import json
from typing import Optional
import pytest
import yaml
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common.by import By
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.remote.webelement import WebElement
from seletools.actions import drag_and_drop
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,
RunsWorkflows,
selenium_test,
SeleniumTestCase,
)
[docs]class TestWorkflowEditor(SeleniumTestCase, RunsWorkflows):
ensure_registered = True
[docs] @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()
# shouldn't have changes on fresh load
save_button = self.components.workflow_editor.save_button
save_button.assert_disabled()
self.screenshot("workflow_editor_blank")
self.hover_over(self.components._.left_panel_drag.wait_for_visible())
self.workflow_editor_maximize_center_pane()
self.screenshot("workflow_editor_center_pane_maximized")
[docs] @selenium_test
def test_edit_annotation(self):
editor = self.components.workflow_editor
annotation = "new_annotation_test"
name = self.create_and_wait_for_new_workflow_in_editor(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)
[docs] @selenium_test
def test_edit_name(self):
name = self.create_and_wait_for_new_workflow_in_editor()
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)
[docs] @selenium_test
def test_edit_license(self):
editor = self.components.workflow_editor
name = self.create_and_wait_for_new_workflow_in_editor()
editor.license_selector.wait_for_visible()
assert "Do not specify" in editor.license_current_value.wait_for_text()
self.workflow_editor_set_license("MIT")
self.workflow_editor_click_save()
self.workflow_index_open_with_name(name)
editor.license_selector.wait_for_visible()
assert "MIT" in editor.license_current_value.wait_for_text()
[docs] @selenium_test
def test_parameter_regex_validation(self):
editor = self.components.workflow_editor
workflow_run = self.components.workflow_run
parameter_name = "text_param"
name = self.create_and_wait_for_new_workflow_in_editor()
self.workflow_editor_add_input("parameter_input")
editor.label_input.wait_for_and_send_keys(parameter_name)
# this really should be parameterized with the repeat name
self.components.tool_form.repeat_insert.wait_for_and_click()
self.components.tool_form.parameter_input(
parameter="parameter_definition|validators_0|regex_match"
).wait_for_and_send_keys("moocow.*")
self.components.tool_form.parameter_input(
parameter="parameter_definition|validators_0|regex_doc"
).wait_for_and_send_keys("input must start with moocow")
self.save_after_node_form_changes()
self.workflow_run_with_name(name)
self.sleep_for(self.wait_types.UX_TRANSITION)
input_element = workflow_run.simplified_input(label=parameter_name).wait_for_and_click()
input_element.send_keys("startswrong")
workflow_run.run_workflow_disabled.wait_for_absent()
workflow_run.run_error.assert_absent_or_hidden()
self.workflow_run_submit()
element = workflow_run.run_error.wait_for_present()
assert "input must start with moocow" in element.text
[docs] @selenium_test
def test_int_parameter_minimum_validation(self):
editor = self.components.workflow_editor
workflow_run = self.components.workflow_run
parameter_name = "int_param"
name = self.create_and_wait_for_new_workflow_in_editor()
self.workflow_editor_add_input("parameter_input")
editor.label_input.wait_for_and_send_keys(parameter_name)
select_field = self.components.tool_form.parameter_select(parameter="parameter_definition|parameter_type")
self.select_set_value(select_field, "integer")
self.components.tool_form.parameter_input(parameter="parameter_definition|min").wait_for_and_send_keys("4")
self.save_after_node_form_changes()
self.workflow_run_with_name(name)
self.sleep_for(self.wait_types.UX_TRANSITION)
input_element = workflow_run.simplified_input(label=parameter_name).wait_for_and_click()
input_element.send_keys("3")
workflow_run.run_workflow_disabled.wait_for_absent()
workflow_run.run_error.assert_absent_or_hidden()
self.workflow_run_submit()
element = workflow_run.run_error.wait_for_present()
# follow up with a bigger PR to just make this (4 <= value) right? need to set default message
# in parameter validators
assert "Value ('3') must fulfill (4 <= value <= +infinity)" in element.text, element.text
[docs] @selenium_test
def test_float_parameter_maximum_validation(self):
editor = self.components.workflow_editor
workflow_run = self.components.workflow_run
parameter_name = "float_param"
name = self.create_and_wait_for_new_workflow_in_editor()
self.workflow_editor_add_input("parameter_input_float")
editor.label_input.wait_for_and_send_keys(parameter_name)
self.components.tool_form.parameter_input(parameter="parameter_definition|max").wait_for_and_send_keys("3.14")
self.save_after_node_form_changes()
self.workflow_run_with_name(name)
self.sleep_for(self.wait_types.UX_TRANSITION)
input_element = workflow_run.simplified_input(label=parameter_name).wait_for_and_click()
input_element.send_keys("3.2")
workflow_run.run_workflow_disabled.wait_for_absent()
workflow_run.run_error.assert_absent_or_hidden()
self.workflow_run_submit()
element = workflow_run.run_error.wait_for_present()
