mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
0391cd4b62
These are collected by pytest only because they are `unittest.TestCase` derived, but normally pytest collects only test classes whose name starts with `Test`, see https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes Also: - Some type annotations
879 lines
37 KiB
Python
879 lines
37 KiB
Python
import json
|
|
|
|
import yaml
|
|
from selenium.webdriver.common.action_chains import ActionChains
|
|
from selenium.webdriver.common.keys import Keys
|
|
|
|
from galaxy_test.base.workflow_fixtures import (
|
|
WORKFLOW_NESTED_SIMPLE,
|
|
WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION,
|
|
WORKFLOW_SELECT_FROM_OPTIONAL_DATASET,
|
|
WORKFLOW_SIMPLE_CAT_TWICE,
|
|
WORKFLOW_SIMPLE_MAPPING,
|
|
WORKFLOW_WITH_INVALID_STATE,
|
|
WORKFLOW_WITH_OLD_TOOL_VERSION,
|
|
WORKFLOW_WITH_OUTPUT_COLLECTION,
|
|
WORKFLOW_WITH_RULES_1,
|
|
WORKFLOW_WITH_RULES_2,
|
|
)
|
|
from .framework import (
|
|
retry_assertion_during_transitions,
|
|
retry_during_transitions,
|
|
RunsWorkflows,
|
|
selenium_test,
|
|
SeleniumTestCase,
|
|
)
|
|
|
|
|
|
class TestWorkflowEditor(SeleniumTestCase, RunsWorkflows):
|
|
|
|
ensure_registered = True
|
|
|
|
@selenium_test
|
|
def test_basics(self):
|
|
editor = self.components.workflow_editor
|
|
annotation = "basic_test"
|
|
name = self.workflow_create_new(annotation=annotation)
|
|
self.assert_wf_name_is(name)
|
|
self.assert_wf_annotation_is(annotation)
|
|
|
|
editor.canvas_body.wait_for_visible()
|
|
editor.tool_menu.wait_for_visible()
|
|
|
|
# shouldn't have changes on fresh load
|
|
save_button = self.components.workflow_editor.save_button
|
|
save_button.wait_for_visible()
|
|
assert save_button.has_class("disabled")
|
|
|
|
self.screenshot("workflow_editor_blank")
|
|
|
|
self.components._.left_panel_drag.wait_for_visible()
|
|
self.components._.left_panel_collapse.wait_for_and_click()
|
|
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
|
|
self.screenshot("workflow_editor_left_collapsed")
|
|
|
|
self.components._.right_panel_drag.wait_for_visible()
|
|
self.components._.right_panel_collapse.wait_for_and_click()
|
|
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
|
|
self.screenshot("workflow_editor_left_and_right_collapsed")
|
|
|
|
@selenium_test
|
|
def test_edit_annotation(self):
|
|
editor = self.components.workflow_editor
|
|
annotation = "new_annotation_test"
|
|
name = self.workflow_create_new(annotation=annotation)
|
|
edit_annotation = self.components.workflow_editor.edit_annotation
|
|
self.assert_wf_annotation_is(annotation)
|
|
|
|
editor.canvas_body.wait_for_visible()
|
|
|
|
new_annotation = "look new annotation"
|
|
edit_annotation.wait_for_and_send_keys(new_annotation)
|
|
self.assert_workflow_has_changes_and_save()
|
|
self.workflow_index_open_with_name(name)
|
|
self.assert_wf_annotation_is(new_annotation)
|
|
|
|
@selenium_test
|
|
def test_edit_name(self):
|
|
editor = self.components.workflow_editor
|
|
name = self.workflow_create_new()
|
|
editor.canvas_body.wait_for_visible()
|
|
new_name = self._get_random_name()
|
|
edit_name = self.components.workflow_editor.edit_name
|
|
edit_name.wait_for_and_send_keys(new_name)
|
|
|
|
self.assert_workflow_has_changes_and_save()
|
|
self.workflow_index_open_with_name(new_name)
|
|
self.assert_wf_name_is(name)
|
|
|
|
@selenium_test
|
|
def test_optional_select_data_field(self):
|
|
editor = self.components.workflow_editor
|
|
workflow_id = self.workflow_populator.upload_yaml_workflow(WORKFLOW_SELECT_FROM_OPTIONAL_DATASET)
|
|
self.workflow_index_open()
|
|
self.workflow_index_click_option("Edit")
|
|
editor = self.components.workflow_editor
|
|
node = editor.node._(label="select_from_dataset_optional")
|
|
node.title.wait_for_and_click()
|
|
self.components.tool_form.parameter_checkbox(parameter="select_single").wait_for_and_click()
