From 8ae03bb51fa8df656b95c1ffafd15e1dd2d7601c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 14 Mar 2024 16:22:42 -0400
Subject: [PATCH 01/19] Swap Datasets list to use standard SwitchToHistory Link
 component, minor enhancement to accept a filter on switchtohistorylink which
 may be generally useful

---
 .../src/components/Dataset/DatasetHistory.vue | 21 -------------------
 client/src/components/Dataset/DatasetList.vue | 10 +++++----
 .../History/SwitchToHistoryLink.vue           |  7 ++++++-
 3 files changed, 12 insertions(+), 26 deletions(-)
 delete mode 100644 client/src/components/Dataset/DatasetHistory.vue

diff --git a/client/src/components/Dataset/DatasetHistory.vue b/client/src/components/Dataset/DatasetHistory.vue
deleted file mode 100644
index 14fc8ac349dc..000000000000
--- a/client/src/components/Dataset/DatasetHistory.vue
+++ /dev/null
@@ -1,21 +0,0 @@
-<template>
-    <div>
-        {{ historyName }}
-    </div>
-</template>
-<script>
-import { mapState } from "pinia";
-import { useHistoryStore } from "stores/historyStore";
-
-export default {
-    props: {
-        item: Object,
-    },
-    computed: {
-        ...mapState(useHistoryStore, ["getHistoryNameById"]),
-        historyName() {
-            return this.getHistoryNameById(this.item.history_id);
-        },
-    },
-};
-</script>
diff --git a/client/src/components/Dataset/DatasetList.vue b/client/src/components/Dataset/DatasetList.vue
index b418d488e914..4d3dee39858d 100644
--- a/client/src/components/Dataset/DatasetList.vue
+++ b/client/src/components/Dataset/DatasetList.vue
@@ -16,7 +16,9 @@
                     <DatasetName :item="row.item" @showDataset="onShowDataset" @copyDataset="onCopyDataset" />
                 </template>
                 <template v-slot:cell(history_id)="row">
-                    <DatasetHistory :item="row.item" />
+                    <SwitchToHistoryLink
+                        :historyId="row.item.history_id"
+                        :filters="{ deleted: row.item.deleted, visible: row.item.visible, hid: row.item.hid }" />
                 </template>
                 <template v-slot:cell(tags)="row">
                     <StatelessTags
@@ -49,17 +51,17 @@ import { copyDataset, getDatasets } from "@/api/datasets";
 import { updateTags } from "@/api/tags";
 import { useHistoryStore } from "@/stores/historyStore";
 
-import DatasetHistory from "./DatasetHistory";
-import DatasetName from "./DatasetName";
+import DatasetName from "./DatasetName.vue";
+import SwitchToHistoryLink from "@/components/History/SwitchToHistoryLink.vue";
 
 export default {
     components: {
-        DatasetHistory,
         DatasetName,
         LoadingSpan,
         DelayedInput,
         UtcDate,
         StatelessTags,
+        SwitchToHistoryLink,
     },
     data() {
         return {
diff --git a/client/src/components/History/SwitchToHistoryLink.vue b/client/src/components/History/SwitchToHistoryLink.vue
index 39fb8e945dc1..d691384ceaac 100644
--- a/client/src/components/History/SwitchToHistoryLink.vue
+++ b/client/src/components/History/SwitchToHistoryLink.vue
@@ -18,6 +18,7 @@ const historyStore = useHistoryStore();
 
 interface Props {
     historyId: string;
+    filters?: Record<string, string | boolean>;
 }
 
 const props = defineProps<Props>();
@@ -30,7 +31,11 @@ const actionText = computed(() => (canSwitch.value ? "Switch to" : "View in new
 
 function onClick(history: HistorySummary) {
     if (canSwitch.value) {
-        historyStore.setCurrentHistory(history.id);
+        if (props.filters) {
+            historyStore.applyFilters(history.id, props.filters);
+        } else {
+            historyStore.setCurrentHistory(history.id);
+        }
         return;
     }
     viewHistoryInNewTab(history);

From 77ad424783771e9ccf1f2ece2f0917bfb6649e62 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 14 Mar 2024 17:16:56 -0400
Subject: [PATCH 02/19] Drop show-in-history option from datasetlist dropdown,
 now that it's in the history column natively, keep the action language the
 same though when applying filter -- maybe revisit this, because the hid
 filtering feels weird.

---
 client/src/components/Dataset/DatasetList.vue         |  2 +-
 client/src/components/Dataset/DatasetName.vue         |  7 -------
 client/src/components/History/SwitchToHistoryLink.vue | 10 +++++++++-
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/client/src/components/Dataset/DatasetList.vue b/client/src/components/Dataset/DatasetList.vue
index 4d3dee39858d..132e2610b4d6 100644
--- a/client/src/components/Dataset/DatasetList.vue
+++ b/client/src/components/Dataset/DatasetList.vue
@@ -17,7 +17,7 @@
                 </template>
                 <template v-slot:cell(history_id)="row">
                     <SwitchToHistoryLink
-                        :historyId="row.item.history_id"
+                        :history-id="row.item.history_id"
                         :filters="{ deleted: row.item.deleted, visible: row.item.visible, hid: row.item.hid }" />
                 </template>
                 <template v-slot:cell(tags)="row">
diff --git a/client/src/components/Dataset/DatasetName.vue b/client/src/components/Dataset/DatasetName.vue
index be8e5382a9c3..a881f591ffab 100644
--- a/client/src/components/Dataset/DatasetName.vue
+++ b/client/src/components/Dataset/DatasetName.vue
@@ -20,10 +20,6 @@
             <span class="name">{{ getName }}</span>
         </b-link>
         <div class="dropdown-menu" aria-labelledby="dataset-dropdown">
-            <a class="dropdown-item" href="#" @click.prevent="showDataset">
-                <span class="fa fa-eye fa-fw mr-1" />
-                <span>Show in History containing dataset</span>
-            </a>
             <a class="dropdown-item" href="#" @click.prevent="copyDataset">
                 <span class="fa fa-copy fa-fw mr-1" />
                 <span>Copy to current History</span>
@@ -56,9 +52,6 @@ export default {
         copyDataset(item) {
             this.$emit("copyDataset", this.item);
         },
-        showDataset(item) {
-            this.$emit("showDataset", this.item);
-        },
     },
 };
 </script>
diff --git a/client/src/components/History/SwitchToHistoryLink.vue b/client/src/components/History/SwitchToHistoryLink.vue
index d691384ceaac..96149ac48bcc 100644
--- a/client/src/components/History/SwitchToHistoryLink.vue
+++ b/client/src/components/History/SwitchToHistoryLink.vue
@@ -27,7 +27,15 @@ const history = computed(() => historyStore.getHistoryById(props.historyId));
 
 const canSwitch = computed(() => !!history.value && !history.value.archived && !history.value.purged);
 
