building up dataset query

HumanBrainProject · Mar 4, 2024 · 024bed2 · 024bed2
1 parent 1a04e7d
commit 024bed2
Show file tree

Hide file tree

Showing 5 changed files with 76 additions and 32 deletions.
diff --git a/apps/nar-v3/src/components/DatasetCard.jsx b/apps/nar-v3/src/components/DatasetCard.jsx
@@ -97,7 +97,7 @@ function SubjectCard(props) {
         )}
       </Stack>
       <Box sx={styles.entity} component={Paper} variant="outlined">
-        <h2>Subject {subject.label}</h2>
+        <h2>Subject {subject.lookupLabel}</h2>
         <p>
           ({props.index + 1} of {props.subjects.length})
         </p>
@@ -343,11 +343,13 @@ function DataFileCard(props) {
 
 function DatasetCard(props) {
   const dataset = props.dataset;
+  const subjects = dataset.studiedSpecimen;
+
   const [subjectIndex, _setSubjectIndex] = useState(0);
   const [sliceIndex, _setSliceIndex] = useState(0);
 
   const setSubjectIndex = (index) => {
-    if (index >= 0 && index < dataset.subjects.length) {
+    if (index >= 0 && index < subjects.length) {
       _setSubjectIndex(index);
       setSliceIndex(0);
     }
@@ -357,7 +359,7 @@ function DatasetCard(props) {
     if (
       index >= 0 &&
       index <
-        dataset.subjects[subjectIndex].states[0].slicePreparation[0].slices
+        subjects[subjectIndex].states[0].slicePreparation[0].slices
           .length
     ) {
       _setSliceIndex(index);
@@ -379,15 +381,15 @@ function DatasetCard(props) {
         </Link>
       </h2>
 
-      {dataset.subjects ? (
+      {subjects ? (
         <Stack
           direction="column"
           alignItems="center"
           spacing={2}
           sx={{ marginBottom: 5 }}
         >
           <SubjectCard
-            subjects={dataset.subjects}
+            subjects={subjects}
             index={subjectIndex}
             setIndex={setSubjectIndex}
           />
@@ -396,15 +398,15 @@ function DatasetCard(props) {
 
           <SlicePreparationCard
             activity={
-              dataset.subjects[subjectIndex].states[0].slicePreparation[0]
+              subjects[subjectIndex].states[0].slicePreparation[0]
             }
           />
 
           <Connection />
 
           <SliceCard
             slices={
-              dataset.subjects[subjectIndex].states[0].slicePreparation[0]
+              subjects[subjectIndex].states[0].slicePreparation[0]
                 .slices
             }
             index={sliceIndex}
@@ -415,7 +417,7 @@ function DatasetCard(props) {
 
           <CellPatchingCard
             activity={
-              dataset.subjects[subjectIndex].states[0].slicePreparation[0]
+              subjects[subjectIndex].states[0].slicePreparation[0]
                 .slices[sliceIndex].cellPatching[0]
             }
           />
@@ -424,7 +426,7 @@ function DatasetCard(props) {
 
           <PatchedCellCard
             cell={
-              dataset.subjects[subjectIndex].states[0].slicePreparation[0]
+              subjects[subjectIndex].states[0].slicePreparation[0]
                 .slices[sliceIndex].cellPatching[0].patchedCells[0]
             }
           />
@@ -433,12 +435,12 @@ function DatasetCard(props) {
 
           <RecordingCard
             recording={
-              dataset.subjects[subjectIndex].states[0].slicePreparation[0]
+              subjects[subjectIndex].states[0].slicePreparation[0]
                 .slices[sliceIndex].cellPatching[0].patchedCells[0]
                 .recordingActivity[0]
             }
             stimulation={
-              dataset.subjects[subjectIndex].states[0].slicePreparation[0]
+              subjects[subjectIndex].states[0].slicePreparation[0]
                 .slices[sliceIndex].cellPatching[0].patchedCells[0]
                 .stimulationActivity[0]
             }
@@ -448,7 +450,7 @@ function DatasetCard(props) {
 
           <DataFileCard
             fileObj={
-              dataset.subjects[subjectIndex].states[0].slicePreparation[0]
+              subjects[subjectIndex].states[0].slicePreparation[0]
                 .slices[sliceIndex].cellPatching[0].patchedCells[0]
                 .recordingActivity[0].files[0]
             }

