Merge branch 'gzi-stderr-update' into 'dev' (200bf9e3) · Commits · NDIP / Galaxy

client/src/components/JobInformation/CodeRow.vue

+13 −18

Original line number	Diff line number	Diff line
		<template>
		<tr
		v-b-tooltip.hover
		:title="`click to ${action}`"
		@mousedown="mouseIsDown = true"
		@mousemove="mouseIsDown ? (mouseMoved = true) : (mouseMoved = false)"
		@mouseup="toggleExpanded()">
		<tr>
		<td>
		{{ codeLabel }}
		</td>
		@@ -13,7 +8,10 @@
		<b-col cols="11">
		<pre :class="codeClass">{{ codeItem }}</pre>
		</b-col>
		<b-col class="nopadding pointer">
		<b-col class="nopadding pointer"
		v-b-tooltip.hover
		:title="`click to ${action}`"
		@mouseup="toggleExpanded()">
		<font-awesome-icon :icon="iconClass" />
		</b-col>
		</b-row>
		@@ -37,10 +35,8 @@ export default {
		},
		data() {
		return {
		mouseIsDown: false,
		mouseMoved: false,
		expanded: false,
		lastHeight: 0,
		lastPos: 0,
		};
		},
		computed: {
		@@ -55,21 +51,20 @@ export default {
		},
		},
		updated() {
		// If the user is at the bottom of the code div, auto scroll for them.
		try {
		var codeDiv = document.querySelector("#stdout").querySelector(".code");
		if (codeDiv.scrollTop >= this.lastHeight - 3000) {
		var codeDiv = this.$el.querySelector(".code");
		if (codeDiv.scrollTop + codeDiv.offsetHeight >= this.lastPos - 5) {
		// scroll is at the bottom
		codeDiv.scrollTop = codeDiv.scrollHeight;
		}
		this.lastHeight = codeDiv.scrollHeight;
		this.lastPos = codeDiv.scrollHeight;
		} catch(exception) {
		console.log("Code div is not present");
		console.debug("Code div is not present");
		}
		},
		methods: {
		toggleExpanded() {
		this.mouseIsDown = false;
		if (this.codeItem && !this.mouseMoved) {
		if (this.codeItem) {
		this.expanded = !this.expanded;
		}
		},

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

+4 −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").reply(200, jobResponse);
		axiosMock.onGet("/api/jobs/test_id?full=True&stdout_position=0&stdout_length=50000&stderr_position=0&stderr_length=50000").reply(200, jobResponse);
		});

		afterEach(() => {
		@@ -48,6 +48,9 @@ describe("JobInformation/JobInformation.vue", () => {
		stdout_position: STDOUT_POSITION,
		stdout_length: STDOUT_LENGTH,
		stdout_text: STDOUT_TEXT,
		stderr_position: STDOUT_POSITION,
		stderr_length: STDOUT_LENGTH,
		stderr_text: STDOUT_TEXT,
		};
		wrapper = mount(JobInformation, {
		propsData,

client/src/components/JobInformation/JobInformation.vue

+9 −15

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 @update:result="updateJob" />
		<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"/>
		<h2 class="h-md">Job Information</h2>
		<table id="job-information" class="tabletip info_data_table">
		<tbody>
		@@ -42,7 +42,7 @@
		</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="stdout_text" />
		<code-row v-if="job" id="stderr" :code-label="'Tool Standard Error'" :code-item="job.tool_stderr" />
		<code-row v-if="job" id="stderr" :code-label="'Tool Standard Error'" :code-item="stderr_text" />
		<code-row
		v-if="job && job.traceback"
		id="traceback"
		@@ -110,6 +110,9 @@ export default {
		stdout_position: 0,
		stdout_length: 50000,
		stdout_text: "",
		stderr_position: 0,
		stderr_length: 50000,
		stderr_text: "",
		};
		},
		computed: {
		@@ -122,19 +125,6 @@ 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_length = 0;
		} else {
		this.stdout_length = 50000;
		}
		} catch(exception) {
		console.log(exception);
		}
		},
		methods: {
		getAppRoot() {
		return getAppRoot();
		@@ -146,6 +136,10 @@ export default {
		this.stdout_text += job.tool_stdout;
		this.stdout_position += job.tool_stdout.length;
		}
		if (job.tool_stderr != null) {
		this.stderr_text += job.tool_stderr;
		this.stderr_position += job.tool_stderr.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, stdout_position = 0, stdout_length = 0 }) {
		const url = `${getAppRoot()}api/jobs/${jobId}?full=True&stdout_position=${stdout_position}&stdout_length=${stdout_length}`;
		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}`;
		try {
		const { data } = await axios.get(url);
		return data;

lib/galaxy/jobs/runners/pulsar.py

+14 −9

Original line number	Diff line number	Diff line
		@@ -657,14 +657,19 @@ class PulsarJobRunner(AsynchronousJobRunner):
		run_results = client.full_status()
		remote_metadata_directory = run_results.get("metadata_directory", None)
		tool_stdout = run_results.get("stdout", "")
		if tool_stdout is None:
		tool_stderr = run_results.get("stderr", "")
		for file in ("tool_stdout", "tool_stderr"):
		if tool_stdout and tool_stderr:
		pass
		try:
		stdout_path = Path(job_wrapper.working_directory) / "outputs" / "tool_stdout"
		stdout_file = open(stdout_path, "r")
		tool_stdout = stdout_file.read()
		file_path = Path(job_wrapper.working_directory) / "outputs" / file
		file_content = open(file_path, "r")
		if tool_stdout is None and file == "tool_stdout":
		tool_stdout = file_content.read()
		elif tool_stderr is None and file == "tool_stderr":
		tool_stderr = file_content.read()
		except Exception:
		pass
		tool_stderr = run_results.get("stderr", "")
		job_stdout = run_results.get("job_stdout")
		job_stderr = run_results.get("job_stderr")
		exit_code = run_results.get("returncode")