Merge branch 'release_24.1' into dev

client/src/api/schema/schema.ts

@@ -5512,6 +5512,15 @@ export interface components {
              */
             url: string;
         };
+        /** GroupUpdatePayload */
+        GroupUpdatePayload: {
+            /** name of the group */
+            name?: string | null;
+            /** role IDs */
+            role_ids?: string[] | null;
+            /** user IDs */
+            user_ids?: string[] | null;
+        };
         /** GroupUserListResponse */
         GroupUserListResponse: components["schemas"]["GroupUserResponse"][];
         /** GroupUserResponse */
@@ -15744,7 +15753,7 @@ export interface operations {
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["GroupCreatePayload"];
+                "application/json": components["schemas"]["GroupUpdatePayload"];
             };
         };
         responses: {

client/src/components/FilesDialog/FilesDialog.vue

@@ -409,6 +409,7 @@ onMounted(() => {
         :is-busy="isBusy"
         :items="items"
         :items-provider="itemsProvider"
+        :provider-url="currentDirectory?.url"
         :total-items="totalItems"
         :modal-show="modalShow"
         :modal-static="modalStatic"

client/src/components/Form/Elements/FormData/FormData.test.js

@@ -3,6 +3,8 @@ import { mount } from "@vue/test-utils";
 import { PiniaVuePlugin } from "pinia";
 import { dispatchEvent, getLocalVue } from "tests/jest/helpers";
 
+import { testDatatypesMapper } from "@/components/Datatypes/test_fixtures";
+import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
 import { useEventStore } from "@/stores/eventStore";
 
 import MountTarget from "./FormData.vue";
@@ -15,6 +17,8 @@ let eventStore;
 function createTarget(propsData) {
     const pinia = createTestingPinia({ stubActions: false });
     eventStore = useEventStore();
+    const datatypesStore = useDatatypesMapperStore();
+    datatypesStore.datatypesMapper = testDatatypesMapper;
     return mount(MountTarget, {
         localVue,
         propsData,

client/src/components/Form/Elements/FormData/FormData.vue

@@ -7,6 +7,7 @@ import { BAlert, BButton, BButtonGroup, BCollapse, BFormCheckbox, BTooltip } fro
 import { computed, onMounted, type Ref, ref, watch } from "vue";
 
 import { getGalaxyInstance } from "@/app";
+import { useDatatypesMapper } from "@/composables/datatypesMapper";
 import { useUid } from "@/composables/utils/uid";
 import { type EventData, useEventStore } from "@/stores/eventStore";
 import { orList } from "@/utils/strings";
@@ -35,6 +36,7 @@ const props = withDefaults(
         };
         extensions?: Array<string>;
         type?: string;
+        collectionTypes?: Array<string>;
         flavor?: string;
         tag?: string;
     }>(),
@@ -45,14 +47,16 @@ const props = withDefaults(
         value: undefined,
         extensions: () => [],
         type: "data",
+        collectionTypes: undefined,
         flavor: undefined,
         tag: undefined,
     }
 );
 
 const eventStore = useEventStore();
+const { datatypesMapper } = useDatatypesMapper();
 
-const $emit = defineEmits(["input"]);
+const $emit = defineEmits(["input", "alert"]);
 
 // Determines wether values should be processed as linked or unlinked
 const currentLinked = ref(true);
@@ -302,6 +306,10 @@ function getSourceType(val: DataOption) {
 function handleIncoming(incoming: Record<string, unknown>, partial = true) {
     if (incoming) {
         const values = Array.isArray(incoming) ? incoming : [incoming];
+        const extensions = values.map((v) => v.extension || v.elements_datatypes).filter((v) => (v ? true : false));
+        if (!canAcceptDatatype(extensions)) {
+            return false;
+        }
         if (values.length > 0) {
             const incomingValues: Array<DataOption> = [];
             values.forEach((v) => {
@@ -311,14 +319,28 @@ function handleIncoming(incoming: Record<string, unknown>, partial = true) {
                 const newName = v.name ? v.name : newId;
                 const newSrc =
                     v.src || (v.history_content_type === "dataset_collection" ? SOURCE.COLLECTION : SOURCE.DATASET);
-                const newValue = {
+                const newValue: DataOption = {
                     id: newId,
                     src: newSrc,
+                    batch: false,
+                    map_over_type: undefined,
                     hid: newHid,
                     name: newName,
                     keep: true,
                     tags: [],
                 };
+                if (v.collection_type && props.collectionTypes?.length > 0) {
+                    if (!props.collectionTypes.includes(v.collection_type)) {
+                        const mapOverType = props.collectionTypes.find((collectionType) =>
+                            v.collection_type.endsWith(collectionType)
+                        );
+                        if (!mapOverType) {
+                            return false;
+                        }
+                        newValue["batch"] = true;
+                        newValue["map_over_type"] = mapOverType;
+                    }
+                }
                 // Verify that new value has corresponding option
                 const keepKey = `${newId}_${newSrc}`;
                 const existingOptions = props.options && props.options[newSrc];
@@ -349,6 +371,7 @@ function handleIncoming(incoming: Record<string, unknown>, partial = true) {
             }
         }
     }
+    return true;
 }
 
