Source code for galaxy_test.selenium.test_collection_builders

from .framework import (
    managed_history,
    selenium_test,
    SeleniumTestCase,
)
from .upload_activity_helpers import UsesUploadActivity



[docs]
class TestCollectionBuilders(SeleniumTestCase, UsesUploadActivity):
    ensure_registered = True


[docs]
    @selenium_test
    @managed_history
    def test_build_list_simple_hidden(self):
        self.upload_context("local-file").stage_local_file(self.get_filename("1.fasta")).start()
        self._wait_for_and_select([1])
        self.history_panel_build_list_auto()
        self.collection_builder_set_name("my cool list")
        self.screenshot("collection_builder_wizard_list")
        self.collection_builder_create()
        self._wait_for_hid_visible(3)
        self._assert_selection_cleared()



[docs]
    @selenium_test
    @managed_history
    def test_build_list_open_keeps_selection(self):
        self.upload_context("local-file").stage_local_file(self.get_filename("1.fasta")).start()
        self._wait_for_and_select([1])
        self.history_panel_build_list_auto()
        self.components.collection_builders.name.wait_for_visible()
        multi_operations = self.navigation.history_panel.multi_operations.selectors
        self.wait_for_visible(multi_operations.selected_content_menu)
        self.wait_for_visible(multi_operations.item_selector)



[docs]
    @selenium_test
    @managed_history
    def test_build_list_and_show_items(self):
        self.upload_context("local-file").stage_local_file(self.get_filename("1.fasta")).start()
        self._wait_for_and_select([1])
        self.history_panel_build_list_auto()
        # this toggles the checkbox to not hide originals
        self.collection_builder_hide_originals()
        self.collection_builder_set_name("my cool list")
        self.collection_builder_create()
        self._wait_for_hid_visible(3)



[docs]
    @selenium_test
    def test_build_list_in_viewed_history(self):
        target_history_id = self.dataset_populator.new_history(name=self._get_random_name())
        self.dataset_populator.new_dataset(target_history_id, content="1\n", wait=True)
        self.history_panel_create_new()
        other_history_id = self.current_history_id()
        self.get(f"histories/view?id={target_history_id}")
        center_panel = self.components._.center_panel
        self.wait_for_and_click(center_panel.descendant(self.components.history_panel.multi_operations.show_button))
        self.history_panel_muli_operation_select_hid(1, history_id=target_history_id)
        self.history_panel_build_list_auto(scope=center_panel.selector)
        self.collection_builder_set_name("viewed history list")
        self.screenshot("collection_builder_wizard_list_viewed_history")
        self.collection_builder_create()
        created_alert = self.components.collection_builders.list_wizard.created_alert
        assert "history it was built from" in created_alert.wait_for_text()
        self.screenshot("collection_builder_wizard_list_created")
        self._wait_on(
            lambda: "viewed history list" in self.history_collection_names(target_history_id),
            "the list in the viewed history",
        )
        assert self.history_collection_names(other_history_id) == []



[docs]
    @selenium_test
    @managed_history
    def test_build_list_keep_extensions(self):
        self._upload_and_select_sample_fastas()
        self.history_panel_build_list_auto()
        self.collection_builder_toggle_remove_extensions()
        self.collection_builder_set_name("list keeping extensions")
        self.collection_builder_create()
        self._wait_for_hid_visible(5)
        identifiers = self._collection_identifiers(5)
        assert identifiers == ["sample1.fasta", "sample2.fasta"]



[docs]
    @selenium_test
    @managed_history
    def test_build_list_advanced_rename_element(self):
        self._upload_and_select_sample_fastas()
        self.history_panel_build_list_advanced_and_select_builder("list")
        self.collection_builder_rename_element(1, "first")
        self.collection_builder_set_name("list with a renamed element")
        self.screenshot("collection_builder_advanced_list")
        self.collection_builder_create()
        self._wait_for_hid_visible(5)
        identifiers = self._collection_identifiers(5)
        assert identifiers == ["first", "sample2"]



