Merge pull request #10755 from mvdbeek/selenium_annotation_fix

Fix currently failing selenium tests, move to github workflow

.github/workflows/selenium.yaml

@@ -0,0 +1,43 @@
+name: Selenium tests
+on: [push, pull_request]
+env:
+  GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR: 'true'
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+        chunk: [0, 1, 2]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - uses: nanasess/setup-chromedriver@master
+      - name: Run tests
+        run: ./run_tests.sh -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
+        working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Selenium test results
+          path: 'galaxy root/database/test_errors'

client/src/components/Sharing.vue

@@ -11,10 +11,16 @@
             <b-button type="submit" variant="primary" @click="setUsername()">Set Username</b-button>
         </div>
         <div v-else>
-            <b-form-checkbox switch v-model="item.importable" @change="onImportable">
+            <b-form-checkbox switch class="make-accessible" v-model="item.importable" @change="onImportable">
                 Make {{ model_class }} accessible.
             </b-form-checkbox>
-            <b-form-checkbox v-if="item.importable" switch v-model="item.published" @change="onPublish">
+            <b-form-checkbox
+                v-if="item.importable"
+                class="make-publishable"
+                switch
+                v-model="item.published"
+                @change="onPublish"
+            >
                 Make {{ model_class }} publicly available in
                 <a :href="published_url" target="_top">Published {{ plural_name }}</a> section.
             </b-form-checkbox>

client/src/components/Tool/ToolFooter.vue

@@ -1,7 +1,11 @@
 <template>
     <div class="tool-footer">
         <!-- <b-button v-b-toggle.collapse-about>About this tool</b-button> -->
-        <b-link :aria-expanded="expanded" aria-controls="collapse-about" @click="expanded = !expanded"
+        <b-link
+            :aria-expanded="expanded"
+            aria-controls="collapse-about"
+            class="collapse-about"
+            @click="expanded = !expanded"
             >About this tool
             <font-awesome-icon :icon="expanded ? 'angle-double-up' : 'angle-double-down'" />
         </b-link>
@@ -17,6 +21,7 @@
                         @click="copyBibtex"
                     />
                     <Citation
+                        class="formatted-reference"
                         v-for="(citation, index) in citations"
                         :key="index"
                         :citation="citation"

client/src/components/Workflow/Editor/Attributes.vue

@@ -27,7 +27,7 @@
         <div id="workflow-annotation-area" class="mt-2">
             <b>Annotation</b>
             <meta itemprop="description" :content="annotation" />
-            <b-textarea id="workflow-annotation" :value="annotation" @change="onAnnotation" />
+            <b-textarea id="workflow-annotation" :value="annotation" @input="onAnnotation" />
             <div class="form-text text-muted">
                 These notes will be visible when this workflow is viewed.
             </div>
@@ -165,7 +165,12 @@ export default {
             this.onAttributes({ tags });
         },
         onAnnotation(annotation) {
-            this.onAttributes({ annotation });
+            if (this.annotationTimeout) {
+                clearTimeout(this.annotationTimeout);
+            }
+            this.annotationTimeout = setTimeout(() => {
+                this.onAttributes({ annotation });
+            }, 300);
         },
         onRename(name) {
             this.onAttributes({ name });
@@ -193,6 +198,9 @@ export default {
                 this.onError(error);
             });
         },
+        beforeDestroy: function () {
+            clearTimeout(this.annotationTimeout);
+        },
     },
 };
 </script>

client/src/components/Workflow/Editor/Node.vue

@@ -292,6 +292,22 @@ export default {
                 this.$emit("onActivate", this);
             });
         },
+        setAnnotation(annotation) {
+            if (this.annotationTimeout) {
+                clearTimeout(this.annotationTimeout);
+            }
+            this.annotationTimeout = setTimeout(() => {
+                this.annotation = annotation;
+            }, 100);
+        },
+        setLabel(label) {
+            if (this.labelTimeout) {
+                clearTimeout(this.labelTimeout);
+            }
+            this.labelTimeout = setTimeout(() => {
+                this.label = label;
+            }, 100);
+        },
         setData(data) {
             this.config_form = data.config_form;
             this.tool_state = data.tool_state;

