mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-11-04 15:35:25 +08:00
Ahmed Awan
04602c3b84
The test would fail because the add items to collection button's disabled/enabled state was not being detected, and hence, we would manually switch tabs and the items would not even have been added to the list yet. Now, we wait for the button to enable, and then adding the items automatically switches tab to Create.
643 lines
28 KiB
Python
643 lines
28 KiB
Python
import json
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from uuid import uuid4
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import yaml
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from selenium.webdriver.common.by import By
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from typing_extensions import Literal
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from galaxy_test.base import rules_test_data
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from galaxy_test.base.workflow_fixtures import (
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WORKFLOW_LIST_PAIRED_MAPPED_OVER_PAIRED,
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WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT,
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WORKFLOW_NESTED_REPLACEMENT_PARAMETER,
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WORKFLOW_NESTED_RUNTIME_PARAMETER,
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WORKFLOW_NESTED_SIMPLE,
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WORKFLOW_RENAME_ON_REPLACEMENT_PARAM,
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WORKFLOW_RUNTIME_PARAMETER_SIMPLE,
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WORKFLOW_SELECT_FROM_OPTIONAL_DATASET,
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WORKFLOW_SIMPLE_CAT_TWICE,
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WORKFLOW_WITH_CUSTOM_REPORT_1,
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WORKFLOW_WITH_CUSTOM_REPORT_1_TEST_DATA,
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WORKFLOW_WITH_DATA_TAG_FILTER,
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WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
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WORKFLOW_WITH_MAPPED_OUTPUT_COLLECTION,
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WORKFLOW_WITH_OLD_TOOL_VERSION,
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WORKFLOW_WITH_RULES_1,
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)
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from .framework import (
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managed_history,
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RunsWorkflows,
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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 TestWorkflowRun(SeleniumTestCase, UsesHistoryItemAssertions, RunsWorkflows):
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ensure_registered = True
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@selenium_test
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@managed_history
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def test_workflow_export_file_rocrate(self):
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self._setup_simple_invocation_for_export_testing()
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invocations = self.components.invocations
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self.workflow_run_wait_for_ok(hid=2)
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invocations.export_tab_disabled.wait_for_absent()
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invocations.export_tab.wait_for_and_click()
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self.screenshot("invocation_export_formats")
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invocations.export_output_format(type="ro-crate").wait_for_and_click()
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invocations.wizard_next_button.wait_for_and_click()
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download_option = invocations.export_destination(destination="download")
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download_option.wait_for_present()
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self.screenshot("invocation_export_rocrate_destinations")
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download_option.wait_for_and_click()
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invocations.wizard_next_button.wait_for_and_click()
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export_button = invocations.wizard_export_button
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export_button.wait_for_present()
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self.screenshot("invocation_export_rocrate_download_options")
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export_button.wait_for_and_click()
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self.sleep_for(self.wait_types.UX_TRANSITION)
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self.screenshot("invocation_export_crate_preparing_download")
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invocations.export_download_link.wait_for_present()
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self.screenshot("invocation_export_crate_download_ready")
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@selenium_test
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@managed_history
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def test_workflow_export_file_native(self):
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self._setup_simple_invocation_for_export_testing()
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invocations = self.components.invocations
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self.workflow_run_wait_for_ok(hid=2)
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invocations.export_tab_disabled.wait_for_absent()
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invocations.export_tab.wait_for_and_click()
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self.screenshot("invocation_export_formats")
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invocations.export_output_format(type="default-file").wait_for_and_click()
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invocations.wizard_next_button.wait_for_and_click()
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download_option = invocations.export_destination(destination="download")
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download_option.wait_for_present()
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self.screenshot("invocation_export_native_destinations")
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download_option.wait_for_and_click()
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invocations.wizard_next_button.wait_for_and_click()
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export_button = invocations.wizard_export_button
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export_button.wait_for_present()
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self.screenshot("invocation_export_native_download_options")
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export_button.wait_for_and_click()
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self.sleep_for(self.wait_types.UX_TRANSITION)
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self.screenshot("invocation_export_native_preparing_download")
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invocations.export_download_link.wait_for_present()
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self.screenshot("invocation_export_native_download_ready")
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@selenium_test
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@managed_history
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def test_simple_execution(self):
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self.perform_upload(self.get_filename("1.fasta"))
