zombie-squirrel 0.8.2__py3-none-any.whl → 0.8.4__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__ = "0.8.2"
+__version__ = "0.8.4"
 
 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
 
 
 @acorns.register_acorn(acorns.NAMES["basics"])
@@ -37,7 +38,13 @@ def asset_basics(force_update: bool = False) -> pd.DataFrame:
         "location",
     ]
 
+    if df.empty and not force_update:
+        raise ValueError(
+            "Cache is empty. Use force_update=True to fetch data from database."
+        )
+
     if df.empty or force_update:
+        setup_logging()
         logging.info("Updating cache for asset basics")
         df = pd.DataFrame(
             columns=[

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
 
 
 @acorns.register_acorn(acorns.NAMES["r2d"])
@@ -22,7 +23,13 @@ def raw_to_derived(force_update: bool = False) -> pd.DataFrame:
         DataFrame with _id and derived_records columns."""
     df = acorns.TREE.scurry(acorns.NAMES["r2d"])
 
+    if df.empty and not force_update:
+        raise ValueError(
+            "Cache is empty. Use force_update=True to fetch data from database."
+        )
+
     if df.empty or force_update:
+        setup_logging()
         logging.info("Updating cache for raw to derived mapping")
         client = MetadataDbClient(
             host=acorns.API_GATEWAY_HOST,
@@ -50,9 +57,10 @@ def raw_to_derived(force_update: bool = False) -> pd.DataFrame:
             source_data_list = derived_record.get("data_description", {}).get("source_data", [])
             derived_id = derived_record["_id"]
             # Add this derived record to each raw record it depends on
-            for source_id in source_data_list:
-                if source_id in raw_to_derived_map:
-                    raw_to_derived_map[source_id].append(derived_id)
+            if source_data_list:
+                for source_id in source_data_list:
+                    if source_id in raw_to_derived_map:
+                        raw_to_derived_map[source_id].append(derived_id)
 
         # Convert to DataFrame
         data = []

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
 
 
 @acorns.register_acorn(acorns.NAMES["d2r"])
@@ -22,7 +23,13 @@ def source_data(force_update: bool = False) -> pd.DataFrame:
         DataFrame with _id and source_data columns."""
     df = acorns.TREE.scurry(acorns.NAMES["d2r"])
 
+    if df.empty and not force_update:
+        raise ValueError(
+            "Cache is empty. Use force_update=True to fetch data from database."
+        )
+
     if df.empty or force_update:
+        setup_logging()
         logging.info("Updating cache for source data")
         client = MetadataDbClient(
             host=acorns.API_GATEWAY_HOST,

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
 
 
 @acorns.register_acorn(acorns.NAMES["upn"])
@@ -22,8 +23,13 @@ def unique_project_names(force_update: bool = False) -> list[str]:
         List of unique project names."""
     df = acorns.TREE.scurry(acorns.NAMES["upn"])
 
+    if df.empty and not force_update:
+        raise ValueError(
+            "Cache is empty. Use force_update=True to fetch data from database."
+        )
+
     if df.empty or force_update:
-        # If cache is missing, fetch data
+        setup_logging()
         logging.info("Updating cache for unique project names")
         client = MetadataDbClient(
             host=acorns.API_GATEWAY_HOST,

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
 
 
 @acorns.register_acorn(acorns.NAMES["usi"])
@@ -22,8 +23,13 @@ def unique_subject_ids(force_update: bool = False) -> list[str]:
         List of unique subject IDs."""
     df = acorns.TREE.scurry(acorns.NAMES["usi"])
 
+    if df.empty and not force_update:
+        raise ValueError(
+            "Cache is empty. Use force_update=True to fetch data from database."
+        )
+
     if df.empty or force_update:
-        # If cache is missing, fetch data
+        setup_logging()
         logging.info("Updating cache for unique subject IDs")
         client = MetadataDbClient(
             host=acorns.API_GATEWAY_HOST,

zombie_squirrel/acorns.py

@@ -45,3 +45,14 @@ 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/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 +1,19 @@
 """Utility functions for zombie-squirrel package."""
 
+import logging
+
+
+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-0.8.2.dist-info → zombie_squirrel-0.8.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: zombie-squirrel
-Version: 0.8.2
+Version: 0.8.4
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT

zombie_squirrel-0.8.4.dist-info/RECORD

@@ -0,0 +1,16 @@
+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,,

zombie_squirrel-0.8.2.dist-info/RECORD

@@ -1,16 +0,0 @@
-zombie_squirrel/__init__.py,sha256=9ab8TQH1uvUteReZQi0QoJfjC32WfRofwMJm6nluA1w,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=cTg016sZbrJH5_As7CqnirumR1hSMn4GiYX0IReoou0,5513
-zombie_squirrel/acorn_contents/raw_to_derived.py,sha256=EFjLP9szzk3Q6jNhyDwxx8rqhG1bFTVmxeCpCAsv6yg,2445
-zombie_squirrel/acorn_contents/source_data.py,sha256=zbw3DnTwXo6xDTZ1uCoIbcYrVBH2r2xZN3trKtxT8cg,1527
-zombie_squirrel/acorn_contents/unique_project_names.py,sha256=Fu0P2DyI91W7xhx1uRk2YVMyFG8WPihDCj7n_A7zL2E,1289
-zombie_squirrel/acorn_contents/unique_subject_ids.py,sha256=dOVn1ObDF86p8S8US__hlyjTGxT0vz01oeGzjoWGFIc,1260
-zombie_squirrel-0.8.2.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
-zombie_squirrel-0.8.2.dist-info/METADATA,sha256=IlGrFVZcitVVqTemTzoZCfoFDKO-xYC4HRskY70ovJI,1898
-zombie_squirrel-0.8.2.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-zombie_squirrel-0.8.2.dist-info/top_level.txt,sha256=FmM0coe4AangURZLjM4JwwRv2B8H6oINYCoZLKLDCKA,16
-zombie_squirrel-0.8.2.dist-info/RECORD,,