From 8d839a65bfa18d45ec387f594e67c5e4062e142c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
<66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 9 Apr 2024 00:15:00 +0000
Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
---
pyflask/apis/neuroconv.py | 2 +-
pyflask/app.py | 6 +-
pyflask/manageNeuroconv/manage_neuroconv.py | 39 ++--
schemas/backend-configuration.schema.ts | 2 +-
schemas/base-metadata.schema.ts | 2 +-
src/renderer/src/stories/JSONSchemaInput.js | 11 +-
src/renderer/src/stories/pages/Page.js | 8 +-
.../data/GuidedBackendConfiguration.js | 187 +++++++++---------
8 files changed, 118 insertions(+), 139 deletions(-)
diff --git a/pyflask/apis/neuroconv.py b/pyflask/apis/neuroconv.py
index a5bca4ec9..b35d2e767 100644
--- a/pyflask/apis/neuroconv.py
+++ b/pyflask/apis/neuroconv.py
@@ -22,7 +22,7 @@
upload_folder_to_dandi,
upload_multiple_filesystem_objects_to_dandi,
get_interface_alignment,
- get_backend_configuration
+ get_backend_configuration,
)
from errorHandlers import notBadRequestException
diff --git a/pyflask/app.py b/pyflask/app.py
index dfaf9ef7a..66846fa03 100644
--- a/pyflask/app.py
+++ b/pyflask/app.py
@@ -111,15 +111,15 @@ def get_cpu_count():
@app.route("/compression/hdf5")
def get_hdf5_compression_methods():
from neuroconv.tools.nwb_helpers import AVAILABLE_HDF5_COMPRESSION_METHODS
+
return list(AVAILABLE_HDF5_COMPRESSION_METHODS)
+
@app.route("/compression/zarr")
def get_zarr_compression_methods():
from neuroconv.tools.nwb_helpers import AVAILABLE_ZARR_COMPRESSION_METHODS
- return list(AVAILABLE_ZARR_COMPRESSION_METHODS)
-
-
+ return list(AVAILABLE_ZARR_COMPRESSION_METHODS)
@app.route("/get-recommended-species")
diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py
index 46d2ddb95..b06e4f422 100644
--- a/pyflask/manageNeuroconv/manage_neuroconv.py
+++ b/pyflask/manageNeuroconv/manage_neuroconv.py
@@ -671,24 +671,20 @@ def get_interface_alignment(info: dict) -> dict:
def get_backend_configuration(info: dict) -> dict:
import numpy as np
- from neuroconv.tools.nwb_helpers import make_or_load_nwbfile, get_default_backend_configuration, HDF5BackendConfiguration, configure_backend
+ from neuroconv.tools.nwb_helpers import (
+ make_or_load_nwbfile,
+ get_default_backend_configuration,
+ HDF5BackendConfiguration,
+ configure_backend,
+ )
backend_configuration = info.get("configuration")
converter, metadata, path_info = get_conversion_info(info)
-
- PROPS_TO_REMOVE = [
- "object_id",
- "dataset_name",
- "location_in_file",
- "dtype"
- ]
+ PROPS_TO_REMOVE = ["object_id", "dataset_name", "location_in_file", "dtype"]
- PROPS_TO_AVOID = [
- "full_shape"
- ]
-
+ PROPS_TO_AVOID = ["full_shape"]
with make_or_load_nwbfile(
nwbfile_path=path_info["file"],
@@ -708,17 +704,15 @@ def get_backend_configuration(info: dict) -> dict:
for key, value in item.items():
# Avoid setting compression options if unspecified
- if (key == 'compression_options' and len(value) == 0):
+ if key == "compression_options" and len(value) == 0:
setattr(configuration.dataset_configurations[name], key, None)
# Avoid certain properties passed to the GUIDE
- elif (key not in PROPS_TO_AVOID):
+ elif key not in PROPS_TO_AVOID:
setattr(configuration.dataset_configurations[name], key, value)
-
configure_backend(nwbfile=nwbfile, backend_configuration=configuration)
-
def custom_encoder(obj):
if isinstance(obj, np.ndarray):
return obj.tolist()
@@ -731,12 +725,12 @@ def custom_encoder(obj):
serialized = json.loads(json.dumps(configuration.dict(), default=custom_encoder))
- dataset_configurations = serialized["dataset_configurations"] # Only provide dataset configurations
+ dataset_configurations = serialized["dataset_configurations"] # Only provide dataset configurations
for dataset in dataset_configurations.values():
for key in PROPS_TO_REMOVE:
del dataset[key]
-
+
return dataset_configurations
@@ -818,7 +812,11 @@ def update_conversion_progress(**kwargs):
