mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 22:06:53 +08:00
John Chilton
377e48918d
This is *not* the tests, it is the components for interacting with Galaxy via Selenium that can be used in any Galaxy UI automation context - not just tests. This includes a tiny CLI framework for building apps that drive Galaxy this way.
383 lines
15 KiB
Python
383 lines
15 KiB
Python
import json
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from base import rules_test_data
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from base.populators import flakey, load_data_dict
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from galaxy.selenium.navigates_galaxy import retry_call_during_transitions
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from .framework import (
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managed_history,
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retry_assertion_during_transitions,
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selenium_test,
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SeleniumTestCase,
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UsesHistoryItemAssertions,
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)
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class ToolFormTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
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@selenium_test
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def test_run_tool_verify_contents_by_peek(self):
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self._run_environment_test_tool()
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self.history_panel_wait_for_hid_ok(1)
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self.history_panel_click_item_title(hid=1)
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self.assert_item_peek_includes(1, "42")
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@selenium_test
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def test_run_tool_verify_dataset_details(self):
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self._run_environment_test_tool()
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self.history_panel_wait_for_hid_ok(1)
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self._check_dataset_details_for_inttest_value(1)
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@selenium_test
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def test_verify_dataset_details_tables(self):
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self._run_environment_test_tool()
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self.history_panel_wait_for_hid_ok(1)
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hda = self.latest_history_item()
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self._check_dataset_details_for_inttest_value(1)
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with self.main_panel():
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dataset_details_key_value_pairs = self._table_to_key_value_elements("table#dataset-details")
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number_found = name_found = format_found = False
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for key, value in dataset_details_key_value_pairs:
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if "Number:" in key.text:
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assert str(hda["hid"]) in value.text
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number_found = True
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if "Name:" in key.text:
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assert hda["name"] in value.text
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name_found = True
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if "Format:" in key.text:
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assert hda["extension"] in value.text
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format_found = True
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assert number_found
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assert name_found
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assert format_found
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def _table_to_key_value_elements(self, table_selector):
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tool_parameters_table = self.wait_for_selector_visible(table_selector)
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tbody_element = tool_parameters_table.find_element_by_css_selector("tbody")
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trs = tbody_element.find_elements_by_css_selector("tr")
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assert trs
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key_value_pairs = []
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for tr in trs:
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tds = tr.find_elements_by_css_selector("td")
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assert tds
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key_value_pairs.append((tds[0], tds[1]))
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return key_value_pairs
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@selenium_test
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def test_rerun(self):
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self._run_environment_test_tool()
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self.history_panel_wait_for_hid_ok(1)
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self.hda_click_primary_action_button(1, "rerun")
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def check_recorded_val():
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inttest_div_element = self.tool_parameter_div("inttest")
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inttest_input_element = inttest_div_element.find_element_by_css_selector("input")
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recorded_val = inttest_input_element.get_attribute("value")
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# Assert form re-rendered with correct value in textbox.
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assert recorded_val == "42", recorded_val
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# These form entries seem to be replaced/updated occasionally
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# causing stale elements.
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retry_call_during_transitions(check_recorded_val)
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self.tool_form_execute()
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self.history_panel_wait_for_hid_ok(2)
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self._check_dataset_details_for_inttest_value(2)
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@selenium_test
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@flakey
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def test_run_data(self):
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test_path = self.get_filename("1.fasta")
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test_path_decoy = self.get_filename("1.txt")
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# Upload form posts bad data if executed two times in a row like this, so
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# wait between uploads. xref https://github.com/galaxyproject/galaxy/issues/5169
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self.perform_upload(test_path)
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self.history_panel_wait_for_hid_ok(1)
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self.perform_upload(test_path_decoy)
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self.history_panel_wait_for_hid_ok(2)
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self.home()
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self.tool_open("head")
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self.tool_set_value("input", "1.fasta", expected_type="data")
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self.screenshot("tool_form_simple_data")
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self.tool_form_execute()
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self.history_panel_wait_for_hid_ok(3)
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latest_hda = self.latest_history_item()
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assert latest_hda["hid"] == 3
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assert latest_hda["name"] == "Select first on data 1"
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@selenium_test
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def test_bibtex_rendering(self):
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self.home()
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# prefetch citations so they will be available quickly when rendering tool form.
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citations_api = self.api_get("tools/bibtex/citations")
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assert len(citations_api) == 29, len(citations_api)
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self.tool_open("bibtex")
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self.components.tool_form.citations.wait_for_visible()
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@retry_assertion_during_transitions
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def assert_citations_visible():
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references = self.components.tool_form.reference.all()
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# This should be 29, but bugs I guess?
