Commit 7136773e authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Rename use_data_store, fix typing

parent 2b2c8b5c

CHANGELOG.md

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### Nova Galaxy, 0.8.0

- `use_data_store()` has been added to the ConnectionHelper class. This functionally does the same thing as create_data_store, but users can choose whether to only use existing upstream data stores. `create_data_store` creates data stores by default and connects to existing ones as well automatically (thanks to Gregory Cage).  [Merge Request 18](https://code.ornl.gov/ndip/public-packages/nova-galaxy/-/merge_requests/18)

- `get_data_store()` has been added to the ConnectionHelper class. This functionally does the same thing as create_data_store, but users can choose whether to only use existing upstream data stores. `create_data_store` creates data stores by default and connects to existing ones as well automatically (thanks to Gregory Cage).  [Merge Request 18](https://code.ornl.gov/ndip/public-packages/nova-galaxy/-/merge_requests/18)

- `Connections.connect()` can now be used with or without the `with` keyword. Consequently, stores can also be created outside a `with` block. `Connection.close()` performs the clean up that exiting the `with` block provides (thanks to Gregory Cage). [Merge Request 18](https://code.ornl.gov/ndip/public-packages/nova-galaxy/-/merge_requests/18)

- Data stores can be cleaned up manually (thanks to Gregory Cage). [Merge Request 18](https://code.ornl.gov/ndip/public-packages/nova-galaxy/-/merge_requests/18)

- Can now wait for the result of a running tool (thanks to Gregory Cage). [Merge Request 18](https://code.ornl.gov/ndip/public-packages/nova-galaxy/-/merge_requests/18)

poetry.lock

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@@ -465,6 +465,24 @@ files = [ 
[package.extras]

toml = ["tomli ; python_full_version <= \"3.11.0a6\""]



[[package]]

name = "deprecated"

version = "1.2.18"

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optional = false

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[package.dependencies]

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[package.extras]

dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools ; python_version >= \"3.12\"", "tox"]



[[package]]

name = "distlib"

version = "0.3.9"
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[[package]]

name = "yarl"

version = "1.19.0"
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[metadata]

lock-version = "2.1"

python-versions = "^3.10"

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pyproject.toml

+1 −0
Original line number Diff line number Diff line
@@ -15,6 +15,7 @@ packages = [ 
python = "^3.10"

bioblend = "^1.5.0"

tomli = "^2.0.2"

deprecated = "^1.2.18"



[build-system]

requires = ["poetry-core"]

src/nova/galaxy/connection.py

+11 −9
Original line number Diff line number Diff line 
"""The NOVA class is responsible for managing interactions with a Galaxy server instance."""



from typing import Any, List, Optional

from typing import Any, List



from bioblend import galaxy

from deprecated import deprecated



from .data_store import Datastore

from .tool import stop_all_tools_in_store
@@ -28,7 +29,7 @@ class ConnectionHelper: 
    be automatically purged after connection is closed, unless Datastore.persist() is called for that store.

    """



    def __init__(self, galaxy_instance: galaxy.GalaxyInstance, galaxy_url: Optional[str]):

    def __init__(self, galaxy_instance: galaxy.GalaxyInstance, galaxy_url: str):

        self.galaxy_instance = galaxy_instance

        self.galaxy_url = galaxy_url

        self.datastores: List[Datastore] = []
@@ -41,11 +42,12 @@ class ConnectionHelper: 
        """Exit method for use with "with" keyword."""

        self.close()



    @deprecated(version="0.8.0", reason="Should use `get_data_store() instead.")

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

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

        return self.use_data_store(name=name, create=True)

        return self.get_data_store(name=name, create=True)



    def use_data_store(self, name: str, create: bool = True) -> Datastore:

    def get_data_store(self, name: str, create: bool = True) -> Datastore:

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

        histories = self.galaxy_instance.histories.get_histories(name=name)

        if len(histories) > 0:
@@ -85,15 +87,15 @@ class Connection: 


    def __init__(

        self,

        galaxy_url: Optional[str] = None,

        galaxy_key: Optional[str] = None,

        galaxy_url: str,

        galaxy_key: str,

    ) -> None:

        """

        Initializes the Connection instance with the provided URL and API key.



        Args:

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

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

            galaxy_url str: URL of the Galaxy instance.

            galaxy_key str: API key for the Galaxy instance.

        """

        self.galaxy_url = galaxy_url

        self.galaxy_api_key = galaxy_key
@@ -101,7 +103,7 @@ class Connection: 


    def _init_galaxy_instance(self) -> None:

        if not self.galaxy_url or not self.galaxy_api_key:

            raise ValueError("Galaxy URL and API key must be provided or set in environment variables.")

            raise ValueError("Galaxy URL and API key must be provided.")

        if not isinstance(self.galaxy_url, str):

            raise ValueError("Galaxy URL must be a string")

        self.galaxy_instance = galaxy.GalaxyInstance(url=self.galaxy_url, key=self.galaxy_api_key)

tests/test_data_store.py

+1 −1
Original line number Diff line number Diff line
@@ -45,7 +45,7 @@ def test_manual_cleanup_store(nova_instance: Connection, galaxy_instance: Galaxy 


def test_manual_connection_close(nova_instance: Connection, galaxy_instance: GalaxyInstance) -> None:

    connection = nova_instance.connect()

    store = connection.use_data_store(name="nova_galaxy_testing")

    store = connection.get_data_store(name="nova_galaxy_testing")

    store.mark_for_cleanup()

    history = galaxy_instance.histories.get_histories(name=store.name)

    assert len(history) > 0