427 lines
15 KiB
Python
Executable File
427 lines
15 KiB
Python
Executable File
#!/bin/python3
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"""
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ECG is a program that automates software environment checking
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for scientific artifacts.
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It is meant to be executed periodically to analyze variations in the
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software environment of the artifact through time.
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"""
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import subprocess
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import json
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import argparse
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import tempfile
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import os
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import requests
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import zipfile
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import tarfile
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import pathlib
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import logging
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import datetime
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import sys
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import string
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def trim(url):
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"""
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Trims given URL to make it contain only lowercase letters and numbers,
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as well as with a maximum length of 128.
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Parameters
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----------
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url: str
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URL to trim.
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Returns
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-------
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str
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Trimmed URL.
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"""
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trimmed = ""
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url_lc = url.lower()
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i = 0
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while i < len(url_lc) and i < 128:
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c = url_lc[i]
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if c in string.ascii_lowercase or c in [str(x) for x in range(0, 10)]:
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trimmed += c
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i += 1
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return trimmed
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def download_file(url, dest):
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"""
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Downloads the file stored at the given URL and returns its hash
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and location.
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Parameters
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----------
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url: str
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URL to the file to download.
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dest: str
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Path to where the file should be stored.
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Returns
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-------
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str
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Hash of the downloaded file.
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"""
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req = requests.get(url)
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file = open(dest, "wb")
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file.write(req.content)
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file.close()
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hash_process = subprocess.run(f"sha256sum {file.name} | cut -d ' ' -f 1 | tr -d '\n'", capture_output=True, shell=True)
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return hash_process.stdout.decode("utf-8")
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def download_sources(config, arthashlog_path, dl_dir, use_cache):
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"""
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Downloads the source of the artifact in 'config'.
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Parameters
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----------
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config: dict
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Parsed config file.
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arthashlog_path: str
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Path to the artifact hash log file.
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dl_dir: str
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Path to the directory where to download the artifact.
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use_cache: bool
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Indicates whether the cache should be used or not.
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Returns
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-------
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temp_dir: str
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Path to the directory where the artifact is downloaded to.
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"""
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url = config["artifact_url"]
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artcache_dir = trim(url)
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artifact_dir = os.path.join(dl_dir, artcache_dir)
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# Checking if artifact in cache. Not downloading if it is:
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if not os.path.exists(artifact_dir) or not use_cache:
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logging.info(f"Downloading artifact from {url}")
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# In case cache was used before:
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if not use_cache:
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os.system(f"rm -rf {artifact_dir}")
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os.mkdir(artifact_dir)
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artifact_file = tempfile.NamedTemporaryFile()
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artifact_path = artifact_file.name
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artifact_hash = download_file(url, artifact_path)
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if config["type"] == "zip":
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artifact = zipfile.ZipFile(artifact_path)
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elif config["type"] == "tar":
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artifact = tarfile.open(artifact_path)
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logging.info(f"Extracting artifact at {artifact_dir}")
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artifact.extractall(artifact_dir)
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# Logging the current hash of the artifact:
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arthashlog_file = open(arthashlog_path, "a")
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now = datetime.datetime.now()
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timestamp = str(datetime.datetime.timestamp(now))
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arthashlog_file.write(f"{timestamp},{artifact_hash}\n")
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arthashlog_file.close()
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else:
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logging.info(f"Cache found for {url}, skipping download")
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return artifact_dir
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def buildstatus_saver(output, buildstatus_path, config_path):
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"""
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Parses the given 'output' to indentify the errors, then saves them to the
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'build_status' file.
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Parameters
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----------
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output: str
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Output of Docker.
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buildstatus_path: str
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Path to the build status file.
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config_path: str
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Path to the config file.
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Returns
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-------
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None
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"""
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# Possible error messages given by 'docker build' and their category.
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# The key is the category, the value is a tuple of error messages belonging to
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# to this category:
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build_errors = {
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"package_unavailable":("Unable to locate package"),
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"baseimage_unavailable":("manifest unknown: manifest unknown")
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}
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file_exists = os.path.exists(buildstatus_path)
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buildstatus_file = open(buildstatus_path, "a")
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artifact_name = os.path.basename(config_path).split(".")[0]
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# # Writing header in case file didn't exist:
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# if not file_exists:
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# buildstatus_file.write("yaml_path,timestamp,error")
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unknown_error = True
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for error_cat, error in build_errors.items():
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if error in output:
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unknown_error = False
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now = datetime.datetime.now()
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timestamp = str(datetime.datetime.timestamp(now))
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buildstatus_file.write(f"{artifact_name},{timestamp},{error_cat}\n")
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if unknown_error:
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now = datetime.datetime.now()
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timestamp = str(datetime.datetime.timestamp(now))
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buildstatus_file.write(f"{artifact_name},{timestamp},unknown_error\n")
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buildstatus_file.close()
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def build_image(config, src_dir, image_name, docker_cache = False):
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"""
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Builds the given Docker image in 'config'.
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Parameters
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----------
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config: dict
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Parsed config file.