 /**
@@ -372,10 +395,36 @@ function onBrowse() {
     }
 }
 
+function canAcceptDatatype(itemDatatypes: string | Array<string>) {
+    if (!(props.extensions?.length > 0)) {
+        return true;
+    }
+    let datatypes: Array<string>;
+    if (!Array.isArray(itemDatatypes)) {
+        datatypes = [itemDatatypes];
+    } else {
+        datatypes = itemDatatypes;
+    }
+    const incompatibleItem = datatypes.find(
+        (extension) => !datatypesMapper.value?.isSubTypeOfAny(extension, props.extensions)
+    );
+    if (incompatibleItem) {
+        return false;
+    }
+    return true;
+}
+
 // Drag/Drop event handlers
 function onDragEnter(evt: MouseEvent) {
     const eventData = eventStore.getDragData();
     if (eventData) {
+        const extensions = (eventData.extension as string) || (eventData.elements_datatypes as Array<string>);
+        if (!canAcceptDatatype(extensions)) {
+            currentHighlighting.value = "warning";
+            $emit("alert", `${extensions} is not an acceptable format for this parameter.`);
+        } else {
+            currentHighlighting.value = "success";
+        }
         dragTarget.value = evt.target;
         dragData.value = eventData;
     }
@@ -384,23 +433,24 @@ function onDragEnter(evt: MouseEvent) {
 function onDragLeave(evt: MouseEvent) {
     if (dragTarget.value === evt.target) {
         currentHighlighting.value = null;
-    }
-}
-
-function onDragOver() {
-    if (dragData.value !== null) {
-        currentHighlighting.value = "warning";
+        $emit("alert", undefined);
     }
 }
 
 function onDrop() {
     if (dragData.value) {
+        let accept = false;
         if (eventStore.multipleDragData) {
-            handleIncoming(Object.values(dragData.value) as any, false);
+            accept = handleIncoming(Object.values(dragData.value) as any, false);
+        } else {
+            accept = handleIncoming(dragData.value);
+        }
+        if (accept) {
+            currentHighlighting.value = "success";
         } else {
-            handleIncoming(dragData.value);
+            currentHighlighting.value = "warning";
         }
-        currentHighlighting.value = "success";
+        $emit("alert", undefined);
         dragData.value = null;
         clearHighlighting();
     }
@@ -468,7 +518,7 @@ const noOptionsWarningMessage = computed(() => {
         :class="currentHighlighting && `ui-dragover-${currentHighlighting}`"
         @dragenter.prevent="onDragEnter"
         @dragleave.prevent="onDragLeave"
-        @dragover.prevent="onDragOver"
+        @dragover.prevent
         @drop.prevent="onDrop">
         <div class="d-flex flex-column">
             <BButtonGroup v-if="variant && variant.length > 1" buttons class="align-self-start">

client/src/components/Form/Elements/FormData/types.ts

@@ -3,6 +3,7 @@ export type DataOption = {
     hid: number;
     is_dataset?: boolean;
     keep: boolean;
+    batch: boolean;
     map_over_type?: string;
     name: string;
     src: string;

client/src/components/Form/FormElement.test.js

@@ -30,7 +30,7 @@ describe("FormElement", () => {
         const error = wrapper.find(".ui-form-error-text");
         expect(error.text()).toBe("error_text");
 
-        await wrapper.setProps({ error: "" });
+        await wrapper.setProps({ error: undefined });
         const no_error = wrapper.findAll(".ui-form-error");
         expect(no_error.length).toBe(0);
 

client/src/components/Form/FormElement.vue

@@ -127,7 +127,7 @@ function onConnect() {
 
 const isHidden = computed(() => attrs.value["hidden"]);
 const elementId = computed(() => `form-element-${props.id}`);
-const hasAlert = computed(() => Boolean(props.error || props.warning));
+const hasAlert = computed(() => alerts.value.length > 0);
 const showPreview = computed(() => (collapsed.value && attrs.value["collapsible_preview"]) || props.disabled);
 const showField = computed(() => !collapsed.value && !props.disabled);
 
