From 47260eb06781e6fe4a107a4a883a27694ec1fe5c Mon Sep 17 00:00:00 2001
From: Andrew Davison <andrew.davison@cnrs.fr>
Date: Thu, 7 Mar 2024 11:33:53 +0100
Subject: [PATCH] Use KeyValueTable component to display metadata

---
 .../__tests__/components/DatasetCard.test.jsx |  4 +-
 .../src/components/CellPatchingCard.jsx       | 54 ++++++----------
 apps/nar-v3/src/components/DataFileCard.jsx   | 34 +++++-----
 apps/nar-v3/src/components/KeyValueTable.jsx  | 42 +++++++++++++
 .../nar-v3/src/components/PatchedCellCard.jsx |  9 +--
 apps/nar-v3/src/components/RecordingCard.jsx  | 62 ++++++++-----------
 apps/nar-v3/src/components/SliceCard.jsx      | 11 ++--
 .../src/components/SlicePreparationCard.jsx   | 35 +++++------
 apps/nar-v3/src/components/SubjectCard.jsx    | 40 +++++-------
 9 files changed, 148 insertions(+), 143 deletions(-)
 create mode 100644 apps/nar-v3/src/components/KeyValueTable.jsx

diff --git a/apps/nar-v3/__tests__/components/DatasetCard.test.jsx b/apps/nar-v3/__tests__/components/DatasetCard.test.jsx
index 5862354..9a4634b 100644
--- a/apps/nar-v3/__tests__/components/DatasetCard.test.jsx
+++ b/apps/nar-v3/__tests__/components/DatasetCard.test.jsx
@@ -2,10 +2,8 @@ import { describe, test, expect } from "vitest";
 import { render, screen } from "@testing-library/react";
 import "@testing-library/jest-dom";
 
-
 import DatasetCard from "../../src/components/DatasetCard";
 
-
 describe("DatasetCard component", () => {
   test("should render without errors", async () => {
     const dataset = {
@@ -545,7 +543,7 @@ describe("DatasetCard component", () => {
           ],
           biologicalSex: "male",
         },
-      ]
+      ],
     };
 
     render(<DatasetCard dataset={dataset} />);
diff --git a/apps/nar-v3/src/components/CellPatchingCard.jsx b/apps/nar-v3/src/components/CellPatchingCard.jsx
index cc70a42..886860d 100644
--- a/apps/nar-v3/src/components/CellPatchingCard.jsx
+++ b/apps/nar-v3/src/components/CellPatchingCard.jsx
@@ -21,12 +21,31 @@ import Box from "@mui/material/Box";
 import Paper from "@mui/material/Paper";
 
 import Connection from "./Connection";
+import KeyValueTable from "./KeyValueTable";
 import styles from "../styles";
 import { formatQuant } from "../utility";
 
 function CellPatchingCard(props) {
   const activity = props.activity;
 
