[15] feat: implement new workflow system

src/components/datasets/Dataset.js

@@ -138,8 +138,7 @@ class Dataset extends Component {
                                        isPrivate={isPrivate} />,
             data_types: <DatasetDataTypes dataset={this.state}
                                           project={this.props.project}
-                                          isPrivate={isPrivate}
-                                          onDatasetIngest={this.props.onDatasetIngest}/>,
+                                          isPrivate={isPrivate} />,
             linked_field_sets: (
                 <>
                     <Typography.Title level={4}>
@@ -295,7 +294,6 @@ Dataset.propTypes = {
     value: datasetPropTypesShape,
 
     onEdit: PropTypes.func,
-    onDatasetIngest: PropTypes.func,
 
     addLinkedFieldSet: PropTypes.func,
     deleteProjectDataset: PropTypes.func,

src/components/datasets/DatasetDataTypes.js

@@ -1,130 +1,157 @@
 import React, {useCallback, useMemo, useState} from "react";
 import { useSelector, useDispatch } from "react-redux";
-import { Button, Col, Row, Table, Typography } from "antd";
-
 import PropTypes from "prop-types";
+
+import { Button, Col, Dropdown, Icon, Menu, Row, Table, Typography } from "antd";
+
+import { useWorkflows } from "../../hooks";
+import { useStartIngestionFlow } from "../manager/workflowCommon";
 import { datasetPropTypesShape, projectPropTypesShape } from "../../propTypes";
 import { clearDatasetDataType } from "../../modules/metadata/actions";
 import { fetchDatasetDataTypesSummariesIfPossible } from "../../modules/datasets/actions";
+
 import genericConfirm from "../ConfirmationModal";
 import DataTypeSummaryModal from "./datatype/DataTypeSummaryModal";
-import { nop } from "../../utils/misc";
 
 const NA_TEXT = <span style={{ color: "#999", fontStyle: "italic" }}>N/A</span>;
 
-const DatasetDataTypes = React.memo(
-    ({isPrivate, project, dataset, onDatasetIngest}) => {
-        const dispatch = useDispatch();
-        const datasetDataTypes = useSelector((state) => Object.values(
-            state.datasetDataTypes.itemsByID[dataset.identifier]?.itemsByID ?? {}));
-        const datasetSummaries = useSelector((state) => state.datasetSummaries.itemsByID[dataset.identifier]);
-        const isFetchingDataset = useSelector(
-            (state) => state.datasetDataTypes.itemsByID[dataset.identifier]?.isFetching);
-
-        const [datatypeSummaryVisible, setDatatypeSummaryVisible] = useState(false);
-        const [selectedDataType, setSelectedDataType] = useState(null);
-
-        const selectedSummary = datasetSummaries?.data?.[selectedDataType?.id] ?? {};
-
-        const handleClearDataType = useCallback((dataType) => {
-            genericConfirm({
-                title: `Are you sure you want to delete the "${dataType.label || dataType.id}" data type?`,
-                content: "Deleting this means all instances of this data type contained in the dataset " +
-                "will be deleted permanently, and will no longer be available for exploration.",
-                onOk: async () => {
-                    await dispatch(clearDatasetDataType(dataset.identifier, dataType.id));
-                    await dispatch(fetchDatasetDataTypesSummariesIfPossible(dataset.identifier));
-                },
-            });
-        }, [dispatch, dataset]);
+const DatasetDataTypes = React.memo(({ isPrivate, project, dataset }) => {
+    const dispatch = useDispatch();
+    const datasetDataTypes = useSelector((state) => Object.values(
+        state.datasetDataTypes.itemsByID[dataset.identifier]?.itemsByID ?? {}));
+    const datasetSummaries = useSelector((state) => state.datasetSummaries.itemsByID[dataset.identifier]);
+    const isFetchingDataset = useSelector(
+        (state) => state.datasetDataTypes.itemsByID[dataset.identifier]?.isFetching);
 
-        const showDataTypeSummary = useCallback((dataType) => {
-            setSelectedDataType(dataType);
-            setDatatypeSummaryVisible(true);
-        }, []);
+    const { workflowsByType } = useWorkflows();
+    const ingestionWorkflows = workflowsByType.ingestion.items;
 