-const actionText = computed(() => (canSwitch.value ? "Switch to" : "View in new tab"));
+const actionText = computed(() => {
+    if (canSwitch.value) {
+        if (props.filters) {
+            return "Show in history";
+        }
+        return "Switch to";
+    }
+    return "View in new tab";
+});
 
 function onClick(history: HistorySummary) {
     if (canSwitch.value) {

From d1725aae152990c8b69460b5b7cf1658d0d4f513 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 14 Mar 2024 13:53:19 -0400
Subject: [PATCH 03/19] Disable published dataset list for anonymous users.

---
 client/src/entry/analysis/menu.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/entry/analysis/menu.js b/client/src/entry/analysis/menu.js
index 495b0ae231a2..78daf6f7b0dd 100644
--- a/client/src/entry/analysis/menu.js
+++ b/client/src/entry/analysis/menu.js
@@ -105,6 +105,7 @@ export function fetchMenu(options = {}) {
                 {
                     title: _l("Datasets"),
                     url: "/datasets/list_published",
+                    hidden: !Galaxy.user.id,
                 },
                 {
                     title: _l("Histories"),

From 23d03da97558ff946eb290840b8cbf48d1ff4a10 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 15 Mar 2024 10:49:13 -0400
Subject: [PATCH 04/19] Update tests to reflect shift of show-in-history
 option.

---
 client/src/components/Dataset/DatasetName.test.js | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/client/src/components/Dataset/DatasetName.test.js b/client/src/components/Dataset/DatasetName.test.js
index f56bd1a55e93..02daca265e0b 100644
--- a/client/src/components/Dataset/DatasetName.test.js
+++ b/client/src/components/Dataset/DatasetName.test.js
@@ -14,10 +14,7 @@ describe("Dataset Name", () => {
         const state = wrapper.findAll(".name");
         expect(state.length).toBe(1);
         expect(state.at(0).text()).toBe("name");
-        const $linkShow = wrapper.find(".dropdown-item:first-child");
-        $linkShow.trigger("click");
-        expect(Array.isArray(wrapper.emitted().showDataset)).toBe(true);
-        const $linkCopy = wrapper.find(".dropdown-item:last-child");
+        const $linkCopy = wrapper.find(".dropdown-item:first-child");
         $linkCopy.trigger("click");
         expect(Array.isArray(wrapper.emitted().copyDataset)).toBe(true);
     });

From b4c5b55aa345cd228e790e4723ef555896f0af5e Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 15 Mar 2024 18:41:23 -0500
Subject: [PATCH 05/19] [24.0] Add Shift+Click select for `ContentItem`
 selector buttons as well

While keyboard select was added in https://github.com/galaxyproject/galaxy/pull/17502 (and polished/fixed) in other PRs, the selector buttons did not allow for Shift+Click selection. This PR adds that.
---
 .../components/History/Content/ContentItem.vue  | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/client/src/components/History/Content/ContentItem.vue b/client/src/components/History/Content/ContentItem.vue
index dc7022d3a824..0236d48f8ac9 100644
--- a/client/src/components/History/Content/ContentItem.vue
+++ b/client/src/components/History/Content/ContentItem.vue
@@ -4,7 +4,7 @@ import { faCheckSquare, faSquare } from "@fortawesome/free-regular-svg-icons";
 import { faArrowCircleDown, faArrowCircleUp, faCheckCircle, faSpinner } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BBadge, BButton, BCollapse } from "bootstrap-vue";
-import { computed } from "vue";
+import { computed, ref } from "vue";
 import { useRoute, useRouter } from "vue-router/composables";
 
 import type { ItemUrls } from "@/components/History/Content/Dataset/index";
@@ -77,6 +77,8 @@ const emit = defineEmits<{
 const entryPointStore = useEntryPointStore();
 const eventStore = useEventStore();
 
+const contentItem = ref<HTMLElement | null>(null);
+
 const jobState = computed(() => {
     return new JobStateSummary(props.item);
 });
@@ -298,6 +300,16 @@ function onTagClick(tag: string) {
     }
 }
 
+function onButtonSelect(e: Event) {
+    const event = e as KeyboardEvent;
+    if (event.shiftKey) {
+        onClick(e);
+    }
+    contentItem.value?.focus();
+    emit("init-key-selection");
+    emit("update:selected", !props.selected);
+}
+
 function toggleHighlights() {
     emit("toggleHighlights", props.item);
 }
@@ -312,6 +324,7 @@ function unexpandedClick(event: Event) {
 <template>
     <div
         :id="contentId"
+        ref="contentItem"
         :class="['content-item m-1 p-0 rounded btn-transparent-background', contentCls, isBeingUsed]"
         :data-hid="id"
         :data-state="dataState"
@@ -322,7 +335,7 @@ function unexpandedClick(event: Event) {
         <div class="p-1 cursor-pointer" draggable @dragstart="onDragStart" @dragend="onDragEnd" @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)">
+                    <BButton v-if="selectable" class="selector p-0" @click.stop="onButtonSelect">
                         <FontAwesomeIcon v-if="selected" fixed-width size="lg" :icon="faCheckSquare" />
                         <FontAwesomeIcon v-else fixed-width size="lg" :icon="faSquare" />
                     </BButton>

