-
- ${this.controls.map(({ name, icon, primary, onClick }) => {
- return html` div:not([hidden])"
- );
- onClick.call(
- this,
- activeContentElement.getAttribute("data-instance"),
- activeContentElement
- );
- }}
- >${name} `;
- })}
-
+ ${this.#controls()}
diff --git a/src/electron/frontend/core/components/JSONSchemaForm.js b/src/electron/frontend/core/components/JSONSchemaForm.js
index 9c9572d3fb..075627d3ee 100644
--- a/src/electron/frontend/core/components/JSONSchemaForm.js
+++ b/src/electron/frontend/core/components/JSONSchemaForm.js
@@ -581,7 +581,8 @@ export class JSONSchemaForm extends LitElement {
const allErrors = flaggedInputs
.map((inputElement) => Array.from(inputElement.nextElementSibling.children).map((li) => li.message))
- .flat();
+ .flat()
+ .filter((v) => !!v);
const nMissingRequired = allErrors.reduce((acc, curr) => {
return (acc += curr.includes(this.#isARequiredPropertyString) ? 1 : 0);
diff --git a/src/electron/frontend/core/components/JSONSchemaInput.js b/src/electron/frontend/core/components/JSONSchemaInput.js
index 9e186fc381..0a3b150a57 100644
--- a/src/electron/frontend/core/components/JSONSchemaInput.js
+++ b/src/electron/frontend/core/components/JSONSchemaInput.js
@@ -501,6 +501,19 @@ export class JSONSchemaInput extends LitElement {
};
}
+ #description;
+ get description() {
+ return this.#description ?? this.schema.description;
+ }
+
+ set description(value) {
+ this.#description = value;
+
+ const descriptionEl = this.shadowRoot.querySelector(".guided--text-input-instructions");
+ if (!descriptionEl) return;
+ descriptionEl.innerHTML = value;
+ }
+
// Enforce dynamic required properties
attributeChangedCallback(key, _, latest) {
super.attributeChangedCallback(...arguments);
@@ -537,6 +550,7 @@ export class JSONSchemaInput extends LitElement {
controls = [];
// required;
validateOnChange = true;
+ allowNaN = true;
constructor(props = {}) {
super();
@@ -664,7 +678,11 @@ export class JSONSchemaInput extends LitElement {
>${(schema.title ? unsafeHTML(schema.title) : null) ?? header(this.path.slice(-1)[0])}`
: ""}
- ${input}${this.controls ? html`
+
+ ${input}${this.controls && this.controls.length
+ ? html`
${descriptionHTML}
`;
@@ -857,6 +875,17 @@ export class JSONSchemaInput extends LitElement {
#render() {
const { validateOnChange, schema, path: fullPath } = this;
+ // Resolve anyof inside the schema
+ const anyOf = schema.anyOf;
+ if (anyOf) {
+ delete schema.anyOf;
+ for (let key in anyOf[0]) {
+ schema[key] = anyOf[0][key];
+ }
+
+ // schema = {...schema, ...anyOf[0]}
+ }
+
this.removeAttribute("data-table");
// Do your best to fill in missing schema values
@@ -907,26 +936,53 @@ export class JSONSchemaInput extends LitElement {
return filesystemSelectorElement;
};
- // Transform to single item if maxItems is 1
- if (isArray && schema.maxItems === 1 && !isTable) {
- return new JSONSchemaInput({
- value: this.value?.[0],
- schema: {
- ...schema.items,
- strict: schema.strict,
- },
- path: fullPath,
- validateEmptyValue: this.validateEmptyValue,
- required: this.required,
- validateOnChange: () => (validateOnChange ? this.#triggerValidation(name, path) : ""),
- form: this.form,
- onUpdate: (value) => this.#updateData(fullPath, [value]),
+ // Transform to single item if maxItems is 1 OR the array has a fixed length
+ if (
+ isArray &&
+ (schema.maxItems === 1 || (schema.maxItems && schema.minItems && schema.maxItems === schema.minItems)) &&
+ !isTable
+ ) {
+ const len = schema.maxItems ?? 1;
+ const array = this.value ?? [];
+
+ // JSONified arrays will convert undefined to null
+ const jsonify = (value) => (value === undefined ? null : value);
+ const jsonschemify = (value) => (value === null ? undefined : value);
+
+ this.required = false;
+
+ const inputs = Array.from({ length: len }).map((_, i) => {
+ const input = new JSONSchemaInput({
+ value: jsonify(array[i]),
+ schema: {
+ ...schema.items,
+ strict: schema.strict,
+ },
+ path: fullPath,
+ validateEmptyValue: this.validateEmptyValue,
+ required: this.required,
+ allowNaN: false,
+ validateOnChange: () => (validateOnChange ? this.#triggerValidation(name, path) : ""),
+ form: this.form,
+ onUpdate: (value) => {
+ array[i] = jsonschemify(value);
+ this.#updateData(fullPath, [...array]);
+ },
+ });
+
+ array[i] = jsonschemify(array[i]);
+
+ return input;
});
+
+ return inputs;
}
if (isArray || canAddProperties) {
// if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
+ const editableInline = ["string", "number"];
+
const allowPatternProperties = isPatternProperties(this.pattern);
const allowAdditionalProperties = isAdditionalProperties(this.pattern);
@@ -949,12 +1005,18 @@ export class JSONSchemaInput extends LitElement {
const fileSystemFormat = isFilesystemSelector(name, itemSchema?.format);
if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
// Create tables if possible
- else if (itemSchema?.type === "string" && !itemSchema.properties) {
+ else if (editableInline.includes(itemSchema?.type) && !itemSchema.properties) {
+ const postprocess = (v) => {
+ if (itemSchema?.type === "number") return parseFloat(v);
+ else return v;
+ };
+
const list = new List({
items: this.value,
- emptyMessage: "No items",
+ emptyMessage: schema.empty ?? "No items selected.",
+ unordered: false,
onChange: ({ items }) => {
- this.#updateData(fullPath, items.length ? items.map((o) => o.value) : undefined);
+ this.#updateData(fullPath, items.length ? items.map((o) => postprocess(o.value)) : undefined);
if (validateOnChange) this.#triggerValidation(name, path);
},
});
@@ -972,6 +1034,7 @@ export class JSONSchemaInput extends LitElement {
};
}),
value: this.value,
+ placeholder: schema.placeholder,
listMode: schema.strict === false ? "click" : "append",
showAllWhenEmpty: false,
onSelect: async ({ label, value }) => {
@@ -981,12 +1044,16 @@ export class JSONSchemaInput extends LitElement {
},
});
- search.style.height = "auto";
- return html`${this.controls}
` : ""}${this.controls}
`
+ : ""}
+ ${search}${list}
`;
+ Object.assign(search.style, { width: "100%" });
+
+ return html`
+
`;
} else {
const input = document.createElement("input");
input.classList.add("guided--input");
- input.placeholder = "Provide an item for the list";
+ input.placeholder = schema.placeholder ?? "Provide an item for the list";
const submitButton = new Button({
label: "Submit",
@@ -1006,11 +1073,13 @@ export class JSONSchemaInput extends LitElement {
});
return html`${search}
+ ${list}
+ validateOnChange && this.#triggerValidation(name, path)}
>
-
`;
}
@@ -1150,6 +1219,7 @@ export class JSONSchemaInput extends LitElement {
const search = new Search({
options,
strict: schema.strict,
+ placeholder: schema.placeholder,
value: {
value: this.value,
key: this.value,
@@ -1188,7 +1258,7 @@ export class JSONSchemaInput extends LitElement {
if (isInteger) schema.type = "number";
const isNumber = schema.type === "number";
- const isRequiredNumber = isNumber && this.required;
+ const isRequiredNumber = isNumber && this.required && this.allowNaN;
const fileSystemFormat = isFilesystemSelector(name, schema.format);
if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
@@ -1240,11 +1310,37 @@ export class JSONSchemaInput extends LitElement {
else if (isNumber) value = newValue = parseFloat(value);
else if (isDateTime) value = newValue = resolveDateTime(value);
+ const isStrict = schema.strict ? true : false;
if (isNumber) {
- if ("min" in schema && newValue < schema.min) newValue = schema.min;
- else if ("max" in schema && newValue > schema.max) newValue = schema.max;
-
- if (isNaN(newValue)) newValue = undefined;
+ // exclusiveMinimum
+ if ("exclusiveMinimum" in schema && newValue <= schema.exclusiveMinimum) {
+ if (isStrict)
+ newValue = this.value; // Set back to last value
+ else newValue = schema.exclusiveMinimum + 1; // (schema.step ?? 1);
+ }
+ // exclusiveMaximum
+ else if ("exclusiveMaximum" in schema && newValue >= schema.exclusiveMaximum) {
+ if (isStrict)
+ newValue = this.value; // Set back to last value
+ else newValue = schema.exclusiveMaximum - 1; // (schema.step ?? 1);
+ }
+ // minimum
+ else if ("minimum" in schema && newValue < schema.minimum) {
+ if (isStrict)
+ newValue = this.value; // Set back to last value
+ else newValue = schema.minimum;
+ }
+ // maximum
+ else if ("maximum" in schema && newValue > schema.maximum) {
+ if (isStrict)
+ newValue = this.value; // Set back to last value
+ else newValue = schema.maximum;
+ }
+ if (isNaN(newValue)) {
