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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")
[docs] @staticmethod def click_menu_item(menu, text): for element in menu.find_elements(By.CSS_SELECTOR, "a"): if element.text == text: return element.click()
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 = list(map(lambda d: d.text, 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) select_field = self.components.tool_form.parameter_data_select(parameter="input1") self.select_set_value(select_field, "test0 (as dataset collection)") 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() references_rendered = len(references) if references_rendered != 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