Merge branch 'main' into fix-nested-form-cell-error-display

environments/environment-Linux.yml

@@ -9,16 +9,16 @@ dependencies:
   - numcodecs = 0.11.0
   # install these from conda-forge so that dependent packages get included in the distributable
   - jsonschema = 4.18.0  # installs jsonschema-specifications
-  - pydantic[email] = 1.10.12  # installs email-validator
   - pip
   - pip:
+      - pyinstaller-hooks-contrib == 2024.2  # Fix needed for pydantic v2; otherwise imports pydantic.compiled
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
-      - dandi >= 0.58.1
+      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@try_remove_packaing_bound#neuroconv[full]
+      - dandi >= 0.60.0
       - pytest == 7.4.0
       - pytest-cov == 4.1.0
       - scikit-learn == 1.4.0

environments/environment-MAC-arm64.yml

@@ -13,7 +13,6 @@ dependencies:
   - pytables = 3.8 # pypi build fails on arm64 so install from conda-forge (used by neuroconv deps)
   # install these from conda-forge so that dependent packages get included in the distributable
   - jsonschema = 4.18.0  # installs jsonschema-specifications
-  - pydantic[email] = 1.10.12  # installs email-validator
   - pip
   - pip:
       - chardet == 5.1.0
@@ -22,7 +21,7 @@ dependencies:
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
-      - dandi >= 0.58.1
+      - dandi >= 0.60.0
       - pytest == 7.4.0
       - pytest-cov == 4.1.0
       - scikit-learn == 1.4.0

environments/environment-MAC.yml

@@ -9,7 +9,6 @@ dependencies:
   - numcodecs = 0.11.0
   # install these from conda-forge so that dependent packages get included in the distributable
   - jsonschema = 4.18.0  # installs jsonschema-specifications
-  - pydantic[email] = 1.10.12  # installs email-validator
   - pip
   - pip:
       - chardet == 5.1.0
@@ -18,7 +17,7 @@ dependencies:
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
-      - dandi >= 0.58.1
+      - dandi >= 0.60.0
       - pytest == 7.4.0
       - pytest-cov == 4.1.0
       - scikit-learn == 1.4.0

environments/environment-Windows.yml

@@ -9,16 +9,16 @@ dependencies:
   - pywin32 = 303
   - git = 2.20.1
   - setuptools = 58.0.4
-  - pydantic[email] = 1.10.12 # installs email-validator
   - pip
   - pip:
+      - pyinstaller-hooks-contrib == 2024.2  # Fix needed for pydantic v2; otherwise imports pydantic.compiled
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
       - flask-cors === 3.0.10
       - flask_restx == 1.1.0
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
-      - dandi >= 0.58.1
+      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@try_remove_packaing_bound#neuroconv[full]
+      - dandi >= 0.60.0
       - pytest == 7.2.2
       - pytest-cov == 4.1.0
       - scikit-learn == 1.4.0

package.json

@@ -1,7 +1,7 @@
 {
   "name": "nwb-guide",
   "productName": "NWB GUIDE",
-  "version": "0.0.14",
+  "version": "0.0.15",
   "description": "NWB GUIDE is a desktop app that provides a no-code user interface for converting neurophysiology data to NWB.",
   "main": "./build/main/main.js",
   "engine": {

src/renderer/src/stories/JSONSchemaForm.js

@@ -21,6 +21,47 @@ const encode = (str) => {
     }
 };
 
+export const get = (path, object, omitted = [], skipped = []) => {
+    // path = path.slice(this.base.length); // Correct for base path
+    if (!path) throw new Error("Path not specified");
+    return path.reduce((acc, curr, i) => {
+        const tempAcc = acc?.[curr] ?? acc?.[omitted.find((str) => acc[str] && acc[str][curr])]?.[curr];
+        if (tempAcc) return tempAcc;
+        else {
+            const level1 = acc?.[skipped.find((str) => acc[str])];
+            if (level1) {
+                // Handle items-like objects
+                const result = get(path.slice(i), level1, omitted, skipped);
+                if (result) return result;
+
+                // Handle pattern properties objects
+                const got = Object.keys(level1).find((key) => {
+                    const result = get(path.slice(i + 1), level1[key], omitted, skipped);
+                    if (result && typeof result === "object") return result; // Schema are objects...
+                });
+
+                if (got) return level1[got];
+            }
+        }
+    }, object);
+};
+
+export const getSchema = (path, schema, base = []) => {
+    if (typeof path === "string") path = path.split(".");
+
+    // NOTE: Still must correct for the base here
+    if (base.length) {
+        const indexOf = path.indexOf(base.slice(-1)[0]);
+        if (indexOf !== -1) path = path.slice(indexOf + 1);
+    }
+
+    // NOTE: Refs are now pre-resolved
+    const resolved = get(path, schema, ["properties", "patternProperties"], ["patternProperties", "items"]);
+    // if (resolved?.["$ref"]) return this.getSchema(resolved["$ref"].split("/").slice(1)); // NOTE: This assumes reference to the root of the schema
+
+    return resolved;
+};
+
 const additionalPropPattern = "additional";
 
 const templateNaNMessage = `<br/><small>Type <b>NaN</b> to represent an unknown value.</small>`;
@@ -235,7 +276,7 @@ export class JSONSchemaForm extends LitElement {
 
         this.groups = props.groups ?? []; // NOTE: We assume properties only belong to one conditional requirement group
 