+ if (isStrict)
+ newValue = this.value; // Set back to last value
+ else newValue = undefined;
+ }
}
if (schema.transform) newValue = schema.transform(newValue, this.value, schema);
@@ -1256,7 +1352,7 @@ export class JSONSchemaInput extends LitElement {
// }
if (isNumber && newValue !== value) {
- ev.target.value = newValue;
+ if (newValue !== undefined) ev.target.value = newValue; // Avoids unnecessary error message
value = newValue;
}
diff --git a/src/electron/frontend/core/components/List.ts b/src/electron/frontend/core/components/List.ts
index 5fe983e47c..e6b8f24fc9 100644
--- a/src/electron/frontend/core/components/List.ts
+++ b/src/electron/frontend/core/components/List.ts
@@ -36,6 +36,11 @@ export class List extends LitElement {
overflow: auto;
}
+ ol {
+ margin: 0px;
+ }
+
+
#empty {
margin: 1rem;
margin-left: -40px;
diff --git a/src/electron/frontend/core/components/Main.js b/src/electron/frontend/core/components/Main.js
index a718756107..7270ac1ec7 100644
--- a/src/electron/frontend/core/components/Main.js
+++ b/src/electron/frontend/core/components/Main.js
@@ -111,7 +111,6 @@ export class Main extends LitElement {
let { page = "", sections = {} } = this.toRender ?? {};
let footer = page?.footer; // Page-specific footer
- let header = page?.header; // Page-specific header
if (page) {
this.to = page.to;
@@ -139,62 +138,99 @@ export class Main extends LitElement {
if (footer === true) footer = {};
if (footer && "onNext" in footer && !("next" in footer)) footer.next = "Next";
+ }
+
+ const footerEl = footer ? (this.footer = new GuidedFooter(footer)) : html``; // Render for grid
+ if (!footer) delete this.footer; // Reset footer
+
+ this.header = new MainHeader(sections, page);
+
+ return html`
+ ${this.header}
+
+ ${input}${submitButton}
+
+ ${input}${submitButton}
+
${list}
- {
+ {
clickEvent.stopPropagation();
if (ALTERNATIVE_MODES.includes(this.listMode)) {
const input = clickEvent.target.value;
diff --git a/src/electron/frontend/core/components/pages/Page.js b/src/electron/frontend/core/components/pages/Page.js
index e340ad6ef5..672068b1eb 100644
--- a/src/electron/frontend/core/components/pages/Page.js
+++ b/src/electron/frontend/core/components/pages/Page.js
@@ -119,18 +119,21 @@ export class Page extends LitElement {
mapSessions = (callback, data = this.info.globalState.results) => mapSessions(callback, data);
- async convert({ preview } = {}) {
+ async convert({ preview, ...conversionOptions } = {}, options = {}) {
const key = preview ? "preview" : "conversion";
delete this.info.globalState[key]; // Clear the preview results
if (preview) {
- const stubs = await this.runConversions({ stub_test: true }, undefined, {
- title: "Creating conversion preview for all sessions...",
- });
+ if (!options.title) options.title = "Running preview conversion on all sessions...";
+
+ const stubs = await this.runConversions({ stub_test: true, ...conversionOptions }, undefined, options);
+
this.info.globalState[key] = { stubs };
} else {
- this.info.globalState[key] = await this.runConversions({}, true, { title: "Running all conversions" });
+ if (!options.title) options.title = "Running all conversions";
+
+ this.info.globalState[key] = await this.runConversions(conversionOptions, true, options);
}
this.unsavedUpdates = true;
@@ -142,7 +145,9 @@ export class Page extends LitElement {
await this.save({}, false);
}
- async runConversions(conversionOptions = {}, toRun, options = {}) {
+ async runConversions(conversionOptions = {}, toRun, options = {}, backendFunctionToRun = null) {
+ const hasCustomFunction = !!backendFunctionToRun;
+
let original = toRun;
if (!Array.isArray(toRun)) toRun = this.mapSessions();
@@ -152,11 +157,14 @@ export class Page extends LitElement {
else if (typeof original === "string") toRun = toRun.filter(({ subject }) => subject === original);
else if (typeof original === "function") toRun = toRun.filter(original);
- const results = {};
+ const conversionOutput = {};
- const swalOpts = await createProgressPopup({ title: `Running conversion`, ...options });
+ const swalOpts = hasCustomFunction
+ ? options
+ : await createProgressPopup({ title: `Running conversion`, ...options });
const { close: closeProgressPopup } = swalOpts;
+
const fileConfiguration = [];
try {
@@ -168,68 +176,87 @@ export class Page extends LitElement {
const sessionResults = globalState.results[subject][session];
+ const configurationCopy = { ...(sessionResults.configuration ?? {}) };
+
const sourceDataCopy = structuredClone(sessionResults.source_data);
- // Resolve the correct session info from all of the metadata for this conversion
- const metadata = resolveMetadata(subject, session, globalState);
+ if (!configurationCopy.backend) configurationCopy.backend = this.workflow.file_format.value;
+ // Resolve the correct session info from all of the metadata for this conversion
const sessionInfo = {
- ...sessionResults,
- metadata,
+ configuration: configurationCopy,
+ metadata: resolveMetadata(subject, session, globalState),
source_data: merge(SourceData, sourceDataCopy),
};
+ const optsCopy = structuredClone(conversionOptions);
+
+ if (optsCopy.configuration === false) {
+ delete sessionInfo.configuration; // Skip backend configuration options if specified as such
+ delete optsCopy.backend;
+ } else {
+ if (typeof optsCopy.configuration === "object") merge(optsCopy.configuration, configurationCopy);
+ }
+
+ delete optsCopy.configuration;
+
const payload = {
- output_folder: conversionOptions.stub_test ? undefined : conversion_output_folder,
+ output_folder: optsCopy.stub_test ? undefined : conversion_output_folder,
project_name: name,
nwbfile_path: file,
overwrite: true, // We assume override is true because the native NWB file dialog will not allow the user to select an existing file (unless they approve the overwrite)
...sessionInfo, // source_data and metadata are passed in here
- ...conversionOptions, // Any additional conversion options override the defaults
+ ...optsCopy, // Any additional conversion options override the defaults
interfaces: globalState.interfaces,
alignment,
timezone: this.workflow.timezone.value,
};
- fileConfiguration.push(payload);
+ if (hasCustomFunction) {
+ const result = await backendFunctionToRun(payload, swalOpts); // Already handling Swal popup
+ const subRef = conversionOutput[subject] ?? (conversionOutput[subject] = {});
+ subRef[session] = result;
+ } else fileConfiguration.push(payload);
}
- const conversionResults = await run(
- `neuroconv/convert`,
- {
- files: fileConfiguration,
- max_workers: 2, // TODO: Make this configurable and confirm default value
- request_id: swalOpts.id,
- },
- {
- title: "Running the conversion",
- onError: () => "Conversion failed with current metadata. Please try again.",
- ...swalOpts,
- }
- ).catch(async (error) => {
- let message = error.message;
-
- if (message.includes("The user aborted a request.")) {
- this.notify("Conversion was cancelled.", "warning");
+ if (fileConfiguration.length) {
+ const results = await run(
+ `neuroconv/convert`,
+ {
+ files: fileConfiguration,
+ max_workers: 2, // TODO: Make this configurable and confirm default value
+ request_id: swalOpts.id,
+ },
+ {
+ title: "Running the conversion",
+ onError: () => "Conversion failed with current metadata. Please try again.",
+ ...swalOpts,
+ }
+ ).catch(async (error) => {
+ let message = error.message;
+
+ if (message.includes("The user aborted a request.")) {
+ this.notify("Conversion was cancelled.", "warning");
+ throw error;
+ }
+
+ this.notify(message, "error");
throw error;
- }
+ });
- this.notify(message, "error");
- throw error;
- });
-
- conversionResults.forEach((info) => {
- const { file } = info;
- const fileName = file.split("/").pop();
- const [subject, session] = fileName.match(/sub-(.+)_ses-(.+)\.nwb/).slice(1);
- const subRef = results[subject] ?? (results[subject] = {});
- subRef[session] = info;
- });
+ results.forEach((info) => {
+ const { file } = info;
+ const fileName = file.split("/").pop();
+ const [subject, session] = fileName.match(/sub-(.+)_ses-(.+)\.nwb/).slice(1);
+ const subRef = conversionOutput[subject] ?? (conversionOutput[subject] = {});
+ subRef[session] = info;
+ });
+ }
} finally {
- await closeProgressPopup();
+ closeProgressPopup && (await closeProgressPopup());
}
- return results;
+ return conversionOutput;
}
// NOTE: Until the shadow DOM is supported in Storybook, we can't use this render function how we'd intend to.