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src_dir: str
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Path to the directory where the artifact is stored.
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image_name: str
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Name of the Docker image.
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docker_cache: bool
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Enables or disables Docker 'build' cache.
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Returns
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-------
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return_code: bool, build_output: str
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Return code and output of Docker 'build'.
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"""
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cache_arg = " --no-cache"
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if docker_cache:
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cache_arg = ""
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logging.info(f"Starting building image {image_name}")
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path = os.path.join(src_dir, config["dockerfile_location"])
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# Using trimmed artifact URL as name:
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build_command = f"docker build{cache_arg} -t {image_name} ."
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build_process = subprocess.run(build_command.split(" "), cwd=path, capture_output=True)
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build_output = f"stdout:\n{build_process.stdout.decode('utf-8')}\nstderr:\n{build_process.stderr.decode('utf-8')}"
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# build_output = build_process.stderr.decode("utf-8")
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logging.info(f"Output of '{build_command}':")
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logging.info(build_output)
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return_code = build_process.returncode
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logging.info(f"Command '{build_command}' exited with code {return_code}")
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return return_code, build_output
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def check_env(config, src_dir, image_name, pkglist_path):
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"""
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Builds a list of all software packages installed in the
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Docker image given in 'config', depending on the package managers
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specified in the configuration, then stores it in a CSV file.
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Parameters
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----------
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config: dict
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Parsed config file.
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src_dir: str
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Path to the directory where the artifact is stored.
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image_name: str
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Name of the Docker image.
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pkglist_path: str
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Path to the package list file.
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Returns
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-------
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None
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"""
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# Commands to list installed packages along with their versions and the name
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# of the package manager, depending on the package managers.
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# Each package manager is associated with a tuple, the first item being
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# the package manager's command, the second being the arguments for the
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# query (they must be separate for the "--entrypoint" argument of Docker
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# 'run', see below), and the third one being the command that will format
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# the output of the query command (this one can be an empty string in case
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# the formatting part is already done using the options of the first command).
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# The first command needs to be run on the container, and the second on the
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# host, to take into account container images that do not have the formatting
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# packages installed.
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pkgmgr_cmd = {
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"dpkg": ("dpkg", "-l", "awk 'NR>5 {print $2 \",\" $3 \",\" \"dpkg\"}'"), \
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"rpm":("rpm", "-qa --queryformat '%{NAME},%{VERSION},rpm\\n'", ""), \
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"pacman":("pacman", "-Q", "awk '{print $0 \",\" $1 \",pacman\"}'"), \
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"pip":("pip", "list", "awk 'NR>2 {print $1 \",\" $2 \",\" \"pip\"}'"), \
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"conda":("/root/.conda/bin/conda", "list -e", "sed 's/=/ /g' | awk 'NR>3 {print $1 \",\" $2 \",conda\"}'")
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}
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# Command to obtain the latest commit hash in a git repository (separated
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# into 2 parts for "--entrypoint"):
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gitcmd = ("git", "log -n 1 --pretty=format:%H")
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logging.info("Checking software environment")
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pkglist_file = open(pkglist_path, "w")
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# pkglist_file.write("package,version,package_manager\n")
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path = os.path.join(src_dir, config["dockerfile_location"])
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# Package managers:
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for pkgmgr in config["package_managers"]:
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# "--entrypoint" requires command and arguments to be separated.
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# This Docker 'run' option is used to prevent the shell from printing
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# a login message, if any.
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pkglist_cmd = pkgmgr_cmd[pkgmgr][0]
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pkglist_cmdargs = pkgmgr_cmd[pkgmgr][1].split(" ")
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listformat_cmd = pkgmgr_cmd[pkgmgr][2]
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logging.info(f"Checking '{pkgmgr}'")
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# pkglist_process = subprocess.run(["docker", "run", "--rm", config["image_name"]] + pkglist_cmd.split(" "), cwd=path, capture_output=True)
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pkglist_process = subprocess.run(["docker", "run", "--rm", "--entrypoint", pkglist_cmd, image_name] + pkglist_cmdargs, cwd=path, capture_output=True)
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format_process = subprocess.run(f"cat << EOF | {listformat_cmd}\n{pkglist_process.stdout.decode('utf-8')}EOF", cwd=path, capture_output=True, shell=True)
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pkglist = format_process.stdout.decode("utf-8")
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pkglist_file.write(pkglist)
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# Git packages:
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logging.info("Checking Git packages")
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for repo in config["git_packages"]:
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pkglist_process = subprocess.run(["docker", "run", "--rm", "-w", repo["location"], "--entrypoint", gitcmd[0], image_name] + gitcmd[1].split(" "), cwd=path, capture_output=True)
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repo_row = f"{repo['name']},{pkglist_process.stdout.decode('utf-8')},git"
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pkglist_file.write(f"{repo_row}\n")
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# Misc packages:
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logging.info("Checking packages obtained outside of a package manager or VCS")
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for pkg in config["misc_packages"]:
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logging.info(f"Downloading package {pkg['name']} from {pkg['url']}")
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pkg_file = tempfile.NamedTemporaryFile()
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pkg_path = pkg_file.name
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pkg_hash = download_file(pkg["url"], pkg_path)
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pkg_row = f"{pkg['name']},{pkg_hash},misc"
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pkglist_file.write(f"{pkg_row}\n")
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# Python venvs:
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logging.info("Checking Python venvs")
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for venv in config["python_venvs"]:
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pipcmd = pkgmgr_cmd["pip"][0]
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pipcmd_args = pkgmgr_cmd["pip"][1]
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pkglist_process = subprocess.run(["docker", "run", "--rm", "-w", venv["path"], "--entrypoint", "source", image_name, ".bin/activate", "&&", pipcmd] + pipcmd_args.split(" "), cwd=path, capture_output=True)
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format_process = subprocess.run(f"cat << EOF | {listformat_cmd}\n{pkglist_process.stdout.decode('utf-8')}EOF", cwd=path, capture_output=True, shell=True)
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pkglist = format_process.stdout.decode("utf-8")
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pkglist_file.write(pkglist)
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pkglist_file.close()
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def remove_image(config, image_name):
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"""
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Removes the Docker image given in 'config'.
