From b84f94590974b90a6ef3c49fc9d368dcbd1c6529 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Thu, 14 Mar 2024 15:19:24 -0500
Subject: [PATCH 01/17] [23.1] Handle missing indexer for a dataset

In case a dataset does not have an indexer, raise an exception.
Fixes the bug mentioned in https://github.com/galaxyproject/galaxy/pull/17639#issuecomment-1995990448
---
 lib/galaxy/webapps/galaxy/services/datasets.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/services/datasets.py b/lib/galaxy/webapps/galaxy/services/datasets.py
index 0d1667a505d..d08fb1a7f33 100644
--- a/lib/galaxy/webapps/galaxy/services/datasets.py
+++ b/lib/galaxy/webapps/galaxy/services/datasets.py
@@ -868,7 +868,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         # 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:
@@ -878,7 +878,7 @@ 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.
@@ -929,7 +929,7 @@ 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"]
 
@@ -981,3 +981,12 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         data = data_provider.get_data(**kwargs)
 
         return data
+
+    def _get_indexer(self, trans, dataset):
+        try:
+            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
+            if indexer is None:
+                raise Exception("No indexer available for this dataset")
+            return indexer
+        except Exception as e:
+            raise galaxy_exceptions.ObjectNotFound(f"Error getting indexer: {util.unicodify(e)}")

From 552fe077cc1522d0dbb268385031e79e4aea36f6 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Mar 2024 16:21:51 +0100
Subject: [PATCH 02/17] Replace deprecated `Model.construct`

---
 lib/galaxy/webapps/galaxy/api/histories.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index c8b23b35c78..410a62410dd 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/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,

From 4fb3cbcd0e0c3bbd6e05b660c67ed4b49d9f8d5a Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Mar 2024 16:41:02 +0100
Subject: [PATCH 03/17] Fix missing serialization_params when listing histories
 in "query mode"

---
 lib/galaxy/webapps/galaxy/api/histories.py      | 4 +++-
 lib/galaxy/webapps/galaxy/services/histories.py | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index 410a62410dd..743d31a48cc 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -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
 
diff --git a/lib/galaxy/webapps/galaxy/services/histories.py b/lib/galaxy/webapps/galaxy/services/histories.py
index ab3fe0e69dc..f759c97fa35 100644
--- a/lib/galaxy/webapps/galaxy/services/histories.py
+++ b/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
@@ -223,7 +224,6 @@ 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],

From 2289f6766d0a48590c37b187c5c54889b5522787 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Mar 2024 16:42:15 +0100
Subject: [PATCH 04/17] Use summary view in the rest of history lists

---
 client/src/components/Grid/configs/histories.ts       | 1 +
 client/src/components/Grid/configs/historiesShared.ts | 1 +
 2 files changed, 2 insertions(+)

diff --git a/client/src/components/Grid/configs/histories.ts b/client/src/components/Grid/configs/histories.ts
index 8216cda7156..08201f24be0 100644
--- a/client/src/components/Grid/configs/histories.ts
+++ b/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,
diff --git a/client/src/components/Grid/configs/historiesShared.ts b/client/src/components/Grid/configs/historiesShared.ts
index 65a65e8a54a..df3fc116438 100644
--- a/client/src/components/Grid/configs/historiesShared.ts
+++ b/client/src/components/Grid/configs/historiesShared.ts
@@ -22,6 +22,7 @@ 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,

From b77ee5c54175d455c427ab6efd5214289b7574ba Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Mar 2024 17:36:21 +0100
Subject: [PATCH 05/17] Set the default view as summary in index_query

For consistency with the existing history index action.
---
 lib/galaxy/webapps/galaxy/services/histories.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/services/histories.py b/lib/galaxy/webapps/galaxy/services/histories.py
index f759c97fa35..3d75284d07e 100644
--- a/lib/galaxy/webapps/galaxy/services/histories.py
+++ b/lib/galaxy/webapps/galaxy/services/histories.py
@@ -226,7 +226,7 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
         """
         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,
         )
 

From 216036cbdd0e52141f3ab208a4582b3ef9b2163d Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Mar 2024 17:45:14 +0100
Subject: [PATCH 06/17] Add API tests for history index serialization

In both modes
---
 lib/galaxy_test/api/test_histories.py | 50 +++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index e263423b2b5..94aabebf5d8 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/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 = ["id", "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 = ["id", "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.