|
|
# External (selenium-side) debounce hack for old backbone input
|
|
# TODO: remove when form elements are all converted.
|
|
self.components.tool_form.parameter_input(parameter="select_single").wait_for_and_send_keys("parameter valu")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.components.tool_form.parameter_input(parameter="select_single").wait_for_and_send_keys("e")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.assert_workflow_has_changes_and_save()
|
|
workflow = self.workflow_populator.download_workflow(workflow_id)
|
|
tool_state = json.loads(workflow["steps"]["0"]["tool_state"])
|
|
assert tool_state["select_single"] == "parameter value"
|
|
# Disable optional button, resets value to null
|
|
self.components.tool_form.parameter_checkbox(parameter="select_single").wait_for_and_click()
|
|
self.assert_workflow_has_changes_and_save()
|
|
workflow = self.workflow_populator.download_workflow(workflow_id)
|
|
tool_state = json.loads(workflow["steps"]["0"]["tool_state"])
|
|
assert tool_state["select_single"] is None
|
|
# Enable button but don't provide a value
|
|
self.components.tool_form.parameter_checkbox(parameter="select_single").wait_for_and_click()
|
|
self.assert_workflow_has_changes_and_save()
|
|
workflow = self.workflow_populator.download_workflow(workflow_id)
|
|
tool_state = json.loads(workflow["steps"]["0"]["tool_state"])
|
|
assert tool_state["select_single"] == ""
|
|
|
|
@selenium_test
|
|
def test_data_input(self):
|
|
editor = self.components.workflow_editor
|
|
|
|
name = self.workflow_create_new()
|
|
self.workflow_editor_add_input(item_name="data_input")
|
|
self.screenshot("workflow_editor_data_input_new")
|
|
editor.label_input.wait_for_and_send_keys("input1")
|
|
editor.annotation_input.wait_for_and_send_keys("my cool annotation")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.screenshot("workflow_editor_data_input_filled_in")
|
|
self.workflow_editor_click_save()
|
|
|
|
self.workflow_index_open_with_name(name)
|
|
data_input_node = editor.node._(label="input1")
|
|
data_input_node.title.wait_for_and_click()
|
|
label = editor.label_input.wait_for_value()
|
|
assert label == "input1", label
|
|
annotation = editor.annotation_input.wait_for_value()
|
|
assert annotation == "my cool annotation", annotation
|
|
data_input_node.destroy.wait_for_and_click()
|
|
data_input_node.wait_for_absent()
|
|
self.screenshot("workflow_editor_data_input_deleted")
|
|
|
|
@selenium_test
|
|
def test_collection_input(self):
|
|
editor = self.components.workflow_editor
|
|
|
|
name = self.workflow_create_new()
|
|
self.workflow_editor_add_input(item_name="data_collection_input")
|
|
self.screenshot("workflow_editor_data_collection_input_new")
|
|
editor.label_input.wait_for_and_send_keys("input1")
|
|
editor.annotation_input.wait_for_and_send_keys("my cool annotation")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.screenshot("workflow_editor_data_collection_input_filled_in")
|
|
self.workflow_editor_click_save()
|
|
|
|
self.workflow_index_open_with_name(name)
|
|
data_input_node = editor.node._(label="input1")
|
|
data_input_node.title.wait_for_and_click()
|
|
label = editor.label_input.wait_for_value()
|
|
assert label == "input1", label
|
|
annotation = editor.annotation_input.wait_for_value()
|
|
assert annotation == "my cool annotation", annotation
|
|
data_input_node.destroy.wait_for_and_click()
|
|
data_input_node.wait_for_absent()
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.screenshot("workflow_editor_data_collection_input_deleted")
|
|
|
|
@selenium_test
|
|
def test_data_column_input_editing(self):
|
|
self.open_in_workflow_editor(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
steps:
|
|
column_param_list:
|
|
tool_id: column_param_list
|
|
state:
|
|
col: ["1","2","3"]
|
|
col_names: ["a", "b", "c"]
|
|
"""
|
|
)
|
|
editor = self.components.workflow_editor
|
|
node = editor.node._(label="column_param_list")
|
|
node.title.wait_for_and_click()
|
|
columns = self.components.tool_form.parameter_textarea(parameter="col")
|
|
textarea_columns = columns.wait_for_visible()
|
|
assert textarea_columns.get_attribute("value") == "1\n2\n3\n"
|
|
column_names = self.components.tool_form.parameter_textarea(parameter="col_names")
|
|
textarea_column_names = column_names.wait_for_visible()
|
|
assert textarea_column_names.get_attribute("value") == "a\nb\nc\n"
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.set_text_element(columns, "4\n5\n6\n")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.assert_workflow_has_changes_and_save()
|
|
self.driver.refresh()
|
|
node.title.wait_for_and_click()
|
|
textarea_columns = columns.wait_for_visible()
|
|
