zombie-squirrel 0.8.3__py3-none-any.whl → 0.8.5__py3-none-any.whl

zombie_squirrel/__init__.py

@@ -3,7 +3,7 @@
 Provides functions to fetch and cache project names, subject IDs, and asset
 metadata from the AIND metadata database with support for multiple backends."""
 
-__version__ = "0.8.3"
+__version__ = "0.8.5"
 
 from zombie_squirrel.acorn_contents.asset_basics import asset_basics  # noqa: F401
 from zombie_squirrel.acorn_contents.raw_to_derived import raw_to_derived  # noqa: F401

zombie_squirrel/acorn_contents/asset_basics.py

@@ -6,6 +6,7 @@ import pandas as pd
 from aind_data_access_api.document_db import MetadataDbClient
 
 import zombie_squirrel.acorns as acorns
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["basics"])
@@ -43,7 +44,12 @@ def asset_basics(force_update: bool = False) -> pd.DataFrame:
         )
 
     if df.empty or force_update:
-        logging.info("Updating cache for asset basics")
+        setup_logging()
+        logging.info(SquirrelMessage(
+            tree=acorns.TREE.__class__.__name__,
+            acorn=acorns.NAMES["basics"],
+            message="Updating cache"
+        ).to_json())
         df = pd.DataFrame(
             columns=[
                 "_id",
@@ -83,7 +89,11 @@ def asset_basics(force_update: bool = False) -> pd.DataFrame:
         BATCH_SIZE = 100
         asset_records = []
         for i in range(0, len(keep_ids), BATCH_SIZE):
-            logging.info(f"Fetching asset basics batch {i // BATCH_SIZE + 1}...")
+            logging.info(SquirrelMessage(
+                tree=acorns.TREE.__class__.__name__,
+                acorn=acorns.NAMES["basics"],
+                message=f"Fetching batch {i // BATCH_SIZE + 1}"
+            ).to_json())
             batch_ids = keep_ids[i: i + BATCH_SIZE]
             batch_records = client.retrieve_docdb_records(
                 filter_query={"_id": {"$in": batch_ids}},

zombie_squirrel/acorn_contents/raw_to_derived.py

@@ -6,6 +6,7 @@ import pandas as pd
 from aind_data_access_api.document_db import MetadataDbClient
 
 import zombie_squirrel.acorns as acorns
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["r2d"])
@@ -28,7 +29,12 @@ def raw_to_derived(force_update: bool = False) -> pd.DataFrame:
         )
 
     if df.empty or force_update:
-        logging.info("Updating cache for raw to derived mapping")
+        setup_logging()
+        logging.info(SquirrelMessage(
+            tree=acorns.TREE.__class__.__name__,
+            acorn=acorns.NAMES["r2d"],
+            message="Updating cache"
+        ).to_json())
         client = MetadataDbClient(
             host=acorns.API_GATEWAY_HOST,
             version="v2",

zombie_squirrel/acorn_contents/source_data.py

@@ -6,6 +6,7 @@ import pandas as pd
 from aind_data_access_api.document_db import MetadataDbClient
 
 import zombie_squirrel.acorns as acorns
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["d2r"])
@@ -28,7 +29,12 @@ def source_data(force_update: bool = False) -> pd.DataFrame:
         )
 
     if df.empty or force_update:
-        logging.info("Updating cache for source data")
+        setup_logging()
+        logging.info(SquirrelMessage(
+            tree=acorns.TREE.__class__.__name__,
+            acorn=acorns.NAMES["d2r"],
+            message="Updating cache"
+        ).to_json())
         client = MetadataDbClient(
             host=acorns.API_GATEWAY_HOST,
             version="v2",

zombie_squirrel/acorn_contents/unique_project_names.py

@@ -6,6 +6,7 @@ import pandas as pd
 from aind_data_access_api.document_db import MetadataDbClient
 
 import zombie_squirrel.acorns as acorns
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["upn"])
@@ -28,8 +29,12 @@ def unique_project_names(force_update: bool = False) -> list[str]:
         )
 
     if df.empty or force_update:
-        # If cache is missing, fetch data
-        logging.info("Updating cache for unique project names")
+        setup_logging()
+        logging.info(SquirrelMessage(
+            tree=acorns.TREE.__class__.__name__,
+            acorn=acorns.NAMES["upn"],
+            message="Updating cache"
+        ).to_json())
         client = MetadataDbClient(
             host=acorns.API_GATEWAY_HOST,
             version="v2",

