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Source code for galaxy_test.selenium.test_workflow_run
import json
from uuid import uuid4
import yaml
from selenium.webdriver.common.by import By
from galaxy_test.base import rules_test_data
from galaxy_test.base.workflow_fixtures import (
WORKFLOW_NESTED_REPLACEMENT_PARAMETER,
WORKFLOW_NESTED_RUNTIME_PARAMETER,
WORKFLOW_NESTED_SIMPLE,
WORKFLOW_RENAME_ON_REPLACEMENT_PARAM,
WORKFLOW_RUNTIME_PARAMETER_SIMPLE,
WORKFLOW_SELECT_FROM_OPTIONAL_DATASET,
WORKFLOW_SIMPLE_CAT_TWICE,
WORKFLOW_WITH_CUSTOM_REPORT_1,
WORKFLOW_WITH_CUSTOM_REPORT_1_TEST_DATA,
WORKFLOW_WITH_DATA_TAG_FILTER,
WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
WORKFLOW_WITH_OLD_TOOL_VERSION,
WORKFLOW_WITH_RULES_1,
)
from .framework import (
managed_history,
RunsWorkflows,
selenium_test,
SeleniumTestCase,
UsesHistoryItemAssertions,
)
[docs]class TestWorkflowRun(SeleniumTestCase, UsesHistoryItemAssertions, RunsWorkflows):
ensure_registered = True
[docs] @selenium_test
@managed_history
def test_workflow_export_file_rocrate(self):
self._setup_simple_invocation_for_export_testing()
invocations = self.components.invocations
self.workflow_run_wait_for_ok(hid=2)
invocations.export_tab.wait_for_and_click()
self.screenshot("invocation_export_formats")
invocations.export_output_format(type="ro-crate").wait_for_and_click()
invocations.wizard_next_button.wait_for_and_click()
download_option = invocations.export_destination(destination="download")
download_option.wait_for_present()
self.screenshot("invocation_export_rocrate_destinations")
download_option.wait_for_and_click()
invocations.wizard_next_button.wait_for_and_click()
export_button = invocations.wizard_export_button
export_button.wait_for_present()
self.screenshot("invocation_export_rocrate_download_options")
export_button.wait_for_and_click()
self.sleep_for(self.wait_types.UX_TRANSITION)
self.screenshot("invocation_export_crate_preparing_download")
invocations.export_download_link.wait_for_present()
self.screenshot("invocation_export_crate_download_ready")
[docs] @selenium_test
@managed_history
def test_workflow_export_file_native(self):
self._setup_simple_invocation_for_export_testing()
invocations = self.components.invocations
self.workflow_run_wait_for_ok(hid=2)
invocations.export_tab.wait_for_and_click()
self.screenshot("invocation_export_formats")
invocations.export_output_format(type="default-file").wait_for_and_click()
invocations.wizard_next_button.wait_for_and_click()
download_option = invocations.export_destination(destination="download")
download_option.wait_for_present()
self.screenshot("invocation_export_native_destinations")
download_option.wait_for_and_click()
invocations.wizard_next_button.wait_for_and_click()
export_button = invocations.wizard_export_button
export_button.wait_for_present()
self.screenshot("invocation_export_native_download_options")
export_button.wait_for_and_click()
self.sleep_for(self.wait_types.UX_TRANSITION)
self.screenshot("invocation_export_native_preparing_download")
invocations.export_download_link.wait_for_present()
self.screenshot("invocation_export_native_download_ready")
[docs] @selenium_test
@managed_history
def test_simple_execution(self):
self.perform_upload(self.get_filename("1.fasta"))
self.wait_for_history()
self.workflow_run_open_workflow(WORKFLOW_SIMPLE_CAT_TWICE)
self.screenshot("workflow_run_simple_ready")
self.workflow_run_submit()
self.sleep_for(self.wait_types.UX_TRANSITION)
self.screenshot("workflow_run_simple_submitted")
self.workflow_run_wait_for_ok(hid=2, expand=True)
self.assert_item_summary_includes(2, "2 sequences")
self.screenshot("workflow_run_simple_complete")
[docs] @selenium_test
@managed_history
def test_expanded_execution_of_simple_workflow(self):
self.perform_upload(self.get_filename("1.fasta"))
self.wait_for_history()
self.workflow_run_open_workflow(WORKFLOW_SIMPLE_CAT_TWICE)
self.workflow_run_ensure_expanded()
self.screenshot("workflow_run_expanded_ready")
self.workflow_run_submit()
self.sleep_for(self.wait_types.UX_TRANSITION)
