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New Ephys Behavior (#586)
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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Cody Baker <[email protected]>
Co-authored-by: CodyCBakerPhD <[email protected]>
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@garrettmflynn @pre-commit-ci @CodyCBakerPhD
4 people authored Mar 13, 2024
1 parent 292ed83 commit 4dd13fc
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Showing 17 changed files with 802 additions and 381 deletions.
3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -36,3 +36,6 @@ src/build
.env
.env.local
.env.production

# Spyder
.spyproject/
353 changes: 289 additions & 64 deletions pyflask/manageNeuroconv/manage_neuroconv.py
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41 changes: 36 additions & 5 deletions schemas/base-metadata.schema.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@ import { header, replaceRefsWithValue } from '../src/renderer/src/stories/forms/

import baseMetadataSchema from './json/base_metadata_schema.json' assert { type: "json" }

const uvMathFormat = `&micro;V`; //`<math xmlns="http://www.w3.org/1998/Math/MathML"><mo>&micro;</mo><mi>V</mi></math>`

function getSpeciesNameComponents(arr: any[]) {
const split = arr[arr.length - 1].split(' - ')
return {
Expand All @@ -13,6 +15,7 @@ function getSpeciesNameComponents(arr: any[]) {
}



function getSpeciesInfo(species: any[][] = []) {


Expand All @@ -34,6 +37,10 @@ function getSpeciesInfo(species: any[][] = []) {

}

const propsToInclude = {
ecephys: ["Device", "ElectrodeGroup", "Electrodes", "ElectrodeColumns", "definitions"]
}

export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, global = false) => {


Expand Down Expand Up @@ -89,17 +96,40 @@ 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) {

// Change rendering order for electrode table columns
const electrodesProp = ecephys.properties["Electrodes"]
for (let name in electrodesProp.properties) {
const interfaceProps = electrodesProp.properties[name].properties
const electrodeItems = interfaceProps["Electrodes"].items.properties
const uvProperties = ["gain_to_uV", "offset_to_uV"]

uvProperties.forEach(prop => {
electrodeItems[prop] = {}
electrodeItems[prop].title = prop.replace('uV', uvMathFormat)
console.log(electrodeItems[prop])
})
interfaceProps["Electrodes"].items.order = ["channel_name", "group_name", "shank_electrode_number", ...uvProperties];
interfaceProps["ElectrodeColumns"].items.order = ["name", "description", "data_type"];

}

}

if (ophys) {

ophys.required = Object.keys(ophys.properties)

const getProp = (name: string) => ophys.properties[name]

if (getProp("TwoPhotonSeries")) {
const tpsItemSchema = getProp("TwoPhotonSeries").items
const tpsItemSchema = getProp("TwoPhotonSeries")?.items

if (tpsItemSchema) {

tpsItemSchema.order = [
"name",
"description",
Expand All @@ -111,8 +141,9 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
}


if (getProp("ImagingPlane")) {
const imagingPlaneItems = getProp("ImagingPlane").items
const imagingPlaneItems = getProp("ImagingPlane")?.items

if (imagingPlaneItems) {
imagingPlaneItems.order = [
"name",
"description",
Expand Down
1 change: 0 additions & 1 deletion src/renderer/src/pages.js
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ import { GuidedSubjectsPage } from "./stories/pages/guided-mode/setup/GuidedSubj
import { GuidedSourceDataPage } from "./stories/pages/guided-mode/data/GuidedSourceData";
import { GuidedMetadataPage } from "./stories/pages/guided-mode/data/GuidedMetadata";
import { GuidedUploadPage } from "./stories/pages/guided-mode/options/GuidedUpload";
// import { GuidedConversionOptionsPage } from "./stories/pages/guided-mode/options/GuidedConversionOptions";
import { GuidedResultsPage } from "./stories/pages/guided-mode/results/GuidedResults";
import { Dashboard } from "./stories/Dashboard";
import { GuidedStubPreviewPage } from "./stories/pages/guided-mode/options/GuidedStubPreview";
Expand Down
126 changes: 87 additions & 39 deletions src/renderer/src/stories/BasicTable.js
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Original file line number Diff line number Diff line change
@@ -1,14 +1,15 @@
import { LitElement, css, html } from "lit";
import { LitElement, css, html, unsafeCSS } from "lit";
import { styleMap } from "lit/directives/style-map.js";
import { header } from "./forms/utils";
import { checkStatus } from "../validation";
import { errorHue, warningHue } from "./globals";
import { emojiFontFamily, errorHue, warningHue } from "./globals";

