From f7932e2742a33bc4d24d9b9ab957e2aef057bc4d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 2 Jan 2025 12:52:10 -0500
Subject: [PATCH] Activity for rule builder imports.

---
 .../Collections/BuildFileSetWizard.vue        | 59 +++++++++++++++++--
 .../src/components/Collections/ListWizard.vue | 35 +++--------
 .../Collections/RulesStandalone.vue           | 35 +++++++++++
 .../common/useCollectionCreator.ts            | 22 ++++++-
 .../Common/Wizard/GenericWizard.vue           | 11 +++-
 .../src/components/Common/Wizard/useWizard.ts |  6 ++
 .../src/components/RuleCollectionBuilder.vue  | 24 +++++---
 .../src/components/Upload/UploadContainer.vue | 14 -----
 client/src/entry/analysis/router.js           | 11 ++++
 client/src/stores/activitySetup.ts            | 14 +++++
 lib/galaxy/webapps/galaxy/buildapp.py         |  1 +
 11 files changed, 176 insertions(+), 56 deletions(-)
 create mode 100644 client/src/components/Collections/RulesStandalone.vue

diff --git a/client/src/components/Collections/BuildFileSetWizard.vue b/client/src/components/Collections/BuildFileSetWizard.vue
index 9d659ce1e528..c74a53202c37 100644
--- a/client/src/components/Collections/BuildFileSetWizard.vue
+++ b/client/src/components/Collections/BuildFileSetWizard.vue
@@ -3,6 +3,8 @@ import { BCardGroup } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
 import { getGalaxyInstance } from "@/app";
+import { attemptCreate, type CollectionCreatorComponent } from "@/components/Collections/common/useCollectionCreator";
+import { rawToTable } from "@/components/Collections/tables";
 import { useWizard } from "@/components/Common/Wizard/useWizard";
 import { useToolRouting } from "@/composables/route";
 
@@ -18,6 +20,7 @@ import SourceFromDatasetAsTable from "./wizard/SourceFromDatasetAsTable.vue";
 import SourceFromPastedData from "./wizard/SourceFromPastedData.vue";
 import SourceFromRemoteFiles from "./wizard/SourceFromRemoteFiles.vue";
 import GenericWizard from "@/components/Common/Wizard/GenericWizard.vue";
+import RuleCollectionBuilder from "@/components/RuleCollectionBuilder.vue";
 
 const isBusy = ref<boolean>(false);
 const { pasteData, tabularDatasetContents, uris, setRemoteFilesFolder, onFtp, setDatasetContents, setPasteTable } =
@@ -26,10 +29,12 @@ const { pasteData, tabularDatasetContents, uris, setRemoteFilesFolder, onFtp, se
 interface Props {
     fileSourcesConfigured: boolean;
     ftpUploadSite?: string;
+    mode: "uploadModal" | "standalone";
 }
 
 const props = defineProps<Props>();
 
+const ruleState = ref(false);
 const creatingWhat = ref<RulesCreatingWhat>("datasets");
 const creatingWhatTitle = computed(() => {
     return creatingWhat.value == "datasets" ? "Datasets" : "Collections";
@@ -37,6 +42,7 @@ const creatingWhatTitle = computed(() => {
 const sourceInstructions = computed(() => {
     return `${creatingWhatTitle.value} can be created from a set or files, URIs, or existing datasets.`;
 });
+const collectionCreator = ref<CollectionCreatorComponent | undefined>();
 
 const sourceFrom = ref<RulesSourceFrom>("remote_files");
 
@@ -65,7 +71,7 @@ const wizard = useWizard({
     },
     "paste-data": {
         label: "Paste data",
-        instructions: "Paste data containing URIs and optional extra metadata.",
+        instructions: "Paste data (or drop file) containing URIs and optional extra metadata.",
         isValid: () => sourceFrom.value === "pasted_table" && pasteData.value.length > 0,
         isSkippable: () => sourceFrom.value !== "pasted_table",
     },
@@ -75,6 +81,13 @@ const wizard = useWizard({
         isValid: () => sourceFrom.value === "dataset_as_table" && tabularDatasetContents.value.length > 0,
         isSkippable: () => sourceFrom.value !== "dataset_as_table",
     },
+    "rule-builder": {
+        label: "Specify Rules",
+        instructions: "Use this form to describe rules for importing",
+        isValid: () => ruleState.value,
+        isSkippable: () => props.mode == "uploadModal",
+        width: "100%",
+    },
 });
 
 const importButtonLabel = computed(() => {
@@ -85,7 +98,7 @@ const importButtonLabel = computed(() => {
     }
 });
 
