Selenium test cases for IGV.

Author: jmchilton

client/src/components/Panels/ActivityPanel.vue

@@ -6,11 +6,13 @@ interface Props {
     title: string;
     goToAllTitle?: string;
     href?: string;
+    goToAllDataDescription?: string;
 }
 
 const props = withDefaults(defineProps<Props>(), {
     goToAllTitle: undefined,
     href: undefined,
+    goToAllDataDescription: undefined,
 });
 
 const emit = defineEmits(["goToAll"]);
@@ -38,7 +40,7 @@ const hasGoToAll = computed(() => props.goToAllTitle && props.href);
                 v-if="hasGoToAll"
                 class="activity-panel-footer"
                 variant="primary"
-                :data-description="`props.mainButtonText button`"
+                :data-description="goToAllDataDescription"
                 :to="props.href"
                 size="sm"
                 @click="emit('goToAll')">

client/src/components/Visualizations/VisualizationPanel.vue

@@ -95,6 +95,7 @@ onMounted(() => {
         :is="props.datasetId ? 'div' : ActivityPanel"
         title="Visualizations"
         :go-to-all-title="datasetId ? undefined : 'Saved Visualizations'"
+        go-to-all-data-description="visualizations show list"
         href="/visualizations/list">
         <template v-slot:header>
             <DelayedInput :delay="100" class="my-2" placeholder="search visualizations" @change="query = $event" />

client/src/utils/navigation/navigation.yml

@@ -697,6 +697,16 @@ visualization:
   selectors:
     activity: '#activity-visualizations'
     matched_plugin: '#center [data-plugin-name*="${id}"]'
+    show_all_button: '[data-description="visualizations show list"]'
+
+igv:
+  selectors:
+    _: ".igv-container"
+    shadow_host: '#app .grid .overflow-hidden .overflow-auto div'
+    current_genome: '.igv-current-genome'
+    settings_button: button.n-button
+    save_button: '[data-description="sidepanel save button"]'
+    name_input: '.n-input__input input'
 
 trs_search:
   selectors:

lib/galaxy/selenium/has_driver.py

@@ -244,6 +244,12 @@ def send_escape(self, element: Optional[WebElement] = None):
     def send_backspace(self, element: Optional[WebElement] = None):
         self._send_key(Keys.BACKSPACE, element)
 
+    def aggressive_clear(self, element: WebElement) -> None:
+        # for when a simple .clear() doesn't work
+        self.driver.execute_script("arguments[0].value = '';", element)
+        for _ in range(25):
+            element.send_keys(Keys.BACKSPACE)
+
     def _send_key(self, key: str, element: Optional[WebElement] = None):
         if element is None:
             self.action_chains().send_keys(key)

lib/galaxy/selenium/navigates_galaxy.py

@@ -83,7 +83,7 @@ class WAIT_TYPES:
     # Creating a new history and loading it into the panel.
     DATABASE_OPERATION = WaitType("database_operation", 10)
     # Wait time for jobs to complete in default environment.
-    JOB_COMPLETION = WaitType("job_completion", 30)
+    JOB_COMPLETION = WaitType("job_completion", 45)
     # Wait time for a GIE to spawn.
     GIE_SPAWN = WaitType("gie_spawn", 30)
     # Wait time for toolshed search
@@ -669,6 +669,15 @@ def select_history_card_operation(self, card_name, action_selector, is_in_extra=
         action_selector = target_card.find_element(By.CSS_SELECTOR, action_selector)
         action_chains.move_to_element(action_selector).click().perform()
 
+    def edit_dataset_dbkey(self, dbkey_text):
+        # precondition: need to be on the dataset edit component
+        self.components.edit_dataset_attributes.dbkey_dropdown.wait_for_and_click()
+        # choose database option from 'Database/Build' dropdown, that equals to dbkey_text
+        self.components.edit_dataset_attributes.dbkey_dropdown_results.dbkey_dropdown_option(
+            dbkey_text=dbkey_text
+        ).wait_for_and_click()
+        self.components.edit_dataset_attributes.save_button.wait_for_and_click()
+
     def get_history_card(self, card_name):
         card_list = self.components.histories.history_cards.all()
         for card in card_list:
@@ -1478,6 +1487,12 @@ def navigate_to_histories_page(self):
         self.components.histories.activity.wait_for_and_click()
         self.components.histories.history_cards.wait_for_present()
 
