Merge pull request #165 from bento-platform/features/beacon-network

feat: Beacon network UI

src/js/components/Beacon/BeaconCommon/BeaconQueryFormUi.tsx

@@ -0,0 +1,307 @@
+import { useCallback, useEffect, useMemo, useState } from 'react';
+import { Button, Card, Col, Form, Row } from 'antd';
+import { useIsAuthenticated } from 'bento-auth-js';
+import { useAppDispatch, useTranslationDefault, useQueryWithAuthIfAllowed } from '@/hooks';
+import VariantsForm from './VariantsForm';
+import Filters from './Filters';
+import SearchToolTip from './ToolTips/SearchToolTip';
+import VariantsInstructions from './ToolTips/VariantsInstructions';
+import { MetadataInstructions } from './ToolTips/MetadataInstructions';
+import BeaconErrorMessage from './BeaconErrorMessage';
+import type {
+  BeaconAssemblyIds,
+  BeaconQueryPayload,
+  BeaconQueryAction,
+  FormFilter,
+  FormValues,
+  PayloadFilter,
+  PayloadVariantsQuery,
+} from '@/types/beacon';
+import type { Section } from '@/types/search';
+import { BOX_SHADOW } from '@/constants/overviewConstants';
+import {
+  FORM_ROW_GUTTERS,
+  CARD_STYLE,
+  BUTTON_AREA_STYLE,
+  BUTTON_STYLE,
+  CARD_STYLES,
+} from '@/constants/beaconConstants';
+
+const STARTER_FILTER = { index: 1, active: true };
+const VARIANTS_FORM_ERROR_MESSAGE =
+  'Variants form should include either an end position or both reference and alternate bases';
+
+// TODOs
+// example searches, either hardcoded or configurable
+// more intuitive variants ui
+
+const BeaconQueryFormUi = ({
+  isFetchingQueryResponse, //used in local beacon only
+  isNetworkQuery,
+  beaconAssemblyIds,
+  querySections,
+  launchQuery,
+  apiErrorMessage,
+}: BeaconQueryFormUiProps) => {
+  const td = useTranslationDefault();
+  const [form] = Form.useForm();
+  const [filters, setFilters] = useState<FormFilter[]>([STARTER_FILTER]);
+  const [hasVariants, setHasVariants] = useState<boolean>(false);
+  const [hasFormError, setHasFormError] = useState<boolean>(false);
+  const [formErrorMessage, setFormErrorMessage] = useState<string>('');
+
+  // remember if user closed alert, so we can force re-render of a new one later
+  const [errorAlertClosed, setErrorAlertClosed] = useState<boolean>(false);
+
+  const dispatch = useAppDispatch();
+  const isAuthenticated = useIsAuthenticated();
+
+  const formInitialValues = useMemo(
+    () => ({
+      'Assembly ID': beaconAssemblyIds.length === 1 && beaconAssemblyIds[0],
+    }),
+    [beaconAssemblyIds]
+  );
+  const uiInstructions = hasVariants ? 'Search by genomic variants, clinical metadata or both.' : '';
+
+  const hasError = hasFormError || !!apiErrorMessage;
+  const showError = hasError && !errorAlertClosed;
+
+  const requestPayload = useCallback(
+    (query: PayloadVariantsQuery, payloadFilters: PayloadFilter[]): BeaconQueryPayload => ({
+      meta: { apiVersion: '2.0.0' },
+      query: { requestParameters: { g_variant: query }, filters: payloadFilters },
+      bento: { showSummaryStatistics: true },
+    }),
+    []
+  );
+
+  const launchEmptyQuery = useCallback(
+    () => dispatch(launchQuery(requestPayload({}, []))),
+    [dispatch, launchQuery, requestPayload]
+  );
+
+  // should not be possible to have both errors simultaneously
+  // and api error is more important
+  const errorMessage = apiErrorMessage || formErrorMessage;
+
+  const clearFormError = () => {
+    setHasFormError(false);
+    setFormErrorMessage('');
+  };
+
+  useEffect(() => {
+    launchEmptyQuery();
+    setHasVariants(beaconAssemblyIds.length > 0 || isNetworkQuery);
+
+    // set assembly id options matching what's in gohan (for local beacon) or in network
+    form.setFieldsValue(formInitialValues);