-const emit = defineEmits(["dismiss"]);
+const emit = defineEmits(["dismiss", "created"]);
 type SelectionType = "raw" | "remote_files";
 type ElementsType = RemoteFile[] | string[][];
 
@@ -101,8 +114,7 @@ interface Entry {
     selectionType: SelectionType;
 }
 
-function launchRuleBuilder() {
-    const Galaxy = getGalaxyInstance();
+const ruleBuilderModalEntryProps = computed(() => {
     let elements: ElementsType | undefined = undefined;
     let selectionType: SelectionType = "raw";
     if (sourceFrom.value == "remote_files") {
@@ -119,12 +131,31 @@ function launchRuleBuilder() {
         selectionType: selectionType,
         elements: elements,
     };
+    return entry;
+});
+
+const ruleBuilderElements = computed(() => {
+    const builderProps = ruleBuilderModalEntryProps.value;
+    let elements;
+    if (builderProps.elements) {
+        elements = builderProps.elements;
+    } else {
+        elements = rawToTable(builderProps.content || "");
+    }
+    return elements;
+});
+
+function launchRuleBuilder() {
+    const Galaxy = getGalaxyInstance();
+    const entry = ruleBuilderModalEntryProps.value;
     Galaxy.currHistoryPanel.buildCollectionFromRules(entry, null, true);
 }
 
 function submit() {
     if (sourceFrom.value == "collection") {
         routeToTool("__APPLY_RULES__");
+    } else if (props.mode == "standalone") {
+        attemptCreate(collectionCreator);
     } else {
         launchRuleBuilder();
     }
@@ -138,6 +169,15 @@ function setCreatingWhat(what: RulesCreatingWhat) {
 function setSourceForm(newValue: RulesSourceFrom) {
     sourceFrom.value = newValue;
 }
+
+function onRuleState(newRuleState: boolean) {
+    ruleState.value = newRuleState;
+}
+
+function onRuleCreate() {
+    // axios response data for job currently sent, not really used but wanted to document what is available.
+    emit("created");
+}
 </script>
 
 <template>
@@ -165,5 +205,16 @@ function setSourceForm(newValue: RulesSourceFrom) {
         <div v-else-if="wizard.isCurrent('select-dataset')">
             <SelectDataset @onChange="setDatasetContents" />
         </div>
+        <div v-else-if="wizard.isCurrent('rule-builder')" style="width: 100%">
+            <RuleCollectionBuilder
+                ref="collectionCreator"
+                grid-implementation="ag"
+                :import-type="creatingWhat"
+                :elements-type="ruleBuilderModalEntryProps.selectionType"
+                :initial-elements="ruleBuilderElements"
+                mode="wizard"
+                @onCreate="onRuleCreate"
+                @validInput="onRuleState" />
+        </div>
     </GenericWizard>
 </template>
diff --git a/client/src/components/Collections/ListWizard.vue b/client/src/components/Collections/ListWizard.vue
index d584f818db52..2f493c06ee22 100644
--- a/client/src/components/Collections/ListWizard.vue
+++ b/client/src/components/Collections/ListWizard.vue
@@ -13,7 +13,11 @@ import { useCollectionBuilderItemSelection } from "@/stores/collectionBuilderIte
 import { errorMessageAsString } from "@/utils/simple-error";
 
 import { useCollectionCreation } from "./common/useCollectionCreation";
-import { type SupportedPairedOrPairedBuilderCollectionTypes } from "./common/useCollectionCreator";
+import {
+    attemptCreate,
+    type CollectionCreatorComponent,
+    type SupportedPairedOrPairedBuilderCollectionTypes,
+} from "./common/useCollectionCreator";
 import { type WhichListBuilder } from "./ListWizard/types";
 import { autoPairWithCommonFilters } from "./pairing";
 
@@ -40,9 +44,6 @@ const creationError = ref<string | null>(null);
 const collectionCreated = ref(false);
 
 type InferrableBuilder = "list" | "list:paired";
-type CollectionCreatorComponent =
-    | InstanceType<typeof ListCollectionCreator>
-    | InstanceType<typeof PairedOrUnpairedListCollectionCreator>;
 const collectionCreator = ref<CollectionCreatorComponent>();
 const { selectedItems } = storeToRefs(store);
 
@@ -155,26 +156,15 @@ const pairedListType = computed(() => {
     return whichBuilder.value == "list:paired_or_unpaired" ? "list:paired_or_unpaired" : "list:paired";
 });
 
