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HumanBrainProject · Mar 5, 2024 · 24c7fb6 · 24c7fb6
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commit 24c7fb6
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Showing 4 changed files with 225 additions and 45 deletions.
diff --git a/apps/nar-v3/src/components/DatasetCard.jsx b/apps/nar-v3/src/components/DatasetCard.jsx
@@ -4,7 +4,7 @@ import Button from "@mui/material/Button";
 import Paper from "@mui/material/Paper";
 import Stack from "@mui/material/Stack";
 import Typography from "@mui/material/Typography";
-import Markdown from 'react-markdown'
+import Markdown from "react-markdown";
 
 import { uuidFromUri } from "../utility.js";
 
@@ -132,7 +132,7 @@ function SubjectCard(props) {
           <dd>{subject.studiedState[0].ageCategory}</dd>
           <dt>Pathologies</dt>
           <dd>
-            {subject.studiedState[0].pathology
+            {subject.studiedState[0].pathology.length > 0
               ? subject.studiedState[0].pathology[0].name
               : "none"}
           </dd>
@@ -161,17 +161,20 @@ function SlicePreparationCard(props) {
           <p>{activity.label}</p>
           <dl>
             <dt>Device name</dt>
-            <dd>{activity.deviceUsage[0].device.name}</dd>
+            <dd>{activity.device[0].device.name}</dd>
             <dt>Device type</dt>
-            <dd>{activity.deviceUsage[0].device.deviceType.name}</dd>
+            <dd>{activity.device[0].device.deviceType}</dd>
             <dt>Manufacturer</dt>
-            <dd>{activity.deviceUsage[0].device.manufacturer.fullName}</dd>
+            <dd>
+              {activity.device[0].device.manufacturer.fullName ||
+                activity.device[0].device.manufacturer.shortName}
+            </dd>
             <dt>Slice thickness</dt>
-            <dd>{formatQuant(activity.deviceUsage[0].sliceThickness)}</dd>
+            <dd>{formatQuant(activity.device[0].sliceThickness)}</dd>
             <dt>Slicing plane</dt>
-            <dd>{activity.deviceUsage[0].slicingPlane.name}</dd>
+            <dd>{activity.device[0].slicingPlane}</dd>
             <dt>Study targets</dt>
-            <dd>{activity.studyTargets.map((item) => item.name).join(", ")}</dd>
+            <dd>{activity.studyTarget.join(", ")}</dd>
             <dt>Temperature</dt>
             <dd>{formatQuant(activity.temperature)}</dd>
             <dt>Dissecting solution (full details to come)</dt>
@@ -243,26 +246,26 @@ function CellPatchingCard(props) {
 
           <dl>
             <dt>Electrode description</dt>
-            <dd>{activity.deviceUsage[0].device.description}</dd>
-            {/* activity.deviceUsage[0].device.deviceType.name */}
-            {/* activity.deviceUsage[0].device.manufacturer.fullName */}
+            <dd>{activity.device[0].device.description}</dd>
+            {/* activity.device[0].device.deviceType.name */}
+            {/* activity.device[0].device.manufacturer.fullName */}
             <dt>Pipette solution (more details to come)</dt>
-            <dd>{activity.deviceUsage[0].pipetteSolution.name}</dd>
+            <dd>{activity.device[0].pipetteSolution.name}</dd>
             <dt>Seal resistance</dt>
             <dd>
-              {activity.deviceUsage[0].sealResistance.values
+              {activity.device[0].sealResistance.value
                 .map((item) => formatQuant(item))
                 .join(", ")}
             </dd>
             <dt>Series resistance</dt>
             <dd>
-              {activity.deviceUsage[0].seriesResistance.values
+              {activity.device[0].seriesResistance.value
                 .map((item) => formatQuant(item))
                 .join(", ")}
             </dd>
             <dt>Holding potential</dt>
             <dd>
-              {activity.deviceUsage[0].holdingPotential.values
+              {activity.device[0].holdingPotential.value
                 .map((item) => formatQuant(item))
                 .join(", ")}
             </dd>
@@ -274,7 +277,7 @@ function CellPatchingCard(props) {
             <dt>Description</dt>
             <dd>{activity.description}</dd>
             <dt>Type</dt>
-            <dd>{activity.variation.name}</dd>
+            <dd>{activity.variation}</dd>
           </dl>
         </Box>
       </>
@@ -444,7 +447,7 @@ function DatasetCard(props) {
   const getSlices = (subjectIndex) => {
     const slicePrep = getSlicePreparation(subjectIndex);
     if (slicePrep) {
-      return slicePrep.slices;
+      return slicePrep.output;
     } else {
       return null;
     }
@@ -454,6 +457,8 @@ function DatasetCard(props) {
     const slices = getSlices(subjectIndex);
     if (slices) {
       const slice = slices[sliceIndex];
+      console.log("cell patching:");
+      console.log(slice.cellPatching[0]);
       return slice.cellPatching[0];
     } else {
       return null;
@@ -463,7 +468,9 @@ function DatasetCard(props) {
   const getPatchedCell = (subjectIndex, sliceIndex) => {
     const cellPatching = getCellPatching(subjectIndex, sliceIndex);
     if (cellPatching) {
-      return cellPatching.patchedCells[0];
+      console.log("patched cell:");
+      console.log(cellPatching.output[0]);
+      return cellPatching.output[0];
     } else {
       return null;
     }
@@ -520,7 +527,9 @@ function DatasetCard(props) {
           View in KG Search
         </Button>
       </h1>
-      <Typography variant="h6" gutterBottom>{formatAuthors(dataset)}</Typography>
+      <Typography variant="h6" gutterBottom>
+        {formatAuthors(dataset)}
+      </Typography>
       <Stack direction="row" spacing={2} alignItems="center">
         <div>
           <b>Licence: </b>
@@ -539,7 +548,9 @@ function DatasetCard(props) {
           {dataset.releaseDate}
         </div>
       </Stack>
-      <Markdown>{dataset.description || dataset.isVersionOf.description}</Markdown>
+      <Markdown>
+        {dataset.description || dataset.isVersionOf.description}
+      </Markdown>
 