@@ -174,6 +174,16 @@ const isEmpty = computed(() => {
 const isRequired = computed(() => attrs.value["optional"] === false);
 const isRequiredType = computed(() => props.type !== "boolean");
 const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !== undefined);
+const formAlert = ref<string>();
+const alerts = computed(() => {
+    return [formAlert.value, props.error, props.warning]
+        .filter((v) => v !== undefined && v !== null)
+        .map((v) => linkify(sanitize(v!, { USE_PROFILES: { html: true } })));
+});
+
+function onAlert(value: string | undefined) {
+    formAlert.value = value;
+}
 </script>
 
 <template>
@@ -182,11 +192,9 @@ const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !
         :id="elementId"
         class="ui-form-element section-row"
         :class="{ alert: hasAlert, 'alert-info': hasAlert }">
-        <div v-if="hasAlert" class="ui-form-error">
+        <div v-for="(alert, index) in alerts" :key="index" class="ui-form-error">
             <FontAwesomeIcon class="mr-1" icon="fa-exclamation" />
-            <span
-                class="ui-form-error-text"
-                v-html="linkify(sanitize(props.error || props.warning, { USE_PROFILES: { html: true } }))" />
+            <span class="ui-form-error-text" v-html="alert" />
         </div>
 
         <div class="ui-form-title">
@@ -288,7 +296,9 @@ const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !
                 :optional="attrs.optional"
                 :options="attrs.options"
                 :tag="attrs.tag"
-                :type="props.type" />
+                :type="props.type"
+                :collection-types="attrs.collection_types"
+                @alert="onAlert" />
             <FormDrilldown
                 v-else-if="props.type === 'drill_down'"
                 :id="id"

client/src/components/SelectionDialog/SelectionDialog.vue

@@ -27,6 +27,7 @@ interface Props {
     isEncoded?: boolean;
     items?: SelectionItem[];
     itemsProvider?: ItemsProvider;
+    providerUrl?: string;
     totalItems?: number;
     leafIcon?: string;
     modalShow?: boolean;
@@ -48,6 +49,7 @@ const props = withDefaults(defineProps<Props>(), {
     isEncoded: false,
     items: () => [],
     itemsProvider: undefined,
+    providerUrl: undefined,
     totalItems: 0,
     leafIcon: "fa fa-file-o",
     modalShow: true,
@@ -127,6 +129,16 @@ watch(
         filtered(props.items);
     }
 );
+
+watch(
+    () => props.providerUrl,
+    () => {
+        // We need to reset the current page when drilling down sub-folders
+        if (props.itemsProvider !== undefined) {
+            currentPage.value = 1;
+        }
+    }
+);
 </script>
 
 <template>

lib/galaxy/managers/groups.py

@@ -17,7 +17,10 @@
 from galaxy.model.db.user import get_users_by_ids
 from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.schema.fields import Security
-from galaxy.schema.groups import GroupCreatePayload
+from galaxy.schema.groups import (
+    GroupCreatePayload,
+    GroupUpdatePayload,
+)
 from galaxy.structured_app import MinimalManagerApp
 
 
@@ -76,7 +79,7 @@ def show(self, trans: ProvidesAppContext, group_id: int):
         item["roles_url"] = self._url_for(trans, "group_roles", group_id=encoded_id)
         return item
 
-    def update(self, trans: ProvidesAppContext, group_id: int, payload: GroupCreatePayload):
+    def update(self, trans: ProvidesAppContext, group_id: int, payload: GroupUpdatePayload):
         """
         Modifies a group.
         """
@@ -86,13 +89,19 @@ def update(self, trans: ProvidesAppContext, group_id: int, payload: GroupCreateP
             self._check_duplicated_group_name(sa_session, name)
             group.name = name
             sa_session.add(group)
-        user_ids = payload.user_ids
-        users = get_users_by_ids(sa_session, user_ids)
-        role_ids = payload.role_ids
-        roles = get_roles_by_ids(sa_session, role_ids)
+
+        users = None
+        if payload.user_ids is not None:
+            users = get_users_by_ids(sa_session, payload.user_ids)
+
+        roles = None
+        if payload.role_ids is not None:
+            roles = get_roles_by_ids(sa_session, payload.role_ids)
+
         self._app.security_agent.set_entity_group_associations(
             groups=[group], roles=roles, users=users, delete_existing_assocs=False
         )
+
         with transaction(sa_session):
             sa_session.commit()