Merge pull request #483 from NeurodataWithoutBorders/global-metadata-…

…on-demand

Global metadata on demand

schemas/base-metadata.schema.ts

@@ -11,4 +11,31 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
 
 }
 
+
+export const instanceSpecificFields = {
+    Subject: ["weight", "subject_id", "age", "date_of_birth", "age__reference"],
+    NWBFile: [
+        "session_id",
+        "session_start_time",
+        "identifier",
+        "data_collection",
+        "notes",
+        "pharmacolocy",
+        "session_description",
+        "slices",
+        "source_script",
+        "source_script_file_name",
+    ],
+};
+
+
+const globalSchema = structuredClone(preprocessMetadataSchema());
+Object.entries(globalSchema.properties).forEach(([globalProp, schema]) => {
+    instanceSpecificFields[globalProp]?.forEach((prop) =>  delete schema.properties[prop]);
+});
+
+export {
+    globalSchema
+}
+
 export default preprocessMetadataSchema()

schemas/json/base_metadata_schema.json

@@ -1,8 +1,6 @@
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
   "$id": "base_metafile.schema.json",
-  "title": "Base schema for the metafile",
-  "description": "Base schema for the metafile",
   "version": "0.1.0",
   "type": "object",
   "required": ["NWBFile"],

src/renderer/src/stories/BasicTable.js

@@ -154,7 +154,7 @@ export class BasicTable extends LitElement {
             } else
                 value =
                     (hasRow ? this.data[row][col] : undefined) ??
-                    // this.template[col] ??
+                    // this.globals[col] ??
                     this.schema.properties[col].default ??
                     "";
             return value;

src/renderer/src/stories/JSONSchemaForm.js

@@ -117,10 +117,12 @@ hr {
   .required label:after {
     content: " *";
     color: #ff0033;
+
   }
 
-  :host([requirementmode="loose"]) .required label:after {
+  :host(:not([validateemptyvalues])) .required label:after {
     color: gray;
+
   }
 
 
@@ -163,7 +165,8 @@ export class JSONSchemaForm extends LitElement {
             required: { type: Object, reflect: false },
             dialogType: { type: String, reflect: false },
             dialogOptions: { type: Object, reflect: false },
-            requirementMode: { type: String, reflect: true },
+            globals: { type: Object, reflect: false },
+            validateEmptyValues: { type: Boolean, reflect: true },
         };
     }
 
@@ -184,6 +187,8 @@ export class JSONSchemaForm extends LitElement {
 
     resolved = {}; // Keep track of actual resolved values—not just what the user provides as results
 
+    states = {};
+
     constructor(props = {}) {
         super();
 
@@ -195,6 +200,8 @@ export class JSONSchemaForm extends LitElement {
         this.results = (props.base ? structuredClone(props.results) : props.results) ?? {}; // Deep clone results in nested forms
         this.globals = props.globals ?? {};
 
+        this.states = props.states ?? {}; // Accordion and other states
+
         this.ignore = props.ignore ?? [];
         this.required = props.required ?? {};
         this.dialogOptions = props.dialogOptions;
@@ -203,7 +210,6 @@ export class JSONSchemaForm extends LitElement {
 
         this.emptyMessage = props.emptyMessage ?? "No properties to render";
 
-        this.requirementMode = props.requirementMode ?? "default";
         this.onlyRequired = props.onlyRequired ?? false;
         this.showLevelOverride = props.showLevelOverride ?? false;
 
@@ -219,6 +225,7 @@ export class JSONSchemaForm extends LitElement {
         if (props.onLoaded) this.onLoaded = props.onLoaded;
         if (props.onUpdate) this.onUpdate = props.onUpdate;
         if (props.renderTable) this.renderTable = props.renderTable;
+        if (props.onOverride) this.onOverride = props.onOverride;
 
         if (props.onStatusChange) this.onStatusChange = props.onStatusChange;
 
@@ -258,6 +265,12 @@ export class JSONSchemaForm extends LitElement {
         if (changedProperties === "options") this.requestUpdate();
     }
 
+    getGlobalValue(path) {
+        if (typeof path === "string") path = path.split(".");
+        const resolved = this.#get(path, this.globals);
+        return resolved;
+    }
+
     // Track resolved values for the form (data only)
     updateData(localPath, value) {
         const path = [...localPath];
@@ -269,12 +282,25 @@ export class JSONSchemaForm extends LitElement {
         const resolvedParent = path.reduce(reducer, this.resolved);
         const hasUpdate = resolvedParent[name] !== value;
 