From c9e9ec1ca358ae8043837586eed25245e0adf705 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 19 Mar 2024 12:56:27 -0500
Subject: [PATCH 06/19] don't initialize shift selection if shiftKey is pressed

---
 client/src/components/History/Content/ContentItem.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/Content/ContentItem.vue b/client/src/components/History/Content/ContentItem.vue
index 0236d48f8ac9..6136f91c2782 100644
--- a/client/src/components/History/Content/ContentItem.vue
+++ b/client/src/components/History/Content/ContentItem.vue
@@ -304,9 +304,10 @@ function onButtonSelect(e: Event) {
     const event = e as KeyboardEvent;
     if (event.shiftKey) {
         onClick(e);
+    } else {
+        emit("init-key-selection");
     }
     contentItem.value?.focus();
-    emit("init-key-selection");
     emit("update:selected", !props.selected);
 }
 

From b734b1dcb433b254916b1edbb9d2888363d36e73 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 21 Mar 2024 18:37:45 +0100
Subject: [PATCH 07/19] Return published histories first in
 display_by_username_and_slug

slugs are not necessarily unique, but they are for published items.  by
returning the published histories first we return the intended history
first, while making it possible for owners to retrieve their now
unpublished histories by the old slug.
---
 lib/galaxy/webapps/galaxy/controllers/history.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index e4746fb6cba0..2c5e2d147ad0 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -97,7 +97,12 @@ def display_by_username_and_slug(self, trans, username, slug, **kwargs):
         session = trans.sa_session
 
         user = session.scalars(select(model.User).filter_by(username=username).limit(1)).first()
-        history = session.scalars(select(model.History).filter_by(user=user, slug=slug, deleted=False).limit(1)).first()
+        history = session.scalars(
+            select(model.History)
+            .filter_by(user=user, slug=slug, deleted=False)
+            .order_by(model.History.importable.desc())
+            .limit(1)
+        ).first()
 
         if history is None:
             raise web.httpexceptions.HTTPNotFound()

From 556580eb8052d1ea769a4e7cf3ca271f47d3902a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 21 Mar 2024 19:07:14 +0100
Subject: [PATCH 08/19] Add comment explaining why we sort

---
 lib/galaxy/webapps/galaxy/controllers/history.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index 2c5e2d147ad0..fd3f1a036f20 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -100,6 +100,7 @@ def display_by_username_and_slug(self, trans, username, slug, **kwargs):
         history = session.scalars(
             select(model.History)
             .filter_by(user=user, slug=slug, deleted=False)
+            # return public histories first if slug is not unique
             .order_by(model.History.importable.desc())
             .limit(1)
         ).first()

From 1d20ce1d6d27914b10418f5ae529e8b619441a87 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Thu, 21 Mar 2024 17:06:05 -0500
Subject: [PATCH 09/19] add a first and last item tracker to `SelectedItems`,
 remove Shift+Ctrl

Modified `SelectedItems` so that for range select, we track the first and last item in a range, along with the anchor. This way, we can persist with a selected range even if the user deselects a few items within it, since we keep track of the beginning and end of the range.

Also, added a CSS indicator to `ContentItem`s which actually indicates which item if the Shift+click range select anchor.
This also removes the `Shift+Ctrl+Click` multiple range select.
---
 .../History/Content/ContentItem.vue           |  25 +--
 .../History/Content/SelectedItems.js          | 147 +++++++++++++++---
 .../History/CurrentHistory/HistoryPanel.vue   |  19 ++-
 3 files changed, 150 insertions(+), 41 deletions(-)

diff --git a/client/src/components/History/Content/ContentItem.vue b/client/src/components/History/Content/ContentItem.vue
index 6136f91c2782..6cfb3135db57 100644
--- a/client/src/components/History/Content/ContentItem.vue
+++ b/client/src/components/History/Content/ContentItem.vue
@@ -35,6 +35,7 @@ interface Props {
     addHighlightBtn?: boolean;
     highlight?: string;
     isDataset?: boolean;
+    isRangeSelectAnchor?: boolean;
     isHistoryItem?: boolean;
     selected?: boolean;
     selectable?: boolean;
@@ -48,6 +49,7 @@ const props = withDefaults(defineProps<Props>(), {
     addHighlightBtn: false,
     highlight: undefined,
     isDataset: true,
+    isRangeSelectAnchor: false,
     isHistoryItem: false,
     selected: false,
     selectable: false,
@@ -58,12 +60,12 @@ const props = withDefaults(defineProps<Props>(), {
 const emit = defineEmits<{
     (e: "update:selected", selected: boolean): void;
     (e: "update:expand-dataset", expand: boolean): void;
-    (e: "shift-select", direction: string): void;
+    (e: "shift-arrow-select", direction: string): void;
     (e: "init-key-selection"): void;
     (e: "arrow-navigate", direction: string): void;
     (e: "hide-selection"): void;
     (e: "select-all"): void;
-    (e: "selected-to", reset: boolean): void;
+    (e: "selected-to"): void;
     (e: "delete", item: any, recursive: boolean): void;
     (e: "undelete"): void;
     (e: "unhide"): void;
@@ -173,6 +175,10 @@ const isBeingUsed = computed(() => {
     return Object.values(itemUrls.value).includes(route.path) ? "being-used" : "";
 });
 
