zombie-squirrel 0.8.4__tar.gz → 0.8.5__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {zombie_squirrel-0.8.4/src/zombie_squirrel.egg-info → zombie_squirrel-0.8.5}/PKG-INFO +2 -2
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/README.md +1 -1
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/__init__.py +1 -1
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorn_contents/asset_basics.py +11 -3
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorn_contents/raw_to_derived.py +6 -2
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorn_contents/source_data.py +6 -2
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorn_contents/unique_project_names.py +6 -2
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorn_contents/unique_subject_ids.py +6 -2
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorns.py +4 -13
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/utils.py +12 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5/src/zombie_squirrel.egg-info}/PKG-INFO +2 -2
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/LICENSE +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/pyproject.toml +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/setup.cfg +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/setup.py +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorn_contents/__init__.py +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/forest.py +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/sync.py +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel.egg-info/SOURCES.txt +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel.egg-info/dependency_links.txt +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel.egg-info/requires.txt +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel.egg-info/top_level.txt +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/tests/test_acorns.py +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/tests/test_sync.py +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/tests/test_trees.py +0 -0
- {zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/tests/test_utils.py +0 -0
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Metadata-Version: 2.4
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Name: zombie-squirrel
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Version: 0.8.
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Version: 0.8.5
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Summary: Generated from aind-library-template
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Author: Allen Institute for Neural Dynamics
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License: MIT
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[](https://github.com/semantic-release/semantic-release)
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<img src="zombie-squirrel_logo.png" width="400" alt="Logo (image from ChatGPT)">
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[](https://github.com/semantic-release/semantic-release)
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<img src="zombie-squirrel_logo.png" width="400" alt="Logo (image from ChatGPT)">
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Provides functions to fetch and cache project names, subject IDs, and asset
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metadata from the AIND metadata database with support for multiple backends."""
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__version__ = "0.8.
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__version__ = "0.8.5"
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from zombie_squirrel.acorn_contents.asset_basics import asset_basics # noqa: F401
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from zombie_squirrel.acorn_contents.raw_to_derived import raw_to_derived # noqa: F401
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{zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorn_contents/asset_basics.py
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from aind_data_access_api.document_db import MetadataDbClient
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import zombie_squirrel.acorns as acorns
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from zombie_squirrel.utils import setup_logging
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from zombie_squirrel.utils import setup_logging, SquirrelMessage
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@acorns.register_acorn(acorns.NAMES["basics"])
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if df.empty or force_update:
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setup_logging()
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logging.info(
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logging.info(SquirrelMessage(
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tree=acorns.TREE.__class__.__name__,
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acorn=acorns.NAMES["basics"],
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message="Updating cache"
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).to_json())
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df = pd.DataFrame(
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columns=[
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"_id",
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BATCH_SIZE = 100
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asset_records = []
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for i in range(0, len(keep_ids), BATCH_SIZE):
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logging.info(
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logging.info(SquirrelMessage(
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tree=acorns.TREE.__class__.__name__,
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acorn=acorns.NAMES["basics"],
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message=f"Fetching batch {i // BATCH_SIZE + 1}"
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).to_json())
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batch_ids = keep_ids[i: i + BATCH_SIZE]
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batch_records = client.retrieve_docdb_records(
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filter_query={"_id": {"$in": batch_ids}},
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{zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorn_contents/raw_to_derived.py
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from aind_data_access_api.document_db import MetadataDbClient
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import zombie_squirrel.acorns as acorns
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from zombie_squirrel.utils import setup_logging
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from zombie_squirrel.utils import setup_logging, SquirrelMessage
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@acorns.register_acorn(acorns.NAMES["r2d"])
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if df.empty or force_update:
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setup_logging()
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logging.info(
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logging.info(SquirrelMessage(
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tree=acorns.TREE.__class__.__name__,
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acorn=acorns.NAMES["r2d"],
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message="Updating cache"
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).to_json())
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client = MetadataDbClient(
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host=acorns.API_GATEWAY_HOST,
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version="v2",
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{zombie_squirrel-0.8.4 → zombie_squirrel-0.8.5}/src/zombie_squirrel/acorn_contents/source_data.py
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from aind_data_access_api.document_db import MetadataDbClient
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import zombie_squirrel.acorns as acorns
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from zombie_squirrel.utils import setup_logging
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from zombie_squirrel.utils import setup_logging, SquirrelMessage
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@acorns.register_acorn(acorns.NAMES["d2r"])
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setup_logging()
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logging.info(
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logging.info(SquirrelMessage(
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tree=acorns.TREE.__class__.__name__,
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acorn=acorns.NAMES["d2r"],
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message="Updating cache"
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).to_json())
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client = MetadataDbClient(
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host=acorns.API_GATEWAY_HOST,
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version="v2",
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from aind_data_access_api.document_db import MetadataDbClient
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import zombie_squirrel.acorns as acorns
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from zombie_squirrel.utils import setup_logging
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from zombie_squirrel.utils import setup_logging, SquirrelMessage
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@acorns.register_acorn(acorns.NAMES["upn"])
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setup_logging()
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logging.info(
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logging.info(SquirrelMessage(
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tree=acorns.TREE.__class__.__name__,
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acorn=acorns.NAMES["upn"],
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message="Updating cache"
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).to_json())
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client = MetadataDbClient(
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host=acorns.API_GATEWAY_HOST,
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version="v2",
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import zombie_squirrel.acorns as acorns
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from zombie_squirrel.utils import setup_logging, SquirrelMessage
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@acorns.register_acorn(acorns.NAMES["usi"])
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setup_logging()
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logging.info(SquirrelMessage(
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tree=acorns.TREE.__class__.__name__,
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acorn=acorns.NAMES["usi"],
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message="Updating cache"
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client = MetadataDbClient(
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host=acorns.API_GATEWAY_HOST,
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version="v2",
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forest_type = os.getenv("FOREST_TYPE", "memory").lower()
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if forest_type == "
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if forest_type == "s3": # pragma: no cover
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logging.info("Using S3 forest for caching")
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TREE = S3Tree()
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elif forest_type == "memory":
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logging.info("Using in-memory forest for caching")
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else:
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raise ValueError(f"Unknown FOREST_TYPE: {forest_type}")
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# --- Acorn registry and names -----------------------------------------------------
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return decorator
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# Import acorn_contents modules to trigger registration
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# This must be done after the registry and decorator are defined
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from zombie_squirrel.acorn_contents import ( # noqa: E402, F401
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asset_basics,
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raw_to_derived,
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source_data,
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"""Utility functions for zombie-squirrel package."""
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import logging
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from pydantic import BaseModel
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class SquirrelMessage(BaseModel):
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"""Structured logging message for zombie-squirrel operations."""
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tree: str
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acorn: str
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message: str
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def to_json(self) -> str:
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"""Convert message to JSON string."""
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return self.model_dump_json()
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def setup_logging():
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Metadata-Version: 2.4
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Name: zombie-squirrel
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Version: 0.8.
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Version: 0.8.5
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Summary: Generated from aind-library-template
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Author: Allen Institute for Neural Dynamics
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License: MIT
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[](https://github.com/semantic-release/semantic-release)
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<img src="zombie-squirrel_logo.png" width="400" alt="Logo (image from ChatGPT)">
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