Add custom Node-RED nodes (#621)

After a bit of playing around we decided to start using custom Node-RED
Nodes instead of creating a new server or adding APIs to device-backend.

These will be used by

* first time setup
* dashboard 2
* portal (replaced with dashboard 2)

Author: sonnyp

.vscode/extensions.json

@@ -0,0 +1,17 @@
+{
+	// See https://go.microsoft.com/fwlink/?LinkId=827846 to learn about workspace recommendations.
+	// Extension identifier format: ${publisher}.${name}. Example: vscode.csharp
+
+	// List of extensions which should be recommended for users of this workspace.
+	"recommendations": [
+		"esbenp.prettier-vscode",
+		"charliermarsh.ruff",
+		"editorconfig.editorconfig",
+		"dbaeumer.vscode-eslint"
+		
+	],
+	// List of extensions recommended by VSCodium that should not be recommended for users of this workspace.
+	"unwantedRecommendations": [
+		
+	]
+}

documentation/docs/community/contribute/tips-and-tricks.md

@@ -52,6 +52,8 @@ Make sure to replace `$planktoscope` with your PlanktoScope hostname, eg. `pksco
 ssh-keygen -t ed25519 -C "pi@$planktoscope" -f ~/.ssh/$planktoscope
 # Make the SSH key accepted by the PlanktoScope
 ssh-copy-id -i ~/.ssh/$planktoscope.pub pi@$planktoscope
+# Add your keys to your SSH agent
+ssh-add -k
 ```
 
 ```

software/distro/setup/planktoscope-app-env/PlanktoScope/cfg80211_regdomain.conf

@@ -0,0 +1 @@
+options cfg80211 ieee80211_regdom=

software/distro/setup/planktoscope-app-env/PlanktoScope/install.sh

@@ -17,3 +17,7 @@ sudo bash -c "cat \"$config_files_root/config.txt.snippet\" >> \"/boot/firmware/
 # Disable the 4 Raspberry logo in the top left corner
 # more space for kernel and system logs
 sudo sed -i -e 's/$/ logo.nologo/' /boot/firmware/cmdline.txt
+
+# Create a file needed by the "set country" Node-RED node
+sudo cp -r "$config_files_root/cfg80211_regdomain.conf" "/etc/modprobe.d/"
+sudo chown -R pi:pi "/etc/modprobe.d/cfg80211_regdomain.conf"

software/distro/setup/planktoscope-app-env/node-red-frontend/install.sh

@@ -23,9 +23,9 @@ if ! sudo apt-get install -y python3-smbus2; then
   pip3 install smbus2==0.4.3
 fi
 
-# Install Node.js 20
-# https://github.com/nodesource/distributions/blob/master/README.md#using-debian-as-root-nodejs-20
-curl -fsSL https://deb.nodesource.com/setup_20.x -o /tmp/nodesource_setup.sh
+# Install Node.js 22
+# https://github.com/nodesource/distributions/blob/master/README.md#using-debian-as-root-nodejs-22
+curl -fsSL https://deb.nodesource.com/setup_22.x -o /tmp/nodesource_setup.sh
 sudo -E bash /tmp/nodesource_setup.sh
 sudo apt-get install -y nodejs
 

software/node-red-dashboard/.gitignore

@@ -1,2 +1,5 @@
 *.backup
 .config.*.json
+/planktoscopehat/context
+/planktoscopehat/projects
+flows_cred.json

software/node-red-dashboard/adafruithat/package.json

@@ -1,22 +1,22 @@
 {
-    "name": "planktoscope-node-red-dashboard",
-    "description": "PlanktoScope graphical user interface",
-    "dependencies": {
-        "@flowfuse/node-red-dashboard": "^1.22.1",
-        "@flowfuse/node-red-dashboard-2-ui-flowviewer": "^1.0.1",
-        "node-red-contrib-cron-plus": "^2.1.0",
-        "node-red-contrib-dir2files": "^0.3.0",
-        "node-red-contrib-gpsd": "^1.0.4",
-        "node-red-contrib-python3-function": "^0.0.4",
-        "node-red-contrib-ui-multistate-switch": "^1.2.2",
-        "node-red-dashboard": "^3.1.2",
-        "node-red-node-pi-gpio": "^2.0.1",
-        "node-red-node-ui-list": "^0.3.6"
-    },
-    "node-red": {
-        "settings": {
-            "flowFile": "flows.json",
-            "credentialsFile": "credentials.json"
-        }
+  "name": "planktoscope-node-red-dashboard",
+  "description": "PlanktoScope graphical user interface",
+  "dependencies": {
+    "@flowfuse/node-red-dashboard": "^1.22.1",
+    "@flowfuse/node-red-dashboard-2-ui-flowviewer": "^1.0.1",
+    "node-red-contrib-cron-plus": "^2.1.0",
+    "node-red-contrib-dir2files": "^0.3.0",
+    "node-red-contrib-gpsd": "^1.0.4",
+    "node-red-contrib-python3-function": "^0.0.4",
+    "node-red-contrib-ui-multistate-switch": "^1.2.2",
+    "node-red-dashboard": "^3.1.2",
+    "node-red-node-pi-gpio": "^2.0.1",
+    "node-red-node-ui-list": "^0.3.6"
+  },
+  "node-red": {
+    "settings": {
+      "flowFile": "flows.json",
+      "credentialsFile": "flows_cred.json"
     }
+  }
 }

