Small fixes (#1256)

* improve error message for 1253

* fix fetch_nwb in Nwbfile per 1243

* update changelog

* lint update

Author: samuelbray32

CHANGELOG.md

@@ -11,12 +11,14 @@
 - Update export process to include `~external` tables #1239
 - Only add merge parts to `source_class_dict` if present in codebase #1237
 - Remove cli module #1250
+- Fix column error in `check_threads` method #1256
 
 ### Pipelines
 
 - Common
     - Set `probe_id` as `probe_description` when inserting from nwb file #1220
     - Default `AnalysisNwbfile.create` permissions are now 777 #1226
+    - Make `Nwbfile.fetch_nwb` functional # 1256
 - Position
     - Allow population of missing `PositionIntervalMap` entries during population
         of `DLCPoseEstimation` #1208

docs/src/api/make_pages.py

@@ -1,5 +1,4 @@
-"""Generate the api pages and navigation.
-"""
+"""Generate the api pages and navigation."""
 
 from pathlib import Path
 

src/spyglass/common/common_nwbfile.py

@@ -75,6 +75,12 @@ def insert_from_relative_file_name(cls, nwb_file_name: str) -> None:
         key["nwb_file_abs_path"] = nwb_file_abs_path
         cls.insert1(key, skip_duplicates=True)
 
+    def fetch_nwb(self):
+        return [
+            get_nwb_file(self.get_abs_path(file))
+            for file in self.fetch("nwb_file_name")
+        ]
+
     @classmethod
     def _get_file_name(cls, nwb_file_name: str) -> str:
         """Get valid nwb file name given substring."""

src/spyglass/utils/dj_mixin.py

@@ -167,10 +167,10 @@ def _nwb_table_tuple(self) -> tuple:
 
         Used to determine fetch_nwb behavior. Also used in Merge.fetch_nwb.
         Implemented as a cached_property to avoid circular imports."""
-        from spyglass.common.common_nwbfile import (  # noqa F401
+        from spyglass.common.common_nwbfile import (
             AnalysisNwbfile,
             Nwbfile,
-        )
+        )  # noqa F401
 
         table_dict = {
             AnalysisNwbfile: "analysis_file_abs_path",
@@ -408,7 +408,7 @@ def _check_delete_permission(self) -> None:
         if None in experimenters:
             raise PermissionError(
                 "Please ensure all Sessions have an experimenter in "
-                + f"SessionExperimenter:\n{sess_summary}"
+                + f"Session.Experimenter:\n{sess_summary}"
             )
 
         user_name = LabMember().get_djuser_name(dj_user)
@@ -841,8 +841,8 @@ def check_threads(self, detailed=False, all_threads=False) -> DataFrame:
                 "Connection ID",  # t.PROCESSLIST_ID -- User connection ID
                 "User",  # t.PROCESSLIST_USER -- User
                 "Host",  # t.PROCESSLIST_HOST -- User machine
-                "Process Database",  # t.PROCESSLIST_DB -- Thread database
                 "Time (s)",  # t.PROCESSLIST_TIME -- Time in seconds
+                "Process Database",  # t.PROCESSLIST_DB -- Thread database
                 "Process",  # t.PROCESSLIST_COMMAND -- Likely Query
                 "State",  # t.PROCESSLIST_STATE
                 "Query",  # t.PROCESSLIST_INFO -- Actual query