+const rangeSelectClass = computed(() => {
+    return props.isRangeSelectAnchor ? "range-select-anchor" : "";
+});
+
 /** Based on the user's keyboard platform, checks if it is the
  * typical key for selection (ctrl for windows/linux, cmd for mac)
  */
@@ -199,7 +205,7 @@ function onKeyDown(event: KeyboardEvent) {
         } else {
             event.preventDefault();
             if ((event.key === "ArrowUp" || event.key === "ArrowDown") && event.shiftKey) {
-                emit("shift-select", event.key);
+                emit("shift-arrow-select", event.key);
             } else if (event.key === "ArrowUp" || event.key === "ArrowDown") {
                 emit("init-key-selection");
             } else if (event.key === "Delete" && !props.selected && !props.item.deleted) {
@@ -217,15 +223,12 @@ function onKeyDown(event: KeyboardEvent) {
 function onClick(e?: Event) {
     const event = e as KeyboardEvent;
     if (event && props.writable) {
-        if (event.shiftKey && isSelectKey(event)) {
-            emit("selected-to", false);
-            return;
-        } else if (isSelectKey(event)) {
+        if (isSelectKey(event)) {
             emit("init-key-selection");
             emit("update:selected", !props.selected);
             return;
         } else if (event.shiftKey) {
-            emit("selected-to", true);
+            emit("selected-to");
             return;
         } else {
             emit("init-key-selection");
@@ -326,7 +329,7 @@ function unexpandedClick(event: Event) {
     <div
         :id="contentId"
         ref="contentItem"
-        :class="['content-item m-1 p-0 rounded btn-transparent-background', contentCls, isBeingUsed]"
+        :class="['content-item m-1 p-0 rounded btn-transparent-background', contentCls, isBeingUsed, rangeSelectClass]"
         :data-hid="id"
         :data-state="dataState"
         tabindex="0"
@@ -450,6 +453,10 @@ function unexpandedClick(event: Event) {
         box-shadow: 0 0 0 0.2rem transparentize($brand-primary, 0.75);
     }
 
+    &.range-select-anchor {
+        box-shadow: 0 0 0 0.2rem transparentize($brand-primary, 0.75);
+    }
+
     &.being-used {
         border-left: 0.25rem solid $brand-primary;
         margin-left: 0rem !important;
diff --git a/client/src/components/History/Content/SelectedItems.js b/client/src/components/History/Content/SelectedItems.js
index 7a0d3a24196f..a93fa5904784 100644
--- a/client/src/components/History/Content/SelectedItems.js
+++ b/client/src/components/History/Content/SelectedItems.js
@@ -11,6 +11,7 @@ export default {
         getItemKey: { type: Function, required: true },
         filterText: { type: String, required: true },
         totalItemsInQuery: { type: Number, required: false },
+        allItems: { type: Array, required: true },
     },
     data() {
         return {
@@ -19,6 +20,8 @@ export default {
             allSelected: false,
             initSelectedItem: null,
             initDirection: null,
+            firstInRange: null,
+            lastInRange: null,
         };
     },
     computed: {
@@ -34,18 +37,27 @@ export default {
         initSelectedKey() {
             return this.initSelectedItem ? this.getItemKey(this.initSelectedItem) : null;
         },
+        lastInRangeIndex() {
+            return this.lastInRange ? this.allItems.indexOf(this.lastInRange) : null;
+        },
+        firstInRangeIndex() {
+            return this.firstInRange ? this.allItems.indexOf(this.firstInRange) : null;
+        },
+        rangeSelectActive() {
+            return this.lastInRange && this.initDirection;
+        },
     },
     methods: {
         setShowSelection(val) {
             this.showSelection = val;
         },
-        selectAllInCurrentQuery(loadedItems = [], force = true) {
+        selectAllInCurrentQuery(force = true) {
             // if we are not forcing selectAll, and all items are already selected; deselect them
             if (!force && this.allSelected) {
                 this.setShowSelection(false);
                 return;
             }
-            this.selectItems(loadedItems);
+            this.selectItems(this.allItems);
             this.allSelected = true;
         },
         isSelected(item) {
@@ -55,19 +67,49 @@ export default {
             const key = this.getItemKey(item);
             return this.items.has(key);
         },
-        setSelected(item, selected) {
+        /** Adds/Removes an item from the selected items
+         *
+         * @param {Object} item - the item to be selected/deselected
+         * @param {Boolean} selected - whether to select or deselect the item
+         * @param {Boolean} checkInRange - whether to check if the item lies outside the range
+         */
+        setSelected(item, selected, checkInRange = true) {
             const key = this.getItemKey(item);
             const newSelected = new Map(this.items);
             selected ? newSelected.set(key, item) : newSelected.delete(key);
             this.items = newSelected;
             this.breakQuerySelection();
+
+            // item selected from panel, range select is active, check if item lies outside the range
+            if (checkInRange && this.rangeSelectActive) {
+                const currentItemIndex = this.allItems.indexOf(item);
+
+                /** If either of the following are `true`, change the range anchor */
+                // if range select was downwards and the current item is below the lastInRange or above the firstInRange
+                if (
+                    this.initDirection === "ArrowDown" &&
+                    (currentItemIndex > this.lastInRangeIndex || currentItemIndex < this.firstInRangeIndex)
+                ) {
+                    this.firstInRange = item;
+                    this.lastInRange = item;
+                }
+                // if range select was upwards and the current item is above the lastInRange or below the firstInRange
+                else if (
+                    this.initDirection === "ArrowUp" &&
+                    (currentItemIndex < this.lastInRangeIndex || currentItemIndex > this.firstInRangeIndex)
+                ) {
+                    this.firstInRange = item;
+                    this.lastInRange = item;
+                }
+            }
         },
-        shiftSelect(item, nextItem, eventKey) {
+        /** Selecting items using `Shift+ArrowUp/ArrowDown` keys */
+        shiftArrowKeySelect(item, nextItem, eventKey) {
             const currentItemKey = this.getItemKey(item);
             if (!this.initSelectedKey) {
                 this.initSelectedItem = item;
                 this.initDirection = eventKey;
-                this.setSelected(item, true);
+                this.setSelected(item, true, false);
             }
             // got back to the initial selected item
             else if (this.initSelectedKey === currentItemKey) {
@@ -75,50 +117,101 @@ export default {
             }
             // same direction
             else if (this.initDirection === eventKey) {
-                this.setSelected(item, true);
+                this.setSelected(item, true, false);
             }
             // different direction
             else {
-                this.setSelected(item, false);
+                this.setSelected(item, false, false);
             }
             if (nextItem) {
-                this.setSelected(nextItem, true);
+                this.setSelected(nextItem, true, false);
             }
         },
-        selectTo(item, prevItem, allItems, reset = true) {
+        /** Range selecting items using `Shift+Click` */
+        rangeSelect(item, prevItem) {
             if (prevItem && item) {
-                // we are staring a new shift+click selectTo from `prevItem`
-                if (!this.initSelectedKey) {
-                    this.initSelectedItem = prevItem;
-                }
+                // either a range select is not active or we have modified a range select (changing the anchor)
+                const noRangeSelectOrModified = !this.initSelectedKey;
+                if (noRangeSelectOrModified) {
+                    // there is a range select active
+                    if (this.rangeSelectActive) {
+                        const currentItemIndex = this.allItems.indexOf(item);
 
