feat: added second dropdown for group comparison estimators and optio…

…ns to select reference dataset
neurostuff · Nov 17, 2023 · 9c7a1f4 · 9c7a1f4
1 parent abc2a18
commit 9c7a1f4
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Showing 20 changed files with 360 additions and 158 deletions.
diff --git a/...alogs/CreateMetaAnalysisSpecificationDialog/CreateMetaAnalysisSpecificationDialogBase.tsx b/...alogs/CreateMetaAnalysisSpecificationDialog/CreateMetaAnalysisSpecificationDialogBase.tsx
@@ -1,20 +1,18 @@
 import { Box, Step, StepLabel, Stepper } from '@mui/material';
-import BaseDialog, { IDialog } from '../BaseDialog';
-import { useEffect, useState } from 'react';
 import { ENavigationButton } from 'components/Buttons/NavigationButtons/NavigationButtons';
-import CreateMetaAnalysisSpecificationSelectionStep from './CreateMetaAnalysisSpecificationSelectionStep/CreateMetaAnalysisSpecificationSelectionStep';
-import { EPropertyType } from 'components/EditMetadata';
-import CreateMetaAnalysisSpecificationAlgorithmStep from './CreateMetaAnalysisSpecificationAlgorithmStep/CreateMetaAnalysisSpecificationAlgorithmStep';
 import { IDynamicValueType } from 'components/MetaAnalysisConfigComponents';
-import CreateMetaAnalysisSpecificationReview from './CreateMetaAnalysisSpecificationReview/CreateMetaAnalysisSpecificationReview';
 import { IAutocompleteObject } from 'components/NeurosynthAutocomplete/NeurosynthAutocomplete';
-import CreateMetaAnalysisSpecificationDetailsStep from './CreateMetaAnalysisSpecificationDetailsStep/CreateMetaAnalysisSpecificationDetailsStep';
 import { useProjectName } from 'pages/Projects/ProjectPage/ProjectStore';
+import { useEffect, useState } from 'react';
+import BaseDialog, { IDialog } from '../BaseDialog';
+import CreateMetaAnalysisSpecificationAlgorithmStep from './CreateMetaAnalysisSpecificationAlgorithmStep/CreateMetaAnalysisSpecificationAlgorithmStep';
+import CreateMetaAnalysisSpecificationDetailsStep from './CreateMetaAnalysisSpecificationDetailsStep/CreateMetaAnalysisSpecificationDetailsStep';
 import {
     IAlgorithmSelection,
     IAnalysesSelection,
 } from './CreateMetaAnalysisSpecificationDialogBase.types';
-import { AnnotationNoteValue } from 'components/HotTables/HotTables.types';
+import CreateMetaAnalysisSpecificationReview from './CreateMetaAnalysisSpecificationReview/CreateMetaAnalysisSpecificationReview';
+import CreateMetaAnalysisSpecificationSelectionStep from './CreateMetaAnalysisSpecificationSelectionStep/CreateMetaAnalysisSpecificationSelectionStep';
 
 const CreateMetaAnalysisSpecificationDialogBase: React.FC<IDialog> = (props) => {
     const projectName = useProjectName();
@@ -24,7 +22,12 @@ const CreateMetaAnalysisSpecificationDialogBase: React.FC<IDialog> = (props) =>
         name: `${projectName} Meta Analysis`,
         description: `this is a meta-analysis for ${projectName}`,
     });
-    const [selection, setSelection] = useState<IAnalysesSelection>();
+    const [selection, setSelection] = useState<IAnalysesSelection>({
+        selectionKey: undefined,
+        selectionValue: undefined,
+        type: undefined,
+        referenceDataset: undefined,
+    });
     const [algorithm, setAlgorithm] = useState<IAlgorithmSelection>({
         estimator: null,
         estimatorArgs: {},
@@ -48,7 +51,12 @@ const CreateMetaAnalysisSpecificationDialogBase: React.FC<IDialog> = (props) =>
             corrector: null,
             correctorArgs: {},
         });
-        setSelection(undefined);
+        setSelection({
+            selectionKey: undefined,
+            selectionValue: undefined,
+            type: undefined,
+            referenceDataset: undefined,
+        });
     };
 
     const handleNavigate = (button: ENavigationButton) => {
@@ -69,15 +77,9 @@ const CreateMetaAnalysisSpecificationDialogBase: React.FC<IDialog> = (props) =>
         });
     };
 