-        const dataTypesColumns = useMemo(() => [
-            {
-                title: "Name",
-                key: "label",
-                render: (dt) =>
-                    isPrivate ? (
-                    <a onClick={() => showDataTypeSummary(dt)}>
-                        {dt.label ?? NA_TEXT}
-                    </a>
-                    ) : dt.label ?? NA_TEXT,
-                defaultSortOrder: "ascend",
-                sorter: (a, b) => a.label.localeCompare(b.label),
+    const [datatypeSummaryVisible, setDatatypeSummaryVisible] = useState(false);
+    const [selectedDataType, setSelectedDataType] = useState(null);
+
+    const selectedSummary = datasetSummaries?.data?.[selectedDataType?.id] ?? {};
+
+    const handleClearDataType = useCallback((dataType) => {
+        genericConfirm({
+            title: `Are you sure you want to delete the "${dataType.label || dataType.id}" data type?`,
+            content: "Deleting this means all instances of this data type contained in the dataset " +
+            "will be deleted permanently, and will no longer be available for exploration.",
+            onOk: async () => {
+                await dispatch(clearDatasetDataType(dataset.identifier, dataType.id));
+                await dispatch(fetchDatasetDataTypesSummariesIfPossible(dataset.identifier));
             },
+        });
+    }, [dispatch, dataset]);
+
+    const showDataTypeSummary = useCallback((dataType) => {
+        setSelectedDataType(dataType);
+        setDatatypeSummaryVisible(true);
+    }, []);
+
+    const startIngestionFlow = useStartIngestionFlow();
+
+    const dataTypesColumns = useMemo(() => [
+        {
+            title: "Name",
+            key: "label",
+            render: (dt) =>
+                isPrivate ? (
+                <a onClick={() => showDataTypeSummary(dt)}>
+                    {dt.label ?? NA_TEXT}
+                </a>
+                ) : dt.label ?? NA_TEXT,
+            defaultSortOrder: "ascend",
+            sorter: (a, b) => a.label.localeCompare(b.label),
+        },
+        {
+            title: "Count",
+            dataIndex: "count",
+            render: (c) => (c ?? NA_TEXT),
+        },
+        ...(isPrivate ? [
             {
-                title: "Count",
-                dataIndex: "count",
-                render: (c) => (c ?? NA_TEXT),
-            },
-            ...(isPrivate ? [
-                {
-                    title: "Actions",
-                    key: "actions",
-                    width: 230,
-                    render: (dt) => (
-                    <Row gutter={10}>
-                        <Col span={12}>
-                            <Button
-                                icon="import"
-                                style={{ width: "100%" }}
-                                onClick={() => (onDatasetIngest || nop)(project, dataset, dt)}
-                            >
-                                Ingest
-                            </Button>
-                        </Col>
-                        <Col span={12}>
-                            <Button
-                                type="danger"
-                                icon="delete"
-                                disabled={ !dt.count || dt.count && dt.count === 0}
-                                onClick={() => handleClearDataType(dt)}
-                                style={{ width: "100%" }}
-                            >
-                                Clear
+                title: "Actions",
+                key: "actions",
+                width: 240,
+                render: (dt) => {
+                    const dtIngestionWorkflows = ingestionWorkflows
+                        .filter((wf) => wf.data_type === dt.id || (wf.tags ?? []).includes(dt.id));
+                    const dtIngestionWorkflowsByID = Object.fromEntries(
+                        dtIngestionWorkflows.map((wf) => [wf.id, wf]));
+
+                    const ingestMenu = (
+                        <Menu onClick={(i) => startIngestionFlow(dtIngestionWorkflowsByID[i.key], {
+                            // TODO: this requires that exactly this input is present, and may break in the future
+                            //  in a bit of a non-obvious way.
+                            "project_dataset": `${project.identifier}:${dataset.identifier}`,
+                        })}>
+                            {dtIngestionWorkflows.map((wf) => (<Menu.Item key={wf.id}>{wf.name}</Menu.Item>))}
+                        </Menu>
+                    );
+
+                    const ingestDropdown = (
+                        <Dropdown overlay={ingestMenu} trigger={["click"]}>
+                            <Button icon="import" style={{ width: "100%" }} disabled={!dtIngestionWorkflows.length}>
+                                Ingest <Icon type="down" />
                             </Button>
-                        </Col>
-                    </Row>
-                    ),
+                        </Dropdown>
+                    );
+
+                    return (
+                        <Row gutter={10}>
+                            <Col span={13}>
+                                {ingestDropdown}
+                            </Col>
+                            <Col span={11}>
+                                <Button
+                                    type="danger"
+                                    icon="delete"
+                                    disabled={ !dt.count || dt.count && dt.count === 0}
+                                    onClick={() => handleClearDataType(dt)}
+                                    style={{ width: "100%" }}
+                                >
+                                    Clear
+                                </Button>
+                            </Col>
+                        </Row>
+                    );
                 },
-            ] : null),
-        ], [isPrivate, project, dataset, onDatasetIngest]);
-
-        const onDataTypeSummaryModalCancel = useCallback(() => setDatatypeSummaryVisible(false), []);
-
-        return (
-            <>
-                <DataTypeSummaryModal
-                    dataType={selectedDataType}
-                    summary={selectedSummary}
-                    visible={datatypeSummaryVisible}
-                    onCancel={onDataTypeSummaryModalCancel}
-                />
-
-                <Typography.Title level={4}>
-                    Data Types
-                </Typography.Title>
-
-                <Table
-                    bordered
-                    dataSource={datasetDataTypes}
-                    rowKey="id"
-                    columns={dataTypesColumns}
-                    loading={isFetchingDataset}
-                />
-            </>
-        );
-    });
+            },
+        ] : null),
+    ], [isPrivate, project, dataset, ingestionWorkflows, startIngestionFlow]);
+
+    const onDataTypeSummaryModalCancel = useCallback(() => setDatatypeSummaryVisible(false), []);
+
+    return (
+        <>
+            <DataTypeSummaryModal
+                dataType={selectedDataType}
+                summary={selectedSummary}
+                visible={datatypeSummaryVisible}
+                onCancel={onDataTypeSummaryModalCancel}
+            />
+
+            <Typography.Title level={4}>
+                Data Types
+            </Typography.Title>
+
+            <Table
+                bordered
+                size="middle"
+                pagination={false}
+                dataSource={datasetDataTypes}
+                rowKey="id"
+                columns={dataTypesColumns}
+                loading={isFetchingDataset}
+            />
+        </>
+    );
+});
 