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self.wait_for_history()
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self.workflow_run_open_workflow(WORKFLOW_SIMPLE_CAT_TWICE)
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self.screenshot("workflow_run_simple_ready")
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self.workflow_run_submit()
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self.sleep_for(self.wait_types.UX_TRANSITION)
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self.screenshot("workflow_run_simple_submitted")
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self.workflow_run_wait_for_ok(hid=2, expand=True)
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self.assert_item_summary_includes(2, "2 sequences")
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self.screenshot("workflow_run_simple_complete")
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@selenium_test
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@managed_history
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def test_expanded_execution_of_simple_workflow(self):
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self.perform_upload(self.get_filename("1.fasta"))
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self.wait_for_history()
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self.workflow_run_open_workflow(WORKFLOW_SIMPLE_CAT_TWICE)
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self.workflow_run_ensure_expanded()
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self.screenshot("workflow_run_expanded_ready")
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self.workflow_run_submit()
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self.sleep_for(self.wait_types.UX_TRANSITION)
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self.screenshot("workflow_run_expanded_submitted")
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self.workflow_run_wait_for_ok(hid=2, expand=True)
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self.assert_item_summary_includes(2, "2 sequences")
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self.screenshot("workflow_run_simple_complete")
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@selenium_test
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@managed_history
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def test_runtime_parameters_simple(self):
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self.perform_upload(self.get_filename("1.txt"))
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self.wait_for_history()
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self.workflow_run_open_workflow(WORKFLOW_RUNTIME_PARAMETER_SIMPLE)
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self.tool_parameter_div("num_lines")
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self.screenshot("workflow_run_runtime_parameters_initial")
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self._set_num_lines_to_3("num_lines")
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self.screenshot("workflow_run_runtime_parameters_modified")
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self.workflow_run_submit()
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self._assert_has_3_lines_after_run(hid=2)
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@selenium_test
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@managed_history
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def test_runtime_parameters_simple_optional(self):
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self.workflow_run_open_workflow(
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"""
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class: GalaxyWorkflow
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inputs: {}
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steps:
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int_step:
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tool_id: expression_null_handling_integer
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runtime_inputs:
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- int_input
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"""
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)
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self.tool_parameter_div("int_input")
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self._set_num_lines_to_3("int_input")
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self.screenshot("workflow_run_optional_runtime_parameters_modified")
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self.workflow_run_submit()
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self.workflow_run_wait_for_ok(hid=1)
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history_id = self.current_history_id()
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content = self.dataset_populator.get_history_dataset_content(history_id, hid=1)
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assert json.loads(content) == 3
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@selenium_test
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@managed_history
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def test_subworkflows_expanded(self):
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self.perform_upload(self.get_filename("1.txt"))
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self.wait_for_history()
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self.workflow_run_open_workflow(WORKFLOW_NESTED_SIMPLE)
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self.workflow_run_ensure_expanded()
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self.components.workflow_run.subworkflow_step_icon.wait_for_visible()
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self.screenshot("workflow_run_nested_collapsed")
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self.components.workflow_run.subworkflow_step_icon.wait_for_and_click()
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self.screenshot("workflow_run_nested_open")
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@selenium_test
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@managed_history
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def test_subworkflow_runtime_parameters(self):
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self.perform_upload(self.get_filename("1.txt"))
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self.wait_for_history()
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self.workflow_run_open_workflow(WORKFLOW_NESTED_RUNTIME_PARAMETER)
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self.workflow_run_ensure_expanded()
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self.components.workflow_run.subworkflow_step_icon.wait_for_visible()
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self.screenshot("workflow_run_nested_parameters_collapsed")
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self.components.workflow_run.subworkflow_step_icon.wait_for_and_click()
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self.screenshot("workflow_run_nested_parameters_open")
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self._set_num_lines_to_3("1|num_lines")
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self.workflow_run_submit()
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self._assert_has_3_lines_after_run(hid=2)
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@selenium_test
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@managed_history
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def test_replacement_parameters(self):
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self.perform_upload(self.get_filename("1.txt"))
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self.wait_for_history()
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self.workflow_run_open_workflow(WORKFLOW_RENAME_ON_REPLACEMENT_PARAM)
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self.workflow_run_ensure_expanded()
