Merge branch 'release_24.0' into dev

client/src/components/DragGhost.vue

@@ -25,7 +25,7 @@ const name = computed(() => {
 
 <template>
     <span id="drag-ghost" class="py-2 px-3 rounded">
-        <FontAwesomeIcon icon="paper-plane" class="mr-1" />
+        <FontAwesomeIcon :icon="faPaperPlane" class="mr-1" />
         <TextShort class="font-weight-bold" :text="name" />
     </span>
 </template>

client/src/components/Grid/configs/histories.ts

@@ -32,6 +32,7 @@ type SortKeyLiteral = "create_time" | "name" | "update_time" | undefined;
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
     const { data, headers } = await historiesFetcher({
+        view: "summary",
         limit,
         offset,
         search,

client/src/components/Grid/configs/historiesShared.ts

@@ -22,6 +22,8 @@ type SortKeyLiteral = "create_time" | "name" | "update_time" | undefined;
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
     const { data, headers } = await historiesFetcher({
+        view: "summary",
+        keys: "username,create_time",
         limit,
         offset,
         search,

client/src/components/History/Content/ContentItem.vue

@@ -317,9 +317,12 @@ function unexpandedClick(event: Event) {
         :data-state="dataState"
         tabindex="0"
         role="button"
+        draggable
+        @dragstart="onDragStart"
+        @dragend="onDragEnd"
         @keydown="onKeyDown">
         <!-- eslint-disable-next-line vuejs-accessibility/click-events-have-key-events, vuejs-accessibility/no-static-element-interactions -->
-        <div class="p-1 cursor-pointer" draggable @dragstart="onDragStart" @dragend="onDragEnd" @click.stop="onClick">
+        <div class="p-1 cursor-pointer" @click.stop="onClick">
             <div class="d-flex justify-content-between">
                 <span class="p-1" data-description="content item header info">
                     <BButton v-if="selectable" class="selector p-0" @click.stop="emit('update:selected', !selected)">

client/src/components/History/CurrentHistory/HistoryPanel.vue

@@ -212,6 +212,36 @@ watch(
     }
 );
 
+function dragSameHistory() {
+    return getDragData().sameHistory;
+}
+
+function getDragData() {
+    const eventStore = useEventStore();
+    const multiple = eventStore.multipleDragData;
+    let data: HistoryItem[] | undefined;
+    let historyId: string | undefined;
+    try {
+        if (multiple) {
+            const dragData = eventStore.getDragData() as Record<string, HistoryItem>;
+            // set historyId to the first history_id in the multiple drag data
+            const firstItem = Object.values(dragData)[0];
+            if (firstItem) {
+                historyId = firstItem.history_id;
+            }
+            data = Object.values(dragData);
+        } else {
+            data = [eventStore.getDragData() as HistoryItem];
+            if (data[0]) {
+                historyId = data[0].history_id;
+            }
+        }
+    } catch (error) {
+        // this was not a valid object for this dropzone, ignore
+    }
+    return { data, sameHistory: historyId === props.history.id, multiple };
+}
+
 function getHighlight(item: HistoryItem) {
     if (unref(isLoading)) {
         return undefined;
@@ -319,45 +349,33 @@ function onOperationError(error: any) {
 }
 
 function onDragEnter(e: DragEvent) {
+    if (dragSameHistory()) {
+        return;
+    }
     dragTarget.value = e.target;
     showDropZone.value = true;
 }
 
+function onDragOver(e: DragEvent) {
+    if (dragSameHistory()) {
+        return;
+    }
+    e.preventDefault();
+}
+
 function onDragLeave(e: DragEvent) {
+    if (dragSameHistory()) {
+        return;
+    }
     if (dragTarget.value === e.target) {
         showDropZone.value = false;
     }
 }
 
