From 58814204e9299f8936f8c23e0e75c36ae02a41e7 Mon Sep 17 00:00:00 2001 From: Mose Mueller Date: Mon, 5 Jun 2023 15:55:19 +0200 Subject: [PATCH] feat: adding database module --- README.md | 34 +- icon_service_base/database/__init__.py | 4 + .../database/influxdb_connection.py | 121 ++++ .../database/postgres_connection.py | 171 ++++++ poetry.lock | 516 ++++++++++++++---- pyproject.toml | 22 + 6 files changed, 751 insertions(+), 117 deletions(-) create mode 100644 icon_service_base/database/__init__.py create mode 100644 icon_service_base/database/influxdb_connection.py create mode 100644 icon_service_base/database/postgres_connection.py diff --git a/README.md b/README.md index 6d3442e..1aad9db 100644 --- a/README.md +++ b/README.md @@ -2,8 +2,22 @@ ICON Service Base is a git repository that contains code shared among all Icon services in a service-oriented architecture. The repository consists of a backend written in Python and a frontend written in TypeScript. +## Modules + +### Database Module + +The Database module provides a robust and scalable solution for interacting with our PostgreSQL and InfluxDB databases. + +#### PostgreSQL + +The PostgreSQL section includes a class for managing PostgreSQL database sessions (`PostgresDatabaseSession`). It provides a Pythonic interface to the SQL language using the `sqlmodel` library, and includes features for managing transactions and handling errors. + +#### InfluxDB + +The InfluxDB section provides a class (`InfluxDBConnection`) to manage connections to an InfluxDB server. This connection is established using credentials provided through environment variables. The class serves as a context manager to handle these connections, automatically opening and closing the connection when needed. It provides functionalities for writing data points to a bucket and creating new buckets. ## Installation + ### Python Make sure you have Python 3.10 or later installed on your system. The dependencies of this package are handled with [`poetry`](https://python-poetry.org/docs/#installation). You can install the `icon_service_base` like so: @@ -13,6 +27,7 @@ poetry add git+ssh://git@gitlab.phys.ethz.ch:tiqi-projects/qchub/icon-services/i ``` ### TypeScript frontend + Make sure you have Node.js and npm or yarn installed on your system. You can install `@icon-services/icon_service_base` like so: ```bash @@ -20,19 +35,26 @@ npm install git+ssh://git@gitlab.phys.ethz.ch:tiqi-projects/qchub/icon-services/ ``` ## Usage + ### Python + The Python code can be used as a library in other ICON services. Import the relevant modules and classes from the `icon_service_base` package in your Python code, as needed. + ### TypeScript Frontend + The frontend code contains the core of the typescript openAPI clients generated by [`openapi-typescript-codegen`](https://github.com/ferdikoomen/openapi-typescript-codegen/tree/master). This needs to be imported in the ICON services like so: ```ts -import { OpenAPI } from '@icon-services/icon_service_base'; -import { request as __request } from '@icon-services/icon_service_base'; -export { ApiError } from "@icon-services/icon_service_base"; -export { CancelablePromise, CancelError } from '@icon-services/icon_service_base'; -export type { OpenAPIConfig } from '@icon-services/icon_service_base'; +import { OpenAPI } from '@icon-services/icon_service_base' +import { request as __request } from '@icon-services/icon_service_base' +export { ApiError } from '@icon-services/icon_service_base' +export { + CancelablePromise, + CancelError, +} from '@icon-services/icon_service_base' +export type { OpenAPIConfig } from '@icon-services/icon_service_base' ``` ## License -This project is licensed under the MIT License. See the [LICENSE](./LICENSE) file for details. \ No newline at end of file +This project is licensed under the MIT License. See the [LICENSE](./LICENSE) file for details. diff --git a/icon_service_base/database/__init__.py b/icon_service_base/database/__init__.py new file mode 100644 index 0000000..a84f36c --- /dev/null +++ b/icon_service_base/database/__init__.py @@ -0,0 +1,4 @@ +from .influxdb_connection import InfluxDBConnection +from .postgres_connection import PostgresDatabaseSession + +__all__ = ["InfluxDBConnection", "PostgresDatabaseSession"] diff --git a/icon_service_base/database/influxdb_connection.py b/icon_service_base/database/influxdb_connection.py new file mode 100644 index 0000000..5cb0595 --- /dev/null +++ b/icon_service_base/database/influxdb_connection.py @@ -0,0 +1,121 @@ +from __future__ import annotations + +from types