Eda notebook

packages/libs/coreui/src/components/theming/UIThemeProvider.tsx

@@ -3,6 +3,7 @@ import { css, Global, ThemeProvider } from '@emotion/react';
 import { useCoreUIFonts } from '../../hooks';
 
 import { UITheme } from './types';
+import colors from '../../definitions/colors';
 
 export type UIThemeProviderProps = {
   theme: UITheme;
@@ -14,13 +15,32 @@ export default function UIThemeProvider({
   children,
 }: UIThemeProviderProps) {
   useCoreUIFonts();
+  // In addition to making the theme available via React Context,
+  // we will also expose the theme as custom CSS properties.
   return (
     <ThemeProvider theme={theme}>
       <Global
         styles={css`
+          :root {
+            ${Object.entries(colors).flatMap(([colorName, byHueOrValue]) =>
+              typeof byHueOrValue === 'string'
+                ? [`--coreui-${colorName}: ${byHueOrValue};`]
+                : Object.entries(byHueOrValue).map(
+                    ([hueName, colorValue]) =>
+                      `--coreui-${colorName}-${hueName}: ${colorValue};`
+                  )
+            )}
+
+            --coreui-color-primary: ${theme.palette.primary.hue[
+              theme.palette.primary.level
+            ]};
+            --coreui-color-secondary: ${theme.palette.secondary.hue[
+              theme.palette.secondary.level
+            ]};
+          }
+
           *:focus-visible {
-            outline: 2px solid
-              ${theme.palette.primary.hue[theme.palette.primary.level]};
+            outline: 2px solid var(--coreui-color-primary);
           }
         `}
       />

packages/libs/eda/src/index.tsx

@@ -60,6 +60,7 @@ import './index.css';
 
 // snackbar
 import makeSnackbarProvider from '@veupathdb/coreui/lib/components/notifications/SnackbarProvider';
+import NotebookRoute from './lib/notebook/NotebookRoute';
 
 // Set singleAppMode to the name of one app, if the eda should use one instance of one app only.
 // Otherwise, let singleAppMode remain undefined or set it to '' to allow multiple app instances.
@@ -169,9 +170,20 @@ initialize({
               <Link to="/maps/studies">All studies</Link>
             </li>
           </ul>
+          <h3>Notebook Links</h3>
+          <ul>
+            <li>
+              <Link to="/notebook">All notebooks</Link>
+            </li>
+          </ul>
         </div>
       ),
     },
+    {
+      path: '/notebook',
+      exact: false,
+      component: () => <NotebookRoute edaServiceUrl={edaEndpoint} />,
+    },
     {
       path: '/eda',
       exact: false,

packages/libs/eda/src/lib/core/components/FilterChipList.tsx

@@ -10,7 +10,7 @@ import { colors, Warning } from '@veupathdb/coreui';
 // Material UI CSS declarations
 const useStyles = makeStyles((theme) => ({
   chips: {
-    display: 'flex',
+    display: 'inline-flex',
     flexWrap: 'wrap',
     '& > *:not(:last-of-type)': {
       // Spacing between chips

packages/libs/eda/src/lib/core/components/VariableLink.tsx

@@ -70,12 +70,12 @@ export const VariableLink = forwardRef(
         tabIndex={0}
         style={finalStyle}
         onKeyDown={(event) => {
-          event.preventDefault();
           if (disabled) {
             return;
           }
           if (event.key === 'Enter' || event.key === ' ') {
             linkConfig.onClick(value);
+            event.preventDefault();
           }
         }}
         onClick={(event) => {

