Merge pull request #513 from NeurodataWithoutBorders/loose-select-dro…

…pdown

Create loose selector (autocomplete) for JSONSchemaForm

pyflask/app.py

@@ -105,6 +105,13 @@ def get_cpu_count():
     return dict(physical=physical, logical=logical)
 
 
+@app.route("/get-recommended-species")
+def get_species():
+    from dandi.metadata import species_map
+
+    return species_map
+
+
 @api.route("/server_shutdown", endpoint="shutdown")
 class Shutdown(Resource):
     def get(self):

schemas/base-metadata.schema.ts

@@ -1,23 +1,90 @@
+import { serverGlobals, resolve } from '../src/renderer/src/server/globals'
+
+import { header } from '../src/renderer/src/stories/forms/utils'
+
 import baseMetadataSchema from './json/base_metadata_schema.json' assert { type: "json" }
 
-export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
+function getSpeciesNameComponents(arr: any[]) {
+    const split = arr[arr.length - 1].split(' - ')
+    return {
+        name: split[0],
+        label: split[1]
+    }
+}
+
+
+function getSpeciesInfo(species: any[][] = []) {
+
+
+    return {
+
+        enumLabels: species.reduce((acc, arr) => {
+            acc[getSpeciesNameComponents(arr).name] = arr[arr.length - 1]
+            return acc
+        }, {}),
+
+        enumKeywords: species.reduce((acc, arr) => {
+            const info = getSpeciesNameComponents(arr)
+            acc[info.name] = info.label ? [`${header(info.label)} — ${arr[0].join(', ')}`] : arr[0]
+            return acc
+        }, {}),
+
+        enum: species.map(arr => getSpeciesNameComponents(arr).name), // Remove common names so this passes the validator
+    }
+
+}
+
+export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, global = false) => {
+
+
+    const copy = structuredClone(schema)
 
     // Add unit to weight
-    schema.properties.Subject.properties.weight.unit = 'kg'
+    const subjectProps = copy.properties.Subject.properties
+    subjectProps.weight.unit = 'kg'
+
+    // subjectProps.order = ['weight', 'age', 'age__reference', 'date_of_birth', 'genotype', 'strain']
 
-    schema.properties.Subject.properties.sex.enumLabels = {
+    subjectProps.sex.enumLabels = {
         M: 'Male',
         F: 'Female',
         U: 'Unknown',
         O: 'Other'
     }
 
+
+      subjectProps.species = {
+        type: 'string',
+        ...getSpeciesInfo(),
+        items: {
+            type: 'string'
+        },
+        strict: false,
+        description: 'The species of your subject.'
+    }
+
+    // Resolve species suggestions
+    resolve(serverGlobals.species, (res) => {
+        const info = getSpeciesInfo(res)
+        Object.assign(subjectProps.species, info)
+    })
+
     // Ensure experimenter schema has custom structure
-    schema.properties.NWBFile.properties.experimenter = baseMetadataSchema.properties.NWBFile.properties.experimenter
+    copy.properties.NWBFile.properties.experimenter = baseMetadataSchema.properties.NWBFile.properties.experimenter
 
     // Override description of keywords
-    schema.properties.NWBFile.properties.keywords.description = 'Terms to describe your dataset (e.g. Neural circuits, V1, etc.)' // Add description to keywords
-    return schema
+    copy.properties.NWBFile.properties.keywords.description = 'Terms to describe your dataset (e.g. Neural circuits, V1, etc.)' // Add description to keywords
+
+
+
+    // Remove non-global properties
+    if (global) {
+        Object.entries(copy.properties).forEach(([globalProp, schema]) => {
+            instanceSpecificFields[globalProp]?.forEach((prop) =>  delete schema.properties[prop]);
+        });
+    }
+
+    return copy
 
 }
 
@@ -39,13 +106,7 @@ export const instanceSpecificFields = {
 };
 
 
-const globalSchema = structuredClone(preprocessMetadataSchema());
-Object.entries(globalSchema.properties).forEach(([globalProp, schema]) => {
-    instanceSpecificFields[globalProp]?.forEach((prop) =>  delete schema.properties[prop]);
-});
+export const globalSchema = preprocessMetadataSchema(undefined, true);
 
-export {
-    globalSchema
-}
 
 export default preprocessMetadataSchema()

schemas/subject.schema.ts

@@ -1,44 +1,27 @@
-import nwbBaseSchema  from './base-metadata.schema'
+import { preprocessMetadataSchema } from './base-metadata.schema'
 
 const removeSubset = (data, subset) => {
     const subsetData = subset.reduce((acc, key) => { acc[key] = data[key]; return acc }, {})
     for (let key in subsetData) delete data[key]
     return subsetData
   }
 