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Parameters
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----------
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config: dict
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Parsed config file.
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image_name: str
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Name of the Docker image.
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Returns
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-------
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None
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"""
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logging.info(f"Removing image '{image_name}'")
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subprocess.run(["docker", "rmi", image_name], capture_output = True)
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def main():
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# Paths:
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config_path = ""
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pkglist_path = "" # Package list being generated
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buildstatus_path = "" # Status of the build process of the image, when it fails
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arthashlog_path = "" # Log of the hash of the downloaded artifact
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cache_dir = "" # Artifact cache directory, when using one. 'None' value indicates no cache.
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use_cache = False
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# Command line arguments parsing:
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parser = argparse.ArgumentParser(
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prog = "ecg",
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description = "ECG is a program that automates software environment checking for scientific artifacts. "
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"It is meant to be executed periodically to analyze variations in the software environment of the artifact through time."
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)
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parser.add_argument('-v', '--verbose',
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action = 'store_true',
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help = "Shows more details on what is being done."
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)
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parser.add_argument(
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"config",
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help = "The path to the configuration file of the artifact's Docker image."
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)
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parser.add_argument(
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"-p", "--pkg-list",
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help = "Path to the file where the package list generated by the program should be written.",
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required = True
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)
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parser.add_argument(
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"-l", "--log-path",
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help = "Path to the file where to log the output of the program.",
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required = True
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)
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parser.add_argument(
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"-b", "--build-status",
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help = "Path to the file where to write the build status of the Docker image given in the configuration file.",
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required = True
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)
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parser.add_argument(
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"-a", "--artifact-hash",
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help = "Path to the file where to write the log of the hash of the downloaded artifact.",
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required = True
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)
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parser.add_argument(
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"-c", "--cache-dir",
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help = "Path to the cache directory, where artifacts that are downloaded will be stored for future usage. " \
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"If not specified, cache is disabled.",
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required = False
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),
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parser.add_argument('--docker-cache',
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action = 'store_true',
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help = "Use cache for Docker 'build'."
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)
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args = parser.parse_args()
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# Setting up the paths of the outputs:
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log_path = "log.txt" # Output of the program
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pkglist_path = args.pkg_list
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log_path = args.log_path
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buildstatus_path = args.build_status
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arthashlog_path = args.artifact_hash
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cache_dir = args.cache_dir
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# Setting up the log: will be displayed both on stdout and to the specified
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# file:
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print(f"Output will be stored in {log_path}")
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logging.basicConfig(filename = log_path, filemode = "w", format = '%(levelname)s: %(message)s', level = logging.INFO)
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if args.verbose:
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logging.getLogger().addHandler(logging.StreamHandler(sys.stdout))
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# Parsing the input file including the configuration of the artifact's
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# image:
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config_path = args.config
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config_file = open(config_path, "r")
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config = json.loads(config_file.read())
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# config = yaml.safe_load(config_file)
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# print(config)
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config_file.close()
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dl_dir = None
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# If not using cache, creates a temporary directory:
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if cache_dir == None:
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tmp_dir = tempfile.TemporaryDirectory()
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dl_dir = tmp_dir.name
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else:
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use_cache = True
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dl_dir = cache_dir
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artifact_dir = download_sources(config, arthashlog_path, dl_dir, use_cache)
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artifact_name = os.path.splitext(os.path.basename(config_path))[0]
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return_code, build_output = build_image(config, artifact_dir, artifact_name, args.docker_cache)
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if return_code == 0:
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check_env(config, artifact_dir, artifact_name, pkglist_path)
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remove_image(config, artifact_name)
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# Creates file if not already:
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pathlib.Path(buildstatus_path).touch()
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else:
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# Creates file if not already:
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pathlib.Path(pkglist_path).touch()
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buildstatus_saver(build_output, buildstatus_path, config_path)
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if __name__ == "__main__":
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main()
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