From 8546cd447eae652f22b6b5d6835adbbe6d74d379 Mon Sep 17 00:00:00 2001 From: arcangelo7 Date: Sun, 29 Sep 2024 00:23:34 +0200 Subject: [PATCH] pandas numpy incompatibily problem solved --- .github/workflows/run_tests.yml | 2 +- .../run/merge/group_entities_to_be_merged.py | 25 +- poetry.lock | 404 ++++++++---------- pyproject.toml | 5 +- 4 files changed, 199 insertions(+), 237 deletions(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 35ee95fd..577e1846 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -27,7 +27,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10"] + python-version: ["3.10"] services: redis: image: redis diff --git a/oc_meta/run/merge/group_entities_to_be_merged.py b/oc_meta/run/merge/group_entities_to_be_merged.py index 0874a69a..d7d28191 100644 --- a/oc_meta/run/merge/group_entities_to_be_merged.py +++ b/oc_meta/run/merge/group_entities_to_be_merged.py @@ -1,4 +1,5 @@ import argparse +import csv import os import pandas as pd @@ -105,7 +106,24 @@ def save_grouped_entities(grouped_data, output_dir): output_file = os.path.join(output_dir, f"{key.split('/')[-1]}.csv") if len(df) > 1: print(f"File with multiple rows: {output_file}") - df.to_csv(output_file, index=False) + + try: + df.to_csv(output_file, index=False) + except AttributeError as e: + print(f"Error saving file {output_file}: {str(e)}") + print(f"DataFrame info:") + print(df.info()) + print(f"DataFrame head:") + print(df.head()) + + # Try an alternative method to save the CSV + try: + df.to_csv(output_file, index=False, encoding='utf-8', quoting=csv.QUOTE_NONNUMERIC) + print(f"Successfully saved using alternative method: {output_file}") + except Exception as alt_e: + print(f"Alternative method also failed: {str(alt_e)}") + except Exception as e: + print(f"Unexpected error saving file {output_file}: {str(e)}") def main(): parser = argparse.ArgumentParser(description='Process CSV and group entities based on SPARQL queries.') @@ -116,8 +134,13 @@ def main(): args = parser.parse_args() df = load_csv(args.csv_file_path) + print(f"Loaded CSV file with {len(df)} rows") + grouped_entities = group_entities(df, args.sparql_endpoint) + print(f"Grouped entities into {len(grouped_entities)} groups") + save_grouped_entities(grouped_entities, args.output_dir) + print("Finished saving grouped entities") if __name__ == "__main__": main() diff --git a/poetry.lock b/poetry.lock index 9996992e..4c13187f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -647,19 +647,19 @@ test = ["pytest (>=6)"] [[package]] name = "fakeredis" -version = "2.24.1" +version = "2.25.0" description = "Python implementation of redis API, can be used for testing purposes." optional = false python-versions = "<4.0,>=3.7" files = [ - {file = "fakeredis-2.24.1-py3-none-any.whl", hash = "sha256:09d3049a29910f80c0ef5789c31bef3dbb9727bd43a67ee8598217f4efd12f35"}, - {file = "fakeredis-2.24.1.tar.gz", hash = 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name = "rdflib" @@ -2757,5 +2695,5 @@ cffi = ["cffi (>=1.11)"] [metadata] lock-version = "2.0" -python-versions = "^3.8" -content-hash = "20b25f8a93d4ea0eef4379102bf51a5bbf47eef5af6881b8a48a9d0c148cdbc7" +python-versions = ">=3.10,<4.0" +content-hash = "578040e7eb82692f6b73a69a718f3cefde46ef6cdefb84764047e9019bfa9423" diff --git a/pyproject.toml b/pyproject.toml index 9dd4c341..7bff3461 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ authors = ["Arcangelo Massari ", "Fabio Mariani", "Simon license = "ISC License" [tool.poetry.dependencies] -python = "^3.8" +python = ">=3.10,<4.0" argparse = "^1.4.0" lxml = ">=4.9.2,<6.0.0" beautifulsoup4 = "^4.11.1" @@ -20,7 +20,6 @@ psutil = "^5.9.0" Pebble = "^5.0.3" time-agnostic-library = ">=4.4.1,<5.0.0" zstandard = "^0.21.0" -pandas = "^2.0.1" sparqlwrapper = "2.0.0" fakeredis = "^2.10.3" ndjson = "^0.3.1" @@ -32,6 +31,8 @@ oc-ocdm = "9.1.0" retrying = "^1.3.4" orjson = "^3.10.7" rdflib-ocdm = "0.3.11" +numpy = "^2.1.1" +pandas = 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