assert textarea_columns.get_attribute("value") == "4\n5\n6\n"
|
|
|
|
@selenium_test
|
|
def test_integer_input(self):
|
|
editor = self.components.workflow_editor
|
|
|
|
name = self.workflow_create_new()
|
|
self.workflow_editor_add_input(item_name="parameter_input")
|
|
self.screenshot("workflow_editor_parameter_input_new")
|
|
editor.label_input.wait_for_and_send_keys("input1")
|
|
editor.annotation_input.wait_for_and_send_keys("my cool annotation")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.screenshot("workflow_editor_parameter_input_filled_in")
|
|
self.workflow_editor_click_save()
|
|
|
|
self.workflow_index_open_with_name(name)
|
|
data_input_node = editor.node._(label="input1")
|
|
data_input_node.title.wait_for_and_click()
|
|
label = editor.label_input.wait_for_value()
|
|
assert label == "input1", label
|
|
annotation = editor.annotation_input.wait_for_value()
|
|
assert annotation == "my cool annotation", annotation
|
|
data_input_node.destroy.wait_for_and_click()
|
|
data_input_node.wait_for_absent()
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.screenshot("workflow_editor_parameter_input_deleted")
|
|
|
|
@selenium_test
|
|
def test_non_data_connections(self):
|
|
self.open_in_workflow_editor(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
inputs:
|
|
input_int: integer
|
|
steps:
|
|
simple_constructs:
|
|
tool_id: simple_constructs
|
|
label: tool_exec
|
|
in:
|
|
inttest: input_int
|
|
cat1:
|
|
# regression test, ensures connecting works in the presence of data input terminals
|
|
tool_id: cat1
|
|
"""
|
|
)
|
|
self.screenshot("workflow_editor_parameter_connection_simple")
|
|
self.assert_connected("input_int#output", "tool_exec#inttest")
|
|
|
|
editor = self.components.workflow_editor
|
|
|
|
tool_node = editor.node._(label="tool_exec")
|
|
tool_input = tool_node.input_terminal(name="inttest")
|
|
tool_input.wait_for_and_click()
|
|
|
|
editor.connector_destroy_callout.wait_for_and_click()
|
|
self.assert_not_connected("input_int#output", "tool_exec#inttest")
|
|
self.screenshot("workflow_editor_parameter_connection_destroyed")
|
|
|
|
# When connected, cannot turn it into a RuntimeValue..
|
|
collapse_input = editor.collapse_icon(name="inttest")
|
|
collapse_input.wait_for_absent_or_hidden()
|
|
|
|
# If it is disconnected, then can specify as RuntimeValue
|
|
connect_icon = editor.connect_icon(name="inttest")
|
|
connect_icon.wait_for_visible()
|
|
connect_icon.wait_for_and_click()
|
|
collapse_input.wait_for_visible()
|
|
|
|
# Also the connector should disappear
|
|
tool_input.wait_for_absent_or_hidden()
|
|
|
|
# Now make it connected again and watch the requests
|
|
connect_icon.wait_for_and_click()
|
|
|
|
tool_input.wait_for_visible()
|
|
collapse_input.wait_for_absent_or_hidden()
|
|
|
|
self.workflow_editor_connect(
|
|
"input_int#output", "tool_exec#inttest", screenshot_partial="workflow_editor_parameter_connection_dragging"
|
|
)
|
|
self.assert_connected("input_int#output", "tool_exec#inttest")
|
|
|
|
@selenium_test
|
|
def test_non_data_map_over_carried_through(self):
|
|
# Use auto_layout=false, which prevents placing any
|
|
# step outside of the scroll area
|
|
# xref: https://github.com/galaxyproject/galaxy/issues/13211
|
|
self.open_in_workflow_editor(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
inputs:
|
|
input_collection:
|
|
type: collection
|
|
collection_type: "list"
|
|
steps:
|
|
param_value_from_file:
|
|
tool_id: param_value_from_file
|
|
in:
|
|
input1: input_collection
|
|
text_input_step:
|
|
tool_id: param_text_option
|
|
in:
|
|
text_param: param_value_from_file/text_param
|
|
collection_input:
|
|
tool_id: identifier_collection
|
|
""",
|
|
auto_layout=False,
|
|
)
|
|
self.workflow_editor_connect("text_input_step#out_file1", "collection_input#input1")
|
|
self.assert_connected("text_input_step#out_file1", "collection_input#input1")
|
|
|
|
def test_connecting_display_in_upload_false_connections(self):
|
|
self.open_in_workflow_editor(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
steps:
|
|
step1:
|
|
tool_id: test_sam_to_bam_conversions
|
|
step2:
|
|
tool_id: test_sam_to_bam_conversions
|
|
"""
|
|
)
|
|
|
|
self.workflow_editor_connect("step1#qname_input_sorted_bam_output", "step2#input5")
|
|
self.assert_connected("step1#qname_input_sorted_bam_output", "step2#input5")
|
|
|
|
@selenium_test
|
|
def test_existing_connections(self):
|
|
self.open_in_workflow_editor(WORKFLOW_SIMPLE_CAT_TWICE)
|
|
|
|
editor = self.components.workflow_editor
|
|
self.assert_connected("input1#output", "first_cat#input1")
|
|
self.screenshot("workflow_editor_connection_simple")
|
|
|
|
cat_node = editor.node._(label="first_cat")
|
|