+    def navigate_to_saved_visualizations(self):
+        self.home()
+        visualizations = self.components.visualization
+        visualizations.activity.wait_for_and_click()
+        visualizations.show_all_button.wait_for_and_click()
+
     def navigate_to_histories_shared_with_me_page(self):
         self.home()
         self.components.histories.activity.wait_for_and_click()
@@ -2111,7 +2126,7 @@ def history_panel_add_tags(self, tags):
     def history_panel_rename(self, new_name):
         editable_text_input_element = self.history_panel_name_input()
         # a simple .clear() doesn't work here since we perform a .blur because of that
-        self.driver.execute_script("arguments[0].value = '';", editable_text_input_element)
+        self.aggressive_clear(editable_text_input_element)
         editable_text_input_element.send_keys(new_name)
         editable_text_input_element.send_keys(self.keys.ENTER)
         return editable_text_input_element
@@ -2200,6 +2215,12 @@ def show_dataset_visualizations(self, hid):
         )
         visualize_tab_button.click()
 
+    def show_dataset_visualization(self, hid: int, visualization_id: str, screenshot_name: Optional[str] = None):
+        self.show_dataset_visualizations(hid)
+        self.components.visualization.matched_plugin(id=visualization_id).wait_for_visible()
+        self.screenshot_if(screenshot_name)
+        self.components.visualization.matched_plugin(id=visualization_id).wait_for_and_click()
+
     def history_panel_item_view_dataset_details(self, hid):
         self.display_dataset(hid)
         self.show_dataset_details(hid)
@@ -2278,7 +2299,9 @@ def history_panel_click_item_title(self, hid, **kwds):
 
     def history_panel_ensure_showing_item_details(self, hid):
         if not self.history_panel_item_showing_details(hid):
-            self.history_panel_click_item_title(hid=hid, wait=True)
+            return self.history_panel_click_item_title(hid=hid, wait=True)
+        else:
+            return self.history_panel_item_component(hid=hid)
 
     def history_panel_item_showing_details(self, hid):
         item_component = self.history_panel_item_component(hid=hid)

lib/galaxy/selenium/smart_components.py

@@ -148,6 +148,11 @@ def wait_for_and_clear_and_send_keys(self, *text):
         dom_element.clear()
         dom_element.send_keys(*text)
 
+    def wait_for_and_clear_aggressive_and_send_keys(self, *text):
+        dom_element = self.wait_for_visible()
+        self._has_driver.aggressive_clear(dom_element)
+        dom_element.send_keys(*text)
+
     def axe_eval(self) -> AxeResults:
         return self._has_driver.axe_eval(context=self._target.element_locator[1])
 

lib/galaxy_test/selenium/test_history_dataset_state.py

@@ -49,12 +49,7 @@ def test_dataset_change_dbkey(self):
         item.dbkey.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("history_panel_edit_dbkey_post_click")
-        self.components.edit_dataset_attributes.dbkey_dropdown.wait_for_and_click()
-        # choose database option from 'Database/Build' dropdown, that equals to dbkey_text
-        self.components.edit_dataset_attributes.dbkey_dropdown_results.dbkey_dropdown_option(
-            dbkey_text=TEST_DBKEY_TEXT
-        ).wait_for_and_click()
-        self.components.edit_dataset_attributes.save_button.wait_for_and_click()
+        self.edit_dataset_dbkey(TEST_DBKEY_TEXT)
         self.sleep_for(self.wait_types.JOB_COMPLETION)
         self.history_panel_wait_for_hid_ok(FIRST_HID)
         self.assert_item_dbkey_displayed_as(FIRST_HID, "apiMel3")

lib/galaxy_test/selenium/test_visualizations.py

@@ -3,12 +3,16 @@
     skip_without_visualization_plugin,
 )
 from .framework import (
+    managed_history,
     selenium_test,
     SeleniumTestCase,
 )
 
+IGV_DEFAULT_GENOME = "hg38"
+HG18_DBKEY_TEXT = "Human Mar. 2006 (NCBI36/hg18) (hg18)"
 
-class TestVisualizations(SeleniumTestCase):
+
+class TestVisualizationsAnonymous(SeleniumTestCase):
 
     @skip_without_datatype("png")
     @skip_without_visualization_plugin("annotate_image")
@@ -17,11 +21,10 @@ def test_charts_image_annotate(self):
         hid = 1
         self.perform_upload(self.get_filename("454Score.png"))
         self.history_panel_wait_for_hid_state(hid, state="ok")
-        self.show_dataset_visualizations(hid)
 
