From 24c7fb6cd94aae5ccde10bb25d196c21ce621dc6 Mon Sep 17 00:00:00 2001
From: Andrew Davison <andrew.davison@cnrs.fr>
Date: Tue, 5 Mar 2024 13:13:25 +0100
Subject: [PATCH] wip

---
 apps/nar-v3/src/components/DatasetCard.jsx |  51 +++--
 apps/nar-v3/src/datastore.js               |  11 +-
 apps/nar-v3/src/globals.js                 |   1 +
 apps/nar-v3/src/routes/dataset.jsx         | 207 +++++++++++++++++++--
 4 files changed, 225 insertions(+), 45 deletions(-)

diff --git a/apps/nar-v3/src/components/DatasetCard.jsx b/apps/nar-v3/src/components/DatasetCard.jsx
index 372cb86..156836c 100644
--- 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
index adacb23..e54cf8f 100644
--- 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
index 47a78d9..02a99e0 100644
--- 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";
\ No newline at end of file
diff --git a/apps/nar-v3/src/routes/dataset.jsx b/apps/nar-v3/src/routes/dataset.jsx
index 5944683..133c5f0 100644
--- a/apps/nar-v3/src/routes/dataset.jsx
+++ b/apps/nar-v3/src/routes/dataset.jsx
@@ -13,14 +13,48 @@ import Navigation from "../components/Navigation";
 import DatasetCard from "../components/DatasetCard";
 import ProgressIndicator from "../components/ProgressIndicator";
 
+const MULTIPLE = { expectSingle: false };
+
 const actorQuery = [
   S("@id"),
   S("@type"),
   S("givenName"),
   S("familyName"),
   S("fullName"),
-  S("shortName")
-]
+  S("shortName"),
+];
+
+const quantValQuery = [
+  S("value"),
+  S("minValue"),
+  S("maxValue"),
+  L("unit/name"),
+  L("minValueUnit/name"),
+  L("maxValueUnit/name"),
+];
+
+const solutionQuery = [
+  S("name"),
+  S("@id"),
+  L(
+    "hasPart",
+    [
+      L("amount", quantValQuery),
+      L("chemicalProduct", [S("name"), S("@id"), S("@type")])
+    ],
+    MULTIPLE
+  ),
+];
+
+const deviceQuery = L("device", [
+  S("lookupLabel"),
+  S("name"),
+  S("@type"),
+  S("internalIdentifier"),
+  S("description"),
+  L("deviceType/name"),
+  L("manufacturer", [S("shortName", S("longName"))]),
+]);
 