+  const data = {
+    "Electrode description": activity.device[0].device.description,
+    "Pipette solution (more details to come)": activity.device[0].pipetteSolution.name,
+    "Seal resistance": activity.device[0].sealResistance.value
+      .map((item) => formatQuant(item))
+      .join(", "),
+    "Series resistance": activity.device[0].seriesResistance.value
+      .map((item) => formatQuant(item))
+      .join(", "),
+    "Holding potential": activity.device[0].holdingPotential.value
+      .map((item) => formatQuant(item))
+      .join(", "),
+    "Bath solution (more details to come)": activity.tissueBathSolution.name,
+    "Bath temperature": formatQuant(activity.bathTemperature),
+    Description: activity.description,
+    Type: activity.variation,
+  };
+
   if (activity) {
     return (
       <>
@@ -34,40 +53,7 @@ function CellPatchingCard(props) {
         <Box sx={styles.activity} component={Paper} variant="outlined">
           <h2>Cell patching</h2>
           <p>{activity.label}</p>
-
-          <dl>
-            <dt>Electrode description</dt>
-            <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.device[0].pipetteSolution.name}</dd>
-            <dt>Seal resistance</dt>
-            <dd>
-              {activity.device[0].sealResistance.value.map((item) => formatQuant(item)).join(", ")}
-            </dd>
-            <dt>Series resistance</dt>
-            <dd>
-              {activity.device[0].seriesResistance.value
-                .map((item) => formatQuant(item))
-                .join(", ")}
-            </dd>
-            <dt>Holding potential</dt>
-            <dd>
-              {activity.device[0].holdingPotential.value
-                .map((item) => formatQuant(item))
-                .join(", ")}
-            </dd>
-
-            <dt>Bath solution (more details to come)</dt>
-            <dd>{activity.tissueBathSolution.name}</dd>
-            <dt>Bath temperature</dt>
-            <dd>{formatQuant(activity.bathTemperature)}</dd>
-            <dt>Description</dt>
-            <dd>{activity.description}</dd>
-            <dt>Type</dt>
-            <dd>{activity.variation}</dd>
-          </dl>
+          <KeyValueTable boldKeys data={data} />
         </Box>
       </>
     );
diff --git a/apps/nar-v3/src/components/DataFileCard.jsx b/apps/nar-v3/src/components/DataFileCard.jsx
index 5fe8f99..78c99e0 100644
--- a/apps/nar-v3/src/components/DataFileCard.jsx
+++ b/apps/nar-v3/src/components/DataFileCard.jsx
@@ -21,33 +21,35 @@ import Paper from "@mui/material/Paper";
 
 import { formatQuant } from "../utility";
 import Connection from "./Connection";
+import KeyValueTable from "./KeyValueTable";
 import styles from "../styles";
 
 function DataFileCard(props) {
   const fileObj = props.fileObj;
 
+  const data = {
+    "Data type": fileObj.dataType ? fileObj.dataType.name : "unknown",
+    Format: fileObj.format ? fileObj.format.name : "unknown",
+    Hash: (
+      <>
+        {fileObj.hash.map((item) => (
+          <span key={item.algorithm}>
+            {item.algorithm}: {item.digest}&nbsp;
+          </span>
+        ))}
+      </>
+    ),
+    Size: formatQuant(fileObj.storageSize),
+  };
+
   if (fileObj) {
     return (
       <>
         <Connection />
         <Box sx={styles.entity} component={Paper} variant="outlined">
           <h2>File {fileObj.name}</h2>
-          <dl>
-            <dt>Data type</dt>
-            <dd>{fileObj.dataType ? fileObj.dataType.name : "unknown"}</dd>
-            <dt>Format</dt>
-            <dd>{fileObj.format ? fileObj.format.name : "unknown"}</dd>
-            <dt>Hash</dt>
-            <dd>
-              {fileObj.hash.map((item) => (
-                <span key={item.algorithm}>
-                  {item.algorithm}: {item.digest}&nbsp;
-                </span>
-              ))}
-            </dd>
-            <dt>Size</dt>
-            <dd>{formatQuant(fileObj.storageSize)}</dd>
-          </dl>
+
+          <KeyValueTable boldKeys data={data} />
         </Box>
       </>
     );
diff --git a/apps/nar-v3/src/components/KeyValueTable.jsx b/apps/nar-v3/src/components/KeyValueTable.jsx
new file mode 100644
index 0000000..e7d6415
--- /dev/null
+++ b/apps/nar-v3/src/components/KeyValueTable.jsx
@@ -0,0 +1,42 @@
+import { isValidElement } from "react";
+import { Table, TableBody, TableRow, TableCell } from "@mui/material";
+
+function KeyValueTable(props) {
+  let formatKey = (key) => {
+    return key;
+  };
+  if (props.boldKeys) {
+    formatKey = (key) => {
+      return <b>{key}</b>;
+    };
+  }
+
+  let rows = [];
+  if (props.data) {
+    for (const [key, value] of Object.entries(props.data)) {
+      let valueStr = value;
+      if (!isValidElement(value)) {
+        // allow passing JSX as values
+        valueStr = String(value);
+        if (Array.isArray(value)) {
+          valueStr = value.join(", ");
+        }
+      }
+
+      rows.push(
+        <TableRow key={key} sx={{ "&:last-child td": { border: 0 } }}>
+          <TableCell>{formatKey(key)}</TableCell>
+          <TableCell sx={{ whiteSpace: "normal", wordBreak: "break-word" }}>{valueStr}</TableCell>
+        </TableRow>
+      );
+    }
+  }
+
+  return (
+      <Table size="small" aria-label="key-value table">
+        <TableBody>{rows}</TableBody>
+      </Table>
+  );
+}
+
+export default KeyValueTable;
diff --git a/apps/nar-v3/src/components/PatchedCellCard.jsx b/apps/nar-v3/src/components/PatchedCellCard.jsx
index f6634dc..4fb75c3 100644
--- a/apps/nar-v3/src/components/PatchedCellCard.jsx
+++ b/apps/nar-v3/src/components/PatchedCellCard.jsx
@@ -20,6 +20,7 @@ import Box from "@mui/material/Box";
 import Paper from "@mui/material/Paper";
 