import * as promises from "../promises";

import "./Button";
import { sortTable } from "./Table";
import tippy from "tippy.js";
import { getIgnore } from "./JSONSchemaForm";

export class BasicTable extends LitElement {
static get styles() {
Expand Down Expand Up @@ -65,6 +66,12 @@ export class BasicTable extends LitElement {
user-select: none;
}
.relative .info {
margin: 0px 5px;
font-size: 80%;
font-family: ${unsafeCSS(emojiFontFamily)};
}
th span {
display: inline-block;
}
Expand Down Expand Up @@ -115,6 +122,7 @@ export class BasicTable extends LitElement {
validateOnChange,
onStatusChange,
onLoaded,
onUpdate,
} = {}) {
super();
this.name = name ?? "data_table";
Expand All @@ -127,6 +135,7 @@ export class BasicTable extends LitElement {
this.ignore = ignore ?? {};

if (validateOnChange) this.validateOnChange = validateOnChange;
if (onUpdate) this.onUpdate = onUpdate;
if (onStatusChange) this.onStatusChange = onStatusChange;
if (onLoaded) this.onLoaded = onLoaded;
}
Expand Down Expand Up @@ -158,9 +167,29 @@ export class BasicTable extends LitElement {
return html`<div class="relative"><span>${header(str)}</span></div>`;
};

#renderHeader = (str, { description }) => {
if (description) return html`<th title="${description}">${this.#renderHeaderContent(str)}</th>`;
return html`<th>${this.#renderHeaderContent(str)}</th>`;
#renderHeader = (prop, { description, title = prop } = {}) => {
const th = document.createElement("th");

const required = this.#itemSchema.required ? this.#itemSchema.required.includes(prop) : false;
const container = document.createElement("div");
container.classList.add("relative");
const span = document.createElement("span");
span.innerHTML = header(title);
if (required) span.setAttribute("required", "");
container.appendChild(span);

// Add Description Tooltip
if (description) {
const span = document.createElement("span");
span.classList.add("info");
span.innerText = "ℹ️";
container.append(span);
tippy(span, { content: `${description[0].toUpperCase() + description.slice(1)}`, allowHTML: true });
}

th.appendChild(container);

return th;
};

#getRowData(row, cols = this.colHeaders) {
Expand All @@ -169,13 +198,12 @@ export class BasicTable extends LitElement {
let value;
if (col === this.keyColumn) {
if (hasRow) value = row;
else return "";
else return;
} else
value =
(hasRow ? this.data[row][col] : undefined) ??
// this.globals[col] ??
this.#itemSchema.properties[col].default ??
"";
this.#itemSchema.properties[col]?.default;
return value;
});
}
Expand Down Expand Up @@ -210,43 +238,52 @@ export class BasicTable extends LitElement {
onStatusChange = () => {};
onLoaded = () => {};

#validateCell = (value, col, parent) => {
#getType = (value, { type, data_type } = {}) => {
let inferred = typeof value;
if (Array.isArray(value)) inferred = "array";
if (value == undefined) inferred = "null";

const original = type || data_type;
let resolved = original;

// Handle based on JSON Schema types
if (type) {
if (resolved === "integer") resolved = "number"; // Map to javascript type
} else if (data_type) {
if (resolved.includes("array")) resolved = "array";
if (resolved.includes("int") || resolved.includes("float")) resolved = "number";
if (resolved.startsWith("bool")) resolved = "boolean";
if (resolved.startsWith("str")) resolved = "string";
}

return {
type: resolved,
original,
inferred,
};
};

#validateCell = (value, col, row, parent) => {
if (!value && !this.validateEmptyCells) return true; // Empty cells are valid
if (!this.validateOnChange) return true;

let result;

const propInfo = this.#itemProps[col] ?? {};
let thisTypeOf = typeof value;
let ogType;
let type = (ogType = propInfo.type || propInfo.data_type);

// Handle based on JSON Schema types
if ("type" in propInfo) {
// Map to javascript type
if (type === "integer") type = "number";

