Merge branch 'release_22.01' into dev

client/src/components/JobStates/CollectionJobStates.vue

@@ -1,5 +1,5 @@
 <template>
-    <div v-if="!jobSourceType || jobSourceType == 'Job' || isTerminal">
+    <div v-if="!jobSourceType || jobSourceType == 'Job' || (isTerminal && !isErrored)">
         {{ simpleDescription }}
     </div>
     <div v-else-if="!jobStatesSummary || !jobStatesSummary.hasDetails()">
@@ -51,6 +51,9 @@ export default {
             return DC_VIEW.collectionDescription(this.collection);
         },
         errorDescription() {
+            if (this.isPopulationFailed) {
+                return `${this.collection.get("populated_state_message")}`;
+            }
             var jobCount = this.jobCount;
             var errorCount = this.jobStatesSummary.numInError();
             return `a ${this.collectionTypeDescription} with ${errorCount} / ${jobCount} jobs in error`;

client/src/components/JobStates/mixin.js

@@ -7,6 +7,9 @@ export default {
         isErrored() {
             return this.jobStatesSummary && this.jobStatesSummary.errored();
         },
+        isPopulationFailed() {
+            return this.jobStatesSummary && this.jobStatesSummary.populationFailed();
+        },
         isTerminal() {
             return this.jobStatesSummary && this.jobStatesSummary.terminal();
         },

client/src/mvc/collection/collection-model.js

@@ -252,6 +252,15 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
                     _.extend(element, {
                         parent_hdca_id: parentHdcaId,
                     });
+
+                    // Warning: MEGA-hack ahead...
+                    if (!element.element_type && !element.object) {
+                        // The DCE has to be in error state... so we simulate it
+                        _.extend(element, {
+                            element_type: "hda",
+                            object: { state: "error" },
+                        });
+                    }
                 });
                 this.elements = new collectionClass(elements);
                 //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );

client/src/mvc/collection/collection-view.js

@@ -62,11 +62,16 @@ var CollectionView = _super.extend(
         },
 
         handleWarning: function ($newRender) {
+            var $warns = $newRender.find(".elements-warning");
+            if (this.model.get("populated_state") === "failed") {
+                var error = _l(`${this.model.get("populated_state_message")}`);
+                $warns.html(`<div class="errormessagesmall">${error}</div>`);
+                return;
+            }
             var viewLength = this.views.length;
             var elementCount = this.model.get("element_count");
             if (elementCount && elementCount !== viewLength) {
                 var warning = _l(`displaying only ${viewLength} of ${elementCount} items`);
-                var $warns = $newRender.find(".elements-warning");
                 $warns.html(`<div class="warningmessagesmall">${warning}</div>`);
             }
         },

client/src/mvc/history/job-states-model.js

@@ -7,6 +7,7 @@ var UPDATE_DELAY = 2000;
 var NON_TERMINAL_STATES = ["new", "queued", "running", "waiting"];
 var ERROR_STATES = ["error", "deleted"];
 var TERMINAL_STATES = ["ok"].concat(ERROR_STATES);
+const POPULATED_STATE_FAILED = "failed";
 /** Fetch state on add or just wait for polling to start. */
 var FETCH_STATE_ON_ADD = false;
 var BATCH_FETCH_STATE = true;
@@ -26,8 +27,12 @@ var JobStatesSummary = Backbone.Model.extend({
         return !this.hasDetails() || this.get("populated_state") == "new";
     },
 
+    populationFailed: function () {
+        return this.get("populated_state") === POPULATED_STATE_FAILED;
+    },
+
     errored: function () {
-        return this.get("populated_state") === "error" || this.anyWithStates(ERROR_STATES);
+        return this.populationFailed() || this.anyWithStates(ERROR_STATES);
     },
 
     states: function () {

lib/galaxy/objectstore/irods.py

@@ -357,7 +357,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         # Ensure the cache directory structure exists (e.g., dataset_#_files/)
         rel_path_dir = os.path.dirname(rel_path)
         if not os.path.exists(self._get_cache_path(rel_path_dir)):
-            os.makedirs(self._get_cache_path(rel_path_dir))
+            os.makedirs(self._get_cache_path(rel_path_dir), exist_ok=True)
         # Now pull in the file
         file_ok = self._download(rel_path)
         self._fix_permissions(self._get_cache_path(rel_path_dir))
@@ -502,7 +502,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         if dir_only and base_dir:
             # for JOB_WORK directory
             if not os.path.exists(rel_path):
-                os.makedirs(rel_path)
+                os.makedirs(rel_path, exist_ok=True)
             log.debug("irods_pt _exists: %s", ipt_timer)
             return True
         log.debug("irods_pt _exists: %s", ipt_timer)
@@ -530,7 +530,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
             # Create given directory in cache
             cache_dir = os.path.join(self.staging_path, rel_path)
             if not os.path.exists(cache_dir):
-                os.makedirs(cache_dir)
+                os.makedirs(cache_dir, exist_ok=True)
 
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")