Ephys Metadata

pyflask/manageNeuroconv/manage_neuroconv.py

@@ -246,6 +246,7 @@ def is_supported_recording_interface(recording_interface, metadata):
 
     Alpha build release should therefore always return False for this.
     """
+
     return (
         recording_interface
         and recording_interface.get_electrode_table_json
@@ -266,40 +267,39 @@ def get_metadata_schema(source_data: Dict[str, dict], interfaces: dict) -> Dict[
     schema = converter.get_metadata_schema()
     metadata = converter.get_metadata()
 
-    # recording_interface = get_first_recording_interface(converter)
+    recording_interface = get_first_recording_interface(converter)
 
-    # if is_supported_recording_interface(recording_interface, metadata):
-    #     metadata["Ecephys"]["Electrodes"] = recording_interface.get_electrode_table_json()
+    if is_supported_recording_interface(recording_interface, metadata):
+        metadata["Ecephys"]["Electrodes"] = recording_interface.get_electrode_table_json()
 
-    #     # Get Electrode metadata
-    #     ecephys_properties = schema["properties"]["Ecephys"]["properties"]
-    #     original_electrodes_schema = ecephys_properties["Electrodes"]
+        # Get Electrode metadata
+        ecephys_properties = schema["properties"]["Ecephys"]["properties"]
+        original_electrodes_schema = ecephys_properties["Electrodes"]
 
-    #     new_electrodes_properties = {
-    #         properties["name"]: {key: value for key, value in properties.items() if key != "name"}
-    #         for properties in original_electrodes_schema["default"]
-    #     }
+        new_electrodes_properties = {
+            properties["name"]: {key: value for key, value in properties.items() if key != "name"}
+            for properties in original_electrodes_schema["default"]
+        }
 
-    #     ecephys_properties["Electrodes"] = {
-    #         "type": "array",
-    #         "minItems": 0,
-    #         "items": {
-    #             "type": "object",
-    #             "properties": new_electrodes_properties,
-    #             "additionalProperties": True,  # Allow for new columns
-    #         },
-    #     }
+        ecephys_properties["Electrodes"] = {
+            "type": "array",
+            "minItems": 0,
+            "items": {
+                "type": "object",
+                "properties": new_electrodes_properties,
+                "additionalProperties": True,  # Allow for new columns
+            },
+        }
 
-    #     metadata["Ecephys"]["ElectrodeColumns"] = original_electrodes_schema["default"]
-    #     defs = ecephys_properties["definitions"]
+        metadata["Ecephys"]["ElectrodeColumns"] = original_electrodes_schema["default"]
+        defs = ecephys_properties["definitions"]
 
-    #     ecephys_properties["ElectrodeColumns"] = {"type": "array", "items": defs["Electrodes"]}
-    #     ecephys_properties["ElectrodeColumns"]["items"]["required"] = list(defs["Electrodes"]["properties"].keys())
-    #     del defs["Electrodes"]
+        ecephys_properties["ElectrodeColumns"] = {"type": "array", "items": defs["Electrodes"]}
+        ecephys_properties["ElectrodeColumns"]["items"]["required"] = list(defs["Electrodes"]["properties"].keys())
+        del defs["Electrodes"]
 
-    # # Delete Ecephys metadata if ElectrodeTable helper function is not available
-    # else:
-    if "Ecephys" in schema["properties"]:
+    # Delete Ecephys metadata if ElectrodeTable helper function is not available
+    elif "Ecephys" in schema["properties"]:
         schema["properties"].pop("Ecephys", dict())
 
     return json.loads(json.dumps(replace_nan_with_none(dict(results=metadata, schema=schema)), cls=NWBMetaDataEncoder))
@@ -451,29 +451,30 @@ def update_conversion_progress(**kwargs):
         else None
     )
 
-    # Update the first recording interface with Ecephys table data
-    # This will be refactored after the ndx-probe-interface integration
-    # recording_interface = get_first_recording_interface(converter)
-
     if "Ecephys" not in info["metadata"]:
         info["metadata"].update(Ecephys=dict())
 
