382 lines
13 KiB
Python
Executable File
382 lines
13 KiB
Python
Executable File
#!/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 argparse
|
|
import tempfile
|
|
import os
|
|
import requests
|
|
import zipfile
|
|
import tarfile
|
|
import pathlib
|
|
import logging
|
|
import datetime
|
|
import sys
|
|
|
|
def trim(url) :
|
|
"""
|
|
Trims given url for cache storage.
|
|
|
|
Parameters
|
|
----------
|
|
url: str
|
|
URL to trim.
|
|
|
|
Returns
|
|
-------
|
|
str
|
|
Trimmed URL.
|
|
"""
|
|
trimmed = ""
|
|
for c in url.lower():
|
|
if c not in "/:;\\'\" *?":
|
|
trimmed += c
|
|
|
|
return trimmed
|
|
|
|
def download_file(url, dest):
|
|
"""
|
|
Downloads the file stored at the given URL and returns its hash
|
|
and location.
|
|
|
|
Parameters
|
|
----------
|
|
url: str
|
|
URL to the file to download.
|
|
dest: str
|
|
Path to where the file should be stored.
|
|
|
|
Returns
|
|
-------
|
|
str
|
|
Hash of the downloaded file.
|
|
"""
|
|
req = requests.get(url)
|
|
file = open(dest, "wb")
|
|
file.write(req.content)
|
|
file.close()
|
|
hash_process = subprocess.run(f"sha256sum {file.name} | cut -d ' ' -f 1 | tr -d '\n'", capture_output=True, shell=True)
|
|
return hash_process.stdout.decode("utf-8")
|
|
|
|
def download_sources(config, arthashlog_path, dl_dir, use_cache):
|
|
"""
|
|
Downloads the source of the artifact in 'config'.
|
|
|
|
Parameters
|
|
----------
|
|
config: dict
|
|
Parsed config file.
|
|
|
|
arthashlog_path: str
|
|
Path to the artifact hash log file.
|
|
|
|
dl_dir: str
|
|
Path to the directory where to download the artifact.
|
|
|
|
use_cache: bool
|
|
Indicates whether the cache should be used or not.
|
|
|
|
Returns
|
|
-------
|
|
temp_dir: str
|
|
Path to the directory where the artifact is downloaded to.
|
|
"""
|
|
url = config["artifact_url"]
|
|
artifact_name = trim(url)
|
|
artifact_dir = os.path.join(dl_dir, artifact_name)
|
|
# Checking if artifact in cache. Not downloading if it is:
|
|
if not os.path.exists(artifact_dir) or not use_cache:
|
|
logging.info(f"Downloading artifact from {url}")
|
|
# In case cache was used before:
|
|
if not use_cache:
|
|
os.system(f"rm -rf {artifact_dir}")
|
|
os.mkdir(artifact_dir)
|
|
artifact_file = tempfile.NamedTemporaryFile()
|
|
artifact_path = artifact_file.name
|
|
artifact_hash = download_file(url, artifact_path)
|
|
if config["type"] == "zip":
|
|
artifact = zipfile.ZipFile(artifact_path)
|
|
elif config["type"] == "tar":
|
|
artifact = tarfile.open(artifact_path)
|
|
logging.info(f"Extracting artifact at {artifact_dir}")
|
|
artifact.extractall(artifact_dir)
|
|
# Logging the current hash of the artifact:
|
|
arthashlog_file = open(arthashlog_path, "a")
|
|
now = datetime.datetime.now()
|
|
timestamp = str(datetime.datetime.timestamp(now))
|
|
arthashlog_file.write(f"{timestamp},{artifact_hash}\n")
|
|
arthashlog_file.close()
|
|
else:
|
|
logging.info(f"Cache found for {url}, skipping download")
|
|
return artifact_dir
|
|
|
|
def buildstatus_saver(output, buildstatus_path, config_path):
|
|
"""
|
|
Parses the given 'output' to indentify the errors, then saves them to the
|
|
'build_status' file.
|
|
|
|
Parameters
|
|
----------
|
|
output: str
|
|
Output of Docker.
