Eda notebook

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.scss

@@ -0,0 +1,35 @@
+.EdaNotebook {
+  .Heading {
+    display: flex;
+    gap: 2em;
+    align-items: baseline;
+  }
+
+  .Paper {
+    max-width: 1250px;
+    padding: 1em;
+    margin: 1em auto;
+    background-color: #f3f3f3;
+    box-shadow: 0 0 2px #b5b5b5;
+
+    > * + * {
+      margin-block-start: 1rem;
+    }
+    h2,
+    h3 {
+      padding: 0;
+    }
+    h3 {
+      font-size: 1em;
+      font-weight: 400;
+      line-height: 1.5;
+    }
+  }
+
+  .Title {
+    fieldset {
+      padding: 0;
+      margin: 0;
+    }
+  }
+}

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

@@ -0,0 +1,101 @@
+// 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.scss';
+
+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="Heading">
+        <h1>EDA Notebook</h1>
+      </div>
+      <div className="Paper">
+        <div>
+          <h2>
+            <SaveableTextEditor
+              className="Title"
+              value={analysisState.analysis?.displayName ?? ''}
+              onSave={analysisState.setName}
+            />
+          </h2>
+          <h3>Study: {safeHtml(studyRecord.displayName)}</h3>
+        </div>
+        {notebookSettings.cells.map((cell, index) => (
+          <ExpandablePanel title={cell.title} subTitle={{}} themeRole="primary">
+            <div style={{ padding: '1em' }}>
+              <NotebookCell
+                analysisState={analysisState}
+                cell={cell}
+                updateCell={(update) => updateCell(update, index)}
+              />
+            </div>
+          </ExpandablePanel>
+        ))}
+      </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;
+  }
+}

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

@@ -0,0 +1,64 @@
+import React, { ComponentType } from 'react';
+import { Route, Switch, useRouteMatch } from 'react-router-dom';
+import { EdaNotebookLandingPage } from './EdaNotebookLandingPage';
+import { EdaNotebookAnalysis } from './EdaNotebookAnalysis';
+import {
+  EDAWorkspaceContainer,
+  useConfiguredAnalysisClient,
+  useConfiguredComputeClient,
+  useConfiguredDataClient,
+  useConfiguredDownloadClient,
+  useConfiguredSubsettingClient,
+} from '../core';
+import { DocumentationContainer } from '../core/components/docs/DocumentationContainer';
+import { QueryClientProvider } from '@tanstack/react-query';
+import { queryClient } from '../core/api/queryClient';
+
+interface Props {
+  edaServiceUrl: string;
+  datasetId?: string;
+  analysisId?: string;
+}
+
+export default function NotebookRoute(props: Props) {
+  const { edaServiceUrl } = props;
+  const match = useRouteMatch();
+  const analysisClient = useConfiguredAnalysisClient(edaServiceUrl);
+  const subsettingClient = useConfiguredSubsettingClient(edaServiceUrl);
+  const downloadClient = useConfiguredDownloadClient(edaServiceUrl);
+  const dataClient = useConfiguredDataClient(edaServiceUrl);
+  const computeClient = useConfiguredComputeClient(edaServiceUrl);
+
+  return (
+    <DocumentationContainer>
+      <QueryClientProvider client={queryClient}>
+        <Switch>
+          <Route
+            exact
+            path={match.path}
+            render={() => (
+              <EdaNotebookLandingPage edaServiceUrl={edaServiceUrl} />
+            )}
+          />
+          <Route
+            path={`${match.path}/:datasetId/:analysisId`}
+            render={(props) => (
+              <EDAWorkspaceContainer
+                studyId={props.match.params.datasetId}
+                analysisClient={analysisClient}
+                subsettingClient={subsettingClient}
+                downloadClient={downloadClient}
+                dataClient={dataClient}
+                computeClient={computeClient}
+              >
+                <EdaNotebookAnalysis
+                  analysisId={props.match.params.analysisId}
+                />
+              </EDAWorkspaceContainer>
+            )}
+          />
+        </Switch>
+      </QueryClientProvider>
+    </DocumentationContainer>
+  );
+}

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

@@ -0,0 +1,58 @@
+import { useMemo } from 'react';
+import { useEntityCounts } from '../core/hooks/entityCounts';
+import { useStudyEntities } from '../core/hooks/workspace';
+import { NotebookCellComponentProps } from './Types';
+import { VariableLinkConfig } from '../core/components/VariableLink';
+import FilterChipList from '../core/components/FilterChipList';
+import Subsetting from '../workspace/Subsetting';
+
+export function SubsettingNotebookCell(
+  props: NotebookCellComponentProps<'subset'>
+) {
+  const { analysisState, cell, updateCell } = props;
+  const { selectedVariable } = cell;
+  const entities = useStudyEntities();
+  const totalCountsResult = useEntityCounts();
+  const filteredCountsResult = useEntityCounts(
+    analysisState.analysis?.descriptor.subset.descriptor
+  );
+  const variableLinkConfig = useMemo(
+    (): VariableLinkConfig => ({
+      type: 'button',
+      onClick: (selectedVariable) => {
+        updateCell({ selectedVariable });
+      },
+    }),
+    [updateCell]
+  );
+  return (
+    <div>
+      <div>
+        <FilterChipList
+          filters={analysisState.analysis?.descriptor.subset.descriptor}
+          entities={entities}
+          selectedEntityId={selectedVariable?.entityId}
+          selectedVariableId={selectedVariable?.variableId}
+          removeFilter={(filter) => {
+            analysisState.setFilters((filters) =>
+              filters.filter(
+                (f) =>
+                  f.entityId !== filter.entityId ||
+                  f.variableId !== filter.variableId
+              )
+            );
+          }}
+          variableLinkConfig={variableLinkConfig}
+        />
+      </div>
+      <Subsetting
+        analysisState={analysisState}
+        entityId={selectedVariable?.entityId ?? ''}
+        variableId={selectedVariable?.variableId ?? ''}
+        totalCounts={totalCountsResult.value}
+        filteredCounts={filteredCountsResult.value}
+        variableLinkConfig={variableLinkConfig}
+      />
+    </div>
+  );
+}