-async function attemptCreate(creator: CollectionCreatorComponent) {
-    // fight typing to workaround https://github.com/vuejs/core/issues/10077
-    interface HasAttemptCreate {
-        attemptCreate: () => Promise<void>;
-    }
-
-    (creator as unknown as HasAttemptCreate).attemptCreate();
-}
-
 async function submit() {
     if (collectionCreator.value) {
-        attemptCreate(collectionCreator.value);
+        attemptCreate(collectionCreator);
     }
 }
 
 async function onCreate(payload: CreateNewCollectionPayload) {
     try {
-        const data = await createHistoryDatasetCollectionInstanceFull(payload);
-        console.log(data);
-        console.log("collection created!");
+        await createHistoryDatasetCollectionInstanceFull(payload);
         collectionCreated.value = true;
     } catch (e) {
         creationError.value = errorMessageAsString(e);
@@ -213,18 +203,9 @@ function goToAutoPairing() {
     wizard.goTo("auto-pairing");
 }
 
-function onRuleCreate() {
-    return 3;
-}
-
-function onRuleCancel() {
-    return 3;
-}
-
 const ruleState = ref(false);
 
 function onRuleState(newRuleState: boolean) {
-    console.log("in on Rule state...");
     ruleState.value = newRuleState;
 }
 </script>
@@ -288,8 +269,6 @@ function onRuleState(newRuleState: boolean) {
                     elements-type="datasets"
                     :initial-elements="selectedItems || []"
                     mode="wizard"
-                    :oncreate="onRuleCreate"
-                    :oncancel="onRuleCancel"
                     @onAttemptCreate="ruleOnAttemptCreate"
                     @validInput="onRuleState" />
             </div>
diff --git a/client/src/components/Collections/RulesStandalone.vue b/client/src/components/Collections/RulesStandalone.vue
new file mode 100644
index 000000000000..fa06e7a4f158
--- /dev/null
+++ b/client/src/components/Collections/RulesStandalone.vue
@@ -0,0 +1,35 @@
+<script setup lang="ts">
+import { BAlert, BContainer, BRow } from "bootstrap-vue";
+import { ref } from "vue";
+
+import { useConfig } from "@/composables/config";
+
+import BuildFileSetWizard from "./BuildFileSetWizard.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+const { config, isConfigLoaded } = useConfig();
+
+const created = ref(false);
+
+function onCreated() {
+    created.value = true;
+}
+</script>
+
+<template>
+    <BContainer>
+        <LoadingSpan v-if="!isConfigLoaded" />
+        <BRow v-else-if="created">
+            <BAlert show variant="success" style="width: 100%">
+                Data imported and should be available in your history.
+            </BAlert>
+        </BRow>
+        <div v-else>
+            <BuildFileSetWizard
+                mode="standalone"
+                :file-sources-configured="config.file_sources_configured"
+                :ftp-upload-site="config.ftp_upload_site"
+                @created="onCreated" />
+        </div>
+    </BContainer>
+</template>
diff --git a/client/src/components/Collections/common/useCollectionCreator.ts b/client/src/components/Collections/common/useCollectionCreator.ts
index d2f76d0f932e..46bce28ff5bf 100644
--- a/client/src/components/Collections/common/useCollectionCreator.ts
+++ b/client/src/components/Collections/common/useCollectionCreator.ts
@@ -1,10 +1,13 @@
-import { computed, ref, watch } from "vue";
+import { computed, type Ref, ref, unref, watch } from "vue";
 
 import { type HistoryItemSummary } from "@/api";
 import { type CollectionElementIdentifiers, type CreateNewCollectionPayload } from "@/api/datasetCollections";
+import type RuleCollectionBuilder from "@/components/RuleCollectionBuilder.vue";
 import STATES from "@/mvc/dataset/states";
 import localize from "@/utils/localization";
 
+import type ListCollectionCreator from "./ListCollectionCreator.vue";
+import type PairedOrUnpairedListCollectionCreator from "./PairedOrUnpairedListCollectionCreator.vue";
 import { useCollectionCreation } from "./useCollectionCreation";
 import { useExtensionFiltering } from "./useExtensionFilter";
 
@@ -28,6 +31,23 @@ export type SupportedPairedOrPairedBuilderCollectionTypes =
     | "list:list"
     | "list:list:paired";
 
