fix missing values from nexus

src/components/Filter/CheckList/Description.tsx

@@ -2,9 +2,22 @@ import { useAtomValue } from 'jotai';
 import { useMemo } from 'react';
 import { unwrap } from 'jotai/utils';
 import { Spin } from 'antd';
+import findKey from 'lodash/findKey';
+import replace from 'lodash/replace';
+import get from 'lodash/get';
+
+import EXPLORE_FIELDS_CONFIG from '@/constants/explore-section/fields-config';
 import { cellTypesByLabelAtom } from '@/state/build-section/cell-types';
 import { FieldType } from '@/constants/explore-section/fields-config/types';
-import EXPLORE_FIELDS_CONFIG from '@/constants/explore-section/fields-config';
+import { ClassNexus } from '@/api/ontologies/types';
+
+// NOTE: this due nexus es aggregation and the resource it self are having different keys name
+// one with underscore, and the other with hyphen
+const getClassByLabel = (label: string, classes: Record<string, ClassNexus>) => {
+  const normalizedLabel = replace(label, /[_-]/g, '');
+  const matchedKey = findKey(classes, (_, key) => replace(key, /[_-]/g, '') === normalizedLabel);
+  return get(classes, matchedKey ?? '', null);
+};
 
 export function CheckListDescription({
   label,
@@ -26,6 +39,6 @@ function ClassDescription({ label }: { label: string }) {
   if (!classes) {
     return <Spin />;
   }
-
-  return <span className="text-primary-1">{classes[label]?.definition}</span>;
+  const classObj = getClassByLabel(label, classes);
+  return <span className="text-primary-1">{classObj?.definition}</span>;
 }

src/components/build-section/virtual-lab/synaptome/molecules/SynapseSet.tsx

@@ -41,8 +41,8 @@ type Props = {
   removeGroup: (index: number | number[]) => void;
 };
 
-const label = (text: string) => (
-  <span className={classNames('text-base font-bold capitalize text-gray-500')}>{text}</span>
+const label = (text: string, cls?: string) => (
+  <span className={classNames('text-base font-bold capitalize text-gray-500', cls)}>{text}</span>
 );
 
 export default function SynapseSet({
@@ -75,9 +75,14 @@ export default function SynapseSet({
     })
   );
 
+  const hasApic = groupedSections.includes('apic');
+
   const targetOptions = groupedSections.map((value) => ({
     value,
-    label: sectionTargetMapping[value as keyof typeof sectionTargetMapping],
+    label:
+      value === 'dend' && !hasApic
+        ? 'Dendrites'
+        : sectionTargetMapping[value as keyof typeof sectionTargetMapping],
   }));
 
   const isAlreadyVisualized = useMemo(
@@ -370,7 +375,7 @@ export default function SynapseSet({
                     displayFormulaHelp && 'justify-between'
                   )}
                 >
-                  {label('Formula')}
+                  {label('Synapse distribution formula', 'normal-case')}
                   {displayFormulaHelp ? (
                     <CloseOutlined className="text-gray-300" onClick={toggleFormulaHelp} />
                   ) : (
@@ -383,7 +388,7 @@ export default function SynapseSet({
                     displayFormulaHelp ? 'mb-4 h-full opacity-100' : 'mb-0 h-0 opacity-0'
                   )}
                 >
-                  More information on formulas here: <br />
+                  Supports advanced math functions (e.g., sin(x), log(x), ...). <br />
                   <a
                     target="_blank"
                     rel="noopener noreferrer"
@@ -397,10 +402,11 @@ export default function SynapseSet({
               <input hidden readOnly name="distribution" value="formula" />
               <Form.Item
                 name={[field.name, 'formula']}
+                extra={<small>x: distance from soma (µm)</small>}
                 rules={[
                   {
                     required: true,
-                    message: 'Please provide a valid formula!',
+                    message: 'Please provide a valid distribution formula!',
                     async validator(_, value) {
                       if (synapses?.[index].distribution !== 'formula') {
                         return Promise.resolve();
@@ -424,7 +430,7 @@ export default function SynapseSet({
                 )}
               >
                 <Input
-                  placeholder="00.3*x*x + 0.004"
+                  placeholder="0.03*x*x + 0.004"
                   size="large"
                   className={classNames(
                     'text-base font-bold italic [&_.ant-input]:text-primary-8',