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self.screenshot("workflow_run_rename_simple_empty")
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self._set_replacement_parameter("replaceme", "moocow")
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self.screenshot("workflow_run_rename_simple_input")
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self.workflow_run_submit()
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output_hid = 2
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self.workflow_run_wait_for_ok(hid=output_hid)
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history_id = self.current_history_id()
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details = self.dataset_populator.get_history_dataset_details(history_id, hid=output_hid)
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assert details["name"] == "moocow suffix", details
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@selenium_test
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@managed_history
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def test_step_parameter_inputs(self):
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self.perform_upload(self.get_filename("1.txt"))
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self.wait_for_history()
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self.workflow_run_open_workflow(
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"""
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class: GalaxyWorkflow
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inputs:
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input_int: integer
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input_data: data
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steps:
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simple_constructs:
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tool_id: simple_constructs
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label: tool_exec
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in:
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inttest: input_int
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files_0|file: input_data
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"""
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)
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self.workflow_run_ensure_expanded()
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workflow_run = self.components.workflow_run
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input_div_element = workflow_run.input_div(label="input_int").wait_for_visible()
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input_element = input_div_element.find_element(By.CSS_SELECTOR, "input")
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input_element.clear()
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input_element.send_keys("12345")
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self.screenshot("workflow_run_step_parameter_input")
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self.workflow_run_submit()
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output_hid = 2
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self.workflow_run_wait_for_ok(hid=output_hid)
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history_id = self.current_history_id()
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content = self.dataset_populator.get_history_dataset_content(history_id, hid=output_hid)
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assert "12345" in content, content
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assert "chr6_hla_hap2" in content
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@selenium_test
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@managed_history
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def test_replacement_parameters_on_subworkflows(self):
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self.perform_upload(self.get_filename("1.txt"))
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self.wait_for_history()
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self.workflow_run_open_workflow(WORKFLOW_NESTED_REPLACEMENT_PARAMETER)
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self.workflow_run_ensure_expanded()
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self.screenshot("workflow_run_rename_subworkflow_empty")
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self._set_replacement_parameter("replaceme", "moocow")
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self.screenshot("workflow_run_rename_subworkflow_input")
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self.workflow_run_submit()
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output_hid = 2
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self.workflow_run_wait_for_ok(hid=output_hid)
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history_id = self.current_history_id()
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details = self.dataset_populator.get_history_dataset_details(history_id, hid=output_hid)
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assert details["name"] == "moocow suffix", details
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@selenium_test
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def test_execution_with_tool_upgrade(self):
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name = self.workflow_upload_yaml_with_random_name(WORKFLOW_WITH_OLD_TOOL_VERSION, exact_tools=True)
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self.workflow_run_with_name(name)
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self.sleep_for(self.wait_types.UX_TRANSITION)
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# Check that this tool form contains a warning about different versions.
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self.assert_message(self.components.workflow_run.warning, contains="tools which have changed")
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self.screenshot("workflow_run_tool_upgrade")
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@selenium_test
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def test_run_form_safe_upgrade_handling(self):
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workflow_with_rules = yaml.safe_load(WORKFLOW_WITH_RULES_1)
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# 0.9.0 is a version that does not exist in WORKFLOW_SAFE_TOOL_VERSION_UPDATES
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workflow_with_rules["steps"]["apply"]["tool_version"] = "0.9.0"
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workflow_with_rules_json = json.dumps(workflow_with_rules)
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name = self.workflow_upload_yaml_with_random_name(workflow_with_rules_json, exact_tools=True)
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self.workflow_run_with_name(name)
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self.sleep_for(self.wait_types.UX_TRANSITION)
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self.assert_message(self.components.workflow_run.warning, contains="tools which have changed")
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# 1.0.0 is a version that exists in WORKFLOW_SAFE_TOOL_VERSION_UPDATES
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workflow_with_rules["steps"]["apply"]["tool_version"] = "1.0.0"
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workflow_with_rules_json = json.dumps(workflow_with_rules)
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name = self.workflow_upload_yaml_with_random_name(workflow_with_rules_json, exact_tools=True)
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self.workflow_run_with_name(name)
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self.sleep_for(self.wait_types.UX_TRANSITION)
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# Check that this tool form does not contain a warning about different versions.
