zombie-squirrel 0.1.0__tar.gz

zombie_squirrel-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2022 Allen Institute for Neural Dynamics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

zombie_squirrel-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: zombie-squirrel
+Version: 0.1.0
+Summary: Generated from aind-library-template
+Author: Allen Institute for Neural Dynamics
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: aind-data-access-api[docdb,rds]
+Dynamic: license-file
+
+# zombie-squirrel
+
+[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
+![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)
+![Python](https://img.shields.io/badge/python->=3.10-blue?logo=python)
+
+## Installation
+
+```bash
+pip install zombie-squirrel
+
+```bash
+uv sync
+```
+
+## Usage
+
+### Set backend
+
+```bash
+export REDSHIFT_SECRETS='/aind/prod/redshift/credentials/readwrite'
+export TREE_SPECIES='REDSHIFT'
+```
+
+Options are 'REDSHIFT', 'MEMORY'.
+
+### Scurry (fetch) data
+
+```python
+import zombie_squirrel as zs
+
+unique_project_names = zs.scurry_project_names()
+```
+
+### Hide the acorns
+
+```python
+from zombie_squirrel.sync import hide_acorns
+hide_acorns()
+```

zombie_squirrel-0.1.0/README.md

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+# zombie-squirrel
+
+[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
+![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)
+![Python](https://img.shields.io/badge/python->=3.10-blue?logo=python)
+
+## Installation
+
+```bash
+pip install zombie-squirrel
+
+```bash
+uv sync
+```
+
+## Usage
+
+### Set backend
+
+```bash
+export REDSHIFT_SECRETS='/aind/prod/redshift/credentials/readwrite'
+export TREE_SPECIES='REDSHIFT'
+```
+
+Options are 'REDSHIFT', 'MEMORY'.
+
+### Scurry (fetch) data
+
+```python
+import zombie_squirrel as zs
+
+unique_project_names = zs.scurry_project_names()
+```
+
+### Hide the acorns
+
+```python
+from zombie_squirrel.sync import hide_acorns
+hide_acorns()
+```

zombie_squirrel-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "zombie-squirrel"
+description = "Generated from aind-library-template"
+license = {text = "MIT"}
+requires-python = ">=3.10"
+authors = [
+    {name = "Allen Institute for Neural Dynamics"}
+]
+classifiers = [
+    "Programming Language :: Python :: 3"
+]
+readme = "README.md"
+dynamic = ["version"]
+
+dependencies = [
+    'aind-data-access-api[docdb,rds]',
+]
+
+[dependency-groups]
+dev = [
+    'black',
+    'coverage',
+    'flake8',
+    'interrogate',
+    'isort',
+    'Sphinx',
+    'furo'
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = {attr = "zombie_squirrel.__version__"}
+
+[tool.black]
+line-length = 79
+target_version = ['py310']
+exclude = '''
+
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | _build
+    | build
+    | dist
+    | .conda
+  )/
+  | .gitignore
+)
+'''
+
+[tool.coverage.run]
+omit = ["*__init__*"]
+source = ["zombie_squirrel", "tests"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "if __name__ == .__main__.:",
+    "^from .* import .*",
+    "^import .*",
+    "pragma: no cover"
+]
+fail_under = 100
+
+[tool.isort]
+line_length = 79
+profile = "black"
+skip = [".conda"]
+
+[tool.interrogate]
+exclude = ["setup.py", "docs", "build", ".conda"]
+fail-under = 100

zombie_squirrel-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

zombie_squirrel-0.1.0/setup.py

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+from setuptools import setup
+
+if __name__ == "__main__":
+    setup()

zombie_squirrel-0.1.0/src/zombie_squirrel/__init__.py

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+"""Init package"""
+__version__ = "0.1.0"
+
+from zombie_squirrel.squirrels import unique_project_names

zombie_squirrel-0.1.0/src/zombie_squirrel/acorns.py

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+# forest_cache/acorns.py
+from abc import ABC, abstractmethod
+import pandas as pd
+import os
+
+from aind_data_access_api.rds_tables import Client, RDSCredentials
+
+
+def prefix_table_name(table_name: str) -> str:
+    return "zs_" + table_name
+
+
+class Acorn(ABC):
+    """Base class for a storage backend (the cache)."""
+
+    def __init__(self) -> None:
+        super().__init__()
+
+    @abstractmethod
+    def hide(self, table_name: str, data: pd.DataFrame) -> None:
+        """Store records in the cache."""
+        pass
+
+    @abstractmethod
+    def scurry(self, table_name: str) -> pd.DataFrame:
+        """Fetch records from the cache."""
+        pass
+
+
+class RedshiftAcorn(Acorn):
+    """Stores and retrieves caches using aind-data-access-api
+    Redshift Client"""
+
+    def __init__(self) -> None:
+        REDSHIFT_SECRETS = os.getenv("REDSHIFT_SECRETS", "/aind/prod/redshift/credentials/readwrite")
+        self.rds_client = Client(
+            credentials=RDSCredentials(aws_secrets_name=REDSHIFT_SECRETS),
+        )
+
+    def hide(self, table_name: str, data: pd.DataFrame) -> None:
+        self.rds_client.overwrite_table_with_df(
+            df=data,
+            table_name=prefix_table_name(table_name),
+        )
+
+    def scurry(self, table_name: str) -> pd.DataFrame:
+        return self.rds_client.read_table(table_name=prefix_table_name(table_name))
+
+
+class MemoryAcorn(Acorn):
+    """A simple in-memory backend for testing or local development."""
+    def __init__(self) -> None:
+        super().__init__()
+        self._store: dict[str, pd.DataFrame] = {}
+
+    def hide(self, table_name: str, data: pd.DataFrame) -> None:
+        self._store[table_name] = data
+
+    def scurry(self, table_name: str) -> pd.DataFrame:
+        return self._store.get(table_name, pd.DataFrame())