|
|
|
|
buildstatus_path: str
|
|
Path to the build status file.
|
|
|
|
config_path: str
|
|
Path to the config file.
|
|
|
|
Returns
|
|
-------
|
|
None
|
|
"""
|
|
# Possible error messages given by 'docker build' and their category.
|
|
# The key is the category, the value is a tuple of error messages belonging to
|
|
# to this category:
|
|
build_errors = {
|
|
"package_unavailable":("Unable to locate package"),
|
|
"baseimage_unavailable":("manifest unknown: manifest unknown")
|
|
}
|
|
|
|
file_exists = os.path.exists(buildstatus_path)
|
|
buildstatus_file = open(buildstatus_path, "a")
|
|
artifact_name = os.path.basename(config_path).split(".")[0]
|
|
# # Writing header in case file didn't exist:
|
|
# if not file_exists:
|
|
# buildstatus_file.write("yaml_path,timestamp,error")
|
|
unknown_error = True
|
|
for error_cat, error in build_errors.items():
|
|
if error in output:
|
|
unknown_error = False
|
|
now = datetime.datetime.now()
|
|
timestamp = str(datetime.datetime.timestamp(now))
|
|
buildstatus_file.write(f"{artifact_name},{timestamp},{error_cat}\n")
|
|
if unknown_error:
|
|
now = datetime.datetime.now()
|
|
timestamp = str(datetime.datetime.timestamp(now))
|
|
buildstatus_file.write(f"{artifact_name},{timestamp},unknown_error\n")
|
|
buildstatus_file.close()
|
|
|
|
def build_image(config, src_dir):
|
|
"""
|
|
Builds the given Docker image in 'config'.
|
|
|
|
Parameters
|
|
----------
|
|
config: dict
|
|
Parsed config file.
|
|
|
|
src_dir: str
|
|
Path to the directory where the artifact is stored.
|
|
|
|
Returns
|
|
-------
|
|
return_code: bool, build_output: str
|
|
Return code and output of Docker 'build'.
|
|
"""
|
|
name = config["image_name"]
|
|
logging.info(f"Starting building image {name}")
|
|
path = os.path.join(src_dir, config["dockerfile_location"])
|
|
build_command = f"docker build -t {config['image_name']} ."
|
|
build_process = subprocess.run(build_command.split(" "), cwd=path, capture_output=True)
|
|
build_output = f"stdout:\n{build_process.stdout.decode('utf-8')}\nstderr:\n{build_process.stderr.decode('utf-8')}"
|
|
# build_output = build_process.stderr.decode("utf-8")
|
|
logging.info(f"Output of '{build_command}':")
|
|
logging.info(build_output)
|
|
return_code = build_process.returncode
|
|
logging.info(f"Command '{build_command}' exited with code {return_code}")
|
|
return return_code, build_output
|
|
|
|
def check_env(config, src_dir, pkglist_path):
|
|
"""
|
|
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 config file.
|
|
|
|
src_dir: str
|
|
Path to the directory where the artifact is stored.
|
|
|
|
pkglist_path: str
|
|
Path to the package list file.
|
|
|
|
Returns
|
|
-------
|
|
None
|
|
"""
|
|
# 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"
|
|
|
|
logging.info("Checking software environment")
|
|
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"]:
|
|
pkglist_cmd = pkgmgr_cmd[pkgmgr][0]
|
|
listformat_cmd = pkgmgr_cmd[pkgmgr][1]
|
|
logging.info(f"Checking '{pkgmgr}'")
|
|
pkglist_process = subprocess.run(["docker", "run", "--rm", config["image_name"]] + pkglist_cmd.split(" "), cwd=path, capture_output=True)
|
|
format_process = subprocess.run(f"cat << EOF | {listformat_cmd}\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 = f"{repo['name']},{pkglist_process.stdout.decode('utf-8')},git"
|
|
pkglist_file.write(f"{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']}")
|
|
pkg_file = tempfile.NamedTemporaryFile()
|
|
pkg_path = pkg_file.name
|
|
pkg_hash = download_file(pkg["url"], pkg_path)
|
|
pkg_row = f"{pkg['name']},{pkg_hash},misc"
|
|
pkglist_file.write(f"{pkg_row}\n")
|
|
pkglist_file.close()
|
|
|
|
def remove_image(config):
|
|
"""
|
|
Removes the Docker image given in 'config'.