-                // `reset = false` in the case user is holding shift+ctrl key
-                if (reset) {
-                    // clear this.items of any other selections
-                    this.items = new Map();
+                        // the current item is outside the range in the same direction;
+                        // the new range will follow the last item in prev range
+                        if (
+                            (this.initDirection === "ArrowDown" && currentItemIndex > this.lastInRangeIndex) ||
+                            (this.initDirection === "ArrowUp" && currentItemIndex < this.lastInRangeIndex)
+                        ) {
+                            this.initSelectedItem = this.lastInRange;
+                        }
+                        // the current item is outside the range in the opposite direction;
+                        // the new range will follow the first item in prev range
+                        else if (
+                            (this.initDirection === "ArrowDown" && currentItemIndex < this.firstInRangeIndex) ||
+                            (this.initDirection === "ArrowUp" && currentItemIndex > this.firstInRangeIndex)
+                        ) {
+                            this.initSelectedItem = this.firstInRange;
+                        } else {
+                            this.initSelectedItem = prevItem;
+                            this.firstInRange = prevItem;
+                        }
+                    }
+                    // there is no range select active
+                    else {
+                        // we are staring a new shift+click rangeSelect from `prevItem`
+                        this.initSelectedItem = prevItem;
+                        this.firstInRange = prevItem;
+                    }
                 }
-                this.setSelected(this.initSelectedItem, true);
 
-                const initItemIndex = allItems.indexOf(this.initSelectedItem);
-                const currentItemIndex = allItems.indexOf(item);
+                const initItemIndex = this.allItems.indexOf(this.initSelectedItem);
+                const currentItemIndex = this.allItems.indexOf(item);
 
+                const lastDirection = this.initDirection;
                 let selections = [];
                 // from allItems, get the items between the init item and the current item
                 if (initItemIndex < currentItemIndex) {
                     this.initDirection = "ArrowDown";
-                    selections = allItems.slice(initItemIndex + 1, currentItemIndex + 1);
+                    selections = this.allItems.slice(initItemIndex + 1, currentItemIndex + 1);
                 } else if (initItemIndex > currentItemIndex) {
                     this.initDirection = "ArrowUp";
-                    selections = allItems.slice(currentItemIndex, initItemIndex);
+                    selections = this.allItems.slice(currentItemIndex, initItemIndex);
+                }
+
+                let deselections;
+                // there is an existing range select; deselect items in certain conditions
+                if (this.rangeSelectActive) {
+                    // if there is an active, uninterrupted range-select and the direction changed;
+                    // deselect the items between the lastInRange and initSelectedItem
+                    if (!noRangeSelectOrModified && lastDirection && lastDirection !== this.initDirection) {
+                        if (this.lastInRangeIndex >= initItemIndex) {
+                            deselections = this.allItems.slice(initItemIndex + 1, this.lastInRangeIndex + 1);
+                        } else {
+                            deselections = this.allItems.slice(this.lastInRangeIndex, initItemIndex);
+                        }
+                    }
+
+                    // if the range has become smaller, deselect items between the lastInRange and the current item
+                    else if (this.lastInRangeIndex < currentItemIndex && this.initDirection === "ArrowUp") {
+                        deselections = this.allItems.slice(this.lastInRangeIndex, currentItemIndex);
+                    } else if (this.lastInRangeIndex > currentItemIndex && this.initDirection === "ArrowDown") {
+                        deselections = this.allItems.slice(currentItemIndex + 1, this.lastInRangeIndex + 1);
+                    }
                 }
+
                 this.selectItems(selections);
+                if (deselections) {
+                    deselections.forEach((deselected) => this.setSelected(deselected, false, false));
+                }
             } else {
                 this.setSelected(item, true);
             }
+            this.lastInRange = item;
         },
+        /** Resets the initial item in a range select (or shiftArrowKeySelect) */
         initKeySelection() {
             this.initSelectedItem = null;
-            this.initDirection = null;
         },
         selectItems(items = []) {
             const newItems = [...this.items.values(), ...items];
@@ -139,6 +232,9 @@ export default {
             this.items = new Map();
             this.allSelected = false;
             this.initKeySelection();
+            this.lastInRange = null;
+            this.firstInRange = null;
+            this.initDirection = null;
         },
         cancelSelection() {
             this.showSelection = false;
@@ -176,12 +272,13 @@ export default {
             setShowSelection: this.setShowSelection,
             selectAllInCurrentQuery: this.selectAllInCurrentQuery,
             selectItems: this.selectItems,
-            selectTo: this.selectTo,
+            rangeSelect: this.rangeSelect,
             isSelected: this.isSelected,
             setSelected: this.setSelected,
             resetSelection: this.reset,
-            shiftSelect: this.shiftSelect,
+            shiftArrowKeySelect: this.shiftArrowKeySelect,
             initKeySelection: this.initKeySelection,
+            initSelectedItem: this.initSelectedItem,
         });
     },
 };
diff --git a/client/src/components/History/CurrentHistory/HistoryPanel.vue b/client/src/components/History/CurrentHistory/HistoryPanel.vue
index 8b2062323cae..4d2858dbddb7 100644
--- a/client/src/components/History/CurrentHistory/HistoryPanel.vue
+++ b/client/src/components/History/CurrentHistory/HistoryPanel.vue
@@ -470,15 +470,17 @@ function setItemDragstart(
                 setShowSelection,
                 selectAllInCurrentQuery,
                 isSelected,
-                selectTo,
+                rangeSelect,
                 setSelected,
-                shiftSelect,
+                shiftArrowKeySelect,
                 initKeySelection,
                 resetSelection,
+                initSelectedItem,
             }"
             :scope-key="queryKey"
             :get-item-key="getItemKey"
             :filter-text="filterText"
+            :all-items="historyItems"
             :total-items-in-query="totalMatchesCount"
             @query-selection-break="querySelectionBreak = true">
             <!-- eslint-disable-next-line vuejs-accessibility/no-static-element-interactions -->
@@ -545,7 +547,7 @@ function setItemDragstart(
                             <HistorySelectionStatus
                                 v-if="showSelection"
                                 :selection-size="selectionSize"
-                                @select-all="selectAllInCurrentQuery(historyItems)"
+                                @select-all="selectAllInCurrentQuery()"
                                 @reset-selection="resetSelection" />
                         </template>
                     </HistoryOperations>
@@ -597,6 +599,9 @@ function setItemDragstart(
                                     :writable="canEditHistory"
                                     :expand-dataset="isExpanded(item)"
                                     :is-dataset="isDataset(item)"
+                                    :is-range-select-anchor="
+                                        initSelectedItem && itemUniqueKey(item) === itemUniqueKey(initSelectedItem)
+                                    "
                                     :highlight="getHighlight(item)"
                                     :selected="isSelected(item)"
                                     :selectable="showSelection"
@@ -613,11 +618,11 @@ function setItemDragstart(
                                     "
                                     @hide-selection="setShowSelection(false)"
                                     @init-key-selection="initKeySelection"
-                                    @shift-select="
-                                        (eventKey) => shiftSelect(item, arrowNavigate(item, eventKey), eventKey)
+                                    @shift-arrow-select="
+                                        (eventKey) => shiftArrowKeySelect(item, arrowNavigate(item, eventKey), eventKey)
                                     "
-                                    @select-all="selectAllInCurrentQuery(historyItems, false)"
-                                    @selected-to="(reset) => selectTo(item, lastItemFocused, historyItems, reset)"
+                                    @select-all="selectAllInCurrentQuery(false)"
+                                    @selected-to="rangeSelect(item, lastItemFocused)"
                                     @tag-click="updateFilterValue('tag', $event)"
                                     @tag-change="onTagChange"
                                     @toggleHighlights="updateFilterValue('related', item.hid)"

