From a90805aefe0426699d849bbe80a87329d054b49f Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Sun, 5 Nov 2023 18:08:40 +0200 Subject: [PATCH] Initial commit --- .github/workflows/run_tests.yml | 59 + .gitignore | 164 ++ .pre-commit-config.yaml | 94 + LICENSE | 674 +++++ Makefile | 25 + README.md | 30 + observer/__init__.py | 33 + observer/azclients.py | 79 + observer/cli.py | 40 + observer/ioc.py | 102 + observer/py.typed | 0 observer/settings.py | 20 + poetry.lock | 4209 +++++++++++++++++++++++++++++ pyproject.toml | 126 + requirements/requirements-dev.txt | 1877 +++++++++++++ requirements/requirements.txt | 1576 +++++++++++ tests/__init__.py | 7 + tests/cli_test.py | 12 + tests/import_test.py | 15 + 19 files changed, 9142 insertions(+) create mode 100644 .github/workflows/run_tests.yml create mode 100644 .gitignore create mode 100644 .pre-commit-config.yaml create mode 100644 LICENSE create mode 100644 Makefile create mode 100644 README.md create mode 100644 observer/__init__.py create mode 100644 observer/azclients.py create mode 100644 observer/cli.py create mode 100644 observer/ioc.py create mode 100644 observer/py.typed create mode 100644 observer/settings.py create mode 100644 poetry.lock create mode 100644 pyproject.toml create mode 100644 requirements/requirements-dev.txt create mode 100644 requirements/requirements.txt create mode 100644 tests/__init__.py create mode 100644 tests/cli_test.py create mode 100644 tests/import_test.py diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml new file mode 100644 index 0000000..3c145f3 --- /dev/null +++ b/.github/workflows/run_tests.yml @@ -0,0 +1,59 @@ +name: test + +on: + push: + branches: + - "main" + - "master" + - "dev" + paths: + - "**.py" + - ".github/workflows/*test*.yml" + - "pyproject.toml" + - "poetry.lock" + - "requirements/requirements*.txt" + pull_request: + paths: + - "**.py" + - ".github/workflows/*test*.yml" + - "pyproject.toml" + - "poetry.lock" + - "requirements/requirements*.txt" + +jobs: + test: + name: "test Python ${{ matrix.python }} on ${{ matrix.os }}" + runs-on: "${{ matrix.os }}" + strategy: + fail-fast: false + matrix: + os: [ "ubuntu-latest" ] + python: [ "3.10", "3.11", "3.12" ] + include: + - os: "macos-latest" + python-version: "3.10" + - os: "macos-latest" + python-version: "3.12" + defaults: + run: + shell: "bash -elo pipefail {0}" + + steps: + - uses: "actions/checkout@main" + - uses: "actions/setup-python@main" + with: + python-version: "${{ matrix.python }}" + - uses: "actions/cache@main" + id: "cache" + with: + path: "${{ env.pythonLocation }}" + key: "test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml', 'requirements/*') }}" + - run: "python --version" + - run: "python -mpip --version" + - run: "python -mpip install -r requirements/requirements-dev.txt" + - run: "python -mpip install ./" + - run: "python -mpip cache info" + - run: "python -mpip freeze" + - run: "pytest --version" + - run: "mypy searvey" + - run: "make cov" diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..4e36d42 --- /dev/null +++ b/.gitignore @@ -0,0 +1,164 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +*.ipynb + +secrets/* diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..2642359 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,94 @@ +--- +ci: + skip: ["mypy", "docs"] + autofix_prs: false +default_language_version: + python: "python3" +fail_fast: false + +repos: + - repo: "https://github.com/pre-commit/pre-commit-hooks" + rev: "v4.5.0" + hooks: + - id: "check-added-large-files" + args: ["--maxkb=40000"] + - id: "check-ast" + - id: "check-byte-order-marker" + - id: "check-case-conflict" + - id: "check-docstring-first" + - id: "check-executables-have-shebangs" + - id: "check-json" + - id: "check-symlinks" + - id: "check-merge-conflict" + - id: "check-vcs-permalinks" + - id: "check-xml" + - id: "check-yaml" + - id: "debug-statements" + - id: "end-of-file-fixer" + exclude: ".