+  }, [beaconAssemblyIds.length, form, formInitialValues, isAuthenticated, isNetworkQuery, launchEmptyQuery]);
+
+  // Disables max query param if user is authenticated and authorized
+  useQueryWithAuthIfAllowed();
+
+  // following GA4GH recommendations, UI is one-based, but API is zero-based, "half-open"
+  // so to convert to zero-based, we only modify the start value
+  // see e.g., https://genome-blog.soe.ucsc.edu/blog/2016/12/12/the-ucsc-genome-browser-coordinate-counting-systems/
+  const convertToZeroBased = (start: string) => Number(start) - 1;
+
+  const packageFilters = useCallback(
+    (values: FormValues): PayloadFilter[] => {
+      // ignore optional first filter when left blank
+      if (filters.length === 1 && !values.filterId1) {
+        return [];
+      }
+
+      return filters
+        .filter((f) => f.active)
+        .map((f) => ({
+          id: values[`filterId${f.index}`],
+          operator: '=',
+          value: values[`filterValue${f.index}`],
+        }));
+    },
+    [filters]
+  );
+
+  const packageBeaconJSON = useCallback(
+    (values: FormValues) => {
+      let query = {} as PayloadVariantsQuery;
+      const payloadFilters = packageFilters(values);
+      const hasVariantsQuery = values?.['Chromosome'] || values?.['Variant start'] || values?.['Reference base(s)'];
+      if (hasVariantsQuery) {
+        query = {
+          referenceName: values['Chromosome'],
+          start: [convertToZeroBased(values['Variant start'])],
+          assemblyId: values['Assembly ID'],
+        };
+        if (values['Variant end']) {
+          query.end = [Number(values['Variant end'])];
+        }
+        if (values['Reference base(s)']) {
+          query.referenceBases = values['Reference base(s)'];
+        }
+        if (values['Alternate base(s)']) {
+          query.alternateBases = values['Alternate base(s)'];
+        }
+      }
+
+      return requestPayload(query, payloadFilters);
+    },
+    [packageFilters, requestPayload]
+  );
+
+  const handleFinish = useCallback(
+    (formValues: FormValues) => {
+      // if bad form, block submit and show user error
+      if (!variantsFormValid(formValues)) {
+        setHasFormError(true);
+        setErrorAlertClosed(false);
+        setFormErrorMessage(td(VARIANTS_FORM_ERROR_MESSAGE));
+        return;
+      }
+
+      clearFormError();
+      setErrorAlertClosed(false);
+      const jsonPayload = packageBeaconJSON(formValues);
+
+      dispatch(launchQuery(jsonPayload));
+    },
+    [dispatch, td, launchQuery, packageBeaconJSON]
+  );
+
+  const handleClearForm = () => {
+    setFilters([STARTER_FILTER]);
+    form.resetFields();
+    form.setFieldsValue(formInitialValues);
+    clearFormError();
+    setErrorAlertClosed(false);
+    launchEmptyQuery();
+  };
+
+  const handleValuesChange = (_: Partial<FormValues>, allValues: FormValues) => {
+    form.validateFields(['Chromosome', 'Variant start', 'Variant end', 'Reference base(s)', 'Alternate base(s)']);
+
+    // clear any existing errors if form now valid
+    if (variantsFormValid(allValues)) {
+      clearFormError();
+    }
+    // can also check filter values here (to e.g. avoid offering duplicate options)
+  };
+
+  const variantsFormValid = (formValues: FormValues) => {
+    // valid variant form states:
+    // empty except possibly autofilled assemblyID (no variant query)
+    // chrom, start, assemblyID, end (range query)
+    // chrom, start, assemblyID, alt, ref (sequence query)
+    // https://docs.genomebeacons.org/variant-queries/
+
+    // as an alternative, we could require "end" always, then form logic would be less convoluted
+    // just set start=end to search for SNPs
+