import TracebackType + +from dotenv import dotenv_values +from influxdb_client import ( # type: ignore + Bucket, + BucketRetentionRules, + BucketsApi, + InfluxDBClient, + WriteApi, +) +from influxdb_client.client.write_api import SYNCHRONOUS # type: ignore +from influxdb_client.rest import ApiException # type: ignore +from loguru import logger + +# Load the environment variables from the .env file +env_vars = dotenv_values() + +# Access the individual environment variables +INFLUXDB_V2_URL = str(env_vars.get("INFLUXDB_V2_URL")) +INFLUXDB_V2_ORG = env_vars.get("INFLUXDB_V2_ORG") +INFLUXDB_V2_TOKEN = env_vars.get("INFLUXDB_V2_TOKEN") + + +class InfluxDBConnection: + """ + The `InfluxDBConnection` class serves as a context manager for a connection + to an InfluxDB server. This connection is established using credentials + provided through environment variables. + + Example usage: + ``` + with InfluxDBConnection() as influx_client: + # Creating a bucket + influx_client.create_bucket( + bucket_name='my_new_bucket', description='This is a new bucket' + ) + + # Writing data to a bucket + record = { + "measurement": "your_measurement", # Replace with your measurement + "tags": { + "example_tag": "tag_value", # Replace with your tag and its value + }, + "fields": { + "example_field": 123, # Replace with your field and its value + }, + "time": "2023-06-05T00:00:00Z", # Replace with your timestamp + } + influx_client.write_api.write( + bucket='my_new_bucket', record=record + ) + ``` + """ + + def __init__(self) -> None: + self.url = INFLUXDB_V2_URL + self.token = INFLUXDB_V2_TOKEN + self.org = INFLUXDB_V2_ORG + self.client: InfluxDBClient + self.write_api: WriteApi + self.buckets_api: BucketsApi | None = None + + def __enter__(self) -> InfluxDBConnection: + self.client = InfluxDBClient(url=self.url, token=self.token, org=self.org) + self.write_api = self.client.write_api(write_options=SYNCHRONOUS) # type: ignore + return self + + def __exit__( + self, + exc_type: type[BaseException] | None, + exc_value: BaseException | None, + exc_traceback: TracebackType | None, + ) -> None: + self.write_api.close() + self.client.__del__() + + def create_bucket( # noqa: CFQ002 + self, + bucket: Bucket | None = None, + bucket_name: str | None = None, + org_id: int | None = None, + retention_rules: BucketRetentionRules | None = None, + description: str | None = None, + org: str | None = None, + ) -> None: + """ + Create a bucket in the InfluxDB instance. This function wraps the create_bucket + from `influxdb_client` in a try-catch block and logs potential errors with + loguru. + + Args: + bucket (Bucket | PostBucketRequest, optional): Bucket instance to be + created. + bucket_name (str, optional): Name of the bucket to be created. + org_id (int, optional): The organization id for the bucket. + retention_rules (BucketRetentionRules, optional): Retention rules for the + bucket. + description (str, optional): Description of the bucket. + org (str, optional): The name of the organization for the bucket. Takes + the ID, Name, or Organization. If not specified, the default value from + `InfluxDBClient.org` is used. + """ + + self.buckets_api = self.client.buckets_api() + try: + self.buckets_api.create_bucket( + bucket=bucket, + bucket_name=bucket_name, + org_id=org_id, + retention_rules=retention_rules, + description=description, + org=org, + ) + except ApiException as e: + if e.status == 422: + logger.debug(e.message) + return + logger.error(e) + return diff --git a/icon_service_base/database/postgres_connection.py b/icon_service_base/database/postgres_connection.py new file mode 100644 index 0000000..90e4c8e --- /dev/null +++ b/icon_service_base/database/postgres_connection.py @@ -0,0 +1,171 @@ +from __future__ import annotations + +import datetime +import json +import re +from types import TracebackType +from typing import Any + +from dateutil.parser import ParserError, parse # type: ignore +from dotenv import dotenv_values +from sqlmodel import Session, SQLModel, create_engine + +# Load the environment variables from the .env file +env_vars = dotenv_values() + +# Access the individual environment variables +POSTGRESQL_USER = env_vars.get("POSTGRESQL_USER") +POSTGRESQL_PASSWORD = env_vars.get("POSTGRESQL_PASSWORD") +POSTGRESQL_HOST = env_vars.get("POSTGRESQL_HOST") +POSTGRESQL_PORT = env_vars.get("POSTGRESQL_PORT") +POSTGRESQL_DATABASE = env_vars.get("POSTGRESQL_DATABASE") + + +def json_loads_or_return_input(input_string: str) -> dict[str, Any] | Any: + """ + Try to parse a string as JSON, if it fails return the original