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assert len(references) > 0, len(references)
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return references
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references = assert_citations_visible()
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doi_resolved_citation = references[0]
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assert "Galaxy: A platform for interactive" in doi_resolved_citation.text
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self.screenshot("tool_form_citations_formatted")
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self.components.tool_form.show_bibtex.wait_for_and_click()
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bibtex_area = self.components.tool_form.bibtex_area.wait_for_visible()
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assert "Galaxy: A platform for interactive" in bibtex_area.text
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self.screenshot("tool_form_citations_bibtex")
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def _check_dataset_details_for_inttest_value(self, hid, expected_value="42"):
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self.hda_click_primary_action_button(hid, "info")
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with self.main_panel():
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self.wait_for_selector_visible("table#dataset-details")
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tool_parameters_table = self.wait_for_selector_visible("table#tool-parameters")
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tbody_element = tool_parameters_table.find_element_by_css_selector("tbody")
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tds = tbody_element.find_elements_by_css_selector("td")
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assert tds
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assert any([expected_value in td.text for td in tds])
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def _run_environment_test_tool(self, inttest_value="42"):
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self.home()
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self.tool_open("environment_variables")
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self.tool_set_value("inttest", inttest_value)
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self.tool_form_execute()
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class LoggedInToolFormTestCase(SeleniumTestCase):
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ensure_registered = True
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@selenium_test
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def test_run_apply_rules_1(self):
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self._apply_rules_and_check(rules_test_data.EXAMPLE_1)
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self.screenshot("tool_apply_rules_example_1_final")
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@selenium_test
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def test_run_apply_rules_2(self):
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self._apply_rules_and_check(rules_test_data.EXAMPLE_2)
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self.screenshot("tool_apply_rules_example_2_final")
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@selenium_test
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def test_run_apply_rules_3(self):
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self._apply_rules_and_check(rules_test_data.EXAMPLE_3)
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self.screenshot("tool_apply_rules_example_3_final")
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@selenium_test
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def test_run_apply_rules_4(self):
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self._apply_rules_and_check(rules_test_data.EXAMPLE_4)
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self.screenshot("tool_apply_rules_example_4_final")
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@selenium_test
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@managed_history
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def test_run_apply_rules_tutorial(self):
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self.home()
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self.upload_rule_start()
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self.upload_rule_set_data_type("Collection")
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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
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https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/treated2fb.txt treated_paired_2
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https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/treated3fb.txt treated_paired_3
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https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated1fb.txt untreated_single_4
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https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated2fb.txt untreated_single_5
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https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated3fb.txt untreated_paired_6
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https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated4fb.txt untreated_paired_7
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""")
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self.screenshot("rules_apply_rules_example_4_1_input_paste")
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self.upload_rule_build()
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rule_builder = self.components.rule_builder
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rule_builder._.wait_for_and_click()
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self.rule_builder_set_mapping("url", "A")
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self.rule_builder_set_mapping("list-identifiers", ["B"])
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self.rule_builder_set_collection_name("flat_count_list")
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self.rule_builder_set_extension("txt")
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self.screenshot("rules_apply_rules_example_4_2_input_rules")
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rule_builder.main_button_ok.wait_for_and_click()
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self.history_panel_wait_for_hid_ok(1)
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self.screenshot("rules_apply_rules_example_4_3_input_ready")
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self.history_multi_view_display_collection_contents(1, "list")
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self.screenshot("rules_apply_rules_example_4_4_input_list")
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self.home()
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add_depth_rules = {
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"rules": [
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{
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"type": "add_column_metadata",
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"value": "identifier0",
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},
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{
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"type": "add_column_regex",
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"target_column": 0,
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"expression": "(.*)_(.*)_.*",
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"group_count": 2
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}
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],
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"mapping": [
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{
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"type": "list_identifiers",
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"columns": [1, 2, 0],
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}
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],
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}
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self._tool_apply_with_source(
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add_depth_rules,
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hid=1,
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landing_screenshot="rules_apply_rules_example_4_5_apply_rules_landing",
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rule_init_screenshot="rules_apply_rules_example_4_6_apply_rules_init_flat",
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rule_complete_screenshot="rules_apply_rules_example_4_7_apply_rules_add_depth"
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)
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self.history_panel_wait_for_hid_ok(16)
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self.history_multi_view_display_collection_contents(16, "list:list:list")
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self.screenshot("rules_apply_rules_example_4_8_nested")
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self.home()
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invert_rules = {
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"rules": [
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{
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"type": "add_column_metadata",
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"value": "identifier0",
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},
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{
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"type": "add_column_metadata",
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"value": "identifier1",