diff --git a/apps/nar-v3/src/example_data/example_patch_clamp_dataset.json b/apps/nar-v3/src/example_data/example_patch_clamp_dataset.json
@@ -5,9 +5,9 @@
   "@type": [
     "https://openminds.ebrains.eu/core/DatasetVersion"
   ],
-  "subjects": [
+  "studiedSpecimen": [
     {
-      "label": "AD-Ctrl_s95",
+      "lookupLabel": "AD-Ctrl_s95",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -1937,7 +1937,7 @@
       ]
     },
     {
-      "label": "AD-Ctrl_s86",
+      "lookupLabel": "AD-Ctrl_s86",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -2947,7 +2947,7 @@
       ]
     },
     {
-      "label": "AD-Ctrl_s76",
+      "lookupLabel": "AD-Ctrl_s76",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -4417,7 +4417,7 @@
       ]
     },
     {
-      "label": "AD-Ctrl_s75",
+      "lookupLabel": "AD-Ctrl_s75",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -5197,7 +5197,7 @@
       ]
     },
     {
-      "label": "AD-Ctrl-s27",
+      "lookupLabel": "AD-Ctrl-s27",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -5747,7 +5747,7 @@
       ]
     },
     {
-      "label": "AD-Ctrl-s31",
+      "lookupLabel": "AD-Ctrl-s31",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -6987,7 +6987,7 @@
       ]
     },
     {
-      "label": "AD-Ctrl-s24",
+      "lookupLabel": "AD-Ctrl-s24",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -8457,7 +8457,7 @@
       ]
     },
     {
-      "label": "APPPS_s96",
+      "lookupLabel": "APPPS_s96",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -10161,7 +10161,7 @@
       ]
     },
     {
-      "label": "APPPS_s87",
+      "lookupLabel": "APPPS_s87",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -12095,7 +12095,7 @@
       ]
     },
     {
-      "label": "APPPS_s77",
+      "lookupLabel": "APPPS_s77",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -13799,7 +13799,7 @@
       ]
     },
     {
-      "label": "APPPS_s26",
+      "lookupLabel": "APPPS_s26",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -14353,7 +14353,7 @@
       ]
     },
     {
-      "label": "APPPS_s22",
+      "lookupLabel": "APPPS_s22",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],
@@ -15827,7 +15827,7 @@
       ]
     },
     {
-      "label": "APPPS_s23",
+      "lookupLabel": "APPPS_s23",
       "@type": [
         "https://openminds.ebrains.eu/core/Subject"
       ],

diff --git a/apps/nar-v3/src/queries.js b/apps/nar-v3/src/queries.js
@@ -59,9 +59,10 @@ function linkProperty(name, structure, options) {
     const defaultOptions = {
         expectSingle: true,
         filter: "",
-        required: false
+        required: false,
+        type: null
     }
-    const {expectSingle, filter, required} = {...defaultOptions, ...options}
+    const {expectSingle, filter, required, type} = {...defaultOptions, ...options}
     let prop = simpleProperty(name);
 
     if (expectSingle) {
@@ -70,6 +71,16 @@ function linkProperty(name, structure, options) {
     if (structure && structure.length > 0) {
         prop.structure = structure
     }
+    if (type) {
+        if (typeof prop.path === 'string') {
+            prop.path = [{
+                "@id": prop.path
+            }]
+        }
+        prop.path[0].typeFilter = {
+            "@id": `https://openminds.ebrains.eu/${type}`
+        }
+    }
     if (filter) {
         prop.filter = {
             op: "CONTAINS",

diff --git a/apps/nar-v3/src/routes/dataset.jsx b/apps/nar-v3/src/routes/dataset.jsx
@@ -1,7 +1,12 @@
 import React from "react";
 import { Await, defer, useLoaderData } from "react-router-dom";
 
-import { buildKGQuery, simpleProperty as S, linkProperty as L, reverseLinkProperty as R } from "../queries";
+import {
+  buildKGQuery,
+  simpleProperty as S,
+  linkProperty as L,
+  reverseLinkProperty as R,
+} from "../queries";
 import { datastore } from "../datastore";
 import { uuidFromUri } from "../utility.js";
 import Navigation from "../components/Navigation";
@@ -19,6 +24,29 @@ const query = buildKGQuery("core/DatasetVersion", [
     S("description"),
     S("shortName"),
   ]),
+  L(
+    "studiedSpecimen",
+    [
+      S("lookupLabel"),
+      L(
+        "studiedState",
+        [
+          L("age", [
+            S("value"),
+            S("minValue"),
+            S("maxValue"),
+            L("unit/name"),
+            L("minValueUnit/name"),
+            L("maxValueUnit/name"),
+          ]),
+          L("ageCategory/name"),
+          L("pathology", [], { expectSingle: false }),
+        ],
+        { expectSingle: false }
+      ),
+    ],
+    { type: "core/Subject", expectSingle: false }
+  ),
 ]);
 
 export async function loader({ params }) {
@@ -47,7 +75,10 @@ function Dataset(props) {
             return (
               <>
                 <Navigation
-                  location={["Datasets", uuidFromUri(dataset.id || dataset["@id"])]}
+                  location={[
+                    "Datasets",
+                    uuidFromUri(dataset.id || dataset["@id"]),
+                  ]}
                 />
                 <DatasetCard dataset={dataset} />
               </>

diff --git a/apps/nar-v3/tmp/build_query.py b/apps/nar-v3/tmp/build_query.py
@@ -58,10 +58,10 @@
         QP("@type"),
         QP(
             f"{vocab}studiedSpecimen",
-            name="subjects",
+            name="studiedSpecimen",
             type_filter=omcore.Subject.type_[0],
             properties=[
-                QP(f"{vocab}lookupLabel", name="label"),
+                QP(f"{vocab}lookupLabel", name="lookupLabel"),
                 QP("@type"),
                 QP(
                     f"{vocab}studiedState",