client/src/components/Workflow/Editor/modules/forms.js

@@ -116,10 +116,13 @@ function _addLabelAnnotation(self, node) {
     inputs.unshift({
         type: "text",
         name: "__annotation",
-        label: "Annotation",
+        label: "Step Annotation",
         fixed: true,
         value: node.annotation,
         area: true,
+        onchange: function (new_annotation) {
+            node.setAnnotation(new_annotation);
+        },
         help: "Add an annotation or notes to this step. Annotations are available when a workflow is viewed.",
     });
     inputs.unshift({
@@ -130,6 +133,7 @@ function _addLabelAnnotation(self, node) {
         help: _l("Add a step label."),
         fixed: true,
         onchange: function (new_label) {
+            node.setLabel(new_label);
             let duplicate = false;
             for (const i in workflow.nodes) {
                 const n = workflow.nodes[i];
@@ -145,7 +149,6 @@ function _addLabelAnnotation(self, node) {
                 "error_text",
                 duplicate && "Duplicate label. Please fix this before saving the workflow."
             );
-            self.form.trigger("change");
         },
     });
 }

lib/galaxy/dependencies/pipfiles/default/Pipfile

@@ -19,6 +19,7 @@ pytest-html = "*"
 pytest-mock = "*"
 pytest-pythonpath = "*"
 pytest-postgresql = "*"
+pytest-shard = "*"
 recommonmark = "*"
 responses = "*"
 selenium = "*"

lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt

@@ -45,6 +45,7 @@ pytest-metadata==1.10.0; python_version >= '2.7' and python_version not in '3.0,
 pytest-mock==3.3.1
 pytest-postgresql==2.5.2
 pytest-pythonpath==0.7.3
+pytest-shard==0.1.1
 pytest==6.1.2
 python-irodsclient==0.8.5
 pytz==2020.4

lib/galaxy/model/item_attrs.py

@@ -113,7 +113,7 @@ def get_item_annotation_obj(db_session, user, item):
 
     # Get annotation association class.
     annotation_assoc_class = _get_annotation_assoc_class(item)
-    if not annotation_assoc_class:
+    if not annotation_assoc_class or item.id is None:
         return None
 
     # Get annotation association object.

lib/galaxy/selenium/navigates_galaxy.py

@@ -216,6 +216,10 @@ class NavigatesGalaxy(HasDriver):
     def history_panel_name(self):
         return self.history_panel_name_element().text
 
+    def make_accessible_and_publishable(self):
+        self.components.histories.sharing.make_accessible.wait_for_and_click()
+        self.components.histories.sharing.make_publishable.wait_for_and_click()
+
     def history_contents(self, history_id=None, view='summary', datasets_only=True):
         if history_id is None:
             history_id = self.current_history_id()

lib/galaxy/selenium/navigation.yml

@@ -286,7 +286,8 @@ histories:
     selectors:
       unshare_user_button: '.unshare_user'
       share_with_a_user_button: '#share_with_a_user'
-      make_accessible_and_publish: '#make_accessible_and_publish'
+      make_accessible: '.make-accessible label'
+      make_publishable: '.make-publishable label'
     labels:
       unshare: 'Unshare'
 
@@ -326,11 +327,8 @@ tool_form:
     options: '#options [data-toggle="dropdown"]'
     execute: 'button#execute'
     parameter_div: 'div.ui-form-element[tour_id="${parameter}"]'
-    citations: '.citations-formatted'
-    reference: '.citations-formatted .formatted-reference'
-    show_bibtex:
-      type: xpath
-      selector: '//a[@class="nav-link" and text()="BibTeX"]'
+    reference: '.formatted-reference'
+    about: '.collapse-about'
 
   labels:
     generate_tour: 'Generate Tour'

lib/galaxy/selenium/sizzle.py

@@ -1,6 +1,6 @@
 """Utilities for using sizzle (jQuery-style) selectors with Selenium."""
 