src/components/build-section/virtual-lab/synaptome/molecules/constants.ts

@@ -29,10 +29,10 @@ export const DEFAULT_SYNAPSE_VALUE: SingleSynaptomeConfig = {
 };
 
 export const sectionTargetMapping = {
-  dend: 'Dendrite',
+  dend: 'Basal Dendrites',
   soma: 'Soma',
-  apic: 'Apical dendrite',
-  basal: 'Basal dendrite',
+  apic: 'Apical dendrites',
+  basal: 'Basal dendrites',
   axon: 'Axon',
 };
 

src/components/explore-section/ExploreSectionListingView/WithControlPanel.tsx

@@ -48,7 +48,6 @@ export default function WithControlPanel({
   );
 
   const data = useUnwrappedValue(dataAtom({ dataType, dataScope, virtualLabInfo, key: dataKey }));
-
   const aggregations = data?.aggs;
 
   return (

src/state/build-section/cell-types.ts

@@ -1,6 +1,10 @@
 import { selectAtom } from 'jotai/utils';
-import esb from 'elastic-builder';
 import { Session } from 'next-auth';
+import esb from 'elastic-builder';
+import toLower from 'lodash/toLower';
+import findKey from 'lodash/findKey';
+import get from 'lodash/get';
+
 import sessionAtom from '@/state/session';
 import { createHeaders } from '@/util/utils';
 import { ClassNexus } from '@/api/ontologies/types';
@@ -61,8 +65,54 @@ export const cellTypesByLabelAtom = selectAtom<
   return cellTypes.hits.hits.reduce(
     (acc: Record<string, ClassNexus>, classObj: ClassESResponse) => {
       acc[classObj._source.label] = classObj._source;
+      // TODO: this is temporary until a fix applied to nexus/entitycore
+      const matchedKey = findKey(
+        TEMPORARY_TYPE_DEFINITION,
+        (_, k) => toLower(k) === toLower(classObj._source.label)
+      );
+      const matchedValue = get(
+        TEMPORARY_TYPE_DEFINITION,
+        matchedKey ?? '',
+        classObj._source?.definition
+      );
+
+      acc[classObj._source.label] = {
+        ...classObj._source,
+        definition: matchedValue,
+      };
       return acc;
     },
     {}
   );
 });
+
+// TODO: this should be fixed in nexus/entitycore level
+const TEMPORARY_TYPE_DEFINITION = {
+  cNAC: 'Continuous non-accommodating electrical type',
+  cADpyr: 'Continuous adapting pyramidal cell electrical type',
+  cACpyr: 'Continuous accommodating pyramidal cell electrical type',
+  bAC: 'Burst accommodating electrical type',
+  cAC: 'Continuous accommodating electrical type',
+  cNAD_lts_dSTR:
+    "Low-threshold spiking, tonically active, slow and regular firing, characteristic 'notch' in the membrane potential during the depolarizing phase of the action potential, depolarizing sag, high input resistance",
+  dAD_htp_dSTR:
+    'delayed spike, adapting or accelerating, input rectification, irregular spiking, high-threshold spike, pacemaker-like firing',
+  dAD_ltb_dSTR:
+    'Delayed spike, adapting or accelerating, input rectification, low resting potential, regular spiking, low-threshold spike, burst firing',
+  bSTUT: 'Burst stuttering electrical type',
+  dNAC: 'Delayed non-accommodating electrical type',
+  GEN_etype: 'Generic excitatory neuron electrical type',
+  GIN_etype: 'Generic inhibitory neuron electrical type',
+  bIR: 'Burst irregular electrical type',
+  bNAC: 'Burst non-accommodating electrical type',
+  cAD_noscltb: 'Continuous adapting non-oscillatory low-threshold bursting electrical type',
+  cIR: 'Continuous irregular electrical type',
+  cNAD_ltb_dSTR:
+    "Low-threshold spiking, tonically active, slow and regular firing, characteristic 'notch' in the membrane potential during the depolarizing phase of the action potential, depolarizing sag, high input resistance",
+  cNAD_noscltb: 'Continuous non-adapting non-oscillatory low-threshold bursting electrical type',
+  cSTUT: 'Continuous stuttering electrical type',
+  dAD_ltb: 'Delayed adapting low-threshold bursting electrical type',
+  dNAD_ltb: 'Delayed non-adapting low-threshold bursting electrical type',
+  dSTUT: 'Delayed stuttering electrical type',
+  bIR_dSTR: 'Tonically active neurons, irregular spiking, burst firing electrical type',
+};