WIP: sample sheets...

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"];

client/src/components/Workflow/Editor/Forms/FormCollectionType.vue

@@ -23,6 +23,7 @@ const collectionTypeOptions = [
     { value: "list", label: "List of Datasets" },
     { value: "paired", label: "Dataset Pair" },
     { value: "list:paired", label: "List of Dataset Pairs" },
+    { value: "sample_sheet", label: "Sample Sheet of Datasets" },
 ];
 
 function updateValue(newValue: string | undefined) {

client/src/components/Workflow/Editor/Forms/FormColumnDefinition.vue

@@ -0,0 +1,56 @@
+<script setup lang="ts">
+import { type SampleSheetColumnDefinition, type SampleSheetColumnDefinitionType } from "@/api";
+
+import FormColumnDefinitionType from "./FormColumnDefinitionType.vue";
+import FormElement from "@/components/Form/FormElement.vue";
+
+interface Props {
+    value: SampleSheetColumnDefinition;
+    index: number;
+    prefix: string; // prefix for ID objects
+}
+
+const props = defineProps<Props>();
+
+const emit = defineEmits(["onChange"]);
+
+function stateCopy(): SampleSheetColumnDefinition {
+    return JSON.parse(JSON.stringify(props.value));
+}
+
+function onName(name: string) {
+    const state = stateCopy();
+    state.name = name;
+    emit("onChange", state, props.index);
+}
+
+function onType(newType: SampleSheetColumnDefinitionType) {
+    const state = stateCopy();
+
+    state.type = newType;
+    emit("onChange", state, props.index);
+}
+</script>
+
+<template>
+    <div>
+        <FormElement
+            :id="prefix + '_name'"
+            :value="value.name"
+            title="Name"
+            type="text"
+            help="Provide a short, unique name to describe this column."
+            @input="onName" />
+        <FormColumnDefinitionType :value="value.type" :prefix="prefix" @onChange="onType" />
+        <FormElement
+            :id="prefix + '_description'"
+            :value="value.description"
+            title="Description"
+            type="text"
+            help="Provide a longer description to help people running this workflow under what is expected to be entered in this column."
+            @input="onName" />
+        TODO: There are more fields to enter here including restrictions and validations that vary based on the type
+        chosen. There will be a lot of overlap with the same validation options for workflow parameters so it might be
+        best to wait until those components can be developed in parallel.
+    </div>
+</template>

