Merge branch 'release_24.2' into merge_24.2_into_dev

client/src/api/datatypes.ts

@@ -0,0 +1,3 @@
+import { type components } from "@/api";
+
+export type CompositeFileInfo = components["schemas"]["CompositeFileInfo"];

client/src/api/histories.ts

@@ -0,0 +1,3 @@
+import { type components } from "@/api";
+
+export type HistoryContentsResult = components["schemas"]["HistoryContentsResult"];

client/src/components/Collections/CollectionCreatorModal.vue

@@ -0,0 +1,329 @@
+<script setup lang="ts">
+import { faCheckCircle, faUndo } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BAlert, BLink, BModal } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
+
+import type { HDASummary, HistoryItemSummary, HistorySummary } from "@/api";
+import { createDatasetCollection } from "@/components/History/model/queries";
+import { useCollectionBuilderItemsStore } from "@/stores/collectionBuilderItemsStore";
+import { useHistoryStore } from "@/stores/historyStore";
+import localize from "@/utils/localization";
+import { orList } from "@/utils/strings";
+
+import type { CollectionType, DatasetPair } from "../History/adapters/buildCollectionModal";
+
+import ListCollectionCreator from "./ListCollectionCreator.vue";
+import PairCollectionCreator from "./PairCollectionCreator.vue";
+import PairedListCollectionCreator from "./PairedListCollectionCreator.vue";
+import Heading from "@/components/Common/Heading.vue";
+import GenericItem from "@/components/History/Content/GenericItem.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+interface Props {
+    historyId: string;
+    showModal: boolean;
+    collectionType: CollectionType;
+    selectedItems?: HistoryItemSummary[];
+    defaultHideSourceItems?: boolean;
+    extensions?: string[];
+    fromRulesInput?: boolean;
+    hideModalOnCreate?: boolean;
+    filterText?: string;
+}
+const props = defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "created-collection", collection: any): void;
+    (e: "update:show-modal", showModal: boolean): void;
+}>();
+
+/** Computed toggle that handles opening and closing the modal */
+const localShowToggle = computed({
+    get: () => props.showModal,
+    set: (value: boolean) => {
+        emit("update:show-modal", value);
+    },
+});
+
+// Create Collection refs
+const creatingCollection = ref(false);
+const createCollectionError = ref<string | null>(null);
+const createdCollection = ref<any>(null);
+
+// History items variables
+const historyItemsError = ref<string | null>(null);
+const collectionItemsStore = useCollectionBuilderItemsStore();
+const historyStore = useHistoryStore();
+const history = computed(() => historyStore.getHistoryById(props.historyId));
+const historyId = computed(() => props.historyId);
+const localFilterText = computed(() => props.filterText || "");
+const historyUpdateTime = computed(() => history.value?.update_time);
+const isFetchingItems = computed(() => collectionItemsStore.isFetching[localFilterText.value]);
+const historyDatasets = computed(() => {
+    if (collectionItemsStore.cachedDatasetsForFilterText) {
+        return collectionItemsStore.cachedDatasetsForFilterText[localFilterText.value] || [];
+    } else {
+        return [];
+    }
+});
+
+/** Flag for the initial fetch of history items */
+const initialFetch = ref(false);
+
+/** Whether a list of items was selected to create a collection from */
+const fromSelection = computed(() => !!props.selectedItems?.length);
+
+/** Items to create the collection from */
+const creatorItems = computed(() => (fromSelection.value ? props.selectedItems : historyDatasets.value));
+
+watch(
+    () => localShowToggle.value,
+    async (show) => {
+        if (show) {
+            await fetchHistoryDatasets();
+            if (!initialFetch.value) {
+                initialFetch.value = true;
+            }
+        }
+    },
+    { immediate: true }
+);
+
+// Fetch items when history ID or update time changes, only if localShowToggle is true
+watch([historyId, historyUpdateTime, localFilterText], async () => {
+    if (localShowToggle.value) {
+        await fetchHistoryDatasets();
+    }
+});
+
+// If there is a change in `historyDatasets`, but we have selected items, we should update the selected items
+watch(
+    () => historyDatasets.value,
+    (newDatasets) => {
+        if (fromSelection.value) {
