Commit 68ef2c43 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Merge branch '26-add-file-type-dataset' into 'main' 

Expose check_url when getting url from tool

See merge request ndip/public-packages/nova-galaxy!17
parents 3d1f8e41 51724ca1

pyproject.toml

+1 −1
Original line number Diff line number Diff line 
[tool.poetry]

name = "nova-galaxy"

version = "0.7.3"

version = "0.7.4"

description = "Utilties for accessing the ORNL Galaxy instance"

authors = ["Greg Watson <watsongr@ornl.gov>", "Gregory Cage <cagege@ornl.gov>"]

readme = "README.md"

src/nova/galaxy/data_store.py

+5 −1
Original line number Diff line number Diff line
@@ -18,7 +18,7 @@ class Datastore: 
        self.name = name

        self.nova_connection = nova_connection

        self.history_id = history_id

        self.persist_store = False

        self.persist_store = True



    def persist(self) -> None:

        """Persist this store even after the nova connection is closed.
@@ -28,6 +28,10 @@ class Datastore: 
        """

        self.persist_store = True



    def mark_for_cleanup(self) -> None:

        """Clean up and delete all content related to this Data Store after the associated connection is closed."""

        self.persist_store = False



    def recover_tools(self, filter_running: bool = True) -> List[Tool]:

        """Recovers all running tools in this data_store.

src/nova/galaxy/dataset.py

+2 −4
Original line number Diff line number Diff line
@@ -163,13 +163,11 @@ class DatasetCollection(AbstractData): 
            raise Exception("Dataset collection is not present in Galaxy.")



    def get_content(self) -> Any:

        """Get a list of the content of this Collection along with info on each element."""

        if self.store and self.id:

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

            info = dataset_client.show_dataset_collection(self.id)

            output = ""

            for element in info["elements"]:

                output += f"{element['element_identifier']}\n"

            return output

            return info["elements"]

        else:

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

src/nova/galaxy/tool.py

+4 −2
Original line number Diff line number Diff line
@@ -168,7 +168,7 @@ class Tool(AbstractWork): 
            return self._job.get_console_output()["stderr"]

        return None



    def get_url(self, max_tries: int = 5) -> Optional[str]:

    def get_url(self, max_tries: int = 5, check_url: bool = False) -> Optional[str]:

        """Get the URL for this tool.



        If this is an interactive tool, then will return the endpoint to the tool. The first call may need to query
@@ -178,9 +178,11 @@ class Tool(AbstractWork): 
        ----------

        max_tries: int

            How many attempts to obtain the url.

        check_url: bool

            Whether to check the URL for a 200 response before returning. If the request is unsuccessful, returns None.

        """

        if self._job:

            return self._job.get_url(max_tries=max_tries, check_url=False)

            return self._job.get_url(max_tries=max_tries, check_url=check_url)

        return None



    def get_uid(self) -> Optional[str]:

tests/test_data_store.py

+2 −0
Original line number Diff line number Diff line
@@ -14,6 +14,7 @@ TEST_INT_TOOL_ID = "interactive_tool_generic_output" 
def test_no_persist_store(nova_instance: Connection, galaxy_instance: GalaxyInstance) -> None:

    with nova_instance.connect() as connection:

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

        store.mark_for_cleanup()

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

        assert len(history) > 0

    history = galaxy_instance.histories.get_histories(name=store.history_id, deleted=False)
@@ -43,6 +44,7 @@ def test_recover_tools(nova_instance: Connection) -> None: 


    with nova_instance.connect() as connection:

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

        store.mark_for_cleanup()

        tools = store.recover_tools()

        assert len(tools) > 0

        assert tools[0].get_url() is not None