|
|
|
|
Parameters
|
|
----------
|
|
config: dict
|
|
Parsed config file.
|
|
|
|
Returns
|
|
-------
|
|
None
|
|
"""
|
|
name = config["image_name"]
|
|
logging.info(f"Removing image '{name}'")
|
|
subprocess.run(["docker", "rmi", name], capture_output = True)
|
|
|
|
def main():
|
|
# Paths:
|
|
config_path = ""
|
|
pkglist_path = "" # Package list being generated
|
|
buildstatus_path = "" # Summary of the build process of the image
|
|
arthashlog_path = "" # Log of the hash of the downloaded artifact
|
|
cache_dir = "" # Artifact cache directory, when using one. 'None' value indicates no cache.
|
|
use_cache = False
|
|
|
|
# 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('-v', '--verbose',
|
|
action = 'store_true',
|
|
help = "Shows more details on what is being done."
|
|
)
|
|
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.",
|
|
required = True
|
|
)
|
|
parser.add_argument(
|
|
"-l", "--log-path",
|
|
help = "Path to the file where to log the output of the program.",
|
|
required = True
|
|
)
|
|
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.",
|
|
required = True
|
|
)
|
|
parser.add_argument(
|
|
"-a", "--artifact-hash",
|
|
help = "Path to the file where to write the log of the hash of the downloaded artifact.",
|
|
required = True
|
|
)
|
|
parser.add_argument(
|
|
"-c", "--cache-dir",
|
|
help = "Path to the cache directory, where artifacts that are downloaded will be stored for future usage. " \
|
|
"If not specified, cache is disabled.",
|
|
required = False
|
|
)
|
|
args = parser.parse_args()
|
|
|
|
# Setting up the paths of the outputs:
|
|
log_path = "log.txt" # Output of the program
|
|
pkglist_path = args.pkg_list
|
|
log_path = args.log_path
|
|
buildstatus_path = args.build_summary
|
|
arthashlog_path = args.artifact_hash
|
|
cache_dir = args.cache_dir
|
|
|
|
# Setting up the log: will be displayed both on stdout and to the specified
|
|
# file:
|
|
print(f"Output will be stored in {log_path}")
|
|
logging.basicConfig(filename = log_path, filemode = "w", format = '%(levelname)s: %(message)s', level = logging.INFO)
|
|
verbose = args.verbose
|
|
if verbose:
|
|
logging.getLogger().addHandler(logging.StreamHandler(sys.stdout))
|
|
|
|
# Parsing the input file including the configuration of the artifact's
|
|
# image:
|
|
config_path = args.config
|
|
config_file = open(config_path, "r")
|
|
config = json.loads(config_file.read())
|
|
# config = yaml.safe_load(config_file)
|
|
# print(config)
|
|
config_file.close()
|
|
|
|
dl_dir = None
|
|
# If not using cache, creates a temporary directory:
|
|
if cache_dir == None:
|
|
tmp_dir = tempfile.TemporaryDirectory()
|
|
dl_dir = tmp_dir.name
|
|
else:
|
|
use_cache = True
|
|
dl_dir = cache_dir
|
|
artifact_dir = download_sources(config, arthashlog_path, dl_dir, use_cache)
|
|
return_code, build_output = build_image(config, artifact_dir)
|
|
if return_code == 0:
|
|
check_env(config, artifact_dir, pkglist_path)
|
|
remove_image(config)
|
|
# Creates file if not already:
|
|
pathlib.Path(buildstatus_path).touch()
|
|
else:
|
|
# Creates file if not already:
|
|
pathlib.Path(pkglist_path).touch()
|
|
buildstatus_saver(build_output, buildstatus_path, config_path)
|
|
|
|
if __name__ == "__main__":
|
|
main()
|