feat: added handling for string selection in specification and mkdachi2

neurostuff · Nov 10, 2023 · ea9e87a · ea9e87a
1 parent 11c9eeb
commit ea9e87a
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Showing 18 changed files with 638 additions and 360 deletions.
diff --git a/...CreateMetaAnalysisSpecificationDetailsStep/CreateMetaAnalysisSpecificationDetailsStep.tsx b/...CreateMetaAnalysisSpecificationDetailsStep/CreateMetaAnalysisSpecificationDetailsStep.tsx
@@ -66,7 +66,7 @@ const CreateMetaAnalysisSpecificationDetailsStep: React.FC<{
                 sx={{ marginBottom: '1rem' }}
                 fullWidth
                 value={details.name}
-                label="name"
+                label="meta-analysis name"
                 name="name"
                 onChange={handleUpdateDetails}
             />
@@ -75,7 +75,7 @@ const CreateMetaAnalysisSpecificationDetailsStep: React.FC<{
                 sx={{ marginBottom: '1rem' }}
                 fullWidth
                 onChange={handleUpdateDetails}
-                label="description"
+                label="meta-analysis description"
                 name="description"
             />
             <NavigationButtons

diff --git a/...alogs/CreateMetaAnalysisSpecificationDialog/CreateMetaAnalysisSpecificationDialogBase.tsx b/...alogs/CreateMetaAnalysisSpecificationDialog/CreateMetaAnalysisSpecificationDialogBase.tsx
@@ -10,6 +10,11 @@ import CreateMetaAnalysisSpecificationReview from './CreateMetaAnalysisSpecifica
 import { IAutocompleteObject } from 'components/NeurosynthAutocomplete/NeurosynthAutocomplete';
 import CreateMetaAnalysisSpecificationDetailsStep from './CreateMetaAnalysisSpecificationDetailsStep/CreateMetaAnalysisSpecificationDetailsStep';
 import { useProjectName } from 'pages/Projects/ProjectPage/ProjectStore';
+import {
+    IAlgorithmSelection,
+    IAnalysesSelection,
+} from './CreateMetaAnalysisSpecificationDialogBase.types';
+import { AnnotationNoteValue } from 'components/HotTables/HotTables.types';
 
 const CreateMetaAnalysisSpecificationDialogBase: React.FC<IDialog> = (props) => {
     const projectName = useProjectName();
@@ -19,16 +24,8 @@ const CreateMetaAnalysisSpecificationDialogBase: React.FC<IDialog> = (props) =>
         name: `${projectName} Meta Analysis`,
         description: `this is a meta-analysis for ${projectName}`,
     });
-    const [selection, setSelection] = useState<{
-        selectionKey: string | undefined;
-        type: EPropertyType;
-    }>();
-    const [algorithm, setAlgorithm] = useState<{
-        estimator: IAutocompleteObject | null;
-        estimatorArgs: IDynamicValueType;
-        corrector: IAutocompleteObject | null;
-        correctorArgs: IDynamicValueType;
-    }>({
+    const [selection, setSelection] = useState<IAnalysesSelection>();
+    const [algorithm, setAlgorithm] = useState<IAlgorithmSelection>({
         estimator: null,
         estimatorArgs: {},
         corrector: null,
@@ -72,10 +69,15 @@ const CreateMetaAnalysisSpecificationDialogBase: React.FC<IDialog> = (props) =>
         });
     };
 
-    const handleChooseSelection = (selectionKey: string, type: EPropertyType) => {
+    const handleChooseSelection = (
+        selectionKey: string,
+        type: EPropertyType,
+        selectionValue?: AnnotationNoteValue
+    ) => {
         setSelection({
             selectionKey,
             type,
+            selectionValue: selectionValue ? selectionValue : undefined,
         });
     };
 