From f4d958f0574491632a50562deba7496efc22392c Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Thu, 21 Mar 2024 17:33:01 -0500
Subject: [PATCH 10/19] fix failing jest because of added `allItems` prop

---
 .../History/Content/SelectedItems.test.js     | 39 ++++++++-----------
 1 file changed, 17 insertions(+), 22 deletions(-)

diff --git a/client/src/components/History/Content/SelectedItems.test.js b/client/src/components/History/Content/SelectedItems.test.js
index d493b1a9cfc7..dbcf8fb55843 100644
--- a/client/src/components/History/Content/SelectedItems.test.js
+++ b/client/src/components/History/Content/SelectedItems.test.js
@@ -6,17 +6,20 @@ import SelectedItems from "./SelectedItems";
 
 const localVue = getLocalVue();
 
-const DEFAULT_PROPS = {
-    scopeKey: "scope",
-    getItemKey: (item) => `item-key-${item.id}`,
-    filterText: "",
-    totalItemsInQuery: 100,
-};
-
 describe("History SelectedItems", () => {
     let wrapper;
     let slotProps;
 
+    const numberOfLoadedItems = 10;
+    const allItems = generateTestItems(numberOfLoadedItems);
+    const DEFAULT_PROPS = {
+        scopeKey: "scope",
+        getItemKey: (item) => `item-key-${item.id}`,
+        filterText: "",
+        totalItemsInQuery: 100,
+        allItems,
+    };
+
     beforeEach(async () => {
         wrapper = shallowMount(SelectedItems, {
             localVue,
@@ -79,10 +82,8 @@ describe("History SelectedItems", () => {
     describe("Query Selection Mode", () => {
         it("is considered a query selection when we select `all items` and the query contains more items than we have currently loaded", async () => {
             const expectedTotalItemsInQuery = 100;
-            const numberOfLoadedItems = 10;
-            const loadedItems = generateTestItems(numberOfLoadedItems);
 
-            await selectAllItemsInCurrentQuery(loadedItems);
+            await selectAllItemsInCurrentQuery();
 
             expect(slotProps.isQuerySelection).toBe(true);
             expect(slotProps.selectionSize).toBe(expectedTotalItemsInQuery);
@@ -90,11 +91,9 @@ describe("History SelectedItems", () => {
 
         it("shouldn't be a query selection when we already have all items loaded", async () => {
             const expectedTotalItemsInQuery = 10;
-            const numberOfLoadedItems = 10;
-            const loadedItems = generateTestItems(numberOfLoadedItems);
             await wrapper.setProps({ totalItemsInQuery: expectedTotalItemsInQuery });
 
-            await selectAllItemsInCurrentQuery(loadedItems);
+            await selectAllItemsInCurrentQuery();
 
             expect(slotProps.isQuerySelection).toBe(false);
             expect(slotProps.selectionSize).toBe(expectedTotalItemsInQuery);
@@ -102,14 +101,12 @@ describe("History SelectedItems", () => {
 
         it("should `break` query selection mode when we unselect an item", async () => {
             const expectedTotalItemsInQuery = 100;
-            const numberOfLoadedItems = 10;
-            const loadedItems = generateTestItems(numberOfLoadedItems);
-            await selectAllItemsInCurrentQuery(loadedItems);
+            await selectAllItemsInCurrentQuery();
             expect(slotProps.isQuerySelection).toBe(true);
             expect(slotProps.selectionSize).toBe(expectedTotalItemsInQuery);
             expect(wrapper.emitted()["query-selection-break"]).toBeUndefined();
 