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assert self.components.workflow_run.warning.is_absent
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@selenium_test
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@managed_history
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def test_execution_with_multiple_inputs(self):
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history_id = self.workflow_run_and_submit(
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WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
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WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
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inputs_specified_screenshot_name="workflow_run_two_inputs",
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ensure_expanded=True,
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)
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self.workflow_run_wait_for_ok(hid=7)
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content = self.dataset_populator.get_history_dataset_content(history_id, hid=7)
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assert "10.0\n30.0\n20.0\n40.0\n" == content
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@selenium_test
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@managed_history
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def test_execution_with_text_default_value_connected_to_restricted_select(self):
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self.workflow_run_open_workflow(
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"""
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class: GalaxyWorkflow
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inputs:
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text_param:
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optional: true
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default: ex2
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restrictOnConnections: true
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type: text
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steps:
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multi_select:
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tool_id: multi_select
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in:
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select_ex:
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source: text_param
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"""
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)
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element = self.components.workflow_run.input_select_field(label="text_param").wait_for_present()
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assert element.text == "Ex2"
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self.workflow_run_submit()
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history_id = self.current_history_id()
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self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
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content = self.dataset_populator.get_history_dataset_content(history_id, hid=1)
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assert content == "ex2"
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@selenium_test
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@managed_history
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def test_execution_with_rules(self):
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history_id = self.workflow_run_and_submit(
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WORKFLOW_WITH_RULES_1,
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WORKFLOW_WITH_RULES_1,
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landing_screenshot_name="workflow_run_rules_landing",
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inputs_specified_screenshot_name="workflow_run_rules",
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ensure_expanded=True,
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)
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self.workflow_run_wait_for_ok(hid=6)
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output_content = self.dataset_populator.get_history_collection_details(history_id, hid=6)
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rules_test_data.check_example_2(output_content, self.dataset_populator)
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@selenium_test
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@managed_history
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def test_execution_with_custom_invocation_report(self):
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history_id = self.workflow_run_and_submit(
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WORKFLOW_WITH_CUSTOM_REPORT_1,
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WORKFLOW_WITH_CUSTOM_REPORT_1_TEST_DATA,
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ensure_expanded=True,