-    const handleChooseSelection = (
-        selectionKey: string,
-        type: EPropertyType,
-        selectionValue?: AnnotationNoteValue
-    ) => {
+    const handleChooseSelection = (selection: IAnalysesSelection) => {
         setSelection({
-            selectionKey,
-            type,
-            selectionValue: selectionValue ? selectionValue : undefined,
+            ...selection,
         });
     };
 

diff --git a/.../CreateMetaAnalysisSpecificationDialog/CreateMetaAnalysisSpecificationDialogBase.types.ts b/.../CreateMetaAnalysisSpecificationDialog/CreateMetaAnalysisSpecificationDialogBase.types.ts
@@ -4,9 +4,10 @@ import { IDynamicValueType } from 'components/MetaAnalysisConfigComponents';
 import { IAutocompleteObject } from 'components/NeurosynthAutocomplete/NeurosynthAutocomplete';
 
 export interface IAnalysesSelection {
-    selectionKey: string;
-    type: EPropertyType;
-    selectionValue?: AnnotationNoteValue;
+    selectionKey: string | undefined;
+    type: EPropertyType | undefined;
+    selectionValue: AnnotationNoteValue | undefined; // defined if type is not a boolean
+    referenceDataset?: string; // defined if multi group analysis is used (i.e. ALESubtraction or MKDAChi2)
 }
 
 export interface IAlgorithmSelection {

diff --git a/...ionDialog/CreateMetaAnalysisSpecificationReview/CreateMetaAnalysisSpecificationReview.tsx b/...ionDialog/CreateMetaAnalysisSpecificationReview/CreateMetaAnalysisSpecificationReview.tsx
@@ -1,4 +1,4 @@
-import { Box, Button } from '@mui/material';
+import { Box, Button, Typography } from '@mui/material';
 import LoadingButton from 'components/Buttons/LoadingButton/LoadingButton';
 import { ENavigationButton } from 'components/Buttons/NavigationButtons/NavigationButtons';
 import { IDynamicValueType } from 'components/MetaAnalysisConfigComponents';
@@ -23,7 +23,7 @@ import { getFilteredAnnotationNotes } from '../CreateMetaAnalysisSpecificationSe
 const CreateMetaAnalysisSpecificationReview: React.FC<{
     onNavigate: (button: ENavigationButton) => void;
     onClose: () => void;
-    selection: IAnalysesSelection | undefined;
+    selection: IAnalysesSelection;
     algorithm: {
         estimator: IAutocompleteObject | null;
         estimatorArgs: IDynamicValueType;
@@ -110,7 +110,15 @@ const CreateMetaAnalysisSpecificationReview: React.FC<{
                     title="Selection"
                     value={selectionText}
                     caption={numSelectedAnnotationsText}
-                ></MetaAnalysisSummaryRow>
+                >
+                    {props.selection.referenceDataset && (
+                        <>
+                            <Typography sx={{ marginTop: '1rem', color: 'gray' }}>
+                                Reference Dataset: {props.selection.referenceDataset}
+                            </Typography>
+                        </>
+                    )}
+                </MetaAnalysisSummaryRow>
                 <MetaAnalysisSummaryRow
                     title="Estimator"
                     value={props.algorithm.estimator?.label || ''}

diff --git a/...teMetaAnalysisSpecificationSelectionStep/CreateMetaAnalysisSpecificationSelectionStep.tsx b/...teMetaAnalysisSpecificationSelectionStep/CreateMetaAnalysisSpecificationSelectionStep.tsx
@@ -6,37 +6,31 @@ import {
     useProjectExtractionStudysetId,
 } from 'pages/Projects/ProjectPage/ProjectStore';
 import { useState } from 'react';
-import SelectAnalysesComponent from './SelectAnalysesComponent/SelectAnalysesComponent';
-import SelectAnalysesSummaryComponent from './SelectAnalysesComponent/SelectAnalysesSummaryComponent';
 import {
     IAlgorithmSelection,
     IAnalysesSelection,
 } from '../CreateMetaAnalysisSpecificationDialogBase.types';
-import { AnnotationNoteValue } from 'components/HotTables/HotTables.types';
+import SelectAnalysesComponent from './SelectAnalysesComponent/SelectAnalysesComponent';
+import { isMultiGroupAlgorithm } from './SelectAnalysesComponent/SelectAnalysesComponent.helpers';
+import SelectAnalysesSummaryComponent from './SelectAnalysesComponent/SelectAnalysesSummaryComponent';
 