self.screenshot("workflow_run_expanded_submitted")
self.workflow_run_wait_for_ok(hid=2, expand=True)
self.assert_item_summary_includes(2, "2 sequences")
self.screenshot("workflow_run_simple_complete")
[docs] @selenium_test
@managed_history
def test_runtime_parameters_simple(self):
self.perform_upload(self.get_filename("1.txt"))
self.wait_for_history()
self.workflow_run_open_workflow(WORKFLOW_RUNTIME_PARAMETER_SIMPLE)
self.tool_parameter_div("num_lines")
self.screenshot("workflow_run_runtime_parameters_initial")
self._set_num_lines_to_3("num_lines")
self.screenshot("workflow_run_runtime_parameters_modified")
self.workflow_run_submit()
self._assert_has_3_lines_after_run(hid=2)
[docs] @selenium_test
@managed_history
def test_runtime_parameters_simple_optional(self):
self.workflow_run_open_workflow(
"""
class: GalaxyWorkflow
inputs: {}
steps:
int_step:
tool_id: expression_null_handling_integer
runtime_inputs:
- int_input
"""
)
self.tool_parameter_div("int_input")
self._set_num_lines_to_3("int_input")
self.screenshot("workflow_run_optional_runtime_parameters_modified")
self.workflow_run_submit()
self.workflow_run_wait_for_ok(hid=1)
history_id = self.current_history_id()
content = self.dataset_populator.get_history_dataset_content(history_id, hid=1)
assert json.loads(content) == 3
[docs] @selenium_test
@managed_history
def test_subworkflows_expanded(self):
self.perform_upload(self.get_filename("1.txt"))
self.wait_for_history()
self.workflow_run_open_workflow(WORKFLOW_NESTED_SIMPLE)
self.workflow_run_ensure_expanded()
self.components.workflow_run.subworkflow_step_icon.wait_for_visible()
self.screenshot("workflow_run_nested_collapsed")
self.components.workflow_run.subworkflow_step_icon.wait_for_and_click()
self.screenshot("workflow_run_nested_open")
[docs] @selenium_test
@managed_history
def test_subworkflow_runtime_parameters(self):
self.perform_upload(self.get_filename("1.txt"))
self.wait_for_history()
self.workflow_run_open_workflow(WORKFLOW_NESTED_RUNTIME_PARAMETER)
self.workflow_run_ensure_expanded()
self.components.workflow_run.subworkflow_step_icon.wait_for_visible()
self.screenshot("workflow_run_nested_parameters_collapsed")
self.components.workflow_run.subworkflow_step_icon.wait_for_and_click()
self.screenshot("workflow_run_nested_parameters_open")
self._set_num_lines_to_3("1|num_lines")
self.workflow_run_submit()
self._assert_has_3_lines_after_run(hid=2)
[docs] @selenium_test
@managed_history
def test_replacement_parameters(self):
self.perform_upload(self.get_filename("1.txt"))
self.wait_for_history()
self.workflow_run_open_workflow(WORKFLOW_RENAME_ON_REPLACEMENT_PARAM)
self.workflow_run_ensure_expanded()
self.screenshot("workflow_run_rename_simple_empty")
self._set_replacement_parameter("replaceme", "moocow")
self.screenshot("workflow_run_rename_simple_input")
self.workflow_run_submit()
output_hid = 2
self.workflow_run_wait_for_ok(hid=output_hid)
history_id = self.current_history_id()
details = self.dataset_populator.get_history_dataset_details(history_id, hid=output_hid)
assert details["name"] == "moocow suffix", details
[docs] @selenium_test
@managed_history
def test_step_parameter_inputs(self):
self.perform_upload(self.get_filename("1.txt"))
self.wait_for_history()
self.workflow_run_open_workflow(
"""
class: GalaxyWorkflow
inputs:
input_int: integer
input_data: data
steps:
simple_constructs:
tool_id: simple_constructs
label: tool_exec
in:
inttest: input_int
files_0|file: input_data
"""
)
self.workflow_run_ensure_expanded()
workflow_run = self.components.workflow_run
input_div_element = workflow_run.input_div(label="input_int").wait_for_visible()
input_element = input_div_element.find_element(By.CSS_SELECTOR, "input")
input_element.clear()
input_element.send_keys("12345")
self.screenshot("workflow_run_step_parameter_input")
self.workflow_run_submit()
output_hid = 2
self.workflow_run_wait_for_ok(hid=output_hid)
history_id = self.current_history_id()
content = self.dataset_populator.get_history_dataset_content(history_id, hid=output_hid)
assert "12345" in content, content