-  const species = [
-    "Mus musculus - House mouse",
-    "Homo sapiens - Human",
-    "Rattus norvegicus - Norway rat",
-    "Rattus rattus - Black rat",
-    "Macaca mulatta - Rhesus monkey",
-    "Callithrix jacchus - Common marmoset",
-    "Drosophila melanogaster - Fruit fly",
-    "Danio rerio - Zebra fish",
-    "Caenorhabditis elegans"
-  ].map(str => str.split(' - ')[0]) // Remove common names so this passes the validator
+export default (schema) => {
 
-nwbBaseSchema.properties.Subject.properties.species = {
-    type: 'string',
-    enum: species,
-    items: {
-        type: 'string'
-    },
-    strict: false,
-    description: 'The species of your subject.'
-}
+  const nwbBaseSchema = preprocessMetadataSchema(schema)
 
-// Sort the subject schema
-const ageGroupKeys = ['age', 'age__reference', 'date_of_birth']
-const genotypeGroupKeys = ['genotype', 'strain']
-const groups = [...ageGroupKeys, ...genotypeGroupKeys]
-const standardOrder = {...nwbBaseSchema.properties.Subject.properties}
-const group = removeSubset(standardOrder, groups)
-const required = removeSubset(standardOrder, nwbBaseSchema.properties.Subject.required)
+    // Sort the subject schema
+  const ageGroupKeys = ['age', 'age__reference', 'date_of_birth']
+  const genotypeGroupKeys = ['genotype', 'strain']
+  const groups = [...ageGroupKeys, ...genotypeGroupKeys]
+  const standardOrder = {...nwbBaseSchema.properties.Subject.properties}
+  const group = removeSubset(standardOrder, groups)
+  const required = removeSubset(standardOrder, nwbBaseSchema.properties.Subject.required)
 
-let newRequiredArray = [...nwbBaseSchema.properties.Subject.required, 'sessions']
+  let newRequiredArray = [...nwbBaseSchema.properties.Subject.required, 'sessions']
 
-export default {
+
+  return {
     ...nwbBaseSchema.properties.Subject,
     properties: {
       sessions: {
@@ -53,3 +36,4 @@ export default {
     },
     required: newRequiredArray
   }
+}

src/renderer/src/globals.js

@@ -1,4 +1,4 @@
-import { path, port } from "./electron/index.js";
+import { path } from "./electron/index.js";
 
 import guideGlobalMetadata from "../../../guideGlobalMetadata.json" assert { type: "json" };
 
@@ -9,7 +9,4 @@ export let runOnLoad = (fn) => {
     else window.addEventListener("load", fn);
 };
 
-// Base Request URL for Python Server
-export const baseUrl = `http://127.0.0.1:${port}`;
-
 export const supportedInterfaces = guideGlobalMetadata.supported_interfaces;

src/renderer/src/index.ts

@@ -10,7 +10,9 @@ import {
 } from './dependencies/globals.js'
 
 import Swal from 'sweetalert2'
-import { loadServerEvents, pythonServerOpened, statusBar } from "./server.js";
+import { loadServerEvents, pythonServerOpened } from "./server/index.js";
+
+import { statusBar } from "./server/globals.js";
 
 // Set the sidebar subtitle to the current app version
 const dashboard = document.querySelector('nwb-dashboard') as Dashboard

