Port changes from main

Author: alejoe91

Dockerfile

@@ -25,7 +25,7 @@ RUN pip install wavpack-numcodecs
 # Install spikeinterface-gui from source
 RUN git clone https://github.com/alejoe91/spikeinterface-gui.git && \
     cd spikeinterface-gui && \
-    git checkout f8198db0ac04232f594dcb1bef80c446e41cd775 && \
+    git checkout a616ff653eea37632cac013bf21a39cdea18c0c1 && \
     pip install . && cd ..
 
 

src/aind_ephys_portal/docdb/database.py

@@ -1,10 +1,8 @@
 """Database access functions for the AIND SIGUI Portal."""
 
 import os
-from typing import Optional, List, Dict, Any
+from typing import List, Dict, Any
 
-import numpy as np
-import pandas as pd
 import panel as pn
 from aind_data_access_api.document_db import MetadataDbClient
 
@@ -81,6 +79,7 @@ def get_asset_by_name(asset_name: str):
     response = client.retrieve_docdb_records(filter_query={"name": {"$regex": asset_name, "$options": "i"}}, limit=0)
     return response
 
+
 @pn.cache(ttl=TIMEOUT_1H)
 def get_raw_asset_by_name(asset_name: str):
     """Get all assets that match a given asset name pattern.
@@ -96,22 +95,22 @@ def get_raw_asset_by_name(asset_name: str):
         List of matching asset records.
     """
     raw_name = _raw_name_from_derived(asset_name)
-    response = client.retrieve_docdb_records(filter_query={"name": {"$regex": raw_name, "$options": "i"},
-                                                           "data_description.data_level": "raw"}, limit=0)
+    response = client.retrieve_docdb_records(
+        filter_query={"name": {"$regex": raw_name, "$options": "i"}, "data_description.data_level": "raw"}, limit=0
+    )
     return response
 
 
 @pn.cache(ttl=TIMEOUT_1H)
 def get_all_ecephys_derived() -> List[Dict[str, Any]]:
     """Get a limited set of all records from the database.
-    
+
     Returns
     -------
     list[dict]
         List of records, limited to 50 entries.
     """
-    filter_query = {"data_description.modality.abbreviation": "ecephys", 
-                    "data_description.data_level": "derived"}
+    filter_query = {"data_description.modality.abbreviation": "ecephys", "data_description.data_level": "derived"}
     response = client.retrieve_docdb_records(
         filter_query=filter_query,
     )

src/aind_ephys_portal/ephys_gui_app.py

@@ -1,4 +1,5 @@
 """SIGUI View main entrypoint"""
+
 import urllib
 import param
 

src/aind_ephys_portal/panel/ephys_gui.py

@@ -29,29 +29,33 @@ def __init__(self, analyzer_path, recording_path, **params):
         # Create initial layout
         self.layout = pn.Column(
             pn.Row(
-                pn.widgets.TextInput(name='Analyzer path', value=self.analyzer_path, height=50, sizing_mode="stretch_width"),
-                pn.widgets.TextInput(name='Recording path (optional)', value=self.recording_path, height=50, sizing_mode="stretch_width"),
-                pn.widgets.Button(name='Launch!', button_type='primary', height=50, sizing_mode="stretch_width"),
-                sizing_mode="stretch_width"
+                pn.widgets.TextInput(
+                    name="Analyzer path", value=self.analyzer_path, height=50, sizing_mode="stretch_width"
+                ),
+                pn.widgets.TextInput(
+                    name="Recording path (optional)", value=self.recording_path, height=50, sizing_mode="stretch_width"
+                ),
+                pn.widgets.Button(name="Launch!", button_type="primary", height=50, sizing_mode="stretch_width"),
+                sizing_mode="stretch_width",
             ),
-            self._create_main_window()
+            self._create_main_window(),
         )
 
         # Store widget references
         self.analyzer_input = self.layout[0][0]
         self.recording_input = self.layout[0][1]
         self.launch_button = self.layout[0][2]
-        
+
         # Setup event handlers
-        self.analyzer_input.param.watch(self.update_values, 'value')
-        self.recording_input.param.watch(self.update_values, 'value')
+        self.analyzer_input.param.watch(self.update_values, "value")
+        self.recording_input.param.watch(self.update_values, "value")
         self.launch_button.on_click(self.on_click)
 
     def _initialize(self):
         if self.analyzer_input.value != "":
             spinner = pn.indicators.LoadingSpinner(value=True, sizing_mode="stretch_width")
             # Create a TextArea widget to display logs
-            log_output = pn.widgets.TextAreaInput(value='', sizing_mode="stretch_both")
+            log_output = pn.widgets.TextAreaInput(value="", sizing_mode="stretch_both")
 
             original_stdout = sys.stdout
             sys.stdout = Tee(original_stdout, log_output)  # Redirect stdout
@@ -61,7 +65,9 @@ def _initialize(self):
 
             self.layout[1] = pn.Row(spinner, log_output)
 
-            print(f"Initializing Ephys GUI for:\nAnalyzer path: {self.analyzer_path}\nRecording path: {self.recording_path}")
+            print(
+                f"Initializing Ephys GUI for:\nAnalyzer path: {self.analyzer_path}\nRecording path: {self.recording_path}"
+            )
 
             self._initialize_analyzer()
             if self.recording_path != "":
@@ -97,14 +103,13 @@ def _set_processed_recording(self):
         print(f"Processed recording loaded: {recording_processed}")
         self.analyzer.set_temporary_recording(recording_processed)
 
-
     def _check_if_s3_folder_exists(self, location):
         bucket_name = location.split("/")[2]
         prefix = "/".join(location.split("/")[3:])
         try:
-            s3 = boto3.client('s3')
+            s3 = boto3.client("s3")
             response = s3.list_objects_v2(Bucket=bucket_name, Prefix=prefix, MaxKeys=1)
-            return 'Contents' in response
+            return "Contents" in response
         except Exception as e:
             return False