zombie_squirrel/acorn_contents/unique_subject_ids.py

@@ -6,6 +6,7 @@ import pandas as pd
 from aind_data_access_api.document_db import MetadataDbClient
 
 import zombie_squirrel.acorns as acorns
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["usi"])
@@ -28,8 +29,12 @@ def unique_subject_ids(force_update: bool = False) -> list[str]:
         )
 
     if df.empty or force_update:
-        # If cache is missing, fetch data
-        logging.info("Updating cache for unique subject IDs")
+        setup_logging()
+        logging.info(SquirrelMessage(
+            tree=acorns.TREE.__class__.__name__,
+            acorn=acorns.NAMES["usi"],
+            message="Updating cache"
+        ).to_json())
         client = MetadataDbClient(
             host=acorns.API_GATEWAY_HOST,
             version="v2",

zombie_squirrel/acorns.py

@@ -16,12 +16,14 @@ API_GATEWAY_HOST = "api.allenneuraldynamics.org"
 
 forest_type = os.getenv("FOREST_TYPE", "memory").lower()
 
-if forest_type == "S3":  # pragma: no cover
+if forest_type == "s3":  # pragma: no cover
     logging.info("Using S3 forest for caching")
     TREE = S3Tree()
-else:
+elif forest_type == "memory":
     logging.info("Using in-memory forest for caching")
     TREE = MemoryTree()
+else:
+    raise ValueError(f"Unknown FOREST_TYPE: {forest_type}")
 
 # --- Acorn registry and names -----------------------------------------------------
 

zombie_squirrel/sync.py

@@ -1,7 +1,5 @@
 """Synchronization utilities for updating all cached data."""
 
-import logging
-
 from .acorns import ACORN_REGISTRY
 
 
@@ -10,9 +8,5 @@ def hide_acorns():
 
     Calls each acorn function with force_update=True to refresh
     all cached data in the tree backend."""
-    logging.basicConfig(
-        level=logging.INFO,
-        format="%(asctime)s %(levelname)s %(message)s"
-    )
     for acorn in ACORN_REGISTRY.values():
         acorn(force_update=True)

zombie_squirrel/utils.py

@@ -1,5 +1,31 @@
 """Utility functions for zombie-squirrel package."""
 
+import logging
+from pydantic import BaseModel
+
+
+class SquirrelMessage(BaseModel):
+    """Structured logging message for zombie-squirrel operations."""
+    tree: str
+    acorn: str
+    message: str
+
+    def to_json(self) -> str:
+        """Convert message to JSON string."""
+        return self.model_dump_json()
+
+
+def setup_logging():
+    """Configure logging for zombie-squirrel package.
+    
+    Sets up INFO level logging with timestamp format.
+    Safe to call multiple times - uses force=True to reconfigure."""
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s %(levelname)s %(message)s",
+        force=True
+    )
+
 
 def prefix_table_name(table_name: str) -> str:
     """Add zombie-squirrel prefix and parquet extension to filenames.

{zombie_squirrel-0.8.3.dist-info → zombie_squirrel-0.8.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: zombie-squirrel
-Version: 0.8.3
+Version: 0.8.5
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT
@@ -21,7 +21,7 @@ Dynamic: license-file
 ![Code Style](https://img.shields.io/badge/code%20style-black-black)
 [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
 ![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
-![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen)
+![Coverage](https://img.shields.io/badge/coverage-99%25-brightgreen)
 ![Python](https://img.shields.io/badge/python->=3.10-blue?logo=python)
 