assert "chr6_hla_hap2" in content
[docs] @selenium_test
@managed_history
def test_replacement_parameters_on_subworkflows(self):
self.perform_upload(self.get_filename("1.txt"))
self.wait_for_history()
self.workflow_run_open_workflow(WORKFLOW_NESTED_REPLACEMENT_PARAMETER)
self.workflow_run_ensure_expanded()
self.screenshot("workflow_run_rename_subworkflow_empty")
self._set_replacement_parameter("replaceme", "moocow")
self.screenshot("workflow_run_rename_subworkflow_input")
self.workflow_run_submit()
output_hid = 2
self.workflow_run_wait_for_ok(hid=output_hid)
history_id = self.current_history_id()
details = self.dataset_populator.get_history_dataset_details(history_id, hid=output_hid)
assert details["name"] == "moocow suffix", details
[docs] @selenium_test
def test_execution_with_tool_upgrade(self):
name = self.workflow_upload_yaml_with_random_name(WORKFLOW_WITH_OLD_TOOL_VERSION, exact_tools=True)
self.workflow_run_with_name(name)
self.sleep_for(self.wait_types.UX_TRANSITION)
# Check that this tool form contains a warning about different versions.
self.assert_message(self.components.workflow_run.warning, contains="tools which have changed")
self.screenshot("workflow_run_tool_upgrade")
[docs] @selenium_test
def test_run_form_safe_upgrade_handling(self):
workflow_with_rules = yaml.safe_load(WORKFLOW_WITH_RULES_1)
# 0.9.0 is a version that does not exist in WORKFLOW_SAFE_TOOL_VERSION_UPDATES
workflow_with_rules["steps"]["apply"]["tool_version"] = "0.9.0"
workflow_with_rules_json = json.dumps(workflow_with_rules)
name = self.workflow_upload_yaml_with_random_name(workflow_with_rules_json, exact_tools=True)
self.workflow_run_with_name(name)
self.sleep_for(self.wait_types.UX_TRANSITION)
self.assert_message(self.components.workflow_run.warning, contains="tools which have changed")
# 1.0.0 is a version that exists in WORKFLOW_SAFE_TOOL_VERSION_UPDATES
workflow_with_rules["steps"]["apply"]["tool_version"] = "1.0.0"
workflow_with_rules_json = json.dumps(workflow_with_rules)
name = self.workflow_upload_yaml_with_random_name(workflow_with_rules_json, exact_tools=True)
self.workflow_run_with_name(name)
self.sleep_for(self.wait_types.UX_TRANSITION)
# Check that this tool form does not contain a warning about different versions.
assert self.components.workflow_run.warning.is_absent
[docs] @selenium_test
@managed_history
def test_execution_with_multiple_inputs(self):
history_id = self.workflow_run_and_submit(
WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
inputs_specified_screenshot_name="workflow_run_two_inputs",
ensure_expanded=True,
)
self.workflow_run_wait_for_ok(hid=7)
content = self.dataset_populator.get_history_dataset_content(history_id, hid=7)
assert "10.0\n30.0\n20.0\n40.0\n" == content
[docs] @selenium_test
@managed_history
def test_execution_with_text_default_value_connected_to_restricted_select(self):
self.workflow_run_open_workflow(
"""
class: GalaxyWorkflow
inputs:
text_param:
optional: true
default: ex2
restrictOnConnections: true
type: text
steps:
multi_select:
tool_id: multi_select
in:
select_ex:
source: text_param
"""
)
element = self.components.workflow_run.input_select_field(label="text_param").wait_for_present()
assert element.text == "Ex2"
self.workflow_run_submit()
history_id = self.current_history_id()
self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
content = self.dataset_populator.get_history_dataset_content(history_id, hid=1)
assert content == "ex2"
[docs] @selenium_test
@managed_history
def test_execution_with_rules(self):
history_id = self.workflow_run_and_submit(
WORKFLOW_WITH_RULES_1,
WORKFLOW_WITH_RULES_1,
landing_screenshot_name="workflow_run_rules_landing",
inputs_specified_screenshot_name="workflow_run_rules",
ensure_expanded=True,
)
self.workflow_run_wait_for_ok(hid=6)
output_content = self.dataset_populator.get_history_collection_details(history_id, hid=6)
rules_test_data.check_example_2(output_content, self.dataset_populator)
[docs] @selenium_test
@managed_history
def test_execution_with_custom_invocation_report(self):
history_id = self.workflow_run_and_submit(
