Merge branch 'stop-job-feature' into 'dev' (ee35008f) · Commits · NDIP / Galaxy

client/src/components/History/Content/Dataset/DatasetActions.vue

+27 −0

Original line number	Diff line number	Diff line
		@@ -61,6 +61,15 @@
		@click.stop="onHighlight">
		<span class="fa fa-sitemap" />
		</b-button>
		<b-button
		v-if="showStop"
		class="stop-btn px-1"
		title="Finish Job Early"
		size="sm"
		variant="link"
		@click.stop="onStop">
		<span class="fa fa-solid fa-stop" />
		</b-button>
		<b-button v-if="showRerun" class="px-1" title="Help" size="sm" variant="link" @click.stop="onRerun">
		<span class="fa fa-question" />
		</b-button>
		@@ -74,6 +83,7 @@ import { copy as sendToClipboard } from "utils/clipboard";
		import { absPath, prependPath } from "@/utils/redirect";
		import { downloadUrlMixin } from "./mixins.js";
		import DatasetDownload from "./DatasetDownload";
		import { stopJob } from "components/History/model/queries";

		export default {
		components: {
		@@ -120,6 +130,9 @@ export default {
		visualizeUrl() {
		return prependPath(this.itemUrls.visualize);
		},
		showStop() {
		return this.item.state == "running";
		},
		},
		methods: {
		onCopyLink() {
		@@ -145,6 +158,20 @@ export default {
		onHighlight() {
		this.$emit("toggleHighlights");
		},
		onStop() {
		stopJob(this.item.creating_job);
		document.querySelector(".stop-btn").classList.add("stopping-job");
		},
		},
		};
		</script>
		<style scoped>
		.stopping-job {
		animation: blink-animation .5s steps(5, start) infinite;
		}
		@keyframes blink-animation {
		to {
		visibility: hidden;
		}
		}
		</style>

+9 −0

Original line number	Diff line number	Diff line
		@@ -53,6 +53,15 @@ export async function deleteContent(content, deleteParams = {}) {
		return doResponse(response);
		}

		/**
		* Stops job and marks it as complete.
		*/
		export async function stopJob(job_id) {
		const url = `api/jobs/${job_id}/finish`;
		const response = await axios.put(prependPath(url));
		return doResponse(response);
		}

		/**
		* Update specific fields on datasets or collections.
		* @param {Object} content content object

+5 −2

Original line number	Diff line number	Diff line
		@@ -739,7 +739,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
		)
		return False

		def stop_job(self, job_wrapper):
		def stop_job(self, job_wrapper, soft_kill=True):
		job = job_wrapper.get_job()
		if not job.job_runner_external_id:
		return
		@@ -778,6 +778,9 @@ class PulsarJobRunner(AsynchronousJobRunner):
		job_id = job.job_runner_external_id
		log.debug(f"Attempt remote Pulsar kill of job with url {pulsar_url} and id {job_id}")
		client = self.get_client(job.destination_params, job_id)
		if soft_kill:
		client.kill(soft_kill=soft_kill)
		else:
		client.kill()

		def recover(self, job, job_wrapper):

+12 −0

Original line number	Diff line number	Diff line
		@@ -270,6 +270,18 @@ class JobManager:
		else:
		return False

		def finish_early(self, job):
		if not job.finished:
		try:
		job.mark_stopped(self.app.config.track_jobs_in_database)
		session = self.app.model.session
		with transaction(session):
		session.commit()
		self.app.job_manager.stop(job, message="")
		return True
		except Exception as e:
		log.error("Job Runner does not support stopping job early.")
		return False

		class JobSearch:
		"""Search for jobs using tool inputs or other jobs"""

+21 −0

Original line number	Diff line number	Diff line
		@@ -339,6 +339,27 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
		exceptions.RequestParameterInvalidException(f"Job with id '{job.tool_id}' is not paused")
		return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)

		@expose_api
		def finish(self, trans: ProvidesUserContext, id, **kwd) -> List[dict]:
		"""
		* PUT /api/jobs/{id}/finish
		Finished a job regardless of execution status (ie early job finish)

		:type id: string
		:param id: Encoded job id

		:rtype: list of dicts
		:returns: list of dictionaries containing output dataset associations
		"""
		job = self.__get_job(trans, id)
		if not job:
		raise exceptions.ObjectNotFound("Could not access job with the given id")
		if job.state == job.states.RUNNING:
		self.job_manager.finish_early(job)
		else:
		exceptions.RequestParameterInvalidException(f"Job with id '{job.tool_id}' is not running.")
		return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)

		@expose_api_anonymous
		def metrics(self, trans: ProvidesUserContext, **kwd):
		"""