Commit c5ac8767 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Merge branch 'stdout-endpoint' into 'dev' 

Add console output endpoint

See merge request !67
parents 15852de1 cc57ae84

client/src/components/JobInformation/JobInformation.test.js

+1 −1
Original line number Diff line number Diff line
@@ -24,7 +24,7 @@ describe("JobInformation/JobInformation.vue", () => { 
    beforeEach(() => {

        axiosMock = new MockAdapter(axios);

        axiosMock.onGet(new RegExp(`api/configuration/decode/*`)).reply(200, { decoded_id: 123 });

        axiosMock.onGet("/api/jobs/test_id?full=True&stdout_position=0&stdout_length=50000&stderr_position=0&stderr_length=50000").reply(200, jobResponse);

        axiosMock.onGet("/api/jobs/test_id?full=True").reply(200, jobResponse);

    });



    afterEach(() => {

client/src/components/JobInformation/JobInformation.vue

+34 −10
Original line number Diff line number Diff line 
<template>

    <div>

        <job-details-provider auto-refresh :jobId="job_id" :stdout_position=stdout_position :stdout_length=stdout_length :stderr_position=stderr_position :stderr_length=stderr_length @update:result="updateJob"/>

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

        <JobConsoleOutputProvider

            auto-refresh="True"

            :job-id="job_id"

            :stdout_position="stdout_position"

            :stdout_length="stdout_length"

            :stderr_position="stderr_position"

            :stderr_length="stderr_length"

            @update:result="updateConsoleOutputs"/>

        <h2 class="h-md">Job Information</h2>

        <table id="job-information" class="tabletip info_data_table">

            <tbody>
@@ -80,7 +88,7 @@ 
import { getAppRoot } from "onload/loadConfig";

import DecodedId from "../DecodedId.vue";

import CodeRow from "./CodeRow.vue";

import { JobDetailsProvider } from "components/providers/JobProvider";

import { JobDetailsProvider, JobConsoleOutputProvider } from "components/providers/JobProvider";

import UtcDate from "components/UtcDate";

import CopyToClipboard from "components/CopyToClipboard";

import JOB_STATES_MODEL from "utils/job-states-model";
@@ -91,6 +99,7 @@ export default { 
        CodeRow,

        DecodedId,

        JobDetailsProvider,

        JobConsoleOutputProvider,

        UtcDate,

        CopyToClipboard,

    },
@@ -131,16 +140,31 @@ export default { 
        },

        updateJob(job) {

            this.job = job;

            // Keep stdout in memory and only fetch new text via JobProvider

            if (job.tool_stdout != null) {

            // Load stored stdout and stderr

            if (this.jobIsTerminal) {

                if (job.tool_stdout) {

                    this.stdout_text += job.tool_stdout;

                    this.stdout_position += job.tool_stdout.length;

                }

            if (job.tool_stderr != null) {

                if (job.tool_stderr) {

                    this.stderr_text += job.tool_stderr;

                    this.stderr_position += job.tool_stderr.length;

                }

            }

        },

        updateConsoleOutputs(output) {

            // Keep stdout in memory and only fetch new text via JobProvider

            if (output && !this.jobIsTerminal) {

                if (output.stdout != null) {

                    this.stdout_text += output.stdout;

                    this.stdout_position += output.stdout.length;

                }

                if (output.stderr != null) {

                    this.stderr_text += output.stderr;

                    this.stderr_position += output.stderr.length;

                }

            }

        }

    },

};

</script>

client/src/components/providers/JobProvider.js

+13 −2
Original line number Diff line number Diff line
@@ -5,8 +5,18 @@ import { rethrowSimple } from "utils/simple-error"; 
import { stateIsTerminal } from "./utils";

import { cleanPaginationParameters } from "./utils";



async function jobDetails({ jobId, stdout_position = 0, stdout_length = 0, stderr_position = 0, stderr_length = 0 }) {

    const url = `${getAppRoot()}api/jobs/${jobId}?full=True&stdout_position=${stdout_position}&stdout_length=${stdout_length}&stderr_position=${stderr_position}&stderr_length=${stderr_length}`;

async function jobDetails({ jobId }) {

    const url = `${getAppRoot()}api/jobs/${jobId}?full=True`;

    try {

        const { data } = await axios.get(url);

        return data;

    } catch (e) {

        rethrowSimple(e);

    }

}



async function jobConsoleOutput({ jobId, stdout_position = 0, stdout_length = 0, stderr_position = 0, stderr_length = 0 }) {

    const url = `${getAppRoot()}api/jobs/${jobId}/console_output?stdout_position=${stdout_position}&stdout_length=${stdout_length}&stderr_position=${stderr_position}&stderr_length=${stderr_length}`;

    try {

        const { data } = await axios.get(url);

        return data;
@@ -26,6 +36,7 @@ async function jobProblems({ jobId }) { 
}



export const JobDetailsProvider = SingleQueryProvider(jobDetails, stateIsTerminal);

export const JobConsoleOutputProvider = SingleQueryProvider(jobConsoleOutput, stateIsTerminal);

export const JobProblemProvider = SingleQueryProvider(jobProblems, stateIsTerminal);



export function jobsProvider(ctx, callback, extraParams = {}) {

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):

        """