From 5a287bd514ef1e25f93d9b4d5454b04c81dad110 Mon Sep 17 00:00:00 2001 From: mdsage1 Date: Wed, 13 Mar 2024 21:08:21 +0000 Subject: [PATCH] add edam etl --- apps/openchallenges/edam-etl/Dockerfile | 3 +- apps/openchallenges/edam-etl/poetry.lock | 318 +++++++++++++++++++- apps/openchallenges/edam-etl/pyproject.toml | 2 + apps/openchallenges/edam-etl/src/main.py | 45 ++- 4 files changed, 362 insertions(+), 6 deletions(-) diff --git a/apps/openchallenges/edam-etl/Dockerfile b/apps/openchallenges/edam-etl/Dockerfile index 31d709a25b..0af4c332c3 100644 --- a/apps/openchallenges/edam-etl/Dockerfile +++ b/apps/openchallenges/edam-etl/Dockerfile @@ -11,10 +11,11 @@ RUN pip install poetry \ && poetry install --with prod --no-root --no-interaction --no-ansi \ && pip cache purge + WORKDIR / COPY docker-entrypoint.sh ./ RUN chmod +x docker-entrypoint.sh ENTRYPOINT ["/docker-entrypoint.sh"] -CMD python "${APP_DIR}/src/main.py" \ No newline at end of file +CMD python "${APP_DIR}/src/main.py" diff --git a/apps/openchallenges/edam-etl/poetry.lock b/apps/openchallenges/edam-etl/poetry.lock index 79a49f5137..c7af18a61e 100644 --- a/apps/openchallenges/edam-etl/poetry.lock +++ b/apps/openchallenges/edam-etl/poetry.lock @@ -1,7 +1,321 @@ # This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. -package = [] + +[[package]] +name = "certifi" +version = "2024.2.2" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.6" +files = [ + {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"}, + {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.3.2" +description = "The Real First Universal Charset Detector. 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"2.31.0" [tool.poetry.group.dev.dependencies] diff --git a/apps/openchallenges/edam-etl/src/main.py b/apps/openchallenges/edam-etl/src/main.py index 191baca385..1b2f7c3f0b 100755 --- a/apps/openchallenges/edam-etl/src/main.py +++ b/apps/openchallenges/edam-etl/src/main.py @@ -2,15 +2,54 @@ from os import getenv +import pandas as pd +import requests + # Get config from the environment variables oc_db_url = getenv("OC_DB_URL") print(f"OC DB URL: {oc_db_url}") +# columns of interest +columns_kept = ["Class ID", "Preferred Label"] + + # TODO Download EDAM concepts from GitHub or S3 bucket (CSV file) -print("[TODO] Download EDAM concepts from GitHub or S3 bucket (CSV file)") +def download_edam_csv(url, version): + response = requests.get(url) + with open(f"EDAM_{version}.csv", "wb") as f: + f.write(response.content) + + +print("Download EDAM concepts from GitHub or S3 bucket (CSV file)") + + +# Transform the TSV to a dataframe w/indices adjusted to start from 0 +def transform_to_dataframe(version): + df = pd.read_csv(f"EDAM_{version}.csv", index_col=0, usecols=columns_kept) + return df + + +# Gather data about the statistics +def print_info_statistics(version, df): + print(f"EDAM Version: {version}") + print(f"Number of Concepts Transformed: {len(df)}") + print("Statistics:") + print(df.describe()) + + +def main(): + version = "1.25" # Change to desired version if changes made + url = "https://github.com/edamontology/edamontology/raw/main/releases/EDAM_1.25.csv" + download_edam_csv(url, version) + df = transform_to_dataframe(version) + print_info_statistics(version, df) + + +if __name__ == "__main__": + main() # TODO Process the EDAM concepts -print("[TODO] Process the EDAM concepts") +# print("[TODO] Process the EDAM concepts") # TODO Push the EDAM concept to the OC challenge service DB -print("[TODO] Push the EDAM concept to the OC challenge service DB") +# print("[TODO] Push the EDAM concept to the OC challenge service DB")