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)
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self.screenshot("workflow_run_invocation_report")
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self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
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invocation_0 = self.workflow_populator.history_invocations(history_id)[0]
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self.get(f"workflows/invocations/report?id={invocation_0['id']}")
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self.wait_for_selector_visible(".markdown-component")
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self.screenshot("workflow_report_custom_1")
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@selenium_test
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@managed_history
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def test_execution_with_null_optional_select_from_data(self):
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history_id = self.workflow_run_and_submit(
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WORKFLOW_SELECT_FROM_OPTIONAL_DATASET,
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)
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self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
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@selenium_test
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@managed_history
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def test_workflow_run_button_disabled_when_required_input_missing(self):
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self.workflow_run_open_workflow(
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"""
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class: GalaxyWorkflow
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inputs:
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text_param:
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type: text
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optional: false
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data_param:
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type: data
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collection_param:
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type: data_collection
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steps: {}
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"""
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)
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workflow_run = self.components.workflow_run
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# None of the required parameters are present
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workflow_run.run_workflow_disabled.wait_for_present()
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# upload datasets and collections
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history_id = self.current_history_id()
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self.dataset_populator.new_dataset(history_id, wait=True)
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self.dataset_collection_populator.create_list_in_history(history_id, wait=True)
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input_element = workflow_run.simplified_input(label="text_param").wait_for_and_click()
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input_element.send_keys("3")
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# Everything is set, workflow is runnable, disabled class should be removed
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workflow_run.run_workflow_disabled.wait_for_absent()
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input_element.clear()
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workflow_run.run_workflow_disabled.wait_for_present()
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@selenium_test
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@managed_history
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def test_workflow_run_tag_filter(self):
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history_id = self.current_history_id()
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dataset = self.dataset_populator.new_dataset(history_id, wait=True)
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self.dataset_populator.tag_dataset(history_id, dataset["id"], tags=["genomescope_model"])
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# Add another possible input that should not be selected
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self.dataset_populator.new_dataset(history_id, wait=True)
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workflow_id, workflow_name = self._create_workflow_with_unique_name(WORKFLOW_WITH_DATA_TAG_FILTER, "ga")
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self.workflow_run_with_name(workflow_name)
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self.workflow_run_submit()
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self.sleep_for(self.wait_types.HISTORY_POLL)
