Add new endpoint for getting stdout and stderr (b03b6abe) · Commits · NDIP / Galaxy

lib/galaxy/managers/jobs.py

+16 −8

Original line number	Diff line number	Diff line
		@@ -228,7 +228,7 @@ class JobManager:
		)
		return self.job_lock()

		def get_accessible_job(self, trans, decoded_job_id, stdout_position=-1, stdout_length=0, stderr_position=-1, stderr_length=0):
		def get_accessible_job(self, trans, decoded_job_id):
		job = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.id == decoded_job_id).first()
		if job is None:
		raise ObjectNotFound()
		@@ -245,8 +245,15 @@ class JobManager:
		if not self.dataset_manager.is_accessible(data_assoc.dataset.dataset, trans.user):
		raise ItemAccessibilityException("You are not allowed to rerun this job.")
		trans.sa_session.refresh(job)
		return job

		def get_job_console_output(self, trans, job, stdout_position=-1, stdout_length=0, stderr_position=-1, stderr_length=0):
		if job is None:
		raise ObjectNotFound()

		# If stdout_length and stdout_position are good values, then load standard out and add it to status
		console_output = dict()
		console_output["state"] = job.state
		if job.state == job.states.RUNNING:
		working_directory = trans.app.object_store.get_filename(
		job, base_dir="job_work", dir_only=True, obj_dir=True
		@@ -256,8 +263,7 @@ class JobManager:
		stdout_path = Path(working_directory) / STDOUT_LOCATION
		stdout_file = open(stdout_path, "r")
		stdout_file.seek(stdout_position)
		job.job_stdout = stdout_file.read(stdout_length)
		job.tool_stdout = job.job_stdout
		console_output["stdout"] = stdout_file.read(stdout_length)
		except Exception as e:
		log.error("Could not read STDOUT: %s", e)
		if stderr_length > 0 and stderr_position > -1:
		@@ -265,11 +271,13 @@ class JobManager:
		stderr_path = Path(working_directory) / STDERR_LOCATION
		stderr_file = open(stderr_path, "r")
		stderr_file.seek(stderr_position)
		job.job_stderr = stderr_file.read(stderr_length)
		job.tool_stderr = job.job_stderr
		console_output["stderr"] = stderr_file.read(stderr_length)
		except Exception as e:
		log.error("Could not read STDERR: %s", e)
		return job
		else:
		console_output["stdout"] = job.tool_stdout
		console_output["stderr"] = job.tool_stderr
		return console_output

		def stop(self, job, message=None):
		if not job.finished:

lib/galaxy/webapps/galaxy/api/jobs.py

+43 −10

Original line number	Diff line number	Diff line
		@@ -178,10 +178,6 @@ class FastAPIJobs:
		id: DecodedDatabaseIdField,
		trans: ProvidesUserContext = DependsOnTrans,
		full: Optional[bool] = False,
		stdout_position: Optional[int] = None,
		stdout_length: Optional[int] = None,
		stderr_position: Optional[int] = None,
		stderr_length: Optional[int] = None,
		) -> Dict[str, Any]:
		"""
		Return dictionary containing description of job data
		@@ -189,17 +185,11 @@ class FastAPIJobs:
		Parameters
		- id: ID of job to return
		- full: Return extra information ?
		- stdout_position: The index of the character to begine reading stdout from
		- stdout_length: How many characters of stdout to read
		"""
		return self.service.show(
		trans,
		id,
		bool(full),
		int(stdout_position) if stdout_position else 0,
		int(stdout_length) if stdout_length else 0,
		int(stderr_position) if stderr_position else 0,
		int(stderr_length) if stderr_length else 0,
		)

		@router.get("/api/jobs")
		@@ -364,6 +354,49 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
		exceptions.RequestParameterInvalidException(f"Job with id '{job.tool_id}' is not running.")
		return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)

		@expose_api
		def console_output(
		self,
		trans: ProvidesUserContext,
		id,
		stdout_position,
		stdout_length,
		stderr_position,
		stderr_length,
		**kwd
		):
		"""
		* GET /api/jobs/{id}/console_output
		Get the stdout and/or stderr of a job.

		:type id: string
		:param id: Encoded job id

		:type stdout_position: int
		:param stdout_position: The index of the character to begin reading stdout from

		:type stdout_length: int
		:param stdout_length: How many characters of stdout to read

		:type stderr_position: int
		:param stderr_position: The index of the character to begin reading stderr from

		:type stderr_length: int
		:param stderr_length: How many characters of stderr to read

		:rtype: dict
		:returns: dict containing stdout and stderr fields
		"""
		job = self.__get_job(trans, id)
		return self.job_manager.get_job_console_output(
		trans,
		job,
		int(stdout_position),
		int(stdout_length),
		int(stderr_position),
		int(stderr_length)
		)

		@expose_api_anonymous
		def metrics(self, trans: ProvidesUserContext, **kwd):
		"""

lib/galaxy/webapps/galaxy/buildapp.py

+7 −0

Original line number	Diff line number	Diff line
		@@ -1007,6 +1007,13 @@ def populate_api_routes(webapp, app):
		webapp.mapper.connect(
		"finish", "/api/jobs/{id}/finish", controller="jobs", action="finish", conditions=dict(method=["PUT"])
		)
		webapp.mapper.connect(
		"console_output",
		"/api/jobs/{id}/console_output",
		controller="jobs",
		action="console_output",
		conditions=dict(method=["GET"])
		)
		webapp.mapper.connect(
		"job_error", "/api/jobs/{id}/error", controller="jobs", action="error", conditions=dict(method=["POST"])
		)

lib/galaxy/webapps/galaxy/services/jobs.py

+1 −5

Original line number	Diff line number	Diff line
		@@ -48,12 +48,8 @@ class JobsService:
		trans: ProvidesUserContext,
		id: DecodedDatabaseIdField,
		full: bool = False,
		stdout_position: int = 0,
		stdout_length: int = 0,
		stderr_position: int = 0,
		stderr_length: int = 0,
		) -> Dict[str, Any]:
		job = self.job_manager.get_accessible_job(trans, id, stdout_position, stdout_length, stderr_position, stderr_length)
		job = self.job_manager.get_accessible_job(trans, id,)
		return view_show_job(trans, job, bool(full))

		def index(