[docs]
    @selenium_test
    @managed_history
    def test_build_paired_list_auto_matched(self):
        uploader = self.upload_context("paste-content")
        uploader.stage_paste_content("forward content", {"name": "basename_1.fasta"})
        uploader.stage_paste_content("reverse content", {"name": "basename_2.fasta"})
        uploader.start()
        self._wait_for_and_select([1, 2])
        self.history_panel_build_list_of_pairs()
        list_wizard = self.components.collection_builders.list_wizard
        self.ag_grid_edit_cell(list_wizard, "identifier", 2, "renamed", clear=True)
        self.collection_builder_set_name("my awesome paired list")
        self.screenshot("collection_builder_paired_list")
        self.collection_builder_create()
        self._wait_for_hid_visible(5)
        collection = self.dataset_populator.get_history_collection_details(self.current_history_id(), hid=5)
        (element,) = collection["elements"]
        assert element["element_identifier"] == "renamed", element["element_identifier"]
        pair = element["object"]["elements"]
        assert [e["element_identifier"] for e in pair] == ["forward", "reverse"]
        assert [e["object"]["name"] for e in pair] == ["basename_1.fasta", "basename_2.fasta"], pair
        self._assert_selection_cleared()
        # switch to hidden filters to see the hidden datasets appear
        self._show_hidden_content()
        self._wait_for_hid_visible(1)
        self._wait_for_hid_visible(2)
        self._wait_for_hid_visible(3)
        self._wait_for_hid_visible(4)



[docs]
    @selenium_test
    @managed_history
    def test_build_paired_list_manual_matched(self):
        uploader = self.upload_context("paste-content")
        uploader.stage_paste_content("forward content", {"name": "thisdoesnotmatch.fasta"})
        uploader.stage_paste_content("reverse content", {"name": "becausethenamesarentalike.fasta"})
        uploader.start()
        self._wait_for_and_select([1, 2])
        self.history_panel_build_list_of_pairs()
        self.collection_builder_pair_rows(0, 1)
        row0 = self.components.collection_builders.list_wizard.row._(index=0)
        row0.unlink_button.wait_for_present()
        row0.link_button.assert_absent()

        self.collection_builder_set_name("my awesome paired list manual match")
        self.screenshot("collection_builder_paired_list_manual_match")
        self.collection_builder_create()
        self._wait_for_hid_visible(5)
        # switch to hidden filters to see the hidden datasets appear
        self._show_hidden_content()
        self._wait_for_hid_visible(1)
        self._wait_for_hid_visible(2)
        self._wait_for_hid_visible(3)
        self._wait_for_hid_visible(4)



[docs]
    @selenium_test
    @managed_history
    def test_build_paired_unpaired_list(self):
        uploader = self.upload_context("paste-content")
        uploader.stage_paste_content("forward content", {"name": "commonprefix_1.fasta"})
        uploader.stage_paste_content("reverse content", {"name": "commonprefix_2.fasta"})
        uploader.stage_paste_content("unmatched", {"name": "unmatched.fasta"})
        uploader.start()
        self._wait_for_and_select([1, 2, 3])
        self.history_panel_build_list_of_paired_or_unpaireds()

        self.collection_builder_set_name("mix of paired and unpaired data")
        self.screenshot("collection_builder_paired_or_unpaired_list")
        self.collection_builder_create()
        self._wait_for_hid_visible(7)