+\\.ipynb" + - id: "mixed-line-ending" + - id: "name-tests-test" + - id: "trailing-whitespace" + + - repo: "https://github.com/pre-commit/pygrep-hooks" + rev: "v1.10.0" + hooks: + - id: "python-check-blanket-noqa" + - id: "python-check-blanket-type-ignore" + - id: "python-use-type-annotations" + + - repo: "https://github.com/asottile/reorder_python_imports" + rev: "v3.12.0" + hooks: + - id: "reorder-python-imports" + args: + - "--py310-plus" + + - repo: "https://github.com/astral-sh/ruff-pre-commit" + rev: "v0.1.3" + hooks: + - id: "ruff" + args: ["--show-fixes"] + - id: "ruff-format" + + - repo: "https://github.com/python-poetry/poetry" + rev: "1.6.0" + hooks: + - id: "poetry-check" + name: "poetry check" + - id: "poetry-check" + name: "poetry check --lock" + args: ["--lock"] + - id: "poetry-lock" + name: "poetry lock --no-update" + args: ["--no-update"] + - id: "poetry-export" + name: "poetry export main" + args: + [ + "--only", + "main", + "-f", + "requirements.txt", + "-o", + "requirements/requirements.txt", + ] + - id: "poetry-export" + name: "poetry export dev" + args: + [ + "--with", + "dev", + "-f", + "requirements.txt", + "-o", + "requirements/requirements-dev.txt", + ] + + - repo: "local" + hooks: + - id: "mypy" + name: "mypy" + entry: "make mypy" + language: "system" + types: ["python"] diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..c0c4d61 --- /dev/null +++ b/Makefile @@ -0,0 +1,25 @@ +.PHONY: list docs + +list: + @LC_ALL=C $(MAKE) -pRrq -f $(lastword $(MAKEFILE_LIST)) : 2>/dev/null | awk -v RS= -F: '/^# File/,/^# Finished Make data base/ {if ($$1 !~ "^[#.]") {print $$1}}' | sort | grep -E -v -e '^[^[:alnum:]]' -e '^$@$$' + +init: + poetry install --sync --with dev + pre-commit install + +style: + pre-commit run ruff-format -a + +lint: + pre-commit run ruff -a + +mypy: + dmypy run observer + +test: + python -m pytest -vlx + +deps: + pre-commit run poetry-lock -a + pre-commit run poetry-check -a + pre-commit run poetry-export -a diff --git a/README.md b/README.md new file mode 100644 index 0000000..b6503ef --- /dev/null +++ b/README.md @@ -0,0 +1,30 @@ +# `observer` + +`observer` is a library/application for: + +- scraping observation data and storing them on Azure +- accessing the scraped data directly from Azure + +Its main purpose is to support `seareport`. +The code may be open source but you won't find it useful since +you won't have access to the Azure Storage Accounts. + +## Usage + +You must define the following env variables (preferably using direnv): + +- `export STORAGE_ACCOUNT=` +- `export CONTAINER_NAME=` + +```python +import observer + +# Parse IOC metadata +ioc = observer.get_ioc_metadata() + +# Create a `pd.DataFrame` containing the last 2 years of a specific station: +acap2 = observer.read_ioc_df("acap2") + +# Create a `pd.DataFrame` containing the last 5 years of a specific station: +acap = observer.read_ioc_df("acap", no_years=5) +``` diff --git a/observer/__init__.py b/observer/__init__.py new file mode 100644 index 0000000..09a5275 --- /dev/null +++ b/observer/__init__.py @@ -0,0 +1,33 @@ +from __future__ import annotations + +import importlib.metadata + +import fastparquet # noqa: F401=unused import + +from .azclients import get_credential +from .azclients import get_obs_client +from .azclients import get_obs_fs +from .azclients import get_storage_options +from .ioc import get_ioc_metadata +from .ioc import get_ioc_parquet_file +from .ioc import read_ioc_df +from .ioc import write_ioc_df +from .settings import get_settings +from .settings import Settings + +__version__ = importlib.metadata.version(__name__) + + +__all__: list[str] = [ + "get_credential", + "get_ioc_metadata", + "get_ioc_parquet_file", + "get_obs_client", + "get_obs_fs", + "get_settings", + "get_storage_options", + "read_ioc_df", + "Settings", + "write_ioc_df", + "__version__", +] diff --git a/observer/azclients.py b/observer/azclients.py new file mode 100644 index 0000000..344e4e2 --- /dev/null +++ b/observer/azclients.py @@ -0,0 +1,79 @@ +from __future__ import annotations + +import logging +import typing as T + +import adlfs +import azure.identity.aio +from azure.storage.blob import BlobServiceClient +from azure.storage.blob import ContainerClient + +from .settings import get_settings + +logger = logging.getLogger(__name__) + +STORAGE_ACCOUNT = "seareport" +CONTAINER_NAME = "obs" + + +def get_credential() -> azure.identity.ChainedTokenCredential: + credential_chain = ( + azure.identity.AzureCliCredential(), + azure.identity.ManagedIdentityCredential(), + ) + credential = azure.identity.ChainedTokenCredential(*credential_chain) + return credential + + +def get_aio_credential() -> azure.identity.aio.ChainedTokenCredential: + credential_chain = ( + azure.identity.aio.AzureCliCredential(), + azure.identity.aio.ManagedIdentityCredential(), + ) + credential = azure.identity.aio.ChainedTokenCredential(*credential_chain) + return credential + + +def get_blob_client( + storage_account: str = "", + credential: azure.identity.ChainedTokenCredential | None = None, +) -> BlobServiceClient: + if not storage_account: + storage_account = get_settings().storage_account + account_url = f"https:{storage_account}.blob.core.windows.net" + if credential is None: + credential = get_credential() + client = BlobServiceClient(account_url=account_url, credential=credential) + return client + + +def get_obs_client( + storage_account: str = "", + container_name: str = "", + credential: azure.identity.ChainedTokenCredential | None = None, +) -> ContainerClient: + settings = get_settings() + if not storage_account: + storage_account = settings.storage_account + if not container_name: + container_name = settings.container_name + blob_client = get_blob_client(storage_account=storage_account, credential=credential) + container_client = blob_client.get_container_client(container=container_name) + return container_client + + +def get_storage_options( + credential: azure.identity.aio.ChainedTokenCredential | None = None, +) -> dict[str, T.Any]: + settings = get_settings() + if credential is None: + credential = get_aio_credential() + return dict(account_name=settings.storage_account, credential=credential) + + +def get_obs_fs( + credential: azure.identity.aio.ChainedTokenCredential | None = None, +) -> adlfs.AzureBlobFileSystem: + storage_options = get_storage_options(credential=credential) + fs = adlfs.AzureBlobFileSystem(**storage_options) + return fs diff --git a/observer/cli.py b/observer/cli.py new file mode 100644 index 0000000..813b052 --- /dev/null +++ b/observer/cli.py @@ -0,0 +1,40 @@ +from __future__ import annotations + +from typing import Annotated + +import typer + +# from .cluster_app import cluster_app +# from .data_app import data_app +# from .model_app import model_app +# from .tools import SHOW_OUTPUT_OPTION +# from .tools import SHOW_TRACEBACK_OPTION +# from ..various import do_login +# from ..various import healthcheck as api_healthcheck + + +app = typer.Typer( + add_completion=False, + add_help_option=True, + no_args_is_help=True, + pretty_exceptions_enable=False, + rich_markup_mode="rich", + help="Observer: Scrape and access observation data", +) +# app.add_typer(cluster_app, name="cluster") +# app.add_typer(data_app, name="data") +# app.add_typer(model_app, name="model") + + +@app.command() +def main( + a: Annotated[str, typer.Option(help="This is option a")], + # timeout: Annotated[int, typer.Option( help="The timeout countdown. If it expires, you probably haven't setup the managed identity correctly.")] = 5, + # no_attempts: Annotated[int, typer.Option(help="How many times to retry to login")] = 3, + # show_output: Annotated[bool, SHOW_OUTPUT_OPTION] = True, + # show_traceback: Annotated[bool, SHOW_TRACEBACK_OPTION] = True, +) -> None: ## fmt: skip + """ + Login to [blue]azure-cli[/blue] and [blue]azcopy[/blue] using [italic]system-managed-identity[/italic]. + + """ diff --git a/observer/ioc.py b/observer/ioc.py new file mode 100644 index 0000000..b7553d3 --- /dev/null +++ b/observer/ioc.py @@ -0,0 +1,102 @@ +from __future__ import annotations + +import typing as T + +import azure.identity.aio +import fastparquet +import pandas as pd + +from .azclients import get_obs_fs +from .azclients import get_storage_options +from .settings import get_settings + + +def _get_metadata_uri() -> str: + settings = get_settings() + uri = f"az://{settings.container_name}/ioc/metadata.parquet" + return uri + + +def _get_station_uri(ioc_code: str) -> str: + settings = get_settings() + uri = f"az://{settings.container_name}/ioc/{ioc_code}.parquet" + return uri + + +def get_ioc_metadata(credential: azure.identity.aio.ChainedTokenCredential | None = None) -> pd.DataFrame: + """ + Return the IOC metadata from Blob + """ + settings = get_settings() + storage_options = get_storage_options(credential=credential) + df = pd.read_parquet( + _get_metadata_uri(), + storage_options=storage_options, + engine=settings.engine, + ) + return df + + +def write_ioc_df( + df: pd.DataFrame, + ioc_code: str, + compression_level: int = 0, + credential: azure.identity.aio.ChainedTokenCredential | None = None, +) -> None: + settings = get_settings() + uri = _get_station_uri(ioc_code) + storage_options = get_storage_options(credential=credential) + if "year" not in df.columns: + df = df.assign(year=df.index.year) + df.to_parquet( + uri, + partition_cols="year", + # file_scheme="hive", + index=True, + storage_options=storage_options, + engine=settings.engine, + compression={ + "_default": { + "type": "zstd", + "args": {"level": compression_level}, + } + }, + ) + + +# def read_ioc_df( +# ioc_code: str, +# credential: azure.identity.aio.ChainedTokenCredential | None = None, +# **kwargs: dict[str, T.Any], +# ) -> pd.DataFrame: +# settings = get_settings() +# storage_options = get_storage_options(credential=credential) +# df = pd.read_parquet( +# path=_get_station_uri(ioc_code), +# storage_options=storage_options, +# engine=settings.engine, +# **kwargs, +# ) +# return df + + +def get_ioc_parquet_file( + ioc_code: str, + credential: azure.identity.aio.ChainedTokenCredential | None = None, + **kwargs: dict[str, T.Any], +) -> pd.DataFrame: + uri = _get_station_uri(ioc_code) + fs = get_obs_fs(credential=credential) + pf = fastparquet.ParquetFile(uri, fs=fs, **kwargs) + return pf + + +def read_ioc_df( + ioc_code: str, + no_years: int = 2, + credential: azure.identity.aio.ChainedTokenCredential | None = None, + **kwargs: dict[str, T.Any], +) -> pd.DataFrame: + pf = get_ioc_parquet_file(ioc_code=ioc_code, credential=credential) + df = pf[-no_years:].to_pandas(columns=pf.columns) + return df diff --git a/observer/py.typed b/observer/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/observer/settings.py b/observer/settings.py new file mode 100644 index 0000000..1ddb311 --- /dev/null +++ b/observer/settings.py @@ -0,0 +1,20 @@ +from functools import lru_cache + +from pydantic import Field +from pydantic_settings import BaseSettings +from pydantic_settings import SettingsConfigDict + + +class Settings(BaseSettings): + model_config = SettingsConfigDict() # secrets_dir="./secrets") + + storage_account: str = Field(min_length=1) + container_name: str = Field(min_length=1) + + engine: str = "fastparquet" + + +@lru_cache +def get_settings() -> Settings: + settings = Settings() + return settings diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..ff66975 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,4209 @@ +# This file is automatically @generated by Poetry 1.6.0 and should not be changed by hand. + +[[package]] +name = "adlfs" +version = "2023.10.0" +description = "Access Azure Datalake Gen1 with fsspec and dask" +optional = false +python-versions = ">=3.8" +files = [ + {file = "adlfs-2023.10.0-py3-none-any.whl", hash = "sha256:dfdc8cc782bd78262435fb1bc2a8cfdbdd80342bb1b1ae9dfff968de912b0b09"}, + {file = "adlfs-2023.10.0.tar.gz", hash = "sha256:f5cf06c5b0074d17d43838d4c434791a98420d9e768b36a1a02c7b3930686543"}, +] + +[package.dependencies] +aiohttp = ">=3.7.0" +azure-core = ">=1.23.1,<2.0.0" +azure-datalake-store = ">=0.0.46,<0.1" +azure-identity = "*" +azure-storage-blob = ">=12.12.0" +fsspec = ">=2023.9.0" + +[package.extras] +docs = ["furo", "myst-parser", "numpydoc", "sphinx"] + +[[package]] +name = "aiohttp" +version = "3.8.6" +description = "Async http client/server 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b/tests/__init__.py @@ -0,0 +1,7 @@ +from __future__ import annotations + +import pathlib + +ROOT = pathlib.Path(__file__).parent.parent +TESTS = ROOT / "tests" +DATA = TESTS / "data" diff --git a/tests/cli_test.py b/tests/cli_test.py new file mode 100644 index 0000000..9c48b30 --- /dev/null +++ b/tests/cli_test.py @@ -0,0 +1,12 @@ +from typer.testing import CliRunner + +from observer.cli import app + +runner = CliRunner() + + +# def test_help(): +# result = runner.invoke(app) +# assert result.exit_code == 0 +# assert "Hello Camila" in result.stdout +# assert "Let's have a coffee in Berlin" in result.stdout diff --git a/tests/import_test.py b/tests/import_test.py new file mode 100644 index 0000000..7cdceb8 --- /dev/null +++ b/tests/import_test.py @@ -0,0 +1,15 @@ +from __future__ import annotations + +import importlib + + +def test_import(): + import observer + + del observer + + +def test_version(): + import observer + + assert observer.__version__ == importlib.metadata.version("observer")