diff --git a/apps/openchallenges/edam-etl/Dockerfile b/apps/openchallenges/edam-etl/Dockerfile index 128d307ce4..685989a045 100644 --- a/apps/openchallenges/edam-etl/Dockerfile +++ b/apps/openchallenges/edam-etl/Dockerfile @@ -12,9 +12,12 @@ RUN groupadd --gid "$USER_GID" "$USERNAME" \ && apt-get update -qq -y && export DEBIAN_FRONTEND=noninteractive \ && apt-get install --no-install-recommends -qq -y \ gosu \ + libmariadb-dev \ + gcc \ && apt-get -y autoclean \ && apt-get -y autoremove \ - && rm -rf /var/lib/apt/lists/* + && rm -rf /var/lib/apt/lists/* + WORKDIR ${APP_DIR} COPY src src/ @@ -24,7 +27,7 @@ COPY pyproject.toml poetry.lock ./ # See /workspaces/sage-monorepo/tools/devcontainers/sage/.devcontainer/Dockerfile RUN pip install --no-cache-dir poetry==1.6.1 \ && poetry config --local virtualenvs.create false \ - && poetry install --with prod --no-root --no-interaction --no-ansi \ + && poetry install --no-root --no-interaction --no-ansi \ && pip cache purge WORKDIR / diff --git a/apps/openchallenges/edam-etl/poetry.lock b/apps/openchallenges/edam-etl/poetry.lock index 07228c961f..0489226a41 100644 --- a/apps/openchallenges/edam-etl/poetry.lock +++ b/apps/openchallenges/edam-etl/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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"typing-extensions" +version = "4.11.0" +description = "Backported and Experimental Type Hints for Python 3.8+" +optional = false +python-versions = ">=3.8" +files = [ + {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, + {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, +] + [[package]] name = "tzdata" version = "2024.1" @@ -425,4 +638,4 @@ zstd = ["zstandard (>=0.18.0)"] [metadata] lock-version = "2.0" python-versions = "3.12.0" -content-hash = "60cfeada182d8e408f67c4cf70ff4d26304af764a67ff223a526f177763c0679" +content-hash = "114844ce577d8eb02f2d3cff10d4597876bc502bbb20b254e4a172f99d609aa3" diff --git a/apps/openchallenges/edam-etl/prepare-python.sh b/apps/openchallenges/edam-etl/prepare-python.sh index 945fe9ca85..9ab5da7ddb 100755 --- a/apps/openchallenges/edam-etl/prepare-python.sh +++ b/apps/openchallenges/edam-etl/prepare-python.sh @@ -12,4 +12,8 @@ eval "$(pyenv init -)" pyenv local $PYTHON_VERSION poetry env use $PYTHON_VERSION -poetry install --with prod,dev \ No newline at end of file +poetry install --with prod,dev + +sudo apt-get update +sudo apt-get install -y libmariadb-dev +pip install packaging diff --git a/apps/openchallenges/edam-etl/pyproject.toml b/apps/openchallenges/edam-etl/pyproject.toml index 7cc52ed8a0..72e56d2853 100644 --- a/apps/openchallenges/edam-etl/pyproject.toml +++ b/apps/openchallenges/edam-etl/pyproject.toml @@ -11,12 +11,9 @@ python = "3.12.0" pandas = "2.2.1" requests = "2.31.0" regex = "2023.12.25" - -[tool.poetry.group.dev.dependencies] - -[tool.poetry.group.prod.dependencies] - -[tool.poetry.group.test.dependencies] +mysql-connector = "^2.2.9" +sqlalchemy = "^2.0.30" +mariadb = "^1.1.10" [build-system] requires = ["poetry-core"] diff --git a/apps/openchallenges/edam-etl/src/main.py b/apps/openchallenges/edam-etl/src/main.py index 8b10bd05f9..13c65b7caf 100755 --- a/apps/openchallenges/edam-etl/src/main.py +++ b/apps/openchallenges/edam-etl/src/main.py @@ -3,6 +3,10 @@ import requests from os import getenv from typing import Optional +import mariadb +import sys +import mysql.connector +from sqlalchemy import create_engine # Get config from the environment variables @@ -11,6 +15,63 @@ print(f"EDAM Version: {VERSION}") print(f"OC DB URL: {OC_DB_URL}") +# Intialize required connection variables from environment variables + +USERNAME = getenv("USERNAME") +PASSWORD = getenv("PASSWORD") +PORT = getenv("PORT") +DB = getenv("DB") +HOST = getenv("HOST") + +def connect_to_mariadb(username: str, password: str, port: str, host: str, database: str, df: pd.DataFrame) -> None: + """Connect to the MariaDB database""" + try: + conn = mariadb.connect( + user = username, + password = password, + host = host, + port = int(port), + database = database + ) + print("Establishing a connection to the MariaDB Platform.") + # Get the cursor + cur = conn.cursor() + print("Connection has been established to MariaDB Platform!") + + # Commit the transaction + conn.commit() + print("The table edam_etl has been added to the edam database!") + + # Create a SQLAlchemy engine from the MySQL Connector connection + engine = create_engine(f'mysql+mysqlconnector://{username}:{password}@{host}/{database}') + + # Drop the table if it exists + cur.execute("DROP TABLE IF EXISTS edam_etl") + + # Create the table with columns + cur.execute(""" + CREATE TABLE edam_etl ( + id INT PRIMARY KEY, + class_id VARCHAR(255), + preferred_label VARCHAR(255) + ) + """) + + #Load the concepts + df.to_sql( + name = "edam_etl", + con = engine, + if_exists = "append", + index = False + ) + + print("The table edam_etl has been populated with the EDAM concepts!") + + # Close the connection + conn.close() + except mariadb.Error as e: + print(f"Error connecting to MariaDB Platform: {e}") + sys.exit(1) def download_edam_csv(url: str, version: str) -> Optional[bool]: """Download EDAM concepts from GitHub or S3 bucket (CSV file)""" @@ -92,7 +153,6 @@ def print_info_statistics(df: pd.DataFrame) -> None: else: print("No data available.") - def main() -> None: """Main function to execute preceding functions""" url: str = ( @@ -101,6 +161,7 @@ def main() -> None: if download_edam_csv(url, VERSION): df: pd.DataFrame = transform_to_dataframe(VERSION) print_info_statistics(df) + connect_to_mariadb(USERNAME, PASSWORD, PORT, HOST, DB, df) if __name__ == "__main__":