@@ -257,7 +284,7 @@ export class Page extends LitElement {
updateSections = () => {
const dashboard = document.querySelector("nwb-dashboard");
- dashboard.updateSections({ sidebar: true, main: true }, this.info.globalState);
+ dashboard.updateSections({ sidebar: true, header: true }, this.info.globalState);
};
#unsaved = false;
diff --git a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedBackendConfiguration.js b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedBackendConfiguration.js
new file mode 100644
index 0000000000..035e576f31
--- /dev/null
+++ b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedBackendConfiguration.js
@@ -0,0 +1,396 @@
+import { JSONSchemaForm, get } from "../../../JSONSchemaForm.js";
+
+import { ManagedPage } from "./ManagedPage.js";
+
+import { onThrow } from "../../../../errors";
+import { merge } from "../../utils.js";
+
+import { html } from "lit";
+
+import { run } from "../options/utils.js";
+import { until } from "lit/directives/until.js";
+
+import { resolve } from "../../../../promises";
+import { InstanceManager } from "../../../InstanceManager.js";
+import { InspectorListItem } from "../../../preview/inspector/InspectorList.js";
+
+import { getResourceUsageBytes } from "../../../../validation/backend-configuration";
+
+import { resolveBackendResults, updateSchema } from "../../../../../../../schemas/backend-configuration.schema";
+import { getInfoFromId } from "./utils.js";
+
+const itemIgnore = {
+ full_shape: true,
+ buffer_shape: true,
+ compression_options: true,
+ filter_options: true,
+};
+
+const backendMap = {
+ zarr: "Zarr",
+ hdf5: "HDF5",
+};
+
+export class GuidedBackendConfigurationPage extends ManagedPage {
+ constructor(...args) {
+ super(...args);
+ this.style.height = "100%"; // Fix main section
+ }
+
+ getBackendConfigurations = (info, options = {}) =>
+ run(`neuroconv/configuration`, info, options).catch((e) => {
+ this.notify(e.message, "error");
+ throw e;
+ });
+
+ beforeSave = () => {
+ merge(this.localState, this.info.globalState);
+ };
+
+ form;
+ instances = [];
+ #getForm = (sub, ses) => {
+ const found = this.instances.find((o) => o.session === ses && o.subject === sub);
+ return found?.instance instanceof JSONSchemaForm ? found.instance : null;
+ };
+
+ header = {};
+
+ workflow = {
+ // Ensure conversion is completed when skipped
+ backend_configuration: {
+ skip: async () => {
+ await this.convert({
+ preview: true,
+ configuration: false,
+ });
+ },
+ },
+ };
+
+ footer = {
+ onNext: async () => {
+ await this.save(); // Save in case the conversion fails
+
+ for (let { instance } of this.instances) {
+ if (instance instanceof JSONSchemaForm) await instance.validate(); // Will throw an error in the callback
+ }
+
+ await this.validate(); // Validate all backend configurations
+
+ await this.convert({ preview: true }, { title: "Running preview conversion on all sessions" }); // Validate by trying to set backend configuration with the latest values
+
+ return this.to(1);
+ },
+ };
+
+ #toggleRendered;
+ #rendered;
+ #updateRendered = (force) =>
+ force || this.#rendered === true
+ ? (this.#rendered = new Promise(
+ (resolve) => (this.#toggleRendered = () => resolve((this.#rendered = true)))
+ ))
+ : this.#rendered;
+
+ get rendered() {
+ return resolve(this.#rendered, () => true);
+ }
+
+ async updated() {
+ await this.rendered;
+ }
+
+ renderInstance = (info) => {
+ const { session, subject, info: configuration } = info;
+ const { results, schema: itemSchema, itemsizes } = configuration;
+
+ let instance;
+ if (Object.keys(results).length === 0) {
+ instance = document.createElement("span");
+ instance.innerText = "No configuration options available for this session";
+ } else {
+ const schema = { type: "object", properties: {} };
+
+ const reorganized = Object.entries(results).reduce((acc, [name, item]) => {
+ const splitName = name.split("/");
+
+ const itemsize = itemsizes[name];
+
+ const resolved = { schema, results: acc };
+
+ const lenSplit = splitName.length;
+ splitName.reduce((acc, key, i) => {
+ const { schema, results } = acc;
+
+ const upperProps = schema.properties ?? (schema.properties = {});
+ if (!schema.required) schema.required = [];
+ schema.required.push(key);
+
+ // Set directly on last iteration
+ if (i === lenSplit - 1) {
+ const { schema, resolved } = resolveBackendResults(itemSchema, item, itemsize);
+ upperProps[key] = schema;
+ results[key] = resolved;
+ updateSchema(schema, item, itemsize);
+ return;
+ }
+
+ // Otherwise drill into the results
+ else {
+ const thisSchema = upperProps[key] ?? (upperProps[key] = {});
+ if (!results[key]) results[key] = {};
+ return { schema: thisSchema, results: results[key] };
+ }
+ }, resolved);
+
+ return acc;
+ }, {});
+
+ const existingForm = this.#getForm(subject, session);
+ if (existingForm) {
+ existingForm.schema = schema; // Update schema
+ existingForm.results = reorganized; // Update resolved values
+ return { session, subject, instance: existingForm };
+ }
+
+ instance = new JSONSchemaForm({
+ schema,
+ results: reorganized,
+ ignore: {
+ "*": itemIgnore,
+ },
+ onUpdate: (updatedPath) => {
+ this.unsavedUpdates = "conversions"; // Trigger conversion updates
+
+ const parentPath = updatedPath.slice(0, -1);
+ const form = instance.getFormElement(parentPath);
+ const name = updatedPath.slice(-1)[0];
+
+ // Update used schema
+ const schema = form.schema;
+ updateSchema(schema, form.results, itemsizes[parentPath.join("/")]);
+
+ // Update rendered description
+ const input = form.inputs[name];
+ input.description = schema.properties[name].description;
+
+ // // Buffer shape depends on chunk shape
+ // if (name === "chunk_shape") form.inputs["buffer_shape"].schema = { ...form.inputs["buffer_shape"].schema }; // Force schema update
+ },
+ onThrow,
+
+ validateOnChange: async (name, _, path, value) => {
+ const errors = [];
+
+ if (name === "chunk_shape") {
+ const input = instance.getFormElement(path).inputs["chunk_shape"];
+
+ const mbUsage = getResourceUsageBytes(value, itemsizes[path.join("/")], 1e6);
+
+ if (mbUsage > 20)
+ errors.push({
+ message:
+ "Recommended maximum chunk size is 20MB. You may want to reduce the size of the chunks.",
+ type: "warning",
+ });
+ // NOTE: Generalize for more axes
+ else if (mbUsage < 10 && value[0] !== input.schema.items.maximum)
+ errors.push({
+ message:
+ "Recommended minimum chunk size is 10MB. You may want to increase the size of the chunks.",
+ type: "warning",
+ });
+ }
+
+ return errors.length ? errors : true;
+ },
+ });
+ }
+
+ return { session, subject, instance };
+ };
+
+ getMissingBackendConfigurations = () => {
+ const toRun = this.mapSessions(({ session, subject }) => {
+ const sesResult = this.info.globalState.results[subject][session].configuration;
+ if (!sesResult) return { subject, session, skip: false };
+
+ const backend = sesResult.backend ?? this.workflow.file_format.value;
+
+ return {
+ subject,
+ session,
+ skip: !!sesResult.results[backend],
+ };
+ }).filter(({ skip }) => !skip);
+
+ return this.runConversions(
+ {},
+ toRun, // All or specific session
+ {
+ title: "Getting backend options",
+ },
+ this.getBackendConfigurations
+ );
+ };
+
+ validate = (toRun) => {
+ if (!toRun)
+ return this.runConversions(
+ {},
+ true,
+ { title: "Validating backend options" },
+ this.getBackendConfigurations
+ );
+
+ const { subject, session } = toRun;
+ return this.runConversions(
+ { configuration: this.info.globalState.results[subject][session].configuration },
+ [{ subject, session }], // All or specific session
+ {
+ title: "Validating backend options",
+ showCancelButton: false,
+ },
+ this.getBackendConfigurations
+ );
+ };
+
+ #getManager = () => {
+ const instances = {};
+
+ // Provide references to local state to each instance
+ this.instances = this.mapSessions(({ subject, session, info }) => {
+ const backend = info.configuration.backend ?? this.workflow.file_format.value; // Use the default backend if none is set
+
+ return this.renderInstance({
+ subject,
+ session,
+ info: {
+ backend,
+ results: info.configuration.results[backend], // Get the configuration options for the current session
+ itemsizes: info.configuration.itemsizes[backend], // Get the item sizes for the current session
+ schema: this.info.globalState.schema.configuration[subject][session][backend], // Get the schema for the current session
+ },
+ });
+ }, this.localState.results);
+
+ this.instances.forEach(({ subject, session, instance }) => {
+ if (!instances[`sub-${subject}`]) instances[`sub-${subject}`] = {};
+ instances[`sub-${subject}`][`ses-${session}`] = instance;
+ });
+
+ const ogManager = this.manager;
+
+ this.manager = new InstanceManager({
+ header: "Sessions",
+ instanceType: "Session",
+ instances,
+
+ controls: [
+ // // NOTE: Removes session-specific control over the backend type since Zarr is not completely supported yet
+ // (id) => {
+ // const instanceInfo = id
+ // .split("/")
+ // .reduce((acc, key) => acc[key.split("-").slice(1).join("-")], this.localState.results);
+
+ // const backend = instanceInfo.configuration.backend ?? this.workflow.file_format.value;
+
+ // return new JSONSchemaInput({
+ // path: [],
+ // schema: {
+ // type: "string",
+ // placeholder: "Select backend type",
+ // enum: Object.keys(backendMap),
+ // enumLabels: backendMap,
+ // strict: true,
+ // },
+ // value: backend,
+ // onUpdate: async (value) => {
+ // if (instanceInfo.configuration.backend === value) return;
+ // instanceInfo.configuration.backend = value; // Ensure new backend choice is persistent
+ // await this.save();
+ // await this.#update();
+ // },
+ // });
+ // },
+ {
+ name: "Save & Validate",
+ primary: true,
+ onClick: async (id) => {
+ const { subject, session } = getInfoFromId(id);
+ await this.save();
+ await this.validate({ session, subject });
+ },
+ },
+ ],
+ });
+
+ if (ogManager) ogManager.replaceWith(this.manager);
+
+ return this.manager;
+ };
+
+ #update = () => {
+ return this.getMissingBackendConfigurations()
+ .then(async (update) => {
+ if (Object.keys(update)) {
+ this.mapSessions(({ subject, session, info }) => {
+ const { results, schema, backend, itemsizes } = info;
+
+ const sesResults = this.localState.results[subject][session];
