merge 24.0 to dev

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

@@ -13,6 +13,7 @@
             @onRefactor="onRefactor"
             @onShow="hideModal" />
         <MessagesModal :title="messageTitle" :message="messageBody" :error="messageIsError" @onHidden="resetMessage" />
+        <SaveChangesModal :nav-url.sync="navUrl" :show-modal.sync="showSaveChangesModal" @on-proceed="onNavigate" />
         <b-modal
             v-model="showSaveAsModal"
             title="Save As a New Workflow"
@@ -147,7 +148,7 @@
     <MarkdownEditor
         v-else
         :markdown-text="markdownText"
-        :markdown-config="markdownConfig"
+        :markdown-config="report"
         mode="report"
         :title="'Workflow Report: ' + name"
         :steps="steps"
@@ -169,7 +170,7 @@
 <script>
 import { Toast } from "composables/toast";
 import { storeToRefs } from "pinia";
-import Vue, { computed, onUnmounted, ref, unref } from "vue";
+import Vue, { computed, nextTick, onUnmounted, ref, unref } from "vue";
 
 import { replaceLabel } from "@/components/Markdown/parse";
 import { getUntypedWorkflowParameters } from "@/components/Workflow/Editor/modules/parameters";
@@ -195,6 +196,7 @@ import WorkflowLint from "./Lint.vue";
 import MessagesModal from "./MessagesModal.vue";
 import WorkflowOptions from "./Options.vue";
 import RefactorConfirmationModal from "./RefactorConfirmationModal.vue";
+import SaveChangesModal from "./SaveChangesModal.vue";
 import StateUpgradeModal from "./StateUpgradeModal.vue";
 import WorkflowGraph from "./WorkflowGraph.vue";
 import MarkdownEditor from "@/components/Markdown/MarkdownEditor.vue";
@@ -207,6 +209,7 @@ export default {
     components: {
         MarkdownEditor,
         FlexPanel,
+        SaveChangesModal,
         StateUpgradeModal,
         ToolPanel,
         FormDefault,
@@ -313,7 +316,6 @@ export default {
     data() {
         return {
             isCanvas: true,
-            markdownConfig: null,
             markdownText: null,
             versions: [],
             parameters: null,
@@ -341,6 +343,8 @@ export default {
             transform: { x: 0, y: 0, k: 1 },
             graphOffset: { left: 0, top: 0, width: 0, height: 0 },
             debounceTimer: null,
+            showSaveChangesModal: false,
+            navUrl: "",
         };
     },
     computed: {
@@ -702,14 +706,21 @@ export default {
             const runUrl = `/workflows/run?id=${this.id}`;
             this.onNavigate(runUrl);
         },
-        async onNavigate(url) {
+        async onNavigate(url, forceSave = false, ignoreChanges = false) {
             if (this.isNewTempWorkflow) {
                 await this.onCreate();
-            } else {
-                await this.onSave(true);
+            } else if (this.hasChanges && !forceSave && !ignoreChanges) {
+                // if there are changes, prompt user to save or discard or cancel
+                this.navUrl = url;
+                this.showSaveChangesModal = true;
+                return;
+            } else if (forceSave) {
+                // when forceSave is true, save the workflow before navigating
+                await this.onSave();
             }
 
             this.hasChanges = false;
+            await nextTick();
             this.$router.push(url);
         },
         onSave(hideProgress = false) {
@@ -787,8 +798,8 @@ export default {
 
             const report = data.report || {};
             const markdown = report.markdown || reportDefault;
+            this.report = report;
             this.markdownText = markdown;
-            this.markdownConfig = report;
             this.hideModal();
             this.stateMessages = getStateUpgradeMessages(data);
             const has_changes = this.stateMessages.length > 0;

