Merge pull request #20259 from mvdbeek/fix_rerun_button_dynamic_tools (36ea7dad) · Commits · NDIP / Galaxy

client/src/components/Tool/ToolForm.vue

+5 −2

Original line number	Diff line number	Diff line
		@@ -219,6 +219,9 @@ export default {
		const { id, version } = this.formConfig;
		return id.endsWith(version) ? id : `${id}/${version}`;
		},
		toolUuid() {
		return this.uuid \|\| this.formConfig.uuid;
		},
		tooltip() {
		if (!this.canMutateHistory) {
		return this.immutableHistoryMessage;
		@@ -287,7 +290,7 @@ export default {
		onUpdate() {
		this.disabled = true;
		console.debug("ToolForm - Updating input parameters.", this.formData);
		updateToolFormData(this.formConfig.id, this.uuid, this.currentVersion, this.history_id, this.formData)
		updateToolFormData(this.formConfig.id, this.toolUuid, this.currentVersion, this.history_id, this.formData)
		.then((data) => {
		this.formConfig = data;
		})
		@@ -339,7 +342,7 @@ export default {
		history_id: historyId,
		tool_id: this.formConfig.id,
		tool_version: this.formConfig.version,
		tool_uuid: this.uuid,
		tool_uuid: this.toolUuid,
		inputs: {
		...this.formData,
		},

lib/galaxy/jobs/init.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -2754,7 +2754,7 @@ class MinimalJobWrapper(HasResourceParameters):

		def _report_error(self):
		job = self.get_job()
		tool = self.app.toolbox.tool_for_job(job)
		tool = self.app.toolbox.tool_for_job(job, check_access=False)
		for dataset in job.output_datasets:
		self.app.error_reports.default_error_plugin.submit_report(dataset, job, tool, user_submission=False)

		@@ -2777,7 +2777,7 @@ class JobWrapper(MinimalJobWrapper):
		job,
		app=app,
		use_persisted_destination=use_persisted_destination,
		tool=app.toolbox.tool_for_job(job, exact=True),
		tool=app.toolbox.tool_for_job(job, exact=True, check_access=False),
		)
		self.queue = queue
		self.job_runner_mapper = JobRunnerMapper(self, queue.dispatcher.url_to_destination, self.app.job_config)

lib/galaxy/managers/datasets.py

+3 −1

Original line number	Diff line number	Diff line
		@@ -758,7 +758,9 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T],
		"""
		dataset = item
		if dataset.creating_job:
		tool = self.app.toolbox.get_tool(dataset.creating_job.tool_id, dataset.creating_job.tool_version)
		tool = self.app.toolbox.tool_for_job(
		dataset.creating_job, exact=False, check_access=True, user=context.get("user")
		)
		if tool and tool.is_workflow_compatible:
		return True
		return False

lib/galaxy/tools/init.py

+17 −2

Original line number	Diff line number	Diff line
		@@ -639,8 +639,15 @@ class ToolBox(AbstractToolBox):
		return tool
		return None

		def tool_for_job(self, job: model.Job, exact=True) -> Optional["Tool"]:
		def tool_for_job(
		self, job: model.Job, exact=True, check_access=True, user: Optional[model.User] = None
		) -> Optional["Tool"]:
		if job.dynamic_tool:
		if check_access:
		if not user:
		return None
		if not job.dynamic_tool.public:
		self.app.dynamic_tool_manager.ensure_can_use_unprivileged_tool(user)
		return self.dynamic_tool_to_tool(job.dynamic_tool)
		else:
		return self.get_tool(job.tool_id, tool_version=job.tool_version, exact=exact)
		@@ -2794,6 +2801,9 @@ class Tool(UsesDictVisibleKeys):
		tool_dict["is_workflow_compatible"] = self.is_workflow_compatible
		tool_dict["xrefs"] = self.xrefs

		if self.dynamic_tool:
		tool_dict["uuid"] = str(self.dynamic_tool.uuid)

		# Fill in ToolShedRepository info
		if hasattr(self, "tool_shed") and self.tool_shed:
		tool_dict["tool_shed_repository"] = {
		@@ -3016,12 +3026,16 @@ class Tool(UsesDictVisibleKeys):

		visit_input_values(tool_inputs, params, mapping_callback)

		def _compare_tool_version(self, job):
		def _compare_tool_version(self, job: Job):
		"""
		Compares a tool version with the tool version from a job (from ToolRunner).
		"""
		tool_id = job.tool_id
		tool_version = job.tool_version
		if job.dynamic_tool_id:
		# This is the exact tool that was used to run the job.
		# We don't need to compare the version.
		return None
		message = ""
		try:
		select_field, tools, tool = self.app.toolbox.get_tool_components(
		@@ -3031,6 +3045,7 @@ class Tool(UsesDictVisibleKeys):
		raise exceptions.MessageException(
		f"This dataset was created by an obsolete tool ({tool_id}). Can't re-run."
		)
		assert tool_id
		if (self.id != tool_id and self.old_id != tool_id) or self.version != tool_version:
		if self.id == tool_id:
		if tool_version:

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

+1 −1

Original line number	Diff line number	Diff line
		@@ -639,7 +639,7 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
		job = self.__get_job(trans, id)
		if not job:
		raise exceptions.ObjectNotFound("Could not access job with the given id")
		tool = self.app.toolbox.get_tool(job.tool_id, kwd.get("tool_version") or job.tool_version)
		tool = self.app.toolbox.tool_for_job(job, exact=False, check_access=True, user=trans.user)
		if tool is None:
		raise exceptions.ObjectNotFound("Requested tool not found")
		if not tool.is_workflow_compatible:

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