Rework wait_for_results and fill in documentation (ca9d3b9e) · Commits · NDIP / Nova Packages / nova-galaxy

src/nova/galaxy/connection.py

+29 −4

Original line number	Diff line number	Diff line
		@@ -26,7 +26,7 @@ class ConnectionHelper:
		"""Manages datastore for current connection.

		Should not be instantiated manually. Use Connection.connect() instead. Any stores created using the connection will
		be automatically purged after connection is closed, unless Datastore.persist() is called for that store.
		be persisted after connection is closed, unless Datastore.mark_for_cleanup() is called for that store.
		"""

		def __init__(self, galaxy_instance: galaxy.GalaxyInstance, galaxy_url: str):
		@@ -44,11 +44,30 @@ class ConnectionHelper:

		@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."""
		"""DEPRECATED. Creates a datastore with the given name or returns an existing data store with that name.

		Parameters
		----------
		name: str
		Name of the data store.
		"""
		return self.get_data_store(name=name, create=True)

		def get_data_store(self, name: str, create: bool = True) -> Datastore:
		"""Creates a datastore with the given name."""
		"""Fetches a datastore with the given name.

		Parameters
		----------
		name: str
		Name of the data store.
		create: bool
		If true, creates a data store if one does not exist with the specified name.

		Returns
		-------
		Datastore
		Returns the specified or newly created data store.
		"""
		histories = self.galaxy_instance.histories.get_histories(name=name)
		if len(histories) > 0:
		store = Datastore(name, self, histories[0]["id"])
		@@ -63,7 +82,13 @@ class ConnectionHelper:
		raise Exception("Data store does not exist and auto creation is set to false.")

		def remove_data_store(self, store: Datastore) -> None:
		"""Permanently deletes the data store with the given name."""
		"""Permanently deletes the data store with the given name.

		Parameters
		----------
		store: Datastore
		The data store to remove from this connection.
		"""
		store.cleanup()
		self.datastores.remove(store)

src/nova/galaxy/job.py

+9 −4

Original line number	Diff line number	Diff line
		@@ -36,6 +36,7 @@ class Job:
		self.galaxy_instance = self.store.nova_connection.galaxy_instance
		self.status = JobStatus()
		self.url: Optional[str] = None
		self.thread: Optional[Thread] = None

		def _run_and_wait(self, params: Optional[Parameters]) -> None:
		"""Runs tools and waits for result."""
		@@ -53,10 +54,10 @@ class Job:
		def run(self, params: Optional[Parameters], wait: bool) -> Optional[Outputs]:
		"""Runs a job in Galaxy."""
		if self.status.state in [WorkState.NOT_STARTED, WorkState.FINISHED, WorkState.ERROR]:
		thread = Thread(target=self._run_and_wait, args=(params,))
		thread.start()
		self.thread = Thread(target=self._run_and_wait, args=(params,))
		self.thread.start()
		if wait:
		thread.join()
		self.join_job_thread()
		return self.get_results()
		return None
		else:
		@@ -127,7 +128,11 @@ class Job:
		self.status.state = WorkState.ERROR
		return self.galaxy_instance.jobs.cancel_job(self.id)

		def wait_for_results(self, timeout: int = 12000) -> None:
		def join_job_thread(self) -> None:
		if self.thread:
		self.thread.join()

		def wait_for_results(self, timeout: float = 12000) -> None:
		"""Wait for job to finish."""
		self.galaxy_instance.jobs.wait_for_job(self.id, maxwait=timeout)

src/nova/galaxy/tool.py

+3 −9

Original line number	Diff line number	Diff line
		@@ -130,16 +130,10 @@ class Tool(AbstractWork):
		return self._job.get_results()
		return None

		def wait_for_results(self, timeout: int = 12000) -> None:
		def wait_for_results(self) -> None:
		"""Wait for this Tool to finish running."""
		if self._job:
		timer = 0
		max_tries = 100
		while timer < max_tries:
		try:
		self._job.wait_for_results(timeout)
		return
		except Exception:
		timer += 1
		self._job.join_job_thread()

		def stop(self) -> None:
		"""Stop the tool, but keep any existing results."""

tests/conftest.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -13,11 +13,11 @@ GALAXY_API_KEY = os.environ.get("NOVA_GALAXY_TEST_GALAXY_KEY")

		@pytest.fixture
		def nova_instance() -> Connection:
		nova = Connection(GALAXY_URL, GALAXY_API_KEY)
		nova = Connection(GALAXY_URL, GALAXY_API_KEY) # type: ignore
		return nova


		@pytest.fixture
		def galaxy_instance() -> GalaxyInstance:
		galaxy = GalaxyInstance(url=GALAXY_URL, key=GALAXY_API_KEY)
		galaxy = GalaxyInstance(url=GALAXY_URL, key=GALAXY_API_KEY) # type: ignore
		return galaxy

tests/test_data_store.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -23,7 +23,7 @@ def test_no_persist_store(nova_instance: Connection, galaxy_instance: GalaxyInst

		def test_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 = connection.get_data_store(name="nova_galaxy_testing")
		store.persist()
		history = galaxy_instance.histories.get_histories(name=store.name)
		assert len(history) > 0
		@@ -35,7 +35,7 @@ def test_persist_store(nova_instance: Connection, galaxy_instance: GalaxyInstanc

		def test_manual_cleanup_store(nova_instance: Connection, galaxy_instance: GalaxyInstance) -> None:
		with nova_instance.connect() as connection:
		store = connection.create_data_store(name="nova_galaxy_testing")
		store = connection.get_data_store(name="nova_galaxy_testing")
		history = galaxy_instance.histories.get_histories(name=store.name)
		assert len(history) > 0
		store.cleanup()
		@@ -59,14 +59,14 @@ def test_manual_connection_close(nova_instance: Connection, galaxy_instance: Gal
		def test_recover_tools(nova_instance: Connection) -> None:
		first_id: Optional[str] = ""
		with nova_instance.connect() as connection:
		store = connection.create_data_store(name="nova_galaxy_testing")
		store = connection.get_data_store(name="nova_galaxy_testing")
		store.persist()
		test_tool = Tool(TEST_INT_TOOL_ID)
		test_tool.run_interactive(data_store=store)
		first_id = test_tool.get_uid()

		with nova_instance.connect() as connection:
		store = connection.create_data_store(name="nova_galaxy_testing")
		store = connection.get_data_store(name="nova_galaxy_testing")
		store.mark_for_cleanup()
		tools = store.recover_tools()
		assert len(tools) > 0