del ecephys_metadata["ElectrodeColumns"]
- return converter, resolved_metadata, dict(file=resolved_output_path, directory=resolved_output_directory, default=default_output_directory)
+ return (
+ converter,
+ resolved_metadata,
+ dict(file=resolved_output_path, directory=resolved_output_directory, default=default_output_directory),
+ )
def convert_to_nwb(info: dict) -> str:
@@ -828,7 +826,6 @@ def convert_to_nwb(info: dict) -> str:
source_data = info.get("source_data", False)
backend_configuration = info.get("configuration")
-
converter, metadata, path_info = get_conversion_info(info)
output_path = path_info["file"]
@@ -840,7 +837,7 @@ def convert_to_nwb(info: dict) -> str:
options = (
{
interface: (
- { "stub_test": run_stub_test } # , "iter_opts": {"report_hook": update_conversion_progress}}
+ {"stub_test": run_stub_test} # , "iter_opts": {"report_hook": update_conversion_progress}}
if available_options.get("properties").get(interface).get("properties", {}).get("stub_test")
else {}
)
diff --git a/schemas/backend-configuration.schema.ts b/schemas/backend-configuration.schema.ts
index 722fa6b77..cba3eef61 100644
--- a/schemas/backend-configuration.schema.ts
+++ b/schemas/backend-configuration.schema.ts
@@ -47,7 +47,7 @@ export const getSchema = (method='hdf5') => {
copy.properties["compression_method"].enum = resolved[method] ?? sharedCompressionMethods
return copy
}
-
+
const setReady: any = {}
diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index f896955e4..d2235616e 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -157,7 +157,7 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
})
const units = ecephys.properties["Units"]
-
+
if (units) {
units.title = "Summarized Units"
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index f423faf73..1c1845fdd 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -926,7 +926,7 @@ export class JSONSchemaInput extends LitElement {
const allowPatternProperties = isPatternProperties(this.pattern);
const allowAdditionalProperties = isAdditionalProperties(this.pattern);
- const editableInline = [ 'string', 'number' ]
+ const editableInline = ["string", "number"];
// Provide default item types
if (isArray) {
@@ -946,15 +946,12 @@ export class JSONSchemaInput extends LitElement {
const fileSystemFormat = isFilesystemSelector(name, itemSchema?.format);
if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
-
// Create tables if possible
else if (editableInline.includes(itemSchema?.type) && !itemSchema.properties) {
-
-
const postprocess = (v) => {
- if (itemSchema?.type === 'number') return parseFloat(v)
- else return v
- }
+ if (itemSchema?.type === "number") return parseFloat(v);
+ else return v;
+ };
const list = new List({
items: this.value,
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index 0480fcb4d..fa85dd222 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -140,12 +140,7 @@ export class Page extends LitElement {
}
}
- async runConversions(
- conversionOptions = {},
- toRun,
- options = {},
- backendFunctionToRun = runConversion
- ) {
+ async runConversions(conversionOptions = {}, toRun, options = {}, backendFunctionToRun = runConversion) {
let original = toRun;
if (!Array.isArray(toRun)) toRun = this.mapSessions();
@@ -200,7 +195,6 @@ export class Page extends LitElement {
const sourceDataCopy = structuredClone(sessionResults.source_data);
-
// Resolve the correct session info from all of the metadata for this conversion
const sessionInfo = {
...sessionResults,
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedBackendConfiguration.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedBackendConfiguration.js
index 2a9a83cfb..de303bb0b 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedBackendConfiguration.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedBackendConfiguration.js
