Add function to get URL after initial run call (0ae029e8) · Commits · NDIP / Nova Packages / nova-galaxy

src/nova/galaxy/job.py

+33 −18

Original line number	Diff line number	Diff line
		@@ -34,6 +34,7 @@ class Job:
		self.store = data_store
		self.galaxy_instance = self.store.nova_connection.galaxy_instance
		self.status = JobStatus()
		self.url: Optional[str] = None

		def _run_and_wait(self, params: Parameters) -> None:
		"""Runs tools and waits for result."""
		@@ -41,6 +42,7 @@ class Job:
		try:
		self.wait_for_results()
		except Exception:
		self.url = None
		self.status.state = WorkState.ERROR

		self.status.state = WorkState.FINISHED
		@@ -64,25 +66,12 @@ class Job:
		self.run(params, False)
		if not wait:
		return None
		timer = max_tries
		while timer > 0:
		try:
		entry_points = self.galaxy_instance.make_get_request(
		f"{self.store.nova_connection.galaxy_url}/api/entry_points?job_id={self.id}"
		)
		for ep in entry_points.json():
		if ep["job_id"] == self.id and ep.get("target", None):
		url = f"{self.store.nova_connection.galaxy_url}{ep['target']}"
		response = self.galaxy_instance.make_get_request(url)
		if response.status_code == 200 or not check_url:
		return url
		except Exception:
		continue
		finally:
		timer -= 1
		time.sleep(1)
		successful_url = self.get_url(max_tries=max_tries, check_url=check_url)
		if successful_url:
		return successful_url
		# If successful_url is None, then there was an issue starting the interactive tool.
		status = self.cancel()
		# if status is false, the job has been in a terminal state already, indicating an error somewhere in execution
		# if status is false, the job has been in a terminal state already, indicating an error somewhere in execution.
		if status:
		raise Exception("Unable to fetch the URL for interactive tool.")
		else:
		@@ -91,6 +80,7 @@ class Job:
		def submit(self, params: Parameters) -> None:
		"""Handles uploading inputs and submitting job."""
		self.status.state = WorkState.UPLOADING_DATA
		self.url = None
		datasets_to_upload = {}

		# Set Tool Inputs
		@@ -115,6 +105,7 @@ class Job:

		def cancel(self, check_results: bool = False) -> bool:
		"""Cancels or stops a job in Galaxy."""
		self.url = None
		if check_results:
		response = self.galaxy_instance.make_get_request(
		f"{self.store.nova_connection.galaxy_url}/api/jobs{self.id}/finish"
		@@ -162,6 +153,30 @@ class Job:
		else:
		raise Exception(f"Job {self.id} has not finished running.")

		def get_url(self, max_tries: int = 100, check_url: bool = True) -> Optional[str]:
		"""Get the URL or endpoint for this tool."""
		if self.url:
		return self.url
		timer = max_tries
		while timer > 0:
		try:
		entry_points = self.galaxy_instance.make_get_request(
		f"{self.store.nova_connection.galaxy_url}/api/entry_points?job_id={self.id}"
		)
		for ep in entry_points.json():
		if ep["job_id"] == self.id and ep.get("target", None):
		url = f"{self.store.nova_connection.galaxy_url}{ep['target']}"
		self.url = url
		response = self.galaxy_instance.make_get_request(url)
		if response.status_code == 200 or not check_url:
		return url
		except Exception:
		continue
		finally:
		timer -= 1
		time.sleep(1)
		return None

		def get_console_output(self) -> Dict[str, str]:
		"""Get all the current console output."""
		out = self.galaxy_instance.make_get_request(

src/nova/galaxy/tool.py

+6 −0

Original line number	Diff line number	Diff line
		@@ -134,6 +134,12 @@ class Tool(AbstractWork):
		return self._job.get_console_output()["stderr"]
		return None

		def get_url(self) -> Optional[str]:
		"""Get the URL for this tool. If this is an interactive tool, then will return the endpoint to the tool."""
		if self._job:
		return self._job.get_url()
		return None


		def stop_all_tools_in_store(data_store: Datastore) -> None:
		"""Stops all the tools from running in a particular store."""

tests/test_run_tool.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -36,6 +36,7 @@ def test_run_tool_interactive(nova_instance: Nova, galaxy_instance: GalaxyInstan
		params.add_input("run_it", True)
		link = test_tool.run_interactive(data_store=store, params=params, check_url=False)
		assert link is not None
		assert test_tool.get_url() is not None
		entry_points = galaxy_instance.make_get_request(
		f"{store.nova_connection.galaxy_url}/api/entry_points?running=true"
		)