 const query = buildKGQuery("core/DatasetVersion", [
   S("@id"),
@@ -31,40 +65,173 @@ const query = buildKGQuery("core/DatasetVersion", [
   L("ethicsAssessment/name"),
   L("license/shortName"),
   S("releaseDate"),
-  L("custodian", actorQuery, { expectSingle: false }),
-  L("author", actorQuery, { expectSingle: false }),
+  L("custodian", actorQuery, MULTIPLE),
+  L("author", actorQuery, MULTIPLE),
   R("isVersionOf", "hasVersion", [
     S("fullName"),
     S("description"),
     S("shortName"),
-    L("custodian", actorQuery, { expectSingle: false }),
-    L("author", actorQuery, { expectSingle: false }),
+    L("custodian", actorQuery, MULTIPLE),
+    L("author", actorQuery, MULTIPLE),
   ]),
   L(
     "studiedSpecimen",
     [
       S("lookupLabel"),
-      L("species", [
-        S("name"),
-        L("species/name")
-      ]),
+      L("species", [S("name"), L("species/name")]),
       L("biologicalSex/name"),
       L(
         "studiedState",
         [
           S("lookupLabel"),
-          L("age", [
-            S("value"),
-            S("minValue"),
-            S("maxValue"),
-            L("unit/name"),
-            L("minValueUnit/name"),
-            L("maxValueUnit/name"),
-          ]),
+          L("age", quantValQuery),
           L("ageCategory/name"),
-          L("pathology", [], { expectSingle: false }),
+          L("pathology", [S("name")], MULTIPLE),
+          R(
+            "slicePreparation",
+            "input",
+            [
+              // slice preparation
+              S("lookupLabel"),
+              S("@type"),
+              L(
+                "device",
+                [
+                  // device usage
+                  S("lookupLabel"),
+                  deviceQuery,
+                  L("sliceThickness", quantValQuery),
+                  L("slicingPlane/name"),
+                ],
+                MULTIPLE
+              ),
+              L("studyTarget/name", [], MULTIPLE),
+              L("temperature", [S("value"), L("unit/name")]),
+              L("tissueBathSolution", solutionQuery),
+              L(
+                "output",
+                [
+                  // slices
+                  S("lookupLabel"),
+                  S("internalIdentifier"),
+                  R("slice", "studiedState", [
+                    S("lookupLabel"),
+                    S("@type"),
+                    S("internalIdentifier"),
+                    L("anatomicalLocation", [S("name"), S("@type")], MULTIPLE),
+                    L("type/name"),
+                  ]),
+                  R("cellPatching", "input", [
+                    S("lookupLabel"),
+                    S("@type"),
+                    L("device", [
+                      // device usage
+                      S("lookupLabel"),
+                      deviceQuery,
+                      L("pipetteSolution", solutionQuery),
+                      L("sealResistance", [
+                        L("value", quantValQuery, MULTIPLE),
+                      ]),
+                      L("seriesResistance", [
+                        L("value", quantValQuery, MULTIPLE),
+                      ]),
+                      L("holdingPotential", [
+                        L("value", quantValQuery, MULTIPLE),
+                      ]),
+                    ], MULTIPLE),
+                    L("tissueBathSolution", solutionQuery),
+                    L("bathTemperature", quantValQuery),
+                    S("description"),
+                    L("variation/name"),
+                    L("output", [
+                      // patched cells
+                      S("lookupLabel"),
+                      S("@type"),
+                      R("cell", "studiedState", [
+                        S("internalIdentifier"),
+                        L(
+                          "anatomicalLocation",
+                          [S("name"), S("@type")],
+                          MULTIPLE
+                        ),
+                        L("type/name"),
+                      ]),
+                      R(
+                        "recordingActivity",
+                        "input",
+                        [
+                          S("lookupLabel"),
+                          S("@type"),
+                          S("description"),
+                          S("internalIdentifier"),
+                          L("device", [
+                            R("metadata", "recordedWith", [
+                              S("name"),
+                              S("additionalRemarks"),
+                              L("samplingFrequency", quantValQuery),
+                              L(
+                                "channel",
+                                [S("internalIdentifier"), L("unit/name")],
+                                MULTIPLE
+                              ),
+                            ]),
+                          ]),
+                          L(
+                            "output",
+                            [
+                              S("@id"),
+                              S("name"),
+                              S("IRI"),
+                              S("dataType/name"),
+                              S("format/name"),
+                              L(
+                                "hash",
+                                [S("algorithm"), S("digest")],
+                                MULTIPLE
+                              ),
+                              L("storageSize", [S("value"), L("unit/name")]),
+                            ],
+                            MULTIPLE
+                          ),
+                        ],
+                        { type: "ephys/RecordingActivity", expectSingle: false }
+                      ),
+                      R(
+                        "stimulationActivity",
+                        "input",
+                        [
+                          S("lookupLabel"),
+                          S("@type"),
+                          L(
+                            "stimulus",
+                            [
+                              S("lookupLabel"),
+                              S("@type"),
+                              L("epoch", quantValQuery),
+                              S("internalIdentifier"),
+                              L("specification", [
+                                S("lookupLabel"),
+                                S("configuration"),
+                              ]),
+                            ],
+                            MULTIPLE
+                          ),
+                        ],
+                        {
+                          type: "stimulation/StimulationActivity",
+                          expectSingle: false,
+                        }
+                      ),
+                    ], MULTIPLE),
+                  ], MULTIPLE),
+                ],
+                MULTIPLE
+              ),
+            ],
+            MULTIPLE
+          ),
         ],
-        { expectSingle: false }
+        MULTIPLE
       ),
     ],
     { type: "core/Subject", expectSingle: false }