-import re
+import json
 
 from selenium.common.exceptions import NoSuchElementException
 from selenium.webdriver.support.ui import WebDriverWait
@@ -119,11 +119,9 @@ def _is_sizzle_loaded(driver):
 
 
 def _make_sizzle_string(sizzle_selector):
-    try:
-        selector = sizzle_selector.decode("utf-8")
-    except (AttributeError, UnicodeEncodeError):
-        selector = sizzle_selector
-    return "return Sizzle(\"{selector}\");".format(selector=re.escape(selector))
+    # Use json.dumps to escape quotes
+    selector = json.dumps(sizzle_selector)
+    return f"return Sizzle({selector});"
 
 
 __all__ = (

lib/galaxy_test/selenium/test_histories_list.py

@@ -43,7 +43,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
 
         # Publish the history
         self.click_grid_popup_option(self.history2_name, 'Share or Publish')
-        self.components.histories.sharing.make_accessible_and_publish.wait_for_and_click()
+        self.make_accessible_and_publishable()
 
         self.navigate_to_histories_page()
 

lib/galaxy_test/selenium/test_published_histories_grid.py

@@ -199,8 +199,7 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
 
     def publish_current_history(self):
         self.click_history_option('Share or Publish')
-        self.components.histories.sharing.make_accessible_and_publish.wait_for_and_click()
-        self.wait_for_selector_clickable('#disable_link_access_and_unpublish')
+        self.make_accessible_and_publishable()
 
     def navigate_to_published_histories_page(self):
         self.home()

lib/galaxy_test/selenium/test_tool_form.py

@@ -124,7 +124,7 @@ class ToolFormTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         citations_api = self.api_get("tools/bibtex/citations")
         assert len(citations_api) == 29, len(citations_api)
         self.tool_open("bibtex")
-        self.components.tool_form.citations.wait_for_visible()
+        self.components.tool_form.about.wait_for_and_click()
 
         @retry_assertion_during_transitions
         def assert_citations_visible():
@@ -138,12 +138,6 @@ class ToolFormTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         assert "Galaxy: A platform for interactive" in doi_resolved_citation.text
         self.screenshot("tool_form_citations_formatted")
 
-        self.components.tool_form.show_bibtex.wait_for_and_click()
-        references = assert_citations_visible()
-        r0text = references[0].text
-        assert "@article{Giardine_2005" in r0text
-        self.screenshot("tool_form_citations_bibtex")
-
     def _check_dataset_details_for_inttest_value(self, hid, expected_value="42"):
         self.hda_click_primary_action_button(hid, "info")
 

lib/galaxy_test/selenium/test_workflow_editor.py

@@ -63,9 +63,6 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         editor.label_input.wait_for_and_send_keys("input1")
         editor.annotation_input.wait_for_and_send_keys("my cool annotation")
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot("workflow_editor_data_input_filled_in PRECLICK")
-        editor.label_input.wait_for_and_click()  # Seems to help force the save of whole annotation.
-        self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("workflow_editor_data_input_filled_in")
         self.workflow_editor_click_save()
 
