Merge branch 'update-job-monitoring' into 'dev' (f2c0f721) · Commits · NDIP / Galaxy

client/src/components/JobInformation/JobInformation.vue

+4 −4

Original line number	Diff line number	Diff line
		<template>
		<div>
		<job-details-provider auto-refresh :jobId="job_id" :stdout_start=stdout_position :stdout_char_count=stdout_char_count @update:result="updateJob" />
		<job-details-provider auto-refresh :jobId="job_id" :stdout_position=stdout_position :stdout_length=stdout_length @update:result="updateJob" />
		<h2 class="h-md">Job Information</h2>
		<table id="job-information" class="tabletip info_data_table">
		<tbody>
		@@ -108,7 +108,7 @@ export default {
		return {
		job: null,
		stdout_position: 0,
		stdout_char_count: 50000,
		stdout_length: 50000,
		stdout_text: "",
		};
		},
		@@ -127,9 +127,9 @@ export default {
		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;
		this.stdout_length = 0;
		} else {
		this.stdout_char_count = 50000;
		this.stdout_length = 50000;
		}
		} catch(exception) {
		console.log(exception);

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

+5 −5

Original line number	Diff line number	Diff line
		@@ -222,7 +222,7 @@ class JobManager:
		)
		return self.job_lock()

		def get_accessible_job(self, trans, decoded_job_id, stdout_start_pos=-1, stdout_count=0):
		def get_accessible_job(self, trans, decoded_job_id, stdout_position=-1, stdout_length=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()
		@@ -240,16 +240,16 @@ class JobManager:
		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:
		# If stdout_length and stdout_position are good values, then load standard out and add it to status
		if job.state == job.states.RUNNING and stdout_length > 0 and stdout_position > -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)
		stdout_file.seek(stdout_position)
		job.job_stdout = stdout_file.read(stdout_length)
		job.tool_stdout = job.job_stdout
		except Exception as e:
		log.error("Could not read STDOUT: %s", e)

+6 −6

Original line number	Diff line number	Diff line
		@@ -178,8 +178,8 @@ class FastAPIJobs:
		id: DecodedDatabaseIdField,
		trans: ProvidesUserContext = DependsOnTrans,
		full: Optional[bool] = False,
		stdout_start_pos: Optional[int] = None,
		stdout_count: Optional[int] = None,
		stdout_position: Optional[int] = None,
		stdout_length: Optional[int] = None,
		) -> Dict[str, Any]:
		"""
		Return dictionary containing description of job data
		@@ -187,15 +187,15 @@ 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
		- 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_start_pos) if stdout_start_pos else 0,
		int(stdout_count) if stdout_count else 0,
		int(stdout_position) if stdout_position else 0,
		int(stdout_length) if stdout_length else 0,
		)

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

+3 −3

Original line number	Diff line number	Diff line
		@@ -48,10 +48,10 @@ class JobsService:
		trans: ProvidesUserContext,
		id: DecodedDatabaseIdField,
		full: bool = False,
		stdout_start_pos: int = 0,
		stdout_count: int = 0,
		stdout_position: int = 0,
		stdout_length: int = 0,
		) -> Dict[str, Any]:
		job = self.job_manager.get_accessible_job(trans, id, stdout_start_pos, stdout_count)
		job = self.job_manager.get_accessible_job(trans, id, stdout_position, stdout_length)
		return view_show_job(trans, job, bool(full))

		def index(