@@ -19,8 +19,8 @@ const getBackendConfigurations = (info, options = {}) => run(`configuration`, in
const itemIgnore = {
full_shape: true,
- compression_options: true
-}
+ compression_options: true,
+};
export class GuidedBackendConfigurationPage extends ManagedPage {
constructor(...args) {
@@ -33,11 +33,11 @@ export class GuidedBackendConfigurationPage extends ManagedPage {
};
form;
- instances = []
+ instances = [];
#getForm = (sub, ses) => {
- const found = this.instances.find(o => o.session === ses && o.subject === sub )
- return found?.instance instanceof JSONSchemaForm ? found.instance : null
- }
+ const found = this.instances.find((o) => o.session === ses && o.subject === sub);
+ return found?.instance instanceof JSONSchemaForm ? found.instance : null;
+ };
header = {
subtitle: "Configure your backend",
@@ -59,7 +59,7 @@ export class GuidedBackendConfigurationPage extends ManagedPage {
if (instance instanceof JSONSchemaForm) await instance.validate(); // Will throw an error in the callback
}
- await this.getBackendConfiguration() // Validate by trying to set backend configuration with the latest values
+ await this.getBackendConfiguration(); // Validate by trying to set backend configuration with the latest values
return this.to(1);
},
@@ -83,113 +83,105 @@ export class GuidedBackendConfigurationPage extends ManagedPage {
}
renderInstance = ({ session, subject, info }) => {
-
- this.localState.results[subject][session].configuration = info
+ this.localState.results[subject][session].configuration = info;
let instance;
if (Object.keys(info).length === 0) {
instance = document.createElement("span");
instance.innerText = "No configuration options available for this session";
- }
-
- else {
-
- const itemSchema = getSchema()
+ } else {
+ const itemSchema = getSchema();
- const schema = { type: 'object', properties: {} }
+ const schema = { type: "object", properties: {} };
- const reorganized = Object.entries(info).reduce((acc, [ name, item ]) => {
+ const reorganized = Object.entries(info).reduce((acc, [name, item]) => {
+ const splitName = name.split("/");
- const splitName = name.split('/')
+ const resolved = { schema, results: acc };
- const resolved = { schema, results: acc }
-
- const lenSplit = splitName.length
+ const lenSplit = splitName.length;
splitName.reduce((acc, key, i) => {
-
- const { schema, results } = acc
-
- const props = schema.properties ?? (schema.properties = {})
-
- // Set directly on last iteration
- if (i === (lenSplit - 1)) {
- props[key] = {...itemSchema}
- if (item.compression_options == null) item.compression_options = {} // Set blank compression options to an empty object
- results[key] = item
- return
- }
-
- // Otherwise drill into the results
- else {
- const thisSchema = props[key] ?? (props[key] = {})
- if (!results[key]) results[key] = {}
- return { schema: thisSchema, results: results[key] }
- }
-
- }, resolved)
-
- return acc
-
- }, {})
-
- const existingForm = this.#getForm(subject, session)
+ const { schema, results } = acc;
+
+ const props = schema.properties ?? (schema.properties = {});
+
+ // Set directly on last iteration
+ if (i === lenSplit - 1) {
+ props[key] = { ...itemSchema };
+ if (item.compression_options == null) item.compression_options = {}; // Set blank compression options to an empty object
+ results[key] = item;
+ return;
+ }
+
+ // Otherwise drill into the results
+ else {
+ const thisSchema = props[key] ?? (props[key] = {});
+ if (!results[key]) results[key] = {};
+ return { schema: thisSchema, results: results[key] };
+ }
+ }, resolved);
+
+ return acc;
+ }, {});
+
+ const existingForm = this.#getForm(subject, session);
if (existingForm) {
- existingForm.results = reorganized // Update resolved values
- return { session, subject, instance: existingForm }
+ existingForm.results = reorganized; // Update resolved values
+ return { session, subject, instance: existingForm };
}
-