cat_input = cat_node.input_terminal(name="input1")
|
|
cat_input.wait_for_and_click()
|
|
editor.connector_destroy_callout.wait_for_visible()
|
|
self.screenshot("workflow_editor_connection_callout")
|
|
editor.connector_destroy_callout.wait_for_and_click()
|
|
self.assert_not_connected("input1#output", "first_cat#input1")
|
|
self.screenshot("workflow_editor_connection_destroyed")
|
|
|
|
self.workflow_editor_connect(
|
|
"input1#output", "first_cat#input1", screenshot_partial="workflow_editor_connection_dragging"
|
|
)
|
|
self.assert_connected("input1#output", "first_cat#input1")
|
|
|
|
@selenium_test
|
|
def test_reconnecting_nodes(self):
|
|
name = self.open_in_workflow_editor(WORKFLOW_SIMPLE_CAT_TWICE)
|
|
self.assert_connected("input1#output", "first_cat#input1")
|
|
self.workflow_editor_destroy_connection("first_cat#input1")
|
|
self.assert_not_connected("input1#output", "first_cat#input1")
|
|
self.workflow_editor_connect("input1#output", "first_cat#input1")
|
|
self.assert_connected("input1#output", "first_cat#input1")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.assert_workflow_has_changes_and_save()
|
|
self.workflow_index_open_with_name(name)
|
|
self.assert_connected("input1#output", "first_cat#input1")
|
|
|
|
@selenium_test
|
|
def test_rendering_output_collection_connections(self):
|
|
self.open_in_workflow_editor(WORKFLOW_WITH_OUTPUT_COLLECTION)
|
|
self.workflow_editor_maximize_center_pane()
|
|
self.screenshot("workflow_editor_output_collections")
|
|
|
|
@selenium_test
|
|
def test_simple_mapping_connections(self):
|
|
self.open_in_workflow_editor(WORKFLOW_SIMPLE_MAPPING)
|
|
self.workflow_editor_maximize_center_pane()
|
|
self.screenshot("workflow_editor_simple_mapping")
|
|
self.assert_connected("input1#output", "cat#input1")
|
|
self.assert_input_mapped("cat#input1")
|
|
self.workflow_editor_destroy_connection("cat#input1")
|
|
self.assert_input_not_mapped("cat#input1")
|
|
self.assert_not_connected("input1#output", "cat#input1")
|
|
self.workflow_editor_connect("input1#output", "cat#input1")
|
|
self.assert_input_mapped("cat#input1")
|
|
|
|
@selenium_test
|
|
def test_rendering_simple_nested_workflow(self):
|
|
self.open_in_workflow_editor(WORKFLOW_NESTED_SIMPLE)
|
|
self.workflow_editor_maximize_center_pane()
|
|
self.screenshot("workflow_editor_simple_nested")
|
|
|
|
@selenium_test
|
|
def test_rendering_rules_workflow_1(self):
|
|
self.open_in_workflow_editor(WORKFLOW_WITH_RULES_1)
|
|
rule_output = "apply#output"
|
|
random_lines_input = "random_lines#input"
|
|
self.workflow_editor_maximize_center_pane()
|
|
self.screenshot("workflow_editor_rules_1")
|
|
self.assert_connected(rule_output, random_lines_input)
|
|
self.assert_input_mapped(random_lines_input)
|
|
self.workflow_editor_destroy_connection(random_lines_input)
|
|
self.assert_not_connected(rule_output, random_lines_input)
|
|
self.assert_input_not_mapped(random_lines_input)
|
|
self.workflow_editor_connect(rule_output, random_lines_input)
|
|
self.assert_connected(rule_output, random_lines_input)
|
|
self.assert_input_mapped(random_lines_input)
|
|
|
|
@selenium_test
|
|
def test_rendering_rules_workflow_2(self):
|
|
self.open_in_workflow_editor(WORKFLOW_WITH_RULES_2)
|
|
self.workflow_editor_maximize_center_pane(collapse_right=False)
|
|
|
|
editor = self.components.workflow_editor
|
|
rule_builder = self.components.rule_builder
|
|
|
|
rule_output = "apply#output"
|
|
copy_list_input = "copy_list#input1"
|
|
|
|
apply_node = editor.node._(label="apply")
|
|
|
|
self.assert_connected(rule_output, copy_list_input)
|
|
self.assert_input_mapped(copy_list_input)
|
|
self.workflow_editor_destroy_connection(copy_list_input)
|
|
self.assert_not_connected(rule_output, copy_list_input)
|
|
self.assert_input_not_mapped(copy_list_input)
|
|
self.workflow_editor_connect(rule_output, copy_list_input)
|
|
self.assert_connected(rule_output, copy_list_input)
|
|
self.assert_input_mapped(copy_list_input)
|
|
|
|
apply_node.title.wait_for_and_click()
|
|
self.screenshot("workflow_editor_rules_2_form")
|
|
self.tool_parameter_edit_rules()
|
|
rule_builder._.wait_for_visible()
|
|
self.screenshot("workflow_editor_rules_2_builder")
|
|
new_rules = dict(
|
|
rules=[{"type": "add_column_metadata", "value": "identifier0"}],
|
|
mapping=[{"type": "list_identifiers", "columns": [0]}],
|
|
)
|
|
self.rule_builder_set_source(json.dumps(new_rules))
|
|
rule_builder.main_button_ok.wait_for_and_click()
|
|
apply_node.title.wait_for_and_click()
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
# screenshot should have async warning about connection removed
|
|
self.screenshot("workflow_editor_rules_2_after_change")
|
|
self.assert_input_not_mapped(copy_list_input)