-async function onDrop(evt: any) {
-    const eventStore = useEventStore();
+async function onDrop() {
     showDropZone.value = false;
-    let data: HistoryItem[] | undefined;
-    let historyId: string | undefined;
-    const multiple = eventStore.multipleDragData;
-    try {
-        if (multiple) {
-            const dragData = eventStore.getDragData() as Record<string, HistoryItem>;
-            // set historyId to the first history_id in the multiple drag data
-            const firstItem = Object.values(dragData)[0];
-            if (firstItem) {
-                historyId = firstItem.history_id;
-            }
-            data = Object.values(dragData);
-        } else {
-            data = [eventStore.getDragData() as HistoryItem];
-            if (data[0]) {
-                historyId = data[0].history_id;
-            }
-        }
-    } catch (error) {
-        // this was not a valid object for this dropzone, ignore
-    }
-
-    if (!data) {
-        return;
-    } else if (historyId === props.history.id) {
-        Toast.error("Cannot copy to the same history");
+    const { data, sameHistory, multiple } = getDragData();
+    if (!data || sameHistory) {
         return;
     }
 
@@ -486,7 +504,7 @@ function setItemDragstart(
                 class="history-layout d-flex flex-column w-100 h-100"
                 @drop.prevent="onDrop"
                 @dragenter.prevent="onDragEnter"
-                @dragover.prevent
+                @dragover="onDragOver"
                 @dragleave.prevent="onDragLeave">
                 <slot name="navigation" :history="history" />
 

client/src/components/TagsMultiselect/HeadlessMultiselect.test.ts

@@ -20,7 +20,7 @@ describe("HeadlessMultiselect", () => {
         });
     };
 
-    const sampleOptions = ["#named", "#named_2", "#named_3", "abc", "def", "ghi"];
+    const sampleOptions = ["name:named", "name:named_2", "name:named_3", "abc", "def", "ghi"];
 
     const selectors = {
         openButton: ".toggle-button",
@@ -197,27 +197,27 @@ describe("HeadlessMultiselect", () => {
             const input = await open(wrapper);
 
             await keyPress(input, "Enter");
-            expect(wrapper.emitted()["input"]?.[0]?.[0]).toEqual(["#named"]);
+            expect(wrapper.emitted()["input"]?.[0]?.[0]).toEqual(["name:named"]);
 
             await keyPress(input, "ArrowDown");
             await keyPress(input, "Enter");
-            expect(wrapper.emitted()["input"]?.[1]?.[0]).toEqual(["#named_2"]);
+            expect(wrapper.emitted()["input"]?.[1]?.[0]).toEqual(["name:named_2"]);
         });
 
         it("deselects options via keyboard", async () => {
             const wrapper = mountWithProps({
                 options: sampleOptions,
-                selected: ["#named", "#named_2", "#named_3"],
+                selected: ["name:named", "name:named_2", "name:named_3"],
             });
 
             const input = await open(wrapper);
 
             await keyPress(input, "Enter");
-            expect(wrapper.emitted()["input"]?.[0]?.[0]).toEqual(["#named_2", "#named_3"]);
+            expect(wrapper.emitted()["input"]?.[0]?.[0]).toEqual(["name:named_2", "name:named_3"]);
 
             await keyPress(input, "ArrowDown");
             await keyPress(input, "Enter");
-            expect(wrapper.emitted()["input"]?.[1]?.[0]).toEqual(["#named", "#named_3"]);
+            expect(wrapper.emitted()["input"]?.[1]?.[0]).toEqual(["name:named", "name:named_3"]);
         });
 
         it("allows for adding new options", async () => {
@@ -243,26 +243,26 @@ describe("HeadlessMultiselect", () => {
             const options = wrapper.findAll(selectors.option);
 
             await options.at(0).trigger("click");
-            expect(wrapper.emitted()["input"]?.[0]?.[0]).toEqual(["#named"]);
+            expect(wrapper.emitted()["input"]?.[0]?.[0]).toEqual(["name:named"]);
 
             await options.at(1).trigger("click");
-            expect(wrapper.emitted()["input"]?.[1]?.[0]).toEqual(["#named_2"]);
+            expect(wrapper.emitted()["input"]?.[1]?.[0]).toEqual(["name:named_2"]);
         });
 
         it("deselects options with mouse", async () => {
             const wrapper = mountWithProps({
                 options: sampleOptions,
-                selected: ["#named", "#named_2", "#named_3"],
+                selected: ["name:named", "name:named_2", "name:named_3"],
             });
 