# see message in test test_int_parameter_minimum_validation about making this a little more human
# friendly.
assert "Value ('3.2') must fulfill (-infinity <= value <= 3.14)" in element.text, element.text
[docs] @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.components.workflows.edit_button.wait_for_and_click()
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()
self.components.tool_form.parameter_input(parameter="select_single").wait_for_and_send_keys("parameter value")
self.save_after_node_form_changes()
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"] == ""
[docs] @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_node.wait_for_and_click()
tool_input = tool_node.input_terminal(name="inttest")
self.hover_over(tool_input.wait_for_visible())
tool_node.connector_destroy_callout(name="inttest").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")
[docs] @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")
[docs] 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")
[docs] @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")
self.hover_over(cat_input.wait_for_visible())
cat_node.connector_destroy_callout(name="input1").wait_for_visible()
self.screenshot("workflow_editor_connection_callout")
cat_node.connector_destroy_callout(name="input1").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")
[docs] @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")
[docs] @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")
[docs] @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")
[docs] @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")
[docs] @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)
[docs] @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)
[docs] @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.components.workflow_editor.save_as_activity.wait_for_and_click()
[docs] @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)
[docs] @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_datatype_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_connection_invalid("create_2#out_file1", "checksum#input")
# Assert save button
save_button = self.components.workflow_editor.save_button
save_button.wait_for_and_click()
# Will trigger confirmation modal
self.components.workflow_editor.save_workflow_confirmation_button.wait_for_and_click()
# Make connection valid again
editor.change_datatype.wait_for_and_click()
editor.select_datatype_text_search.wait_for_and_send_keys("tabular")
editor.select_datatype(datatype="tabular").wait_for_and_click()
# Assert connection is valid
self.assert_connected("create_2#out_file1", "checksum#input")
[docs] @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")
[docs] @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")
[docs] @pytest.mark.xfail
@selenium_test
def test_edit_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
"""
)
editor = self.components.workflow_editor
node = editor.node._(label="nested_workflow")
node.wait_for_and_click()
editor.edit_subworkflow.wait_for_and_click()
node = editor.node._(label="create_2")
node.wait_for_and_click()
[docs] @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.components.workflows.edit_button.wait_for_and_click()
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_datatype_text_search.wait_for_and_send_keys("bam")
editor.select_datatype(datatype="bam").wait_for_and_click()
editor.add_tags_button.wait_for_and_click()
editor.add_tags_input.wait_for_and_send_keys("#crazynewtag" + Keys.ENTER + Keys.ESCAPE)
editor.remove_tags_button.wait_for_and_click()
editor.remove_tags_input.wait_for_and_send_keys("#oldboringtag" + Keys.ENTER + Keys.ESCAPE)
self.sleep_for(self.wait_types.UX_RENDER)
cat_node.clone.wait_for_and_click()
cloned_node = editor.node.by_id(id=2)
cloned_node.wait_for_and_click()
editor.label_input.wait_for_and_send_keys(Keys.BACKSPACE * 20)
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"]
[docs] @selenium_test
def test_editor_embed_workflow(self):
self.setup_subworkflow()
[docs] def setup_subworkflow(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:
input_collection:
type: collection
collection_type: "list"
steps:
- tool_id: multiple_versions
tool_version: 0.1
label: multiple_versions
state:
foo: bar
"""
)
self.workflow_index_open()
self.components.workflows.edit_button.wait_for_and_click()
editor = self.components.workflow_editor
editor.canvas_body.wait_for_visible()
self.workflow_editor_add_subworkflow(child_workflow_name)
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"]["2"]