// Convert to json schema type
if (Array.isArray(value)) thisTypeOf = "array";
if (value == undefined) thisTypeOf = "null";
} else if ("data_type" in propInfo) {
if (type.includes("array")) type = "array";
if (type.includes("int") || type.includes("float")) type = "number";
if (type.startsWith("bool")) type = "boolean";
if (type.startsWith("str")) type = "string";
}
let { type, original, inferred } = this.#getType(value, propInfo);

// Check if required
if (!value && "required" in this.#itemSchema.required.includes(col))
if (!value && "required" in this.#itemSchema && this.#itemSchema.required.includes(col))
result = [{ message: `${col} is a required property`, type: "error" }];
// If not required, check matching types for values that are defined
else if (value !== "" && thisTypeOf !== type)
result = [{ message: `${col} is expected to be of type ${ogType}, not ${thisTypeOf}`, type: "error" }];
// If not required, check matching types (if provided) for values that are defined
else if (value !== "" && type && inferred !== type)
result = [{ message: `${col} is expected to be of type ${original}, not ${inferred}`, type: "error" }];
// Otherwise validate using the specified onChange function
else result = this.validateOnChange(col, parent, value, this.#itemProps[col]);
else result = this.validateOnChange([row, col], parent, value, this.#itemProps[col]);

// Will run synchronously if not a promise result
return promises.resolve(result, () => {
return promises.resolve(result, (result) => {
let info = {
title: undefined,
warning: undefined,
Expand Down Expand Up @@ -277,7 +314,7 @@ export class BasicTable extends LitElement {

const results = this.#data.map((v, i) => {
return v.map((vv, j) => {
const info = this.#validateCell(vv, this.colHeaders[j], { ...this.data[rows[i]] }); // Could be a promise or a basic response
const info = this.#validateCell(vv, this.colHeaders[j], i, { ...this.data[rows[i]] }); // Could be a promise or a basic response
return promises.resolve(info, (info) => {
if (info === true) return;
const td = this.shadowRoot.getElementById(`i${i}_j${j}`);
Expand Down Expand Up @@ -336,7 +373,7 @@ export class BasicTable extends LitElement {
let data = text.split("\n").map((row) =>
row.split("\t").map((v) => {
try {
return JSON.parse(v);
return eval(v);
} catch {
return v.trim();
}
Expand All @@ -356,19 +393,24 @@ export class BasicTable extends LitElement {
Object.keys(data).forEach((row) => {
const cols = structuredData[row];
const latest = (this.data[this.keyColumn ? cols[this.keyColumn] : row] = {});
Object.entries(cols).forEach(([key, value]) => (key in this.#itemProps ? (latest[key] = value) : "")); // Only include data from schema
Object.entries(cols).forEach(([key, value]) => {
if (key in this.#itemProps) {
const { type } = this.#getType(value, this.#itemProps[key]);
if (type === "string") value = `${value}`; // Convert to string if necessary
latest[key] = value;
}
}); // Only include data from schema
});

this.onUpdate(null, null, value); // Update the whole table
if (this.onUpdate) this.onUpdate([], data); // Update the whole table
}

// Render Code
render() {
this.#updateRendered();

this.schema = this.schema; // Always update the schema
const entries = this.#itemProps;
for (let key in this.ignore) delete entries[key];
for (let key in this.ignore["*"] ?? {}) delete entries[key];

// Add existing additional properties to the entries variable if necessary
if (this.#itemSchema.additionalProperties) {
Expand All @@ -384,6 +426,10 @@ export class BasicTable extends LitElement {
}, entries);
}

// Ignore any additions in the ignore configuration
for (let key in this.ignore) delete entries[key];
for (let key in this.ignore["*"] ?? {}) delete entries[key];

// Sort Columns by Key Column and Requirement
const keys =
(this.#keys =
Expand Down Expand Up @@ -418,7 +464,9 @@ export class BasicTable extends LitElement {
${data.map(
(row, i) =>
html`<tr>
${row.map((col, j) => html`<td id="i${i}_j${j}"><div>${col}</div></td>`)}
${row.map(
(col, j) => html`<td id="i${i}_j${j}"><div>${JSON.stringify(col)}</div></td>`
)}
</tr>`
)}
</tbody>
Expand Down
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