zombie-squirrel 0.8.4__py3-none-any.whl → 0.8.6__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__ = "0.8.4"
+__version__ = "0.8.6"
 
 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

@@ -6,7 +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
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["basics"])
@@ -45,7 +45,11 @@ def asset_basics(force_update: bool = False) -> pd.DataFrame:
 
     if df.empty or force_update:
         setup_logging()
-        logging.info("Updating cache for asset basics")
+        logging.info(SquirrelMessage(
+            tree=acorns.TREE.__class__.__name__,
+            acorn=acorns.NAMES["basics"],
+            message="Updating cache"
+        ).to_json())
         df = pd.DataFrame(
             columns=[
                 "_id",
@@ -85,7 +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

@@ -6,7 +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
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["r2d"])
@@ -30,7 +30,11 @@ def raw_to_derived(force_update: bool = False) -> pd.DataFrame:
 
     if df.empty or force_update:
         setup_logging()
-        logging.info("Updating cache for raw to derived mapping")
+        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

@@ -6,7 +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
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["d2r"])
@@ -30,7 +30,11 @@ def source_data(force_update: bool = False) -> pd.DataFrame:
 
     if df.empty or force_update:
         setup_logging()
-        logging.info("Updating cache for source data")
+        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

@@ -6,7 +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
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["upn"])
@@ -30,7 +30,11 @@ def unique_project_names(force_update: bool = False) -> list[str]:
 
     if df.empty or force_update:
         setup_logging()
-        logging.info("Updating cache for unique project names")
+        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

@@ -6,7 +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
+from zombie_squirrel.utils import setup_logging, SquirrelMessage
 
 
 @acorns.register_acorn(acorns.NAMES["usi"])
@@ -30,7 +30,11 @@ def unique_subject_ids(force_update: bool = False) -> list[str]:
 
     if df.empty or force_update:
         setup_logging()
-        logging.info("Updating cache for unique subject IDs")
+        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

@@ -9,6 +9,7 @@ from zombie_squirrel.forest import (
     MemoryTree,
     S3Tree,
 )
+from zombie_squirrel.utils import SquirrelMessage
 
 # --- Backend setup ---------------------------------------------------
 
@@ -16,12 +17,22 @@ API_GATEWAY_HOST = "api.allenneuraldynamics.org"
 
 forest_type = os.getenv("FOREST_TYPE", "memory").lower()
 
-if forest_type == "S3":  # pragma: no cover
-    logging.info("Using S3 forest for caching")
+if forest_type == "s3":  # pragma: no cover
+    logging.info(SquirrelMessage(
+        tree="S3Tree",
+        acorn="system",
+        message="Initializing S3 forest for caching"
+    ).to_json())
     TREE = S3Tree()
-else:
-    logging.info("Using in-memory forest for caching")
+elif forest_type == "memory":
+    logging.info(SquirrelMessage(
+        tree="MemoryTree",
+        acorn="system",
+        message="Initializing in-memory forest for caching"
+    ).to_json())
     TREE = MemoryTree()
+else:
+    raise ValueError(f"Unknown FOREST_TYPE: {forest_type}")
 
 # --- Acorn registry and names -----------------------------------------------------
 
@@ -45,14 +56,3 @@ def register_acorn(name: str):
         return func
 
     return decorator
-
-
-# Import acorn_contents modules to trigger registration
-# This must be done after the registry and decorator are defined
-from zombie_squirrel.acorn_contents import (  # noqa: E402, F401
-    asset_basics,
-    raw_to_derived,
-    source_data,
-    unique_project_names,
-    unique_subject_ids,
-)

zombie_squirrel/forest.py

@@ -8,7 +8,7 @@ import boto3
 import duckdb
 import pandas as pd
 
-from zombie_squirrel.utils import get_s3_cache_path, prefix_table_name
+from zombie_squirrel.utils import get_s3_cache_path, prefix_table_name, SquirrelMessage
 
 
 class Tree(ABC):
@@ -53,7 +53,11 @@ class S3Tree(Tree):
             Key=s3_key,
             Body=parquet_buffer.getvalue(),
         )
-        logging.info(f"Stored cache to S3: s3://{self.bucket}/{s3_key}")
+        logging.info(SquirrelMessage(
+            tree="S3Tree",
+            acorn=table_name,
+            message=f"Stored cache to s3://{self.bucket}/{s3_key}"
+        ).to_json())
 
     def scurry(self, table_name: str) -> pd.DataFrame:
         """Fetch DataFrame from S3 parquet file."""
@@ -68,14 +72,18 @@ class S3Tree(Tree):
                 )
             """
             result = duckdb.query(query).to_df()
-            logging.info(
-                f"Retrieved cache from S3: s3://{self.bucket}/{s3_key}"
-            )
+            logging.info(SquirrelMessage(
+                tree="S3Tree",
+                acorn=table_name,
+                message=f"Retrieved cache from s3://{self.bucket}/{s3_key}"
+            ).to_json())
             return result
         except Exception as e:
-            logging.warning(
-                f"Error fetching from cache {s3_key}: {e}"
-            )
+            logging.warning(SquirrelMessage(
+                tree="S3Tree",
+                acorn=table_name,
+                message=f"Error fetching from cache {s3_key}: {e}"
+            ).to_json())
             return pd.DataFrame()
 
