Merge branch 'release_24.0' into dev

client/src/components/History/CurrentCollection/CollectionOperations.vue

@@ -18,6 +18,8 @@ const rerunUrl = computed(() =>
 const showCollectionDetailsUrl = computed(() =>
     props.dsc.job_source_type == "Job" ? `/jobs/${props.dsc.job_source_id}/view` : null
 );
+const disableDownload = props.dsc.populated_state !== "ok";
+
 function onDownload() {
     window.location.href = downloadUrl.value;
 }
@@ -28,6 +30,7 @@ function onDownload() {
             <b-button-group>
                 <b-button
                     title="Download Collection"
+                    :disabled="disableDownload"
                     class="rounded-0 text-decoration-none"
                     size="sm"
                     variant="link"

client/src/components/Login/ChangePassword.vue

@@ -5,6 +5,7 @@ import { ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { withPrefix } from "@/utils/redirect";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 interface Props {
     token?: string;
@@ -36,8 +37,7 @@ async function submit() {
         router.push("/");
     } catch (error: any) {
         variant.value = "danger";
-        const errMsg = error.response && error.response.data && error.response.data.err_msg;
-        message.value = errMsg || "Password change failed for an unknown reason.";
+        message.value = errorMessageAsString(error, "Password change failed for an unknown reason.");
     }
 }
 </script>

client/src/components/Login/LoginForm.vue

@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import axios, { type AxiosError } from "axios";
+import axios from "axios";
 import {
     BAlert,
     BButton,
@@ -18,6 +18,7 @@ import { useRouter } from "vue-router/composables";
 
 import localize from "@/utils/localization";
 import { withPrefix } from "@/utils/redirect";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import NewUserConfirmation from "@/components/Login/NewUserConfirmation.vue";
 import ExternalLogin from "@/components/User/ExternalIdentities/ExternalLogin.vue";
@@ -106,14 +107,13 @@ async function submitLogin() {
         }
     } catch (e) {
         loading.value = false;
-        const error = e as AxiosError<{ err_msg?: string }>;
         messageVariant.value = "danger";
-        const message = error.response && error.response.data && error.response.data.err_msg;
+        const message = errorMessageAsString(e, "Login failed for an unknown reason.");
 
         if (connectExternalProvider.value && message && message.toLowerCase().includes("invalid")) {
             messageText.value = message + " Try logging in to the existing account through an external provider below.";
         } else {
-            messageText.value = message || "Login failed for an unknown reason.";
+            messageText.value = message;
         }
         if (message === "Invalid password.") {
             passwordState.value = false;
@@ -132,10 +132,8 @@ async function resetLogin() {
         messageVariant.value = "info";
         messageText.value = response.data.message;
     } catch (e) {
-        const error = e as AxiosError<{ err_msg?: string }>;
         messageVariant.value = "danger";
-        const errMsg = error.response?.data && error.response.data.err_msg;
-        messageText.value = errMsg || "Password reset failed for an unknown reason.";
+        messageText.value = errorMessageAsString(e, "Password reset failed for an unknown reason.");
     } finally {
         loading.value = false;
     }

client/src/components/Login/NewUserConfirmation.vue

@@ -15,6 +15,7 @@ import { ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { withPrefix } from "@/utils/redirect";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 interface Props {
     termsUrl?: string;
@@ -58,8 +59,7 @@ async function submit() {
             }
         } catch (error: any) {
             messageVariant.value = "danger";
-            const errMsg = error.response.data && error.response.data.err_msg;
-            messageText.value = errMsg || "Login failed for an unknown reason.";
+            messageText.value = errorMessageAsString(error, "Login failed for an unknown reason.");
         }
     }
 }

client/src/components/Login/RegisterForm.vue

@@ -19,6 +19,7 @@ import { computed, ref } from "vue";
 import { Toast } from "@/composables/toast";
 import localize from "@/utils/localization";
 import { withPrefix } from "@/utils/redirect";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import ExternalLogin from "@/components/User/ExternalIdentities/ExternalLogin.vue";
 