-    resolved_metadata = replace_none_with_nan(
-        info["metadata"], resolve_references(converter.get_metadata_schema())
-    )  # Ensure Ophys NaN values are resolved
+    # Ensure Ophys NaN values are resolved
+    resolved_metadata = replace_none_with_nan(info["metadata"], resolve_references(converter.get_metadata_schema()))
 
-    # if is_supported_recording_interface(recording_interface, info["metadata"]):
-    #     electrode_column_results = ecephys_metadata["ElectrodeColumns"]
-    #     electrode_results = ecephys_metadata["Electrodes"]
+    # Update the first recording interface with Ecephys table data
+    # NOTE: This will be refactored after the ndx-probe-interface integration
+    recording_interface = get_first_recording_interface(converter)
+
+    ecephys_metadata = resolved_metadata["Ecephys"]
 
-    #     recording_interface.update_electrode_table(
-    #         electrode_table_json=electrode_results, electrode_column_info=electrode_column_results
-    #     )
+    if is_supported_recording_interface(recording_interface, info["metadata"]):
+        electrode_column_results = ecephys_metadata["ElectrodeColumns"]
+        electrode_results = ecephys_metadata["Electrodes"]
+
+        recording_interface.update_electrode_table(
+            electrode_table_json=electrode_results, electrode_column_info=electrode_column_results
+        )
 
-    #     # Update with the latest metadata for the electrodes
-    #     ecephys_metadata["Electrodes"] = electrode_column_results
+        # Update with the latest metadata for the electrodes
+        ecephys_metadata["Electrodes"] = electrode_column_results
 
-    # ecephys_metadata.pop("ElectrodeColumns", dict())
+    ecephys_metadata.pop("ElectrodeColumns", dict())
 
     # Actually run the conversion
     converter.run_conversion(

schemas/base-metadata.schema.ts

@@ -4,6 +4,11 @@ import { header, replaceRefsWithValue } from '../src/renderer/src/stories/forms/
 
 import baseMetadataSchema from './json/base_metadata_schema.json' assert { type: "json" }
 
+const propsToInclude = {
+    ecephys: ["Device", "ElectrodeGroup", "Electrodes", "ElectrodeColumns", "definitions"]
+}
+
+
 function getSpeciesNameComponents(arr: any[]) {
     const split = arr[arr.length - 1].split(' - ')
     return {
@@ -41,8 +46,6 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
 
     copy.additionalProperties = false
 
-
-
     copy.required = Object.keys(copy.properties) // Require all properties at the top level
 
     copy.order = [ "NWBFile", "Subject" ]
@@ -89,9 +92,18 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
     // Override description of keywords
     nwbProps.keywords.description = 'Terms to describe your dataset (e.g. Neural circuits, V1, etc.)' // Add description to keywords
 
-
+    const ecephys = copy.properties.Ecephys
     const ophys = copy.properties.Ophys
 
+    if (ecephys) {
+        // Only include a select group of Ecephys metadata here
+        const ecephysProps = ecephys.properties;
+        Object.keys(ecephysProps).forEach((k) => (!propsToInclude.ecephys.includes(k) ? delete ecephysProps[k] : ""));
+
+        // Change rendering order for electrode table columns
+        ecephysProps["Electrodes"].items.order = ["channel_name", "group_name", "shank_electrode_number"];
+    }
+
     if (ophys) {
 
         ophys.required = Object.keys(ophys.properties)

src/renderer/src/stories/BasicTable.js

@@ -234,7 +234,7 @@ export class BasicTable extends LitElement {
             if (type.includes("int") || type.includes("float")) type = "number";
             if (type.startsWith("bool")) type = "boolean";
             if (type.startsWith("str")) type = "string";
-        }
+        } else type = "string"; // Default to string type
 
         // Check if required
         if (!value && "required" in this.#itemSchema.required.includes(col))
@@ -367,6 +367,7 @@ export class BasicTable extends LitElement {
         this.#updateRendered();
 
         const entries = this.#itemProps;
+
         for (let key in this.ignore) delete entries[key];
         for (let key in this.ignore["*"] ?? {}) delete entries[key];
 

src/renderer/src/stories/JSONSchemaForm.js

@@ -1275,7 +1275,6 @@ export class JSONSchemaForm extends LitElement {
                 results,
                 additionalPropPattern
             );
-
             return [...rendered, additionalElement];
         }
 

