Merge pull request #22102 from mvdbeek/fix-transient-ci-failures

Fix transient ci failures

Author: martenson

client/src/components/BaseComponents/GTabs.vue

@@ -167,7 +167,9 @@ const TabTitleContent = defineComponent({
                     role="tab"
                     href="#"
                     :aria-selected="index === activeIndex"
+                    :aria-controls="tab.id"
                     :aria-disabled="tab.disabled"
+                    :data-tab-title="tab.title"
                     v-bind="tab.titleLinkAttributes"
                     @click.prevent="!tab.disabled && setActive(index)">
                     <TabTitleContent :tab="tab" />

client/src/components/FilesDialog/FilesDialog.vue

@@ -265,6 +265,7 @@ function load() {
     if (urlTracker.isAtRoot.value || errorMessage.value) {
         itemsProvider.value = undefined;
         errorMessage.value = undefined;
+        isBusy.value = true;
         fetchFileSources(props.filterOptions)
             .then((results) => {
                 const convertedItems = results
@@ -274,13 +275,15 @@ function load() {
                 const sortedItems = convertedItems.sort(sortPrivateFileSourcesFirst);
                 items.value = sortedItems;
                 formatRows();
-                optionsShow.value = true;
                 showTime.value = false;
                 showDetails.value = true;
                 totalItems.value = convertedItems.length;
+                isBusy.value = false;
+                optionsShow.value = true;
             })
             .catch((error) => {
                 errorMessage.value = errorMessageAsString(error);
+                isBusy.value = false;
             });
     } else {
         if (!urlTracker.current.value) {
@@ -303,17 +306,20 @@ function load() {
             return;
         }
 
+        isBusy.value = true;
         browseRemoteFiles(urlTracker.current.value?.url, false, props.requireWritable)
             .then((result) => {
                 items.value = filterByMode(result.entries).map(entryToRecord);
                 totalItems.value = result.totalMatches;
                 formatRows();
-                optionsShow.value = true;
                 showTime.value = true;
                 showDetails.value = false;
+                isBusy.value = false;
+                optionsShow.value = true;
             })
             .catch((error) => {
                 errorMessage.value = errorMessageAsString(error);
+                isBusy.value = false;
             });
     }
 }

client/src/components/SelectionDialog/SelectionDialog.vue

@@ -196,7 +196,7 @@ defineExpose({
             {{ errorMessage }}
         </BAlert>
         <div v-else>
-            <div v-if="optionsShow">
+            <div v-if="optionsShow" data-description="selection dialog options">
                 <BTable
                     small
                     hover

client/src/utils/navigation/navigation.yml

@@ -552,6 +552,7 @@ files_dialog:
     ftp_details: 'span[title="details-gxftp://"]'
     row: 'span[title="label-${uri}"]'
     back_btn: '#back-btn'
+    options_ready: '[data-description="selection dialog options"] .selection-dialog-table[aria-busy="false"]'
 
 history_export:
   selectors:
@@ -1159,18 +1160,10 @@ custom_tools:
 admin:
   allowlist:
     selectors:
-      toolshed:
-        type: xpath
-        selector: '//a[contains(text(), "Toolshed Tools")]'
-      local:
-        type: xpath
-        selector: '//a[contains(text(), "Local Tools")]'
-      sanitized:
-        type: xpath
-        selector: '//a[contains(text(), "HTML Sanitized")]'
-      rendered_active:
-        type: xpath
-        selector: '//div[contains(@class, "active")]//a[contains(text(), "HTML Rendered")]'
+      toolshed: 'a[data-tab-title="Toolshed Tools"]'
+      local: 'a[data-tab-title="Local Tools"]'
+      sanitized: 'a[data-tab-title="HTML Sanitized"]'
+      rendered_active: '.tab-pane.active a[data-tab-title="HTML Rendered"]'
 
   manage_dependencies:
     selectors:

client/src/utils/navigation/schema.ts

@@ -301,6 +301,7 @@ interface Rootfiles_dialog extends Component {
     ftp_details: SelectorTemplate;
     row: SelectorTemplate;
     back_btn: SelectorTemplate;
+    options_ready: SelectorTemplate;
 }
 interface Roothistory_export extends Component {
     export_link: SelectorTemplate;

lib/galaxy/jobs/__init__.py

@@ -2231,24 +2231,27 @@ def fail(message=job.info, exception=None):
                 dataset.full_delete()
                 collected_bytes = 0
 
