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Source code for galaxy_test.selenium.test_tool_form
import json
from typing import (
Any,
Dict,
List,
)
import pytest
from selenium.webdriver.common.by import By
from galaxy.model.unittest_utils.store_fixtures import one_hda_model_store_dict
from galaxy.selenium.navigates_galaxy import retry_call_during_transitions
from galaxy.util.unittest_utils import skip_if_github_down
from galaxy_test.base import rules_test_data
from galaxy_test.base.populators import (
flakey,
stage_rules_example,
)
from .framework import (
managed_history,
retry_assertion_during_transitions,
selenium_test,
SeleniumTestCase,
UsesHistoryItemAssertions,
)
[docs]class TestToolForm(SeleniumTestCase, UsesHistoryItemAssertions):
[docs] @selenium_test
def test_run_tool_verify_contents_by_peek(self):
self._run_environment_test_tool()
self.history_panel_wait_for_hid_ok(1)
self.history_panel_click_item_title(hid=1)
self.assert_item_peek_includes(1, "42")
[docs] @selenium_test
def test_run_tool_verify_dataset_details(self):
self._run_environment_test_tool()
self.history_panel_wait_for_hid_ok(1)
self._check_dataset_details_for_inttest_value(1)
[docs] @selenium_test
def test_verify_dataset_details_tables(self):
self._run_environment_test_tool()
self.history_panel_wait_for_hid_ok(1)
hda = self.latest_history_item()
self._check_dataset_details_for_inttest_value(1)
dataset_details_key_value_pairs = self._table_to_key_value_elements("table#dataset-details")
number_found = name_found = format_found = False
for key, value in dataset_details_key_value_pairs:
if "Number" in key.text:
assert str(hda["hid"]) in value.text
number_found = True
if "Name" in key.text:
assert hda["name"] in value.text
name_found = True
if "Format" in key.text:
assert hda["extension"] in value.text
format_found = True
assert number_found
assert name_found
assert format_found
job_outputs = self._table_to_key_value_elements("table#job-outputs")
assert job_outputs[0][0].text == "environment_variables"
generic_item = job_outputs[0][1]
assert "1: environment_variables" in generic_item.text
generic_item.click()
self.sleep_for(self.wait_types.UX_RENDER)
assert generic_item.find_element(By.CSS_SELECTOR, "pre").text == "42\nmoo\nNOTTHREE"
generic_item.find_element(By.CSS_SELECTOR, "[title='Run Job Again']").click()
self.components.tool_form.execute.wait_for_visible()
[docs] @selenium_test
def test_drilldown_tool(self):
self._open_drilldown_test_tool()
# click first option in first drilldown component
self.wait_for_and_click(self.components.tool_form.drilldown_expand)
self.wait_for_and_click(self.components.tool_form.drilldown_option)
# click select all in second drilldown component
self.wait_for_and_click(self.components.tool_form.drilldown_select_all(parameter="dd_recurse"))
self.tool_form_execute()
self.history_panel_wait_for_hid_ok(1)
# click hid 1 in history panel
self.history_panel_click_item_title(hid=1)
# assert that the dataset peek is d = a dd_recurse = a,b,c
self.assert_item_peek_includes(1, "dd a")
self.assert_item_peek_includes(1, "dd_recurse aa,aba,abb,ba,bba,bbb")
def _open_drilldown_test_tool(self):
self.home()
self.tool_open("drill_down")
def _table_to_key_value_elements(self, table_selector):
tool_parameters_table = self.wait_for_selector_visible(table_selector)
tbody_element = tool_parameters_table.find_element(By.CSS_SELECTOR, "tbody")
trs = tbody_element.find_elements(By.CSS_SELECTOR, "tr")
assert trs
key_value_pairs = []
for tr in trs:
tds = tr.find_elements(By.CSS_SELECTOR, "td")
assert tds
key_value_pairs.append((tds[0], tds[1]))
return key_value_pairs
[docs] @selenium_test
def test_repeat_reordering(self):
self.home()
self.tool_open("text_repeat")
def assert_input_order(inputs: List[str]):
