crab/clone_repos.py

import pandas as pd
import argparse, os, sys, subprocess
from tqdm import tqdm
import shutil

tqdm.pandas()

EXCLUSION_LIST = [
    "edmcouncil/idmp",
]

def clone(repo: str, dest: str, row: pd.Series, force: bool = False, verbose: bool = False) -> None:
    """
    Clones a GitHub repository into a local directory.

    Args:
        repo (str): The repository to clone, in the format "owner/repo_name".
        force (bool, optional): If `True`, re-clones the repository even if it already exists. Defaults to `False`.
    """
    local_repo_path = os.path.join(dest, repo)
    if not force and os.path.exists(local_repo_path):
        # if verbose: print(f"Skipping {repo}, already exists")
        return 
    if verbose: print(f"Cloning {repo}")
    proc = subprocess.run(
        ["git", "clone", "--depth", "1", f"https://github.com/{repo}", local_repo_path],
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE
    )
    if proc.returncode != 0:
        row["successfully_cloned"] = False
        print(f"Failed to clone {repo}", file=sys.stderr)
        print(f"Error message was:", file=sys.stderr)
        error_msg = proc.stderr.decode()
        print(error_msg, file=sys.stderr)
        row["error_msg"] = error_msg
    else:
        row["successfully_cloned"] = True

def get_build_file(root: str, repo: str, row: pd.Series, verbose: bool = False):
    """
    Get the path to the build file of a repository. The build file is either a
    `pom.xml`, `build.gradle`, or `build.xml` file.

    Args:
        root (str): The root directory in which the repository is located.
        repo (str): The name of the repository.

    Returns:
        str | None: The path to the repository if it is valid, `None` otherwise
    """
    path = os.path.join(root, repo)
    # Check if the given path is a directory
    if not os.path.isdir(path):
        error_msg = f"The path {path} is not a valid directory."
        print(error_msg, file=sys.stderr)
        row["error_msg"] = error_msg
        return None

    to_keep = ["pom.xml", "build.gradle", "build.xml"]
    for entry in os.scandir(path):
        if entry.is_file() and entry.name in to_keep:
            if verbose: print(f"Found {entry.name} in {repo} root, so keeping it and returning")
            row["depth_of_build_file"] = 0
            return os.path.join(path, entry.name)
    
    # List files in the immediate subdirectories
    for entry in os.scandir(path):
        if entry.is_dir():
            for sub_entry in os.scandir(entry.path):
                if sub_entry.is_file() and sub_entry.name in to_keep:
                    if verbose: print(f"Found {sub_entry.name} in {repo} first level, so keeping it and returning")
                    row["depth_of_build_file"] = 1
                    return os.path.join(path, entry.name, sub_entry.name)

    row["error_msg"] = "No build file found"
    return None

def has_tests(path: str, build_file: str, row: pd.Series) -> bool:
    with open(build_file, "r") as f:
        content = f.read()

        for library in ["junit", "testng", "mockito"]:
            if library in content:
                row["detected_source_of_tests"] = library + " library in build file"
                return True

        for keyword in ["testImplementation", "functionalTests", "bwc_tests_enabled"]:
            if keyword in content:
                row["detected_source_of_tests"] = keyword + " keyword in build file"
                return False

    test_dirs = [
        "src/test/java",
        "src/test/kotlin",
        "src/test/groovy",
        "test",
    ]
    for td in test_dirs:
        if os.path.exists(os.path.join(path, td)):
            row["detected_source_of_tests"] = td + " dir exists in repo"
            return True

    row["error_msg"] = "No tests found"
    return False

def remove_dir(dir: str) -> None:
    """
    Removes a directory and all its contents. Removes parent directorie if it is empty after removing child (dir).

    Args:
        dir (str): The directory to remove.
    """
    shutil.rmtree(dir)
    parent = os.path.abspath(os.path.join(dir, os.path.pardir))
    if os.listdir(parent) == []:
        shutil.rmtree(parent)


def process_row(row, dest: str, force: bool = False, verbose: bool = False):
    repo = row["name"]
    if repo in EXCLUSION_LIST:
        row["error_msg"] = "Repo in exclusion list"
        if verbose: print(f"Skipping {repo}, in exclusion list")
        return

    if force:
        clone(repo, dest, row, verbose=verbose)

    repo_path = os.path.join(dest, repo)
    if not os.path.exists(repo_path):
        row["error_msg"] = "Repo not cloned"
        return

    build_file = get_build_file(dest, repo, row)
    if build_file is None:
        if verbose: print(f"Removing {repo}, no build file")
        remove_dir(repo_path)
        return
    
    if not has_tests(repo_path, build_file, row):
        if verbose: print(f"Removing {repo}, no test suites")
        remove_dir(repo_path)
        return
    # if verbose: print(f"Keeping {repo}")

    # Check for compilation and tests

    # If repo was not removed, then it is a good repo
    row["good_repo_for_crab"] = True

def clone_repos(file: str, dest: str, force: bool =False, verbose: bool = False) -> None:
    """
    Download the repos listed in the file passed as argument. The downloaded repos will be placed in the folder that is named as the dest argument.


    Arguments:
        file (str): The name of the file to download the repos from. Must be a .csv.gz file (downloaded from https://seart-ghs.si.usi.ch)
        dest (str): The name of the root directory in which to download the repos
        verbose (bool): If `True`, outputs detailed process information. Defaults to `False`.
    """
    if verbose: print(f"Reading CSV file {file}")
    df = pd.read_csv(file)

    df["successfully_cloned"] = None
    df["build_system"] = None
    df["depth_of_build_file"] = None
    df["detected_source_of_tests"] = None
    df["error_msg"] = None
    df["good_repo_for_crab"] = False
    df["n_tests"] = None
    df["n_tests_with_grep"] = None
    df["n_tests_passed"] = None
    df["n_tests_failed"] = None
    df["n_tests_skipped"] = None

    try:
        if verbose: print("Processing repositories")
        df.progress_apply(lambda row: process_row(row, dest, force=force, verbose=verbose), axis=1)
    except KeyboardInterrupt:
        print("Keyboard interrupt detected. Stopping the processing of the repos...")

    if verbose: print("Writing results...")
    df.to_csv("results.csv.gz", index=False)


if __name__ == "__main__":
    # whtie the code to parse the arguments here
    parser = argparse.ArgumentParser(description="Clone repos from a given file")
    parser.add_argument("file", default="results.csv.gz", help="The file to download the repos from. Default is 'results.csv.gz'")
    parser.add_argument("-d", "--dest", default="./results/", help="The root directory in which to download the repos. Default is './results/'")
    parser.add_argument("-f", "--force", action="store_true", help="Force the download of the repos")
    parser.add_argument("-v", "--verbose", action="store_true", help="Make the program verbose")
    args = parser.parse_args()

    clone_repos(args.file, args.dest, force=args.force, verbose=args.verbose)