+        const globalValue = this.getGlobalValue(localPath);
+
         // NOTE: Forms with nested forms will handle their own state updates
-        if (!value) {
-            delete resultParent[name];
-            delete resolvedParent[name];
+        if (this.isUndefined(value)) {
+            const globalValue = this.getGlobalValue(localPath);
+
+            // Continue to resolve and re-render...
+            if (globalValue) {
+                value = resolvedParent[name] = globalValue;
+                const input = this.getInput(localPath);
+                if (input) {
+                    input.updateData(globalValue);
+                    this.onOverride(name, globalValue, path);
+                }
+            } else resolvedParent[name] = undefined;
+
+            resultParent[name] = undefined; // NOTE: Will be removed when stringified
         } else {
-            resultParent[name] = value;
+            resultParent[name] = value === globalValue ? undefined : value; // Retain association with global value
             resolvedParent[name] = value;
         }
 
@@ -317,7 +343,7 @@ export class JSONSchemaForm extends LitElement {
     validate = async (resolved) => {
         // Check if any required inputs are missing
         const requiredButNotSpecified = await this.#validateRequirements(resolved); // get missing required paths
-        const isValid = this.requirementMode === "loose" ? true : !requiredButNotSpecified.length;
+        const isValid = !requiredButNotSpecified.length;
 
         // Print out a detailed error message if any inputs are missing
         let message = isValid ? "" : `${requiredButNotSpecified.length} required inputs are not specified properly.`;
@@ -366,7 +392,10 @@ export class JSONSchemaForm extends LitElement {
 
     #get = (path, object = this.resolved, omitted = []) => {
         // path = path.slice(this.base.length); // Correct for base path
-        return path.reduce((acc, curr) => (acc = acc[curr] ?? acc?.[omitted.find((str) => acc[str])]?.[curr]), object);
+        return path.reduce(
+            (acc, curr) => (acc = acc?.[curr] ?? acc?.[omitted.find((str) => acc[str])]?.[curr]),
+            object
+        );
     };
 
     #checkRequiredAfterChange = async (localPath) => {
@@ -482,7 +511,7 @@ export class JSONSchemaForm extends LitElement {
 
                 if (typeof isRequired === "object" && !Array.isArray(isRequired))
                     invalid.push(...(await this.#validateRequirements(resolved[name], isRequired, path)));
-                else if (!resolved[name]) invalid.push(path);
+                else if (this.isUndefined(resolved[name]) && this.validateEmptyValues) invalid.push(path);
             }
         }
 
@@ -493,14 +522,15 @@ export class JSONSchemaForm extends LitElement {
     onInvalid = () => {};
     onLoaded = () => {};
     onUpdate = () => {};
+    onOverride = () => {};
 
-    #deleteExtraneousResults = (results, schema) => {
-        for (let name in results) {
-            if (!schema.properties || !(name in schema.properties)) delete results[name];
-            else if (results[name] && typeof results[name] === "object" && !Array.isArray(results[name]))
-                this.#deleteExtraneousResults(results[name], schema.properties[name]);
-        }
-    };
+    // #deleteExtraneousResults = (results, schema) => {
+    //     for (let name in results) {
+    //         if (!schema.properties || !(name in schema.properties)) delete results[name];
+    //         else if (results[name] && typeof results[name] === "object" && !Array.isArray(results[name]))
+    //             this.#deleteExtraneousResults(results[name], schema.properties[name]);
+    //     }
+    // };
 
     #getRenderable = (schema = {}, required, path, recursive = false) => {
         const entries = Object.entries(schema.properties ?? {});
@@ -594,21 +624,26 @@ export class JSONSchemaForm extends LitElement {
         return this.shadowRoot.querySelector(`[data-name="${link.name}"]`);
     };
 
