Merge pull request #721 from NeurodataWithoutBorders/fix-ophys-table-…

…popup-and-validation

Fix Ophys Table Popup

.github/workflows/pyflask-build-and-dist-tests.yml

@@ -1,4 +1,4 @@
-name: Build Tests — Flask
+name: Build Tests
 on:
   schedule:
     - cron: "0 16 * * *"  # Daily at noon EST
@@ -15,7 +15,7 @@ env:
 
 jobs:
   testing:
-    name: PyFlask build and distributable tests on ${{ matrix.os }}
+    name: PyInstaller on ${{ matrix.os }}  # Will read on the dashboard as 'Build Tests / PyInstaller on {os}'
     runs-on: ${{ matrix.os }}
     defaults:
       run:

.github/workflows/testing-live-services.yml

@@ -1,4 +1,4 @@
-name: Dev Tests (Live Services)
+name: Dev Tests (Live)
 on:
   schedule:
     - cron: "0 16 * * *"  # Daily at noon EST
@@ -13,7 +13,7 @@ env:
 
 jobs:
   testing:
-    name: Dev tests with live services on ${{ matrix.os }}
+    name: Services on ${{ matrix.os }}  # Will read on the dashboard as 'Dev Tests (Live) / Services on {os}'
     runs-on: ${{ matrix.os }}
     defaults:
       run:

.github/workflows/testing.yml

@@ -13,7 +13,7 @@ env:
 
 jobs:
   testing:
-    name: Dev tests on ${{ matrix.os }}
+    name: ${{ matrix.os }}  # Will read on the dashboard as 'Dev Tests / {os}'
     runs-on: ${{ matrix.os }}
     defaults:
       run:

schemas/base-metadata.schema.ts

@@ -5,6 +5,7 @@ import { header, replaceRefsWithValue } from '../src/renderer/src/stories/forms/
 import baseMetadataSchema from './json/base_metadata_schema.json' assert { type: "json" }
 
 import { merge } from '../src/renderer/src/stories/pages/utils'
+import { drillSchemaProperties } from '../src/renderer/src/stories/pages/guided-mode/data/utils'
 
 const UV_MATH_FORMAT = `&micro;V`; //`<math xmlns="http://www.w3.org/1998/Math/MathML"><mo>&micro;</mo><mi>V</mi></math>`
 const UV_PROPERTIES = ["gain_to_uV", "offset_to_uV"]
@@ -71,8 +72,20 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
 
     const copy = replaceRefsWithValue(structuredClone(schema))
 
-    copy.additionalProperties = false
+    // NEUROCONV PATCH: Correct for incorrect array schema
+    drillSchemaProperties(
+        copy,
+        (_, schema) => {
+            if (schema.properties && schema.type === "array") {
+                schema.items = { type: "object", properties: schema.properties, required: schema.required };
+                delete schema.properties;
+                delete schema.required;
+            }
+        },
+        {}
+    );
 
+    copy.additionalProperties = false
 
 
     copy.required = Object.keys(copy.properties) // Require all properties at the top level

src/renderer/src/stories/InstanceManager.js

@@ -223,7 +223,6 @@ export class InstanceManager extends LitElement {
 
     // Correct bug where multiple instances are selected
     updated = () => {
-        console.log(this);
         const selected = Array.from(this.shadowRoot.querySelectorAll("[selected]"));
         if (selected.length > 0)
             selected.slice(1).forEach((element) => {
@@ -376,7 +375,6 @@ export class InstanceManager extends LitElement {
         this.#items = [];
 
         const instances = this.#render();
-        console.log(this.#items);
 
         const hasMultiple = this.#hasMultiple();
 

src/renderer/src/stories/JSONSchemaForm.js

@@ -517,8 +517,9 @@ export class JSONSchemaForm extends LitElement {
                 if (e.message.includes("is not of a type(s)")) {
                     if (resolvedSchema.type === "number") {
                         if (resolvedValue === "NaN") return;
-                        else if (resolvedValue === null) return;
-                        else if (isRow) e.message = `${e.message}. ${templateNaNMessage}`;
+                        else if (resolvedValue === null) {
+                            if (schema.type !== "array") return; // Allow null in non-tables
+                        } else if (isRow) e.message = `${e.message}. ${templateNaNMessage}`;
                     } else if (resolvedSchema.type === "string") {
                         if ("properties" in resolvedSchema) return; // Allow for constructing types from object types
                     }

src/renderer/src/stories/JSONSchemaInput.js

@@ -174,8 +174,6 @@ export function createTable(fullPath, { onUpdate, onThrow, overrides = {} }) {
 
         merge(overrides.schema, schemaCopy, { arrays: true });
 
