Merge branch 'gzi-job-monitoring' into 'dev' (5f7690f3) · Commits · NDIP / Galaxy

client/src/components/JobInformation/JobInformation.vue

+23 −2

Original line number	Diff line number	Diff line
		<template>
		<div>
		<job-details-provider auto-refresh :jobId="job_id" @update:result="updateJob" />
		<job-details-provider auto-refresh :jobId="job_id" :stdout_start=stdout_position :stdout_char_count=stdout_char_count @update:result="updateJob" />
		<h3>Job Information</h3>
		<table id="job-information" class="tabletip info_data_table">
		<tbody>
		@@ -37,7 +37,7 @@
		</td>
		</tr>
		<code-row v-if="job" id="command-line" :code-label="'Command Line'" :code-item="job.command_line" />
		<code-row v-if="job" id="stdout" :code-label="'Tool Standard Output'" :code-item="job.tool_stdout" />
		<code-row v-if="job" id="stdout" :code-label="'Tool Standard Output'" :code-item="stdout_text" />
		<code-row v-if="job" id="stderr" :code-label="'Tool Standard Error'" :code-item="job.tool_stderr" />
		<code-row
		v-if="job && job.traceback"
		@@ -103,6 +103,9 @@ export default {
		data() {
		return {
		job: null,
		stdout_position: 0,
		stdout_char_count: 50000,
		stdout_text: "",
		};
		},
		computed: {
		@@ -115,12 +118,30 @@ export default {
		return this.job && !JOB_STATES_MODEL.NON_TERMINAL_STATES.includes(this.job.state);
		},
		},
		updated() {
		try {
		const stdout_block = document.querySelector("#stdout").querySelector(".code");
		// if user is scrolled above the bottom of the code element, then no need to update the stdout
		if (stdout_block.scrollTop <= stdout_block.scrollHeight - 3000) {
		this.stdout_char_count = 0;
		} else {
		this.stdout_char_count = 50000;
		}
		} catch(exception) {
		console.log(exception);
		}
		},
		methods: {
		getAppRoot() {
		return getAppRoot();
		},
		updateJob(job) {
		this.job = job;
		// Keep stdout in memory and only fetch new text via JobProvider
		if (job.tool_stdout != null) {
		this.stdout_text += job.tool_stdout;
		this.stdout_position += job.tool_stdout.length;
		}
		},
		},
		};

client/src/components/providers/JobProvider.js

+2 −2

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

		async function jobDetails({ jobId }) {
		const url = `${getAppRoot()}api/jobs/${jobId}?full=True`;
		async function jobDetails({ jobId, stdout_start = 0, stdout_char_count = 0 }) {
		const url = `${getAppRoot()}api/jobs/${jobId}?full=True&stdout_start_pos=${stdout_start}&stdout_count=${stdout_char_count}`;
		try {
		const { data } = await axios.get(url);
		return data;

lib/galaxy/jobs/runners/pulsar.py

+5 −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 +645,10 @@ 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(job_wrapper.working_directory) / "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

+15 −2

Original line number	Diff line number	Diff line
		import json
		import logging
		import typing
		from pathlib import Path
		from datetime import (
		date,
		datetime,
		@@ -56,7 +57,7 @@ from galaxy.util.search import (
		parse_filters_structured,
		RawTextTerm,
		)

		import traceback
		log = logging.getLogger(__name__)


		@@ -219,7 +220,7 @@ 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_start_pos=-1, stdout_count=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()
		@@ -236,6 +237,18 @@ 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 stdout_count and stdout_start_pos are good values, then load standard out and add it to status
		if job.state == job.states.RUNNING and stdout_count > 0 and stdout_start_pos > -1:
		try:
		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"
		stdout_file = open(stdout_path, "r")
		stdout_file.seek(stdout_start_pos)
		job.job_stdout = stdout_file.read(stdout_count)
		job.tool_stdout = job.job_stdout
		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: