Merge branch 'main' into 425-add-new-analysis-button-in-map

.github/workflows/pr-check.yml

@@ -14,7 +14,7 @@ jobs:
         with:
           node-version: '14'
           cache: 'yarn'
-      - uses: nrwl/nx-set-shas@v3
+      - uses: nrwl/nx-set-shas@v3.0.0
       - run: yarn
       - run: yarn nx affected --target=build-npm-modules --parallel=3
       - run: yarn nx affected --target=compile:check

packages/libs/components/package.json

@@ -12,6 +12,7 @@
     "@typescript-eslint/parser": "^5.46.0",
     "@veupathdb/coreui": "workspace:^",
     "@visx/axis": "^3.1.0",
+    "@visx/brush": "^3.0.1",
     "@visx/gradient": "^1.0.0",
     "@visx/group": "^1.0.0",
     "@visx/hierarchy": "^1.0.0",

packages/libs/components/src/components/plotControls/EzTimeFilter.tsx

@@ -0,0 +1,252 @@
+/* eslint-disable @typescript-eslint/no-use-before-define */
+import React, { useEffect, useMemo } from 'react';
+import { scaleTime, scaleLinear } from '@visx/scale';
+import { Brush } from '@visx/brush';
+// add ResizeTriggerAreas type
+import { Bounds, ResizeTriggerAreas } from '@visx/brush/lib/types';
+import { Group } from '@visx/group';
+import { max, extent } from 'd3-array';
+import { BrushHandleRenderProps } from '@visx/brush/lib/BrushHandle';
+import { AxisBottom } from '@visx/axis';
+import { millisecondTodate } from '../../utils/date-format-change';
+import { Bar } from '@visx/shape';
+import { debounce } from 'lodash';
+
+export type EZTimeFilterDataProp = {
+  x: string;
+  y: number;
+};
+
+export type EzTimeFilterProps = {
+  /** Ez time filter data  */
+  data: EZTimeFilterDataProp[];
+  /** current state of selectedRange */
+  selectedRange: { start: string; end: string } | undefined;
+  /** update function selectedRange */
+  setSelectedRange: (
+    selectedRange: { start: string; end: string } | undefined
+  ) => void;
+  /** width */
+  width?: number;
+  /** height */
+  height?: number;
+  /** color of the selected range */
+  brushColor?: string;
+  /** axis tick and tick label color */
+  axisColor?: string;
+  /** opacity of selected brush */
+  brushOpacity?: number;
+  /** debounce rate in millisecond */
+  debounceRateMs?: number;
+  /** all user-interaction disabled */
+  disabled?: boolean;
+};
+
+// using forwardRef
+function EzTimeFilter(props: EzTimeFilterProps) {
+  const {
+    data,
+    // set default width and height
+    width = 720,
+    height = 100,
+    brushColor = 'lightblue',
+    axisColor = '#000',
+    brushOpacity = 0.4,
+    selectedRange,
+    setSelectedRange,
+    // set a default debounce time in milliseconds
+    debounceRateMs = 500,
+    disabled = false,
+  } = props;
+
+  const resizeTriggerAreas: ResizeTriggerAreas[] = disabled
+    ? []
+    : ['left', 'right'];
+
+  // define default values
+  const margin = { top: 0, bottom: 10, left: 10, right: 10 };
+  const selectedBrushStyle = {
+    fill: disabled ? 'lightgray' : brushColor,
+    stroke: disabled ? 'lightgray' : brushColor,
+    fillOpacity: brushOpacity,
+    // need to set this to be 1?
+    strokeOpacity: 1,
+  };
+
+  // axis props
+  const axisBottomTickLabelProps = {
+    textAnchor: 'middle' as const,
+    fontFamily: 'Arial',
+    fontSize: 10,
+    fill: axisColor,
+  };
+
+  // accessors for data
+  const getXData = (d: EZTimeFilterDataProp) => new Date(d.x);
+  const getYData = (d: EZTimeFilterDataProp) => d.y;
+
+  const onBrushChange = useMemo(
+    () =>
+      debounce((domain: Bounds | null) => {
+        if (!domain) return;
+
+        const { x0, x1 } = domain;
+
+        const selectedDomain = {
+          // x0 and x1 are millisecond value
+          start: millisecondTodate(x0),
+          end: millisecondTodate(x1),
+        };
+
+        setSelectedRange(selectedDomain);
+      }, debounceRateMs),
+    [setSelectedRange]
+  );
+
+  // Cancel any pending onBrushChange requests when this component is unmounted
+  useEffect(() => {
+    return () => {
+      onBrushChange.cancel();
+    };
+  }, []);
+
+  // bounds
+  const xBrushMax = Math.max(width - margin.left - margin.right, 0);
+  // take 80 % of given height considering axis tick/tick labels at the bottom
+  const yBrushMax = Math.max(0.8 * height - margin.top - margin.bottom, 0);
+
+  // scaling
+  const xBrushScale = useMemo(
+    () =>
+      scaleTime<number>({
+        range: [0, xBrushMax],
+        domain:
+          data != null ? (extent(data, getXData) as [Date, Date]) : undefined,
