From ff0fabf334673e28f7823e57a3886cfb2773babc Mon Sep 17 00:00:00 2001
From: CBroz1 <CBrozdowski@yahoo.com>
Date: Fri, 15 Dec 2023 15:21:21 -0600
Subject: [PATCH] Changelog, docstrings, delay import with cache properties
---
CHANGELOG.md | 1 +
src/spyglass/__init__.py | 2 +-
src/spyglass/common/__init__.py | 5 +-
src/spyglass/settings.py | 1 +
src/spyglass/utils/dj_mixin.py | 111 ++++++++++++++++++++++++++++----
5 files changed, 103 insertions(+), 17 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4da58f2d2..55d0666d5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
- Add SpikeSorting V1 pipeline #651
- Refactor restriction use in `delete_downstream_merge` #703
- Minor fixes to LFPBandV1 populator #706
+- Add `cautious_delete` to Mixin class, intial implementation. #710
## [0.4.3] (November 7, 2023)
diff --git a/src/spyglass/__init__.py b/src/spyglass/__init__.py
index 3f8887d2d..524235c1a 100644
--- a/src/spyglass/__init__.py
+++ b/src/spyglass/__init__.py
@@ -1,4 +1,4 @@
-from .settings import config
+from .settings import config # ensure loaded config dirs
try:
import ndx_franklab_novela
diff --git a/src/spyglass/common/__init__.py b/src/spyglass/common/__init__.py
index 47c00beb0..79219f277 100644
--- a/src/spyglass/common/__init__.py
+++ b/src/spyglass/common/__init__.py
@@ -1,5 +1,6 @@
-import spyglass as sg
+from ..utils.dj_mixin import SpyglassMixin # isort:skip
+from ..settings import prepopulate
from ..utils.nwb_helper_fn import (
close_nwb_files,
estimate_sampling_rate,
@@ -73,5 +74,5 @@
from .populate_all_common import populate_all_common
from .prepopulate import populate_from_yaml, prepopulate_default
-if sg.config["prepopulate"]:
+if prepopulate:
prepopulate_default()
diff --git a/src/spyglass/settings.py b/src/spyglass/settings.py
index 9ae32639b..ed131c557 100644
--- a/src/spyglass/settings.py
+++ b/src/spyglass/settings.py
@@ -440,3 +440,4 @@ def debug_mode(self) -> bool:
waveform_dir = sg_config.waveform_dir
video_dir = sg_config.video_dir
debug_mode = sg_config.debug_mode
+prepopulate = config.get("prepopulate", False)
diff --git a/src/spyglass/utils/dj_mixin.py b/src/spyglass/utils/dj_mixin.py
index 50c02bcb5..91f51f542 100644
--- a/src/spyglass/utils/dj_mixin.py
+++ b/src/spyglass/utils/dj_mixin.py
@@ -2,20 +2,58 @@
from datajoint.table import logger as dj_logger
from datajoint.utils import user_choice
-from spyglass.common.common_nwbfile import AnalysisNwbfile, Nwbfile
from spyglass.utils.dj_helper_fn import fetch_nwb
-from spyglass.utils.dj_merge_tables import delete_downstream_merge
class SpyglassMixin:
- """Mixin for Spyglass DataJoint tables ."""
+ """Mixin for Spyglass DataJoint tables.
+
+ Provides methods for fetching NWBFile objects and checking user permission
+ prior to deleting. As a mixin class, all Spyglass tables can inherit custom
+ methods from a central location.
+
+ Methods
+ -------
+ fetch_nwb(*attrs, **kwargs)
+ Fetch NWBFile object from relevant table. Uses either a foreign key to
+ a NWBFile table (including AnalysisNwbfile) or a _nwb_table attribute to
+ determine which table to use.
+ cautious_delete(force_permission=False, *args, **kwargs)
+ Check user permissions before deleting table rows. Permission is granted
+ to users listed as admin in LabMember table or to users on a team with
+ with the Session experimenter(s). If the table where the delete is
+ executed cannot be linked to a Session, a warning is printed and the
+ delete continues. If the Session has no experimenter, or if the user is
+ not on a team with the Session experimenter(s), a PermissionError is
+ raised. `force_permission` can be set to True to bypass permission check.
+ cdel(*args, **kwargs)
+ Alias for cautious_delete.