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},
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{
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"type": "add_column_metadata",
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"value": "identifier2",
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},
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],
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"mapping": [
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{
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"type": "list_identifiers",
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"columns": [1, 0, 2],
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}
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],
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}
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self._tool_apply_with_source(
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invert_rules,
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rule_init_screenshot="rules_apply_rules_example_4_9_apply_rules_init_nested",
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rule_complete_screenshot="rules_apply_rules_example_4_10_apply_rules_inverted"
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)
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self.history_panel_wait_for_hid_ok(24)
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self.history_multi_view_display_collection_contents(24, "list:list:list")
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self.screenshot("rules_apply_rules_example_4_11_inverted")
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self.home()
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filter_rules = {
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"rules": [
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{
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"type": "add_column_metadata",
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"value": "identifier0",
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},
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{
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"type": "add_filter_regex",
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"target_column": 0,
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"expression": ".*_single_.*",
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"invert": False,
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}
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],
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"mapping": [
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{
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"type": "list_identifiers",
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"columns": [0],
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}
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],
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}
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self._tool_apply_with_source(
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filter_rules,
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hid=1,
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rule_complete_screenshot="rules_apply_rules_example_4_12_apply_rules_filter"
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)
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self.history_panel_wait_for_hid_ok(28)
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self.history_multi_view_display_collection_contents(28, "list")
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self.screenshot("rules_apply_rules_example_4_13_filtered")
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self.home()
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filter_and_nest_rules = {
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"rules": [
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{
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"type": "add_column_metadata",
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"value": "identifier0",
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},
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{
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"type": "add_filter_regex",
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"target_column": 0,
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"expression": ".*_single_.*",
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"invert": False,
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},
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{
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"type": "add_column_regex",
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"target_column": 0,
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"expression": "(.*)_single_.*",
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"group_count": 1
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}
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],
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"mapping": [
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{
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"type": "list_identifiers",
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"columns": [1, 0],
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}
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],
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}
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self._tool_apply_with_source(
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filter_and_nest_rules,
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hid=1,
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rule_complete_screenshot="rules_apply_rules_example_4_14_apply_rules_filtered_and_nested"
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)
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self.history_panel_wait_for_hid_ok(32)
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self.history_multi_view_display_collection_contents(32, "list:list")
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self.screenshot("rules_apply_rules_example_4_15_filtered_and_nested")
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def _apply_rules_and_check(self, example):
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rule_builder = self.components.rule_builder
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self.home()
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history_id = self.current_history_id()
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inputs, _, _ = load_data_dict(history_id, {"input": example["test_data"]}, self.dataset_populator, self.dataset_collection_populator)
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self.dataset_populator.wait_for_history(history_id)
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self.home()
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self._tool_open_apply_rules()
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self.screenshot("tool_apply_rules_landing")
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self.tool_parameter_edit_rules()
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rule_builder._.wait_for_visible()
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self.screenshot("tool_apply_rules_builder_landing")
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self.rule_builder_set_source(json.dumps(example["rules"]))
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self.screenshot("tool_apply_rules_after")
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rule_builder.main_button_ok.wait_for_and_click()
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self.tool_form_execute()
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output_hid = example["output_hid"]
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self.history_panel_wait_for_hid_ok(output_hid)
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output_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=output_hid, wait=False)
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example["check"](output_hdca, self.dataset_populator)
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def _tool_apply_with_source(self, rules_json, hid=None, landing_screenshot=None, rule_init_screenshot=None, rule_complete_screenshot=None):
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self._tool_open_apply_rules()
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if hid:
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self.tool_set_value("input", "%s:" % hid, expected_type="data_collection")
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if landing_screenshot:
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self.screenshot(landing_screenshot)
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rule_builder = self.components.rule_builder
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self.tool_parameter_edit_rules()
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rule_builder._.wait_for_visible()
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if rule_init_screenshot:
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self.screenshot(rule_init_screenshot)
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self.rule_builder_set_source(json.dumps(rules_json))
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if rule_complete_screenshot:
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self.screenshot(rule_complete_screenshot)
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rule_builder.main_button_ok.wait_for_and_click()
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self.tool_form_execute()
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def _tool_open_apply_rules(self):
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self.tool_open("__APPLY_RULES__", outer=True) # may appear twice in panel, grab top-level link
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