client/src/components/Workflow/Editor/Forms/FormColumnDefinitions.vue

@@ -0,0 +1,148 @@
+<script setup lang="ts">
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faCaretDown, faCaretUp, faPlus, faTrashAlt } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BLink } from "bootstrap-vue";
+import { computed } from "vue";
+
+import { type SampleSheetColumnDefinition, type SampleSheetColumnDefinitions } from "@/api";
+import localize from "@/utils/localization";
+
+import FormColumnDefinition from "./FormColumnDefinition.vue";
+import FormCard from "@/components/Form/FormCard.vue";
+
+library.add(faPlus, faTrashAlt, faCaretUp, faCaretDown);
+
+interface Props {
+    value: SampleSheetColumnDefinitions;
+}
+
+const props = defineProps<Props>();
+
+function addColumn() {
+    const state = stateCopy();
+    state.push({ type: "int", name: "column" });
+    emit("onChange", state);
+}
+
+function stateCopy(): SampleSheetColumnDefinition[] {
+    return JSON.parse(JSON.stringify(props.value || []));
+}
+
+function onRemove(index: number) {
+    const state = stateCopy();
+    state.splice(index, 1);
+    emit("onChange", state);
+}
+
+function titleForColumnDefinition(index: number) {
+    return `Column ${index + 1}`;
+}
+
+function getPrefix(index: number) {
+    const name = `column_definition_${index}`;
+    return name;
+}
+
+function getButtonId(index: number, direction: "up" | "down") {
+    const prefix = getPrefix(index);
+    return `${prefix}_${direction}`;
+}
+
+function swap(index: number, swapWith: number, direction: "up" | "down") {
+    // the FormRepeat version does cool highlighting - probably worth implementing
+    // on next pass
+    const state = stateCopy();
+    if (swapWith >= 0 && swapWith < state.length && index >= 0 && index < state.length) {
+        const wasSwapped = state[swapWith] as SampleSheetColumnDefinition;
+        state[swapWith] = state[index] as SampleSheetColumnDefinition;
+        state[index] = wasSwapped;
+    }
+    emit("onChange", state);
+}
+
+function onChildUpdate(childState: SampleSheetColumnDefinition, index: number) {
+    const state = stateCopy();
+    state[index] = childState;
+    emit("onChange", state);
+}
+
+const deleteTooltip = computed(() => {
+    return localize(`Click to delete column definition`);
+});
+
+const emit = defineEmits(["onChange"]);
+</script>
+
+<template>
+    <div class="ui-form-element section-row">
+        <div class="ui-form-title">
+            <span class="ui-form-title-text">Column definitions</span>
+        </div>
+        <FormCard
+            v-for="(columnDefinition, index) in value"
+            v-bind:key="index"
+            data-description="column definition block"
+            class="card"
+            :title="titleForColumnDefinition(index)">
+            <template v-slot:operations>
+                <!-- code modelled after FormRepeat -->
+                <span class="float-right">
+                    <b-button-group>
+                        <b-button
+                            :id="getButtonId(index, 'up')"
+                            v-b-tooltip.hover.bottom
+                            title="move up"
+                            role="button"
+                            variant="link"
+                            size="sm"
+                            class="ml-0"
+                            @click="() => swap(index, index - 1, 'up')">
+                            <FontAwesomeIcon icon="caret-up" />
+                        </b-button>
+                        <b-button
+                            :id="getButtonId(index, 'down')"
+                            v-b-tooltip.hover.bottom
+                            title="move down"
+                            role="button"
+                            variant="link"
+                            size="sm"
+                            class="ml-0"
+                            @click="() => swap(index, index + 1, 'down')">
+                            <FontAwesomeIcon icon="caret-down" />
+                        </b-button>
+                    </b-button-group>
+
+                    <span v-b-tooltip.hover.bottom :title="deleteTooltip">
+                        <b-button
+                            title="delete"
+                            role="button"
+                            variant="link"
+                            size="sm"
+                            class="ml-0"
+                            @click="() => onRemove(index)">
+                            <FontAwesomeIcon icon="trash-alt" />
+                        </b-button>
+                    </span>
+                </span>
+            </template>
+            <template v-slot:body>
+                <FormColumnDefinition
+                    :index="index"
+                    :value="columnDefinition"
+                    :prefix="getPrefix(index)"
+                    @onChange="onChildUpdate" />
+            </template>
+        </FormCard>
+        <BLink @click="addColumn">Add column.</BLink>
+    </div>
+</template>
+
+<style lang="scss" scoped>
+@import "../../../Form/_form-elements.scss";
+
+.column-definition-list {
+    padding: 0px;
+    list-style-type: none;
+}
+</style>

client/src/components/Workflow/Editor/Forms/FormInputCollection.vue

@@ -1,20 +1,23 @@
 <script setup lang="ts">
 import { computed, toRef } from "vue";
 
+import { type SampleSheetColumnDefinitions } from "@/api";
 import type { DatatypesMapperModel } from "@/components/Datatypes/model";
 import type { Step } from "@/stores/workflowStepStore";
 
 import { useToolState } from "../composables/useToolState";
 
 import FormElement from "@/components/Form/FormElement.vue";
 import FormCollectionType from "@/components/Workflow/Editor/Forms/FormCollectionType.vue";
+import FormColumnDefinitions from "@/components/Workflow/Editor/Forms/FormColumnDefinitions.vue";
 import FormDatatype from "@/components/Workflow/Editor/Forms/FormDatatype.vue";
 
 interface ToolState {
     collection_type: string | null;
     optional: boolean;
     format: string | null;
     tag: string | null;
+    column_definitions: SampleSheetColumnDefinitions;
 }
 
 const props = defineProps<{
@@ -34,6 +37,7 @@ function cleanToolState(): ToolState {
             optional: false,
             tag: null,
             format: null,
+            column_definitions: null,
         };
     }
 }
@@ -64,9 +68,16 @@ function onCollectionType(newCollectionType: string | null) {
     emit("onChange", state);
 }
 
+function onColumnDefinitions(newColumnDefinitions: SampleSheetColumnDefinitions) {
+    const state = cleanToolState();
+    console.log(newColumnDefinitions);
+    state.column_definitions = newColumnDefinitions;
+    emit("onChange", state);
+}
+
 const formatsAsList = computed(() => {
-    const formatStr = toolState.value?.format as (string | string[] | null);
-    if (formatStr && (typeof formatStr === "string")) {
+    const formatStr = toolState.value?.format as string | string[] | null;
+    if (formatStr && typeof formatStr === "string") {
         return formatStr.split(/\s*,\s*/);
     } else if (formatStr) {
         return formatStr;
@@ -100,5 +111,9 @@ emit("onChange", cleanToolState());
             type="text"
             help="Tags to automatically filter inputs"
             @input="onTags" />
+        <FormColumnDefinitions
+            v-if="toolState?.collection_type == 'sample_sheet'"
+            :value="toolState?.column_definitions"
+            @onChange="onColumnDefinitions" />
     </div>
 </template>

client/src/components/Workflow/Editor/modules/collectionTypeDescription.ts

@@ -129,7 +129,7 @@ export class CollectionTypeDescription implements CollectionTypeDescriptor {
     }
 }
 
