study-docker-repro-longevity/ecg.py

#!/bin/python3

"""
    ECG is a program that automates software environment checking
    for scientific artifacts.

    It is meant to be executed periodically to analyze variations in the
    software environment of the artifact through time.
"""

import subprocess
import json
import yaml
import argparse
import tempfile
import os
import requests
import zipfile
import io
import tarfile
import pathlib
import logging
import datetime
import sys

# Paths:
pkglist_path = "pkglist.csv" # Package list being generated
log_path = "log.txt" # Output of the program
buildstatus_path = "build_status.csv" # Summary of the build process of the image

# Commands to list installed packages along with their versions and the name
# of the package manager, depending on the package managers.
# Each package manager is associated with a tuple, the first item being
# the query command, and the second being the command that will format
# the output of the query command (this one can be an empty string in case
# the formatting part is already done using the options of the first command).
# The first needs to be run on the container, and the second on the host,
# to take into account container images that do not have the formatting
# packages installed.
pkgmgr_cmd = {
    "dpkg": ("dpkg -l", "awk 'NR>5 {print $2 \",\" $3 \",\" \"dpkg\"}'"), \
    "rpm":("rpm -qa --queryformat '%{NAME},%{VERSION},rpm\\n'", ""), \
    "pacman":("pacman -Q", "awk '{print $0 \",\" $1 \",pacman\"}'"), \
    "pip":("pip freeze", "sed 's/==/,/g' | awk '{print $0 \",pip\"}'"), \
    "conda":("/root/.conda/bin/conda list -e", "sed 's/=/ /g' | awk 'NR>3 {print $1 \",\" $2 \",conda\"}'")
}

# Command to obtain the latest commit hash in a git repository:
gitcmd = "git log -n 1 --pretty=format:%H"

def download_sources(config):
    """
        Downloads the source of the artifact in 'config'.

        Parameters
        ----------
        config: dict
            Parsed YAML config file.

        Returns
        -------
        temp_dir: tempfile.TemporaryDirectory
            The directory where the artifact is downloaded to.
    """
    url = config["artifact_url"]
    logging.info(f"Downloading artifact from {url}")
    temp_dir = tempfile.TemporaryDirectory()
    req = requests.get(url)
    if config["type"] == "zip":
        artifact = zipfile.ZipFile(io.BytesIO(req.content))
    elif config["type"] == "tgz":
        artifact = tarfile.open(fileobj=io.BytesIO(req.content))
    logging.info(f"Extracting artifact at {temp_dir.name}")
    artifact.extractall(temp_dir.name)
    return temp_dir

def build_image(config, src_dir):
    """
        Builds the given Docker image in 'config'.

        Parameters
        ----------
        config: dict
            Parsed YAML config file.

        src_dir: tempfile.TemporaryDirectory
            The directory where the artifact is stored.

        Returns
        -------
        return_code: int
            Return code of the Docker 'build' command.
    """
    name = config["image_name"]
    logging.info(f"Starting building image {name}")
    path = os.path.join(src_dir, config["dockerfile_location"])
    build_command = "docker build -t " + config["image_name"] + " ."
    build_process = subprocess.run(build_command.split(" "), cwd=path, capture_output=True)
    logging.info(f"Output of '{build_command}':")
    logging.info(build_process.stdout)
    return_code = build_process.returncode
    logging.info(f"Command '{build_command}' exited with code {return_code}")
    return return_code == 0

def check_env(config, src_dir):
    """
        Builds a list of all software packages installed in the
        Docker image given in 'config', depending on the package managers
        specified in the configuration, then stores it in a CSV file.

        Parameters
        ----------
        config: dict
            Parsed YAML config file.

        src_dir: tempfile.TemporaryDirectory
            The directory where the artifact is stored.