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invocations = self.workflow_populator.workflow_invocations(workflow_id=workflow_id)
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invocation = self.workflow_populator.get_invocation(invocations[-1]["id"])
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assert invocation["inputs"]["0"]["id"] == dataset["id"]
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@selenium_test
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@managed_history
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|
def test_workflow_run_list_paired_or_unpaired_with_paired_list(self):
|
|
history_id = self.current_history_id()
|
|
self.perform_upload_of_pasted_content(
|
|
{
|
|
"foo_1.fasta": "forward content",
|
|
"foo_2.fasta": "reverse content",
|
|
}
|
|
)
|
|
self.history_panel_wait_for_and_select([1, 2])
|
|
self.history_panel_build_list_of_pairs()
|
|
self.collection_builder_set_name("my awesome paired list")
|
|
self.collection_builder_create()
|
|
self.history_panel_wait_for_hid_ok(5)
|
|
self._create_and_run_workflow_with_unique_name(WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT)
|
|
self.workflow_run_submit()
|
|
self.history_panel_wait_for_hid_ok(6)
|
|
content = self.dataset_populator.get_history_dataset_content(history_id, hid=6)
|
|
assert content.strip() == "forward content\nreverse content"
|
|
|
|
@selenium_test
|
|
@managed_history
|
|
def test_workflow_run_list_paired_or_unpaired_with_flat_list(self):
|
|
history_id = self.current_history_id()
|
|
self.perform_upload_of_pasted_content(
|
|
{
|
|
"foo_1.fasta": "forward content",
|
|
"foo_2.fasta": "reverse content",
|
|
}
|
|
)
|
|
self.history_panel_wait_for_and_select([1, 2])
|
|
self.history_panel_build_list_advanced_and_select_builder("list")
|
|
self.collection_builder_set_name("my awesome flat list")
|
|
self.collection_builder_create()
|
|
self.history_panel_wait_for_hid_ok(5)
|
|
self._create_and_run_workflow_with_unique_name(WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT)
|
|
self.workflow_run_submit()
|
|
self.history_panel_wait_for_hid_ok(6)
|
|
content = self.dataset_populator.get_history_dataset_content(history_id, hid=6)
|
|
assert content.strip() == "reverse content\nforward content"
|
|
|
|
@selenium_test
|
|
@managed_history
|
|
def test_workflow_run_list_paired_or_unpaired_with_mixed_list(self):
|
|
history_id = self.current_history_id()
|
|
self.perform_upload_of_pasted_content(
|
|
{
|
|
"foo_1.fasta": "forward content",
|
|
"foo_2.fasta": "reverse content",
|
|
"other.fasta": "unpaired content",
|
|
}
|
|
)
|
|
self.history_panel_wait_for_and_select([1, 2, 3])
|
|
self.history_panel_build_list_of_paired_or_unpaireds()
|
|
self.collection_builder_set_name("my awesome flat list")
|
|
self.collection_builder_create()
|
|
self.history_panel_wait_for_hid_ok(7)
|
|
self._create_and_run_workflow_with_unique_name(WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT)
|
|
self.workflow_run_submit()
|
|
self.history_panel_wait_for_hid_ok(8)
|
|
content = self.dataset_populator.get_history_dataset_content(history_id, hid=8)
|
|
assert content.strip() == "forward content\nreverse content\nunpaired content"
|
|
|
|
@selenium_test
|
|
@managed_history
|
|
def test_upload_dataset_from_workflow_simple(self):
|
|
history_id = self.current_history_id()
|
|
self._create_and_run_workflow_with_unique_name(WORKFLOW_SIMPLE_CAT_TWICE)
|
|
workflow_run = self.components.workflow_run
|
|
input = workflow_run.input._(label="input1")
|
|
input.upload.wait_for_and_click()
|
|
self._upload_hello_world_for_input(input)
|
|
self.workflow_run_submit()
|
|
self.history_panel_wait_for_hid_ok(2)
|
|
content = self.dataset_populator.get_history_dataset_content(history_id, hid=2)
|
|
assert content.strip() == "hello world\nhello world"
|
|
|
|
@selenium_test
|
|
@managed_history
|
|
def test_modal_upload_updates_form(self):
|
|
history_id = self.current_history_id()
|
|
self.perform_upload_of_pasted_content("goodbye land")
|
|
|
|
self._create_and_run_workflow_with_unique_name(WORKFLOW_WITH_MAPPED_OUTPUT_COLLECTION)
|
|
workflow_run = self.components.workflow_run
|
|
input = workflow_run.input._(label="input1")
|
|
input.upload.wait_for_and_click()
|
|
|
|
self.perform_upload_of_pasted_content("hello world", on_current_page=True)
|
|
|
|
self.history_panel_wait_for_hid_ok(2)
|
|
|
|
builder = workflow_run.input.collection_builder._(label="input1")
|
|
# it is a div so I don't think it works to click directly but we can go to it and click
|
|
# on that part of the screen.
|
|
element = builder.element_by_hid(hid=2).wait_for_present()
|
|
action_chains = self.action_chains()
|
|
action_chains.move_to_element(element)
|
|
action_chains.click()
|
|
action_chains.perform()
|
|
|
|
input.collection_tab_build_link.wait_for_and_click()
|
|
builder.create.wait_for_and_click()
|
|
|
|
self.workflow_run_submit()
|
|
self.history_panel_wait_for_hid_ok(5)
|
|
content = self.dataset_populator.get_history_dataset_content(history_id, hid=6)
|
|
