galaxyproject · jmchilton · Dec 10, 2024 · Dec 10, 2024 · Dec 13, 2024 · Dec 11, 2024
diff --git a/client/package.json b/client/package.json
@@ -45,6 +45,8 @@
     "@types/jest": "^29.5.12",
     "@vueuse/core": "^10.5.0",
     "@vueuse/math": "^10.9.0",
+    "ag-grid-community": "^30",
+    "ag-grid-vue": "^30",
     "assert": "^2.1.0",
     "axios": "^1.6.2",
     "babel-runtime": "^6.26.0",
@@ -106,11 +108,13 @@
     "vega-embed": "^6.26.0",
     "vega-lite": "^5.21.0",
     "vue": "^2.7.14",
+    "vue-class-component": "^7.2.6",
     "vue-echarts": "^7.0.3",
     "vue-infinite-scroll": "^2.0.2",
     "vue-multiselect": "^2.1.7",
     "vue-observe-visibility": "^1.0.0",
     "vue-prismjs": "^1.2.0",
+    "vue-property-decorator": "^9.1.2",
     "vue-router": "^3.6.5",
     "vue-rx": "^6.2.0",
     "vue-virtual-scroll-list": "^2.3.5",

diff --git a/client/src/api/index.ts b/client/src/api/index.ts
@@ -312,4 +312,8 @@ export type ObjectExportTaskResponse = components["schemas"]["ObjectExportTaskRe
 export type ExportObjectRequestMetadata = components["schemas"]["ExportObjectRequestMetadata"];
 export type ExportObjectResultMetadata = components["schemas"]["ExportObjectResultMetadata"];
 
+export type SampleSheetColumnDefinition = components["schemas"]["SampleSheetColumnDefinition"];
+export type SampleSheetColumnDefinitionType = SampleSheetColumnDefinition["type"];
+export type SampleSheetColumnDefinitions = SampleSheetColumnDefinition[] | null;
+
 export type AsyncTaskResultSummary = components["schemas"]["AsyncTaskResultSummary"];
diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
@@ -4060,6 +4060,23 @@ export interface paths {
         patch?: never;
         trace?: never;
     };
+    "/api/sample_sheet_workbook/generate": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Create an XLSX workbook for a sample sheet definition. */
+        get: operations["dataset_collections__workbook_download"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
     "/api/short_term_storage/{storage_request_id}": {
         parameters: {
             query?: never;
@@ -6929,6 +6946,11 @@ export interface components {
              * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`.
              */
             collection_type?: string | null;
+            /**
+             * Column Definitions
+             * @description Specify definitions for row data if collection_type if sample_sheet
+             */
+            column_definitions?: components["schemas"]["SampleSheetColumnDefinition"][] | null;
             /**
              * Content
              * @description Depending on the `source` it can be:
@@ -6982,6 +7004,13 @@ export interface components {
              * @description The name of the new collection.
              */
             name?: string | null;
+            /**
+             * Row data
+             * @description Specify rows of metadata data corresponding to an indentifier if collection_type is sample_sheet
+             */
+            rows?: {
+                [key: string]: (string | number | boolean)[];
+            } | null;
             /**
              * Source
              * @description The source of the content. Can be other history element to be copied or library elements.
@@ -7136,6 +7165,11 @@ export interface components {
              * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`.
              */
             collection_type?: string | null;
+            /**
+             * Column Definitions
+             * @description Specify definitions for row data if collection_type if sample_sheet
+             */
+            column_definitions?: components["schemas"]["SampleSheetColumnDefinition"][] | null;
             /**
              * Copy Elements
              * @description Whether to create a copy of the source HDAs for the new collection.
@@ -7174,6 +7208,13 @@ export interface components {
              * @description The name of the new collection.
              */
             name?: string | null;
+            /**
+             * Row data
+             * @description Specify rows of metadata data corresponding to an indentifier if collection_type is sample_sheet
+             */
+            rows?: {
+                [key: string]: (string | number | boolean)[];
+            } | null;
         };
         /** CreatePagePayload */
         CreatePagePayload: {
@@ -7774,6 +7815,11 @@ export interface components {
          * @description Dataset Collection Element summary information.
          */
         DCESummary: {
+            /**
+             * Columns
+             * @description A row (or list of columns) of data associated with this element
+             */
+            columns?: (string | number | boolean)[] | null;
             /**
              * Element Identifier
              * @description The actual name of this element.
@@ -10376,6 +10422,11 @@ export interface components {
              * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`.
              */
             collection_type?: string | null;
+            /**
+             * Column Definitions
+             * @description Column data associated with each element of this collection.
+             */
+            column_definitions?: components["schemas"]["SampleSheetColumnDefinition"][] | null;
             /**
              * Contents URL
              * @description The relative URL to access the contents of this History.
@@ -10515,6 +10566,11 @@ export interface components {
              * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`.
              */
             collection_type: string;
+            /**
+             * Column Definitions
+             * @description Column data associated with each element of this collection.
+             */
+            column_definitions?: components["schemas"]["SampleSheetColumnDefinition"][] | null;
             /**
              * Contents URL
              * @description The relative URL to access the contents of this History.
@@ -15735,6 +15791,24 @@ export interface components {
         RootModel_Dict_str__int__: {
             [key: string]: number;
         };
+        /** SampleSheetColumnDefinition */
+        SampleSheetColumnDefinition: {
+            /** Description */
+            description?: string | null;
+            /** Name */
+            name: string;
+            /** Restrictions */
+            restrictions?: string[] | null;
+            /** Suggestions */
+            suggestions?: string[] | null;
+            /**
+             * Type
+             * @enum {string}
+             */
+            type: "string" | "int" | "float" | "boolean";
+            /** Validators */
+            validators?: Record<string, never>[] | null;
+        };
         /** SearchJobsPayload */
         SearchJobsPayload: {
             /**
@@ -31902,6 +31976,50 @@ export interface operations {
             };
         };
     };
+    dataset_collections__workbook_download: {
+        parameters: {
+            query: {
+                /** @description Base64 encoding of column definitions. */
+                column_definitions: string;
+                /** @description Filename of the workbook download to generate */
+                filename?: string | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
     serve_api_short_term_storage__storage_request_id__get: {
         parameters: {
             query?: never;