-            await unselectItem(loadedItems[0]);
+            await unselectItem(allItems[0]);
 
             expect(slotProps.isQuerySelection).toBe(false);
             expect(slotProps.selectionSize).toBe(numberOfLoadedItems - 1);
@@ -117,9 +114,7 @@ describe("History SelectedItems", () => {
         });
 
         it("should `break` query selection mode when the total number of items changes", async () => {
-            const numberOfLoadedItems = 10;
-            const loadedItems = generateTestItems(numberOfLoadedItems);
-            await selectAllItemsInCurrentQuery(loadedItems);
+            await selectAllItemsInCurrentQuery();
             expect(slotProps.isQuerySelection).toBe(true);
             expect(wrapper.emitted()["query-selection-break"]).toBeUndefined();
 
@@ -146,8 +141,8 @@ describe("History SelectedItems", () => {
 
         it("should match the number of items in query when selecting all items", async () => {
             const expectedTotalItemsInQuery = 100;
-            const loadedItems = []; // Even if there are no explicit items selected
-            await selectAllItemsInCurrentQuery(loadedItems);
+            await wrapper.setProps({ allItems: generateTestItems(0) }); // Even if there are no explicit items selected
+            await selectAllItemsInCurrentQuery();
             expect(slotProps.isQuerySelection).toBe(true);
             expect(slotProps.selectionSize).toBe(expectedTotalItemsInQuery);
         });

From 343ca94c621601fb1fdc379a1857c491969bd1bc Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 22 Mar 2024 12:19:11 -0400
Subject: [PATCH 11/19] Enable 'Data' menu for single users.  Historically this
 was only published stuff, but now has more and needs to be accessible.

---
 client/src/entry/analysis/menu.js | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/client/src/entry/analysis/menu.js b/client/src/entry/analysis/menu.js
index 78daf6f7b0dd..ae776271496a 100644
--- a/client/src/entry/analysis/menu.js
+++ b/client/src/entry/analysis/menu.js
@@ -41,18 +41,9 @@ export function fetchMenu(options = {}) {
     }
 
     //
-    // 'Data Items' or Libraries tab.
+    // 'Data' tab.
     //
-    if (Galaxy.config.single_user) {
-        // Single user can still use libraries, especially as we may grow that
-        // functionality as a representation for external data.  The rest is
-        // hidden though.
-        menu.push({
-            title: _l("Data Libraries"),
-            url: "/libraries",
-            id: "libraries",
-        });
-    } else if (Galaxy.user.id) {
+    if (Galaxy.user.id) {
         menu.push({
             id: "resources",
             title: _l("Data"),

From eb0557275f9130603e03d29240dac20c74678a44 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Fri, 22 Mar 2024 09:58:17 -0700
Subject: [PATCH 12/19] drop non-existent menu item

---
 client/src/entry/analysis/menu.js | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/client/src/entry/analysis/menu.js b/client/src/entry/analysis/menu.js
index 78daf6f7b0dd..53c1b5b83159 100644
--- a/client/src/entry/analysis/menu.js
+++ b/client/src/entry/analysis/menu.js
@@ -102,11 +102,6 @@ export function fetchMenu(options = {}) {
                     url: "/libraries",
                     target: "_top",
                 },
-                {
-                    title: _l("Datasets"),
-                    url: "/datasets/list_published",
-                    hidden: !Galaxy.user.id,
-                },
                 {
                     title: _l("Histories"),
                     url: "/histories/list_published",

From 896d7fec1929f34176dffdcf698972003d8ab250 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 22 Mar 2024 17:24:57 +0100
Subject: [PATCH 13/19] Simplify nested collection joins

by joining via dataset collection element, and only bringing
in the dataset collection if we're filtering against the collection.
---
 lib/galaxy/model/__init__.py | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index dcb4e9d55a55..d8ac3d2233ca 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -6270,16 +6270,17 @@ def attribute_columns(column_collection, attributes, nesting_level=None):
 
         while ":" in depth_collection_type:
             nesting_level += 1
-            inner_dc = alias(DatasetCollection)
             inner_dce = alias(DatasetCollectionElement)
+            inner_dc = alias(DatasetCollection)
             order_by_columns.append(inner_dce.c.element_index)
-            q = q.join(
-                inner_dc, and_(inner_dc.c.id == dce.c.child_collection_id, dce.c.dataset_collection_id == dc.c.id)
-            ).outerjoin(inner_dce, inner_dce.c.dataset_collection_id == inner_dc.c.id)
-            q = q.add_columns(
-                *attribute_columns(inner_dce.c, element_attributes, nesting_level),
-                *attribute_columns(inner_dc.c, collection_attributes, nesting_level),
-            )
+            q = q.join(inner_dce, inner_dce.c.dataset_collection_id == dce.c.child_collection_id)
+            if collection_attributes:
+                q = q.join(inner_dc, inner_dc.c.id == dce.c.child_collection_id)
+            q = q.add_columns(*attribute_columns(inner_dce.c, element_attributes, nesting_level))
+            if collection_attributes:
+                q = q.add_columns(
+                    *attribute_columns(inner_dc.c, collection_attributes, nesting_level),
+                )
             dce = inner_dce
             dc = inner_dc
             depth_collection_type = depth_collection_type.split(":", 1)[1]
@@ -6293,7 +6294,11 @@ def attribute_columns(column_collection, attributes, nesting_level=None):
             or return_entities
             and not return_entities == (DatasetCollectionElement,)
         ):
-            q = q.join(HistoryDatasetAssociation).join(Dataset)
+            q = q.join(HistoryDatasetAssociation)
+            if HistoryDatasetAssociation not in return_entities:
+                # if we do return HDAs we'll be joining on the dataset implicitly,
+                # so join here only if we're not already joining on dataset
+                q = q.join(Dataset)
         if dataset_permission_attributes:
             q = q.join(DatasetPermissions)
         q = (