for index, input in enumerate(inputs):
parameter_input = self.components.tool_form.parameter_input(parameter=f"the_repeat_{index}|texttest")
parameter_value = parameter_input.wait_for_value()
assert parameter_value == input
self.components.tool_form.repeat_insert.wait_for_and_click()
self.tool_set_value("the_repeat_0|texttest", "Text A")
self.components.tool_form.repeat_insert.wait_for_and_click()
self.tool_set_value("the_repeat_1|texttest", "Text B")
self.components.tool_form.repeat_insert.wait_for_and_click()
self.tool_set_value("the_repeat_2|texttest", "Text C")
assert_input_order(["Text A", "Text B", "Text C"])
self.components.tool_form.repeat_move_up(parameter="the_repeat_1").wait_for_and_click()
assert_input_order(["Text B", "Text A", "Text C"])
self.components.tool_form.repeat_move_up(parameter="the_repeat_2").wait_for_and_click()
assert_input_order(["Text B", "Text C", "Text A"])
self.components.tool_form.repeat_move_up(parameter="the_repeat_1").wait_for_and_click()
assert_input_order(["Text C", "Text B", "Text A"])
self.components.tool_form.repeat_move_up(parameter="the_repeat_0").wait_for_and_click()
assert_input_order(["Text C", "Text B", "Text A"])
self.tool_form_execute()
self.history_panel_wait_for_hid_ok(1)
details = [d.text for d in self._get_dataset_tool_parameters(1)]
assert details == ["texttest", "Text C", "texttest", "Text B", "texttest", "Text A"]
[docs] @selenium_test
def test_rerun(self):
self._run_environment_test_tool()
self.history_panel_wait_for_hid_ok(1)
self.hda_click_primary_action_button(1, "rerun")
def check_recorded_val():
inttest_div_element = self.tool_parameter_div("inttest")
inttest_input_element = inttest_div_element.find_element(By.CSS_SELECTOR, "input")
recorded_val = inttest_input_element.get_attribute("value")
# Assert form re-rendered with correct value in textbox.
assert recorded_val == "42", recorded_val
# These form entries seem to be replaced/updated occasionally
# causing stale elements.
retry_call_during_transitions(check_recorded_val)
self.tool_form_execute()
self.history_panel_wait_for_hid_ok(2)
self._check_dataset_details_for_inttest_value(2)
[docs] @selenium_test
def test_rerun_deleted_dataset(self):
# upload a first dataset that should not become selected on re-run
test_path = self.get_filename("1.tabular")
self.perform_upload(test_path)
self.history_panel_wait_for_hid_ok(1)
self.tool_open("column_param")
self.select_set_value("#col", "3")
self.tool_form_execute()
self.history_panel_wait_for_hid_ok(2)
# delete source dataset and click re-run on resulting dataset
item = self.history_panel_item_component(hid=1)
item.delete_button.wait_for_and_click()
item = self.history_panel_item_component(hid=2)
item.title.wait_for_and_click()
item.rerun_button.wait_for_and_click()
# validate initial warnings
error_input1 = self.components.tool_form.parameter_error(parameter="input1").wait_for_visible()
error_col = self.components.tool_form.parameter_error(parameter="col").wait_for_visible()
assert (
error_input1.text
== "parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
)
assert error_col.text == "parameter 'col': an invalid option ('3') was selected (valid options: 1)"
# validate errors when inputs are missing
self.components.tool_form.parameter_data_input_collection(parameter="input1").wait_for_and_click()
self.sleep_for(self.wait_types.UX_TRANSITION)
error_input1 = self.components.tool_form.parameter_error(parameter="input1").wait_for_visible()
error_col = self.components.tool_form.parameter_error(parameter="col").wait_for_visible()
error_col_names = self.components.tool_form.parameter_error(parameter="col_names").wait_for_visible()
assert error_input1.text == "Please provide a value for this option."