-        console.log(schemaPath, nestedIgnore);
-
         const tableMetadata = {
             keyColumn: tempPropertyKey,
             schema: schemaCopy,
@@ -928,7 +926,6 @@ export class JSONSchemaInput extends LitElement {
             const allowPatternProperties = isPatternProperties(this.pattern);
             const allowAdditionalProperties = isAdditionalProperties(this.pattern);
 
-            // Provide default item types
             // Provide default item types
             if (isArray) {
                 const hasItemsRef = "items" in schema && "$ref" in schema.items;
@@ -1016,7 +1013,7 @@ export class JSONSchemaInput extends LitElement {
                     });
                 }
 
-                const externalPath = this.form ? [...this.form.base, ...resolvedFullPath] : resolvedFullPath;
+                const externalPath = this.form?.base ? [...this.form.base, ...resolvedFullPath] : resolvedFullPath;
 
                 const table = createTable.call(this, externalPath, {
                     onUpdate: updateFunction,

src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js

@@ -245,7 +245,6 @@ export class GuidedMetadataPage extends ManagedPage {
 
         const ophys = schema.properties.Ophys;
         if (ophys) {
-            // Set most Ophys tables to have minItems / maxItems equal (i.e. no editing possible)
             drillSchemaProperties(
                 schema,
                 (path, schema, target, isPatternProperties, parentSchema) => {
@@ -258,11 +257,14 @@ export class GuidedMetadataPage extends ManagedPage {
 
                         if (schema.type === "array") {
                             if (name !== "Device" && target) {
-                                if (name in target)
-                                    schema.minItems = schema.maxItems = target[name].length; // Skip unresolved deep in pattern properties)
-                                // Remove Ophys requirements if left initially undefined
-                                else if (parentSchema.required.includes(name))
-                                    parentSchema.required = parentSchema.required.filter((n) => n !== name);
+                                // Set most Ophys tables to have minItems / maxItems equal (i.e. no editing possible)
+                                if (name in target) schema.minItems = schema.maxItems = target[name].length;
+                                // Remove Ophys property requirement if left initially undefined
+                                else {
+                                    target[name] = []; // Initialize empty array
+                                    if (parentSchema.required.includes(name))
+                                        parentSchema.required = parentSchema.required.filter((n) => n !== name);
+                                }
                             }
                         }
                     }
@@ -272,6 +274,7 @@ export class GuidedMetadataPage extends ManagedPage {
         }
 
         console.log("schema", structuredClone(schema), structuredClone(results));
+
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,

src/renderer/src/stories/pages/guided-mode/data/utils.js

@@ -88,12 +88,6 @@ export function resolveProperties(properties = {}, target, globals = {}) {
     for (let name in properties) {
         const info = properties[name];
 
-        // NEUROCONV PATCH: Correct for incorrect array schema
-        if (info.properties && info.type === "array") {
-            info.items = { type: "object", properties: info.properties, required: info.required };
-            delete info.properties;
-        }
-
         const props = info.properties;
 
         if (!(name in target)) {

src/renderer/src/stories/table/cells/base.ts

@@ -126,7 +126,6 @@ export class TableCellBase extends LitElement {
             this.setAttribute('editing', '')
 
             const listenForEnter = (ev: KeyboardEvent) => {
-                console.log(ev)
 
                 if (ev.key === 'Enter') {
                     ev.preventDefault()

src/renderer/src/stories/table/cells/input.ts

@@ -44,6 +44,8 @@ export class NestedEditor extends LitElement {
         const schema = this.schema
 
 
+        console.log('schema', schema, 'data', data)
+        const container = document.createElement('div')
         const input = this.#input = new JSONSchemaInput({
             schema,
             value: data,
@@ -59,9 +61,10 @@ export class NestedEditor extends LitElement {
             renderTable: (name, metadata, path) => new SimpleTable(metadata) // NOTE: Would be most ideal to have a reference to the containing input...
         })
 
-        input.style.padding = '25px 50px'
+        container.style.padding = '25px'
+        container.append(input)
 
-        modal.append(input)
+        modal.append(container)
 
         modal.open = true
     }