             await open(wrapper);
             const options = wrapper.findAll(selectors.option);
 
             await options.at(0).trigger("click");
-            expect(wrapper.emitted()["input"]?.[0]?.[0]).toEqual(["#named_2", "#named_3"]);
+            expect(wrapper.emitted()["input"]?.[0]?.[0]).toEqual(["name:named_2", "name:named_3"]);
 
             await options.at(1).trigger("click");
-            expect(wrapper.emitted()["input"]?.[1]?.[0]).toEqual(["#named", "#named_3"]);
+            expect(wrapper.emitted()["input"]?.[1]?.[0]).toEqual(["name:named", "name:named_3"]);
         });
     });
 });

client/src/components/TagsMultiselect/HeadlessMultiselect.vue

@@ -15,6 +15,7 @@ import { computed, nextTick, ref, watch } from "vue";
 import Vue2Teleport from "vue2-teleport";
 
 import { useUid } from "@/composables/utils/uid";
+import { normalizeTag } from "@/stores/userTagsStore";
 
 library.add(faCheck, faChevronUp, faPlus, faTags, faTimes);
 
@@ -147,6 +148,8 @@ function getOptionWithId(id: number) {
  * was not part of the provided options
  */
 function onOptionSelected(option: string) {
+    option = normalizeTag(option);
+
     if (!optionsAsSet.value.has(option)) {
         emit("addOption", option);
         return;
@@ -318,7 +321,7 @@ whenever(isOpen, async () => {
                     :data-parent-id="props.id"
                     class="headless-multiselect__option"
                     role="option"
-                    :aria-selected="props.selected.includes(option)"
+                    :aria-selected="props.selected.includes(normalizeTag(option))"
                     :class="{
                         invalid: i === 0 && !searchValueValid,
                         highlighted: highlightedOption === i,
@@ -332,7 +335,7 @@ whenever(isOpen, async () => {
                         {{ option }}
                     </span>
 
-                    <span v-if="props.selected.includes(option)" class="headless-multiselect__info">
+                    <span v-if="props.selected.includes(normalizeTag(option))" class="headless-multiselect__info">
                         <template v-if="highlightedOption === i">
                             <FontAwesomeIcon
                                 class="headless-multiselect__needs-highlight"

client/src/components/TagsMultiselect/StatelessTags.test.js

@@ -3,11 +3,11 @@ import { useToast } from "composables/toast";
 import { getLocalVue } from "tests/jest/helpers";
 import { computed } from "vue";
 
-import { useUserTagsStore } from "@/stores/userTagsStore";
+import { normalizeTag, useUserTagsStore } from "@/stores/userTagsStore";
 
 import StatelessTags from "./StatelessTags";
 
-const autocompleteTags = ["#named_user_tag", "abc", "my_tag"];
+const autocompleteTags = ["name:named_user_tag", "abc", "my_tag"];
 const toggleButton = ".toggle-button";
 
 const localVue = getLocalVue();
@@ -28,6 +28,12 @@ useUserTagsStore.mockReturnValue({
     onMultipleNewTagsSeen: jest.fn(),
 });
 
+function normalize(tag) {
+    return tag.replace(/^#/, "name:");
+}
+
+normalizeTag.mockImplementation(normalize);
+
 jest.mock("composables/toast");
 const warningMock = jest.fn((message, title) => {
     return { message, title };
@@ -88,7 +94,7 @@ describe("StatelessTags", () => {
         expect(visibleOptions.length).toBe(autocompleteTags.length);
 
         visibleOptions.wrappers.forEach((option, i) => {
-            expect(option.text()).toContain(autocompleteTags[i]);
+            expect(normalize(option.text())).toContain(autocompleteTags[i]);
         });
     });
 

client/src/components/TagsMultiselect/StatelessTags.vue

@@ -111,7 +111,7 @@ function onTagClicked(tag: string) {
 
             <HeadlessMultiselect
                 :options="userTags"
-                :selected="tags"
+                :selected="props.value"
                 :placeholder="props.placeholder"
                 :validator="isValid"
                 @addOption="onAddTag"

client/src/stores/userTagsStore.ts

@@ -20,13 +20,13 @@ class UserTagStoreDatabase extends Dexie {
 
     constructor() {
         super("userTagStoreDatabase");
-        this.version(1).stores({ tags: "++id, userHash, lastUsed" });
+        this.version(2).stores({ tags: "++id, userHash, lastUsed, tag" });
     }
 }
 
 const maxDbEntriesPerUser = 10000;
 