+ if (!sesResults.configuration) sesResults.configuration = {};
+ if (!sesResults.configuration.results) sesResults.configuration.results = {};
+ if (!sesResults.configuration.itemsizes) sesResults.configuration.itemsizes = {};
+
+ sesResults.configuration.itemsizes[backend] = itemsizes; // Set the item sizes for the current session
+ sesResults.configuration.results[backend] = results; // Set the configuration options for the current session
+
+ // Set the schema for the current session
+ const path = [subject, session, backend];
+ path.reduce((acc, key, i) => {
+ if (i === path.length - 1) acc[key] = schema;
+ if (!acc[key]) acc[key] = {};
+ return acc[key];
+ }, this.localState.schema.configuration);
+ }, update);
+
+ await this.save(); // Save data as soon as it arrives from the server
+ }
+
+ return this.#getManager();
+ })
+
+ .catch((error) => {
+ const split = error.message.split(":");
+ console.error(error);
+ return new InspectorListItem({
+ message: split.length > 1 ? error.message.split(":")[1].slice(1) : error.message,
+ type: "error",
+ });
+ });
+ };
+
+ render() {
+ delete this.manager; // Delete any existing manager
+
+ this.#updateRendered(true);
+
+ const globalSchemas = this.info.globalState.schema;
+ if (!globalSchemas.configuration) globalSchemas.configuration = {};
+
+ this.localState = {
+ results: structuredClone(this.info.globalState.results),
+ schema: { configuration: structuredClone(globalSchemas.configuration) },
+ };
+
+ const promise = this.#update();
+
+ const untilResult = until(promise, html`Loading form contents...`);
+ promise.then(() => this.#toggleRendered());
+ return untilResult;
+ }
+}
+
+customElements.get("nwbguide-guided-backend-configuration-page") ||
+ customElements.define("nwbguide-guided-backend-configuration-page", GuidedBackendConfigurationPage);
diff --git a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedPathExpansion.js b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedPathExpansion.js
index af89aea7da..2805deec60 100644
--- a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedPathExpansion.js
@@ -178,9 +178,6 @@ export class GuidedPathExpansionPage extends Page {
#initialize = () => (this.localState = merge(this.info.globalState.structure, { results: {} }));
workflow = {
- subject_id: {},
- session_id: {},
- base_directory: {},
locate_data: {
skip: () => {
this.#initialize();
diff --git a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedSourceData.js b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedSourceData.js
index 8bda2a9e54..9eeaafa610 100644
--- a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedSourceData.js
@@ -220,11 +220,6 @@ export class GuidedSourceDataPage extends ManagedPage {
if (this.#globalModal) this.#globalModal.remove();
}
- updated() {
- const dashboard = document.querySelector("nwb-dashboard");
- const page = dashboard.page;
- }
-
render() {
this.localState = { results: structuredClone(this.info.globalState.results ?? {}) };
diff --git a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedStructure.js b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedStructure.js
index 03ad6d742a..6bf9f36087 100644
--- a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedStructure.js
+++ b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedStructure.js
@@ -35,6 +35,10 @@ export class GuidedStructurePage extends Page {
this.searchModal.toggle(false);
};
+ Object.assign(this.addButton.style, {
+ marginTop: "10px",
+ });
+
this.addButton.innerText = "Add Format";
this.addButton.onClick = () => {
this.search.shadowRoot.querySelector("input").focus();
diff --git a/src/electron/frontend/core/components/pages/guided-mode/options/GuidedInspectorPage.js b/src/electron/frontend/core/components/pages/guided-mode/options/GuidedInspectorPage.js
index 036712a9fa..80e96c708e 100644
--- a/src/electron/frontend/core/components/pages/guided-mode/options/GuidedInspectorPage.js
+++ b/src/electron/frontend/core/components/pages/guided-mode/options/GuidedInspectorPage.js
@@ -47,10 +47,6 @@ export class GuidedInspectorPage extends Page {
});
}
- workflow = {
- multiple_sessions: {},
- };
-
headerButtons = [
new Button({
label: "JSON",
diff --git a/src/electron/frontend/core/components/pages/guided-mode/options/utils.js b/src/electron/frontend/core/components/pages/guided-mode/options/utils.js
index 259c49c74b..7e6e8bc439 100644
--- a/src/electron/frontend/core/components/pages/guided-mode/options/utils.js
+++ b/src/electron/frontend/core/components/pages/guided-mode/options/utils.js
@@ -102,8 +102,8 @@ export const run = async (pathname, payload, options = {}) => {
export const runConversion = async (info, options = {}) =>
run(`neuroconv/convert`, info, {
title: "Running the conversion",
- onError: (results) => {
- if (results.message.includes("already exists")) {
+ onError: (error) => {
+ if (error.message.includes("already exists")) {
return "File already exists. Please specify another location to store the conversion results";
} else {
return "Conversion failed with current metadata. Please try again.";
diff --git a/src/electron/frontend/core/components/pages/guided-mode/setup/Preform.js b/src/electron/frontend/core/components/pages/guided-mode/setup/Preform.js
index 7ba682da87..5e9f128abd 100644
--- a/src/electron/frontend/core/components/pages/guided-mode/setup/Preform.js
+++ b/src/electron/frontend/core/components/pages/guided-mode/setup/Preform.js
@@ -2,7 +2,7 @@ import { html } from "lit";
import { JSONSchemaForm } from "../../../JSONSchemaForm.js";
import { Page } from "../../Page.js";
import { onThrow } from "../../../../errors";
-
+import { merge } from "../../utils.js";
import timezoneSchema from "../../../../../../../schemas/timezone.schema";
// ------------------------------------------------------------------------------
@@ -10,6 +10,12 @@ import timezoneSchema from "../../../../../../../schemas/timezone.schema";
// ------------------------------------------------------------------------------
const questions = {
+ timezone: {
+ ...timezoneSchema,
+ title: "What timezone is your data in?",
+ required: true,
+ },
+
multiple_sessions: {
type: "boolean",
title: "Will this pipeline be run on multiple sessions?",
@@ -41,7 +47,7 @@ const questions = {
type: "boolean",
title: "Would you like to locate the source data programmatically?",
dependencies: {
- multiple_sessions: { default: false },
+ multiple_sessions: {},
},
default: false,
},
@@ -57,15 +63,32 @@ const questions = {
},
},
- timezone: {
- ...timezoneSchema,
- title: "What timezone is your data in?",
- required: true,
+ file_format: {
+ type: "string",
+ enum: ["hdf5", "zarr"],
+ enumLabels: {
+ hdf5: "HDF5",
+ zarr: "Zarr",
+ },
+ strict: true,
+ title: "What file format would you like to use?",
+ description: "Choose a default file format for your data.",
+ default: "hdf5",
+ ignore: true, // NOTE: This ensures that users can only use the default (HDF5) format
+ },
+
+ backend_configuration: {
+ type: "boolean",
+ title: "Would you like to customize low-level data storage options?",
+
+ description:
+ "Dataset chunking, compression, etc.
This also allows you to change file formats per-session", + default: false, }, upload_to_dandi: { type: "boolean", - title: "Would you like to upload your data to DANDI?", + title: "Will you publish data on DANDI?", default: true, }, }; @@ -92,7 +115,7 @@ const getSchema = (questions) => { else Object.entries(deps).forEach(([dep, opts]) => { if (!acc[dep]) acc[dep] = []; - acc[dep].push({ name, ...opts }); + acc[dep].push({ name, default: info.default, ...opts }); }); } return acc; @@ -108,6 +131,11 @@ const getSchema = (questions) => { return acc; }, []); + const ignore = Object.entries(questions).reduce((acc, [name, info]) => { + if (info.ignore) acc[name] = true; + return acc; + }, {}); + const projectWorkflowSchema = { type: "object", properties: Object.entries(questions).reduce((acc, [name, info]) => { @@ -123,6 +151,7 @@ const getSchema = (questions) => { schema: structuredClone(projectWorkflowSchema), defaults, dependents, + ignore, }; }; @@ -142,9 +171,11 @@ export class GuidedPreform extends Page { subtitle: "Answer the following questions to simplify your workflow through the GUIDE", }; + #setWorkflow = () => (this.info.globalState.project.workflow = this.state); // NOTE: Defaults already populated + beforeSave = async () => { await this.form.validate(); - this.info.globalState.project.workflow = this.state; + this.#setWorkflow(); }; footer = { @@ -155,7 +186,7 @@ export class GuidedPreform extends Page { }; updateForm = () => { - const { schema, dependents, defaults } = getSchema(questions); + const { schema, dependents, defaults, ignore } = getSchema(questions); const projectState = this.info.globalState.project ?? {}; if (!projectState.workflow) projectState.workflow = {}; @@ -168,6 +199,7 @@ export class GuidedPreform extends Page { this.form = new JSONSchemaForm({ schema, + ignore, results: this.state, validateEmptyValues: false, // Only show errors after submission validateOnChange: function (name, parent, path, value) { @@ -193,28 +225,46 @@ export class GuidedPreform extends Page { condition = (v) => dependent.condition.some((condition) => v == condition); else console.warn("Invalid condition", dependent.condition); + // Is set to true if (uniformDeps.every(({ name }) => condition(parent[name]))) { dependentParent.removeAttribute(attr); if ("required" in dependent) dependentEl.required = dependent.required; if ("__cached" in dependent) dependentEl.updateData(dependent.__cached); - } else { + } + + // Is set to false + else { if (dependentEl.value !== undefined) dependent.__cached = dependentEl.value; dependentEl.updateData(dependent.default); dependentParent.setAttribute(attr, true); if ("required" in dependent) dependentEl.required = !dependent.required; } }); + + const { upload_to_dandi, file_format } = parent; + + // Only check file format because of global re-render + if (name === "file_format") { + if (upload_to_dandi === true && file_format === "zarr") + return [ + { + type: "error", + message: + "
Set blank to disable filtering" + copy.properties.compression_method.description = "The specified compression method to apply to this dataset.
