Merge pull request #133 from kbase/hist_scatter

RE2022-278 RE2022-280 add basic histogram and scatter

package.json

@@ -26,18 +26,24 @@
     "@types/dompurify": "^3.0.0",
     "@types/leaflet": "^1.9.3",
     "@types/marked": "^4.0.8",
+    "@types/plotly.js": "^2.12.30",
+    "@types/react-plotly.js": "^2.6.3",
     "ajv": "^8.12.0",
+    "canvas": "^2.11.2",
     "d3-zoom": "^3.0.0",
     "dompurify": "^3.0.1",
+    "downsample-lttb-ts": "^0.0.6",
     "jest-fetch-mock": "^3.0.3",
     "leaflet": "^1.9.4",
     "marked": "^4.2.12",
     "node-sass": "^9.0.0",
+    "plotly.js": "^2.27.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
     "react-error-boundary": "^3.1.4",
     "react-hook-form": "^7.47.0",
     "react-hot-toast": "^2.4.1",
+    "react-plotly.js": "^2.6.0",
     "react-popper": "^2.3.0",
     "react-redux": "^8.0.5",
     "react-router-dom": "^6.11.1",

src/common/api/collectionsApi.ts

@@ -241,6 +241,15 @@ interface CollectionsResults {
     data?: null;
     count?: number;
   };
+  getAttribHistogram: {
+    bins: number[];
+    values: number[];
+  };
+  getAttribScatter: {
+    xcolumn: string;
+    ycolumn: string;
+    data: { x: number; y: number }[];
+  };
   getGenomeAttribsMeta: {
     count: number;
     columns: Array<ColumnMeta>;
@@ -377,6 +386,23 @@ interface CollectionsParams {
     collection_id: Collection['id'];
     load_ver_override?: Collection['ver_tag'];
   };
+  getAttribHistogram: {
+    collection_id: Collection['id'];
+    column: string;
+    match_id?: Match['match_id'];
+    selection_id?: Selection['selection_id'];
+    load_ver_override?: Collection['ver_tag'];
+    filters?: Record<string, string>;
+  };
+  getAttribScatter: {
+    collection_id: Collection['id'];
+    xcolumn: string;
+    ycolumn: string;
+    match_id?: Match['match_id'];
+    selection_id?: Selection['selection_id'];
+    load_ver_override?: Collection['ver_tag'];
+    filters?: Record<string, string>;
+  };
   getMicroTrait: {
     collection_id: Collection['id'];
     start_after?: KBaseId;
@@ -683,6 +709,36 @@ export const collectionsApi = baseApi.injectEndpoints({
         }),
     }),
 
+    getAttribHistogram: builder.query<
+      CollectionsResults['getAttribHistogram'],
+      CollectionsParams['getAttribHistogram']
+    >({
+      query: ({ collection_id, ...options }) =>
+        collectionsService({
+          method: 'GET',
+          url: encode`/collections/${collection_id}/data_products/genome_attribs/hist`,
+          params: options,
+          headers: {
+            authorization: `Bearer ${store.getState().auth.token}`,
+          },
+        }),
+    }),
+
+    getAttribScatter: builder.query<
+      CollectionsResults['getAttribScatter'],
+      CollectionsParams['getAttribScatter']
+    >({
+      query: ({ collection_id, ...options }) =>
+        collectionsService({
+          method: 'GET',
+          url: encode`/collections/${collection_id}/data_products/genome_attribs/scatter`,
+          params: options,
+          headers: {
+            authorization: `Bearer ${store.getState().auth.token}`,
+          },
+        }),
+    }),
+
     getMicroTrait: builder.query<
       CollectionsResults['getMicroTrait'],
       CollectionsParams['getMicroTrait']
@@ -876,6 +932,8 @@ export const {
   listTaxaCountRanks,
   getTaxaCountRank,
   getGenomeAttribs,
+  getAttribHistogram,
+  getAttribScatter,
   getGenomeAttribsMeta,
   getMicroTrait,
   getMicroTraitMeta,

src/common/components/Loader.tsx

@@ -1,5 +1,9 @@
-import { faSpinner } from '@fortawesome/free-solid-svg-icons';
+import {
+  faExclamationCircle,
+  faSpinner,
+} from '@fortawesome/free-solid-svg-icons';
 import { FontAwesomeIcon } from '@fortawesome/react-fontawesome';
+import { Box, Chip, Stack } from '@mui/material';
 
