Merge branch 'release_22.05' into dev

client/gulpfile.js

@@ -121,6 +121,13 @@ function buildPlugins(callback, forceRebuild) {
                                     shell: true,
                                 }
                             ).status === 0;
+                        if (!skipBuild) {
+                            // Hash exists and is outdated, triggering a rebuild.
+                            // Stage current hash to .orig for debugging and to
+                            // force a plugin rebuild in the event of a failure
+                            // (i.e. -- we're committed to a new build of this plugin).
+                            fs.renameSync(hashFilePath, `${hashFilePath}.orig`)
+                        }
                     } else {
                         console.log(`No build hashfile detected for ${pluginName}, generating now.`);
                     }

client/src/components/History/Content/ContentItem.vue

@@ -91,7 +91,7 @@
 <script>
 import { backboneRoute, iframeAdd } from "components/plugins/legacyNavigation";
 import { StatelessTags } from "components/Tags";
-import { STATES } from "./model/states";
+import { STATES, HIERARCHICAL_COLLECTION_JOB_STATES } from "./model/states";
 import CollectionDescription from "./Collection/CollectionDescription";
 import ContentOptions from "./ContentOptions";
 import DatasetDetails from "./Dataset/DatasetDetails";
@@ -151,9 +151,9 @@ export default {
         },
         state() {
             if (this.item.job_state_summary) {
-                for (const key of ["error", "failed", "paused", "upload", "running"]) {
-                    if (this.item.job_state_summary[key] > 0) {
-                        return key;
+                for (const state of HIERARCHICAL_COLLECTION_JOB_STATES) {
+                    if (this.item.job_state_summary[state] > 0) {
+                        return state;
                     }
                 }
                 return "ok";

client/src/components/History/Content/model/states.js

@@ -19,12 +19,17 @@ export const STATES = {
         status: "success",
         text: "No data.",
     },
-    /** the tool producing this dataset failed */
+    /** the tool producing this dataset has errored */
     error: {
         status: "danger",
         text: "An error occurred with this dataset:",
         icon: "exclamation-triangle",
     },
+    /** the job has failed, this is not a dataset but a job state used in the collection job state summary. */
+    failed: {
+        status: "danger",
+        icon: "exclamation-triangle",
+    },
     /** metadata discovery/setting failed or errored (but otherwise ok) */
     failed_metadata: {
         status: "danger",
@@ -74,3 +79,8 @@ export const STATES = {
         spin: true,
     },
 };
+
+/** We want to display a single state for a dataset collection whose elements may have mixed states.
+ * This list is ordered from highest to lowest priority. If any element is in error state the whole collection should be in error.
+ */
+export const HIERARCHICAL_COLLECTION_JOB_STATES = ["error", "failed", "queued", "upload", "paused", "running", "new"];

client/src/components/History/Content/model/states.test.js

@@ -0,0 +1,10 @@
+import { STATES, HIERARCHICAL_COLLECTION_JOB_STATES } from "./states";
+
+describe("States", () => {
+    it("check if all reduced states exist and have a status set", async () => {
+        HIERARCHICAL_COLLECTION_JOB_STATES.forEach((jobState) => {
+            const alertState = STATES[jobState];
+            expect(alertState.status).toBeDefined();
+        });
+    });
+});

config/plugins/visualizations/PCA_3Dplot/package.json

@@ -8,6 +8,6 @@
         "d3": "^7.4.4"
     },
     "scripts": {
-        "build": "mkdir static/dist && cp node_modules/pca-js/pca.min.js node_modules/plotly.js/dist/plotly.min.js node_modules/d3/dist/d3.min.js static/dist"
+        "build": "mkdir -p static/dist && cp node_modules/pca-js/pca.min.js node_modules/plotly.js/dist/plotly.min.js node_modules/d3/dist/d3.min.js static/dist"
     }
 }

lib/galaxy/model/__init__.py

@@ -2885,7 +2885,7 @@ def disk_size(cls):
             .distinct()
         )
         # postgres needs an alias on FROM
-        distinct_datasets_alias = aliased(distinct_datasets, name="datasets")
+        distinct_datasets_alias = aliased(distinct_datasets.subquery(), name="datasets")
         # then, bind as property of history using the cls.id
         size_query = (
             select([func.coalesce(func.sum(distinct_datasets_alias.c.dataset_size), 0)])

lib/galaxy/webapps/base/webapp.py

@@ -448,7 +448,7 @@ def get_user(self):
     def set_user(self, user):
         """Set the current user."""
         if self.galaxy_session:
-            if user.bootstrap_admin_user:
+            if user and not user.bootstrap_admin_user:
                 self.galaxy_session.user = user
                 self.sa_session.add(self.galaxy_session)
                 self.sa_session.flush()

lib/galaxy/webapps/galaxy/api/datasets.py

@@ -2,7 +2,10 @@
 API operations on the contents of a history dataset.
 """
 import logging
-from io import IOBase
+from io import (
+    BytesIO,
+    IOBase,
+)
 from typing import (
     Any,
     cast,
@@ -255,6 +258,8 @@ def display(
                 return FileResponse(file_name, headers=headers)
         elif isinstance(display_data, ZipstreamWrapper):
             return StreamingResponse(display_data.response(), headers=headers)
+        elif isinstance(display_data, bytes):
+            return StreamingResponse(BytesIO(display_data), headers=headers)
         return StreamingResponse(display_data, headers=headers)
 
     @router.get(