 const CreateMetaAnalysisSpecificationSelectionStep: React.FC<{
-    onChooseSelection: (
-        selectionKey: string,
-        type: EPropertyType,
-        selectionValue?: AnnotationNoteValue
-    ) => void;
+    onChooseSelection: (selection: IAnalysesSelection) => void;
     onNavigate: (button: ENavigationButton) => void;
-    selection: IAnalysesSelection | undefined;
+    selection: IAnalysesSelection;
     algorithm: IAlgorithmSelection;
 }> = (props) => {
     const annotationId = useProjectExtractionAnnotationId();
     const studysetId = useProjectExtractionStudysetId();
-    const [selectedValue, setSelectedValue] = useState<IAnalysesSelection | undefined>(
-        props.selection
-    );
+    const [selectedValue, setSelectedValue] = useState<IAnalysesSelection>(props.selection);
+
+    const isMultiGroup = isMultiGroupAlgorithm(props.algorithm?.estimator);
 
     const handleNavigate = (button: ENavigationButton) => {
         if (selectedValue?.selectionKey && selectedValue?.type !== EPropertyType.NONE)
-            props.onChooseSelection(
-                selectedValue.selectionKey,
-                selectedValue.type,
-                selectedValue.selectionValue
-            );
+            props.onChooseSelection({
+                ...selectedValue,
+            });
         props.onNavigate(button);
     };
 
@@ -57,7 +51,7 @@ const CreateMetaAnalysisSpecificationSelectionStep: React.FC<{
                 <SelectAnalysesComponent
                     selectedValue={selectedValue}
                     onSelectValue={(val) => setSelectedValue(val)}
-                    annotationdId={annotationId || ''}
+                    annotationId={annotationId || ''}
                     algorithm={props.algorithm}
                 />
 
@@ -79,7 +73,8 @@ const CreateMetaAnalysisSpecificationSelectionStep: React.FC<{
                         sx={{ width: '200px' }}
                         disabled={
                             !selectedValue?.selectionKey ||
-                            selectedValue?.selectionValue === undefined
+                            selectedValue?.selectionValue === undefined ||
+                            (isMultiGroup && !selectedValue?.referenceDataset) // needs ref dataset for multigroup algos
                         }
                         onClick={() => handleNavigate(ENavigationButton.NEXT)}
                     >

diff --git a/...ysisSpecificationSelectionStep/SelectAnalysesComponent/SelectAnalysesComponent.helpers.ts b/...ysisSpecificationSelectionStep/SelectAnalysesComponent/SelectAnalysesComponent.helpers.ts
@@ -3,6 +3,7 @@ import { AnnotationNoteValue } from 'components/HotTables/HotTables.types';
 import { NoteCollectionReturn } from 'neurostore-typescript-sdk';
 import { IAnalysesSelection } from '../../CreateMetaAnalysisSpecificationDialogBase.types';
 import { IAutocompleteObject } from 'components/NeurosynthAutocomplete/NeurosynthAutocomplete';
+import { DEFAULT_REFERENCE_DATASETS } from './SelectAnalysesComponent.types';
 