        Returns
        -------
        None
    """
    pkglist_file = open(pkglist_path, "w")
    pkglist_file.write("Package,Version,Package manager\n")
    path = os.path.join(src_dir, config["dockerfile_location"])
    for pkgmgr in config["package_managers"]:
        logging.info(f"Checking '{pkgmgr}'")
        pkglist_process = subprocess.run(["docker", "run", "--rm", config["image_name"]] + pkgmgr_cmd[pkgmgr][0].split(" "), cwd=path, capture_output=True)
        format_process = subprocess.run("cat << EOF | " + pkgmgr_cmd[pkgmgr][1] + "\n" + pkglist_process.stdout.decode("utf-8") + "EOF", cwd=path, capture_output=True, shell=True)
        pkglist = format_process.stdout.decode("utf-8")
        pkglist_file.write(pkglist)
    if "git_packages" in config.keys():
        logging.info("Checking Git packages")
        for repo in config["git_packages"]:
            pkglist_process = subprocess.run(["docker", "run", "--rm", "-w", repo["location"], config["image_name"]] + gitcmd.split(" "), cwd=path, capture_output=True)
            repo_row = repo["name"] + "," + pkglist_process.stdout.decode("utf-8") + ",git"
            pkglist_file.write(repo_row + "\n")
    if "misc_packages" in config.keys():
        logging.info("Checking packages obtained outside of a package manager or VCS")
        for pkg in config["misc_packages"]:
            logging.info(f"Downloading package {pkg["name"]} from {pkg["url"]}")
            req = requests.get(pkg["url"])
            pkg_file = tempfile.NamedTemporaryFile()
            pkg_file.write(req.content)
            pkglist_process = subprocess.run("sha256sum " + pkg_file.name + " | cut -zd ' ' -f 1", cwd=path, capture_output=True, shell=True)
            pkg_row = pkg["name"] + "," + pkglist_process.stdout.decode("utf-8") + ",misc"
            pkglist_file.write(pkg_row + "\n")
    pkglist_file.close()

def remove_image(config):
    """
        Removes the Docker image given in 'config'.

        Parameters
        ----------
        config: dict
            Parsed YAML config file.

        Returns
        -------
        None
    """
    name = config["image_name"]
    logging.info(f"Removing image '{name}'")
    subprocess.run(["docker", "rmi", name], capture_output = True)

def main():
    global pkglist_path, log_path, buildstatus_path

    # Command line arguments parsing:
    parser = argparse.ArgumentParser(
        prog = "ecg",
        description = "ECG is a program that automates software environment checking for scientific artifacts. "
            "It is meant to be executed periodically to analyze variations in the software environment of the artifact through time."
    )
    parser.add_argument(
        "config",
        help = "The path to the configuration file of the artifact's Docker image."
    )
    parser.add_argument(
        "-p", "--pkg-list",
        help = "Path to the file where the package list generated by the program should be written."
    )
    parser.add_argument(
        "-l", "--log-path",
        help = "Path to the file where to log the output of the program."
    )
    parser.add_argument(
        "-b", "--build-summary",
        help = "Path to the file where to write the build summary of the Docker image given in the configuration file."
    )
    parser.add_argument(
        "-c", "--cache-dir",
        help = "Path to the cache directory, where artifact that are downloaded will be stored for future usage."
    )
    parser.add_argument('-v', '--verbose',
        action = 'store_true',
        help = "Shows more details on what is being done.")
    args = parser.parse_args()

    # Setting up the paths of the outputs:
    if args.pkg_list != None:
        pkglist_path = args.pkg_list
    if args.log_path != None:
        log_path = args.log_path
    if args.build_summary != None:
        buildstatus_path = args.build_summary

    # Setting up the log: will be displayed both on stdout and to the specified
    # file:
    logging.basicConfig(filename = log_path, filemode = "w", format = '%(levelname)s: %(message)s', level = logging.INFO)
    logging.getLogger().addHandler(logging.StreamHandler(sys.stdout))

    # Parsing the input YAML file including the configuration of
    # the artifact's image:
    config_file = open(args.config, "r")
    config = yaml.safe_load(config_file)
    config_file.close()

    verbose = args.verbose

    # if verbose:
    #    logging.info(f"Output will be stored in {output}")

    src_dir = download_sources(config)
    successful_build = build_image(config, src_dir.name)
    if successful_build:
        check_env(config, src_dir.name)
        remove_image(config)

if __name__ == "__main__":
    main()