-        self.components.visualization.matched_plugin(id="annotate_image").wait_for_visible()
-        self.screenshot("visualization_plugins_png")
-        self.components.visualization.matched_plugin(id="annotate_image").wait_for_and_click()
+        self.show_dataset_visualization(
+            hid, visualization_id="annotate_image", screenshot_name="visualization_plugins_png"
+        )
 
         with self.visualization_panel():
             self.wait_for_selector("#image-annotate")
@@ -33,11 +36,9 @@ def test_charts_tabulator(self):
         hid = 1
         self.perform_upload(self.get_filename("1.tabular"))
         self.history_panel_wait_for_hid_state(hid, state="ok")
-        self.show_dataset_visualizations(hid)
-
-        self.components.visualization.matched_plugin(id="tabulator").wait_for_visible()
-        self.screenshot("visualization_plugins_tabulator")
-        self.components.visualization.matched_plugin(id="tabulator").wait_for_and_click()
+        self.show_dataset_visualization(
+            hid, visualization_id="tabulator", screenshot_name="visualization_plugins_tabulator"
+        )
 
         with self.visualization_panel():
             self.wait_for_selector(".tabulator-table")
@@ -49,13 +50,67 @@ def test_charts_h5web(self):
         hid = 1
         self.perform_upload(self.get_filename("chopper.h5"))
         self.history_panel_wait_for_hid_state(hid, state="ok")
-        self.show_dataset_visualizations(hid)
-
-        self.components.visualization.matched_plugin(id="h5web").wait_for_visible()
-        self.screenshot("visualization_plugins_h5")
-        self.components.visualization.matched_plugin(id="h5web").wait_for_and_click()
+        self.show_dataset_visualization(hid, visualization_id="h5web", screenshot_name="visualization_plugins_h5")
 
         with self.visualization_panel():
             # Look for the h5web-explorer-tree identifier to verify it loads.
             self.wait_for_selector("#h5web-explorer-tree")
             self.screenshot("visualization_plugin_charts_h5web_landing")
+
+
+class TestVisualizations(SeleniumTestCase):
+    ensure_registered = True
+
+    @selenium_test
+    @managed_history
+    @skip_without_visualization_plugin("igv")
+    def test_igv_loads_correct_genome(self):
+        hid = 1
+        self.perform_upload(self.get_filename("1.bed"))
+        self.history_panel_wait_for_hid_state(hid, state="ok")
+        self.show_dataset_visualization(hid, visualization_id="igv", screenshot_name="visualization_plugins_igv")
+
+        with self.visualization_panel():
+            self._wait_for_igv_container()
+            self.screenshot("visualization_plugin_igv_landing_default_genome")
+            current_genome_text = self._igv_current_genome()
+            assert IGV_DEFAULT_GENOME in current_genome_text
+
+        dataset_component = self.history_panel_ensure_showing_item_details(hid)
+        dataset_component.dbkey.wait_for_and_click()
+        self.edit_dataset_dbkey(HG18_DBKEY_TEXT)
+
+        self.show_dataset_visualization(hid, visualization_id="igv")
+
+        with self.visualization_panel():
+            self._wait_for_igv_container()
+            current_genome_text = self._igv_current_genome()
+            self.screenshot("visualization_plugin_igv_landing_genome_from_dbkey_apimel3")
+            assert "hg18" in current_genome_text
+
+            igv = self.components.igv
+            igv.save_button.assert_absent_or_hidden()
+            igv.settings_button.wait_for_and_click()
+            self.sleep_for(self.wait_types.UX_TRANSITION)
+            igv.name_input.wait_for_and_clear_aggressive_and_send_keys("igv with hg18")
+            igv.save_button.wait_for_and_click()
+            self.sleep_for(self.wait_types.UX_TRANSITION)
+
+        self.navigate_to_saved_visualizations()
+
+    def _igv_current_genome(self):
+        igv = self.components.igv
+        element = igv.shadow_host.wait_for_present()
+        shadow_root = element.shadow_root
+        igv_current_genome = self.navigation.igv.selectors.current_genome
+        current_genome_element = shadow_root.find_element(*igv_current_genome.component_locator)
+        return current_genome_element.text
+
+    def _wait_for_igv_container(self):
+        igv = self.components.igv
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        element = igv.shadow_host.wait_for_present()
+        shadow_root = element.shadow_root
+
+        igv_root_container = self.navigation.igv.selectors._
+        shadow_root.find_element(*igv_root_container.component_locator)