 /**
  * Component for rendering loading states
@@ -13,8 +17,29 @@ export const Loader = (props: {
   children?: React.ReactNode | React.ReactNode[];
   /** Overrides the loader style to render a custom loader*/
   render?: React.ReactNode | React.ReactNode[];
+  size?: [width: string, height: string];
+  error?: string;
 }) => {
-  if (props.loading ?? true) {
+  const isLoading = props.loading ?? true;
+  if (props.size && (isLoading || props.error)) {
+    const {
+      size: [width, height],
+      ...forwardProps
+    } = props;
+    return (
+      <Box sx={{ width, height, position: 'relative' }}>
+        <Stack
+          direction="row"
+          justifyContent="center"
+          alignItems="center"
+          sx={{ width: 1, height: '100%' }}
+        >
+          <Loader {...forwardProps} />
+        </Stack>
+      </Box>
+    );
+  }
+  if (isLoading) {
     if (props.render !== undefined) return <>{props.render}</>;
     switch (props.type) {
       case 'text':
@@ -23,6 +48,16 @@ export const Loader = (props: {
       default:
         return <FontAwesomeIcon icon={faSpinner} spin />;
     }
+  }
+  if (props.error) {
+    return (
+      <Chip
+        icon={<FontAwesomeIcon icon={faExclamationCircle} />}
+        variant="outlined"
+        color="error"
+        label={props.error}
+      />
+    );
   } else {
     return <>{props.children}</>;
   }

src/features/collections/data_products/AttribHistogram.tsx

@@ -0,0 +1,59 @@
+import { ComponentProps, useMemo } from 'react';
+import Plot from 'react-plotly.js';
+import { getAttribHistogram } from '../../../common/api/collectionsApi';
+import { parseError } from '../../../common/api/utils/parseError';
+import { Loader } from '../../../common/components/Loader';
+import { useFilters } from '../collectionsSlice';
+import { useTableViewParams } from './GenomeAttribs';
+
+export const AttribHistogram = ({
+  collection_id,
+  column,
+  size = [600, 600],
+}: {
+  collection_id: string;
+  column: string;
+  size?: [width: number, height: number];
+}) => {
+  const { filterMatch, filterSelection, columnMeta } =
+    useFilters(collection_id);
+  const viewParams = useTableViewParams(collection_id, {
+    filtered: true,
+    selected: Boolean(filterMatch),
+    matched: Boolean(filterSelection),
+  });
+  const { data, isLoading, error } = getAttribHistogram.useQuery({
+    ...viewParams,
+    column,
+  });
+  const plotData: ComponentProps<typeof Plot>['data'] = useMemo(() => {
+    if (!data) return [];
+    const bins = data.bins ?? [];
+    const values = data.values ?? [];
+    const binStarts = bins.slice(0, -1);
+    const binWidths = bins.slice(1).map((end, index) => end - bins[index]);
+    return [{ type: 'bar', x: binStarts, width: binWidths, y: values }];
+  }, [data]);
+  if (plotData && !isLoading && !error) {
+    return (
+      <Plot
+        data={plotData}
+        layout={{
+          height: size[1],
+          width: size[0],
+          title: column,
+          xaxis: { title: { text: columnMeta?.[column]?.display_name } },
+          yaxis: { title: { text: 'Count' } },
+        }}
+      />
+    );
+  } else {
+    return (
+      <Loader
+        loading={isLoading}
+        size={[`${size[0]}px`, `${size[1]}px`]}
+        error={error ? parseError(error).message : undefined}
+      />
+    );
+  }
+};