@@ -98,16 +100,17 @@ const CreateMetaAnalysisSpecificationDialogBase: React.FC<IDialog> = (props) =>
             dialogTitle="Create Meta-Analysis Specification"
             isOpen={props.isOpen}
             fullWidth
-            maxWidth="md"
+            dialogTitleSx={{ padding: '1rem 0rem 0rem 4rem' }}
+            maxWidth="lg"
             onCloseDialog={handleCloseDialog}
         >
-            <Box>
+            <Box sx={{ padding: '2rem' }}>
                 <Stepper activeStep={activeStep}>
                     <Step>
-                        <StepLabel>Select Analyses</StepLabel>
+                        <StepLabel>Enter Specification</StepLabel>
                     </Step>
                     <Step>
-                        <StepLabel>Enter Specification</StepLabel>
+                        <StepLabel>Select Analyses</StepLabel>
                     </Step>
                     <Step>
                         <StepLabel>Enter Details</StepLabel>
@@ -118,16 +121,17 @@ const CreateMetaAnalysisSpecificationDialogBase: React.FC<IDialog> = (props) =>
                 </Stepper>
                 <Box sx={{ marginTop: '1rem' }}>
                     {activeStep === 0 && (
-                        <CreateMetaAnalysisSpecificationSelectionStep
-                            onChooseSelection={handleChooseSelection}
-                            selection={selection}
+                        <CreateMetaAnalysisSpecificationAlgorithmStep
+                            onChooseAlgorithm={handleChooseAlgorithm}
+                            algorithm={algorithm}
                             onNavigate={handleNavigate}
                         />
                     )}
                     {activeStep === 1 && (
-                        <CreateMetaAnalysisSpecificationAlgorithmStep
-                            onChooseAlgorithm={handleChooseAlgorithm}
+                        <CreateMetaAnalysisSpecificationSelectionStep
+                            onChooseSelection={handleChooseSelection}
                             algorithm={algorithm}
+                            selection={selection}
                             onNavigate={handleNavigate}
                         />
                     )}

diff --git a/.../CreateMetaAnalysisSpecificationDialog/CreateMetaAnalysisSpecificationDialogBase.types.ts b/.../CreateMetaAnalysisSpecificationDialog/CreateMetaAnalysisSpecificationDialogBase.types.ts
@@ -0,0 +1,17 @@
+import { EPropertyType } from 'components/EditMetadata';
+import { AnnotationNoteValue } from 'components/HotTables/HotTables.types';
+import { IDynamicValueType } from 'components/MetaAnalysisConfigComponents';
+import { IAutocompleteObject } from 'components/NeurosynthAutocomplete/NeurosynthAutocomplete';
+
+export interface IAnalysesSelection {
+    selectionKey: string;
+    type: EPropertyType;
+    selectionValue?: AnnotationNoteValue;
+}
+
+export interface IAlgorithmSelection {
+    estimator: IAutocompleteObject | null;
+    estimatorArgs: IDynamicValueType;
+    corrector: IAutocompleteObject | null;
+    correctorArgs: IDynamicValueType;
+}
diff --git a/...ionDialog/CreateMetaAnalysisSpecificationReview/CreateMetaAnalysisSpecificationReview.tsx b/...ionDialog/CreateMetaAnalysisSpecificationReview/CreateMetaAnalysisSpecificationReview.tsx
@@ -1,17 +1,6 @@
-import {
-    Box,
-    Button,
-    Divider,
-    FormControl,
-    InputLabel,
-    MenuItem,
-    Select,
-    Typography,
-} from '@mui/material';
+import { Box, Button } from '@mui/material';
 import LoadingButton from 'components/Buttons/LoadingButton/LoadingButton';
 import { ENavigationButton } from 'components/Buttons/NavigationButtons/NavigationButtons';
-import { getFilteredAnnotationNotes } from 'components/Dialogs/CreateMetaAnalysisSpecificationDialog/CreateMetaAnalysisSpecificationSelectionStep/SelectAnalysesComponent/SelectAnalysesComponent';
-import { EPropertyType } from 'components/EditMetadata';
 import { IDynamicValueType } from 'components/MetaAnalysisConfigComponents';
 import DynamicInputDisplay from 'components/MetaAnalysisConfigComponents/DynamicInputDisplay/DynamicInputDisplay';
 import MetaAnalysisSummaryRow from 'components/MetaAnalysisConfigComponents/MetaAnalysisSummaryRow/MetaAnalysisSummaryRow';
@@ -26,18 +15,15 @@ import {
     useProjectExtractionStudysetId,
     useProjectId,
 } from 'pages/Projects/ProjectPage/ProjectStore';
-import { useState } from 'react';
+import { useMemo } from 'react';
 import { useHistory } from 'react-router-dom';
+import { IAnalysesSelection } from '../CreateMetaAnalysisSpecificationDialogBase.types';
+import { getFilteredAnnotationNotes } from '../CreateMetaAnalysisSpecificationSelectionStep/SelectAnalysesComponent/SelectAnalysesComponent.helpers';
 