 

zombie_squirrel/utils.py

@@ -1,6 +1,18 @@
 """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():

{zombie_squirrel-0.8.4.dist-info → zombie_squirrel-0.8.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: zombie-squirrel
-Version: 0.8.4
+Version: 0.8.6
 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-0.8.6.dist-info/RECORD

@@ -0,0 +1,16 @@
+zombie_squirrel/__init__.py,sha256=xHHJ6bd_QrBfJVqejcucILL05-9V1SHbB3EFC4ebf70,693
+zombie_squirrel/acorns.py,sha256=Sb5bYUGhvTvtWpRn7IuymBbFQ5-WhO6DOJf0hRZ-azI,1484
+zombie_squirrel/forest.py,sha256=hsXBJrtAs4LnAabpIBp88ByDeDXfrK0AePqdkVMz-e8,3262
+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-0.8.6.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
+zombie_squirrel-0.8.6.dist-info/METADATA,sha256=dNdtuz95_8ZWfhRivvf8cUH4gtXGLO0d_6eaGfsHnt8,1897
+zombie_squirrel-0.8.6.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+zombie_squirrel-0.8.6.dist-info/top_level.txt,sha256=FmM0coe4AangURZLjM4JwwRv2B8H6oINYCoZLKLDCKA,16
+zombie_squirrel-0.8.6.dist-info/RECORD,,

zombie_squirrel-0.8.4.dist-info/RECORD

@@ -1,16 +0,0 @@
-zombie_squirrel/__init__.py,sha256=V1ZXhNO1h3PxKP-k5yb8YtU1sgw0ie8JduMXfR3C7Zo,693
-zombie_squirrel/acorns.py,sha256=oFrRkE3P6Mf9ZUCM8JmzDPBdc4gnoc-gVau7kWt0EJY,1429
-zombie_squirrel/forest.py,sha256=v0K1u0EA0OptzxocFC-fPEi6xYcnJ9SoWJ6aiPF4jLg,2939
-zombie_squirrel/sync.py,sha256=51ufe4n_3CvYrfTKW4KHngY4k-E9k0I_HGdWOIHY-bA,366
-zombie_squirrel/utils.py,sha256=v9IsbICSflk5TjSFSgcEoL0FSyU-M8_fn3OYdkjBu8Y,983
-zombie_squirrel/acorn_contents/__init__.py,sha256=N4Wun9kn44_nCwV4g6naEVzf76ozOgEoupAHLYpiGsI,224
-zombie_squirrel/acorn_contents/asset_basics.py,sha256=_vbZS7fa_u-2J592aKWzFd3jFFBZMU7PnrVeF4WWrkw,5741
-zombie_squirrel/acorn_contents/raw_to_derived.py,sha256=iQ5L12VJm2GVUU9J9HjLcr_YhMcHYFGLtXzfqmLrgNM,2718
-zombie_squirrel/acorn_contents/source_data.py,sha256=boO6kd8ksdYzg_LBhmvTFfI1vjJuIFRUKWSC40TVwnA,1755
-zombie_squirrel/acorn_contents/unique_project_names.py,sha256=inHOXd1_XeUVFGv9HT9m4GXE3vN9qbPR0H6aEtzVAZo,1475
-zombie_squirrel/acorn_contents/unique_subject_ids.py,sha256=J9F_I0iR5HU6D2gme6vdC-kMGPxb6F6TfoW1zX1x-PM,1446
-zombie_squirrel-0.8.4.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
-zombie_squirrel-0.8.4.dist-info/METADATA,sha256=FDGupBmCDrMY4maTCb-U2xJeZ0mSp02dWyWI4K2iplA,1898
-zombie_squirrel-0.8.4.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-zombie_squirrel-0.8.4.dist-info/top_level.txt,sha256=FmM0coe4AangURZLjM4JwwRv2B8H6oINYCoZLKLDCKA,16
-zombie_squirrel-0.8.4.dist-info/RECORD,,