instance = new JSONSchemaForm({
schema,
results: reorganized,
ignore: {
- '*': itemIgnore
+ "*": itemIgnore,
},
onUpdate: (updatedPath) => {
- console.log(updatedPath)
- this.unsavedUpdates = true
+ console.log(updatedPath);
+ this.unsavedUpdates = true;
},
onThrow,
// validateOnChange: validate,
- })
+ });
}
return { session, subject, instance };
-
};
getBackendConfiguration = (config = true, opts = {}) => {
-
- if (!opts.title && config === true) opts.title = "Getting backend options for all sessions"
-
+ if (!opts.title && config === true) opts.title = "Getting backend options for all sessions";
return this.runConversions(
- {},
+ {},
config, // All or specific session
- opts,
+ opts,
getBackendConfigurations
- )
- }
+ );
+ };
- #needsUpdate = {}
+ #needsUpdate = {};
render() {
-
- this.#needsUpdate = {}
+ this.#needsUpdate = {};
this.#updateRendered(true);
this.localState = { results: structuredClone(this.info.globalState.results ?? {}) };
const renderInstances = (toIterate) => {
-
const instances = {};
- this.instances = toIterate ? this.mapSessions(this.renderInstance, toIterate) : this.mapSessions(({ subject, session, info }) => this.renderInstance({ subject, session, info: info.configuration }), toIterate);
-
+ this.instances = toIterate
+ ? this.mapSessions(this.renderInstance, toIterate)
+ : this.mapSessions(
+ ({ subject, session, info }) =>
+ this.renderInstance({ subject, session, info: info.configuration }),
+ toIterate
+ );
+
this.instances.forEach(({ subject, session, instance }) => {
if (!instances[`sub-${subject}`]) instances[`sub-${subject}`] = {};
instances[`sub-${subject}`][`ses-${session}`] = instance;
});
-
+
this.manager = new InstanceManager({
header: "Sessions",
instanceType: "Session",
@@ -199,48 +191,48 @@ export class GuidedBackendConfigurationPage extends ManagedPage {
name: "Update",
primary: true,
onClick: async (key) => {
-
const { subject, session } = getInfoFromId(key);
- const existingForm = this.#getForm(subject, session)
- await existingForm.validate()
+ const existingForm = this.#getForm(subject, session);
+ await existingForm.validate();
- const merged = merge(this.localState, structuredClone(this.info.globalState))
+ const merged = merge(this.localState, structuredClone(this.info.globalState));
- const results = await this.getBackendConfiguration( [
+ const results = await this.getBackendConfiguration(
+ [
+ {
+ subject,
+ session,
+ globalState: merged,
+ },
+ ],
{
- subject,
- session,
- globalState:merged,
- },
- ],
- {
- title: `Configuring backend for ${key}`
- }).catch(() => {})
-
-
+ title: `Configuring backend for ${key}`,
+ }
+ ).catch(() => {});
+
if (!results) return;
// Update existing instance
- this.renderInstance({ subject, session, info: results[subject][session] })
+ this.renderInstance({ subject, session, info: results[subject][session] });
- await this.save() // Save if properly returned
-
+ await this.save(); // Save if properly returned
},
},
- ]
- })
-
- return this.manager
-
- }
-
+ ],
+ });
- const hasAll = this.mapSessions(({ session, subject}) => !!this.info.globalState.results[subject][session].configuration)
- if (hasAll.every((v) => v === true)) return renderInstances()
+ return this.manager;
+ };
+ const hasAll = this.mapSessions(
+ ({ session, subject }) => !!this.info.globalState.results[subject][session].configuration
+ );
+ if (hasAll.every((v) => v === true)) return renderInstances();
- const promise = this.getBackendConfiguration().then((backendOptions) => renderInstances(backendOptions)).catch((error) => html`${error}
`);
+ const promise = this.getBackendConfiguration()
+ .then((backendOptions) => renderInstances(backendOptions))
+ .catch((error) => html`${error}
`);
const untilResult = until(promise, html`Loading form contents...`);
@@ -249,7 +241,6 @@ export class GuidedBackendConfigurationPage extends ManagedPage {
});
return untilResult;
-
}
}