       {subjects ? (
         <Stack

diff --git a/apps/nar-v3/src/datastore.js b/apps/nar-v3/src/datastore.js
@@ -1,4 +1,4 @@
-import { kgUrl } from "./globals";
+import { kgUrl, kgDefaultStage } from "./globals";
 import { buildKGQuery, simpleProperty as S, linkProperty as L, reverseLinkProperty as R } from "./queries";
 import { uuidFromUri } from "./utility.js";
 import examplePatchClampData from "./example_data/example_patch_clamp_dataset.json";
@@ -31,7 +31,8 @@ class DataStore {
       "patch clamp recordings summary": {},
       "patch clamp recordings detail": {}
     };
-    this.cache["datasets detail"][uuidFromUri(examplePatchClampData["@id"])] = examplePatchClampData;
+    //this.cache["datasets detail"][uuidFromUri(examplePatchClampData["@id"])] = examplePatchClampData;
+    this.cache["datasets detail"]["example"] = examplePatchClampData;
   }
 
   buildRequestConfig(method="GET", body={}) {
@@ -58,7 +59,7 @@ class DataStore {
     return result;
   }
 
-  async getKGItem(cacheLabel, kgQuery, instanceId, stage = "RELEASED") {
+  async getKGItem(cacheLabel, kgQuery, instanceId, stage = kgDefaultStage) {
     console.log("getKGItem " + cacheLabel + instanceId);
     if (!this.cache[cacheLabel][instanceId]) {
       const searchParams = {stage: stage, instanceId: instanceId};
@@ -69,7 +70,7 @@ class DataStore {
     return this.cache[cacheLabel][instanceId];
   }
 
-  async getKGData(cacheLabel, kgQuery, searchFilters, stage = "RELEASED", size = 1000, from = 0) {
+  async getKGData(cacheLabel, kgQuery, searchFilters, stage = kgDefaultStage, size = 1000, from = 0) {
     console.log("getKGData " + cacheLabel);
     if (isEmpty(this.cache[cacheLabel])) {
       // if the cache is empty we need to fill it
@@ -94,7 +95,7 @@ class DataStore {
     return itemArray
   }
 
-  async count(kgQuery, searchFilters, stage = "RELEASED") {
+  async count(kgQuery, searchFilters, stage = kgDefaultStage) {
     let searchParams = {
       returnTotalResults: true,
       stage: stage,

diff --git a/apps/nar-v3/src/globals.js b/apps/nar-v3/src/globals.js
@@ -1 +1,2 @@
 export const kgUrl = "https://core.kg.ebrains.eu/v3";
+export const kgDefaultStage = "IN_PROGRESS";
Original file line number	Diff line number	Diff line change
		@@ -1 +1,2 @@
		export const kgUrl = "https://core.kg.ebrains.eu/v3";
		export const kgDefaultStage = "IN_PROGRESS";