assert subworkflow_step["name"] == child_workflow_name
assert subworkflow_step["type"] == "subworkflow"
assert subworkflow_step["subworkflow"]["a_galaxy_workflow"] == "true"
self.workflow_editor_connect("input_collection#output", f"{child_workflow_name}#input1")
self.assert_connected("input_collection#output", f"{child_workflow_name}#input1")
self.assert_workflow_has_changes_and_save()
workflow = self.workflow_populator.download_workflow(parent_workflow_id)
subworkflow_step = workflow["steps"]["2"]
assert subworkflow_step["input_connections"]["input1"]["input_subworkflow_step_id"] == 0
return child_workflow_name
[docs] @selenium_test
def test_editor_insert_steps(self):
steps_to_insert = self.workflow_upload_yaml_with_random_name(WORKFLOW_SIMPLE_CAT_TWICE)
annotation = "insert step test"
self.workflow_create_new(annotation=annotation)
self.workflow_editor_add_input(item_name="data_input")
editor = self.components.workflow_editor
editor.canvas_body.wait_for_visible()
self.workflow_editor_add_steps(steps_to_insert)
self.assert_connected("input1#output", "first_cat#input1")
self.assert_workflow_has_changes_and_save()
workflow_id = self.driver.current_url.split("id=")[1]
workflow = self.workflow_populator.download_workflow(workflow_id)
assert len(workflow["steps"]) == 3
[docs] @selenium_test
def test_editor_create_conditional_step(self):
editor = self.components.workflow_editor
self.workflow_create_new(annotation="simple when step definition")
# Insert a boolean parameter
self.workflow_editor_add_input(item_name="parameter_input")
param_type_element = editor.param_type_form.wait_for_present()
self.switch_param_type(param_type_element, "Boolean")
editor.label_input.wait_for_and_send_keys("param_input")
# Insert cat tool
self.tool_open("cat")
self.sleep_for(self.wait_types.UX_RENDER)
editor.label_input.wait_for_and_send_keys("downstream_step")
# Insert head tool
self.tool_open("head")
self.components.workflow_editor.tool_bar.auto_layout.wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
editor.label_input.wait_for_and_send_keys("conditional_step")
# Connect head to cat
self.workflow_editor_connect("conditional_step#out_file1", "downstream_step#input1")
self.assert_connected("conditional_step#out_file1", "downstream_step#input1")
# Make head tool conditional
conditional_node = editor.node._(label="conditional_step")
conditional_node.input_terminal(name="input").wait_for_present()
# Assert no when input before making step conditional
conditional_node.input_terminal(name="when").wait_for_absent()
conditional_toggle = editor.step_when.wait_for_present()
self.action_chains().move_to_element(conditional_toggle).click().perform()
# Toggling conditional should cause when input to appear
conditional_node.input_terminal(name="when").wait_for_present()
self.action_chains().move_to_element(conditional_toggle).click().perform()
# Toggling conditional should cause when input to disappear
conditional_node.input_terminal(name="when").wait_for_absent()
self.action_chains().move_to_element(conditional_toggle).click().perform()
conditional_node.input_terminal(name="when").wait_for_present()
# Output connection should be invalid, as output from conditional step is potentially null
self.assert_connection_invalid("conditional_step#out_file1", "downstream_step#input1")
downstream_step = editor.node._(label="downstream_step")
downstream_step.destroy.wait_for_and_click()
downstream_step.wait_for_absent()
# Connect boolean input to when
self.workflow_editor_connect("param_input#output", "conditional_step#when")
self.assert_connected("param_input#output", "conditional_step#when")
# Change boolean input parameter to invalid parameter type
editor.node._(label="param_input").wait_for_and_click()
param_type_element = editor.param_type_form.wait_for_present()
self.switch_param_type(param_type_element, "Text")
self.assert_connection_invalid("param_input#output", "conditional_step#when")
self.workflow_editor_destroy_connection("conditional_step#when")
# Make sure the when input is still shown
conditional_node.input_terminal(name="when").wait_for_present()
# Assert save button is disabled because of disconnected when
save_button = self.components.workflow_editor.save_button
save_button.wait_for_visible()
# TODO: hook up best practice panel, disable save when "when" not connected
# assert save_button.has_class("disabled")
[docs] def test_conditional_subworkflow_step(self):
child_workflow_name = self.setup_subworkflow()
editor = self.components.workflow_editor
# Insert a boolean parameter
self.workflow_editor_add_input(item_name="parameter_input")
