Merge branch 'backend-configuration' of https://github.com/NeurodataW…

…ithoutBorders/nwb-guide into backend-configuration

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

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")

pyflask/manageNeuroconv/manage_neuroconv.py

@@ -703,13 +703,7 @@ def get_backend_configuration(info: dict) -> dict:
 
     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"]
 
     with make_or_load_nwbfile(
         nwbfile_path=path_info["file"],
@@ -737,12 +731,12 @@ 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
 
 
@@ -824,7 +818,11 @@ 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:
@@ -834,7 +832,6 @@ 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"]
@@ -846,7 +843,7 @@ 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 {}
             )

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 = {}
 

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"

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,

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,