Commit 485406af authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Add stderr loading to job status

parent ef6ba69f

lib/galaxy/managers/jobs.py

+25 −13
Original line number Diff line number Diff line
@@ -66,6 +66,8 @@ from galaxy.util.search import ( 


log = logging.getLogger(__name__)



STDOUT_LOCATION = "outputs/tool_stdout"

STDERR_LOCATION = "outputs/tool_stderr"



class JobLock(BaseModel):

    active: bool = Field(title="Job lock status", description="If active, jobs will not dispatch")
@@ -226,7 +228,7 @@ class JobManager: 
        )

        return self.job_lock()



    def get_accessible_job(self, trans, decoded_job_id, stdout_position=-1, stdout_length=0):

    def get_accessible_job(self, trans, decoded_job_id, stdout_position=-1, stdout_length=0, stderr_position=-1, stderr_length=0):

        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()
@@ -245,18 +247,28 @@ class JobManager: 
        trans.sa_session.refresh(job)



        # If stdout_length and stdout_position are good values, then load standard out and add it to status

        if job.state == job.states.RUNNING and stdout_length > 0 and stdout_position > -1:

            try:

        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

            )

                stdout_path = Path(working_directory) / "outputs" / "tool_stdout"

            if stdout_length > 0 and stdout_position > -1:

                try:

                    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

                except Exception as e:

                    log.error("Could not read STDOUT: %s", e)

            if stderr_length > 0 and stderr_position > -1:

                try:

                    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

                except Exception as e:

                    log.error("Could not read STDERR: %s", e)

        return job



    def stop(self, job, message=None):

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

+4 −0
Original line number Diff line number Diff line
@@ -180,6 +180,8 @@ class FastAPIJobs: 
        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
@@ -196,6 +198,8 @@ class FastAPIJobs: 
            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")

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

+3 −1
Original line number Diff line number Diff line
@@ -50,8 +50,10 @@ class JobsService: 
        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)

        job = self.job_manager.get_accessible_job(trans, id, stdout_position, stdout_length, stderr_position, stderr_length)

        return view_show_job(trans, job, bool(full))



    def index(