src/renderer/src/server/globals.ts

@@ -0,0 +1,79 @@
+import { isElectron, app, port } from '../electron/index.js'
+
+import serverSVG from "../stories/assets/server.svg?raw";
+import webAssetSVG from "../stories/assets/web_asset.svg?raw";
+import wifiSVG from "../stories/assets/wifi.svg?raw";
+
+// Base Request URL for Python Server
+export const baseUrl = `http://127.0.0.1:${port}`;
+
+const isPromise = (o) => typeof o === 'object' && typeof o.then === 'function'
+
+export const resolve = (object, callback) => {
+  if (isPromise(object)) {
+    return new Promise(resolvePromise => {
+        object.then((res) => resolvePromise((callback) ? callback(res) : res))
+    })
+  } else return (callback) ? callback(object) : object
+}
+
+// -------------------------------------------------
+
+import { StatusBar } from "../stories/status/StatusBar.js";
+import { unsafeSVG } from "lit/directives/unsafe-svg.js";
+
+const appVersion = app?.getVersion();
+
+export const statusBar = new StatusBar({
+  items: [
+    { label: unsafeSVG(webAssetSVG), value: isElectron ? appVersion ?? 'ERROR' : 'Web' },
+    { label: unsafeSVG(wifiSVG) },
+    { label: unsafeSVG(serverSVG) }
+  ]
+})
+
+
+let serverCallbacks: Function[] = []
+export const onServerOpen = (callback:Function) => {
+  if (statusBar.items[2].status === true) return callback()
+  else {
+    return new Promise(res => {
+        serverCallbacks.push(() => {
+            res(callback())
+        })
+
+    })
+ }
+}
+
+export const activateServer = () => {
+ statusBar.items[2].status = true
+
+ serverCallbacks.forEach(cb => cb())
+ serverCallbacks = []
+}
+
+export const serverGlobals = {
+    species: new Promise((res, rej) => {
+      onServerOpen(() => {
+        fetch(new URL("get-recommended-species", baseUrl))
+          .then((res) => res.json())
+          .then((species) => {
+            res(species)
+            serverGlobals.species = species
+          })
+          .catch(() => rej());
+      });
+    }),
+    cpus: new Promise((res, rej) => {
+      onServerOpen(() => {
+        fetch(new URL("cpus", baseUrl))
+          .then((res) => res.json())
+          .then((cpus) => {
+            res(cpus)
+            serverGlobals.cpus = cpus
+          })
+          .catch(() => rej());
+      });
+    })
+  }

src/renderer/src/server.ts → src/renderer/src/server/index.ts

@@ -1,31 +1,13 @@
-import { isElectron, electron, app } from './electron/index.js'
+import { isElectron, electron, app, port } from '../electron/index.js'
 const { ipcRenderer } = electron;
 
 import {
   notyf,
-} from './dependencies/globals.js'
-
-import { baseUrl } from './globals.js'
+} from '../dependencies/globals.js'
 
 import Swal from 'sweetalert2'
 
-
-import { StatusBar } from "./stories/status/StatusBar.js";
-import { unsafeSVG } from "lit/directives/unsafe-svg.js";
-import serverSVG from "./stories/assets/server.svg?raw";
-import webAssetSVG from "./stories/assets/web_asset.svg?raw";
-import wifiSVG from "./stories/assets/wifi.svg?raw";
-
-const appVersion = app?.getVersion();
-
-export const statusBar = new StatusBar({
-  items: [
-    { label: unsafeSVG(webAssetSVG), value: isElectron ? appVersion ?? 'ERROR' : 'Web' },
-    { label: unsafeSVG(wifiSVG) },
-    { label: unsafeSVG(serverSVG) }
-  ]
-})
-
+import { activateServer, baseUrl } from './globals.js';
 
 // Check if the Flask server is live
 const serverIsLiveStartup = async () => {
@@ -39,27 +21,6 @@ const serverIsLiveStartup = async () => {
     else throw new Error('Error preloading Flask imports')
   })
 
-
-let serverCallbacks: Function[] = []
-export const onServerOpen = (callback:Function) => {
-  if (statusBar.items[2].status === true) return callback()
-  else {
-    return new Promise(res => {
-        serverCallbacks.push(() => {
-            res(callback())
-        })
-
-    })
- }
-}
-
-export const activateServer = () => {
- statusBar.items[2].status = true
-
- serverCallbacks.forEach(cb => cb())
- serverCallbacks = []
-}
-
 export async function pythonServerOpened() {
 
   // Confirm requests are actually received by the server

src/renderer/src/stories/JSONSchemaForm.js

@@ -376,7 +376,7 @@ export class JSONSchemaForm extends LitElement {
         let message = isValid
             ? ""
             : requiredButNotSpecified.length === 1
-              ? `<b>${requiredButNotSpecified[0]}</b> is not defined`
+              ? `<b>${header(requiredButNotSpecified[0])}</b> is not defined`
               : `${requiredButNotSpecified.length} required inputs are not specified properly`;
         if (requiredButNotSpecified.length !== nMissingRequired)
             console.warn("Disagreement about the correct error to throw...");
@@ -387,7 +387,6 @@ export class JSONSchemaForm extends LitElement {
         if (flaggedInputs.length) {
             flaggedInputs[0].focus();
             if (!message) {
-                console.log(flaggedInputs);
                 if (flaggedInputs.length === 1)
                     message = `<b>${header(flaggedInputs[0].path.join("."))}</b> is not valid`;
                 else message = `${flaggedInputs.length} invalid form values`;