From 234e6bd00d3323925a1a5c841b3db01e024f1adb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 22 Mar 2024 19:49:25 +0100
Subject: [PATCH 14/19] Return to outerjoin on dce

---
 lib/galaxy/model/__init__.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index d8ac3d2233ca..b087eec862fd 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -6273,7 +6273,7 @@ def attribute_columns(column_collection, attributes, nesting_level=None):
             inner_dce = alias(DatasetCollectionElement)
             inner_dc = alias(DatasetCollection)
             order_by_columns.append(inner_dce.c.element_index)
-            q = q.join(inner_dce, inner_dce.c.dataset_collection_id == dce.c.child_collection_id)
+            q = q.outerjoin(inner_dce, inner_dce.c.dataset_collection_id == dce.c.child_collection_id)
             if collection_attributes:
                 q = q.join(inner_dc, inner_dc.c.id == dce.c.child_collection_id)
             q = q.add_columns(*attribute_columns(inner_dce.c, element_attributes, nesting_level))
@@ -6294,11 +6294,7 @@ def attribute_columns(column_collection, attributes, nesting_level=None):
             or return_entities
             and not return_entities == (DatasetCollectionElement,)
         ):
-            q = q.join(HistoryDatasetAssociation)
-            if HistoryDatasetAssociation not in return_entities:
-                # if we do return HDAs we'll be joining on the dataset implicitly,
-                # so join here only if we're not already joining on dataset
-                q = q.join(Dataset)
+            q = q.join(HistoryDatasetAssociation).join(Dataset)
         if dataset_permission_attributes:
             q = q.join(DatasetPermissions)
         q = (

From c2904121248431a2795621e9edd6b5e85b9c4d89 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 23:49:18 -0400
Subject: [PATCH 15/19] Fix creation and association of new histories w/ brand
 new single/remote user

---
 lib/galaxy/webapps/base/webapp.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index c3c1dd8bbcf2..824abb45cbeb 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -936,8 +936,8 @@ def get_or_create_default_history(self):
             if default_history:
                 history = default_history
                 self.set_history(history)
-        else:
-            history = self.new_history()
+            else:
+                history = self.new_history()
 
         return history
 

From 1fdbb121dcfe21027fd08d07b3e27736c3a50663 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 20 Mar 2024 08:06:41 +0100
Subject: [PATCH 16/19] Create new history if user has no history AND for
 anonymous users

---
 lib/galaxy/webapps/base/webapp.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 824abb45cbeb..cd897139c4c7 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -938,6 +938,8 @@ def get_or_create_default_history(self):
                 self.set_history(history)
             else:
                 history = self.new_history()
+        else:
+            history = self.new_history()
 
         return history
 

From e3805c7bfb7b164b0b1c73aea0e391b919cbe4cb Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 20 Mar 2024 07:58:42 -0400
Subject: [PATCH 17/19] Refactoring for clarity.

---
 lib/galaxy/webapps/base/webapp.py | 26 +++++++++-----------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index cd897139c4c7..b9430a3774c0 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -912,36 +912,28 @@ def get_or_create_default_history(self):
         Gets or creates a default history and associates it with the current
         session.
         """
+
+        # Just return the current history if one exists and is not deleted.
         history = self.galaxy_session.current_history
         if history and not history.deleted:
             return history
 
+        # Look for an existing history that has the default name, is not
+        # deleted, and is empty. If this exists, we associate it with the
+        # current session and return it.
         user = self.galaxy_session.user
         if user:
-            # Look for default history that (a) has default name + is not deleted and
-            # (b) has no datasets. If suitable history found, use it; otherwise, create
-            # new history.
             stmt = select(self.app.model.History).filter_by(
                 user=user, name=self.app.model.History.default_name, deleted=False
             )
             unnamed_histories = self.sa_session.scalars(stmt)
-            default_history = None
             for history in unnamed_histories:
                 if history.empty:
-                    # Found suitable default history.
-                    default_history = history
-                    break
-
-            # Set or create history.
-            if default_history:
-                history = default_history
-                self.set_history(history)
-            else:
-                history = self.new_history()
-        else:
-            history = self.new_history()
+                    self.set_history(history)
+                    return history
 
-        return history
+        # No suitable history found, create a new one.
+        return self.new_history()
 
     def get_most_recent_history(self):
         """

From ed69e0f821ca5cab31baf908ea56329a7605bb29 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 12 Mar 2024 14:07:47 +0100
Subject: [PATCH 18/19] Npz sniffing: do not read the whole file

takes to much memory
---
 lib/galaxy/datatypes/binary.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index cc6702cd589f..fd58af3dcc97 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -4137,9 +4137,7 @@ def sniff(self, filename: str) -> bool:
         try:
             npz = np.load(filename)
             if isinstance(npz, np.lib.npyio.NpzFile):
-                for f in npz.files:
-                    if isinstance(npz[f], np.ndarray):
-                        return True
+                return True
         except Exception:
             return False
         return False

From 28c19ebadf42b13edf8e44ec55efcab6d61683f4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 12 Mar 2024 18:24:24 +0100
Subject: [PATCH 19/19] Assert that at least one file in npz zipfile ends with
 .npy

from https://pydoc.dev/numpy/latest/numpy.lib.npyio.NpzFile.html:

> NpzFile is used to load files in the NumPy .npz data archive format. It assumes that files in the archive have a .npy extension, other files are ignored.
---
 lib/galaxy/datatypes/binary.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index fd58af3dcc97..456dacc5ba05 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -4135,9 +4135,9 @@ def __init__(self, **kwd):
 
     def sniff(self, filename: str) -> bool:
         try:
-            npz = np.load(filename)
-            if isinstance(npz, np.lib.npyio.NpzFile):
-                return True
+            with np.load(filename) as npz:
+                if isinstance(npz, np.lib.npyio.NpzFile) and any(f.filename.endswith(".npy") for f in npz.zip.filelist):
+                    return True
         except Exception:
             return False
         return False