+ """
+
+ _nwb_table_dict = {}
+ _delete_dependencies = []
+ _merge_delete_func = None
# ------------------------------- fetch_nwb -------------------------------
- _nwb_table_dict = {
- AnalysisNwbfile: "analysis_file_abs_path",
- Nwbfile: "nwb_file_abs_path",
- }
+ @property
+ def _table_dict(self):
+ """Dict mapping NWBFile table to path attribute name.
+
+ Used to delay import of NWBFile tables until needed, avoiding circular
+ imports.
+ """
+ if not self.__nwb_table_dict:
+ from spyglass.common.common_nwbfile import ( # noqa F401
+ AnalysisNwbfile,
+ Nwbfile,
+ )
+
+ self.__nwb_table_dict = {
+ AnalysisNwbfile: "analysis_file_abs_path",
+ Nwbfile: "nwb_file_abs_path",
+ }
+ return self.__nwb_table_dict
def fetch_nwb(self, *attrs, **kwargs):
"""Fetch NWBFile object from relevant table.
@@ -27,12 +65,14 @@ def fetch_nwb(self, *attrs, **kwargs):
'-> AnalysisNwbfile' in its definition can use a _nwb_table attribute to
specify which table to use.
"""
+ _nwb_table_dict = self._table_dict
+ analysis_table, nwb_table = _nwb_table_dict.keys()
if not hasattr(self, "_nwb_table"):
self._nwb_table = (
- AnalysisNwbfile
+ analysis_table
if "-> AnalysisNwbfile" in self.definition
- else Nwbfile
+ else nwb_table
if "-> Nwbfile" in self.definition
else None
)
@@ -45,13 +85,42 @@ def fetch_nwb(self, *attrs, **kwargs):
return fetch_nwb(
self,
- (self._nwb_table, self._nwb_table_dict[self._nwb_table]),
+ (self._nwb_table, _nwb_table_dict[self._nwb_table]),
*attrs,
**kwargs,
)
# -------------------------------- delete ---------------------------------
+ @property
+ def _delete_deps(self) -> list:
+ """List of tables required for delete permission check.
+
+ Used to delay import of tables until needed, avoiding circular imports.
+ """
+ print("Getting delete deps")
+ if not self._delete_dependencies:
+ print("Importing delete deps")
+ from spyglass.common import LabMember, LabTeam, Session # noqa F401
+
+ self._delete_dependencies = [LabMember, LabTeam, Session]
+ print("Returning delete deps")
+ return self._delete_dependencies
+
+ @property
+ def _merge_del_func(self) -> callable:
+ """Callable: delete_downstream_merge function.
+
+ Used to delay import of func until needed, avoiding circular imports.
+ """
+ if not self._merge_delete_func:
+ from spyglass.utils.dj_merge_tables import ( # noqa F401
+ delete_downstream_merge,
+ )
+
+ self._merge_delete_func = delete_downstream_merge
+ return self._merge_delete_func
+
def _find_session(
self,
table: dj.user_tables.UserTable,
@@ -108,7 +177,7 @@ def _check_delete_permission(self) -> None:
Permission denied because (a) Session has no experimenter, or (b)
user is not on a team with Session experimenter(s).
"""
- from spyglass.common import LabMember, LabTeam, Session # noqa F401
+ LabMember, LabTeam, Session = self._delete_deps
dj_user = dj.config["database.user"]
if dj_user in LabMember().admin: # bypass permission check for admin
@@ -141,13 +210,27 @@ def _check_delete_permission(self) -> None:
# Rename to `delete` when we're ready to use it
# TODO: Intercept datajoint delete confirmation prompt for merge deletes
- def cautious_delete(self, force_permission=False, *args, **kwargs):
- """Delete table rows after checking user permission."""
+ def cautious_delete(self, force_permission: bool = False, *args, **kwargs):
+ """Delete table rows after checking user permission.
+
+ Permission is granted to users listed as admin in LabMember table or to
+ users on a team with with the Session experimenter(s). If the table
+ cannot be linked to Session, a warning is printed and the delete
+ continues. If the Session has no experimenter, or if the user is not on
+ a team with the Session experimenter(s), a PermissionError is raised.
+
+ Parameters
+ ----------
+ force_permission : bool, optional
+ Bypass permission check. Default False.
+ *args, **kwargs : Any
+ Passed to datajoint.table.Table.delete.
+ """
if not force_permission:
self._check_delete_permission()
- merge_deletes = delete_downstream_merge(
+ merge_deletes = self._merge_del_func(
self,
restriction=self.restriction,
dry_run=True,