 <img src="zombie-squirrel_logo.png" width="400" alt="Logo (image from ChatGPT)">

zombie_squirrel-0.8.5.dist-info/RECORD

@@ -0,0 +1,16 @@
+zombie_squirrel/__init__.py,sha256=VuYcirFF0r9h-Rn0WZsLuMZgNPONe0KmzKSxK45yV_s,693
+zombie_squirrel/acorns.py,sha256=ZjGZMzVcV44dI56Efrj_m4yZCV88UPBvOp-IBQ7pAc4,1224
+zombie_squirrel/forest.py,sha256=v0K1u0EA0OptzxocFC-fPEi6xYcnJ9SoWJ6aiPF4jLg,2939
+zombie_squirrel/sync.py,sha256=51ufe4n_3CvYrfTKW4KHngY4k-E9k0I_HGdWOIHY-bA,366
+zombie_squirrel/utils.py,sha256=hyXoWstJ7rUYZVmazEtt5hXJ4SAMbfmlQMDUmBlfFZw,1280
+zombie_squirrel/acorn_contents/__init__.py,sha256=N4Wun9kn44_nCwV4g6naEVzf76ozOgEoupAHLYpiGsI,224
+zombie_squirrel/acorn_contents/asset_basics.py,sha256=PYN1NQsTVVCdLVd7JgTMTf5uepABOKVtSe4Sx_wrA1g,6037
+zombie_squirrel/acorn_contents/raw_to_derived.py,sha256=7y2xA7GLC2hMj_Z7gz-uBOKiVdzGjBtQ2lsgHzASnOg,2853
+zombie_squirrel/acorn_contents/source_data.py,sha256=I7A3mHqVO4C4880w82LNlBHZZ72uSHw3eCwrKtVCnSI,1901
+zombie_squirrel/acorn_contents/unique_project_names.py,sha256=VAS0CZzsC9ObPM39KfrIjYPDIVcqu9H9wyZz8styznQ,1612
+zombie_squirrel/acorn_contents/unique_subject_ids.py,sha256=H_eb3ucayNOdt4GtW26qckqvX6qGcRU59Q_D9NlnSbg,1585
+zombie_squirrel-0.8.5.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
+zombie_squirrel-0.8.5.dist-info/METADATA,sha256=pXffN2yY6CD9ygtZhqGxeWF1VVL_qg4ZunrKKO23c8w,1897
+zombie_squirrel-0.8.5.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+zombie_squirrel-0.8.5.dist-info/top_level.txt,sha256=FmM0coe4AangURZLjM4JwwRv2B8H6oINYCoZLKLDCKA,16
+zombie_squirrel-0.8.5.dist-info/RECORD,,

zombie_squirrel-0.8.3.dist-info/RECORD

@@ -1,16 +0,0 @@
-zombie_squirrel/__init__.py,sha256=46-EAdFSa5UsVaOENsqKKw2wVBlGRDrQojdWE4SU14s,693
-zombie_squirrel/acorns.py,sha256=BLhySoLfb7D6IfbNMOhxbLJba-8Wp-L9e1w_2KozjjM,1134
-zombie_squirrel/forest.py,sha256=v0K1u0EA0OptzxocFC-fPEi6xYcnJ9SoWJ6aiPF4jLg,2939
-zombie_squirrel/sync.py,sha256=9cpfSzTj0cQz4-d3glMAOejCZgekMirLc-dwEFFQhlg,496
-zombie_squirrel/utils.py,sha256=kojQpHUKlRJD7WEZDfcpQIZTj9iUrtX5_6F-gWWzJW0,628
-zombie_squirrel/acorn_contents/__init__.py,sha256=N4Wun9kn44_nCwV4g6naEVzf76ozOgEoupAHLYpiGsI,224
-zombie_squirrel/acorn_contents/asset_basics.py,sha256=EZ4jGiO2JYyMZuhZ0DsCyOtEk2jL_oAqAO6HPVwrhY8,5669
-zombie_squirrel/acorn_contents/raw_to_derived.py,sha256=Ld9gbYDmg6hVvB4ai_T1A4mAiU7shSq_ZEDSg4HPJ3M,2646
-zombie_squirrel/acorn_contents/source_data.py,sha256=XoepH1EZUYy4QTLzXW5sP8zBn1mjoMVDLtWfy0TPHoA,1683
-zombie_squirrel/acorn_contents/unique_project_names.py,sha256=k0ePwdrDHDe5rvdPZOfL1X9VlsUZcMtTkUWDw_vuZkw,1445
-zombie_squirrel/acorn_contents/unique_subject_ids.py,sha256=nsew2-bHCcmxfaYCWzjUEx9T2cohL_E7OuRsQjJl8KY,1416
-zombie_squirrel-0.8.3.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
-zombie_squirrel-0.8.3.dist-info/METADATA,sha256=HpbkwFYI5U0OzKDRyYUXASOjxlcbUks6GmL-EreBt4U,1898
-zombie_squirrel-0.8.3.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-zombie_squirrel-0.8.3.dist-info/top_level.txt,sha256=FmM0coe4AangURZLjM4JwwRv2B8H6oINYCoZLKLDCKA,16
-zombie_squirrel-0.8.3.dist-info/RECORD,,