-function normalizeTag(tag: string) {
+export function normalizeTag(tag: string) {
     return tag.replace(/^#/, "name:");
 }
 
@@ -113,12 +113,17 @@ export const useUserTagsStore = defineStore("userTagsStore", () => {
         await until(dbLoaded).toBe(true);
         tag = normalizeTag(tag);
 
-        const storedTag = tags.value.find((o) => o.tag === tag);
-        const id = storedTag?.id;
+        const dbTag = await db.tags.get({ tag });
 
-        if (id !== undefined) {
-            // put instead of update, because `removeOldestEntries` may have deleted this tag on init
-            await db.tags.put({ ...storedTag, lastUsed: Date.now() } as StoredTag, id);
+        if (dbTag) {
+            await db.tags.update(dbTag, { lastUsed: Date.now() });
+        } else {
+            const storedTag = tags.value.find((o) => o.tag === tag);
+            const id = storedTag?.id;
+
+            if (id !== undefined) {
+                await db.tags.add({ ...storedTag, lastUsed: Date.now() } as StoredTag);
+            }
         }
     }
 

lib/galaxy/managers/histories.py

@@ -215,6 +215,7 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
             total_matches = None
         if payload.sort_by == "username":
             sort_column = model.User.username
+            stmt = stmt.add_columns(sort_column)
         else:
             sort_column = getattr(model.History, payload.sort_by)
         if payload.sort_desc:

lib/galaxy/webapps/galaxy/api/histories.py

@@ -191,7 +191,7 @@ class FastAPIHistories:
                 trans, serialization_params, filter_query_params, deleted_only=deleted, all_histories=all
             )
         else:
-            payload = HistoryIndexQueryPayload.construct(
+            payload = HistoryIndexQueryPayload.model_construct(
                 show_own=show_own,
                 show_published=show_published,
                 show_shared=show_shared,
@@ -201,7 +201,9 @@ class FastAPIHistories:
                 offset=offset,
                 search=search,
             )
-            entries, total_matches = self.service.index_query(trans, payload, include_total_count=True)
+            entries, total_matches = self.service.index_query(
+                trans, payload, serialization_params, include_total_count=True
+            )
             response.headers["total_matches"] = str(total_matches)
             return entries
 

lib/galaxy/webapps/galaxy/services/datasets.py

@@ -891,12 +891,11 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
 
         extra_info = None
         mode = kwargs.get("mode", "Auto")
-        indexer = None
 
         # Coverage mode uses index data.
         if mode == "Coverage":
             # Get summary using minimal cutoffs.
-            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
+            indexer = self._get_indexer(trans, dataset)
             return indexer.get_data(chrom, low, high, **kwargs)
 
         # TODO:
@@ -906,7 +905,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         # If mode is Auto, need to determine what type of data to return.
         if mode == "Auto":
             # Get stats from indexer.
-            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
+            indexer = self._get_indexer(trans, dataset)
             stats = indexer.get_data(chrom, low, high, stats=True)
 
             # If stats were requested, return them.
@@ -956,8 +955,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
                 )
 
             # Get mean depth.
-            if not indexer:
-                indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
+            indexer = self._get_indexer(trans, dataset)
             stats = indexer.get_data(chrom, low, high, stats=True)
             mean_depth = stats["data"]["mean"]
 