Set blank to disable compression" + delete copy.properties.compression_method.default // Remove gzip as the default compression method + copy.description = `Full Shape: ${full_shape.join(' x ')}
Source size: ${getResourceUsage(full_shape, itemsize)}`; // This is static + + updateSchema(copy, results, itemsize) + + return { schema: copy, resolved: results } +} + + +const propertiesToUpdate = [ + 'chunk_shape', + // 'buffer_shape' +] + +// const bufferShapeDescription = (value, itemsize) => { +// return `Expected RAM usage: ${getResourceUsage(value, itemsize)}.`; +// } + +const chunkShapeDescription = (value, itemsize) => { + const hasNull = value.includes(null) || value.includes(undefined); // Both null after JSON processing + const diskSpaceMessage = hasNull ? 'Disk space usage will be determined automatically' : `Disk space usage per chunk: ${getResourceUsage(value, itemsize)}`; + return `${diskSpaceMessage}
Leave blank to auto-specify the axis`; +} + + +export const updateSchema = (schema, results, itemsize) => { + + const { + chunk_shape, + // buffer_shape, + full_shape + } = results; + + + const chunkSchema = schema.properties.chunk_shape; + const chunkArraySchema = chunkSchema.anyOf?.[0] || chunkSchema; + // const bufferSchema = schema.properties.buffer_shape; + + const shapeMax = full_shape[0] + + if (propertiesToUpdate.includes('chunk_shape')) { + chunkArraySchema.items.minimum = 1 + chunkArraySchema.maxItems = chunkArraySchema.minItems = chunk_shape.length; + chunkArraySchema.items.maximum = shapeMax + chunkArraySchema.description = chunkShapeDescription( + chunk_shape, + itemsize + ); + + } + + // if (propertiesToUpdate.includes('buffer_shape')) { + // bufferSchema.items.minimum = 1 + // bufferSchema.items.maximum = shapeMax + // bufferSchema.items.step = chunk_shape[0] // Constrain to increments of chunk size + // bufferSchema.strict = true + + // bufferSchema.maxItems = bufferSchema.minItems = buffer_shape.length; + // bufferSchema.description = bufferShapeDescription( + // buffer_shape, + // itemsize + // ); + // } +} diff --git a/src/schemas/base-metadata.schema.ts b/src/schemas/base-metadata.schema.ts index 466993ebe3..1dfa0de588 100644 --- a/src/schemas/base-metadata.schema.ts +++ b/src/schemas/base-metadata.schema.ts @@ -174,10 +174,11 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa order: ["channel_name", "group_name", "shank_electrode_number", ...UV_PROPERTIES] }) - if (ecephys.properties["Units"]) { + const units = ecephys.properties["Units"] - ecephys.properties["Units"].title = "Summarized Units" + if (units) { + units.title = "Summarized Units" updateEcephysTable("Units", copy, { properties: { @@ -187,7 +188,6 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa }, order: ["unit_id", "unit_name", "clu_id", "group_id"] }) - } } diff --git a/src/schemas/dandi-upload.schema.ts b/src/schemas/dandi-upload.schema.ts index d39a05234b..16b416a8db 100644 --- a/src/schemas/dandi-upload.schema.ts +++ b/src/schemas/dandi-upload.schema.ts @@ -32,12 +32,12 @@ onServerOpen(async () => { .then((res) => res.json()) .then(({ physical, logical }) => { const { number_of_jobs, number_of_threads } = additionalSettings as any; - number_of_jobs.max = physical; - number_of_threads.max = logical / physical; + number_of_jobs.maximum = physical; + number_of_threads.maximum = logical / physical; setReady.cpus({ number_of_jobs, number_of_threads }) }) .catch(() => { - if (isStorybook) setReady.cpus({ number_of_jobs: { max: 1, default: 1 }, number_of_threads: { max: 1, default: 1 } }) + if (isStorybook) setReady.cpus({ number_of_jobs: { maximum: 1, default: 1 }, number_of_threads: { maximum: 1, default: 1 } }) }); }); diff --git a/src/schemas/json/dandi/create.json b/src/schemas/json/dandi/create.json index aeca70a26b..faedd35041 100644 --- a/src/schemas/json/dandi/create.json +++ b/src/schemas/json/dandi/create.json @@ -27,7 +27,8 @@ "main": "Main Archive" }, "enum": ["main", "staging"], - "description": "Which DANDI server to upload to.
Note: The Development Server is recommended for developers, or users learning to use DANDI" + "description": "Which DANDI server to upload to.
Note: The Development Server is recommended for developers, or users learning to use DANDI", + "strict": true }, "description": {
This also allows you to change file formats per-session", + default: false, }, upload_to_dandi: { type: "boolean", - title: "Would you like to upload your data to DANDI?", + title: "Will you publish data on DANDI?", default: true, }, }; @@ -92,7 +115,7 @@ const getSchema = (questions) => { else Object.entries(deps).forEach(([dep, opts]) => { if (!acc[dep]) acc[dep] = []; - acc[dep].push({ name, ...opts }); + acc[dep].push({ name, default: info.default, ...opts }); }); } return acc; @@ -108,6 +131,11 @@ const getSchema = (questions) => { return acc; }, []); + const ignore = Object.entries(questions).reduce((acc, [name, info]) => { + if (info.ignore) acc[name] = true; + return acc; + }, {}); + const projectWorkflowSchema = { type: "object", properties: Object.entries(questions).reduce((acc, [name, info]) => { @@ -123,6 +151,7 @@ const getSchema = (questions) => { schema: structuredClone(projectWorkflowSchema), defaults, dependents, + ignore, }; }; @@ -142,9 +171,11 @@ export class GuidedPreform extends Page { subtitle: "Answer the following questions to simplify your workflow through the GUIDE", }; + #setWorkflow = () => (this.info.globalState.project.workflow = this.state); // NOTE: Defaults already populated + beforeSave = async () => { await this.form.validate(); - this.info.globalState.project.workflow = this.state; + this.#setWorkflow(); }; footer = { @@ -155,7 +186,7 @@ export class GuidedPreform extends Page { }; updateForm = () => { - const { schema, dependents, defaults } = getSchema(questions); + const { schema, dependents, defaults, ignore } = getSchema(questions); const projectState = this.info.globalState.project ?? {}; if (!projectState.workflow) projectState.workflow = {}; @@ -168,6 +199,7 @@ export class GuidedPreform extends Page { this.form = new JSONSchemaForm({ schema, + ignore, results: this.state, validateEmptyValues: false, // Only show errors after submission validateOnChange: function (name, parent, path, value) { @@ -193,28 +225,46 @@ export class GuidedPreform extends Page { condition = (v) => dependent.condition.some((condition) => v == condition); else console.warn("Invalid condition", dependent.condition); + // Is set to true if (uniformDeps.every(({ name }) => condition(parent[name]))) { dependentParent.removeAttribute(attr); if ("required" in dependent) dependentEl.required = dependent.required; if ("__cached" in dependent) dependentEl.updateData(dependent.__cached); - } else { + } + + // Is set to false + else { if (dependentEl.value !== undefined) dependent.__cached = dependentEl.value; dependentEl.updateData(dependent.default); dependentParent.setAttribute(attr, true); if ("required" in dependent) dependentEl.required = !dependent.required; } }); + + const { upload_to_dandi, file_format } = parent; + + // Only check file format because of global re-render + if (name === "file_format") { + if (upload_to_dandi === true && file_format === "zarr") + return [ + { + type: "error", + message: + "
Zarr files are not supported by DANDI
Please change the file format to HDF5 or disable DANDI upload.", + }, + ]; + } }, - // Immediately re-render boolean values + // Save all changes onUpdate: async (path, value) => { - if (typeof value === "boolean") { - this.unsavedUpdates = true; - this.info.globalState.project.workflow = this.state; - this.updateSections(); // Trigger section changes with new workflow - await this.save({}, false); // Save new workflow and section changes - } + const willUpdateFlow = typeof value === "boolean"; + this.unsavedUpdates = true; + this.#setWorkflow(); + if (willUpdateFlow) this.updateSections(); // Trigger section changes with new workflow + await this.save({}, false); // Save new workflow and section changes }, + onThrow, // groups: [ // { diff --git a/src/electron/frontend/core/components/pages/settings/SettingsPage.js b/src/electron/frontend/core/components/pages/settings/SettingsPage.js index d5ea234eab..5c70885068 100644 --- a/src/electron/frontend/core/components/pages/settings/SettingsPage.js +++ b/src/electron/frontend/core/components/pages/settings/SettingsPage.js @@ -32,7 +32,8 @@ import examplePipelines from "../../../../../../example_pipelines.yml"; import { run } from "../guided-mode/options/utils.js"; import { joinPath } from "../../../globals"; import { Modal } from "../../Modal"; -import { ProgressBar, humanReadableBytes } from "../../ProgressBar"; +import { ProgressBar } from "../../ProgressBar"; +import { humanReadableBytes } from "../../utils/size"; const DATA_OUTPUT_PATH = joinPath(testDataFolderPath, "single_session_data"); const DATASET_OUTPUT_PATH = joinPath(testDataFolderPath, "multi_session_dataset"); diff --git a/src/electron/frontend/core/components/table/cells/input.ts b/src/electron/frontend/core/components/table/cells/input.ts index 17572ead1d..4c02b508de 100644 --- a/src/electron/frontend/core/components/table/cells/input.ts +++ b/src/electron/frontend/core/components/table/cells/input.ts @@ -43,8 +43,6 @@ export class NestedEditor extends LitElement { const schema = this.schema - - console.log('schema', schema, 'data', data) const container = document.createElement('div') const input = this.