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Source code for galaxy_test.selenium.test_tool_form
import json
import pytest
from galaxy.selenium.navigates_galaxy import retry_call_during_transitions
from galaxy_test.base import rules_test_data
from galaxy_test.base.populators import (
flakey,
skip_if_github_down,
stage_rules_example,
)
from .framework import (
managed_history,
retry_assertion_during_transitions,
selenium_test,
SeleniumTestCase,
UsesHistoryItemAssertions,
)
[docs]class ToolFormTestCase(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)
with self.main_panel():
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
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_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
@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")
assert len(citations_api) == 29, 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()
assert len(references) == 29
return references
references = assert_citations_visible()
doi_resolved_citation = references[1]
assert "enabling efficient sequence analysis" in doi_resolved_citation.text
self.screenshot("tool_form_citations_formatted")
def _check_dataset_details_for_inttest_value(self, hid, expected_value="42"):
self.hda_click_primary_action_button(hid, "info")
with self.main_panel():
self.wait_for_selector_visible("table#dataset-details")
tool_parameters_table = self.wait_for_selector_visible("table#tool-parameters")
tbody_element = tool_parameters_table.find_element_by_css_selector("tbody")
tds = tbody_element.find_elements_by_css_selector("td")
assert tds
assert any([expected_value in td.text for td in 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 LoggedInToolFormTestCase(SeleniumTestCase):
ensure_registered = True
[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("Collection")
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):
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.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", "%s:" % 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