packages/libs/eda/src/lib/notebook/EdaNotebook.css

@@ -0,0 +1,116 @@
+.EdaNotebook {
+  .Heading {
+    display: flex;
+    gap: 2em;
+    align-items: baseline;
+  }
+
+  .Paper {
+    /* A4 dimensions */
+    --paper-width: 2480px;
+    --paper-height: 3508px;
+    --paper-scale: 0.5;
+
+    width: calc(var(--paper-width) * var(--paper-scale));
+    /* height: calc(var(--paper-height) * var(--paper-scale)); */
+
+    padding: 2em;
+    margin: 1em auto;
+
+    /* background-color: #f3f3f3; */
+    box-shadow: 0 0 2px #b5b5b5;
+
+    > * + * {
+      margin-block-start: 1rem;
+    }
+
+    .Heading {
+      display: flex;
+      flex-direction: row;
+      justify-content: space-between;
+      gap: 0.5em;
+
+      h1 {
+        padding: 0;
+        font-size: 1.75em;
+      }
+
+      h2 {
+        font-size: 1em;
+        font-weight: bold;
+        padding: 0.25em 0.5em;
+        color: var(--coreui-color-primary, black);
+        border: 2px solid;
+        border-radius: 0.25em;
+        background-color: color-mix(
+          in srgb,
+          var(--coreui-color-primary) 5%,
+          transparent
+        );
+      }
+    }
+
+    > details {
+      border: 1px solid;
+      border-color: color-mix(
+        in srgb,
+        var(--coreui-color-primary) 30%,
+        transparent
+      );
+      border-top-left-radius: 0.5em;
+      border-top-right-radius: 0.5em;
+      border-bottom-left-radius: 0.5em;
+      border-bottom-right-radius: 0.5em;
+
+      > summary {
+        padding: 0.75em;
+        cursor: pointer;
+        font-size: 1.2em;
+        font-weight: 500;
+        background-color: color-mix(
+          in srgb,
+          var(--coreui-color-primary) 10%,
+          transparent
+        );
+
+        &:hover {
+          background-color: color-mix(
+            in srgb,
+            var(--coreui-color-primary) 20%,
+            transparent
+          );
+        }
+
+        &:active {
+          background-color: color-mix(
+            in srgb,
+            var(--coreui-color-primary) 15%,
+            transparent
+          );
+        }
+
+        transition: background-color 100ms ease-in;
+      }
+
+      &[open] > summary {
+        border-bottom: 1px solid;
+        border-color: color-mix(
+          in srgb,
+          var(--coreui-color-primary) 30%,
+          transparent
+        );
+      }
+
+      > div {
+        padding: 1em;
+      }
+    }
+  }
+
+  .Title {
+    fieldset {
+      padding: 0;
+      margin: 0;
+    }
+  }
+}