[docs]
    @selenium_test
    @managed_history
    def test_build_list_of_lists(self):
        uploader = self.upload_context("paste-content")
        uploader.stage_paste_content("forward content 1", {"name": "foo1.txt"})
        uploader.stage_paste_content("reverse content 1", {"name": "bar1.txt"})
        uploader.stage_paste_content("forward content 2", {"name": "foo2.txt"})
        uploader.stage_paste_content("forward content 2", {"name": "bar2.txt"})
        uploader.start()
        self._wait_for_and_select([1, 2, 3, 4])
        self.history_panel_build_list_of_lists(screenshot_name="collection_builder_which_builder_list_list")
        self.list_wizard_click_cell_and_send_keys("outerIdentifier", 2, "outer1")
        self.list_wizard_click_cell_and_send_keys("outerIdentifier", 3, "outer1")
        self.list_wizard_click_cell_and_send_keys("outerIdentifier", 4, "outer2")
        self.list_wizard_click_cell_and_send_keys("outerIdentifier", 5, "outer2")
        self.collection_builder_set_name("nested list")
        self.screenshot("collection_builder_list_list")
        self.collection_builder_create()
        self._wait_for_hid_visible(9)



[docs]
    @selenium_test
    @managed_history
    def test_build_paired_list_show_original(self):
        uploader = self.upload_context("paste-content")
        uploader.stage_paste_content("forward content", {"name": "thisdoesnotmatch.fasta"})
        uploader.stage_paste_content("reverse content", {"name": "becausethenamesarentalike.fasta"})
        uploader.start()
        self._wait_for_and_select([1, 2])
        self.history_panel_build_list_of_pairs()

        self.collection_builder_pair_rows(0, 1)
        row0 = self.components.collection_builders.list_wizard.row._(index=0)
        row0.unlink_button.wait_for_present()
        row0.link_button.assert_absent()

        self.collection_builder_hide_originals()
        self.collection_builder_set_name("my awesome paired list shown originals")
        self.collection_builder_create()
        self._wait_for_hid_visible(5)
        self._wait_for_hid_visible(1)
        self._wait_for_hid_visible(2)
        self._show_hidden_content()
        self._wait_for_hid_visible(3)
        self._wait_for_hid_visible(4)



[docs]
    @selenium_test
    @managed_history
    def test_build_simple_list_via_rules_hidden(self):
        self.upload_context("paste-content").stage_paste_content("fasta content", {"name": "1.fasta"}).start()
        self._wait_for_and_select([1])
        self.history_panel_build_rule_builder_for_selection()
        self.collection_builder_set_name("my cool list from rules originals hidden")
        self.screenshot("collection_builder_rules_list")
        self.collection_builder_create()
        self._wait_for_hid_visible(3)
        self._show_hidden_content()
        self._wait_for_hid_visible(1)
        self._wait_for_hid_visible(2)


    def _wait_for_hid_visible(self, hid, state="ok"):
        # takes a little while for these things to upload and end up in the history
        timeout = self.wait_length(self.wait_types.JOB_COMPLETION)
        row_selector = self.content_item_by_attributes(hid=hid, state=state)
        self.wait_for_visible(row_selector, timeout=timeout)

    def _assert_selection_cleared(self):
        multi_operations = self.navigation.history_panel.multi_operations.selectors
        self.wait_for_absent(multi_operations.selected_content_menu)
        self.wait_for_absent(multi_operations.item_selector)

    def _collection_dropdown(self, option_description):
        return self.use_bootstrap_dropdown(option=option_description, menu="selected content menu")

    def _wait_for_and_select(self, hids):
        self.history_panel_wait_for_and_select(hids)

    def _upload_and_select_sample_fastas(self):
        """Paste ``sample1.fasta`` and ``sample2.fasta`` (hids 1, 2) and select both."""
        uploader = self.upload_context("paste-content")
        uploader.stage_paste_content("content 1", {"name": "sample1.fasta"})
        uploader.stage_paste_content("content 2", {"name": "sample2.fasta"})
        uploader.start()
        self._wait_for_and_select([1, 2])

    def _collection_identifiers(self, hid):
        """Sorted element identifiers of collection ``hid``, via the API."""
        collection = self.dataset_populator.get_history_collection_details(self.current_history_id(), hid=hid)
        return sorted(e["element_identifier"] for e in collection["elements"])

    def _show_hidden_content(self):
        """Filter the history panel to hidden items."""
        self.history_panel_filter("visible:false")