Refactor stdout loading in job details screen to keep stdout in memory (415567dd) · Commits · NDIP / Galaxy

client/src/components/JobInformation/JobInformation.vue

+14 −25

Original line number	Diff line number	Diff line
		<template>
		<div>
		<job-details-provider auto-refresh :jobId="job_id" :page_start=stdout_start :page_end=stdout_end @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"
		@@ -103,11 +103,9 @@ export default {
		data() {
		return {
		job: null,
		stdout_start: 1,
		stdout_end: 3,
		stdout_page_length: 5000,
		stdout_live: true,
		stdout_old: false,
		stdout_position: 0,
		stdout_char_count: 50000,
		stdout_text: "",
		};
		},
		computed: {
		@@ -123,18 +121,14 @@ export default {
		updated() {
		try {
		const stdout_block = document.querySelector("#stdout").querySelector(".code");
		if (stdout_block.scrollTop <= .25 * stdout_block.scrollHeight) {
		this.stdout_live = false;
		this.stdout_old = true;
		} else if (stdout_block.scrollTop >= .75 * stdout_block.scrollHeight) {
		this.stdout_live = true;
		this.stdout_old = false;
		// 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_live = false;
		this.stdout_old = false;
		this.stdout_char_count = 50000;
		}
		} catch(exception) {
		console.log("Can not find code div.");
		console.log(exception);
		}
		},
		methods: {
		@@ -143,16 +137,11 @@ export default {
		},
		updateJob(job) {
		this.job = job;
		if (this.job.tool_stdout.length >= this.stdout_page_length * 3 && this.stdout_live) {
		this.stdout_start += 1;
		this.stdout_end += 1;
		// 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;
		}
		if (!this.stdout_live && this.stdout_old) {
		this.stdout_start = this.stdout_start > 1 ? this.stdout_start - 1: 1;
		this.stdout_end = this.stdout_end > 3 ? this.stdout_end - 1: 3;
		}


		},
		},
		};

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, page_start = 0, page_end = 0 }) {
		const url = `${getAppRoot()}api/jobs/${jobId}?full=True&stdout_start=${page_start}&stdout_end=${page_end}`;
		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/managers/jobs.py

+6 −8

Original line number	Diff line number	Diff line
		@@ -60,7 +60,6 @@ from galaxy.util.search import (
		import traceback
		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")
		@@ -221,7 +220,7 @@ class JobManager:
		)
		return self.job_lock()

		def get_accessible_job(self, trans, decoded_job_id, stdout_start=0, stdout_end=0):
		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()
		@@ -239,18 +238,17 @@ class JobManager:
		raise ItemAccessibilityException("You are not allowed to rerun this job.")
		trans.sa_session.refresh(job)

		if job.state == job.states.RUNNING and stdout_start > 0:
		# 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:
		stdout_path = Path(".").parent.parent.parent.parent.parent / "database/jobs_directory/000" / str(
		job.id) / "outputs/tool_stdout"
		stdout_file = open(stdout_path, "r")
		number_of_pages = stdout_end - stdout_start + 1 if stdout_end > 0 else 1
		stdout_file.seek((stdout_start - 1) * STDOUT_PAGE_SIZE_CHARS)
		job.job_stdout = stdout_file.read(STDOUT_PAGE_SIZE_CHARS * number_of_pages)
		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)
		log.error(traceback.format_exc())
		return job

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

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

+5 −3

Original line number	Diff line number	Diff line
		@@ -178,8 +178,8 @@ class FastAPIJobs:
		id: EncodedDatabaseIdField,
		trans: ProvidesUserContext = DependsOnTrans,
		full: Optional[bool] = False,
		stdout_start: Optional[int] = None,
		stdout_end: Optional[int] = None,
		stdout_start_pos: Optional[int] = None,
		stdout_count: Optional[int] = None,
		) -> Dict[str, Any]:
		"""
		Return dictionary containing description of job data
		@@ -187,8 +187,10 @@ class FastAPIJobs:
		Parameters
		- id: ID of job to return
		- full: Return extra information ?
		- stdout_start_pos: The index of the character to begine reading stdout from
		- stdout_count: How many characters of stdout to read
		"""
		return self.service.show(trans, id, bool(full), int(stdout_start) if stdout_start else 0, int(stdout_end) if stdout_end else 0)
		return self.service.show(trans, id, bool(full), int(stdout_start_pos) if stdout_start_pos else 0, int(stdout_count) if stdout_count else 0)

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

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

+3 −3

Original line number	Diff line number	Diff line
		@@ -48,11 +48,11 @@ class JobsService:
		trans: ProvidesUserContext,
		id: EncodedDatabaseIdField,
		full: bool = False,
		stdout_start: int = 0,
		stdout_end: int = 0,
		stdout_start_pos: int = 0,
		stdout_count: int = 0,
		) -> Dict[str, Any]:
		id = trans.app.security.decode_id(id)
		job = self.job_manager.get_accessible_job(trans, id, stdout_start, stdout_end)
		job = self.job_manager.get_accessible_job(trans, id, stdout_start_pos, stdout_count)
		return view_show_job(trans, job, bool(full))

		def index(