|
|
# changing output collection type remove outbound connections, so this
|
|
# this needs to be re-connected. Remove this re-connection if we upgrade
|
|
# the workflow editor to try to re-establish the connection with different
|
|
# mapping.
|
|
self.workflow_editor_connect(rule_output, copy_list_input)
|
|
self.assert_connected(rule_output, copy_list_input)
|
|
# Regardless - this rules now say to connect a list to a list instead of a list
|
|
# to a list:list, so there should be no mapping anymore even after connected.
|
|
self.assert_input_not_mapped(copy_list_input)
|
|
|
|
@selenium_test
|
|
def test_save_as(self):
|
|
name = self.workflow_upload_yaml_with_random_name(WORKFLOW_SIMPLE_CAT_TWICE)
|
|
self.workflow_index_open()
|
|
self.workflow_index_open_with_name(name)
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.screenshot("workflow_editor_edit_menu")
|
|
self.workflow_editor_click_option("Save As")
|
|
|
|
@selenium_test
|
|
def test_editor_tool_upgrade(self):
|
|
workflow_populator = self.workflow_populator
|
|
workflow_id = workflow_populator.upload_yaml_workflow(
|
|
"""class: GalaxyWorkflow
|
|
inputs: []
|
|
steps:
|
|
- tool_id: multiple_versions
|
|
tool_version: 0.1
|
|
label: multiple_versions
|
|
state:
|
|
foo: bar
|
|
""",
|
|
exact_tools=True,
|
|
)
|
|
self.workflow_index_open()
|
|
self.workflow_index_click_option("Edit")
|
|
editor = self.components.workflow_editor
|
|
editor.node._(label="multiple_versions").wait_for_and_click()
|
|
editor.tool_version_button.wait_for_and_click()
|
|
assert self.select_dropdown_item("Switch to 0.2"), "Switch to tool version dropdown item not found"
|
|
self.screenshot("workflow_editor_version_update")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.assert_workflow_has_changes_and_save()
|
|
workflow = self.workflow_populator.download_workflow(workflow_id)
|
|
assert workflow["steps"]["0"]["tool_version"] == "0.2"
|
|
|
|
@selenium_test
|
|
def test_editor_tool_upgrade_message(self):
|
|
workflow_populator = self.workflow_populator
|
|
workflow_populator.upload_yaml_workflow(WORKFLOW_WITH_OLD_TOOL_VERSION, exact_tools=True)
|
|
self.workflow_index_open()
|
|
self.workflow_index_click_option("Edit")
|
|
self.assert_modal_has_text("Using version '0.2' instead of version '0.0.1'")
|
|
self.screenshot("workflow_editor_tool_upgrade")
|
|
self.components.workflow_editor.modal_button_continue.wait_for_and_click()
|
|
self.assert_workflow_has_changes_and_save()
|
|
|
|
@selenium_test
|
|
def test_editor_subworkflow_tool_upgrade_message(self):
|
|
workflow_populator = self.workflow_populator
|
|
embedded_workflow = yaml.safe_load(WORKFLOW_WITH_OLD_TOOL_VERSION)
|
|
# Create invalid tool state
|
|
embedded_workflow["steps"]["mul_versions"]["state"]["inttest"] = "Invalid"
|
|
outer_workflow = yaml.safe_load(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
inputs:
|
|
outer_input: data
|
|
steps:
|
|
nested_workflow:
|
|
run: {}
|
|
in:
|
|
input1: outer_input
|
|
"""
|
|
)
|
|
outer_workflow["steps"]["nested_workflow"]["run"] = embedded_workflow
|
|
workflow_populator.upload_yaml_workflow(json.dumps(outer_workflow), exact_tools=True)
|
|
self.workflow_index_open()
|
|
self.workflow_index_click_option("Edit")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.assert_modal_has_text("Using version '0.2' instead of version '0.0.1'")
|
|
self.assert_modal_has_text("parameter 'inttest': an integer or workflow parameter is required")
|
|
self.screenshot("workflow_editor_subworkflow_tool_upgrade")
|
|
self.components.workflow_editor.modal_button_continue.wait_for_and_click()
|
|
self.assert_workflow_has_changes_and_save()
|
|
|
|
@staticmethod
|
|
def set_text_element(element, value):
|
|
# Try both, no harm here
|
|
element.wait_for_and_send_keys(Keys.CONTROL, "a")
|
|
element.wait_for_and_send_keys(Keys.COMMAND, "a")
|
|
element.wait_for_and_send_keys(Keys.BACKSPACE)
|
|
element.wait_for_and_send_keys(value)
|
|
|
|
@selenium_test
|
|
def test_change_datatype(self):
|
|
self.open_in_workflow_editor(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
inputs: []
|
|
steps:
|
|
- tool_id: create_2
|
|
label: create_2
|
|
- tool_id: checksum
|
|
label: checksum
|
|
in:
|
|
input: create_2/out_file1
|
|
"""
|
|
)
|
|
editor = self.components.workflow_editor
|
|
self.assert_connected("create_2#out_file1", "checksum#input")
|
|
node = editor.node._(label="create_2")
|
|
node.wait_for_and_click()
|
|
editor.configure_output(output="out_file1").wait_for_and_click()
|
|
