Commit 23aadd11 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Provide an option to get stdout as part of api status request

parent d2c74366

lib/galaxy/jobs/runners/pulsar.py

+6 −0
Original line number Diff line number Diff line
@@ -8,6 +8,7 @@ import logging 
import os

import re

import subprocess

from pathlib import Path

from time import sleep



import packaging.version
@@ -644,6 +645,11 @@ class PulsarJobRunner(AsynchronousJobRunner): 
            run_results = client.full_status()

            remote_metadata_directory = run_results.get("metadata_directory", None)

            stdout = run_results.get("stdout", "")

            if stdout == "":

                stdout_path = Path(".").parent.parent.parent.parent.parent / "database/jobs_directory/000" / str(

                    run_results["job_id"]) / "outputs/tool_stdout"

                stdout_file = open(stdout_path, "r")

                stdout = stdout_file.read()

            stderr = run_results.get("stderr", "")

            exit_code = run_results.get("returncode", None)

            pulsar_outputs = PulsarOutputs.from_status_response(run_results)

lib/galaxy/managers/jobs.py

+12 −8
Original line number Diff line number Diff line
@@ -60,6 +60,7 @@ from galaxy.util.search import ( 


log = logging.getLogger(__name__)



STDOUT_PAGE_SIZE_CHARS = 5000



class JobLock(BaseModel):

    active: bool = Field(title="Job lock status", description="If active, jobs will not dispatch")
@@ -220,7 +221,7 @@ class JobManager: 
        )

        return self.job_lock()



    def get_accessible_job(self, trans, decoded_job_id):

    def get_accessible_job(self, trans, decoded_job_id, stdout_page=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()
@@ -237,17 +238,20 @@ 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)

        if job.state == job.states.RUNNING:

        if job.state == job.states.RUNNING and stdout_page != 0:

            try:

                stdout_path = Path(".").parent.parent.parent.parent.parent / "database/jobs_directory/000" / str(

                    job.id) / "outputs/tool_stdout"

                stdout_file = open(stdout_path, "r")

                # stderr_file = open("../../../../../database/jobs_directory/000/" + str(job.id) + "/outputs/tool_stderr")

                job.job_stdout = stdout_file.read()

                stdout_file = open(stdout_path, "rb")

                if stdout_page < 0:

                    stdout_file.seek((stdout_page) * STDOUT_PAGE_SIZE_CHARS, 2)

                    job.job_stdout = stdout_file.read(STDOUT_PAGE_SIZE_CHARS).decode("utf-8")

                else:

                    stdout_file.seek((stdout_page - 1) * STDOUT_PAGE_SIZE_CHARS)

                    job.job_stdout = stdout_file.read(STDOUT_PAGE_SIZE_CHARS).decode("utf-8")

                job.tool_stdout = job.job_stdout

                # job.stderr = stderr_file.read()

            except:

                log.error("Could not load std out")

            except Exception as e:

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

        return job



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

lib/galaxy/webapps/galaxy/api/job_files.py

+5 −1
Original line number Diff line number Diff line
@@ -104,6 +104,10 @@ class JobFilesAPIController(BaseGalaxyAPIController): 
        target_dir = os.path.dirname(path)

        util.safe_makedirs(target_dir)

        try:

            if os.path.exists(path):

                with open(path, 'ab') as dest:

                    shutil.copyfileobj(open(input_file.name, 'rb'), dest)

            else:

                shutil.move(input_file.name, path)

        finally:

            try:

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

+2 −1
Original line number Diff line number Diff line
@@ -178,6 +178,7 @@ class FastAPIJobs: 
        id: EncodedDatabaseIdField,

        trans: ProvidesUserContext = DependsOnTrans,

        full: Optional[bool] = False,

        stdout_page: Optional[int] = None,

    ) -> Dict[str, Any]:

        """

        Return dictionary containing description of job data
@@ -186,7 +187,7 @@ class FastAPIJobs: 
        - id: ID of job to return

        - full: Return extra information ?

        """

        return self.service.show(trans, id, bool(full))

        return self.service.show(trans, id, bool(full), int(stdout_page) if stdout_page else 0)



    @router.get("/api/jobs")

    def index(

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

+2 −1
Original line number Diff line number Diff line
@@ -48,9 +48,10 @@ class JobsService: 
        trans: ProvidesUserContext,

        id: EncodedDatabaseIdField,

        full: bool = False,

        stdout_page: int = 0,

    ) -> Dict[str, Any]:

        id = trans.app.security.decode_id(id)

        job = self.job_manager.get_accessible_job(trans, id)

        job = self.job_manager.get_accessible_job(trans, id, stdout_page)

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



    def index(