-        this.validateEmptyValues = props.validateEmptyValues ?? true;
+        this.validateEmptyValues = props.validateEmptyValues === undefined ? true : props.validateEmptyValues; // false = validate when not empty, true = always validate, null = never validate
 
         if (props.onInvalid) this.onInvalid = props.onInvalid;
         if (props.sort) this.sort = props.sort;
@@ -387,16 +428,16 @@ export class JSONSchemaForm extends LitElement {
 
                 const isRow = typeof rowName === "number";
 
-                const resolvedValue = e.path.reduce((acc, token) => acc[token], resolved);
+                const resolvedValue = e.instance; // Get offending value
+                const schema = e.schema; // Get offending schema
 
                 // ------------ Exclude Certain Errors ------------
-
                 // Allow for constructing types from object types
                 if (e.message.includes("is not of a type(s)") && "properties" in schema && schema.type === "string")
                     return;
 
                 // Ignore required errors if value is empty
-                if (e.name === "required" && !this.validateEmptyValues && !(e.property in e.instance)) return;
+                if (e.name === "required" && this.validateEmptyValues === null && !(e.property in e.instance)) return;
 
                 // Non-Strict Rule
                 if (schema.strict === false && e.message.includes("is not one of enum values")) return;
@@ -423,6 +464,8 @@ export class JSONSchemaForm extends LitElement {
     };
 
     validate = async (resolved = this.resolved) => {
+        if (this.validateEmptyValues === false) this.validateEmptyValues = true;
+
         // Validate against the entire JSON Schema
         const copy = structuredClone(resolved);
         delete copy.__disabled;
@@ -506,30 +549,7 @@ export class JSONSchemaForm extends LitElement {
         return true;
     };
 
-    #get = (path, object = this.resolved, omitted = [], skipped = []) => {
-        // path = path.slice(this.base.length); // Correct for base path
-        if (!path) throw new Error("Path not specified");
-        return path.reduce((acc, curr, i) => {
-            const tempAcc = acc?.[curr] ?? acc?.[omitted.find((str) => acc[str] && acc[str][curr])]?.[curr];
-            if (tempAcc) return tempAcc;
-            else {
-                const level1 = acc?.[skipped.find((str) => acc[str])];
-                if (level1) {
-                    // Handle items-like objects
-                    const result = this.#get(path.slice(i), level1, omitted, skipped);
-                    if (result) return result;
-
-                    // Handle pattern properties objects
-                    const got = Object.keys(level1).find((key) => {
-                        const result = this.#get(path.slice(i + 1), level1[key], omitted, skipped);
-                        if (result && typeof result === "object") return result; // Schema are objects...
-                    });
-
-                    if (got) return level1[got];
-                }
-            }
-        }, object);
-    };
+    #get = (path, object = this.resolved, omitted = [], skipped = []) => get(path, object, omitted, skipped);
 
     #checkRequiredAfterChange = async (localPath) => {
         const path = [...localPath];
@@ -550,22 +570,7 @@ export class JSONSchemaForm extends LitElement {
         return this.#schema;
     }
 
-    getSchema(path, schema = this.schema) {
-        if (typeof path === "string") path = path.split(".");
-
-        // NOTE: Still must correct for the base here
-        if (this.base.length) {
-            const base = this.base.slice(-1)[0];
-            const indexOf = path.indexOf(base);
-            if (indexOf !== -1) path = path.slice(indexOf + 1);
-        }
-
-        // NOTE: Refs are now pre-resolved
-        const resolved = this.#get(path, schema, ["properties", "patternProperties"], ["patternProperties", "items"]);
-        // if (resolved?.["$ref"]) return this.getSchema(resolved["$ref"].split("/").slice(1)); // NOTE: This assumes reference to the root of the schema
-
-        return resolved;
-    }
+    getSchema = (path, schema = this.schema) => getSchema(path, schema, this.base);
 
     #renderInteractiveElement = (name, info, required, path = [], value, propertyType) => {
         let isRequired = this.#isRequired([...path, name]);
@@ -653,7 +658,7 @@ export class JSONSchemaForm extends LitElement {
                 // if (typeof isRequired === "object" && !Array.isArray(isRequired))
                 //     invalid.push(...(await this.#validateRequirements(resolved[name], isRequired, path)));
                 // else
-                if (this.isUndefined(resolved[name]) && this.validateEmptyValues) invalid.push(path);
+                if (this.isUndefined(resolved[name]) && this.validateEmptyValues !== null) invalid.push(path);
             }
         }
 