editor.change_datatype.wait_for_and_click()
|
|
editor.select_dataype_text_search.wait_for_and_send_keys("bam")
|
|
editor.select_datatype(datatype="bam").wait_for_and_click()
|
|
editor.node.output_data_row(output_name="out_file1", extension="bam").wait_for_visible()
|
|
self.assert_not_connected("create_2#out_file1", "checksum#input")
|
|
|
|
@selenium_test
|
|
def test_change_datatype_post_job_action_lost_regression(self):
|
|
self.open_in_workflow_editor(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
inputs: []
|
|
steps:
|
|
- tool_id: create_2
|
|
label: create_2
|
|
outputs:
|
|
out_file1:
|
|
change_datatype: bam
|
|
- tool_id: metadata_bam
|
|
label: metadata_bam
|
|
in:
|
|
input_bam: create_2/out_file1
|
|
"""
|
|
)
|
|
self.assert_connected("create_2#out_file1", "metadata_bam#input_bam")
|
|
editor = self.components.workflow_editor
|
|
node = editor.node._(label="create_2")
|
|
node.wait_for_and_click()
|
|
self.assert_connected("create_2#out_file1", "metadata_bam#input_bam")
|
|
|
|
@selenium_test
|
|
def test_change_datatype_in_subworkflow(self):
|
|
self.open_in_workflow_editor(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
inputs: []
|
|
steps:
|
|
nested_workflow:
|
|
run:
|
|
class: GalaxyWorkflow
|
|
inputs: []
|
|
steps:
|
|
- tool_id: create_2
|
|
label: create_2
|
|
outputs:
|
|
out_file1:
|
|
change_datatype: bam
|
|
outputs:
|
|
workflow_output:
|
|
outputSource: create_2/out_file1
|
|
metadata_bam:
|
|
tool_id: metadata_bam
|
|
"""
|
|
)
|
|
editor = self.components.workflow_editor
|
|
node = editor.node._(label="nested_workflow")
|
|
node.wait_for_and_click()
|
|
node.output_data_row(output_name="workflow_output", extension="bam").wait_for_visible()
|
|
# Move canvas, so terminals are in viewport
|
|
self.move_center_of_canvas(xoffset=100, yoffset=100)
|
|
self.workflow_editor_connect("nested_workflow#workflow_output", "metadata_bam#input_bam")
|
|
self.assert_connected("nested_workflow#workflow_output", "metadata_bam#input_bam")
|
|
|
|
@selenium_test
|
|
def test_editor_duplicate_node(self):
|
|
workflow_id = self.workflow_populator.upload_yaml_workflow(WORKFLOW_SIMPLE_CAT_TWICE)
|
|
self.workflow_index_open()
|
|
self.workflow_index_click_option("Edit")
|
|
editor = self.components.workflow_editor
|
|
cat_node = editor.node._(label="first_cat")
|
|
cat_node.wait_for_and_click()
|
|
self.set_text_element(editor.label_input, "source label")
|
|
# Select node using new label, ensures labels are synced between side panel and node
|
|
cat_node = editor.node._(label="source label")
|
|
self.assert_workflow_has_changes_and_save()
|
|
editor.annotation_input.wait_for_and_send_keys("source annotation")
|
|
self.assert_workflow_has_changes_and_save()
|
|
editor.configure_output(output="out_file1").wait_for_and_click()
|
|
output_label = editor.label_output(output="out_file1")
|
|
self.set_text_element(output_label, "workflow output label")
|
|
self.set_text_element(editor.rename_output, "renamed_output")
|
|
editor.change_datatype.wait_for_and_click()
|
|
editor.select_dataype_text_search.wait_for_and_send_keys("bam")
|
|
editor.select_datatype(datatype="bam").wait_for_and_click()
|
|
self.set_text_element(editor.add_tags, "#crazynewtag")
|
|
self.set_text_element(editor.remove_tags, "#oldboringtag")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
cat_node.clone.wait_for_and_click()
|
|
editor.label_input.wait_for_and_send_keys("cloned label")
|
|
output_label = editor.label_output(output="out_file1")
|
|
self.set_text_element(output_label, "cloned output label")
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.assert_workflow_has_changes_and_save()
|
|
edited_workflow = self.workflow_populator.download_workflow(workflow_id)
|
|
source_step = next(iter(step for step in edited_workflow["steps"].values() if step["label"] == "source label"))
|
|
cloned_step = next(iter(step for step in edited_workflow["steps"].values() if step["label"] == "cloned label"))
|
|
assert source_step["annotation"] == cloned_step["annotation"] == "source annotation"
|
|
assert source_step["workflow_outputs"][0]["label"] == "workflow output label"
|
|
assert cloned_step["workflow_outputs"][0]["label"] == "cloned output label"
|
|
assert len(source_step["post_job_actions"]) == len(cloned_step["post_job_actions"]) == 4
|
|
assert source_step["post_job_actions"] == cloned_step["post_job_actions"]
|
|
|
|
@selenium_test
|
|
def test_editor_embed_workflow(self):
|
|
workflow_populator = self.workflow_populator
|
|
child_workflow_name = self._get_random_name()
