diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py
index 27727640b..890ddefa4 100644
--- a/pyflask/manageNeuroconv/manage_neuroconv.py
+++ b/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(
diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 7fea3bd08..a82a1adba 100644
--- a/schemas/base-metadata.schema.ts
+++ b/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)
diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index c56e8329e..801f75d90 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/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];
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index c7e4d865f..77239650a 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -1275,7 +1275,6 @@ export class JSONSchemaForm extends LitElement {
results,
additionalPropPattern
);
-
return [...rendered, additionalElement];
}
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
index dbec3445f..be24f28a1 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/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: [
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
index fee0343cf..56c389e33 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/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);
diff --git a/src/renderer/src/stories/pages/guided-mode/storyStates.ts b/src/renderer/src/stories/pages/guided-mode/storyStates.ts
index 211ee2c5c..76ba4afbd 100644
--- a/src/renderer/src/stories/pages/guided-mode/storyStates.ts
+++ b/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: {
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 86fe647a1..491deb29a 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/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
diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index 1dca267cb..57f244d26 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/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`${renderer}
${editor}
`
diff --git a/src/renderer/src/stories/table/convert.ts b/src/renderer/src/stories/table/convert.ts
index cef7a43a4..b046b8410 100644
--- a/src/renderer/src/stories/table/convert.ts
+++ b/src/renderer/src/stories/table/convert.ts
@@ -1,5 +1,4 @@
export const renderValue = (value: any, schema: any) => {
-
if (schema.type === 'number' || schema.type === 'integer') {
if (value === null) return ''
}
diff --git a/src/renderer/src/validation/index.js b/src/renderer/src/validation/index.js
index 524795f83..075599877 100644
--- a/src/renderer/src/validation/index.js
+++ b/src/renderer/src/validation/index.js
@@ -13,7 +13,8 @@ export async function validateOnChange(name, parent, path, value) {
let functions = [];
const fullPath = [...path, name];
- const toIterate = fullPath; //fullPathNoRows // fullPath
+
+ const toIterate = fullPath;
const copy = { ...parent }; // Validate on a copy of the parent
if (arguments.length > 3) copy[name] = value; // Update value on copy
@@ -37,6 +38,7 @@ export async function validateOnChange(name, parent, path, value) {
// Otherwise set the last wildcard
else {
lastWildcard = typeof acc["*"] === "string" ? acc["*"].replace(`{*}`, `${name}`) : acc["*"];
+
overridden = false; // Re-enable if a new one is specified below
}
} else if (lastWildcard && typeof lastWildcard === "object") {