From a7ea52841748437acfb172e11f513eed6f2fcceb Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 15 Mar 2024 13:10:36 +0100
Subject: [PATCH 07/17] Temporarily avoid checking id not present in API test

Until the HistoryMinimal model gets replaced by the CustomHistory again.
---
 lib/galaxy_test/api/test_histories.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index 94aabebf5d8..a3c8e28a9f8 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -155,7 +155,7 @@ class TestHistoriesApi(ApiTestCase, BaseHistories):
 
         # Expect only specific keys
         expected_keys = ["name"]
-        unexpected_keys = ["id", "deleted", "state"]
+        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:
@@ -181,7 +181,7 @@ class TestHistoriesApi(ApiTestCase, BaseHistories):
 
         # Expect only specific keys
         expected_keys = ["name"]
-        unexpected_keys = ["id", "deleted", "state"]
+        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:

From 0def903a895d57f41aa50c5f538b34912dc04d00 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 15 Mar 2024 13:34:44 +0100
Subject: [PATCH 08/17] fix id unknown

---
 client/src/stores/userTagsStore.ts | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/client/src/stores/userTagsStore.ts b/client/src/stores/userTagsStore.ts
index ce5b449a155..36a20a92b15 100644
--- a/client/src/stores/userTagsStore.ts
+++ b/client/src/stores/userTagsStore.ts
@@ -20,7 +20,7 @@ class UserTagStoreDatabase extends Dexie {
 
     constructor() {
         super("userTagStoreDatabase");
-        this.version(1).stores({ tags: "++id, userHash, lastUsed" });
+        this.version(2).stores({ tags: "++id, userHash, lastUsed, tag" });
     }
 }
 
@@ -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);
+            }
         }
     }
 

From 61efe13f4711027a5449102c17dba561ea9adbd3 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 15 Mar 2024 13:45:02 +0100
Subject: [PATCH 09/17] fix sorting and toggling for named tags

---
 .../src/components/TagsMultiselect/HeadlessMultiselect.vue | 7 +++++--
 client/src/components/TagsMultiselect/StatelessTags.vue    | 2 +-
 client/src/stores/userTagsStore.ts                         | 2 +-
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/client/src/components/TagsMultiselect/HeadlessMultiselect.vue b/client/src/components/TagsMultiselect/HeadlessMultiselect.vue
index 3a07de33a79..95660d1ced8 100644
--- a/client/src/components/TagsMultiselect/HeadlessMultiselect.vue
+++ b/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"
diff --git a/client/src/components/TagsMultiselect/StatelessTags.vue b/client/src/components/TagsMultiselect/StatelessTags.vue
index 413def84e2a..dfc30060dbb 100644
--- a/client/src/components/TagsMultiselect/StatelessTags.vue
+++ b/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"
diff --git a/client/src/stores/userTagsStore.ts b/client/src/stores/userTagsStore.ts
index 36a20a92b15..d8eaacb957b 100644
--- a/client/src/stores/userTagsStore.ts
+++ b/client/src/stores/userTagsStore.ts
@@ -26,7 +26,7 @@ class UserTagStoreDatabase extends Dexie {
 
 const maxDbEntriesPerUser = 10000;
 
-function normalizeTag(tag: string) {
+export function normalizeTag(tag: string) {
     return tag.replace(/^#/, "name:");
 }
 

From da7349abcc4d7d623ccda1fa9f82948a23b650fa Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 15 Mar 2024 14:55:08 +0100
Subject: [PATCH 10/17] fix tests

---
 .../HeadlessMultiselect.test.ts               | 22 +++++++++----------
 .../TagsMultiselect/StatelessTags.test.js     | 12 +++++++---
 2 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/client/src/components/TagsMultiselect/HeadlessMultiselect.test.ts b/client/src/components/TagsMultiselect/HeadlessMultiselect.test.ts
index ca97b4615ba..4ef562b2efd 100644
--- a/client/src/components/TagsMultiselect/HeadlessMultiselect.test.ts
+++ b/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"]);
         });
     });
 });
diff --git a/client/src/components/TagsMultiselect/StatelessTags.test.js b/client/src/components/TagsMultiselect/StatelessTags.test.js
index 63a35000093..54a35a19bb3 100644
--- a/client/src/components/TagsMultiselect/StatelessTags.test.js
+++ b/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]);
         });
     });
 

From 3578159625585715ab1a3a7df0a6f93aa1c89269 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 15 Mar 2024 17:19:39 +0100
Subject: [PATCH 11/17] Add missing keys expected by shared histories listing

---
 client/src/components/Grid/configs/historiesShared.ts | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/Grid/configs/historiesShared.ts b/client/src/components/Grid/configs/historiesShared.ts
index df3fc116438..7052c4d3e35 100644
--- a/client/src/components/Grid/configs/historiesShared.ts
+++ b/client/src/components/Grid/configs/historiesShared.ts
@@ -23,6 +23,7 @@ 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",
+        keys: "username,create_time",
         limit,
         offset,
         search,

