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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") 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 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 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 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() 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_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() 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("workflows/invocations/report?id=%s" % 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): 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, tour_id): # for random_lines num_lines parameter as runtime parameter in workflow form. div = self.tool_parameter_div(tour_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, tour_id, value): # for random_lines num_lines parameter as runtime parameter in workflow form. div = self.tool_parameter_div(tour_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)