assert error_col.text == "parameter 'col': requires a value, but no legal values defined"
assert error_col_names.text == "parameter 'col_names': requires a value, but no legal values defined"
# validate warnings when inputs are restored
self.components.tool_form.parameter_data_input_single(parameter="input1").wait_for_and_click()
self.sleep_for(self.wait_types.UX_TRANSITION)
error_input1 = self.components.tool_form.parameter_error(parameter="input1").wait_for_visible()
error_col = self.components.tool_form.parameter_error(parameter="col").wait_for_visible()
assert (
error_input1.text
== "parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
)
assert error_col.text == "parameter 'col': an invalid option ('3') was selected (valid options: 1)"
[docs] @selenium_test
def test_rerun_dataset_collection_element(self):
# upload a first dataset that should not become selected on re-run
test_path = self.get_filename("1.fasta")
self.perform_upload(test_path)
self.history_panel_wait_for_hid_ok(1)
history_id = self.current_history_id()
# upload a nested collection
self.dataset_collection_populator.create_list_of_list_in_history(
history_id,
collection_type="list:list",
wait=True,
).json()["id"]
self.tool_open("identifier_multiple")
self.components.tool_form.parameter_data_input_collection(parameter="input1").wait_for_and_click()
self.sleep_for(self.wait_types.UX_RENDER)
select_field = self.components.tool_form.parameter_data_select(parameter="input1")
self.select_set_value(select_field, "list:list")
self.sleep_for(self.wait_types.UX_RENDER)
self.tool_form_execute()
self.history_panel_wait_for_hid_ok(7)
self.history_panel_expand_collection(7)
self.sleep_for(self.wait_types.UX_RENDER)
self.history_panel_click_item_title(1)
self.sleep_for(self.wait_types.UX_RENDER)
self.hda_click_primary_action_button(1, "rerun")
self.sleep_for(self.wait_types.UX_RENDER)
self.tool_form_execute()
self.components.history_panel.collection_view.back_to_history.wait_for_and_click()
self.history_panel_wait_for_hid_ok(9)
[docs] @selenium_test
@flakey
def test_run_data(self):
test_path = self.get_filename("1.fasta")
test_path_decoy = self.get_filename("1.txt")
# Upload form posts bad data if executed two times in a row like this, so
# wait between uploads. xref https://github.com/galaxyproject/galaxy/issues/5169
self.perform_upload(test_path)
self.history_panel_wait_for_hid_ok(1)
self.perform_upload(test_path_decoy)
self.history_panel_wait_for_hid_ok(2)
self.home()
self.tool_open("head")
self.tool_set_value("input", "1.fasta", expected_type="data")
self.screenshot("tool_form_simple_data")
self.tool_form_execute()
self.history_panel_wait_for_hid_ok(3)
latest_hda = self.latest_history_item()
assert latest_hda["hid"] == 3
assert latest_hda["name"] == "Select first on data 1"
[docs] @selenium_test
def test_bibtex_rendering(self):
self.home()
# prefetch citations so they will be available quickly when rendering tool form.
citations_api = self.api_get("tools/bibtex/citations")
citation_count = len(citations_api)
self.tool_open("bibtex")
self.components.tool_form.about.wait_for_and_click()
@retry_assertion_during_transitions
def assert_citations_visible():
references = self.components.tool_form.reference.all()
if (references_rendered := len(references)) != citation_count:
citations_api = self.api_get("tools/bibtex/citations")
current_citation_count = len(citations_api)
message = f"Expected {citation_count} references to be rendered, {references_rendered} actually rendered. Currently the API yields {current_citation_count} references"
raise AssertionError(message)
return references
references = assert_citations_visible()
doi_resolved_citation = references[0]
assert "platform for interactive" in doi_resolved_citation.text
self.screenshot("tool_form_citations_formatted")
def _check_dataset_details_for_inttest_value(self, hid, expected_value="42"):
tds = self._get_dataset_tool_parameters(hid)
assert tds
assert any(expected_value in td.text for td in tds)
def _get_dataset_tool_parameters(self, hid):
self.hda_click_details(hid)
self.components.dataset_details._.wait_for_visible()
tool_parameters_table = self.components.dataset_details.tool_parameters.wait_for_visible()
tbody_element = tool_parameters_table.find_element(By.CSS_SELECTOR, "tbody")
tds = tbody_element.find_elements(By.CSS_SELECTOR, "td")
return tds
def _run_environment_test_tool(self, inttest_value="42"):
self.home()
self.tool_open("environment_variables")
self.tool_set_value("inttest", inttest_value)
self.tool_form_execute()
[docs]class TestLoggedInToolForm(SeleniumTestCase):
ensure_registered = True
[docs] @selenium_test
def test_dataset_state_filtering(self):