@@ -75,7 +72,7 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         label = editor.label_input.wait_for_value()
         assert label == "input1", label
         annotation = editor.annotation_input.wait_for_value()
-        assert annotation == "my cool annotation"
+        assert annotation == "my cool annotation", annotation
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.screenshot("workflow_editor_data_input_deleted")
@@ -89,7 +86,6 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         self.screenshot("workflow_editor_data_collection_input_new")
         editor.label_input.wait_for_and_send_keys("input1")
         editor.annotation_input.wait_for_and_send_keys("my cool annotation")
-        editor.label_input.wait_for_and_click()  # Seems to help force the save of whole annotation.
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("workflow_editor_data_collection_input_filled_in")
         self.workflow_editor_click_save()
@@ -100,7 +96,7 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         label = editor.label_input.wait_for_value()
         assert label == "input1", label
         annotation = editor.annotation_input.wait_for_value()
-        assert annotation == "my cool annotation"
+        assert annotation == "my cool annotation", annotation
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.sleep_for(self.wait_types.UX_RENDER)
@@ -115,7 +111,6 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         self.screenshot("workflow_editor_parameter_input_new")
         editor.label_input.wait_for_and_send_keys("input1")
         editor.annotation_input.wait_for_and_send_keys("my cool annotation")
-        editor.label_input.wait_for_and_click()  # Seems to help force the save of whole annotation.
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("workflow_editor_parameter_input_filled_in")
         self.workflow_editor_click_save()
@@ -126,7 +121,7 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         label = editor.label_input.wait_for_value()
         assert label == "input1", label
         annotation = editor.annotation_input.wait_for_value()
-        assert annotation == "my cool annotation"
+        assert annotation == "my cool annotation", annotation
         data_input_node.destroy.wait_for_and_click()
         data_input_node.wait_for_absent()
         self.sleep_for(self.wait_types.UX_RENDER)
@@ -146,16 +141,16 @@ steps:
       inttest: input_int
 """)
         self.screenshot("workflow_editor_parameter_connection_simple")
-        self.assert_connected("input_int#output", "simple_constructs#inttest")
+        self.assert_connected("input_int#output", "tool_exec#inttest")
 
         editor = self.components.workflow_editor
 
-        tool_node = editor.node._(label="simple_constructs")
+        tool_node = editor.node._(label="tool_exec")
         tool_input = tool_node.input_terminal(name="inttest")
         tool_input.wait_for_and_click()
 
         editor.connector_destroy_callout.wait_for_and_click()
-        self.assert_not_connected("input_int#output", "simple_constructs#inttest")
+        self.assert_not_connected("input_int#output", "tool_exec#inttest")
         self.screenshot("workflow_editor_parameter_connection_destroyed")
 
         # When connected, cannot turn it into a RuntimeValue..
@@ -177,8 +172,8 @@ steps:
         tool_input.wait_for_visible()
         collapse_input.wait_for_absent_or_hidden()
 
-        self.workflow_editor_connect("input_int#output", "simple_constructs#inttest", screenshot_partial="workflow_editor_parameter_connection_dragging")
-        self.assert_connected("input_int#output", "simple_constructs#inttest")
+        self.workflow_editor_connect("input_int#output", "tool_exec#inttest", screenshot_partial="workflow_editor_parameter_connection_dragging")
+        self.assert_connected("input_int#output", "tool_exec#inttest")
 
     @selenium_test
     def test_existing_connections(self):

run_tests.sh

@@ -393,7 +393,7 @@ do
           ;;
       -selenium|--selenium)
           GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
-          test_script="./scripts/functional_tests.py"
+          test_script="pytest"
           report_file="./run_selenium_tests.html"
           skip_client_build=""
           selenium_test=1;
@@ -617,8 +617,8 @@ setup_python
 if [ -n "$framework_test" -o -n "$installed_test" -o -n "$migrated_test" -o -n "$data_managers_test" ] ; then
     [ -n "$test_id" ] && selector="-k $test_id" || selector=""
     extra_args="test/functional/test_toolbox_pytest.py $selector $marker"
-elif [ -n "$selenium_test" ] ; then
-    extra_args="$selenium_script -selenium"
+elif [ -n "$selenium_script" ]; then
+    extra_args="$selenium_script"
 elif [ -n "$toolshed_script" ]; then
     extra_args="$toolshed_script"
 elif [ -n "$api_script" ]; then