WORKFLOW_WITH_CUSTOM_REPORT_1,
WORKFLOW_WITH_CUSTOM_REPORT_1_TEST_DATA,
ensure_expanded=True,
)
self.screenshot("workflow_run_invocation_report")
self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
invocation_0 = self.workflow_populator.history_invocations(history_id)[0]
self.get(f"workflows/invocations/report?id={invocation_0['id']}")
self.wait_for_selector_visible(".embedded-dataset")
self.screenshot("workflow_report_custom_1")
[docs] @selenium_test
@managed_history
def test_execution_with_null_optional_select_from_data(self):
history_id = self.workflow_run_and_submit(
WORKFLOW_SELECT_FROM_OPTIONAL_DATASET,
)
self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
[docs] @selenium_test
@managed_history
def test_workflow_run_button_disabled_when_required_input_missing(self):
self.workflow_run_open_workflow(
"""
class: GalaxyWorkflow
inputs:
text_param:
type: text
optional: false
data_param:
type: data
collection_param:
type: data_collection
steps: {}
"""
)
workflow_run = self.components.workflow_run
# None of the required parameters are present
workflow_run.run_workflow_disabled.wait_for_present()
# upload datasets and collections
history_id = self.current_history_id()
self.dataset_populator.new_dataset(history_id, wait=True)
self.dataset_collection_populator.create_list_in_history(history_id, wait=True)
input_element = workflow_run.simplified_input(label="text_param").wait_for_and_click()
input_element.send_keys("3")
# Everything is set, workflow is runnable, disabled class should be removed
workflow_run.run_workflow_disabled.wait_for_absent()
input_element.clear()
workflow_run.run_workflow_disabled.wait_for_present()
[docs] @selenium_test
@managed_history
def test_workflow_run_tag_filter(self):
history_id = self.current_history_id()
dataset = self.dataset_populator.new_dataset(history_id, wait=True)
self.dataset_populator.tag_dataset(history_id, dataset["id"], tags=["genomescope_model"])
# Add another possible input that should not be selected
self.dataset_populator.new_dataset(history_id, wait=True)
wf = json.loads(WORKFLOW_WITH_DATA_TAG_FILTER)
wf["name"] = str(uuid4())
workflow_id = self.workflow_populator.create_workflow(wf)
self.workflow_run_with_name(wf["name"])
self.workflow_run_submit()
self.sleep_for(self.wait_types.HISTORY_POLL)
invocations = self.workflow_populator.workflow_invocations(workflow_id=workflow_id)
invocation = self.workflow_populator.get_invocation(invocations[-1]["id"])
assert invocation["inputs"]["0"]["id"] == dataset["id"]
def _assert_has_3_lines_after_run(self, hid):
self.workflow_run_wait_for_ok(hid=hid)
history_id = self.current_history_id()
content = self.dataset_populator.get_history_dataset_content(history_id, hid=hid)
assert len([x for x in content.split("\n") if x]) == 3, content
def _set_num_lines_to_3(self, element_id):
# for random_lines num_lines parameter as runtime parameter in workflow form.
div = self.tool_parameter_div(element_id)
input_element = div.find_element(By.CSS_SELECTOR, "input")
# runtime parameters not being set to tool default value:
# https://github.com/galaxyproject/galaxy/pull/7157
# initial_value = input_element.get_attribute("value")
# assert initial_value == "1", initial_value
input_element.clear()
input_element.send_keys("3")
def _set_replacement_parameter(self, element_id, value):
# for random_lines num_lines parameter as runtime parameter in workflow form.
div = self.tool_parameter_div(element_id)
input_element = div.find_element(By.CSS_SELECTOR, "input")
initial_value = input_element.get_attribute("value")
assert initial_value == "", initial_value
input_element.clear()
input_element.send_keys(value)
def _setup_simple_invocation_for_export_testing(self):
# precondition: refresh history
self.perform_upload(self.get_filename("1.fasta"))
self.wait_for_history()
self.workflow_run_open_workflow(WORKFLOW_SIMPLE_CAT_TWICE)
self.workflow_run_submit()
history_id = self.current_history_id()
self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
return self.workflow_populator.history_invocations(history_id)[0]