#input = new JSONSchemaInput({ schema, diff --git a/src/electron/frontend/core/components/utils/size.ts b/src/electron/frontend/core/components/utils/size.ts new file mode 100644 index 0000000000..2e08881342 --- /dev/null +++ b/src/electron/frontend/core/components/utils/size.ts @@ -0,0 +1,20 @@ +export function humanReadableBytes(size: number | string) { + + // Define the units + const units = ['B', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB', 'ZB', 'YB']; + + // Initialize the index to 0 + let index = 0; + + // Convert the size to a floating point number + size = parseFloat(size); + + // Loop until the size is less than 1024 and increment the unit + while (size >= 1000 && index < units.length - 1) { + size /= 1000; + index += 1; + } + + // Return the size formatted with 2 decimal places and the appropriate unit + return `${size.toFixed(2)} ${units[index]}`; +} diff --git a/src/electron/frontend/core/pages.js b/src/electron/frontend/core/pages.js index 11f042adcf..3371f27950 100644 --- a/src/electron/frontend/core/pages.js +++ b/src/electron/frontend/core/pages.js @@ -4,9 +4,13 @@ import { GuidedHomePage } from "./components/pages/guided-mode/GuidedHome"; import { GuidedNewDatasetPage } from "./components/pages/guided-mode/setup/GuidedNewDatasetInfo"; import { GuidedStructurePage } from "./components/pages/guided-mode/data/GuidedStructure"; import { sections } from "./components/pages/globals"; + import { GuidedSubjectsPage } from "./components/pages/guided-mode/setup/GuidedSubjects"; + import { GuidedSourceDataPage } from "./components/pages/guided-mode/data/GuidedSourceData"; import { GuidedMetadataPage } from "./components/pages/guided-mode/data/GuidedMetadata"; +import { GuidedBackendConfigurationPage } from "./components/pages/guided-mode/data/GuidedBackendConfiguration"; + import { GuidedUploadPage } from "./components/pages/guided-mode/options/GuidedUpload"; import { GuidedResultsPage } from "./components/pages/guided-mode/results/GuidedResults"; import { Dashboard } from "./components/Dashboard"; @@ -125,6 +129,12 @@ const pages = { section: sections[1], }), + backend: new GuidedBackendConfigurationPage({ + title: "Backend Configuration", + label: "Backend configuration", + section: sections[1], + }), + inspect: new GuidedInspectorPage({ title: "Inspector Report", label: "Validate metadata", diff --git a/src/electron/frontend/core/validation/backend-configuration.ts b/src/electron/frontend/core/validation/backend-configuration.ts new file mode 100644 index 0000000000..16431dc93c --- /dev/null +++ b/src/electron/frontend/core/validation/backend-configuration.ts @@ -0,0 +1,7 @@ +import { humanReadableBytes } from "../components/utils/size"; + +const prod = (arr: number[]) => arr.reduce((accumulator, currentValue) => accumulator * currentValue, 1); + +export const getResourceUsageBytes = (shape: number[], itemsize: number, scale=1e9) => prod(shape) * (itemsize / scale) // Default to GB + +export const getResourceUsage = (shape: number[], itemsize: number) => humanReadableBytes(getResourceUsageBytes(shape, itemsize, 1)) diff --git a/src/pyflask/app.py b/src/pyflask/app.py index 28b0f8a308..3301c21a88 100644 --- a/src/pyflask/app.py +++ b/src/pyflask/app.py @@ -107,10 +107,15 @@ def post(self): type = payload["type"] header = payload["header"] inputs = payload["inputs"] - traceback = payload["traceback"] + traceback = payload.get("traceback", "") + + message = f"{header}\n{'-'*len(header)}\n\n{json.dumps(inputs, indent=2)}\n" + + if traceback: + message += f"\n{traceback}\n" - message = f"{header}\n{'-'*len(header)}\n\n{json.dumps(inputs, indent=2)}\n\n{traceback}\n" selected_logger = getattr(api.logger, type) + api.logger.info(f"Logging {type} message: {header}") selected_logger(message) diff --git a/src/pyflask/manageNeuroconv/__init__.py b/src/pyflask/manageNeuroconv/__init__.py index 0793acb240..8401b0f374 100644 --- a/src/pyflask/manageNeuroconv/__init__.py +++ b/src/pyflask/manageNeuroconv/__init__.py @@ -7,6 +7,7 @@ generate_test_data, get_all_converter_info, get_all_interface_info, + get_backend_configuration, get_interface_alignment, get_metadata_schema, get_source_schema, diff --git a/src/pyflask/manageNeuroconv/manage_neuroconv.py b/src/pyflask/manageNeuroconv/manage_neuroconv.py index f875874459..2d7825411b 100644 --- a/src/pyflask/manageNeuroconv/manage_neuroconv.py +++ b/src/pyflask/manageNeuroconv/manage_neuroconv.py @@ -510,6 +510,9 @@ def on_recording_interface(name, recording_interface): if has_ecephys: + if "definitions" not in ecephys_schema: + ecephys_schema["definitions"] = ecephys_properties["definitions"] + has_electrodes = "ElectrodeColumns" in ecephys_metadata original_units_schema = ecephys_properties.pop("UnitProperties", None) @@ -863,52 +866,45 @@ def get_interface_alignment(info: dict) -> dict: ) -def convert_to_nwb( +def create_file( info: dict, - log_url=None, -) -> str: - """Function used to convert the source data to NWB format using the specified metadata.""" + log_url: Optional[str] = None, +) -> dict: import requests - from neuroconv import NWBConverter from tqdm_publisher import TQDMProgressSubscriber - url = info.get("url", None) - request_id = info.get("request_id", None) - - nwbfile_path = Path(info["nwbfile_path"]) - custom_output_directory = info.get("output_folder") project_name = info.get("project_name") + run_stub_test = info.get("stub_test", False) - default_output_base = STUB_SAVE_FOLDER_PATH if run_stub_test else CONVERSION_SAVE_FOLDER_PATH - default_output_directory = default_output_base / project_name - try: + overwrite = info.get("overwrite", False) - # add a subdirectory to a filepath if stub_test is true - resolved_output_base = Path(custom_output_directory) if custom_output_directory else default_output_base - resolved_output_directory = resolved_output_base / project_name - resolved_output_path = resolved_output_directory / nwbfile_path + # Progress update info + url = info.get("url") + request_id = info.get("request_id") - # Remove symlink placed at the default_output_directory if this will hold real data - if resolved_output_directory == default_output_directory and default_output_directory.is_symlink(): - default_output_directory.unlink() + # Backend configuration info + backend_configuration = info.get("configuration", {}) + backend = backend_configuration.get("backend", "hdf5") - resolved_output_path.parent.mkdir(exist_ok=True, parents=True) # Ensure all parent directories exist + converter, metadata, path_info = get_conversion_info(info) - resolved_source_data = replace_none_with_nan( - info["source_data"], resolve_references(get_custom_converter(info["interfaces"]).get_source_schema()) - ) + nwbfile_path = path_info["file"] - converter = instantiate_custom_converter( - source_data=resolved_source_data, - interface_class_dict=info["interfaces"], - alignment_info=info.get("alignment", dict()), - ) + try: + + # Delete files manually if using Zarr + if overwrite: + if nwbfile_path.exists(): + if nwbfile_path.is_dir(): + rmtree(nwbfile_path) + else: + nwbfile_path.unlink() def update_conversion_progress(message): update_dict = dict(request_id=request_id, **message) - if (url) or not run_stub_test: + if url or not run_stub_test: requests.post(url=url, json=update_dict) else: progress_handler.announce(update_dict) @@ -938,126 +934,273 @@ def update_conversion_progress(message): progress_bar_options=progress_bar_options, ) - # Ensure Ophys NaN values are resolved - resolved_metadata = replace_none_with_nan(info["metadata"], resolve_references(converter.get_metadata_schema())) + run_conversion_kwargs = dict( + metadata=metadata, + nwbfile_path=nwbfile_path, + overwrite=overwrite, + conversion_options=options, + backend=backend, + ) - ecephys_metadata = resolved_metadata.get("Ecephys") + if not run_stub_test: + run_conversion_kwargs.update(dict(backend_configuration=update_backend_configuration(info))) - if ecephys_metadata: + converter.run_conversion(**run_conversion_kwargs) - # Quick fix to remove units - has_units = "Units" in ecephys_metadata + except Exception as e: + if log_url: + requests.post( + url=log_url, + json=dict( + header=f"Conversion failed for {project_name} — {nwbfile_path} (convert_to_nwb)", + inputs=dict(info=info), + traceback=traceback.format_exc(), + type="error", + ), + ) - if has_units: + raise e - ## NOTE: Currently do not allow editing units properties - # shared_units_columns = ecephys_metadata["UnitColumns"] - # for interface_name, interface_unit_results in ecephys_metadata["Units"].items(): - # interface = converter.data_interface_objects[interface_name] - # update_sorting_properties_from_table_as_json( - # interface, - # unit_table_json=interface_unit_results, - # unit_column_info=shared_units_columns, - # ) +def