param_type_element = editor.param_type_form.wait_for_present()
self.switch_param_type(param_type_element, "Boolean")
editor.label_input.wait_for_and_send_keys("param_input")
self.components.workflow_editor.tool_bar.auto_layout.wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
conditional_node = editor.node._(label=child_workflow_name)
conditional_node.wait_for_and_click()
conditional_toggle = editor.step_when.wait_for_present()
self.action_chains().move_to_element(conditional_toggle).click().perform()
conditional_node.input_terminal(name="when").wait_for_present()
self.workflow_editor_connect("param_input#output", f"{child_workflow_name}#when")
self.assert_connected("param_input#output", f"{child_workflow_name}#when")
self.assert_workflow_has_changes_and_save()
[docs] def switch_param_type(self, element, param_type):
self.action_chains().move_to_element(element).click().pause(1).send_keys(param_type).pause(1).send_keys(
Keys.ENTER
).perform()
[docs] def tab_to(self, accessible_name, direction="forward"):
for _ in range(100):
ac = self.action_chains()
if direction == "backwards":
ac.key_down(Keys.SHIFT)
ac.send_keys(Keys.TAB)
if direction == "backwards":
ac.key_down(Keys.SHIFT)
ac.perform()
if accessible_name in self.driver.switch_to.active_element.accessible_name:
return self.driver.switch_to.active_element
else:
raise Exception(f"Could not tab to element containing '{accessible_name}' in aria-label")
[docs] @selenium_test
def test_workflow_output_handling(self):
self.open_in_workflow_editor(
"""
class: GalaxyWorkflow
inputs: []
outputs:
first_out:
outputSource: first/out_file1
second_out:
outputSource: second/out_file1
steps:
first:
tool_id: create_2
second:
tool_id: create_2
""",
auto_layout=True,
)
editor = self.components.workflow_editor
# assert both steps have one workflow output each
first = editor.node._(label="first")
first.workflow_output_toggle_active(name="out_file1").wait_for_visible()
first.workflow_output_toggle_active(name="out_file2").wait_for_absent()
second = editor.node._(label="second")
second.workflow_output_toggle_active(name="out_file1").wait_for_visible()
second.workflow_output_toggle_active(name="out_file2").wait_for_absent()
# toggle out_file1 on second step, both outputs not active
second.workflow_output_toggle(name="out_file1").wait_for_and_click()
# just toggling outputs doesn't set a label
second.workflow_output_toggle_active(name="out_file1").wait_for_absent()
second.workflow_output_toggle_active(name="out_file2").wait_for_absent()
# switch to first node
editor.node._(label="first").wait_for_and_click()
# toggle out_file1 on first step
first.workflow_output_toggle(name="out_file1").wait_for_and_click()
first.workflow_output_toggle_active(name="out_file1").wait_for_absent()
# turn out_file1 back on
first.workflow_output_toggle(name="out_file1").wait_for_and_click()
first.workflow_output_toggle_active(name="out_file1").wait_for_visible()
# turn out_file1 off
first.workflow_output_toggle(name="out_file1").wait_for_and_click()
first.workflow_output_toggle_active(name="out_file1").wait_for_absent()
editor.node._(label="second").wait_for_and_click()
editor.node._(label="first").wait_for_and_click()
# make sure workflow outputs are both off for second step
first.workflow_output_toggle_active(name="out_file1").wait_for_absent()
first.workflow_output_toggle_active(name="out_file2").wait_for_absent()
# add an output label
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")
# should indicate active workflow output
first.workflow_output_toggle_active(name="out_file1").wait_for_visible()
self.set_text_element(output_label, "")
# deleting label also deletes active output
first.workflow_output_toggle_active(name="out_file1").wait_for_absent()
# set duplicate label
output_label = editor.label_output(output="out_file1")
self.set_text_element(output_label, "workflow output label")
editor.node._(label="second").wait_for_and_click()
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")
# should show error
editor.duplicate_label_error(output="out_file1").wait_for_visible()
# make label unique
self.set_text_element(output_label, "workflow output label2")
# should not show error
editor.duplicate_label_error(output="out_file1").wait_for_absent()
[docs] @selenium_test
def test_map_over_output_indicator(self):
self.open_in_workflow_editor(
"""
class: GalaxyWorkflow
inputs:
list:
type: collection
collection_type: "list"
nested_list:
type: collection
collection_type: "list:list"
steps:
filter:
tool_id: __FILTER_FROM_FILE__
"""
)