@@ -81,8 +82,7 @@ async function submit() {
         window.location.href = props.redirect || withPrefix("/");
     } catch (error: any) {
         disableCreate.value = false;
-        const errMsg = error.response.data && error.response.data.err_msg;
-        messageText.value = errMsg || "Registration failed for an unknown reason.";
+        messageText.value = errorMessageAsString(error, "Registration failed for an unknown reason.");
     }
 }
 </script>
@@ -215,7 +215,6 @@ async function submit() {
         </div>
     </div>
 </template>
-
 <style scoped lang="scss">
 .embed-container {
     position: relative;

client/src/components/Markdown/parse.ts

@@ -13,7 +13,7 @@ type WorkflowLabelKind = "input" | "output" | "step";
 const SINGLE_QUOTE = "'";
 const DOUBLE_QUOTE = '"';
 
-export function splitMarkdown(markdown: string, preserveWhitespace: boolean = false) {
+export function splitMarkdown(markdown: string, preserveWhitespace = false) {
     const sections: Section[] = [];
     const markdownErrors = [];
     let digest = markdown;

client/src/components/Popper/usePopper.ts

@@ -186,19 +186,14 @@ export function usePopperjs(
 
             case "hover": {
                 on(referenceRef.value!, "mouseover", doMouseover);
-                on(popperRef.value!, "mouseover", doMouseover);
                 on(referenceRef.value!, "mouseout", doMouseout);
-                on(popperRef.value!, "mouseout", doMouseout);
                 on(referenceRef.value!, "mousedown", doMouseout);
-                on(popperRef.value!, "mousedown", doMouseout);
                 break;
             }
 
             case "focus": {
                 on(referenceRef.value!, "focus", doOpen);
-                on(popperRef.value!, "focus", doOpen);
                 on(referenceRef.value!, "blur", doClose);
-                on(popperRef.value!, "blur", doClose);
                 break;
             }
 
@@ -218,16 +213,11 @@ export function usePopperjs(
         off(referenceRef.value!, "click", doToggle);
 
         off(referenceRef.value!, "mouseover", doMouseover);
-        off(popperRef.value!, "mouseover", doMouseover);
         off(referenceRef.value!, "mouseout", doMouseout);
-        off(popperRef.value!, "mouseout", doMouseout);
         off(referenceRef.value!, "mousedown", doMouseout);
-        off(popperRef.value!, "mousedown", doMouseout);
 
         off(referenceRef.value!, "focus", doOpen);
-        off(popperRef.value!, "focus", doOpen);
         off(referenceRef.value!, "blur", doClose);
-        off(popperRef.value!, "blur", doClose);
     };
     const doCloseForDocument = (e: Event) => {
         if (referenceRef.value?.contains(e.target as Element)) {

client/src/components/User/DiskUsage/Visualizations/service.ts

@@ -35,7 +35,7 @@ export async function fetchAllHistoriesSizeSummary(): Promise<ItemSizeSummary[]>
 
 export async function fetchHistoryContentsSizeSummary(
     historyId: string,
-    limit: number = 5000,
+    limit = 5000,
     objectStoreId: string | null = null
 ) {
     const q = ["purged", "history_content_type"];

client/src/components/User/ExternalIdentities/ExternalLogin.vue

@@ -1,6 +1,7 @@
 <script setup lang="ts">
 import axios, { type AxiosError } from "axios";
 import { BAlert, BButton, BForm, BFormCheckbox, BFormGroup } from "bootstrap-vue";
+import { errorMessageAsString } from "utils/simple-error";
 import { computed, onMounted, ref } from "vue";
 import Multiselect from "vue-multiselect";
 
@@ -82,10 +83,8 @@ async function submitOIDCLogin(idp: string) {
             window.location = data.redirect_uri;
         }
     } catch (e) {
-        const error = e as AxiosError<{ err_msg?: string }>;
         messageVariant.value = "danger";
-        const message = error.response?.data && error.response.data.err_msg;
-        messageText.value = message || "Login failed for an unknown reason.";
+        messageText.value = errorMessageAsString(e, "Login failed for an unknown reason.");
     } finally {
         loading.value = false;
     }
@@ -113,10 +112,8 @@ async function submitCILogon(idp: string | null) {
             window.location = data.redirect_uri;
         }
     } catch (e) {
-        const error = e as AxiosError<{ err_msg?: string }>;
         messageVariant.value = "danger";
-        const message = error.response?.data && error.response.data.err_msg;
-        messageText.value = message || "Login failed for an unknown reason.";
+        messageText.value = errorMessageAsString(e, "Login failed for an unknown reason.");
     } finally {
         loading.value = false;
     }

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

@@ -392,17 +392,18 @@ export default {
             }
         });
 
