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Source code for galaxy_test.selenium.test_workflow_run
import yaml
from galaxy_test.base import rules_test_data
from galaxy_test.base.populators import load_data_dict
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_DYNAMIC_OUTPUT_COLLECTION,
WORKFLOW_WITH_OLD_TOOL_VERSION,
WORKFLOW_WITH_RULES_1,
)
from .framework import (
managed_history,
selenium_test,
SeleniumTestCase,
UsesHistoryItemAssertions,
)
[docs]class WorkflowRunTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
ensure_registered = True
[docs] @selenium_test
@managed_history
def test_simple_execution(self):
self.perform_upload(self.get_filename("1.fasta"))
self.wait_for_history()
self.open_in_workflow_run(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")
if self.is_beta_history():
item = self.content_item_by_attributes(hid=2, state="ok")
item.wait_for_present()
item.title.wait_for_and_click()
else:
self.history_panel_wait_for_hid_ok(2, allowed_force_refreshes=1)
self.history_panel_click_item_title(hid=2, wait=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.open_in_workflow_run(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_subworkflows_simple(self):
self.perform_upload(self.get_filename("1.txt"))
self.wait_for_history()
self.open_in_workflow_run(WORKFLOW_NESTED_SIMPLE)
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.open_in_workflow_run(WORKFLOW_NESTED_RUNTIME_PARAMETER)
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.open_in_workflow_run(WORKFLOW_RENAME_ON_REPLACEMENT_PARAM)
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
if self.is_beta_history():
self.content_item_by_attributes(hid=output_hid, state="ok").wait_for_present()
else:
self.history_panel_wait_for_hid_ok(output_hid, allowed_force_refreshes=1)
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.open_in_workflow_run("""
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
""")
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
if self.is_beta_history():
self.content_item_by_attributes(hid=output_hid, state="ok").wait_for_present()
else:
self.history_panel_wait_for_hid_ok(output_hid, allowed_force_refreshes=1)
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.open_in_workflow_run(WORKFLOW_NESTED_REPLACEMENT_PARAMETER)
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
if self.is_beta_history():
self.content_item_by_attributes(hid=output_hid, state="ok").wait_for_present()
else:
self.history_panel_wait_for_hid_ok(output_hid, allowed_force_refreshes=1)
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="different versions")
self.screenshot("workflow_run_tool_upgrade")
[docs] @selenium_test
@managed_history
def test_execution_with_multiple_inputs(self):
history_id, inputs = self.workflow_run_setup_inputs(WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION)
self.open_in_workflow_run(WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION)
self.workflow_run_specify_inputs(inputs)
self.screenshot("workflow_run_two_inputs")
self.workflow_run_submit()
if self.is_beta_history():
timeout = self.wait_length(self.wait_types.JOB_COMPLETION)
item = self.content_item_by_attributes(hid=7, state="ok")
self.wait_for_present(item, timeout=timeout)
else:
self.history_panel_wait_for_hid_ok(7, allowed_force_refreshes=1)
content = self.dataset_populator.get_history_dataset_content(history_id, hid=7)
self.assertEqual("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.open_in_workflow_run("""
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, inputs = self.workflow_run_setup_inputs(WORKFLOW_WITH_RULES_1)
self.open_in_workflow_run(WORKFLOW_WITH_RULES_1)
self.workflow_run_specify_inputs(inputs)
self.screenshot("workflow_run_rules")
self.workflow_run_submit()
if self.is_beta_history():
timeout = self.wait_length(self.wait_types.JOB_COMPLETION)
item = self.content_item_by_attributes(hid=6, state="ok")
self.wait_for_present(item, timeout=timeout)
else:
self.history_panel_wait_for_hid_ok(6, allowed_force_refreshes=1)
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, inputs = self.workflow_run_setup_inputs(WORKFLOW_WITH_CUSTOM_REPORT_1_TEST_DATA)
self.open_in_workflow_run(WORKFLOW_WITH_CUSTOM_REPORT_1)
self.workflow_run_specify_inputs(inputs)
self.workflow_run_submit()
self.sleep_for(self.wait_types.UX_TRANSITION)
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):
self.open_in_workflow_run(WORKFLOW_SELECT_FROM_OPTIONAL_DATASET)
self.workflow_run_submit()
history_id = self.current_history_id()
self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
[docs] def open_in_workflow_run(self, yaml_content):
name = self.workflow_upload_yaml_with_random_name(yaml_content)
self.workflow_run_with_name(name)
[docs] def workflow_run_setup_inputs(self, content):
history_id = self.current_history_id()
yaml_content = yaml.safe_load(content)
if "test_data" in yaml_content:
test_data = yaml_content["test_data"]
else:
test_data = yaml_content
inputs, _, _ = load_data_dict(history_id, test_data, self.dataset_populator, self.dataset_collection_populator)
self.dataset_populator.wait_for_history(history_id)
return history_id, inputs
[docs] def workflow_run_specify_inputs(self, inputs):
workflow_run = self.components.workflow_run
for label, value in inputs.items():
input_div_element = workflow_run.input_data_div(label=label).wait_for_visible()
self.select2_set_value(input_div_element, "%d: " % value["hid"])
[docs] def workflow_run_with_name(self, name):
self.workflow_index_open()
self.workflow_index_search_for(name)
self.workflow_click_option(".workflow-run")
def _assert_has_3_lines_after_run(self, hid):
if self.is_beta_history():
self.content_item_by_attributes(hid=hid, state="ok").wait_for_present()
else:
self.history_panel_wait_for_hid_ok(hid, allowed_force_refreshes=1)
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)