+            // find each selected item in the new datasets, and update it
+            props.selectedItems?.forEach((selectedItem) => {
+                const newDataset = newDatasets.find((dataset) => dataset.id === selectedItem.id);
+                if (newDataset) {
+                    Object.assign(selectedItem, newDataset);
+                }
+            });
+        }
+    }
+);
+
+const modalTitle = computed(() => {
+    if (props.collectionType === "list") {
+        return localize(
+            `Create a collection from a list of ${fromSelection.value ? "selected" : ""} ${
+                props.extensions?.length ? orList(props.extensions) : ""
+            } datasets`
+        );
+    } else if (props.collectionType === "list:paired") {
+        return localize(
+            `Create a collection of ${fromSelection.value ? "selected" : ""} ${
+                props.extensions?.length ? orList(props.extensions) : ""
+            } dataset pairs`
+        );
+    } else if (props.collectionType === "paired") {
+        return localize(
+            `Create a ${props.extensions?.length ? orList(props.extensions) : ""} dataset pair collection ${
+                fromSelection.value ? "from selected items" : ""
+            }`
+        );
+    } else {
+        return localize("Create a collection");
+    }
+});
+
+// Methods
+function createListCollection(elements: HDASummary[], name: string, hideSourceItems: boolean) {
+    const returnedElems = elements.map((element) => ({
+        id: element.id,
+        name: element.name,
+        //TODO: this allows for list:list even if the implementation does not - reconcile
+        src: "src" in element ? element.src : element.history_content_type == "dataset" ? "hda" : "hdca",
+    }));
+    return createHDCA(returnedElems, "list", name, hideSourceItems);
+}
+
+function createListPairedCollection(elements: DatasetPair[], name: string, hideSourceItems: boolean) {
+    const returnedElems = elements.map((pair) => ({
+        collection_type: "paired",
+        src: "new_collection",
+        name: pair.name,
+        element_identifiers: [
+            {
+                name: "forward",
+                id: pair.forward.id,
+                src: "src" in pair.forward ? pair.forward.src : "hda",
+            },
+            {
+                name: "reverse",
+                id: pair.reverse.id,
+                src: "src" in pair.reverse ? pair.reverse.src : "hda",
+            },
+        ],
+    }));
+    return createHDCA(returnedElems, "list:paired", name, hideSourceItems);
+}
+
+function createPairedCollection(elements: DatasetPair, name: string, hideSourceItems: boolean) {
+    const { forward, reverse } = elements;
+    const returnedElems = [
+        { name: "forward", src: "src" in forward ? forward.src : "hda", id: forward.id },
+        { name: "reverse", src: "src" in reverse ? reverse.src : "hda", id: reverse.id },
+    ];
+    return createHDCA(returnedElems, "paired", name, hideSourceItems);
+}
+
+async function createHDCA(
+    element_identifiers: any[],
+    collection_type: CollectionType,
+    name: string,
+    hide_source_items: boolean,
+    options = {}
+) {
+    try {
+        creatingCollection.value = true;
+        const collection = await createDatasetCollection(history.value as HistorySummary, {
+            collection_type,
+            name,
+            hide_source_items,
+            element_identifiers,
+            options,
+        });
+
+        emit("created-collection", collection);
+        createdCollection.value = collection;
+
+        if (props.hideModalOnCreate) {
+            hideModal();
+        }
+    } catch (error) {
+        createCollectionError.value = error as string;
+    } finally {
+        creatingCollection.value = false;
+    }
+}
+
+async function fetchHistoryDatasets() {
+    const { error } = await collectionItemsStore.fetchDatasetsForFiltertext(
+        historyId.value,
+        historyUpdateTime.value,
+        localFilterText.value
+    );
+    if (error) {
+        historyItemsError.value = error;
+        console.error("Error fetching history items:", historyItemsError.value);
+    } else {
+        historyItemsError.value = null;
+    }
+}
+
+function hideModal() {
+    localShowToggle.value = false;
+}
+
+function resetModal() {
+    createCollectionError.value = null;
