Added a lot of comments.

README.md

@@ -14,4 +14,4 @@ This repository previously contained substantial other material, such as metadat
 such as [openMINDS](https://openminds-documentation.readthedocs.io/).
 
 ### Acknowledgements
-This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements 720270, 785907 and 945539 (Human Brain Project SGA1, SGA2 and SGA3).
+This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements 720270, 785907 and 945539 (Human Brain Project SGA1, SGA2 and SGA3), and in EBRAINS 2.0, funded from the EU Horizon Europe programme under grant agreement 101147319.

apps/nar-v3/README.md

@@ -0,0 +1,32 @@
+# Neural Activity Resource app
+
+Code for the Neural Activity Resource app.
+
+This is an experimental interface for in-depth metadata in the [EBRAINS Knowledge Graph](https://kg.ebrains.eu).
+It is not yet intended for public use.
+
+Copyright 2017, Centre National de la Recherche Scientifique and Forschungszentrum Jülich;
+Copyright 2018-2024 Centre National de la Recherche Scientifique
+
+Code is licenced under the Apache 2.0 licence.
+
+## Developers' Guide
+
+The main code repository is https://gitlab.ebrains.eu/data-services/neural-activity-resource.
+
+The app is implemented using React Router v6, with Material UI for layout and design.
+Data are retrieved from the EBRAINS Knowledge Graph using the [KG Core API](https://docs.kg.ebrains.eu/).
+
+To run a development server, you will need to obtain an EBRAINS IAM authorization token,
+paste it into src/main.jsx, then run:
+
+  $ npm run dev
+
+### Deployment
+
+The app is deployed to https://nar.apps.tc.humanbrainproject.eu using Kubernetes.
+See the "deployment" folder and .gitlab-ci.yml for more details.
+
+
+## Acknowledgements
+This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreement 945539 (Human Brain Project SGA3), and in EBRAINS 2.0, funded from the EU Horizon Europe programme under grant agreement 101147319.

apps/nar-v3/src/auth.js

@@ -1,3 +1,25 @@
+/*
+This file contains functions for authentication.
+
+It is based on code written by the Collaboratory team at EBRAINS AISBL, formerly at EPFL.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import Keycloak from "keycloak-js";
 
 // We start by configuring the Keycloak javascript client

apps/nar-v3/src/components/ControlledTerm.jsx

@@ -1,3 +1,28 @@
+/*
+The Controlled Term component provides a rich display of information
+about a term from the openMINDS controlled terminologies.
+
+At present, it displays the standardised name of the term.
+
+TODO: add links to external resources, such an ontology definitions.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import Tooltip from "@mui/material/Tooltip";
 
 function ControlledTerm(props) {

apps/nar-v3/src/components/DatasetList.jsx

@@ -1,3 +1,22 @@
+/*
+The DatasetList component displays a table with summary information
+about datasets, and links to the individual dataset views.
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
 import { Link as RouterLink } from "react-router-dom";
 import Table from "@mui/material/Table";
 import TableBody from "@mui/material/TableBody";

apps/nar-v3/src/components/KeyValueTable.jsx

@@ -1,3 +1,24 @@
+/*
+The KeyValueTable component represents the content of a dictionary
+as a table.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import { isValidElement } from "react";
 import { Table, TableBody, TableRow, TableCell } from "@mui/material";
 

apps/nar-v3/src/components/Navigation.jsx

@@ -1,3 +1,27 @@
+/*
+This file provides several components used in navigating the app:
+
+  Navigation - a "breadcrumb" style bar showing where the user is in the app
+  NavigateNext - a CSS button for moving to the next item in a list
+  NavigatePrevious - a CSS button for moving to the previous item in a list
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import { Link, Typography, Toolbar, Breadcrumbs } from "@mui/material";
 import { Link as RouterLink, useLocation } from "react-router-dom";
 

apps/nar-v3/src/components/PatchClampRecordingCard.jsx

@@ -1,3 +1,24 @@
+/*
+The PatchClampRecordingCard component displays metadata about recordings
+from an individual neuron using the patch clamp technique.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import Link from "@mui/material/Link";
 
 import { uuidFromUri } from "../utility.js";

apps/nar-v3/src/components/PatchClampRecordingList.jsx

@@ -1,3 +1,23 @@
+/*
+The PatchClampRecordinList component displays a list of neurons
+whose activity has been recorded using the patch clamp technique.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
 import { Link as RouterLink } from "react-router-dom";
 
 function uuidFromUri(uri) {

apps/nar-v3/src/datastore.js

@@ -1,3 +1,23 @@
+/*
+This file contains functions for retrieving data from the KG Core API of the
+EBRAINS Knowledge Graph. It also contains a cache, to reduce the number of requests.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
 import { kgUrl, kgDefaultStage } from "./globals";
 //import examplePatchClampData from "./example_data/example_patch_clamp_dataset.json";
 

apps/nar-v3/src/main.jsx

@@ -1,3 +1,24 @@
+/*
+This is the main entry point to the Neural Activity Resource app,
+which is built with React Router v6, using the data loader pattern.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import React from "react";
 import ReactDOM from "react-dom/client";
 import { createBrowserRouter, RouterProvider } from "react-router-dom";

apps/nar-v3/src/queries.js

@@ -1,3 +1,27 @@
+/*
+This file contains functions for building queries for the KG Core API
+of the EBRAINS Knowledge Graph.
+
+These functions are used in routes/queryLibrary.js to create a library
+of pre-defined queries, which are then used by the functions in datastore.js
+to retrieve data from the KG.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
 function buildKGQuery(baseType, structure) {
   return {
     "@context": {

apps/nar-v3/src/routes/dataset.jsx

@@ -1,3 +1,23 @@
+/*
+The dataset route displays the metadata for a single dataset.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import React from "react";
 import { Await, defer, useLoaderData } from "react-router-dom";
 

apps/nar-v3/src/routes/datasets.jsx

@@ -1,3 +1,24 @@
+/*
+The datasets route displays a table with summary information
+from all suitable "neural activity" datasets in the EBRAINS Knowledge Graph.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import React from "react";
 import { Await, defer, useLoaderData } from "react-router-dom";
 

apps/nar-v3/src/routes/home.jsx

@@ -1,3 +1,24 @@
+/*
+The home route is the entry point to the Neural Activity Resource app.
+It has links to different ways of viewing the metadata in the EBRAINS Knowledge Graph.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import React from "react";
 import { Await, defer, useLoaderData, Link as RouterLink } from "react-router-dom";
 

apps/nar-v3/src/routes/patchClampRecording.jsx

@@ -1,3 +1,24 @@
+/*
+The "patch clamp recording" route displays metadata about recordings from
+single neurons. Each page shows the recordings from one individual neuron.
+
+
+Copyright 2024 Andrew P. Davison, CNRS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
 import React from "react";
 import { Await, defer, useLoaderData } from "react-router-dom";