+export type CollectionCreatorComponent =
+    | InstanceType<typeof ListCollectionCreator>
+    | InstanceType<typeof PairedOrUnpairedListCollectionCreator>
+    | InstanceType<typeof RuleCollectionBuilder>;
+
+export async function attemptCreate(creator: CollectionCreatorComponent | Ref<CollectionCreatorComponent | undefined>) {
+    const creatorValue: CollectionCreatorComponent | undefined = unref(creator);
+    // fight typing to workaround https://github.com/vuejs/core/issues/10077
+    interface HasAttemptCreate {
+        attemptCreate: () => Promise<void>;
+    }
+
+    if (creatorValue) {
+        (creatorValue as unknown as HasAttemptCreate).attemptCreate();
+    }
+}
+
 export function useCollectionCreator(props: CommonCollectionBuilderProps, emit?: EmitsName) {
     const removeExtensions = ref(true);
     const hideSourceItems = ref(props.defaultHideSourceItems || false);
diff --git a/client/src/components/Common/Wizard/GenericWizard.vue b/client/src/components/Common/Wizard/GenericWizard.vue
index b51e60df43ae..dc75454e5f0f 100644
--- a/client/src/components/Common/Wizard/GenericWizard.vue
+++ b/client/src/components/Common/Wizard/GenericWizard.vue
@@ -125,6 +125,15 @@ const stepsGridColumnsTemplate = computed(() => {
             .join(" ") + " max-content"
     );
 });
+
+const bodyStyle = computed(() => {
+    const width = props.use.current.value.width;
+    if (width) {
+        return { width: width };
+    } else {
+        return {};
+    }
+});
 </script>
 
 <template>
@@ -158,7 +167,7 @@ const stepsGridColumnsTemplate = computed(() => {
             <div class="step-content">
                 <span class="h-md step-instructions" v-text="props.use.current.value.instructions" />
 
-                <div class="step-body">
+                <div class="step-body" :style="bodyStyle">
                     <slot>
                         <p>
                             Missing body for step <b>{{ props.use.current.value.label }}</b>
diff --git a/client/src/components/Common/Wizard/useWizard.ts b/client/src/components/Common/Wizard/useWizard.ts
index f863347fdad6..569b687d621a 100644
--- a/client/src/components/Common/Wizard/useWizard.ts
+++ b/client/src/components/Common/Wizard/useWizard.ts
@@ -25,6 +25,12 @@ export interface WizardStep {
      * This is useful for optional or conditional steps.
      */
     isSkippable: () => boolean;
+
+    /**
+     * Hack added by John, someone component in CSS should undo this or come up
+     * with an alternative that doesn't require this to be set.
+     */
+    hackBodyWidth?: string;
 }
 
 /**
diff --git a/client/src/components/RuleCollectionBuilder.vue b/client/src/components/RuleCollectionBuilder.vue
index f506fa5179eb..9099abd30421 100644
--- a/client/src/components/RuleCollectionBuilder.vue
+++ b/client/src/components/RuleCollectionBuilder.vue
@@ -553,7 +553,7 @@
                 )
             }}
         </RuleModalHeader>
-        <RuleModalFooter>
+        <RuleModalFooter v-if="mode == 'modal'">
             <b-button class="creator-cancel-btn" tabindex="-1" @click="cancel">{{ l("Close") }}</b-button>
         </RuleModalFooter>
     </StateDiv>
@@ -563,7 +563,7 @@
         <RuleModalMiddle>
             <p class="errormessagelarge">{{ errorMessage }}</p>
         </RuleModalMiddle>
-        <RuleModalFooter>
+        <RuleModalFooter v-if="mode == 'modal'">
             <b-button v-b-tooltip.hover :title="titleCancel" class="creator-cancel-btn" tabindex="-1" @click="cancel">{{
                 l("Close")
             }}</b-button>
@@ -671,14 +671,16 @@ export default {
             required: false,
             default: true,
         },
-        // Callbacks sent in by modal code.
+        // Callbacks sent in by modal code, optional if mode is not modal
         oncancel: {
-            required: true,
+            required: false,
             type: Function,
+            default: null,
         },
         oncreate: {
-            required: true,
+            required: false,
             type: Function,
+            default: null,
         },
         ftpUploadSite: {
             type: String,
@@ -1178,7 +1180,6 @@ export default {
             }
         },
         validInput: function (newState) {
-            console.log("watching validInput....");
             this.$emit("validInput", newState);
         },
     },
@@ -1372,7 +1373,11 @@ export default {
                     this.doFullJobCheck(jobId);
                 } else {
                     refreshContentsWrapper();
-                    this.oncreate();
+                    this.$emit("onCreate", jobResponse.data);
+                    if (this.oncreate) {
+                        // legacy non-event handling
+                        this.oncreate();
+                    }
                 }
             };
             const doJobCheck = () => {
@@ -1470,7 +1475,10 @@ export default {
                 this.resetSource();
                 if (this.state !== "error") {
                     this.saveRulesFn(this.ruleSourceJson);
-                    this.oncreate();
+                    this.$emit("onCreate");
+                    if (this.oncreate) {
+                        this.oncreate();
+                    }
                 }
             } else {
                 const Galaxy = getGalaxyInstance();
diff --git a/client/src/components/Upload/UploadContainer.vue b/client/src/components/Upload/UploadContainer.vue
index 9922d1325adb..7b918c349545 100644
--- a/client/src/components/Upload/UploadContainer.vue
+++ b/client/src/components/Upload/UploadContainer.vue
@@ -13,7 +13,6 @@ import { storeToRefs } from "pinia";
 import { computed, onMounted, ref } from "vue";
 