 const CreateMetaAnalysisSpecificationReview: React.FC<{
     onNavigate: (button: ENavigationButton) => void;
     onClose: () => void;
-    selection:
-        | {
-              selectionKey: string | undefined;
-              type: EPropertyType;
-          }
-        | undefined;
+    selection: IAnalysesSelection | undefined;
     algorithm: {
         estimator: IAutocompleteObject | null;
         estimatorArgs: IDynamicValueType;
@@ -56,37 +42,57 @@ const CreateMetaAnalysisSpecificationReview: React.FC<{
     const { data: annotations } = useGetAnnotationById(annotationId);
     const { createMetaAnalysis, isLoading, isError } = useCreateAlgorithmSpecification();
     const { enqueueSnackbar } = useSnackbar();
-    const [showAdvanced, setShowAdvanced] = useState(false);
+    // TODO: implement studyset snapshot
+    // const [showAdvanced, setShowAdvanced] = useState(false);
 
     const handleCreateSpecification = async () => {
-        if (props.algorithm?.estimator?.label && props.selection?.selectionKey) {
-            const metaAnalysis = await createMetaAnalysis(
-                projectId,
-                EAnalysisType.CBMA,
-                props.algorithm.estimator,
-                props.algorithm.corrector,
-                studysetId,
-                annotationId,
-                props.selection?.selectionKey,
-                props.details.name,
-                props.details.description,
-                props.algorithm.estimatorArgs,
-                props.algorithm.correctorArgs
-            );
-            if (!metaAnalysis.data.specification || !metaAnalysis.data.id)
-                throw new Error('no specification ID found when creating a meta-analysis');
+        if (!props.algorithm?.estimator?.label || !props.selection?.selectionKey) return;
+        if (!props.selection || !props.selection.selectionValue) return;
+
+        const conditions = [props.selection.selectionValue] as string[] | boolean[];
+        const weights = [1];
+
+        const metaAnalysis = await createMetaAnalysis(
+            projectId,
+            EAnalysisType.CBMA,
+            props.algorithm.estimator,
+            props.algorithm.corrector,
+            studysetId,
+            annotationId,
+            props.selection?.selectionKey,
+            props.details.name,
+            props.details.description,
+            props.algorithm.estimatorArgs,
+            props.algorithm.correctorArgs,
+            conditions,
+            weights
+        );
+        if (!metaAnalysis.data.specification || !metaAnalysis.data.id)
+            throw new Error('no specification ID found when creating a meta-analysis');
 
-            enqueueSnackbar('created meta analysis specification successfully', {
-                variant: 'success',
-            });
-            history.push(`/projects/${projectId}/meta-analyses/${metaAnalysis.data.id}`);
-        }
+        enqueueSnackbar('created meta analysis specification successfully', {
+            variant: 'success',
+        });
+        history.push(`/projects/${projectId}/meta-analyses/${metaAnalysis.data.id}`);
     };
 
-    const selectedAnnotations = getFilteredAnnotationNotes(
-        (annotations?.notes || []) as NoteCollectionReturn[],
-        props.selection?.selectionKey
-    );
+    const numSelectedAnnotationsText = useMemo(() => {
+        const selectedAnnotations = getFilteredAnnotationNotes(
+            (annotations?.notes || []) as NoteCollectionReturn[],
+            props.selection
+        );
+        const totalNumAnnotations = (annotations?.notes || []).length;
+        return `${selectedAnnotations.length} / ${totalNumAnnotations} analyses selected`;
+    }, [annotations?.notes, props.selection]);
+
+    const selectionText = useMemo(() => {
+        if (!props.selection) return '';
+        const selectionKey = props.selection.selectionKey;
+        const selectionValue = props.selection.selectionValue
+            ? `: ${props.selection.selectionValue}`
+            : '';
+        return `${selectionKey} ${selectionValue}`;
+    }, [props.selection]);
 
     return (
         <StateHandlerComponent
@@ -102,10 +108,8 @@ const CreateMetaAnalysisSpecificationReview: React.FC<{
                 />
                 <MetaAnalysisSummaryRow
                     title="Selection"
-                    value={props.selection?.selectionKey || ''}
-                    caption={`${selectedAnnotations.length} / ${
-                        (annotations?.notes || []).length
-                    } analyses selected`}
+                    value={selectionText}
+                    caption={numSelectedAnnotationsText}
                 ></MetaAnalysisSummaryRow>
                 <MetaAnalysisSummaryRow
                     title="Estimator"
@@ -131,7 +135,7 @@ const CreateMetaAnalysisSpecificationReview: React.FC<{
                         )}
                     </MetaAnalysisSummaryRow>
                 )}
-                <Box>
+                {/* <Box>
                     <Button color="info" onClick={() => setShowAdvanced((prev) => !prev)}>
                         {showAdvanced ? 'hide' : 'show'} advanced
                     </Button>
@@ -163,7 +167,7 @@ const CreateMetaAnalysisSpecificationReview: React.FC<{
                             </FormControl>
                         </Box>
                     )}
-                </Box>
+                </Box> */}
             </Box>
             <Box sx={{ marginTop: '1rem', display: 'flex', justifyContent: 'space-between' }}>
                 <Button