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

@@ -0,0 +1,97 @@
+<script setup lang="ts">
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faSave, faTimes, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton, BModal } from "bootstrap-vue";
+import { ref } from "vue";
+
+import localize from "@/utils/localization";
+
+library.add(faSave, faTimes, faTrash);
+
+interface Props {
+    /** Show the save changes modal */
+    showModal: boolean;
+    /** The URL to navigate to before saving/ignoring changes */
+    navUrl: string;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    showModal: false,
+});
+
+const busy = ref(false);
+
+const emit = defineEmits<{
+    /** Proceed with or without saving the changes */
+    (e: "on-proceed", url: string, forceSave: boolean, ignoreChanges: boolean): void;
+    /** Update the nav URL prop */
+    (e: "update:nav-url", url: string): void;
+    /** Update the show modal boolean prop */
+    (e: "update:show-modal", showModal: boolean): void;
+}>();
+
+const title = localize("You have unsaved changes. Do you want to save them before proceeding?");
+const body = localize(
+    "Click 'Save' to save your changes and proceed, 'Don't Save' to discard them and proceed, or 'Cancel' to return to the editor."
+);
+
+const buttonTitles = {
+    cancel: localize("Do not run proceed and return to editor"),
+    dontSave: localize("Discard changes and proceed"),
+    save: localize("Save changes and proceed"),
+};
+
+function closeModal() {
+    emit("update:show-modal", false);
+    emit("update:nav-url", "");
+}
+
+function dontSave() {
+    busy.value = true;
+    emit("on-proceed", props.navUrl, false, true);
+}
+
+function saveChanges() {
+    busy.value = true;
+    closeModal();
+    emit("on-proceed", props.navUrl, true, false);
+}
+</script>
+
+<template>
+    <BModal :title="title" :visible="props.showModal" @close="closeModal" @hide="closeModal">
+        <div>
+            {{ body }}
+        </div>
+        <template v-slot:modal-footer>
+            <BButton
+                v-b-tooltip.noninteractive.hover
+                :title="buttonTitles['cancel']"
+                variant="secondary"
+                :disabled="busy"
+                @click="closeModal">
+                <FontAwesomeIcon :icon="faTimes" />
+                {{ localize("Cancel") }}
+            </BButton>
+            <BButton
+                v-b-tooltip.noninteractive.hover
+                :title="buttonTitles['dontSave']"
+                variant="danger"
+                :disabled="busy"
+                @click="dontSave">
+                <FontAwesomeIcon :icon="faTrash" />
+                {{ localize("Don't Save") }}
+            </BButton>
+            <BButton
+                v-b-tooltip.noninteractive.hover
+                :title="buttonTitles['save']"
+                variant="primary"
+                :disabled="busy"
+                @click="saveChanges">
+                <FontAwesomeIcon :icon="faSave" />
+                {{ localize("Save") }}
+            </BButton>
+        </template>
+    </BModal>
+</template>

client/src/stores/workflowStepStore.ts

@@ -340,6 +340,7 @@ export const useWorkflowStepStore = defineScopedStore("workflowStepStore", (work
 
         del(steps.value, stepId.toString());
         del(stepExtraInputs.value, stepId);
+        del(stepMapOver.value, stepId.toString());
     }
 
     return {

doc/source/admin/galaxy_options.rst

@@ -1453,7 +1453,7 @@
     This option has no effect if the file specified by
     object_store_config_file exists. Otherwise, if this option is set,
     it overrides any other objectstore settings.
-    The syntax, available instrumenters, and documentation of their
+    The syntax, available storage plugins, and documentation of their
     options is explained in detail in the object store sample
     configuration file, `object_store_conf.sample.yml`
 :Default: ``None``
@@ -2606,8 +2606,20 @@
 
 :Description:
     The upload store is a temporary directory in which files uploaded
-    by the tus middleware or server will be placed. Defaults to
-    new_file_path if not set.
+    by the tus middleware or server for user uploads will be placed.
+    Defaults to new_file_path if not set.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``tus_upload_store_job_files``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    The upload store is a temporary directory in which files uploaded
+    by the tus middleware or server for remote job files (Pulsar) will
+    be placed. Defaults to tus_upload_store if not set.
 :Default: ``None``
 :Type: str
 
@@ -4030,6 +4042,23 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~
+``oidc_scope_prefix``
+~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Sets the prefix for OIDC scopes specific to this Galaxy instance.
+    If an API call is made against this Galaxy instance using an OIDC
+    bearer token, any scopes must be prefixed with this value e.g.
+    https://galaxyproject.org/api. More concretely, to request all
+    permissions that the user has, the scope would have to be
+    specified as "<prefix>:*". e.g "https://galaxyproject.org/api:*".
+    Currently, only * is recognised as a valid scope, and future
+    iterations may provide more fine-grained scopes.
+:Default: ``https://galaxyproject.org/api``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~
 ``auth_config_file``
 ~~~~~~~~~~~~~~~~~~~~
@@ -5439,9 +5468,9 @@
 :Type: str
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``help_forum_tool_panel_integration_enabled``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_help_forum_tool_panel_integration``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
     Enable the integration of the Galaxy Help Forum in the tool panel.