+    const empty = !(
+      formValues['Chromosome'] ||
+      formValues['Variant start'] ||
+      formValues['Variant end'] ||
+      formValues['Reference base(s)'] ||
+      formValues['Alternate base(s)']
+    );
+    const rangeQuery =
+      formValues['Chromosome'] && formValues['Variant start'] && formValues['Variant end'] && formValues['Assembly ID'];
+
+    const sequenceQuery =
+      formValues['Chromosome'] &&
+      formValues['Variant start'] &&
+      formValues['Assembly ID'] &&
+      formValues['Reference base(s)'] &&
+      formValues['Alternate base(s)'];
+    return empty || rangeQuery || sequenceQuery;
+  };
+
+  const searchButtonText = isNetworkQuery ? 'Search Network' : 'Search Beacon';
+
+  return (
+    <div style={{ paddingBottom: 8, display: 'flex', justifyContent: 'center', width: '100%' }}>
+      <Card
+        title={td('Search')}
+        style={{ borderRadius: '10px', maxWidth: '1200px', width: '100%', ...BOX_SHADOW }}
+        styles={CARD_STYLES}
+      >
+        <p style={{ margin: '-8px 0 8px 0', padding: '0', color: 'grey' }}>{td(uiInstructions)}</p>
+        <Form form={form} onFinish={handleFinish} layout="vertical" onValuesChange={handleValuesChange}>
+          <Row gutter={FORM_ROW_GUTTERS}>
+            {hasVariants && (
+              <Col xs={24} lg={12}>
+                <Card
+                  title={td('entities.Variants')}
+                  style={CARD_STYLE}
+                  styles={CARD_STYLES}
+                  extra={
+                    <SearchToolTip>
+                      <VariantsInstructions />
+                    </SearchToolTip>
+                  }
+                >
+                  <VariantsForm beaconAssemblyIds={beaconAssemblyIds} />
+                </Card>
+              </Col>
+            )}
+            <Col xs={24} lg={hasVariants ? 12 : 24}>
+              <Card
+                title={
+                  <div style={{ display: 'flex', justifyContent: 'space-between' }}>
+                    <>{td('Metadata')}</>
+                  </div>
+                }
+                style={CARD_STYLE}
+                styles={CARD_STYLES}
+                extra={
+                  <SearchToolTip>
+                    <MetadataInstructions />
+                  </SearchToolTip>
+                }
+              >
+                <Filters
+                  filters={filters}
+                  setFilters={setFilters}
+                  form={form}
+                  querySections={querySections}
+                  isNetworkQuery={isNetworkQuery}
+                />
+              </Card>
+            </Col>
+          </Row>
+          <Row>
+            <Col span={24}>
+              {showError && (
+                <BeaconErrorMessage
+                  message={`${td('Beacon error')}: ${errorMessage}`}
+                  onClose={() => setErrorAlertClosed(true)}
+                />
+              )}
+              <div style={BUTTON_AREA_STYLE}>
+                <Button type="primary" htmlType="submit" loading={isFetchingQueryResponse} style={BUTTON_STYLE}>
+                  {td(searchButtonText)}
+                </Button>
+                <Button onClick={handleClearForm} style={BUTTON_STYLE}>
+                  {td('Clear Form')}
+                </Button>
+              </div>
+            </Col>
+          </Row>
+        </Form>
+      </Card>
+    </div>
+  );
+};
+
+export interface BeaconQueryFormUiProps {
+  isFetchingQueryResponse: boolean;
+  isNetworkQuery: boolean;
+  beaconAssemblyIds: BeaconAssemblyIds;
+  querySections: Section[];
+  launchQuery: BeaconQueryAction;
+  apiErrorMessage?: string;
+}
+
+export default BeaconQueryFormUi;