+      }),
+    [data, xBrushMax]
+  );
+
+  const yBrushScale = useMemo(
+    () =>
+      scaleLinear({
+        range: [yBrushMax, 0],
+        domain: [0, max(data, getYData) || 1],
+        // set zero: false so that it does not include zero line in the middle of y-axis
+        // this is useful when all data have zeros
+        zero: false,
+      }),
+    [data, yBrushMax]
+  );
+
+  // initial selectedRange position
+  const initialBrushPosition = useMemo(
+    () =>
+      selectedRange != null
+        ? {
+            start: { x: xBrushScale(new Date(selectedRange.start)) },
+            end: { x: xBrushScale(new Date(selectedRange.end)) },
+          }
+        : undefined,
+    [selectedRange, xBrushScale]
+  );
+
+  // compute bar width manually as scaleTime is used for Bar chart
+  const barWidth = xBrushMax / data.length;
+
+  // data bar color
+  const defaultColor = '#333';
+
+  // this makes/fakes the brush as a controlled component
+  const brushKey =
+    initialBrushPosition != null
+      ? initialBrushPosition.start + ':' + initialBrushPosition.end
+      : 'no_brush';
+
+  return (
+    <div
+      style={{
+        // centering time filter
+        textAlign: 'center',
+        pointerEvents: disabled ? 'none' : 'all',
+      }}
+    >
+      <svg width={width} height={height}>
+        <Group left={margin.left} top={margin.top}>
+          {/* use Bar chart */}
+          {data.map((d, i) => {
+            const barHeight = yBrushMax - yBrushScale(getYData(d));
+            return (
+              <React.Fragment key={i}>
+                <Bar
+                  key={`bar-${i.toString()}`}
+                  x={xBrushScale(getXData(d))}
+                  // In SVG bar chart, y-coordinate increases downward, i.e.,
+                  // y-coordinates of the top and bottom of the bars are 0 and yBrushMax, respectively
+                  // Also, under current yBrushScale, dataY = 0 -> barHeight = 0; dataY = 1 -> barHeight = 60
+                  // Thus, to mimick the bar shape of the ez time filter mockup,
+                  // starting y-coordinate for dataY = 1 sets to be 1/4*yBrushMax.
+                  // And, the height prop is set to be 1/2*yBrushMax so that
+                  // the bottom side of a bar has 1/4*yBrushMax space with respect to the x-axis line
+                  y={barHeight === 0 ? yBrushMax : (1 / 4) * yBrushMax}
+                  height={(1 / 2) * barHeight}
+                  // set the last data's barWidth to be 0 so that it does not overflow to dragging area
+                  width={i === data.length - 1 ? 0 : barWidth}
+                  fill={defaultColor}
+                />
+              </React.Fragment>
+            );
+          })}
+          <AxisBottom
+            top={yBrushMax}
+            scale={xBrushScale}
+            numTicks={width > 520 ? 10 : 5}
+            stroke={axisColor}
+            tickStroke={axisColor}
+            tickLabelProps={axisBottomTickLabelProps}
+          />
+          <Brush
+            key={brushKey}
+            xScale={xBrushScale}
+            yScale={yBrushScale}
+            width={xBrushMax}
+            height={yBrushMax}
+            margin={margin}
+            handleSize={8}
+            // resize
+            resizeTriggerAreas={resizeTriggerAreas}
+            brushDirection="horizontal"
+            initialBrushPosition={initialBrushPosition}
+            onChange={onBrushChange}
+            onClick={disabled ? () => {} : () => setSelectedRange(undefined)}
+            selectedBoxStyle={selectedBrushStyle}
+            useWindowMoveEvents
+            disableDraggingSelection={disabled}
+            renderBrushHandle={(props) => <BrushHandle {...props} />}
+          />
+        </Group>
+      </svg>
+    </div>
+  );
+}
+
+// define brush handle shape and position
+function BrushHandle({ x, height, isBrushActive }: BrushHandleRenderProps) {
+  const pathWidth = 8;
+  const pathHeight = 15;
+  if (!isBrushActive) {
+    return null;
+  }
+  return (
+    <Group left={x + pathWidth / 2} top={(height - pathHeight) / 2}>
+      <path
+        fill="#f2f2f2"
+        d="M -4.5 0.5 L 3.5 0.5 L 3.5 15.5 L -4.5 15.5 L -4.5 0.5 M -1.5 4 L -1.5 12 M 0.5 4 L 0.5 12"
+        stroke="#999999"
+        strokeWidth="1"
+        style={{ cursor: 'ew-resize' }}
+      />
+    </Group>
+  );
+}
+
+export default EzTimeFilter;