 DatasetDataTypes.propTypes = {
     isPrivate: PropTypes.bool,
     project: projectPropTypesShape,
     dataset: datasetPropTypesShape,
-    onDatasetIngest: PropTypes.func,
 };
 
 export default DatasetDataTypes;

src/components/explorer/IndividualExperiments.js

@@ -7,7 +7,7 @@ import { Button, Descriptions, Icon, Popover, Table, Tooltip, Typography } from
 
 import { experimentPropTypesShape, experimentResultPropTypesShape, individualPropTypesShape } from "../../propTypes";
 import { getFileDownloadUrlsFromDrs } from "../../modules/drs/actions";
-import { guessFileType } from "../../utils/guessFileType";
+import { guessFileType } from "../../utils/files";
 
 import { useDeduplicatedIndividualBiosamples, useIndividualResources } from "./utils";
 import { VIEWABLE_FILE_EXTENSIONS } from "../display/FileDisplay";

src/components/explorer/IndividualTracks.js

@@ -9,7 +9,7 @@ import { BENTO_PUBLIC_URL, BENTO_URL } from "../../config";
 import { individualPropTypesShape } from "../../propTypes";
 import { getIgvUrlsFromDrs } from "../../modules/drs/actions";
 import { setIgvPosition } from "../../modules/explorer/actions";
-import { guessFileType } from "../../utils/guessFileType";
+import { guessFileType } from "../../utils/files";
 import {useDeduplicatedIndividualBiosamples} from "./utils";
 
 const SQUISHED_CALL_HEIGHT = 10;