-        # Calculate dataset hash
-        for dataset_assoc in output_dataset_associations:
-            dataset = dataset_assoc.dataset.dataset
-            if not dataset.purged and dataset.state == Dataset.states.OK and not dataset.hashes:
-                if self.app.config.calculate_dataset_hash == "always" or (
-                    self.app.config.calculate_dataset_hash == "upload" and job.tool_id in ("upload1", "__DATA_FETCH__")
-                ):
-                    # Calculate dataset hash via a celery task
-                    if self.app.config.enable_celery_tasks:
-                        from galaxy.celery.tasks import compute_dataset_hash
-
-                        extra_files_path = dataset.extra_files_path if dataset.extra_files_path_exists() else None
-                        request = ComputeDatasetHashTaskRequest(
-                            dataset_id=dataset.id,
-                            extra_files_path=extra_files_path,
-                            hash_function=self.app.config.hash_function,
-                        )
-                        compute_dataset_hash.delay(request=request)
+        # Calculate dataset hash - only if the job completed successfully,
+        # otherwise dataset files may be missing/invalid (e.g. failed fetch from 404 URL).
+        if final_job_state == job.states.OK:
+            for dataset_assoc in output_dataset_associations:
+                dataset = dataset_assoc.dataset.dataset
+                if not dataset.purged and dataset.state == Dataset.states.OK and not dataset.hashes:
+                    if self.app.config.calculate_dataset_hash == "always" or (
+                        self.app.config.calculate_dataset_hash == "upload"
+                        and job.tool_id in ("upload1", "__DATA_FETCH__")
+                    ):
+                        # Calculate dataset hash via a celery task
+                        if self.app.config.enable_celery_tasks:
+                            from galaxy.celery.tasks import compute_dataset_hash
+
+                            extra_files_path = dataset.extra_files_path if dataset.extra_files_path_exists() else None
+                            request = ComputeDatasetHashTaskRequest(
+                                dataset_id=dataset.id,
+                                extra_files_path=extra_files_path,
+                                hash_function=self.app.config.hash_function,
+                            )
+                            compute_dataset_hash.delay(request=request)
 
         user = job.user
         if user and collected_bytes > 0 and quota_source_info is not None and quota_source_info.use:

lib/galaxy/managers/datasets.py

@@ -18,6 +18,7 @@
     model,
 )
 from galaxy.datatypes import sniff
+from galaxy.exceptions import ObjectInvalid
 from galaxy.managers import (
     base,
     deletable,
@@ -164,11 +165,18 @@ def compute_hash(self, request: ComputeDatasetHashTaskRequest):
             return
         # For files in extra_files_path
         extra_files_path = request.extra_files_path
-        if extra_files_path:
-            extra_dir = dataset.extra_files_path_name
-            file_path = self.app.object_store.get_filename(dataset, extra_dir=extra_dir, alt_name=extra_files_path)
-        else:
-            file_path = dataset.get_file_name()
+        try:
+            if extra_files_path:
+                extra_dir = dataset.extra_files_path_name
+                file_path = self.app.object_store.get_filename(dataset, extra_dir=extra_dir, alt_name=extra_files_path)
+            else:
+                file_path = dataset.get_file_name()
+        except ObjectInvalid:
+            log.warning(
+                "Unable to calculate hash for dataset [%s]: object is invalid (dataset may have failed or been purged).",
+                dataset.id,
+            )
+            return
         hash_function = request.hash_function
         calculated_hash_value = memory_bound_hexdigest(hash_func_name=hash_function, path=file_path)
         dataset_hash = model.DatasetHash(

test/integration_selenium/test_history_import_export_ftp.py

@@ -30,8 +30,13 @@ def create_user_ftp_dir(self):
         user_ftp_dir = os.path.join(self.ftp_dir(), email)
         os.makedirs(user_ftp_dir)
 
+    def _wait_for_files_dialog_ready(self):
+        """Wait for the files dialog to finish loading and display its options."""
+        self.components.files_dialog.options_ready.wait_for_visible()
+
     def _export_to_ftp_with_filename(self, filename: str):
         self.components.history_export.directory_input.wait_for_and_click()
+        self._wait_for_files_dialog_ready()
         self.components.files_dialog.ftp_label.wait_for_and_click()
         self.components.upload.file_dialog_ok.wait_for_and_click()
         self.components.history_export.name_input.wait_for_and_send_keys(filename)
@@ -72,6 +77,7 @@ def test_history_import_export(self):
         history_import = gx_selenium_context.components.history_import
         history_import.radio_button_remote_files.wait_for_and_click()
         history_import.open_files_dialog.wait_for_and_click()
+        self._wait_for_files_dialog_ready()
         files_dialog.ftp_label.wait_for_and_click()
         files_dialog.row(uri="gxftp://my_export.tar.gz").wait_for_and_click()
 
@@ -128,6 +134,7 @@ def test_history_export_tracking(self):
 
         # Select FTP file source
         self.components.history_export.directory_input.wait_for_and_click()
+        self._wait_for_files_dialog_ready()
         self.components.files_dialog.ftp_label.wait_for_and_click()
         self.components.upload.file_dialog_ok.wait_for_and_click()