packages/libs/eda/src/lib/notebook/EdaNotebookAnalysis.tsx

@@ -0,0 +1,97 @@
+// Notes
+// =====
+//
+// - For now, we will only support "fixed" notebooks. If we want to allow "custom" notebooks,
+//   we have to make some decisions.
+// - Do we want a top-down data flow? E.g., subsetting is global for an analysis.
+// - Do we want to separate compute config from visualization? If so, how do we
+//   support that in the UI?
+// - Do we want text-based cells?
+// - Do we want download cells? It could have a preview.
+//
+
+import React, { useCallback, useMemo } from 'react';
+import { useAnalysis, useStudyRecord } from '../core';
+import { safeHtml } from '@veupathdb/wdk-client/lib/Utils/ComponentUtils';
+import { SaveableTextEditor } from '@veupathdb/wdk-client/lib/Components';
+import { ExpandablePanel } from '@veupathdb/coreui';
+import { NotebookCell as NotebookCellType } from './Types';
+import { NotebookCell } from './NotebookCell';
+
+import './EdaNotebook.css';
+
+interface NotebookSettings {
+  /** Ordered array of notebook cells */
+  cells: NotebookCellType[];
+}
+
+const NOTEBOOK_UI_SETTINGS_KEY = '@@NOTEBOOK@@';
+
+interface Props {
+  analysisId: string;
+}
+
+export function EdaNotebookAnalysis(props: Props) {
+  const { analysisId } = props;
+  const studyRecord = useStudyRecord();
+  const analysisState = useAnalysis(
+    analysisId === 'new' ? undefined : analysisId
+  );
+  const { analysis } = analysisState;
+  const notebookSettings = useMemo((): NotebookSettings => {
+    const storedSettings =
+      analysis?.descriptor.subset.uiSettings[NOTEBOOK_UI_SETTINGS_KEY];
+    if (storedSettings == null)
+      return {
+        cells: [
+          {
+            type: 'subset',
+            title: 'Subset data',
+          },
+        ],
+      };
+    return storedSettings as any as NotebookSettings;
+  }, [analysis]);
+  const updateCell = useCallback(
+    (cell: Partial<Omit<NotebookCellType, 'type'>>, cellIndex: number) => {
+      const oldCell = notebookSettings.cells[cellIndex];
+      const newCell = { ...oldCell, ...cell };
+      const nextCells = notebookSettings.cells.concat();
+      nextCells[cellIndex] = newCell;
+      const nextSettings = {
+        ...notebookSettings,
+        cells: nextCells,
+      };
+      analysisState.setVariableUISettings({
+        [NOTEBOOK_UI_SETTINGS_KEY]: nextSettings,
+      });
+    },
+    [analysisState, notebookSettings]
+  );
+  return (
+    <div className="EdaNotebook">
+      <div className="Paper">
+        <div className="Heading">
+          <h1>
+            <SaveableTextEditor
+              className="Title"
+              value={analysisState.analysis?.displayName ?? ''}
+              onSave={analysisState.setName}
+            />
+          </h1>
+          <h2>{safeHtml(studyRecord.displayName)}</h2>
+        </div>
+        {notebookSettings.cells.map((cell, index) => (
+          <details>
+            <summary>{cell.title}</summary>
+            <NotebookCell
+              analysisState={analysisState}
+              cell={cell}
+              updateCell={(update) => updateCell(update, index)}
+            />
+          </details>
+        ))}
+      </div>
+    </div>
+  );
+}

packages/libs/eda/src/lib/notebook/EdaNotebookLandingPage.tsx

@@ -0,0 +1,37 @@
+import React from 'react';
+import { useWdkStudyRecords } from '../core/hooks/study';
+import { useConfiguredSubsettingClient } from '../core/hooks/client';
+import { Link, useRouteMatch } from 'react-router-dom';
+import { safeHtml } from '@veupathdb/wdk-client/lib/Utils/ComponentUtils';
+
+interface Props {
+  edaServiceUrl: string;
+}
+
+export function EdaNotebookLandingPage(props: Props) {
+  const subsettingClient = useConfiguredSubsettingClient(props.edaServiceUrl);
+  const datasets = useWdkStudyRecords(subsettingClient);
+  const { url } = useRouteMatch();
+  return (
+    <div>
+      <h1>EDA Notebooks</h1>
+      <div>
+        <h2>Start a new notebook</h2>
+        <ul>
+          {datasets?.map((dataset) => (
+            <li>
+              {safeHtml(
+                dataset.displayName,
+                { to: `${url}/${dataset.attributes.dataset_id as string}/new` },
+                Link
+              )}
+            </li>
+          ))}
+        </ul>
+      </div>
+      <hr />
+      <div>MY NOTEBOOKS</div>
+      <div>SHARED NOTEBOOKS</div>
+    </div>
+  );
+}

packages/libs/eda/src/lib/notebook/NotebookCell.tsx

@@ -0,0 +1,28 @@
+import { AnalysisState } from '../core';
+import { NotebookCell as NotebookCellType } from './Types';
+import { SubsettingNotebookCell } from './SubsettingNotebookCell';
+
+interface Props {
+  analysisState: AnalysisState;
+  cell: NotebookCellType;
+  updateCell: (cell: Partial<Omit<NotebookCellType, 'type'>>) => void;
+}
+
+/**
+ * Top-level component that delegates to imeplementations of NotebookCell variants.
+ */
+export function NotebookCell(props: Props) {
+  const { cell, analysisState, updateCell } = props;
+  switch (cell.type) {
+    case 'subset':
+      return (
+        <SubsettingNotebookCell
+          cell={cell}
+          analysisState={analysisState}
+          updateCell={updateCell}
+        />
+      );
+    default:
+      return null;
+  }
+}