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galaxy/test/selenium_tests/test_workflow_run.py
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John Chilton ad650897d6 Implement workflow invocation reports. 
Implement markdown backend and frontend components as well generator plugin framework to allow customizable workflow invocation reports.

Architectural Choices on the Client

Old-style embedded objects vs components

In theory, this could make really nice use of excellent VueJS components for dataset display, dataset collection display, workflow display, etc.. These aren't available yet, we don't even really have Backbone stuff that exist very well outside history panels, so this re-uses "components" from Galaxy Pages for datasets and reuses the collection display for history panels as a stand-alone display for collections (I got this trick from DIsplayStructured.vue). This isn't ideal and I know that but at least reusing things this way will provide a path forward for migrating both pages and this new Markdown language (which could easily replace or co-exist with pages HTML someday) together seamlessly as the real modern components become available and doesn't increase the overall work needed to integrate newer style components. In fact, this might even be the impetus for creating and polishing more of these components.

markdown-it vs markdown-it-vue

I tried this with markdown-it-vue also but it added very little in terms of reducing client code, obscured entirely how to attach plugins to the markdown rendering process, and brought in many, many more extra packages that we don't need or want.

Given there is no representation of invocations in the GUI and not editor for reports config this is a bit challenging still. But here is goes:

- Source Galaxy's virtualenv.
- Login to a user and grab an API key, set in the following command:
- ``GALAXY_TEST_EXTERNAL=http://localhost:8080 GALAXY_TEST_USER_API_KEY=38175dfc69d9009992b69efcca8b209b pytest test/api/test_workflows.py::WorkflowsApiTestCase::test_workflow_invocation_report_custom``
- In the web browser go to http://localhost:8080/api/invocations and grab the latest invocation ID. Replace it in the follow query string.
- Navigate to http://localhost:8080/workflows/invocations/report?id=c887f1d0da42bdfe
2019-08-30 09:43:01 -04:00

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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_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,
)
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)
@selenium_test
@managed_history
def test_execution_with_custom_invocation_repoprt(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-item.dataset")
self.screenshot("workflow_report_custom_1")
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()
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
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)
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