More test coverage for workflow running with collections. (6c9bc27d) · Commits · NDIP / Galaxy

lib/galaxy/selenium/navigates_galaxy.py

+12 −0

Original line number	Diff line number	Diff line
		@@ -605,6 +605,18 @@ class NavigatesGalaxy(HasDriver):
		raise self.prepend_timeout_message(e, message)
		return history_item_selector_state

		def history_panel_wait_for_and_select(self, hids: List[int]):
		"""
		Waits for uploads to pass through queued, running, ok. Not all the states are not guaranteed
		depending on how fast the upload goes compared to the history polling updates, it might just
		skip to the end for a really fast upload
		"""
		for hid in hids:
		self.history_panel_wait_for_hid_ok(hid)
		self.history_panel_multi_operations_show()
		for hid in hids:
		self.history_panel_muli_operation_select_hid(hid)

		@retry_during_transitions
		def get_grid_entry_names(self, selector):
		self.sleep_for(self.wait_types.UX_RENDER)

lib/galaxy_test/base/workflow_fixtures.py

+12 −0

Original line number	Diff line number	Diff line
		@@ -892,6 +892,18 @@ steps:
		"""


		WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT = """
		class: GalaxyWorkflow
		inputs:
		- id: input_list
		type: collection
		collection_type: "list:paired_or_unpaired"
		steps:
		- tool_id: collection_list_paired_or_unpaired
		in:
		f1: input_list
		"""


		WORKFLOW_WITH_OUTPUTS = """
		class: GalaxyWorkflow

lib/galaxy_test/selenium/test_collection_builders.py

+1 −10

Original line number	Diff line number	Diff line
		@@ -175,16 +175,7 @@ class TestCollectionBuilders(SeleniumTestCase):
		return self.use_bootstrap_dropdown(option=option_description, menu="selected content menu")

		def _wait_for_and_select(self, hids):
		"""
		Waits for uploads to pass through queued, running, ok. Not all the states are not guaranteed
		depending on how fast the upload goes compared to the history polling updates, it might just
		skip to the end for a really fast upload
		"""
		for hid in hids:
		self.history_panel_wait_for_hid_ok(hid)
		self.history_panel_multi_operations_show()
		for hid in hids:
		self.history_panel_muli_operation_select_hid(hid)
		self.history_panel_wait_for_and_select(hids)

		def _show_hidden_content(self):
		"""Switches the hidden filter toggle on"""

lib/galaxy_test/selenium/test_workflow_run.py

+66 −1

Original line number	Diff line number	Diff line
		@@ -8,6 +8,7 @@ from typing_extensions import Literal
		from galaxy_test.base import rules_test_data
		from galaxy_test.base.workflow_fixtures import (
		WORKFLOW_LIST_PAIRED_MAPPED_OVER_PAIRED,
		WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT,
		WORKFLOW_NESTED_REPLACEMENT_PARAMETER,
		WORKFLOW_NESTED_RUNTIME_PARAMETER,
		WORKFLOW_NESTED_SIMPLE,
		@@ -402,6 +403,70 @@ steps: {}
		invocation = self.workflow_populator.get_invocation(invocations[-1]["id"])
		assert invocation["inputs"]["0"]["id"] == dataset["id"]

		@selenium_test
		@managed_history
		def test_workflow_run_list_paired_or_unpaired_with_paired_list(self):
		history_id = self.current_history_id()
		self.perform_upload_of_pasted_content(
		{
		"foo_1.fasta": "forward content",
		"foo_2.fasta": "reverse content",
		}
		)
		self.history_panel_wait_for_and_select([1, 2])
		self.history_panel_build_list_of_pairs()
		self.collection_builder_set_name("my awesome paired list")
		self.collection_builder_create()
		self.history_panel_wait_for_hid_ok(5)
		self._create_and_run_workflow_with_unique_name(WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT)
		self.workflow_run_submit()
		self.history_panel_wait_for_hid_ok(6)
		content = self.dataset_populator.get_history_dataset_content(history_id, hid=6)
		assert content.strip() == "forward content\nreverse content"

		@selenium_test
		@managed_history
		def test_workflow_run_list_paired_or_unpaired_with_flat_list(self):
		history_id = self.current_history_id()
		self.perform_upload_of_pasted_content(
		{
		"foo_1.fasta": "forward content",
		"foo_2.fasta": "reverse content",
		}
		)
		self.history_panel_wait_for_and_select([1, 2])
		self.history_panel_build_list_advanced_and_select_builder("list")
		self.collection_builder_set_name("my awesome flat list")
		self.collection_builder_create()
		self.history_panel_wait_for_hid_ok(5)
		self._create_and_run_workflow_with_unique_name(WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT)
		self.workflow_run_submit()
		self.history_panel_wait_for_hid_ok(6)
		content = self.dataset_populator.get_history_dataset_content(history_id, hid=6)
		assert content.strip() == "reverse content\nforward content"

		@selenium_test
		@managed_history
		def test_workflow_run_list_paired_or_unpaired_with_mixed_list(self):
		history_id = self.current_history_id()
		self.perform_upload_of_pasted_content(
		{
		"foo_1.fasta": "forward content",
		"foo_2.fasta": "reverse content",
		"other.fasta": "unpaired content",
		}
		)
		self.history_panel_wait_for_and_select([1, 2, 3])
		self.history_panel_build_list_of_paired_or_unpaireds()
		self.collection_builder_set_name("my awesome flat list")
		self.collection_builder_create()
		self.history_panel_wait_for_hid_ok(7)
		self._create_and_run_workflow_with_unique_name(WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT)
		self.workflow_run_submit()
		self.history_panel_wait_for_hid_ok(8)
		content = self.dataset_populator.get_history_dataset_content(history_id, hid=8)
		assert content.strip() == "forward content\nreverse content\nunpaired content"

		@selenium_test
		@managed_history
		def test_upload_dataset_from_workflow_simple(self):

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