Merge remote-tracking branch 'upstream/release_23.1' into dev

client/package.json

@@ -50,7 +50,6 @@
     "d3-zoom": "^3.0.0",
     "d3v3": "npm:d3@3",
     "date-fns": "^2.28.0",
-    "date-fns-tz": "^1.3.3",
     "decode-uri-component": "^0.2.1",
     "dom-to-image": "^2.6.0",
     "dompurify": "^3.0.1",

client/src/components/DatasetInformation/DatasetInformation.test.js

@@ -1,8 +1,7 @@
 import { mount } from "@vue/test-utils";
 import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
-import { parseISO } from "date-fns";
-import { formatInTimeZone } from "date-fns-tz";
+import { format, parseISO } from "date-fns";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
@@ -68,7 +67,7 @@ describe("DatasetInformation/DatasetInformation", () => {
     it("Date should be formatted", async () => {
         const date = datasetInfoTable.find(".utc-time").text();
         const parsedDate = parseISO(`${datasetResponse.create_time}Z`);
-        const formattedDate = `${formatInTimeZone(parsedDate, "Etc/Zulu", "eeee MMM do H:mm:ss yyyy")} UTC`;
+        const formattedDate = format(parsedDate, "eeee MMM do H:mm:ss yyyy zz");
         expect(date).toBe(formattedDate);
     });
 

client/src/components/UtcDate.test.js

@@ -2,6 +2,7 @@ import { shallowMount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
 
 import UtcDate from "./UtcDate.vue";
+import { format, parseISO } from "date-fns";
 
 describe("UTCDate component", () => {
     const localVue = getLocalVue();
@@ -17,6 +18,6 @@ describe("UTCDate component", () => {
         expect(wrapper.text()).toContain("years ago");
 
         await wrapper.setProps({ mode: "pretty" });
-        expect(wrapper.text()).toBe("Wednesday Oct 21st 16:29:00 2015 UTC");
+        expect(wrapper.text()).toBe(format(parseISO("2015-10-21T16:29:00.000Z"), "eeee MMM do H:mm:ss yyyy zz"));
     });
 });

client/src/components/UtcDate.vue

@@ -1,7 +1,6 @@
 <script setup lang="ts">
-import { formatDistanceToNow, parseISO } from "date-fns";
-import { formatInTimeZone } from "date-fns-tz";
 import { computed } from "vue";
+import { format, formatDistanceToNow, parseISO } from "date-fns";
 
 interface UtcDateProps {
     date: string;
@@ -12,13 +11,12 @@ const props = withDefaults(defineProps<UtcDateProps>(), {
     mode: "date",
 });
 
-// Component assumes ISO format date, but note that in Galaxy this won't have
-// TZinfo -- it will always be Zulu
 const parsedDate = computed(() => parseISO(`${props.date}Z`));
 const elapsedTime = computed(() => formatDistanceToNow(parsedDate.value, { addSuffix: true }));
 const fullISO = computed(() => parsedDate.value.toISOString());
-const pretty = computed(() => `${formatInTimeZone(parsedDate.value, "Etc/Zulu", "eeee MMM do H:mm:ss yyyy")} UTC`);
+const pretty = computed(() => format(parsedDate.value, "eeee MMM do H:mm:ss yyyy zz"));
 </script>
+
 <template>
     <span v-if="mode == 'date'" class="utc-time" :title="elapsedTime">
         {{ fullISO }}

client/src/components/Workflow/Editor/Forms/FormConditional.vue

@@ -36,7 +36,7 @@ function onSkipBoolean(value: boolean) {
         id="__conditional"
         :value="conditionalDefined"
         title="Conditionally skip step?"
-        help="Set to true and connect a boolean parameter that determines whether step will be skipped"
+        help="Set to true and connect a boolean parameter that determines whether the step should run. The step runs if the parameter value is true and will be skipped if the parameter value is false"
         type="boolean"
         @input="onSkipBoolean"></FormElement>
     <!-- We don't seem to have a disabled text field

client/yarn.lock

@@ -4703,11 +4703,6 @@ data-urls@^3.0.2:
     whatwg-mimetype "^3.0.0"
     whatwg-url "^11.0.0"
 
-date-fns-tz@^1.3.3:
-  version "1.3.6"
-  resolved "https://registry.npmjs.org/date-fns-tz/-/date-fns-tz-1.3.6.tgz"
-  integrity sha512-C8q7mErvG4INw1ZwAFmPlGjEo5Sv4udjKVbTc03zpP9cu6cp5AemFzKhz0V68LGcWEtX5mJudzzg3G04emIxLA==
-
 date-fns@^2.28.0:
   version "2.29.1"
   resolved "https://registry.npmjs.org/date-fns/-/date-fns-2.29.1.tgz"

lib/galaxy/tools/actions/__init__.py

@@ -663,11 +663,15 @@ def handle_output(name, output, hidden=None):
             job.state = job.states.SKIPPED
             for output_collection in output_collections.out_collections.values():
                 output_collection.mark_as_populated()
+            for hdca in output_collections.out_collection_instances.values():
+                hdca.visible = False
             object_store_populator = ObjectStorePopulator(trans.app, trans.user)
             for data in out_data.values():
                 object_store_populator.set_object_store_id(data)
                 data.extension = "expression.json"
                 data.state = "ok"
+                data.blurb = "skipped"
+                data.visible = False
                 with open(data.dataset.file_name, "w") as out:
                     out.write(json.dumps(None))
         job.preferred_object_store_id = preferred_object_store_id

lib/galaxy/web_stack/handlers.py

@@ -336,7 +336,7 @@ def _assign_mem_self_handler(self, obj, method, configured, queue_callback=None,
                 HANDLER_ASSIGNMENT_METHODS.MEM_SELF,
                 configured,
             )
-        if flush():
+        if flush:
             _timed_flush_obj(obj)
         queue_callback()
         return self.app.config.server_name