zombie_squirrel-0.1.0/src/zombie_squirrel/squirrels.py

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+"""Squirrels: functions to fetch and cache data from MongoDB."""
+import pandas as pd
+from typing import Any, Callable, Optional
+from zombie_squirrel.acorns import RedshiftAcorn, MemoryAcorn
+from aind_data_access_api.document_db import MetadataDbClient
+import os
+
+# --- Backend setup ---------------------------------------------------
+
+API_GATEWAY_HOST = "api.allenneuraldynamics.org"
+
+tree_type = os.getenv("TREE_SPECIES", "memory").lower()
+
+if tree_type == "redshift":
+    ACORN = RedshiftAcorn()
+else:
+    ACORN = MemoryAcorn()
+
+# --- Squirrel registry -----------------------------------------------------
+
+SQUIRREL_REGISTRY: dict[str, Callable[[], Any]] = {}
+
+
+def register_squirrel(name: str):
+    """Decorator for registering new squirrels."""
+    def decorator(func):
+        SQUIRREL_REGISTRY[name] = func
+        return func
+    return decorator
+
+
+# --- Squirrels -----------------------------------------------------
+
+
+@register_squirrel("unique-project-names")
+def unique_project_names(force_update: bool = False) -> list[str]:
+    df = ACORN.scurry("unique-project-names")
+
+    if df.empty or force_update:
+        # If cache is missing, fetch data
+        client = MetadataDbClient(
+            host=API_GATEWAY_HOST,
+            version="v2",
+        )
+        unique_project_names = client.aggregate_docdb_records(
+            pipeline=[
+                {"$group": {"_id": "$data_description.project_name"}},
+                {"$project": {"project_name": "$_id", "_id": 0}},
+            ]
+        )
+        df = pd.DataFrame(unique_project_names)
+        ACORN.hide("unique-project-names", df)
+
+    return df["project_name"].tolist()
+
+
+@register_squirrel("unique-subject-ids")
+def unique_subject_ids(force_update: bool = False) -> list[str]:
+    df = ACORN.scurry("unique-subject-ids")
+
+    if df.empty or force_update:
+        # If cache is missing, fetch data
+        client = MetadataDbClient(
+            host=API_GATEWAY_HOST,
+            version="v2",
+        )
+        unique_subject_ids = client.aggregate_docdb_records(
+            pipeline=[
+                {"$group": {"_id": "$subject.subject_id"}},
+                {"$project": {"subject_id": "$_id", "_id": 0}},
+            ]
+        )
+        df = pd.DataFrame(unique_subject_ids)
+        ACORN.hide("unique-subject-ids", df)
+
+    return df["subject_id"].tolist()

zombie_squirrel-0.1.0/src/zombie_squirrel/sync.py

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+"""Sync all acorns"""
+from .squirrels import SQUIRREL_REGISTRY
+
+
+def hide_acorns():
+    for squirrel in SQUIRREL_REGISTRY.values():
+        squirrel(force_update=True)

zombie_squirrel-0.1.0/src/zombie_squirrel.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: zombie-squirrel
+Version: 0.1.0
+Summary: Generated from aind-library-template
+Author: Allen Institute for Neural Dynamics
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: aind-data-access-api[docdb,rds]
+Dynamic: license-file
+
+# zombie-squirrel
+
+[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
+![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)
+![Python](https://img.shields.io/badge/python->=3.10-blue?logo=python)
+
+## Installation
+
+```bash
+pip install zombie-squirrel
+
+```bash
+uv sync
+```
+
+## Usage
+
+### Set backend
+
+```bash
+export REDSHIFT_SECRETS='/aind/prod/redshift/credentials/readwrite'
+export TREE_SPECIES='REDSHIFT'
+```
+
+Options are 'REDSHIFT', 'MEMORY'.
+
+### Scurry (fetch) data
+
+```python
+import zombie_squirrel as zs
+
+unique_project_names = zs.scurry_project_names()
+```
+
+### Hide the acorns
+
+```python
+from zombie_squirrel.sync import hide_acorns
+hide_acorns()
+```

zombie_squirrel-0.1.0/src/zombie_squirrel.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+setup.py
+src/zombie_squirrel/__init__.py
+src/zombie_squirrel/acorns.py
+src/zombie_squirrel/squirrels.py
+src/zombie_squirrel/sync.py
+src/zombie_squirrel.egg-info/PKG-INFO
+src/zombie_squirrel.egg-info/SOURCES.txt
+src/zombie_squirrel.egg-info/dependency_links.txt
+src/zombie_squirrel.egg-info/requires.txt
+src/zombie_squirrel.egg-info/top_level.txt

zombie_squirrel-0.1.0/src/zombie_squirrel.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

zombie_squirrel-0.1.0/src/zombie_squirrel.egg-info/requires.txt

@@ -0,0 +1 @@
+aind-data-access-api[docdb,rds]

zombie_squirrel-0.1.0/src/zombie_squirrel.egg-info/top_level.txt

@@ -0,0 +1 @@
+zombie_squirrel