string. + """ + try: + return json.loads(input_string) + except (TypeError, json.JSONDecodeError): + return input_string + + +def parse_datetime_or_return_str(input_string: str) -> datetime.datetime | str: + try: + # Attempts to parse the string as a datetime object + return parse(input_string) + except ParserError: + # If parsing fails, return the original input string + return input_string + + +def is_datetime_format(input_string: str) -> bool: + """ + Check if a string is in datetime format. + """ + try: + parse(input_string) + return True + except ParserError: + return False + + +def json_dumps(data: Any) -> str | list: + """ + Serialize a Python object into a JSON-formatted string, with custom handling for + datetime and list objects. + """ + # 'Infinity' is an unallowed token in JSON, thus make it a string + # https://stackoverflow.com/questions/48356938/store-infinity-in-postgres-json-via-django + pattern = r"(-?Infinity)" + result: str | list + + if isinstance(data, str): + if is_datetime_format(data): + result = json.dumps(data) + else: + result = data + elif isinstance(data, datetime.datetime): + result = json.dumps(str(data)) + elif isinstance(data, list): + result = [json_dumps(element) for element in data] + else: + if isinstance(data, SQLModel): + serialized_data = data.json() + else: + serialized_data = json.dumps(data) + result = re.sub(pattern, r'"\1"', serialized_data) + return result + + +def deserialize_json_dict(json_string: str) -> Any: + """ + Deserialize a JSON string into a Python dictionary. + """ + # 'Infinity' is an unallowed token in JSON, thus we made it a string. Now, convert + # it back + pattern = r'"(-?Infinity)"' + json_string = re.sub(pattern, r"\1", json_string) + result: Any + + val = json.loads(json_string) + json_dict_or_val = json_loads_or_return_input(val) + if isinstance(json_dict_or_val, str): + result = parse_datetime_or_return_str(json_dict_or_val) + else: + result = json_dict_or_val + return result + + +# the docs state that +# "You should normally have a single engine object for your whole application +# and re-use it everywhere." +database_engine = create_engine( + f"postgresql://{POSTGRESQL_USER}:{POSTGRESQL_PASSWORD}@{POSTGRESQL_HOST}:" + f"{POSTGRESQL_PORT}/{POSTGRESQL_DATABASE}", + echo=False, + json_serializer=json_dumps, + json_deserializer=deserialize_json_dict, +) + + +class PostgresDatabaseSession(Session): + """A class to represent a session with the PostgreSQL database. + + This class inherits from SQLModel's Session class and implements Python's context + manager protocol. This class helps to ensure that sessions are properly opened + and closed, even in cases of error. + + The main goal of this class is to provide a way to manage persistence operations + for ORM-mapped objects. + + Attributes: + bind: Represents the database engine to which this session is bound. + + Example: + This class is designed to be used with a context manager (the 'with' keyword). + Here's how you can use it to query data from a table represented by a SQLModel + class named 'YourModel': + + ```python + from your_module.models import YourModel # replace with your model + from sqlmodel import select + + with PostgresDatabaseSession() as session: + row = session.exec(select(YourModel).limit(1)).all() + ``` + + You can also use it to add new data to the table: + + ```python + with PostgresDatabaseSession() as session: + new_row = YourModel(...) # replace ... with your data + session.add(new_row) + session.commit() + ``` + """ + + def __init__(self) -> None: + """Initializes a new session bound to the database engine.""" + + super().__init__(bind=database_engine) + + def __enter__(self) -> PostgresDatabaseSession: + """Begins the runtime context related to the database session.""" + + super().__enter__() + return self + + def __exit__( + self, + exc_type: type[BaseException] | None, + exc_value: BaseException | None, + exc_traceback: TracebackType | None, + ) -> None: + """Ends the runtime context related to the database session. + + Ensures that the session is properly closed, even in the case of an error. + """ + + super().__exit__(exc_type, exc_value, exc_traceback) diff --git a/poetry.lock b/poetry.lock index ea53817..c71d893 100644 --- a/poetry.lock +++ b/poetry.lock @@ -17,22 +17,22 @@ vine = ">=5.0.0" [[package]] name = "attrs" -version = "22.2.0" +version = "23.1.0" description = "Classes Without Boilerplate" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "attrs-22.2.0-py3-none-any.whl", hash = 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