 import Connection from "./Connection";
+import KeyValueTable from "./KeyValueTable";
 import styles from "../styles";
 
 function PatchedCellCard(props) {
@@ -27,15 +28,15 @@ function PatchedCellCard(props) {
     const cell = props.cell.cell;
 
     if (cell) {
+      const data = {
+        Location: cell.anatomicalLocation.map((item) => item.name).join(", "),
+      };
       return (
         <>
           <Connection />
           <Box sx={styles.entity} component={Paper} variant="outlined">
             <h2>Patched cell #{cell.internalIdentifier}</h2>
-            <dl>
-              <dt>Location</dt>
-              <dd>{cell.anatomicalLocation.map((item) => item.name).join(", ")}</dd>
-            </dl>
+            <KeyValueTable boldKeys data={data} />
           </Box>
         </>
       );
diff --git a/apps/nar-v3/src/components/RecordingCard.jsx b/apps/nar-v3/src/components/RecordingCard.jsx
index 4beef45..9c50a38 100644
--- a/apps/nar-v3/src/components/RecordingCard.jsx
+++ b/apps/nar-v3/src/components/RecordingCard.jsx
@@ -17,11 +17,11 @@ See the License for the specific language governing permissions and
 limitations under the License.
 */
 
-import { Fragment } from "react";
 import Box from "@mui/material/Box";
 import Paper from "@mui/material/Paper";
 
 import Connection from "./Connection";
+import KeyValueTable from "./KeyValueTable";
 import styles from "../styles";
 import { formatQuant, formatUnits } from "../utility";
 
@@ -30,6 +30,26 @@ function RecordingCard(props) {
   const stimulation = props.stimulation;
 
   if (recording) {
+    const recordingData = {
+      Description: recording.description,
+      "Additional remarks": recording.device.metadata.additionalRemarks,
+      "Sampling frequency": formatQuant(recording.device.metadata.samplingFrequency),
+      Channels: (
+        <ul>
+          {recording.device.metadata.channel.map((item) => (
+            <li key={item.internalIdentifier}>
+              {item.internalIdentifier} ({formatUnits(item.unit)})
+            </li>
+          ))}
+        </ul>
+      ),
+    };
+    const stimulationData = {
+      Type: "Current injection",
+      Description: stimulation.stimulus[0].lookupLabel,
+      "Epoch duration": formatQuant(stimulation.stimulus[0].epoch),
+      Identifier: stimulation.stimulus[0].internalIdentifier,
+    };
     const stimulusSpec = JSON.parse(stimulation.stimulus[0].specification.configuration);
 
     return (
@@ -38,46 +58,14 @@ function RecordingCard(props) {
         <Box sx={styles.activity} component={Paper} variant="outlined">
           <h2>Recording</h2>
           <p>{recording.label}</p>
-          <dl>
-            <dt>Description</dt>
-            <dd>{recording.description}</dd>
-            <dt>Additional remarks</dt>
-            <dd>{recording.device.metadata.additionalRemarks}</dd>
-            <dt>Sampling frequency</dt>
-            <dd>{formatQuant(recording.device.metadata.samplingFrequency)}</dd>
-            <dt>Channels</dt>
-            <dd>
-              <ul>
-                {recording.device.metadata.channel.map((item) => (
-                  <li key={item.internalIdentifier}>
-                    {item.internalIdentifier} ({formatUnits(item.unit)})
-                  </li>
-                ))}
-              </ul>
-            </dd>
-          </dl>
+          <KeyValueTable boldKeys data={recordingData} />
 
