Merge pull request #14296 from mvdbeek/deleted_discarded_file_not_found_tweaks (48487c56) · Commits · NDIP / Galaxy

client/src/components/Workflow/WorkflowDropdown.vue

+3 −3

Original line number	Diff line number	Diff line
		@@ -101,9 +101,9 @@ export default {
		return `${getAppRoot()}workflows/${this.workflow.id}/invocations`;
		},
		urlViewShared() {
		return `${getAppRoot()}workflow/display_by_username_and_slug?username=${this.workflow.owner}&slug=${
		this.workflow.slug
		}`;
		return `${getAppRoot()}workflow/display_by_username_and_slug?username=${
		this.workflow.owner
		}&slug=${encodeURIComponent(this.workflow.slug)}`;
		},
		readOnly() {
		return !!this.workflow.shared;

lib/galaxy/datatypes/interval.py

+4 −2

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@ from galaxy.datatypes.util.gff_util import (
		parse_gff3_attributes,
		parse_gff_attributes,
		)
		from galaxy.model import DatasetInstance
		from galaxy.util import compression_utils
		from . import (
		data,
		@@ -167,10 +168,11 @@ class Interval(Tabular):
		else:
		empty_line_count += 1

		def displayable(self, dataset):
		def displayable(self, dataset: DatasetInstance):
		try:
		return (
		dataset.has_data()
		not dataset.dataset.purged
		and dataset.has_data()
		and dataset.state == dataset.states.OK
		and dataset.metadata.columns > 0
		and dataset.metadata.data_lines != 0

lib/galaxy/datatypes/tabular.py

+4 −2

Original line number	Diff line number	Diff line
		@@ -34,6 +34,7 @@ from galaxy.datatypes.sniff import (
		iter_headers,
		validate_tabular,
		)
		from galaxy.model import DatasetInstance
		from galaxy.util import compression_utils
		from . import dataproviders

		@@ -90,10 +91,11 @@ class TabularData(data.Text):
		if dataset.metadata.comment_lines:
		dataset.blurb = f"{dataset.blurb}, {util.commaify(str(dataset.metadata.comment_lines))} comments"

		def displayable(self, dataset):
		def displayable(self, dataset: DatasetInstance):
		try:
		return (
		dataset.has_data()
		not dataset.dataset.purged
		and dataset.has_data()
		and dataset.state == dataset.states.OK
		and dataset.metadata.columns > 0
		and dataset.metadata.data_lines != 0

lib/galaxy/webapps/galaxy/controllers/dataset.py

+55 −48

Original line number	Diff line number	Diff line
		@@ -25,6 +25,7 @@ from galaxy.managers.hdas import (
		HDAManager,
		)
		from galaxy.managers.histories import HistoryManager
		from galaxy.model import Dataset
		from galaxy.model.item_attrs import (
		UsesAnnotations,
		UsesItemRatings,
		@@ -147,17 +148,27 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
		except Exception:
		data = None
		if not data:
		raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable(f"Invalid reference dataset id: {str(hda_id)}.")
		raise web.httpexceptions.HTTPNotFound(f"Invalid reference dataset id: {str(hda_id)}.")
		if not self._can_access_dataset(trans, data):
		return trans.show_error_message("You are not allowed to access this dataset")
		if data.purged:
		return trans.show_error_message("The dataset you are attempting to view has been purged.")
		if data.deleted and not (trans.user_is_admin or (data.history and trans.get_user() == data.history.user)):
		elif data.deleted and not (trans.user_is_admin or (data.history and trans.get_user() == data.history.user)):
		return trans.show_error_message("The dataset you are attempting to view has been deleted.")
		if data.state == trans.model.Dataset.states.UPLOAD:
		elif data.state == Dataset.states.UPLOAD:
		return trans.show_error_message(
		"Please wait until this dataset finishes uploading before attempting to view it."
		)
		elif data.state == Dataset.states.DISCARDED:
		return trans.show_error_message("The dataset you are attempting to view has been discarded.")
		elif data.state == Dataset.states.DEFERRED:
		return trans.show_error_message(
		"The dataset you are attempting to view has deferred data. You can only use this dataset as input for jobs."
		)
		elif data.state == Dataset.states.PAUSED:
		return trans.show_error_message(
		"The dataset you are attempting to view is in paused state. One of the inputs for the job that creates this dataset has failed."
		)
		return data

		@web.expose
		@@ -563,11 +574,9 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
		@web.expose
		def display_by_username_and_slug(self, trans, username, slug, filename=None, preview=True):
		"""Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id."""
		id = slug
		decoded_id = self.decode_id(id)
		dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
		dataset = self.hda_manager.error_if_uploading(dataset)
		if dataset:
		dataset = self._check_dataset(trans, slug)
		if not isinstance(dataset, trans.app.model.DatasetInstance):
		return dataset
		# Filename used for composite types.
		if filename:
		return self.display(trans, dataset_id=slug, filename=filename)
		@@ -610,8 +619,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
		num_ratings=num_ratings,
		first_chunk=first_chunk,
		)
		else:
		raise web.httpexceptions.HTTPNotFound()

		@web.expose
		def get_item_content_async(self, trans, id):

lib/galaxy/webapps/galaxy/services/dataset_collections.py

+8 −1

Original line number	Diff line number	Diff line
		@@ -9,6 +9,7 @@ from pydantic import (
		BaseModel,
		Extra,
		Field,
		ValidationError,
		)

		from galaxy import exceptions
		@@ -254,4 +255,10 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
		return result

		rval = [serialize_element(el) for el in contents]
		try:
		return DatasetCollectionContentElements.parse_obj(rval)
		except ValidationError:
		log.exception(
		f"Serializing DatasetCollectionContentsElements failed. Collection is populated: {hdca.collection.populated}"
		)
		raise