From ec4ce219f74cbabc9c141546d8c543aeaf525723 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 15 Mar 2024 17:21:46 -0400
Subject: [PATCH 12/17] Fix usage of DISTINCT

---
 lib/galaxy/managers/histories.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index bebd0344678..9f5140c39aa 100644
--- a/lib/galaxy/managers/histories.py
+++ b/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:

From 86fcb4dcaac760cf4e3ee85ce0965f71bb4d02c2 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 15 Mar 2024 17:27:20 -0500
Subject: [PATCH 13/17] [24.0] Prevent dragover for item from same history in
 history panel

We would allow users to dragover items from the same history over its panel and render the dropzone, this prevents that entirely.
Fixes https://github.com/galaxyproject/galaxy/issues/17743
---
 client/src/components/DragGhost.vue           |  2 +-
 .../History/CurrentHistory/HistoryPanel.vue   | 76 ++++++++++++-------
 2 files changed, 48 insertions(+), 30 deletions(-)

diff --git a/client/src/components/DragGhost.vue b/client/src/components/DragGhost.vue
index ae4dbfc6eaa..bc15f7c46af 100644
--- a/client/src/components/DragGhost.vue
+++ b/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>
diff --git a/client/src/components/History/CurrentHistory/HistoryPanel.vue b/client/src/components/History/CurrentHistory/HistoryPanel.vue
index 8b2062323ca..ab8bc7d6358 100644
--- a/client/src/components/History/CurrentHistory/HistoryPanel.vue
+++ b/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" />
 

From 694958b21cf3968fce6b6a65e1a1b716e8abe3c3 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 15 Mar 2024 17:59:50 -0500
Subject: [PATCH 14/17] make whole `ContentItem` draggable

---
 client/src/components/History/Content/ContentItem.vue | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/Content/ContentItem.vue b/client/src/components/History/Content/ContentItem.vue
index dc7022d3a82..11ecbf1df64 100644
--- a/client/src/components/History/Content/ContentItem.vue
+++ b/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)">

From a20c3deb25c6c2fc70bb7f17dc5eb6915df8c484 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 16 Mar 2024 17:26:29 +0100
Subject: [PATCH 15/17] Don't require history to calculate anon disk usage

This is probably the simplest way to fix the anon user issue.
If we don't have a history the size is 0, that's fairly simple.

We might still want to do https://github.com/galaxyproject/galaxy/pull/17755
for those FastAPI endpoints that do actually require a default history.
---
 lib/galaxy/webapps/galaxy/services/users.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/services/users.py b/lib/galaxy/webapps/galaxy/services/users.py
index 91bcf390c0a..fa820748c11 100644
--- a/lib/galaxy/webapps/galaxy/services/users.py
+++ b/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 {

From 4b1b600139c6f04c81d789c939ae3b21222ab47a Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Sat, 16 Mar 2024 17:46:08 -0700
Subject: [PATCH 16/17] fix oidc logout test

which relied on receiving 400
---
 test/integration/oidc/test_auth_oidc.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/integration/oidc/test_auth_oidc.py b/test/integration/oidc/test_auth_oidc.py
index 1674e935307..29ff1c18b2b 100644
--- a/test/integration/oidc/test_auth_oidc.py
+++ b/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

From d6914b73879c9096251e74181e87aa1a80ea9af4 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 15 Mar 2024 15:55:10 -0500
Subject: [PATCH 17/17] exception without the `try/catch` block

Also, improve clarity a bit...
---
 lib/galaxy/webapps/galaxy/services/datasets.py | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/services/datasets.py b/lib/galaxy/webapps/galaxy/services/datasets.py
index d08fb1a7f33..b7a53cd9f91 100644
--- a/lib/galaxy/webapps/galaxy/services/datasets.py
+++ b/lib/galaxy/webapps/galaxy/services/datasets.py
@@ -863,7 +863,6 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
 
         extra_info = None
         mode = kwargs.get("mode", "Auto")
-        indexer = None
 
         # Coverage mode uses index data.
         if mode == "Coverage":
@@ -928,8 +927,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
                 )
 
             # Get mean depth.
-            if not indexer:
-                indexer = self._get_indexer(trans, dataset)
+            indexer = self._get_indexer(trans, dataset)
             stats = indexer.get_data(chrom, low, high, stats=True)
             mean_depth = stats["data"]["mean"]
 
@@ -983,10 +981,9 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         return data
 
     def _get_indexer(self, trans, dataset):
-        try:
-            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
-            if indexer is None:
-                raise Exception("No indexer available for this dataset")
-            return indexer
-        except Exception as e:
-            raise galaxy_exceptions.ObjectNotFound(f"Error getting indexer: {util.unicodify(e)}")
+        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