# upload an ok (HID 1) and a discarded (HID 2) dataset and run a tool
# normally HID 2 would be selected but since it is discarded - it won't
# be an option so verify the result was run with HID 1.
test_path = self.get_filename("1.fasta")
self.perform_upload(test_path)
self.history_panel_wait_for_hid_ok(1)
history_id = self.current_history_id()
self.dataset_populator.create_contents_from_store(
history_id,
store_dict=one_hda_model_store_dict(include_source=False),
)
self.home()
self.tool_open("head")
self.components.tool_form.execute.wait_for_visible()
self.screenshot("tool_form_with_filtered_discarded_input")
self.tool_form_execute()
self.history_panel_wait_for_hid_ok(3)
latest_hda = self.latest_history_item()
assert latest_hda["hid"] == 3
assert latest_hda["name"] == "Select first on data 1"
[docs] @selenium_test
def test_run_apply_rules_1(self):
self._apply_rules_and_check(rules_test_data.EXAMPLE_1)
self.screenshot("tool_apply_rules_example_1_final")
[docs] @selenium_test
def test_run_apply_rules_2(self):
self._apply_rules_and_check(rules_test_data.EXAMPLE_2)
self.screenshot("tool_apply_rules_example_2_final")
[docs] @selenium_test
def test_run_apply_rules_3(self):
self._apply_rules_and_check(rules_test_data.EXAMPLE_3)
self.screenshot("tool_apply_rules_example_3_final")
[docs] @selenium_test
def test_run_apply_rules_4(self):
self._apply_rules_and_check(rules_test_data.EXAMPLE_4)
self.screenshot("tool_apply_rules_example_4_final")
[docs] @selenium_test
@managed_history
@skip_if_github_down
@pytest.mark.gtn_screenshot
@pytest.mark.local
def test_run_apply_rules_tutorial(self):
self.home()
self.upload_rule_start()
self.upload_rule_set_data_type("Collections")
self.components.upload.rule_source_content.wait_for_and_send_keys(
"""https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/treated1fb.txt treated_single_1
https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/treated2fb.txt treated_paired_2
https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/treated3fb.txt treated_paired_3
https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated1fb.txt untreated_single_4
https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated2fb.txt untreated_single_5
https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated3fb.txt untreated_paired_6
https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated4fb.txt untreated_paired_7
"""
)
self.screenshot("rules_apply_rules_example_4_1_input_paste")
self.upload_rule_build()
rule_builder = self.components.rule_builder
rule_builder._.wait_for_and_click()
self.rule_builder_set_mapping("url", "A")
self.rule_builder_set_mapping("list-identifiers", ["B"])
self.rule_builder_set_collection_name("flat_count_list")
self.rule_builder_set_extension("txt")
self.screenshot("rules_apply_rules_example_4_2_input_rules")
rule_builder.main_button_ok.wait_for_and_click()
self.history_panel_wait_for_hid_ok(1)
self.screenshot("rules_apply_rules_example_4_3_input_ready")
self.history_multi_view_display_collection_contents(1, "list")
self.screenshot("rules_apply_rules_example_4_4_input_list")
self.home()
add_depth_rules = {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
},
{"type": "add_column_regex", "target_column": 0, "expression": "(.*)_(.*)_.*", "group_count": 2},
],
"mapping": [
{
"type": "list_identifiers",
"columns": [1, 2, 0],
}
],
}
self._tool_apply_with_source(
add_depth_rules,
hid=1,
landing_screenshot="rules_apply_rules_example_4_5_apply_rules_landing",
rule_init_screenshot="rules_apply_rules_example_4_6_apply_rules_init_flat",
rule_complete_screenshot="rules_apply_rules_example_4_7_apply_rules_add_depth",
)
self.history_panel_wait_for_hid_ok(16)
self.history_multi_view_display_collection_contents(16, "list:list:list")