|
|
workflow_populator.upload_yaml_workflow(WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION, name=child_workflow_name)
|
|
parent_workflow_id = workflow_populator.upload_yaml_workflow(
|
|
"""class: GalaxyWorkflow
|
|
inputs: []
|
|
steps:
|
|
- tool_id: multiple_versions
|
|
tool_version: 0.1
|
|
label: multiple_versions
|
|
state:
|
|
foo: bar
|
|
"""
|
|
)
|
|
self.workflow_index_open()
|
|
self.workflow_index_click_option("Edit")
|
|
editor = self.components.workflow_editor
|
|
editor.canvas_body.wait_for_visible()
|
|
editor.tool_menu.wait_for_visible()
|
|
editor.tool_menu_section_link(section_name="workflows").wait_for_and_click()
|
|
editor.workflow_link(workflow_title=child_workflow_name).wait_for_and_click()
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.assert_workflow_has_changes_and_save()
|
|
workflow = self.workflow_populator.download_workflow(parent_workflow_id)
|
|
subworkflow_step = workflow["steps"]["1"]
|
|
assert subworkflow_step["name"] == child_workflow_name
|
|
assert subworkflow_step["type"] == "subworkflow"
|
|
assert subworkflow_step["subworkflow"]["a_galaxy_workflow"] == "true"
|
|
|
|
@selenium_test
|
|
def test_editor_invalid_tool_state(self):
|
|
workflow_populator = self.workflow_populator
|
|
workflow_populator.upload_yaml_workflow(WORKFLOW_WITH_INVALID_STATE, exact_tools=True)
|
|
self.workflow_index_open()
|
|
self.workflow_index_click_option("Edit")
|
|
self.assert_modal_has_text("Using version '0.2' instead of version '0.0.1'")
|
|
self.assert_modal_has_text("Using default: '1'")
|
|
self.screenshot("workflow_editor_invalid_state")
|
|
|
|
@selenium_test
|
|
def test_missing_tools(self):
|
|
workflow_populator = self.workflow_populator
|
|
workflow_populator.upload_yaml_workflow(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
inputs:
|
|
- id: input1
|
|
steps:
|
|
- tool_id: missing
|
|
label: first_cat
|
|
state:
|
|
foo: bar
|
|
"""
|
|
)
|
|
self.workflow_index_open()
|
|
self.workflow_index_click_option("Edit")
|
|
self.assert_modal_has_text("Tool is not installed")
|
|
self.screenshot("workflow_editor_missing_tool")
|
|
|
|
@selenium_test
|
|
def test_workflow_bookmarking(self):
|
|
@retry_during_transitions
|
|
def assert_workflow_bookmarked_status(target_status):
|
|
name_matches = [c.text == new_workflow_name for c in self.components.tool_panel.workflow_names.all()]
|
|
status = any(name_matches)
|
|
assert status == target_status
|
|
|
|
new_workflow_name = self.workflow_create_new(clear_placeholder=True)
|
|
|
|
# Assert workflow not initially bookmarked.
|
|
assert_workflow_bookmarked_status(False)
|
|
|
|
self.components.workflow_editor.canvas_body.wait_for_visible()
|
|
self.wait_for_selector_absent_or_hidden(self.modal_body_selector())
|
|
self.components.masthead.workflow.wait_for_and_click()
|
|
|
|
self.components.tool_panel.search.wait_for_and_send_keys(new_workflow_name)
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.components.workflows.bookmark_link.wait_for_and_click()
|
|
self.components.masthead.workflow.wait_for_and_click()
|
|
self.sleep_for(self.wait_types.UX_TRANSITION)
|
|
|
|
# search for bookmark in tools menu
|
|
self.components.tool_panel.search.wait_for_and_send_keys(new_workflow_name)
|
|
assert_workflow_bookmarked_status(True)
|
|
|
|
def workflow_editor_maximize_center_pane(self, collapse_left=True, collapse_right=True):
|
|
if collapse_left:
|
|
self.components._.left_panel_collapse.wait_for_and_click()
|
|
if collapse_right:
|
|
self.components._.right_panel_collapse.wait_for_and_click()
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
|
|
def workflow_editor_connect(self, source, sink, screenshot_partial=None):
|
|
source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
|
|
source_element = self.find_element_by_selector(f"#{source_id}")
|
|
sink_element = self.find_element_by_selector(f"#{sink_id}")
|
|
|
|
ac = self.action_chains()
|
|
ac = ac.move_to_element(source_element).click_and_hold()
|
|
if screenshot_partial:
|
|
ac = ac.move_to_element_with_offset(sink_element, -5, 0)
|
|
ac.perform()
|
|
self.sleep_for(self.wait_types.UX_RENDER)
|
|
self.screenshot(screenshot_partial)
|
|
ac = self.action_chains()
|
|
|
|
ac = ac.move_to_element(sink_element).release().perform()
|
|
|
|
def assert_connected(self, source, sink):
|
|
source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
|
|
self.components.workflow_editor.connector_for(source_id=source_id, sink_id=sink_id).wait_for_visible()
|
|
|
|
def assert_not_connected(self, source, sink):
