galaxy/test/selenium_tests/test_workflow_run.py

import yaml
from base import rules_test_data
from base.populators import load_data_dict
from 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_SIMPLE_CAT_TWICE,
    WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
    WORKFLOW_WITH_OLD_TOOL_VERSION,
    WORKFLOW_WITH_RULES_1,
)

from .framework import (
    managed_history,
    selenium_test,
    SeleniumTestCase,
    UsesHistoryItemAssertions,
)


class WorkflowRunTestCase(SeleniumTestCase, UsesHistoryItemAssertions):

    ensure_registered = True

    @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")

    @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)

    @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")

    @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)

    @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

    @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

    @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

    @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_warning_message(contains="different versions")
        self.screenshot("workflow_run_tool_upgrade")

    @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)

    @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)

    def open_in_workflow_run(self, yaml_content):
        name = self.workflow_upload_yaml_with_random_name(yaml_content)
        self.workflow_run_with_name(name)

    def workflow_run_setup_inputs(self, content):
        history_id = self.current_history_id()
        test_data = yaml.safe_load(content)["test_data"]
        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

    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"])

    def workflow_run_with_name(self, name):
        self.workflow_index_open()
        self.workflow_index_search_for(name)
        self.workflow_index_click_option("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)