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

@@ -236,6 +236,8 @@ export class GuidedMetadataPage extends ManagedPage {
                 // JSON Schema Exceptions
                 if (error.message.includes('does not conform to the "date-time" format.')) return false;
                 if (error.message.includes('not allowed to have the additional property "Ecephys".')) return false; // NOTE: Remove after including Ecephys metadata
+                if (error.message.includes('not allowed to have the additional property "ElectricalSeriesAP'))
+                    return false; // NOTE: Remove after including Icephys metadata
             },
 
             groups: [

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

@@ -124,15 +124,9 @@ export class GuidedSourceDataPage extends ManagedPage {
 
                     const { results: metadata, schema } = result;
 
-                    // Always delete Ecephys if absent ( NOTE: temporarily manually removing from schema on backend...)
-                    const alwaysDelete = ["Ecephys"];
-                    alwaysDelete.forEach((k) => {
-                        if (!metadata[k]) delete info.metadata[k]; // Delete directly on metadata
-                    });
-
-                    for (let key in info.metadata) {
-                        if (!alwaysDelete.includes(key) && !(key in schema.properties)) metadata[key] = undefined;
-                    }
+                    // for (let key in info.metadata) {
+                    //     if (!alwaysDelete.includes(key) && !(key in schema.properties)) metadata[key] = undefined;
+                    // }
 
                     // Merge metadata results with the generated info
                     merge(metadata, info.metadata);

src/renderer/src/stories/pages/guided-mode/storyStates.ts

@@ -1,5 +1,5 @@
 import nwbBaseSchema from "../../../../../../schemas/base-metadata.schema";
-// import exephysExampleSchema from "../../../../../../schemas/json/ecephys_metadata_schema_example.json";
+import exephysExampleSchema from "../../../../../../schemas/json/ecephys_metadata_schema_example.json";
 
 import { dashboard } from "../../../pages.js";
 import { activateServer } from "../../../server/globals";
@@ -12,7 +12,7 @@ export const PageTemplate = (args = {}) => {
 };
 
 
-// nwbBaseSchema.properties.Ecephys = exephysExampleSchema;
+nwbBaseSchema.properties.Ecephys = exephysExampleSchema;
 
 export const globalState = {
     project: {

src/renderer/src/stories/table/Cell.ts

@@ -110,7 +110,7 @@ export class TableCell extends LitElement {
     }
 
     set value(value) {
-        if (!value) value = []
+        // if (!value) value = []
 
         if (this.input) this.input.set(renderValue(value, this.schema)) // Allow null to be set directly
         this.#value = this.input

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

@@ -235,14 +235,12 @@ export class TableCellBase extends LitElement {
         const editor = this.#editor = this.#render('editor')
         const renderer = this.#renderer = this.#render('renderer')
 
-
         this.addEventListener('blur', (ev) => {
             ev.stopPropagation()
             this.toggle(false)
         })
 
 
-
         if (!editor || !renderer || renderer === editor) return editor || renderer
 
         return html`<div class="renderer">${renderer}</div><div id="editor">${editor}</div>`

src/renderer/src/stories/table/convert.ts

@@ -1,5 +1,4 @@
 export const renderValue = (value: any, schema: any) => {
-
     if (schema.type === 'number' || schema.type === 'integer') {
         if (value === null) return ''
     }

src/renderer/src/validation/index.js

@@ -13,7 +13,8 @@ export async function validateOnChange(name, parent, path, value) {
     let functions = [];
 
     const fullPath = [...path, name];
-    const toIterate = fullPath; //fullPathNoRows // fullPath
+
+    const toIterate = fullPath;
 
     const copy = { ...parent }; // Validate on a copy of the parent
     if (arguments.length > 3) copy[name] = value; // Update value on copy
@@ -37,6 +38,7 @@ export async function validateOnChange(name, parent, path, value) {
                 // Otherwise set the last wildcard
                 else {
                     lastWildcard = typeof acc["*"] === "string" ? acc["*"].replace(`{*}`, `${name}`) : acc["*"];
+
                     overridden = false; // Re-enable if a new one is specified below
                 }
             } else if (lastWildcard && typeof lastWildcard === "object") {