src/js/components/Beacon/Filter.tsx → src/js/components/Beacon/BeaconCommon/Filter.tsx

@@ -13,6 +13,7 @@ import type {
 import type { Section, Field } from '@/types/search';
 
 // TODOs:
+// rewrite to use beacon specification filters instead of bento public "querySections"
 // any search key (eg "sex") selected in one filter should not available in other
 // for clarity they should probably appear, but be greyed out
 // this requires rendering select options as <Option> components

src/js/components/Beacon/Filters.tsx → src/js/components/Beacon/BeaconCommon/Filters.tsx

@@ -1,26 +1,51 @@
 import type { Dispatch, SetStateAction } from 'react';
-import { useAppSelector } from '@/hooks';
 import { useTranslation } from 'react-i18next';
-import { Button, Form, Space, Tooltip } from 'antd';
+import { Button, Form, Space, Switch, Tooltip } from 'antd';
 import type { FormInstance } from 'antd/es/form';
+
+import { DEFAULT_TRANSLATION } from '@/constants/configConstants';
+import { useBeaconNetwork } from '@/features/beacon/hooks';
+import { toggleQuerySectionsUnionOrIntersection } from '@/features/beacon/network.store';
+import { useAppSelector, useAppDispatch } from '@/hooks';
 import type { FormFilter } from '@/types/beacon';
 import type { SearchFieldResponse } from '@/types/search';
-import { DEFAULT_TRANSLATION } from '@/constants/configConstants';
+
 import Filter from './Filter';
 
+const NetworkFilterToggle = () => {
+  const dispatch = useAppDispatch();
+  const { isQuerySectionsUnion } = useBeaconNetwork();
+
+  return (
+    <Tooltip title="Choose all search filters across the network, or only those common to all beacons.">
+      <div style={{ display: 'flex', alignItems: 'center' }}>
+        <Switch
+          onChange={() => dispatch(toggleQuerySectionsUnionOrIntersection())}
+          checked={isQuerySectionsUnion}
+          style={{ margin: '5px' }}
+        />
+        <p style={{ margin: '5px' }}>{isQuerySectionsUnion ? 'show all filters' : 'common filters only'}</p>
+      </div>
+    </Tooltip>
+  );
+};
+
 // ideally:
 // - should not permit you to make multiple queries on the same key (Redmine #1688)
 
 const BUTTON_STYLE = { margin: '10px 0' };
 
-const Filters = ({ filters, setFilters, form, querySections }: FiltersProps) => {
+const Filters = ({ filters, setFilters, form, querySections, isNetworkQuery }: FiltersProps) => {
   const { t: td } = useTranslation(DEFAULT_TRANSLATION);
 
   const maxFilters = useAppSelector((state) => state.config.maxQueryParameters);
   const maxQueryParametersRequired = useAppSelector((state) => state.config.maxQueryParametersRequired);
   const activeFilters = filters.filter((f) => f.active);
   const hasMaxFilters = maxQueryParametersRequired && activeFilters.length >= maxFilters;
 
+  // don't need to pull filters from state
+  // we only need to know *which* state we are in, so it can be shown in the switch
+
   // UI starts with an optional filter, which can be left blank
   const isRequired = filters.length > 1;
 
@@ -45,6 +70,7 @@ const Filters = ({ filters, setFilters, form, querySections }: FiltersProps) =>
             {td('Add Filter')}
           </Button>
         </Tooltip>
+        {isNetworkQuery && <NetworkFilterToggle />}
       </Space>
       <div style={{ display: 'flex', flexDirection: 'column' }}>
         {activeFilters.map((f) => (
@@ -67,6 +93,7 @@ export interface FiltersProps {
   setFilters: Dispatch<SetStateAction<FormFilter[]>>;
   form: FormInstance;
   querySections: SearchFieldResponse['sections'];
+  isNetworkQuery: boolean;
 }
 
 export default Filters;

src/js/components/Beacon/BeaconCommon/ToolTips/MetadataInstructions.tsx

@@ -0,0 +1,9 @@
+import { ToolTipText } from './ToolTipText';
+import { useTranslationDefault } from '@/hooks';
+
+const METADATA_INSTRUCTIONS = 'Search over clinical or phenotypic properties.';
+
+export const MetadataInstructions = () => {
+  const td = useTranslationDefault();
+  return <ToolTipText>{td(METADATA_INSTRUCTIONS)}</ToolTipText>;
+};