 // TODO: instead of hardcoding this, we should add a property to the meta-analysis spec with something like: "multi-group" or something similar
 export const MULTIGROUP_ALGORITHMS = ['MKDAChi2', 'ALESubtraction'];
@@ -87,3 +88,9 @@ export const annotationNotesToTableFormatHelper = (
 
     return tableFormat;
 };
+
+export const selectedReferenceDatasetIsDefault = (selectedReferenceDataset: string | undefined) => {
+    if (!selectedReferenceDataset) return false;
+
+    return DEFAULT_REFERENCE_DATASETS.some((x) => x.label === selectedReferenceDataset);
+};
diff --git a/...etaAnalysisSpecificationSelectionStep/SelectAnalysesComponent/SelectAnalysesComponent.tsx b/...etaAnalysisSpecificationSelectionStep/SelectAnalysesComponent/SelectAnalysesComponent.tsx
@@ -11,63 +11,96 @@ import {
 } from '../../CreateMetaAnalysisSpecificationDialogBase.types';
 import SelectAnalysesComponentTable from './SelectAnalysesComponentTable';
 import SelectAnalysesStringValue from './SelectAnalysesStringValue';
-import { isMultiGroupAlgorithm } from './SelectAnalysesComponent.helpers';
+import {
+    isMultiGroupAlgorithm,
+    selectedReferenceDatasetIsDefault,
+} from './SelectAnalysesComponent.helpers';
 import SelectAnalysesMultiGroupComponent from './SelectAnalysesMultiGroupComponent';
+import { DEFAULT_REFERENCE_DATASETS } from './SelectAnalysesComponent.types';
 
 const SelectAnalysesComponent: React.FC<{
-    annotationdId: string;
-    selectedValue: IAnalysesSelection | undefined;
-    onSelectValue: (value: IAnalysesSelection | undefined) => void;
+    annotationId: string;
+    selectedValue: IAnalysesSelection;
+    onSelectValue: (value: IAnalysesSelection) => void;
     algorithm: IAlgorithmSelection;
 }> = (props) => {
-    const { annotationdId, selectedValue, onSelectValue, algorithm } = props;
-    const { data: annotation } = useGetAnnotationById(annotationdId);
+    const { annotationId, selectedValue, onSelectValue, algorithm } = props;
+    const { data: annotation } = useGetAnnotationById(annotationId);
 
     // we need some notion of "touched" in order to know if the input is being seen for the first time (so we can set some default value)
     // versus the input being cleared (in which case we dont do anything)
     const selectionOccurred = useRef<boolean>(false);
 
     useEffect(() => {
-        if (selectedValue?.selectionKey) {
+        if (selectedValue.selectionKey) {
             selectionOccurred.current = true;
             return;
-        }
-
-        if (!selectionOccurred.current && 'included' in (annotation?.note_keys || {})) {
-            onSelectValue({
+        } else if (!selectionOccurred.current && 'included' in (annotation?.note_keys || {})) {
+            const initialVal: IAnalysesSelection = {
                 selectionKey: 'included',
                 type: EPropertyType.BOOLEAN,
                 selectionValue: true,
-            });
+            };
+
+            if (isMultiGroupAlgorithm(algorithm?.estimator)) {
+                initialVal.referenceDataset = DEFAULT_REFERENCE_DATASETS[0].label;
+            }
+
+            onSelectValue(initialVal);
             selectionOccurred.current = true;
         }
-    }, [selectedValue?.selectionKey, annotation, onSelectValue, selectionOccurred]);
+    }, [
+        selectedValue.selectionKey,
+        annotation,
+        onSelectValue,
+        selectionOccurred,
+        algorithm?.estimator,
+    ]);
 
     const options = useMemo(() => {
         return Object.entries(annotation?.note_keys || {})
             .map(([key, value]) => ({
                 selectionKey: key,
                 type: value as EPropertyType,
+                selectionValue: undefined,
+                referenceDataset: undefined,
             }))
             .filter((x) => x.type === EPropertyType.BOOLEAN || x.type === EPropertyType.STRING);
     }, [annotation?.note_keys]);
 
     const stringInclusionColSelected = selectedValue?.type === EPropertyType.STRING;
-    const showTable = stringInclusionColSelected
+    const showInclusionSummary = stringInclusionColSelected
         ? !!selectedValue?.selectionValue
         : !!selectedValue?.selectionKey;
-    const isMultiGroup = isMultiGroupAlgorithm(algorithm?.estimator);
+    const showMultiGroup = isMultiGroupAlgorithm(algorithm?.estimator);
 