+    createdCollection.value = null;
+}
+</script>
+
+<template>
+    <BModal
+        id="collection-creator-modal"
+        v-model="localShowToggle"
+        :busy="(fromSelection && isFetchingItems) || creatingCollection"
+        modal-class="ui-modal collection-creator-modal"
+        :hide-footer="!createdCollection && !createCollectionError"
+        :ok-disabled="!!createdCollection || !!createCollectionError"
+        :cancel-title="localize('Exit')"
+        footer-class="d-flex justify-content-between"
+        :ok-title="localize('Create Collection')"
+        @hidden="resetModal">
+        <template v-slot:modal-header>
+            <Heading class="w-100" size="sm">
+                <div class="d-flex justify-content-between unselectable w-100">
+                    <div>{{ modalTitle }}</div>
+                    <div v-if="!!history">
+                        From history: <b>{{ history.name }}</b>
+                    </div>
+                </div>
+            </Heading>
+        </template>
+        <BAlert v-if="isFetchingItems && !initialFetch" variant="info" show>
+            <LoadingSpan :message="localize('Loading items')" />
+        </BAlert>
+        <BAlert v-else-if="!fromSelection && historyItemsError" variant="danger" show>
+            {{ historyItemsError }}
+        </BAlert>
+        <BAlert v-else-if="!creatorItems?.length" variant="info" show>
+            {{ localize("No items available to create a collection.") }}
+        </BAlert>
+        <BAlert v-else-if="creatingCollection" variant="info" show>
+            <LoadingSpan :message="localize('Creating collection')" />
+        </BAlert>
+        <BAlert v-else-if="createCollectionError" variant="danger" show>
+            {{ createCollectionError }}
+            <BLink class="text-decoration-none" @click.stop.prevent="resetModal">
+                <FontAwesomeIcon :icon="faUndo" fixed-width />
+                {{ localize("Try again") }}
+            </BLink>
+        </BAlert>
+        <div v-else-if="createdCollection">
+            <BAlert variant="success" show>
+                <FontAwesomeIcon :icon="faCheckCircle" class="text-success" fixed-width />
+                {{ localize("Collection created successfully.") }}
+                <BLink v-if="!fromSelection" class="text-decoration-none" @click.stop.prevent="resetModal">
+                    <FontAwesomeIcon :icon="faUndo" fixed-width />
+                    {{ localize("Create another collection") }}
+                </BLink>
+            </BAlert>
+
+            <!-- TODO: This is a bit shady, better if we confirm it is a collection type -->
+            <GenericItem :item-id="createdCollection.id" item-src="hdca" />
+        </div>
+        <ListCollectionCreator
+            v-else-if="props.collectionType === 'list'"
+            :history-id="props.historyId"
+            :initial-elements="creatorItems"
+            :default-hide-source-items="props.defaultHideSourceItems"
+            :from-selection="fromSelection"
+            :extensions="props.extensions"
+            @clicked-create="createListCollection"
+            @on-cancel="hideModal" />
+        <PairedListCollectionCreator
+            v-else-if="props.collectionType === 'list:paired'"
+            :history-id="props.historyId"
+            :initial-elements="creatorItems"
+            :default-hide-source-items="props.defaultHideSourceItems"
+            :from-selection="fromSelection"
+            :extensions="props.extensions"
+            @clicked-create="createListPairedCollection"
+            @on-cancel="hideModal" />
+        <PairCollectionCreator
+            v-else-if="props.collectionType === 'paired'"
+            :history-id="props.historyId"
+            :initial-elements="creatorItems"
+            :default-hide-source-items="props.defaultHideSourceItems"
+            :from-selection="fromSelection"
+            :extensions="props.extensions"
+            @clicked-create="createPairedCollection"
+            @on-cancel="hideModal" />
+    </BModal>
+</template>
+
+<style lang="scss">
+/** NOTE: Not using `<style scoped> here because these classes are
+`BModal` `body-class` and `content-class` and don't seem to work
+with scoped */
+.collection-creator-modal {
+    .modal-dialog {
+        width: 85%;
+        max-width: 100%;
+    }
+}
+</style>