 import { canMutateHistory } from "@/api";
-import BuildFileSetWizard from "@/components/Collections/BuildFileSetWizard";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useUploadStore } from "@/stores/uploadStore";
 import { uploadPayload } from "@/utils/upload-payload.js";
@@ -205,19 +204,6 @@ defineExpose({
                 :history-id="currentHistoryId"
                 v-on="$listeners" />
         </BTab>
-        <BTab
-            v-if="showRules"
-            id="rule-based-import"
-            title="Rule-based (beta)"
-            button-id="tab-title-link-rule-based-import"
-            no-body>
-            <BuildFileSetWizard
-                :file-sources-configured="fileSourcesConfigured"
-                :ftp-upload-site="currentUserId && ftpUploadSite"
-                :has-callback="hasCallback"
-                :history-id="currentHistoryId"
-                v-on="$listeners" />
-        </BTab>
         <DefaultBox
             v-if="showRegular || showCollection"
             v-show="regularTabActive || collectionTabActive"
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 1da3e853b418..6112acbc6df4 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -68,6 +68,7 @@ import { patchRouterPush } from "./router-push";
 
 import AboutGalaxy from "@/components/AboutGalaxy.vue";
 import ListWizard from "@/components/Collections/ListWizard.vue";
+import RulesStandalone from "@/components/Collections/RulesStandalone.vue";
 import EditFileSourceInstance from "@/components/FileSources/Instances/EditInstance.vue";
 import ManageFileSourceIndex from "@/components/FileSources/Instances/ManageIndex.vue";
 import UpgradeFileSourceInstance from "@/components/FileSources/Instances/UpgradeInstance.vue";
@@ -504,6 +505,16 @@ export function getRouter(Galaxy) {
                         component: TourRunner,
                         props: true,
                     },
+                    {
+                        path: "rules",
+                        component: RulesStandalone,
+                        props: (route) => {
+                            return {
+                                mode: "standalone",
+                                ...route.query,
+                            };
+                        },
+                    },
                     {
                         path: "tools/list",
                         component: ToolsList,
diff --git a/client/src/stores/activitySetup.ts b/client/src/stores/activitySetup.ts
index af494b4b0409..60e1277a224d 100644
--- a/client/src/stores/activitySetup.ts
+++ b/client/src/stores/activitySetup.ts
@@ -13,6 +13,7 @@ import {
     faList,
     faPlay,
     faSitemap,
+    faTable,
     faUpload,
     faWrench,
 } from "@fortawesome/free-solid-svg-icons";
@@ -164,6 +165,19 @@ export const defaultActivities = [
         to: "/libraries",
         visible: true,
     },
+    {
+        anonymous: true,
+        description: "Rule-based advanced import of datasets or collections.",
+        icon: faTable,
+        id: "rules",
+        mutable: false,
+        optional: true,
+        panel: false,
+        title: "Rule-based Data Import",
+        tooltip: "Launch rule-based advanced import of datasets or collections",
+        to: "/rules",
+        visible: false,
+    },
 ] as const;
 
 export function convertDropData(data: EventData): Activity | null {
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 5514bb9f8f0e..5918834bd6d6 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -285,6 +285,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     webapp.add_client_route("/collection/new_list")
     webapp.add_client_route("/jobs/submission/success")
     webapp.add_client_route("/jobs/{job_id}/view")
+    webapp.add_client_route("/rules")
     webapp.add_client_route("/wizard")
     webapp.add_client_route("/workflows/list")
     webapp.add_client_route("/workflows/list_published")