-const collectionTypeRegex = /^(list|paired)(:(list|paired))*$/;
+const collectionTypeRegex = /^((list|paired)(:(list|paired))*|sample_sheet)$/;
 
 export function isValidCollectionTypeStr(collectionType: string | undefined) {
     if (collectionType) {

client/src/stores/workflowStepStore.ts

@@ -1,5 +1,6 @@
 import { computed, del, ref, set } from "vue";
 
+import { type SampleSheetColumnDefinitions } from "@/api";
 import { type CollectionTypeDescriptor } from "@/components/Workflow/Editor/modules/collectionTypeDescription";
 import { type Connection, getConnectionId, useConnectionStore } from "@/stores/workflowConnectionStore";
 import { assertDefined } from "@/utils/assertions";
@@ -71,6 +72,7 @@ export interface DataStepInput extends BaseStepInput {
 export interface DataCollectionStepInput extends BaseStepInput {
     input_type: "dataset_collection";
     collection_types: string[];
+    column_definitions: SampleSheetColumnDefinitions;
 }
 
 export interface ParameterStepInput extends Omit<BaseStepInput, "input_type"> {

lib/galaxy/managers/collections.py

@@ -176,6 +176,8 @@ def create(
         completed_job=None,
         output_name=None,
         fields=None,
+        column_definitions=None,
+        rows=None,
     ):
         """
         PRECONDITION: security checks on ability to add to parent
@@ -201,6 +203,8 @@ def create(
                 copy_elements=copy_elements,
                 history=history,
                 fields=fields,
+                column_definitions=column_definitions,
+                rows=rows,
             )
 
         implicit_inputs = []
@@ -288,6 +292,8 @@ def create_dataset_collection(
         copy_elements=False,
         history=None,
         fields=None,
+        column_definitions=None,
+        rows=None,
     ):
         # Make sure at least one of these is None.
         assert element_identifiers is None or elements is None
@@ -324,9 +330,12 @@ def create_dataset_collection(
 
         if elements is not self.ELEMENTS_UNINITIALIZED:
             type_plugin = collection_type_description.rank_type_plugin()
-            dataset_collection = builder.build_collection(type_plugin, elements, fields=fields)
+            dataset_collection = builder.build_collection(
+                type_plugin, elements, fields=fields, column_definitions=column_definitions, rows=rows
+            )
         else:
             # TODO: Pass fields here - need test case first.
+            # TODO: same with column definitions I think.
             dataset_collection = model.DatasetCollection(populated=False)
         dataset_collection.collection_type = collection_type
         return dataset_collection
@@ -783,10 +792,16 @@ def __init_rule_data(self, elements, collection_type_description, parent_identif
             identifiers = parent_identifiers + [element.element_identifier]
             if not element.is_collection:
                 data.append([])
+                columns = None
+                collection_type_str = collection_type_description.collection_type
+                if collection_type_str == "sample_sheet":
+                    columns = element.columns
+                    assert isinstance(columns, list)
                 source = {
                     "identifiers": identifiers,
                     "dataset": element_object,
                     "tags": element_object.make_tag_string_list(),
+                    "columns": columns,
                 }
                 sources.append(source)
             else:

lib/galaxy/managers/collections_util.py

@@ -9,6 +9,7 @@
     exceptions,
     model,
 )
+from galaxy.model.dataset_collections.types.sample_sheet_util import validate_column_definitions
 from galaxy.util import string_as_bool
 
 log = logging.getLogger(__name__)
@@ -33,13 +34,18 @@ def api_payload_to_create_params(payload):
         message = f"Missing required parameters {missing_parameters}"
         raise exceptions.ObjectAttributeMissingException(message)
 
+    column_definitions = payload.get("column_definitions", None)
+    validate_column_definitions(column_definitions)
+
     params = dict(
         collection_type=payload.get("collection_type"),
         element_identifiers=payload.get("element_identifiers"),
         name=payload.get("name", None),
         hide_source_items=string_as_bool(payload.get("hide_source_items", False)),
         copy_elements=string_as_bool(payload.get("copy_elements", False)),
         fields=payload.get("fields", None),
+        column_definitions=column_definitions,
+        rows=payload.get("rows", None),
     )
     return params