-    const handleSelectColumn = (selectedVal: IAnalysesSelection | null | undefined) => {
-        const update = selectedVal;
-        if (update) {
-            if (update.type === EPropertyType.BOOLEAN) {
-                update.selectionValue = true;
-            } else {
-                update.selectionValue = undefined;
-            }
+    const handleSelectColumn = (newVal: IAnalysesSelection | undefined) => {
+        if (newVal?.selectionKey === selectedValue.selectionKey) return; // we selected the same option that is already selected
+
+        const referenceDatasetIsNowInvalid = !selectedReferenceDatasetIsDefault(
+            selectedValue.referenceDataset
+        );
+        if (!newVal) {
+            onSelectValue({
+                selectionKey: undefined,
+                type: undefined,
+                selectionValue: undefined,
+                referenceDataset: referenceDatasetIsNowInvalid
+                    ? undefined
+                    : selectedValue.referenceDataset,
+            });
+            return;
         }
-        onSelectValue(update || undefined);
+
+        const update: IAnalysesSelection = {
+            selectionKey: newVal.selectionKey,
+            type: newVal.type,
+            selectionValue: newVal.type === EPropertyType.BOOLEAN ? true : undefined,
+            referenceDataset: referenceDatasetIsNowInvalid
+                ? undefined
+                : selectedValue.referenceDataset,
+        };
+        onSelectValue(update);
     };
 
     return (
@@ -83,7 +116,7 @@ const SelectAnalysesComponent: React.FC<{
                 isOptionEqualToValue={(option, value) =>
                     option?.selectionKey === value?.selectionKey
                 }
-                value={selectedValue}
+                value={selectedValue?.selectionKey ? selectedValue : undefined}
                 size="medium"
                 inputPropsSx={{
                     color: NeurosynthTableStyles[selectedValue?.type || EPropertyType.NONE],
@@ -100,7 +133,7 @@ const SelectAnalysesComponent: React.FC<{
                     </ListItem>
                 )}
                 getOptionLabel={(option) => option?.selectionKey || ''}
-                onChange={(_event, newVal, _reason) => handleSelectColumn(newVal)}
+                onChange={(_event, newVal, _reason) => handleSelectColumn(newVal || undefined)}
                 options={options}
             />
             {stringInclusionColSelected && (
@@ -112,13 +145,13 @@ const SelectAnalysesComponent: React.FC<{
                     }}
                 >
                     <SelectAnalysesStringValue
+                        annotationId={annotationId}
                         selectedValue={selectedValue}
                         onSelectValue={(newVal) => onSelectValue(newVal)}
-                        allNotes={annotation?.notes as NoteCollectionReturn[] | undefined}
                     />
                 </Box>
             )}
-            {showTable && (
+            {showInclusionSummary && (
                 <Box
                     sx={{
                         marginTop: '1rem',
@@ -130,7 +163,14 @@ const SelectAnalysesComponent: React.FC<{
                     />
                 </Box>
             )}
-            {isMultiGroup && <SelectAnalysesMultiGroupComponent algorithm={algorithm} />}
+            {showMultiGroup && (
+                <SelectAnalysesMultiGroupComponent
+                    onSelectValue={(newVal) => onSelectValue(newVal)}
+                    annotationId={annotationId}
+                    selectedValue={selectedValue}
+                    algorithm={algorithm}
+                />
+            )}
         </Box>
     );
 };

diff --git a/...alysisSpecificationSelectionStep/SelectAnalysesComponent/SelectAnalysesComponent.types.ts b/...alysisSpecificationSelectionStep/SelectAnalysesComponent/SelectAnalysesComponent.types.ts
@@ -0,0 +1,12 @@
+import { IAutocompleteObject } from 'components/NeurosynthAutocomplete/NeurosynthAutocomplete';
+
+export type IMultiGroupOption = IAutocompleteObject & {
+    type: string;
+    id: string;
+};
+
+export const DEFAULT_REFERENCE_DATASETS: IMultiGroupOption[] = [
+    { label: 'Neurostore Dataset', description: '', type: 'Reference Dataset', id: 'neurostore' },
+    { label: 'Neuroquery Dataset', description: '', type: 'Reference Dataset', id: 'neuroquery' },
+    { label: 'Neurosynth Dataset', description: '', type: 'Reference Dataset', id: 'neurosynth' },
+];