-        function resetStores() {
+        async function resetStores() {
             hasChanges.value = false;
             connectionStore.$reset();
             stepStore.$reset();
             stateStore.$reset();
             commentStore.$reset();
             undoRedoStore.$reset();
+            await nextTick();
         }
 
-        onUnmounted(() => {
-            resetStores();
+        onUnmounted(async () => {
+            await resetStores();
             emit("update:confirmation", false);
         });
 
@@ -574,7 +575,7 @@ export default {
             hide_modal(); // hide other modals created in utilities also...
         },
         async onRefactor(response) {
-            this.resetStores();
+            await this.resetStores();
             await fromSimple(this.id, response.workflow);
             this._loadEditorData(response.workflow);
         },
@@ -887,7 +888,7 @@ export default {
         },
         async _loadCurrent(id, version) {
             if (!this.isNewTempWorkflow) {
-                this.resetStores();
+                await this.resetStores();
                 this.onWorkflowMessage("Loading workflow...", "progress");
 
                 try {

lib/galaxy/files/sources/invenio.py

@@ -167,7 +167,7 @@ def _create_entry(
         record = self.repository.create_draft_record(entry_data["name"], public_name, user_context=user_context)
         return {
             "uri": self.repository.to_plugin_uri(record["id"]),
-            "name": record["metadata"]["title"],
+            "name": record["title"],
             "external_link": record["links"]["self_html"],
         }
 
@@ -253,6 +253,7 @@ def create_draft_record(
         response = requests.post(self.records_url, json=create_record_request, headers=headers)
         self._ensure_response_has_expected_status_code(response, 201)
         record = response.json()
+        record["title"] = self._get_record_title(record)
         return record
 
     def upload_file_to_draft_record(
@@ -359,16 +360,23 @@ def _get_records_from_response(self, response: dict) -> List[RemoteDirectory]:
         for record in records:
             uri = self.to_plugin_uri(record_id=record["id"])
             path = self.plugin.to_relative_path(uri)
+            name = self._get_record_title(record)
             rval.append(
                 {
                     "class": "Directory",
-                    "name": record["metadata"]["title"],
+                    "name": name,
                     "uri": uri,
                     "path": path,
                 }
             )
         return rval
 
+    def _get_record_title(self, record: InvenioRecord) -> str:
+        title = record.get("title")
+        if not title and "metadata" in record:
+            title = record["metadata"].get("title")
+        return title or "No title"
+
     def _get_record_files_from_response(self, record_id: str, response: dict) -> List[RemoteFile]:
         files_enabled = response.get("enabled", False)
         if not files_enabled:

lib/galaxy/managers/hdcas.py

@@ -9,6 +9,7 @@
 from typing import Dict
 
 from galaxy import model
+from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.managers import (
     annotatable,
     base,
@@ -40,6 +41,8 @@ def stream_dataset_collection(dataset_collection_instance, upstream_mod_zip=Fals
 
 
 def write_dataset_collection(dataset_collection_instance, archive):
+    if not dataset_collection_instance.collection.populated_optimized:
+        raise RequestParameterInvalidException("Attempt to write dataset collection that has not been populated yet")
     names, hdas = get_hda_and_element_identifiers(dataset_collection_instance)
     for name, hda in zip(names, hdas):
         if hda.state != hda.states.OK:

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -626,8 +626,7 @@ def download_dataset_collection_history_content(
         """Download the content of a history dataset collection as a `zip` archive
         while maintaining approximate collection structure.
         """
-        archive = self.service.get_dataset_collection_archive_for_download(trans, id)
-        return StreamingResponse(archive.response(), headers=archive.get_headers())
+        return self._download_collection(trans, id)
 
     @router.get(
         "/api/dataset_collections/{id}/download",
@@ -644,8 +643,7 @@ def download_dataset_collection(
         """Download the content of a history dataset collection as a `zip` archive
         while maintaining approximate collection structure.
         """
-        archive = self.service.get_dataset_collection_archive_for_download(trans, id)
-        return StreamingResponse(archive.response(), headers=archive.get_headers())
+        return self._download_collection(trans, id)
 
     @router.post(
         "/api/histories/{history_id}/contents/dataset_collections/{id}/prepare_download",
@@ -1089,3 +1087,7 @@ def materialize_to_history(
         )
         rval = self.service.materialize(trans, materialize_request)
         return rval
+
+    def _download_collection(self, trans, id):
+        archive = self.service.get_dataset_collection_archive_for_download(trans, id)
+        return StreamingResponse(archive.response(), headers=archive.get_headers())