           <h2>Stimulation</h2>
           <p>{stimulation.label}</p>
-          <dl>
-            <dt>Type</dt>
-            <dd>Current injection</dd>
-            <dt>Description</dt>
-            <dd>{stimulation.stimulus[0].lookupLabel}</dd>
-            <dt>Epoch duration</dt>
-            <dd>{formatQuant(stimulation.stimulus[0].epoch)}</dd>
-            <dt>Identifier</dt>
-            <dd>{stimulation.stimulus[0].internalIdentifier}</dd>
-          </dl>
+          <KeyValueTable boldKeys data={stimulationData} />
+
           <h3>Specification</h3>
-          <dl>
-            {Object.entries(stimulusSpec).map((item, index) => (
-              <Fragment key={index}>
-                <dt key={`key${index}`}>{item[0]}</dt>
-                <dd key={`value${index}`}>{item[1]}</dd>
-              </Fragment>
-            ))}
-          </dl>
+          <KeyValueTable boldKeys data={stimulusSpec} />
         </Box>
       </>
     );
diff --git a/apps/nar-v3/src/components/SliceCard.jsx b/apps/nar-v3/src/components/SliceCard.jsx
index 1ef2375..49e2e87 100644
--- a/apps/nar-v3/src/components/SliceCard.jsx
+++ b/apps/nar-v3/src/components/SliceCard.jsx
@@ -21,6 +21,7 @@ import Paper from "@mui/material/Paper";
 import Stack from "@mui/material/Stack";
 
 import Connection from "./Connection";
+import KeyValueTable from "./KeyValueTable";
 import { NavigateNext, NavigatePrevious } from "./Navigation";
 import styles from "../styles";
 
@@ -29,6 +30,11 @@ function SliceCard(props) {
     const slice = props.slices[props.index].slice;
 
     if (slice) {
+      const data = {
+        "Location (todo: add link outs)": slice.anatomicalLocation
+          .map((item) => item.name)
+          .join(", "),
+      };
       return (
         <>
           <Connection />
@@ -45,10 +51,7 @@ function SliceCard(props) {
               <p>
                 ({props.index + 1} of {props.slices.length})
               </p>
-              <dl>
-                <dt>Location (todo: add link outs)</dt>
-                <dd>{slice.anatomicalLocation.map((item) => item.name).join(", ")}</dd>
-              </dl>
+              <KeyValueTable boldKeys data={data} />
             </Box>
             <Stack sx={{ width: "60px" }} justifyContent="center">
               {props.index < props.slices.length - 1 ? (
diff --git a/apps/nar-v3/src/components/SlicePreparationCard.jsx b/apps/nar-v3/src/components/SlicePreparationCard.jsx
index 44f8c86..5a19cfb 100644
--- a/apps/nar-v3/src/components/SlicePreparationCard.jsx
+++ b/apps/nar-v3/src/components/SlicePreparationCard.jsx
@@ -22,39 +22,32 @@ import Paper from "@mui/material/Paper";
 
 import { formatQuant } from "../utility";
 import Connection from "./Connection";
+import KeyValueTable from "./KeyValueTable";
 import styles from "../styles";
 
 function SlicePreparationCard(props) {
   const activity = props.activity;
 