@@ -875,7 +880,7 @@ export class JSONSchemaForm extends LitElement {
                             type: "error",
                             missing: true,
                         });
-                    } else {
+                    } else if (this.validateEmptyValues === null) {
                         warnings.push({
                             message: `${schema.title ?? header(name)} is a suggested property.`,
                             type: "warning",

src/renderer/src/stories/JSONSchemaInput.js

@@ -505,6 +505,7 @@ export class JSONSchemaInput extends LitElement {
     constructor(props) {
         super();
         Object.assign(this, props);
+        if (props.validateEmptyValue === false) this.validateEmptyValue = true; // False is treated as required but not triggered if empty
     }
 
     // onUpdate = () => {}

src/renderer/src/stories/Search.js

@@ -455,7 +455,8 @@ export class Search extends LitElement {
       }}
 
       @blur=${(blurEvent) => {
-          if (blurEvent.relatedTarget.classList.contains("option")) return;
+          const relatedTarget = blurEvent.relatedTarget;
+          if (relatedTarget && relatedTarget.classList.contains("option")) return;
           this.submit();
       }}
 

src/renderer/src/stories/forms/GlobalFormModal.ts

@@ -70,7 +70,7 @@ export function createFormModal ({
     else removeProperties(schemaCopy.properties, propsToRemove)
 
     const globalForm = new JSONSchemaForm({
-        validateEmptyValues: false,
+        validateEmptyValues: null,
         schema: schemaCopy,
         emptyMessage: "No properties to edit globally.",
         onThrow,

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

@@ -2,7 +2,7 @@ import { html } from "lit";
 import { Page } from "../../Page.js";
 
 // For Multi-Select Form
-import { JSONSchemaForm } from "../../../JSONSchemaForm.js";
+import { JSONSchemaForm, getSchema } from "../../../JSONSchemaForm.js";
 import { OptionalSection } from "../../../OptionalSection.js";
 import { run } from "../options/utils.js";
 import { onThrow } from "../../../../errors";
@@ -25,6 +25,13 @@ export async function autocompleteFormatString(path) {
 
     const { base_directory } = path.reduce((acc, key) => acc[key] ?? {}, this.form.resolved);
 
+    const schema = getSchema(path, this.info.globalState.schema.source_data);
+
+    const isFile = "file_path" in schema.properties;
+    const pathType = isFile ? "file" : "directory";
+
+    const description = isFile ? schema.properties.file_path.description : schema.properties.folder_path.description;
+
     const notify = (message, type) => {
         if (notification) this.dismiss(notification);
         return (notification = this.notify(message, type));
@@ -48,14 +55,15 @@ export async function autocompleteFormatString(path) {
 
     const propOrder = ["path", "subject_id", "session_id"];
     const form = new JSONSchemaForm({
+        validateEmptyValues: false,
         schema: {
             type: "object",
             properties: {
                 path: {
                     type: "string",
-                    title: "Example Filesystem Entry",
-                    format: ["file", "directory"],
-                    description: "Provide an example filesystem entry for the selected interface",
+                    title: `Example ${isFile ? "File" : "Folder"}`,
+                    format: pathType,
+                    description: description ?? `Provide an example ${pathType} for the selected interface`,
                 },
                 subject_id: {
                     type: "string",
@@ -73,6 +81,9 @@ export async function autocompleteFormatString(path) {
             const value = parent[name];
 
             if (name === "path") {
+                const toUpdate = ["subject_id", "session_id"];
+                toUpdate.forEach((key) => form.getFormElement([key]).requestUpdate());
+
                 if (value) {
                     if (fs.lstatSync(value).isSymbolicLink())
                         return [
@@ -122,7 +133,7 @@ export async function autocompleteFormatString(path) {
 
     return new Promise((resolve) => {
         const button = new Button({
-            label: "Create",
+            label: "Submit",
             primary: true,
             onClick: async () => {
                 await form.validate().catch((e) => {
@@ -432,7 +443,7 @@ export class GuidedPathExpansionPage extends Page {
         const form = (this.form = new JSONSchemaForm({
             ...structureState,
             onThrow,
-            validateEmptyValues: false,
+            validateEmptyValues: null,
 
             controls,
 

src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js

@@ -86,7 +86,7 @@ export class GuidedNewDatasetPage extends Page {
         this.form = new JSONSchemaForm({
             schema,
             results: this.state,
-            // validateEmptyValues: false,
+            // validateEmptyValues: null,
             dialogOptions: {
                 properties: ["createDirectory"],
             },

src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js

@@ -87,7 +87,7 @@ export class GuidedSubjectsPage extends Page {
         const modal = (this.#globalModal = createGlobalFormModal.call(this, {
             header: "Global Subject Metadata",
             key: "Subject",
-            validateEmptyValues: false,
+            validateEmptyValues: null,
             schema,
             formProps: {
                 validateOnChange: (localPath, parent, path) => {

src/renderer/src/stories/preview/inspector/InspectorList.js

@@ -76,7 +76,8 @@ export class InspectorListItem extends LitElement {
                 border-radius: 10px;
                 overflow: hidden;
                 text-wrap: wrap;
-                padding: 25px;
+                padding: 10px;
+                font-size: 12px;
                 margin: 0 0 1em;
             }