diff --git a/client/src/components/Collections/CollectionCreatorModal.vue b/client/src/components/Collections/CollectionCreatorModal.vue
@@ -16,6 +16,7 @@ import type { CollectionType, DatasetPair } from "../History/adapters/buildColle
 import ListCollectionCreator from "./ListCollectionCreator.vue";
 import PairCollectionCreator from "./PairCollectionCreator.vue";
 import PairedListCollectionCreator from "./PairedListCollectionCreator.vue";
+import SampleSheetCollectionCreator from "./SampleSheetCollectionCreator.vue";
 import Heading from "@/components/Common/Heading.vue";
 import GenericItem from "@/components/History/Content/GenericItem.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
@@ -313,6 +314,15 @@ function resetModal() {
             :extensions="props.extensions"
             @clicked-create="createPairedCollection"
             @on-cancel="hideModal" />
+        <SampleSheetCollectionCreator
+            v-else-if="props.collectionType === 'sample_sheet'"
+            :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>
 

diff --git a/client/src/components/Collections/SampleSheetCollectionCreator.vue b/client/src/components/Collections/SampleSheetCollectionCreator.vue
@@ -0,0 +1,32 @@
+<script lang="ts" setup>
+import SampleSheetGrid from "./sheet/SampleSheetGrid.vue";
+
+const initialElements = [
+    ["https://zenodo.org/records/3263975/files/DRR000770.fastqsanger.gz", 1, "treatment1", false],
+    ["https://zenodo.org/records/3263975/files/DRR000771.fastqsanger.gz", 2, "treatment1", false],
+    ["https://zenodo.org/records/3263975/files/DRR000772.fastqsanger.gz", 1, "none", true],
+    ["https://zenodo.org/records/3263975/files/DRR000773.fastqsanger.gz", 1, "treatment2", false],
+    ["https://zenodo.org/records/3263975/files/DRR000774.fastqsanger.gz", 2, "treatment3", false],
+];
+
+const columnDefinitions = [
+    { name: "replicate number", type: "int", description: "The replicate number of this sample." },
+    {
+        name: "treatment",
+        type: "string",
+        restrictions: ["treatment1", "treatment2", "none"],
+        description: "The treatment code for this sample.",
+    },
+    {
+        name: "is control?",
+        type: "boolean",
+        description: "Was this sample a control? If TRUE, please ensure treatment is set to none.",
+    },
+];
+</script>
+
+<template>
+    <div class="sample-sheet-collection-creator">
+        <SampleSheetGrid :initial-elements="initialElements" :columnDefinitions="columnDefinitions" />
+    </div>
+</template>