+    isUndefined(value) {
+        return value === undefined || value === "";
+    }
+
     // Assume this is going to return as a Promise—even if the change function isn't returning one
     triggerValidation = async (name, path = [], checkLinks = true) => {
         const parent = this.#get(path, this.resolved);
 
         const pathToValidate = [...(this.base ?? []), ...path];
 
         const valid =
-            !this.validateEmptyValues && !(name in parent)
+            !this.validateEmptyValues && parent[name] === undefined
                 ? true
                 : await this.validateOnChange(name, parent, pathToValidate);
 
         const localPath = [...path, name]; // Use basePath to augment the validation
         const externalPath = [...this.base, name];
 
         const isRequired = this.#isRequired(localPath);
+
         let warnings = Array.isArray(valid)
             ? valid.filter((info) => info.type === "warning" && (!isRequired || !info.missing))
             : [];
@@ -635,15 +670,22 @@ export class JSONSchemaForm extends LitElement {
             }
         } else {
             // For non-links, throw a basic requirement error if the property is required
-            if (!errors.length && isRequired && !parent[name]) {
-                // Skip simple required checks in loose mode
-                if (this.requirementMode !== "loose") {
-                    const schema = this.getSchema(localPath);
+            if (!errors.length && isRequired && this.isUndefined(parent[name])) {
+                const schema = this.getSchema(localPath);
+
+                // Throw at least a basic warning if the property is required and missing
+                if (this.validateEmptyValues) {
                     errors.push({
                         message: `${schema.title ?? header(name)} is a required property.`,
                         type: "error",
                         missing: true,
-                    }); // Throw at least a basic error if the property is required
+                    });
+                } else {
+                    warnings.push({
+                        message: `${schema.title ?? header(name)} is a suggested property.`,
+                        type: "warning",
+                        missing: true,
+                    });
                 }
             }
         }
@@ -805,6 +847,8 @@ export class JSONSchemaForm extends LitElement {
                     results: { ...results[name] },
                     globals: this.globals?.[name],
 
+                    states: this.states,
+
                     mode: this.mode,
 
                     onUpdate: (internalPath, value) => {
@@ -833,15 +877,19 @@ export class JSONSchemaForm extends LitElement {
                         this.checkAllLoaded();
                     },
                     renderTable: (...args) => this.renderTable(...args),
+                    onOverride: (...args) => this.onOverride(...args),
                     base: [...this.base, ...localPath],
                 });
 
+                if (!this.states[headerName]) this.states[headerName] = {};
+                this.states[headerName].subtitle = `${
+                    this.#getRenderable(info, required[name], localPath, true).length
+                } fields`;
+                this.states[headerName].content = this.#nestedForms[name];
+
                 const accordion = new Accordion({
                     sections: {
-                        [headerName]: {
-                            subtitle: `${this.#getRenderable(info, required[name], localPath, true).length} fields`,
-                            content: this.#nestedForms[name],
-                        },
+                        [headerName]: this.states[headerName],
                     },
                 });
 

src/renderer/src/stories/JSONSchemaInput.js

@@ -121,6 +121,12 @@ export class JSONSchemaInput extends LitElement {
 
         const el = this.getElement();
         if (el.type === "checkbox") el.checked = value;
+        else if (el.classList.contains("list"))
+            el.children[0].items = value
+                ? value.map((value) => {
+                      return { value };
+                  })
+                : [];
         else el.value = value;
 
         return true;
@@ -311,7 +317,7 @@ export class JSONSchemaInput extends LitElement {
             });
 
             return html`
-                <div class="schema-input" @change=${() => validateOnChange && this.#triggerValidation(name, path)}>
+                <div class="schema-input list" @change=${() => validateOnChange && this.#triggerValidation(name, path)}>
                     ${list} ${addButton}
                 </div>
             `;

src/renderer/src/stories/SimpleTable.js

@@ -163,7 +163,7 @@ export class SimpleTable extends LitElement {
     constructor({
         schema,
         data,
-        template,
+        globals,
         keyColumn,
         validateOnChange,
         validateEmptyCells,
@@ -178,7 +178,7 @@ export class SimpleTable extends LitElement {
         this.schema = schema ?? {};
         this.data = data ?? [];
         this.keyColumn = keyColumn;
-        this.template = template ?? {};
+        this.globals = globals ?? {};
         this.validateEmptyCells = validateEmptyCells ?? true;
         this.deferLoading = deferLoading ?? false;
         this.maxHeight = maxHeight ?? "";
@@ -334,7 +334,7 @@ export class SimpleTable extends LitElement {
             } else
                 value =
                     (hasRow ? this.data[row][col] : undefined) ??
-                    this.template[col] ??
+                    this.globals[col] ??
                     this.schema.properties[col].default ??
                     "";
             return value;
@@ -631,7 +631,7 @@ export class SimpleTable extends LitElement {
         }
         // Update data on passed object
         else {
-            if (value == undefined || value === "") delete target[rowName][header];
+            if (value == undefined || value === "") target[rowName][header] = undefined;
             else target[rowName][header] = value;
         }