assert content.strip() == "hello world"
|
|
|
|
@selenium_test
|
|
@managed_history
|
|
def test_upload_list_from_workflow_simple(self):
|
|
self._create_and_run_workflow_with_unique_name(WORKFLOW_WITH_MAPPED_OUTPUT_COLLECTION)
|
|
workflow_run = self.components.workflow_run
|
|
input = workflow_run.input._(label="input1")
|
|
input.upload.wait_for_and_click()
|
|
input.collection_tab_upload_link.wait_for_and_click()
|
|
builder = workflow_run.input.collection_builder._(label="input1")
|
|
self._upload_hello_world_for_input(builder, count=2)
|
|
builder.create.wait_for_and_click()
|
|
self.workflow_run_submit()
|
|
self.history_panel_wait_for_hid_ok(6)
|
|
|
|
@selenium_test
|
|
@managed_history
|
|
def test_upload_list_paired_from_workflow(self):
|
|
history_id = self.current_history_id()
|
|
self._create_and_run_workflow_with_unique_name(WORKFLOW_LIST_PAIRED_MAPPED_OVER_PAIRED)
|
|
workflow_run = self.components.workflow_run
|
|
input = workflow_run.input._(label="input_list")
|
|
input.upload.wait_for_and_click()
|
|
input.collection_tab_upload_link.wait_for_and_click()
|
|
builder = workflow_run.input.collection_builder._(label="input_list")
|
|
self._upload_hello_world_for_input(builder, count=2)
|
|
builder.create.wait_for_and_click()
|
|
self.workflow_run_submit()
|
|
self.history_panel_wait_for_hid_ok(6)
|
|
content = self.dataset_populator.get_history_dataset_content(history_id, hid=7)
|
|
assert content.strip() == "hello world\nhello world"
|
|
|
|
@selenium_test
|
|
@managed_history
|
|
def test_upload_list_paired_or_unpaired_from_workflow(self):
|
|
history_id = self.current_history_id()
|
|
self.perform_upload_of_pasted_content(
|
|
{
|
|
"foo_1.fasta": "forward content",
|
|
"foo_2.fasta": "reverse content",
|
|
"other.fasta": "unpaired content",
|
|
}
|
|
)
|
|
self.history_panel_wait_for_hid_ok(3)
|
|
self._create_and_run_workflow_with_unique_name(WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT)
|
|
workflow_run = self.components.workflow_run
|
|
input = workflow_run.input._(label="input_list")
|
|
input.upload.wait_for_and_click()
|
|
builder = workflow_run.input.collection_builder._(label="input_list")
|
|
builder.element_by_hid(hid=3).wait_for_present()
|
|
# self.sleep_for(self.wait_types.UX_TRANSITION)
|
|
builder.select_all.wait_for_and_click()
|
|
input.collection_tab_build_link.wait_for_and_click()
|
|
builder.create.wait_for_and_click()
|
|
self.workflow_run_submit()
|
|
|
|
self.history_panel_wait_for_hid_ok(8)
|
|
content = self.dataset_populator.get_history_dataset_content(history_id, hid=8)
|
|
assert content.strip() == "unpaired content\nreverse content\nforward content"
|
|
|
|
def _upload_hello_world_for_input(self, workflow_input, count=1, from_hid=1):
|
|
# assumes fresh history...
|
|
for i in range(count):
|
|
workflow_input.create_button.wait_for_and_click()
|
|
url = self.dataset_populator.base64_url_for_string("hello world")
|
|
workflow_input.paste_content(n=i).wait_for_and_send_keys(url)
|
|
workflow_input.title(n=i).wait_for_and_clear_and_send_keys(f"hello world.{i + 1}.fastq")
|
|
|
|
workflow_input.embedded_start_button.wait_for_and_click()
|
|
workflow_input.use_button_disabled.wait_for_absent()
|
|
workflow_input.use_button.wait_for_and_click()
|
|
|
|
def _create_and_run_workflow_with_unique_name(
|
|
self, workflow_contents: str, format: Literal["ga", "gxformat2"] = "gxformat2"
|
|
):
|
|
workflow_id, workflow_name = self._create_workflow_with_unique_name(workflow_contents, format)
|
|
self.workflow_run_with_name(workflow_name)
|
|
return workflow_id, workflow_name
|
|
|
|
def _create_workflow_with_unique_name(
|
|
self, workflow_contents: str, format: Literal["ga", "gxformat2"] = "gxformat2"
|
|
):
|
|
workflow_name = str(uuid4())
|
|
if format == "gxformat2":
|
|
wf = yaml.safe_load(workflow_contents)
|
|
wf["name"] = workflow_name
|
|
workflow_id = self.workflow_populator.upload_yaml_workflow(wf)
|
|
else:
|
|
wf = json.loads(workflow_contents)
|
|
wf["name"] = workflow_name
|
|
workflow_id = self.workflow_populator.create_workflow(wf)
|
|
return (workflow_id, workflow_name)
|
|
|
|
def _assert_has_3_lines_after_run(self, hid):
|
|
self.workflow_run_wait_for_ok(hid=hid)
|
|
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, element_id):
|
|
# for random_lines num_lines parameter as runtime parameter in workflow form.
|
|
div = self.tool_parameter_div(element_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, element_id, value):
|
|
# for random_lines num_lines parameter as runtime parameter in workflow form.
|
|
div = self.tool_parameter_div(element_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)
|
|
|
|
def _setup_simple_invocation_for_export_testing(self):
|
|
# precondition: refresh history
|
|
self.perform_upload(self.get_filename("1.fasta"))
|
|
self.wait_for_history()
|
|
self.workflow_run_open_workflow(WORKFLOW_SIMPLE_CAT_TWICE)
|
|
self.workflow_run_submit()
|
|
history_id = self.current_history_id()
|
|
self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
|
|
return self.workflow_populator.history_invocations(history_id)[0]
|