]["id"]

        self.galaxy_instance.histories.delete_history(history_id=history, purge=True)

src/nova/galaxy/tool.py

+3 −3
Original line number Diff line number Diff line
@@ -35,8 +35,6 @@ class Tool(AbstractWork): 
        """Runs this tool in a blocking manner and returns a map of the output datasets and collections."""

        outputs: Dict[Any, AbstractData] = {}

        galaxy_instance = data_store.nova.galaxy_instance

        history_id = galaxy_instance.histories.get_histories(name=data_store.name)[0]["id"]



        datasets_to_upload = {}



        # Set Tool Inputs
@@ -52,7 +50,9 @@ class Tool(AbstractWork): 
            tool_inputs.set_dataset_param(param, val)



        # Run tool and wait for job to finish

        results = galaxy_instance.tools.run_tool(history_id=history_id, tool_id=self.id, tool_inputs=tool_inputs)

        results = galaxy_instance.tools.run_tool(

            history_id=data_store.history_id, tool_id=self.id, tool_inputs=tool_inputs

        )



        for job in results["jobs"]:

            galaxy_instance.jobs.wait_for_job(job_id=job["id"])