|
|
source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
|
|
self.components.workflow_editor.connector_for(source_id=source_id, sink_id=sink_id).wait_for_absent()
|
|
|
|
def open_in_workflow_editor(self, yaml_content, auto_layout=True):
|
|
name = self.workflow_upload_yaml_with_random_name(yaml_content)
|
|
self.workflow_index_open()
|
|
self.workflow_index_open_with_name(name)
|
|
if auto_layout:
|
|
self.workflow_editor_click_option("Auto Layout")
|
|
return name
|
|
|
|
def workflow_editor_source_sink_terminal_ids(self, source, sink):
|
|
editor = self.components.workflow_editor
|
|
|
|
source_node_label, source_output = source.split("#", 1)
|
|
sink_node_label, sink_input = sink.split("#", 1)
|
|
|
|
source_node = editor.node._(label=source_node_label)
|
|
sink_node = editor.node._(label=sink_node_label)
|
|
|
|
source_node.wait_for_visible()
|
|
sink_node.wait_for_visible()
|
|
|
|
output_terminal = source_node.output_terminal(name=source_output)
|
|
input_terminal = sink_node.input_terminal(name=sink_input)
|
|
|
|
output_element = output_terminal.wait_for_visible()
|
|
input_element = input_terminal.wait_for_visible()
|
|
|
|
source_id = output_element.get_attribute("id")
|
|
sink_id = input_element.get_attribute("id")
|
|
|
|
return source_id, sink_id
|
|
|
|
def workflow_editor_add_input(self, item_name="data_input"):
|
|
editor = self.components.workflow_editor
|
|
|
|
# Make sure we're on the the workflow editor and not clicking the main tool panel.
|
|
editor.canvas_body.wait_for_visible()
|
|
|
|
editor.tool_menu.wait_for_visible()
|
|
editor.tool_menu_section_link(section_name="inputs").wait_for_and_click()
|
|
editor.tool_menu_item_link(item_name=item_name).wait_for_and_click()
|
|
|
|
def workflow_editor_destroy_connection(self, sink):
|
|
editor = self.components.workflow_editor
|
|
|
|
sink_node_label, sink_input_name = sink.split("#", 1)
|
|
sink_node = editor.node._(label=sink_node_label)
|
|
sink_input = sink_node.input_terminal(name=sink_input_name)
|
|
sink_input.wait_for_and_click()
|
|
editor.connector_destroy_callout.wait_for_and_click()
|
|
|
|
def assert_input_mapped(self, sink):
|
|
editor = self.components.workflow_editor
|
|
sink_node_label, sink_input_name = sink.split("#", 1)
|
|
sink_node = editor.node._(label=sink_node_label)
|
|
sink_mapping_icon = sink_node.input_mapping_icon(name=sink_input_name)
|
|
sink_mapping_icon.wait_for_visible()
|
|
|
|
def assert_input_not_mapped(self, sink):
|
|
editor = self.components.workflow_editor
|
|
sink_node_label, sink_input_name = sink.split("#", 1)
|
|
sink_node = editor.node._(label=sink_node_label)
|
|
sink_mapping_icon = sink_node.input_mapping_icon(name=sink_input_name)
|
|
sink_mapping_icon.wait_for_absent_or_hidden()
|
|
|
|
def workflow_index_open_with_name(self, name):
|
|
self.workflow_index_open()
|
|
self.workflow_index_search_for(name)
|
|
self.workflow_index_click_option("Edit")
|
|
|
|
def workflow_upload_yaml_with_random_name(self, content):
|
|
workflow_populator = self.workflow_populator
|
|
name = self._get_random_name()
|
|
workflow_populator.upload_yaml_workflow(content, name=name)
|
|
return name
|
|
|
|
@retry_assertion_during_transitions
|
|
def assert_wf_name_is(self, expected_name):
|
|
edit_name_element = self.components.workflow_editor.edit_name.wait_for_visible()
|
|
actual_name = edit_name_element.get_attribute("value")
|
|
assert expected_name in actual_name, f"'{expected_name}' unequal name '{actual_name}'"
|
|
|
|
@retry_assertion_during_transitions
|
|
def assert_wf_annotation_is(self, expected_annotation):
|
|
edit_annotation = self.components.workflow_editor.edit_annotation
|
|
edit_annotation_element = edit_annotation.wait_for_visible()
|
|
actual_annotation = edit_annotation_element.get_attribute("value")
|
|
assert (
|
|
expected_annotation in actual_annotation
|
|
), f"'{expected_annotation}' unequal annotation '{actual_annotation}'"
|
|
|
|
@retry_assertion_during_transitions
|
|
def assert_modal_has_text(self, expected_text):
|
|
modal_element = self.components.workflow_editor.state_modal_body.wait_for_visible()
|
|
text = modal_element.text
|
|
assert expected_text in text, f"Failed to find expected text [{expected_text}] in modal text [{text}]"
|
|
|
|
def move_center_of_canvas(self, xoffset=0, yoffset=0):
|
|
canvas = self.find_element_by_id("canvas-container")
|
|
chains = ActionChains(self.driver)
|
|
chains.click_and_hold(canvas).move_by_offset(xoffset=xoffset, yoffset=yoffset).release().perform()
|