self.assert_node_output_is("filter#output_filtered", "any")
self.workflow_editor_connect("list#output", "filter#input")
self.assert_node_output_is("filter#output_filtered", "list")
self.workflow_editor_connect("nested_list#output", "filter#how|filter_source")
self.assert_node_output_is("filter#output_filtered", "list", "list:list:list")
self.workflow_editor_destroy_connection("filter#how|filter_source")
self.assert_node_output_is("filter#output_filtered", "list")
[docs] @selenium_test
def test_editor_snapping(self):
editor = self.components.workflow_editor
self.workflow_create_new(annotation="simple workflow")
self.sleep_for(self.wait_types.UX_RENDER)
self.tool_open("cat")
self.sleep_for(self.wait_types.UX_RENDER)
editor.label_input.wait_for_and_send_keys("tool_node")
# activate snapping and set it to max (200)
editor.tool_bar.tool(tool="toggle_snap").wait_for_and_click()
editor.tool_bar.snapping_distance.wait_for_and_click()
self.action_chains().send_keys(Keys.RIGHT * 10).perform()
# move the node a bit
tool_node = editor.node._(label="tool_node").wait_for_present()
self.action_chains().move_to_element(tool_node).click_and_hold().move_by_offset(12, 3).release().perform()
# check if editor position is snapped
top, left = self.get_node_position("tool_node")
assert top % 200 == 0
assert left % 200 == 0
# move the node a bit more
tool_node = editor.node._(label="tool_node").wait_for_present()
self.action_chains().move_to_element(tool_node).click_and_hold().move_by_offset(207, -181).release().perform()
# check if editor position is snapped
top, left = self.get_node_position("tool_node")
assert top % 200 == 0
assert left % 200 == 0
[docs] @selenium_test
def test_editor_selection(self):
editor = self.components.workflow_editor
self.workflow_create_new(annotation="simple workflow")
self.sleep_for(self.wait_types.UX_RENDER)
canvas = editor.canvas_body.wait_for_visible()
# place tool in center of canvas
self.tool_open("cat")
self.sleep_for(self.wait_types.UX_RENDER)
editor.label_input.wait_for_and_send_keys("tool_node")
tool_node = editor.node._(label="tool_node").wait_for_present()
self.mouse_drag(from_element=tool_node, to_element=canvas, to_offset=(0, -100))
# select the node
editor.node_inspector_close.wait_for_and_click()
self.action_chains().move_to_element(tool_node).key_down(Keys.SHIFT).click().key_up(Keys.SHIFT).perform()
self.sleep_for(self.wait_types.UX_RENDER)
assert editor.tool_bar.selection_count.wait_for_visible().text.find("1 step") != -1
# duplicate it
editor.tool_bar.duplicate_selection.wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
assert editor.tool_bar.selection_count.wait_for_visible().text.find("1 step") != -1
# move the node
tool_node_new = editor.node._(label="tool_node 2").wait_for_present()
self.mouse_drag(from_element=tool_node_new, to_element=canvas, to_offset=(0, 100))
# clear selection
editor.tool_bar.clear_selection.wait_for_and_click()
editor.tool_bar.selection_count.wait_for_absent_or_hidden()
# select both using box
tool_node_original = editor.node._(label="tool_node").wait_for_present()
editor.tool_bar.tool(tool="box_select").wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
self.mouse_drag(
from_element=tool_node_original, from_offset=(150, -100), to_element=tool_node_new, to_offset=(-150, 100)
)
self.sleep_for(self.wait_types.UX_RENDER)
assert editor.tool_bar.selection_count.wait_for_visible().text.find("2 steps") != -1
# delete steps
editor.tool_bar.delete_selection.wait_for_and_click()
editor.tool_bar.selection_count.wait_for_absent_or_hidden()
editor.node._(label="tool_node").wait_for_absent()
editor.node._(label="tool_node 2").wait_for_absent()
# place comments
editor.tool_bar.tool(tool="text_comment").wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
self.mouse_drag(from_element=canvas, from_offset=(-100, -200), to_element=canvas, to_offset=(100, 0))
editor.tool_bar.tool(tool="markdown_comment").wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
self.mouse_drag(from_element=canvas, from_offset=(-100, 0), to_element=canvas, to_offset=(100, 200))
# select both using box select
editor.tool_bar.tool(tool="box_select").wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
self.mouse_drag(from_element=canvas, from_offset=(-110, -210), to_element=canvas, to_offset=(110, 210))
assert editor.tool_bar.selection_count.wait_for_visible().text.find("2 comments") != -1
# deselect one using box select
editor.tool_bar.select_mode_remove.wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
self.mouse_drag(from_element=canvas, from_offset=(-110, -210), to_element=canvas, to_offset=(110, 10))