diff --git a/...teMetaAnalysisSpecificationSelectionStep/CreateMetaAnalysisSpecificationSelectionStep.tsx b/...teMetaAnalysisSpecificationSelectionStep/CreateMetaAnalysisSpecificationSelectionStep.tsx
@@ -7,26 +7,36 @@ import {
 } from 'pages/Projects/ProjectPage/ProjectStore';
 import { useState } from 'react';
 import SelectAnalysesComponent from './SelectAnalysesComponent/SelectAnalysesComponent';
-import SelectAnalysesSummaryComponent from './SelectAnalysesSummaryComponent/SelectAnalysesSummaryComponent';
+import SelectAnalysesSummaryComponent from './SelectAnalysesComponent/SelectAnalysesSummaryComponent';
+import {
+    IAlgorithmSelection,
+    IAnalysesSelection,
+} from '../CreateMetaAnalysisSpecificationDialogBase.types';
+import { AnnotationNoteValue } from 'components/HotTables/HotTables.types';
 
 const CreateMetaAnalysisSpecificationSelectionStep: React.FC<{
-    onChooseSelection: (selectionKey: string, type: EPropertyType) => void;
+    onChooseSelection: (
+        selectionKey: string,
+        type: EPropertyType,
+        selectionValue?: AnnotationNoteValue
+    ) => void;
     onNavigate: (button: ENavigationButton) => void;
-    selection: { selectionKey: string | undefined; type: EPropertyType } | undefined;
+    selection: IAnalysesSelection | undefined;
+    algorithm: IAlgorithmSelection;
 }> = (props) => {
     const annotationId = useProjectExtractionAnnotationId();
     const studysetId = useProjectExtractionStudysetId();
-    const [selectedValue, setSelectedValue] = useState<
-        | {
-              selectionKey: string | undefined;
-              type: EPropertyType;
-          }
-        | undefined
-    >(props.selection);
+    const [selectedValue, setSelectedValue] = useState<IAnalysesSelection | undefined>(
+        props.selection
+    );
 
     const handleNavigate = (button: ENavigationButton) => {
         if (selectedValue?.selectionKey && selectedValue?.type !== EPropertyType.NONE)
-            props.onChooseSelection(selectedValue.selectionKey, selectedValue.type);
+            props.onChooseSelection(
+                selectedValue.selectionKey,
+                selectedValue.type,
+                selectedValue.selectionValue
+            );
         props.onNavigate(button);
     };
 
@@ -39,19 +49,16 @@ const CreateMetaAnalysisSpecificationSelectionStep: React.FC<{
                 </Typography>
             </Box>
             <Box>
-                <Typography gutterBottom>
+                <Typography gutterBottom sx={{ marginBottom: '1rem' }}>
                     Select the <b>annotation inclusion column</b> that you would like to use to
                     select the analyses for your meta-analysis.
                 </Typography>
-                <Typography sx={{ color: 'warning.dark', marginBottom: '1rem' }}>
-                    At the moment, only boolean columns will be supported. We will be adding support
-                    for the other types in the near future.
-                </Typography>
 
                 <SelectAnalysesComponent
                     selectedValue={selectedValue}
                     onSelectValue={(val) => setSelectedValue(val)}
                     annotationdId={annotationId || ''}
+                    algorithm={props.algorithm}
                 />
 
                 <Box
@@ -69,7 +76,11 @@ const CreateMetaAnalysisSpecificationSelectionStep: React.FC<{
                     />
                     <Button
                         variant="contained"
-                        disabled={!selectedValue?.selectionKey}
+                        sx={{ width: '200px' }}
+                        disabled={
+                            !selectedValue?.selectionKey ||
+                            selectedValue?.selectionValue === undefined
+                        }
                         onClick={() => handleNavigate(ENavigationButton.NEXT)}
                     >
                         next