update_backend_configuration(info: dict) -> dict: - # ecephys_metadata["UnitProperties"] = [ - # {"name": entry["name"], "description": entry["description"]} for entry in shared_units_columns - # ] + from neuroconv.tools.nwb_helpers import ( + get_default_backend_configuration, + make_nwbfile_from_metadata, + ) - del ecephys_metadata["Units"] - del ecephys_metadata["UnitColumns"] + PROPS_TO_IGNORE = ["full_shape"] - has_electrodes = "Electrodes" in ecephys_metadata - if has_electrodes: + info_from_frontend = info.get("configuration", {}) + backend = info_from_frontend.get("backend", "hdf5") + backend_configuration_from_frontend = info_from_frontend.get("results", {}).get(backend, {}) - shared_electrode_columns = ecephys_metadata["ElectrodeColumns"] + converter, metadata, __ = get_conversion_info(info) - for interface_name, interface_electrode_results in ecephys_metadata["Electrodes"].items(): - name_split = interface_name.split(" — ") + nwbfile = make_nwbfile_from_metadata(metadata=metadata) + converter.add_to_nwbfile(nwbfile, metadata=metadata) - if len(name_split) == 1: - sub_interface = name_split[0] - elif len(name_split) == 2: - sub_interface, sub_sub_interface = name_split + backend_configuration = get_default_backend_configuration(nwbfile=nwbfile, backend=backend) - interface_or_subconverter = converter.data_interface_objects[sub_interface] + for location_in_file, dataset_configuration in backend_configuration_from_frontend.items(): + for key, value in dataset_configuration.items(): + if key not in PROPS_TO_IGNORE: + # Pydantic models only allow setting of attributes + setattr(backend_configuration.dataset_configurations[location_in_file], key, value) - if isinstance(interface_or_subconverter, NWBConverter): - subconverter = interface_or_subconverter + return backend_configuration - update_recording_properties_from_table_as_json( - recording_interface=subconverter.data_interface_objects[sub_sub_interface], - electrode_table_json=interface_electrode_results, - electrode_column_info=shared_electrode_columns, - ) - else: - interface = interface_or_subconverter - update_recording_properties_from_table_as_json( - recording_interface=interface, - electrode_table_json=interface_electrode_results, - electrode_column_info=shared_electrode_columns, - ) +def get_backend_configuration(info: dict) -> dict: - ecephys_metadata["Electrodes"] = [ - {"name": entry["name"], "description": entry["description"]} for entry in shared_electrode_columns - ] + import numpy as np - del ecephys_metadata["ElectrodeColumns"] + PROPS_TO_REMOVE = [ + # Immutable + "object_id", + "dataset_name", + "location_in_file", + "dtype", + ] - # Correct timezone in metadata fields - resolved_metadata["NWBFile"]["session_start_time"] = datetime.fromisoformat( - resolved_metadata["NWBFile"]["session_start_time"] - ).replace(tzinfo=zoneinfo.ZoneInfo(info["timezone"])) + info["overwrite"] = True # Always overwrite the file - if "date_of_birth" in resolved_metadata["Subject"]: - resolved_metadata["Subject"]["date_of_birth"] = datetime.fromisoformat( - resolved_metadata["Subject"]["date_of_birth"] - ).replace(tzinfo=zoneinfo.ZoneInfo(info["timezone"])) + backend = info.get("backend", "hdf5") + configuration = update_backend_configuration(info) - # Actually run the conversion - converter.run_conversion( - metadata=resolved_metadata, - nwbfile_path=resolved_output_path, - overwrite=info.get("overwrite", False), - conversion_options=options, - ) + def custom_encoder(obj): + if isinstance(obj, np.ndarray): + return obj.tolist() + if isinstance(obj, np.dtype): + return str(obj) + raise TypeError(f"Object of type {obj.__class__.__name__} is not JSON serializable") - # Create a symlink between the fake data and custom data - if not resolved_output_directory == default_output_directory: - if default_output_directory.exists(): - # If default default_output_directory is not a symlink, delete all contents and create a symlink there - if not default_output_directory.is_symlink(): - rmtree(default_output_directory) + # Provide metadata on configuration dictionary + configuration_dict = configuration.dict() - # If the location is already a symlink, but points to a different output location - # remove the existing symlink before creating a new one - elif ( - default_output_directory.is_symlink() - and default_output_directory.readlink() is not resolved_output_directory - ): - default_output_directory.unlink() + itemsizes = {} + for key, dataset in configuration_dict["dataset_configurations"].items(): + itemsizes[key] = dataset["dtype"].itemsize - # Create a pointer to the actual conversion outputs - if not default_output_directory.exists(): - os.symlink(resolved_output_directory, default_output_directory) + serialized = json.loads(json.dumps(configuration_dict, default=custom_encoder)) - return dict(file=str(resolved_output_path)) + dataset_configurations = serialized["dataset_configurations"] # Only provide dataset configurations - except Exception as e: - if log_url: - requests.post( - url=log_url, - json=dict( - header=f"Conversion failed for {project_name} — {nwbfile_path} (convert_to_nwb)", - inputs=dict(info=info), - traceback=traceback.format_exc(), - type="error", - ), - ) + for dataset in dataset_configurations.values(): + for key in PROPS_TO_REMOVE: + del dataset[key] - raise e + schema = list(configuration.schema()["$defs"].values())[0] + for key in PROPS_TO_REMOVE: + existed = schema["properties"].pop(key, None) # Why is dtype not included but the rest are? + if existed: + schema["required"].remove(key) + + return dict(results=dataset_configurations, schema=schema, backend=backend, itemsizes=itemsizes) + + +def get_conversion_path_info(info: dict) -> dict: + """Function used to resolve the path details for the conversion.""" + + nwbfile_path = Path(info["nwbfile_path"]) + custom_output_directory = info.get("output_folder") + project_name = info.get("project_name") + run_stub_test = info.get("stub_test", False) + default_output_base = STUB_SAVE_FOLDER_PATH if run_stub_test else CONVERSION_SAVE_FOLDER_PATH + default_output_directory = default_output_base / project_name + + # add a subdirectory to a filepath if stub_test is true + resolved_output_base = Path(custom_output_directory) if custom_output_directory else default_output_base + resolved_output_directory = resolved_output_base / project_name + resolved_output_path = resolved_output_directory / nwbfile_path + + return dict(file=resolved_output_path, directory=resolved_output_directory, default=default_output_directory) + + +def get_conversion_info(info: dict) -> dict: + """Function used to organize the required information for conversion.""" + + from neuroconv import NWBConverter + + path_info = get_conversion_path_info(info) + resolved_output_path = path_info["file"] + resolved_output_directory = path_info["directory"] + default_output_directory = path_info["default"] + + # Remove symlink placed at the default_output_directory if this will hold real data + if resolved_output_directory == default_output_directory and default_output_directory.is_symlink(): + default_output_directory.unlink() + + resolved_output_path.parent.mkdir(exist_ok=True, parents=True) # Ensure all parent directories exist + + resolved_source_data = replace_none_with_nan( + info["source_data"], resolve_references(get_custom_converter(info["interfaces"]).get_source_schema()) + ) + + converter = instantiate_custom_converter( + source_data=resolved_source_data, + interface_class_dict=info["interfaces"], + alignment_info=info.get("alignment", dict()), + ) + + # Ensure Ophys NaN values are resolved + resolved_metadata = replace_none_with_nan(info["metadata"], resolve_references(converter.get_metadata_schema())) + + ecephys_metadata = resolved_metadata.get("Ecephys") + + if ecephys_metadata: + + # Quick fix to remove units + has_units = "Units" in ecephys_metadata + + if has_units: + + ## NOTE: Currently do not allow editing units properties + # shared_units_columns = ecephys_metadata["UnitColumns"] + # for interface_name, interface_unit_results in ecephys_metadata["Units"].items(): + # interface = converter.data_interface_objects[interface_name] + + # update_sorting_properties_from_table_as_json( + # interface, + # unit_table_json=interface_unit_results, + # unit_column_info=shared_units_columns, + # ) + + # ecephys_metadata["UnitProperties"] = [ + # {"name": entry["name"], "description": entry["description"]} for entry in shared_units_columns + # ] + + del ecephys_metadata["Units"] + del ecephys_metadata["UnitColumns"] + + has_electrodes = "Electrodes" in ecephys_metadata + if has_electrodes: + + shared_electrode_columns = ecephys_metadata["ElectrodeColumns"] + + for interface_name, interface_electrode_results in ecephys_metadata["Electrodes"].items(): + name_split = interface_name.split(" — ") + + if len(name_split) == 1: + sub_interface = name_split[0] + elif len(name_split) == 2: + sub_interface, sub_sub_interface = name_split + + interface_or_subconverter = converter.data_interface_objects[sub_interface] + + if isinstance(interface_or_subconverter, NWBConverter): + subconverter = interface_or_subconverter + + update_recording_properties_from_table_as_json( + recording_interface=subconverter.data_interface_objects[sub_sub_interface], + electrode_table_json=interface_electrode_results, + electrode_column_info=shared_electrode_columns, + ) + else: + interface = interface_or_subconverter + + update_recording_properties_from_table_as_json( + recording_interface=interface, + electrode_table_json=interface_electrode_results, + electrode_column_info=shared_electrode_columns, + ) + + ecephys_metadata["Electrodes"] = [ + {"name": entry["name"], "description": entry["description"]} for entry in shared_electrode_columns + ] + + del ecephys_metadata["ElectrodeColumns"] + + # Correct timezone in metadata fields + resolved_metadata["NWBFile"]["session_start_time"] = datetime.fromisoformat( + resolved_metadata["NWBFile"]["session_start_time"] + ).replace(tzinfo=zoneinfo.ZoneInfo(info["timezone"])) + + if "date_of_birth" in resolved_metadata["Subject"]: + resolved_metadata["Subject"]["date_of_birth"] = datetime.fromisoformat( + resolved_metadata["Subject"]["date_of_birth"] + ).replace(tzinfo=zoneinfo.ZoneInfo(info["timezone"])) + + return ( + converter, + resolved_metadata, + path_info, + ) + + +def convert_to_nwb( + info: dict, + log_url: Optional[str] = None, +) -> str: + """Function used to convert the source data to NWB format using the specified metadata.""" + + path_info = get_conversion_path_info(info) + output_path = path_info["file"] + resolved_output_directory = path_info["directory"] + default_output_directory = path_info["default"] + + create_file(info, log_url=log_url) + + # Create a symlink between the fake data and custom data + if not resolved_output_directory == default_output_directory: + if default_output_directory.exists(): + # If default default_output_directory is not a symlink, delete all contents and create a symlink there + if not default_output_directory.is_symlink(): + rmtree(default_output_directory) + + # If the location is already a symlink, but points to a different output location + # remove the existing symlink before creating a new one + elif ( + default_output_directory.is_symlink() + and default_output_directory.readlink() is not resolved_output_directory + ): + default_output_directory.unlink() + + # Create a pointer to the actual conversion outputs + if not default_output_directory.exists(): + os.symlink(resolved_output_directory, default_output_directory) + + return dict(file=str(output_path)) def convert_all_to_nwb( diff --git a/src/pyflask/namespaces/neuroconv.py b/src/pyflask/namespaces/neuroconv.py index 3d37dcc156..fc3fba9814 100644 --- a/src/pyflask/namespaces/neuroconv.py +++ b/src/pyflask/namespaces/neuroconv.py @@ -7,6 +7,7 @@ convert_all_to_nwb, get_all_converter_info, get_all_interface_info, + get_backend_configuration, get_interface_alignment, get_metadata_schema, get_source_schema, @@ -93,6 +94,13 @@ def post(self): return get_interface_alignment(neuroconv_namespace.payload) +@neuroconv_namespace.route("/configuration") +class GetBackendConfiguration(Resource): + @neuroconv_namespace.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"}) + def post(self): + return get_backend_configuration(neuroconv_namespace.payload) + + validate_parser = neuroconv_namespace.parser() validate_parser.add_argument("parent", type=dict, required=True) validate_parser.add_argument("function_name", type=str, required=True) diff --git a/src/schemas/backend-configuration.schema.ts b/src/schemas/backend-configuration.schema.ts new file mode 100644 index 0000000000..2b36b5aedf --- /dev/null +++ b/src/schemas/backend-configuration.schema.ts @@ -0,0 +1,80 @@ +import { getResourceUsage } from "../../src/electron/frontend/core/validation/backend-configuration" + +export const resolveBackendResults = (schema, results, itemsize) => { + const copy = structuredClone(schema) + + // results.buffer_shape = results.chunk_shape.map(() => null); // Provide an unspecified buffer shape for now + + // Do not handle compression options or any filter options for now + if (copy.properties.compression_options) results.compression_options = null; + if (copy.properties.filter_methods) results.filter_methods = [] + if (copy.properties.filter_options) results.filter_options = null; + + + const { full_shape } = results; + if (copy.properties.filter_methods) copy.properties.filter_methods.description = "The ordered collection of filtering methods to apply to this dataset prior to compression.Set blank to disable filtering" + copy.properties.compression_method.description = "The specified compression method to apply to this dataset.
Set blank to disable compression" + delete copy.properties.compression_method.default // Remove gzip as the default compression method + copy.description = `Full Shape: ${full_shape.join(' x ')}
Source size: ${getResourceUsage(full_shape, itemsize)}`; // This is static + + updateSchema(copy, results, itemsize) + + return { schema: copy, resolved: results } +} + + +const propertiesToUpdate = [ + 'chunk_shape', + // 'buffer_shape' +] + +// const bufferShapeDescription = (value, itemsize) => { +// return `Expected RAM usage: ${getResourceUsage(value, itemsize)}.`; +// } + +const chunkShapeDescription = (value, itemsize) => { + const hasNull = value.includes(null) || value.includes(undefined); // Both null after JSON processing + const diskSpaceMessage = hasNull ? 'Disk space usage will be determined automatically' : `Disk space usage per chunk: ${getResourceUsage(value, itemsize)}`; + return `${diskSpaceMessage}
Leave blank to auto-specify the axis`; +} + + +export const updateSchema = (schema, results, itemsize) => { + + const { + chunk_shape, + // buffer_shape, + full_shape + } = results; + + + const chunkSchema = schema.properties.chunk_shape; + const chunkArraySchema = chunkSchema.anyOf?.[0] || chunkSchema; + // const bufferSchema = schema.properties.buffer_shape; + + const shapeMax = full_shape[0] + + if (propertiesToUpdate.includes('chunk_shape')) { + chunkArraySchema.items.minimum = 1 + chunkArraySchema.maxItems = chunkArraySchema.minItems = chunk_shape.length; + chunkArraySchema.items.maximum = shapeMax + chunkArraySchema.description = chunkShapeDescription( + chunk_shape, + itemsize + ); + + } + + // if (propertiesToUpdate.includes('buffer_shape')) { + // bufferSchema.items.minimum = 1 + // bufferSchema.items.maximum = shapeMax + // bufferSchema.items.step = chunk_shape[0] // Constrain to increments of chunk size + // bufferSchema.strict = true + + // bufferSchema.maxItems = bufferSchema.minItems = buffer_shape.length; + // bufferSchema.description = bufferShapeDescription( + // buffer_shape, + // itemsize + // ); + // } +} diff --git a/src/schemas/base-metadata.schema.ts b/src/schemas/base-metadata.schema.ts index 466993ebe3..1dfa0de588 100644 --- a/src/schemas/base-metadata.schema.ts +++ b/src/schemas/base-metadata.schema.ts @@ -174,10 +174,11 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa order: ["channel_name", "group_name", "shank_electrode_number", ...UV_PROPERTIES] }) - if (ecephys.properties["Units"]) { + const units = ecephys.properties["Units"] - ecephys.properties["Units"].title = "Summarized Units" + if (units) { + units.title = "Summarized Units" updateEcephysTable("Units", copy, { properties: { @@ -187,7 +188,6 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa }, order: ["unit_id", "unit_name", "clu_id", "group_id"] }) - } } diff --git a/src/schemas/dandi-upload.schema.ts b/src/schemas/dandi-upload.schema.ts index d39a05234b..16b416a8db 100644 --- a/src/schemas/dandi-upload.schema.ts +++ b/src/schemas/dandi-upload.schema.ts @@ -32,12 +32,12 @@ onServerOpen(async () => { .then((res) => res.json()) .then(({ physical, logical }) => { const { number_of_jobs, number_of_threads } = additionalSettings as any; - number_of_jobs.max = physical; - number_of_threads.max = logical / physical; + number_of_jobs.maximum = physical; + number_of_threads.maximum = logical / physical; setReady.cpus({ number_of_jobs, number_of_threads }) }) .catch(() => { - if (isStorybook) setReady.cpus({ number_of_jobs: { max: 1, default: 1 }, number_of_threads: { max: 1, default: 1 } }) + if (isStorybook) setReady.cpus({ number_of_jobs: { maximum: 1, default: 1 }, number_of_threads: { maximum: 1, default: 1 } }) }); }); diff --git a/src/schemas/json/dandi/create.json b/src/schemas/json/dandi/create.json index aeca70a26b..faedd35041 100644 --- a/src/schemas/json/dandi/create.json +++ b/src/schemas/json/dandi/create.json @@ -27,7 +27,8 @@ "main": "Main Archive" }, "enum": ["main", "staging"], - "description": "Which DANDI server to upload to.
Note: The Development Server is recommended for developers, or users learning to use DANDI" + "description": "Which DANDI server to upload to.
Note: The Development Server is recommended for developers, or users learning to use DANDI", + "strict": true }, "description": {