self.sleep_for(self.wait_types.UX_RENDER)
assert editor.tool_bar.selection_count.wait_for_visible().text.find("1 comment") != -1
[docs] def create_and_wait_for_new_workflow_in_editor(self, annotation: Optional[str] = None) -> str:
editor = self.components.workflow_editor
name = self.workflow_create_new(annotation=annotation)
editor.canvas_body.wait_for_visible()
return name
[docs] def get_node_position(self, label: str):
node = self.components.workflow_editor.node._(label=label).wait_for_present()
return self.get_element_position(node)
[docs] def get_element_position(self, element: WebElement):
left = element.value_of_css_property("left")
top = element.value_of_css_property("top")
left_stripped = "".join(char for char in left if char.isdigit())
top_stripped = "".join(char for char in top if char.isdigit())
return (int(left_stripped), int(top_stripped))
[docs] def get_element_size(self, element: WebElement):
width = element.value_of_css_property("width")
height = element.value_of_css_property("height")
width_stripped = "".join(char for char in width if char.isdigit())
height_stripped = "".join(char for char in height if char.isdigit())
return (int(width_stripped), int(height_stripped))
[docs] def assert_node_output_is(self, label: str, output_type: str, subcollection_type: Optional[str] = None):
editor = self.components.workflow_editor
node_label, output_name = label.split("#")
node = editor.node._(label=node_label)
node.wait_for_present()
output_element = node.output_terminal(name=output_name).wait_for_visible()
self.hover_over(output_element)
element = self.components._.tooltip_inner.wait_for_present()
assert f"output is {output_type}" in element.text, element.text
if subcollection_type is None:
assert "mapped-over" not in element.text
else:
fragment = " and mapped-over to produce a "
if subcollection_type == "list:paired":
fragment += "list of pairs dataset collection"
elif subcollection_type == "list:list":
fragment += "list of lists dataset collection"
elif subcollection_type.count(":") > 1:
fragment += f"dataset collection with {subcollection_type.count(':') + 1} levels of nesting"
else:
fragment += f"{subcollection_type}"
assert fragment in element.text
self.click_center()
[docs] def workflow_editor_maximize_center_pane(self, collapse_left=True, collapse_right=True):
self.sleep_for(self.wait_types.UX_RENDER)
editor = self.components.workflow_editor
if collapse_right and not editor.node_inspector.is_absent:
editor.node_inspector_close.wait_for_and_click()
if collapse_left and not self.components._.active_nav_item.is_absent:
self.components._.active_nav_item.wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
[docs] 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_by_offset(10, 10)
ac.perform()
self.sleep_for(self.wait_types.UX_RENDER)
self.screenshot(screenshot_partial)
drag_and_drop(self.driver, source_element, sink_element)
[docs] 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()
[docs] def assert_connection_invalid(self, source, sink):
source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
self.components.workflow_editor.connector_invalid_for(source_id=source_id, sink_id=sink_id).wait_for_present()
[docs] 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()
[docs] 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.components.workflow_editor.tool_bar.auto_layout.wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
return name
[docs] 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_present()
sink_node.wait_for_present()
output_terminal = source_node.output_terminal(name=source_output)
input_terminal = sink_node.input_terminal(name=sink_input)
output_element = output_terminal.wait_for_present()
input_element = input_terminal.wait_for_present()
source_id = output_element.get_attribute("id").replace("|", r"\|")
sink_id = input_element.get_attribute("id").replace("|", r"\|")
return source_id, sink_id
[docs] 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).wait_for_visible()
self.hover_over(sink_input)
sink_node.connector_destroy_callout(name=sink_input_name).wait_for_and_click()
[docs] def workflow_index_open_with_name(self, name):
self.workflow_index_open()
self.workflow_index_search_for(name)
self.components.workflows.edit_button.wait_for_and_click()
[docs] @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}'"
[docs] @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}'"
[docs] @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}]"
[docs] 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()