software/node-red-dashboard/planktoscopehat/nodes/README.md

@@ -0,0 +1,43 @@
+# nodes
+
+Custom Node-RED modules for the PlanktoScope
+
+- https://nodered.org/docs/creating-nodes/
+- https://github.com/node-red/node-red-node-test-helper/
+- https://nodejs.org/docs/latest-v20.x/api/test.html
+- https://nodejs.org/docs/latest-v20.x/api/assert.html
+
+## Development
+
+```sh
+cd nodes
+npm install
+npm test
+```
+
+Run excotaxa:
+
+https://github.com/ecotaxa/ecotaxa_front/tree/master/docker/all_in_one
+
+Note:
+
+On Fedora you need to disable SELinux with
+
+```sh
+sudo setenforce 0
+```
+
+Start node-red manually
+
+```sh
+sudo systemctl stop node-red
+node-red --settings /home/pi/PlanktoScope/software/node-red-dashboard/settings.js
+```
+
+## Tests
+
+Currently broken
+
+```
+node --test ecotaxa.test.js
+```

software/node-red-dashboard/planktoscopehat/nodes/api/country.js

@@ -0,0 +1,49 @@
+import { readFile, writeFile } from "fs/promises"
+
+// We don't use files from "sudo dpkg-query -L wireless-regdb"
+// because the tool to read them crda was removed in Bookworm
+export async function getWifiRegulatoryDomains() {
+  const iso3166tab = await readFile("/usr/share/zoneinfo/iso3166.tab", {
+    encoding: "utf8",
+  })
+  let countries = []
+  for (const line of iso3166tab.split("\n")) {
+    if (line.startsWith("#")) continue
+    const [value, label] = line.split("\t")
+    if (value && label) {
+      countries.push({ value, label })
+    }
+  }
+  countries = countries.sort((a, b) => {
+    return a.label.localeCompare(b.label)
+  })
+
+  return countries
+}
+
+const path = "/etc/modprobe.d/cfg80211_regdomain.conf"
+
+// We don't use `iw reg get` and `iw reg set`
+// because
+// * it is temporary
+// * wifi needs to be disconnected for get to reflect set
+export async function setWifiRegulatoryDomain(code) {
+  await writeFile(path, `options cfg80211 ieee80211_regdom=${code}`)
+}
+
+// TODO: set by default to 00 which is global setting
+export async function getWifiRegulatoryDomain() {
+  let data
+
+  try {
+    data = await readFile(path, {
+      encoding: "utf8",
+    })
+  } catch (err) {
+    if (err.code !== "ENOENT") throw err
+    data = ""
+  }
+
+  const [, code] = data.match(/options cfg80211 ieee80211_regdom=(.*$)/)
+  return code || null
+}

software/node-red-dashboard/planktoscopehat/nodes/api/ecotaxa.js

@@ -0,0 +1,73 @@
+import { openAsBlob } from "node:fs"
+import { extname, basename } from "node:path"
+
+import mime from "mime"
+
+export async function login({ api_url, username, password }) {
+  const req = await fetch(new URL("login", api_url), {
+    method: "POST",
+    headers: {
+      "Content-Type": "application/json",
+    },
+    body: JSON.stringify({ username, password }),
+  })
+  const token = await req.json()
+  return token
+}
+
+// async function createProject({api_url, token, title }) {
+//   const req = await fetch(new URL("projects/create", api_url), {
+//     method: "POST",
+//     headers: {
+//       "Content-Type": "application/json",
+//       Authorization: `Bearer ${token}`,
+//     },
+//     body: JSON.stringify({
+//       // "clone_of_id": 2,
+//       title: "My new project title",
+//       // "instrument": "PlanktoScope test",
+//       // "visible": True,
+//     }),
+//   })
+//   const project_id = await req.json()
+//   return project_id
+// }
+
+export async function uploadFile({ api_url, token, path }) {
+  const type = mime.getType(extname(path))
+  const blob = await openAsBlob(path, { type })
+  const file = new File([blob], basename(path), { type: blob.type })
+
+  const form = new FormData()
+  form.append("file", file)
+
+  const req = await fetch(new URL("my_files/", api_url), {
+    method: "POST",
+    headers: {
+      Authorization: `Bearer ${token}`,
+    },
+    body: form,
+  })
+  const res = await req.json()
+  return res
+}
+
+export async function importFile({ api_url, token, project_id, path }) {
+  const req = await fetch(new URL(`file_import/${project_id}`, api_url), {
+    method: "POST",
+    headers: {
+      Authorization: `Bearer ${token}`,
+      "Content-Type": "application/json",
+    },
+    body: JSON.stringify({
+      source_path: path,
+      // "taxo_mappings": {"23444": 76543},
+      // "skip_loaded_files": False,
+      // "skip_existing_objects": False,
+      // "update_mode": "Yes",
+    }),
+  })
+
+  const result = await req.json()
+  return result
+}