self.screenshot("rules_apply_rules_example_4_8_nested")
self.home()
invert_rules = {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
},
{
"type": "add_column_metadata",
"value": "identifier1",
},
{
"type": "add_column_metadata",
"value": "identifier2",
},
],
"mapping": [
{
"type": "list_identifiers",
"columns": [1, 0, 2],
}
],
}
self._tool_apply_with_source(
invert_rules,
rule_init_screenshot="rules_apply_rules_example_4_9_apply_rules_init_nested",
rule_complete_screenshot="rules_apply_rules_example_4_10_apply_rules_inverted",
)
self.history_panel_wait_for_hid_ok(24)
self.history_multi_view_display_collection_contents(24, "list:list:list")
self.screenshot("rules_apply_rules_example_4_11_inverted")
self.home()
filter_rules = {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
},
{
"type": "add_filter_regex",
"target_column": 0,
"expression": ".*_single_.*",
"invert": False,
},
],
"mapping": [
{
"type": "list_identifiers",
"columns": [0],
}
],
}
self._tool_apply_with_source(
filter_rules, hid=1, rule_complete_screenshot="rules_apply_rules_example_4_12_apply_rules_filter"
)
self.history_panel_wait_for_hid_ok(28)
self.history_multi_view_display_collection_contents(28, "list")
self.screenshot("rules_apply_rules_example_4_13_filtered")
self.home()
filter_and_nest_rules = {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
},
{
"type": "add_filter_regex",
"target_column": 0,
"expression": ".*_single_.*",
"invert": False,
},
{"type": "add_column_regex", "target_column": 0, "expression": "(.*)_single_.*", "group_count": 1},
],
"mapping": [
{
"type": "list_identifiers",
"columns": [1, 0],
}
],
}
self._tool_apply_with_source(
filter_and_nest_rules,
hid=1,
rule_complete_screenshot="rules_apply_rules_example_4_14_apply_rules_filtered_and_nested",
)
self.history_panel_wait_for_hid_ok(32)
self.history_multi_view_display_collection_contents(32, "list:list")
self.screenshot("rules_apply_rules_example_4_15_filtered_and_nested")
def _apply_rules_and_check(self, example: Dict[str, Any]) -> None:
rule_builder = self.components.rule_builder
self.home()
history_id = self.current_history_id()
stage_rules_example(self.api_interactor_for_logged_in_user(), history_id, example)
self.dataset_populator.wait_for_history(history_id)
self.home()
self._tool_open_apply_rules()
self.screenshot("tool_apply_rules_landing")
self.tool_parameter_edit_rules()
rule_builder._.wait_for_visible()
self.screenshot("tool_apply_rules_builder_landing")
self.rule_builder_set_source(json.dumps(example["rules"]))
self.screenshot("tool_apply_rules_after")
rule_builder.main_button_ok.wait_for_and_click()
self.tool_form_execute()
output_hid = example["output_hid"]
self.home()
self.history_panel_wait_for_hid_ok(output_hid)
output_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=output_hid, wait=False)
example["check"](output_hdca, self.dataset_populator)
def _tool_apply_with_source(
self, rules_json, hid=None, landing_screenshot=None, rule_init_screenshot=None, rule_complete_screenshot=None
):
self._tool_open_apply_rules()
if hid:
self.tool_set_value("input", f"{hid}:", expected_type="data_collection")
if landing_screenshot:
self.screenshot(landing_screenshot)
rule_builder = self.components.rule_builder
self.tool_parameter_edit_rules()
rule_builder._.wait_for_visible()
if rule_init_screenshot:
self.screenshot(rule_init_screenshot)
self.rule_builder_set_source(json.dumps(rules_json))
if rule_complete_screenshot:
self.screenshot(rule_complete_screenshot)
rule_builder.main_button_ok.wait_for_and_click()
self.tool_form_execute()
def _tool_open_apply_rules(self):
self.tool_open("__APPLY_RULES__", outer=True) # may appear twice in panel, grab top-level link