Commit f929c6ed authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Add job console output endpoint and update job schema

parent c63538d9

client/src/components/JobInformation/JobInformation.vue

+2 −2
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ 
    <div>

        <JobDetailsProvider auto-refresh :job-id="job_id" @update:result="updateJob"/>

        <JobConsoleOutputProvider

            auto-refresh="True"

            auto-refresh

            :job-id="job_id"

            :stdout_position="stdout_position"

            :stdout_length="stdout_length"
@@ -166,7 +166,7 @@ export default { 
                    this.stderr_position += output.stderr.length;

                }

            }

        }

        },

    },

};

</script>

lib/galaxy/schema/jobs.py

+6 −0
Original line number Diff line number Diff line
@@ -207,6 +207,12 @@ class JobOutput(Model): 
    value: EncodedDataItemSourceId = Field(default=Required, title="Dataset", description="The associated dataset.")





class JobConsoleOutput(Model):

    state: str = Field(None, title="Job State", description="The current job's state")

    stdout: Optional[str] = Field(None, title="STDOUT", description="Job STDOUT text")

    stderr: Optional[str] = Field(None, title="STDERR", description="Job STDERR text")





class JobParameter(Model):

    text: str = Field(

        default=Required,

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

+31 −0
Original line number Diff line number Diff line
@@ -41,6 +41,7 @@ from galaxy.schema.fields import DecodedDatabaseIdField 
from galaxy.schema.jobs import (

    DeleteJobPayload,

    EncodedJobDetails,

    JobConsoleOutput,

    JobDestinationParams,

    JobDisplayParametersSummary,

    JobErrorSummary,
@@ -360,6 +361,36 @@ class FastAPIJobs: 
            output_associations.append(JobOutputAssociation(name=association.name, dataset=association.dataset))

        return output_associations



    @router.get(

        "/api/jobs/{job_id}/console_output",

        name="get_console_output",

        summary="Returns STDOUT and STDERR from job.",

    )

    def console_output(

            self,

            job_id: Annotated[DecodedDatabaseIdField, JobIdPathParam],

            stdout_position: int,

            stdout_length: int,

            stderr_position: int,

            stderr_length: int,

            trans: ProvidesUserContext = DependsOnTrans,

    ) -> JobConsoleOutput:

        """

        Get the stdout and/or stderr of a job. The position parameters are the index

        of where to start reading stdout/stderr. The length parameterscontrol how much

        stdout/stderr is read.

        """

        job = self.service.get_job(trans, job_id)

        output = self.service.job_manager.get_job_console_output(

            trans,

            job,

            int(stdout_position),

            int(stdout_length),

            int(stderr_position),

            int(stderr_length),

        )

        return JobConsoleOutput(state=output["state"], stdout=output["stdout"], stderr=output["stderr"])



    @router.get(

        "/api/jobs/{job_id}/parameters_display",

        name="resolve_parameters_display",