@@ -1008,3 +1006,11 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         data = data_provider.get_data(**kwargs)
 
         return data
+
+    def _get_indexer(self, trans, dataset):
+        indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
+        if indexer is None:
+            msg = f"No indexer available for dataset {self.encode_id(dataset.id)}"
+            log.exception(msg)
+            raise galaxy_exceptions.ObjectNotFound(msg)
+        return indexer

lib/galaxy/webapps/galaxy/services/histories.py

@@ -216,6 +216,7 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
         self,
         trans,
         payload: HistoryIndexQueryPayload,
+        serialization_params: SerializationParams,
         include_total_count: bool = False,
     ) -> Tuple[List[AnyHistoryView], int]:
         """Return a list of History accessible by the user
@@ -223,10 +224,9 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
         :rtype:     list
         :returns:   dictionaries containing History details
         """
-        serialization_params = SerializationParams(default_view="detailed")
         entries, total_matches = self.manager.index_query(trans, payload, include_total_count)
         return (
-            [self._serialize_history(trans, entry, serialization_params) for entry in entries],
+            [self._serialize_history(trans, entry, serialization_params, default_view="summary") for entry in entries],
             total_matches,
         )
 

lib/galaxy/webapps/galaxy/services/users.py

@@ -122,10 +122,9 @@ class UsersService(ServiceBase):
     def _anon_user_api_value(self, trans: ProvidesHistoryContext):
         """Return data for an anonymous user, truncated to only usage and quota_percent"""
         if not trans.user and not trans.history:
-            # Can't return info about this user, may not have a history yet.
-            # return {}
-            raise glx_exceptions.MessageException(err_msg="The user has no history, which should always be the case.")
-        usage = self.quota_agent.get_usage(trans, history=trans.history)
+            usage = None
+        else:
+            usage = self.quota_agent.get_usage(trans, history=trans.history)
         percent = self.quota_agent.get_percent(trans=trans, usage=usage)
         usage = usage or 0
         return {

lib/galaxy_test/api/test_histories.py

@@ -140,6 +140,56 @@ class TestHistoriesApi(ApiTestCase, BaseHistories):
         assert len(index_response) == 1
         assert index_response[0]["name"] == expected_history_name
 
+    def test_index_views(self):
+        # Make sure there is at least one history
+        self._create_history(f"TestHistoryForViews_{uuid4()}")["id"]
+        # By default the view is summary
+        index_response = self._get("histories").json()
+        for history in index_response:
+            assert "state" not in history
+
+        # Change the view to detailed
+        index_response = self._get("histories?view=detailed").json()
+        for history in index_response:
+            assert "state" in history
+
+        # Expect only specific keys
+        expected_keys = ["name"]
+        unexpected_keys = ["deleted", "state"]
+        index_response = self._get(f"histories?keys={','.join(expected_keys)}").json()
+        for history in index_response:
+            for key in expected_keys:
+                assert key in history
+            for key in unexpected_keys:
+                assert key not in history
+
+    def test_index_search_mode_views(self):
+        # Make sure there is at least one history
+        expected_name_contains = "SearchMode"
+        self._create_history(f"TestHistory{expected_name_contains}_{uuid4()}")["id"]
+        # By default the view is summary
+        data = dict(search=expected_name_contains, show_published=False)
+        index_response = self._get("histories", data=data).json()
+        for history in index_response:
+            assert "state" not in history
+
+        # Change the view to detailed
+        data = dict(search=expected_name_contains, show_published=False)
+        index_response = self._get("histories?view=detailed", data=data).json()
+        for history in index_response:
+            assert "state" in history
+
+        # Expect only specific keys
+        expected_keys = ["name"]
+        unexpected_keys = ["deleted", "state"]
+        data = dict(search=expected_name_contains, show_published=False, keys=",".join(expected_keys))
+        index_response = self._get("histories", data=data).json()
+        for history in index_response:
+            for key in expected_keys:
+                assert key in history
+            for key in unexpected_keys:
+                assert key not in history
+
     def test_index_case_insensitive_contains_query(self):
         # Create the histories with a different user to ensure the test
         # is not conflicted with the current user's histories.

test/integration/oidc/test_auth_oidc.py

@@ -296,7 +296,8 @@ class TestGalaxyOIDCLoginIntegration(AbstractTestCases.BaseKeycloakIntegrationTe
         response = session.get(response.json()["redirect_uri"], verify=False)
         # make sure we can no longer request the user
         response = session.get(self._api_url("users/current"))
-        self._assert_status_code_is(response, 400)
+        self._assert_status_code_is(response, 200)
+        assert "email" not in response.json()
 
     def test_auth_by_access_token_logged_in_once(self):
         # login at least once