   if (activity) {
+    const data = {
+      "Device name": activity.device[0].device.name,
+      "Device type": activity.device[0].device.deviceType,
+      Manufacturer:
+        activity.device[0].device.manufacturer.fullName ||
+        activity.device[0].device.manufacturer.shortName,
+      "Slice thickness": formatQuant(activity.device[0].sliceThickness),
+      "Slicing plane": activity.device[0].slicingPlane,
+      "Study targets": activity.studyTarget.join(", "),
+      Temperature: formatQuant(activity.temperature),
+      "Dissecting solution (full details to come)": activity.tissueBathSolution.name,
+    };
     return (
       <>
         <Connection />
         <Box sx={styles.activity} component={Paper} variant="outlined">
           <h2>Slice preparation</h2>
           <p>{activity.label}</p>
-          <dl>
-            <dt>Device name</dt>
-            <dd>{activity.device[0].device.name}</dd>
-            <dt>Device type</dt>
-            <dd>{activity.device[0].device.deviceType}</dd>
-            <dt>Manufacturer</dt>
-            <dd>
-              {activity.device[0].device.manufacturer.fullName ||
-                activity.device[0].device.manufacturer.shortName}
-            </dd>
-            <dt>Slice thickness</dt>
-            <dd>{formatQuant(activity.device[0].sliceThickness)}</dd>
-            <dt>Slicing plane</dt>
-            <dd>{activity.device[0].slicingPlane}</dd>
-            <dt>Study targets</dt>
-            <dd>{activity.studyTarget.join(", ")}</dd>
-            <dt>Temperature</dt>
-            <dd>{formatQuant(activity.temperature)}</dd>
-            <dt>Dissecting solution (full details to come)</dt>
-            <dd>{activity.tissueBathSolution.name}</dd>
-          </dl>
+          <KeyValueTable boldKeys data={data} />
         </Box>
       </>
     );
diff --git a/apps/nar-v3/src/components/SubjectCard.jsx b/apps/nar-v3/src/components/SubjectCard.jsx
index 6b247d8..e9a676b 100644
--- a/apps/nar-v3/src/components/SubjectCard.jsx
+++ b/apps/nar-v3/src/components/SubjectCard.jsx
@@ -22,6 +22,7 @@ import Stack from "@mui/material/Stack";
 
 import { formatUnits } from "../utility";
 import { NavigateNext, NavigatePrevious } from "./Navigation";
+import KeyValueTable from "./KeyValueTable";
 import styles from "../styles";
 
 function AgeDisplay(props) {
@@ -60,6 +61,20 @@ function SubjectCard(props) {
     }
   }
 
+  const data = {
+    Species: species,
+    Strain: strain,
+    Age: <AgeDisplay age={subject.studiedState[0].age} />,
+    "Age category": subject.studiedState[0].ageCategory,
+    Pathologies:
+      subject.studiedState[0].pathology.length > 0
+        ? subject.studiedState[0].pathology[0].name
+        : "none",
+  };
+  if (!strain) {
+    delete data.Strain;
+  }
+
   return (
     <Stack direction="row" spacing={1}>
       <Stack sx={{ width: "60px" }} justifyContent="center">
@@ -75,30 +90,7 @@ function SubjectCard(props) {
           ({props.index + 1} of {props.subjects.length})
         </p>
         {/* todo: add subject group information */}
-        <dl>
-          <dt>Species</dt>
-          <dd>{species}</dd>
-          {strain ? (
-            <>
-              <dt>Strain</dt>
-              <dd>{strain}</dd>
-            </>
-          ) : (
-            ""
-          )}
-          <dt>Age</dt>
-          <dd>
-            <AgeDisplay age={subject.studiedState[0].age} />
-          </dd>
-          <dt>Age category</dt>
-          <dd>{subject.studiedState[0].ageCategory}</dd>
-          <dt>Pathologies</dt>
-          <dd>
-            {subject.studiedState[0].pathology.length > 0
-              ? subject.studiedState[0].pathology[0].name
-              : "none"}
-          </dd>
-        </dl>
+        <KeyValueTable boldKeys data={data} />
       </Box>
       <Stack sx={{ width: "60px" }} justifyContent="center">
         {props.index < props.subjects.length - 1 ? (