github_backup.py

#!/usr/bin/env python

from __future__ import print_function

import argparse
import base64
import calendar
import codecs
import errno
import getpass
import json
import logging
import os
import platform
import re
import select
import socket
import ssl
import subprocess
import sys
import time
from datetime import datetime
from http.client import IncompleteRead
from urllib.error import HTTPError, URLError
from urllib.parse import quote as urlquote
from urllib.parse import urlencode, urlparse
from urllib.request import HTTPRedirectHandler, Request, build_opener, urlopen

try:
    from . import __version__

    VERSION = __version__
except ImportError:
    VERSION = "unknown"

FNULL = open(os.devnull, "w")
FILE_URI_PREFIX = "file://"
logger = logging.getLogger(__name__)

https_ctx = ssl.create_default_context()
if not https_ctx.get_ca_certs():
    import warnings

    warnings.warn(
        "\n\nYOUR DEFAULT CA CERTS ARE EMPTY.\n"
        + "PLEASE POPULATE ANY OF:"
        + "".join(
            ["\n - " + x for x in ssl.get_default_verify_paths() if type(x) is str]
        )
        + "\n",
        stacklevel=2,
    )
    import certifi

    https_ctx = ssl.create_default_context(cafile=certifi.where())


def logging_subprocess(
    popenargs, stdout_log_level=logging.DEBUG, stderr_log_level=logging.ERROR, **kwargs
):
    """
    Variant of subprocess.call that accepts a logger instead of stdout/stderr,
    and logs stdout messages via logger.debug and stderr messages via
    logger.error.
    """
    child = subprocess.Popen(
        popenargs, stdout=subprocess.PIPE, stderr=subprocess.PIPE, **kwargs
    )
    if sys.platform == "win32":
        logger.info(
            "Windows operating system detected - no subprocess logging will be returned"
        )

    log_level = {child.stdout: stdout_log_level, child.stderr: stderr_log_level}

    def check_io():
        if sys.platform == "win32":
            return
        ready_to_read = select.select([child.stdout, child.stderr], [], [], 1000)[0]
        for io in ready_to_read:
            line = io.readline()
            if not logger:
                continue
            if not (io == child.stderr and not line):
                logger.log(log_level[io], line[:-1])

    # keep checking stdout/stderr until the child exits
    while child.poll() is None:
        check_io()

    check_io()  # check again to catch anything after the process exits

    rc = child.wait()

    if rc != 0:
        print("{} returned {}:".format(popenargs[0], rc), file=sys.stderr)
        print("\t", " ".join(popenargs), file=sys.stderr)

    return rc


def mkdir_p(*args):
    for path in args:
        try:
            os.makedirs(path)
        except OSError as exc:  # Python >2.5
            if exc.errno == errno.EEXIST and os.path.isdir(path):
                pass
            else:
                raise


def mask_password(url, secret="*****"):
    parsed = urlparse(url)

    if not parsed.password:
        return url
    elif parsed.password == "x-oauth-basic":
        return url.replace(parsed.username, secret)

    return url.replace(parsed.password, secret)


def parse_args(args=None):
    parser = argparse.ArgumentParser(description="Backup a github account")
    parser.add_argument("user", metavar="USER", type=str, help="github username")
    parser.add_argument(
        "-u", "--username", dest="username", help="username for basic auth"
    )
    parser.add_argument(
        "-p",
        "--password",
        dest="password",
        help="password for basic auth. "
        "If a username is given but not a password, the "
        "password will be prompted for.",
    )
    parser.add_argument(
        "-t",
        "--token",
        dest="token_classic",
        help="personal access, OAuth, or JSON Web token, or path to token (file://...)",
    )  # noqa
    parser.add_argument(
        "-f",
        "--token-fine",
        dest="token_fine",
        help="fine-grained personal access token (github_pat_....), or path to token (file://...)",
    )  # noqa
    parser.add_argument(
        "-q",
        "--quiet",
        action="store_true",
        dest="quiet",
        help="supress log messages less severe than warning, e.g. info",
    )
    parser.add_argument(
        "--as-app",
        action="store_true",
        dest="as_app",
        help="authenticate as github app instead of as a user.",
    )
    parser.add_argument(
        "-o",
        "--output-directory",
        default=".",
        dest="output_directory",
        help="directory at which to backup the repositories",
    )
    parser.add_argument(
        "-l",
        "--log-level",
        default="info",
        dest="log_level",
        help="log level to use (default: info, possible levels: debug, info, warning, error, critical)",
    )
    parser.add_argument(
        "-i",
        "--incremental",
        action="store_true",
        dest="incremental",
        help="incremental backup",
    )
    parser.add_argument(
        "--incremental-by-files",
        action="store_true",
        dest="incremental_by_files",
        help="incremental backup based on modification date of files",
    )
    parser.add_argument(
        "--starred",
        action="store_true",
        dest="include_starred",
        help="include JSON output of starred repositories in backup",
    )
    parser.add_argument(
        "--all-starred",
        action="store_true",
        dest="all_starred",
        help="include starred repositories in backup [*]",
    )
    parser.add_argument(
        "--watched",
        action="store_true",
        dest="include_watched",
        help="include JSON output of watched repositories in backup",
    )
    parser.add_argument(
        "--followers",
        action="store_true",
        dest="include_followers",
        help="include JSON output of followers in backup",
    )
    parser.add_argument(
        "--following",
        action="store_true",
        dest="include_following",
        help="include JSON output of following users in backup",
    )
    parser.add_argument(
        "--all",
        action="store_true",
        dest="include_everything",
        help="include everything in backup (not including [*])",
    )
    parser.add_argument(
        "--issues",
        action="store_true",
        dest="include_issues",
        help="include issues in backup",
    )
    parser.add_argument(
        "--issue-comments",
        action="store_true",
        dest="include_issue_comments",
        help="include issue comments in backup",
    )
    parser.add_argument(
        "--issue-events",
        action="store_true",
        dest="include_issue_events",
        help="include issue events in backup",
    )
    parser.add_argument(
        "--pulls",
        action="store_true",
        dest="include_pulls",
        help="include pull requests in backup",
    )
    parser.add_argument(
        "--pull-comments",
        action="store_true",
        dest="include_pull_comments",
        help="include pull request review comments in backup",
    )
    parser.add_argument(
        "--pull-commits",
        action="store_true",
        dest="include_pull_commits",
        help="include pull request commits in backup",
    )
    parser.add_argument(
        "--pull-details",
        action="store_true",
        dest="include_pull_details",
        help="include more pull request details in backup [*]",
    )
    parser.add_argument(
        "--labels",
        action="store_true",
        dest="include_labels",
        help="include labels in backup",
    )
    parser.add_argument(
        "--hooks",
        action="store_true",
        dest="include_hooks",
        help="include hooks in backup (works only when authenticated)",
    )  # noqa
    parser.add_argument(
        "--milestones",
        action="store_true",
        dest="include_milestones",
        help="include milestones in backup",
    )
    parser.add_argument(
        "--repositories",
        action="store_true",
        dest="include_repository",
        help="include repository clone in backup",
    )
    parser.add_argument(
        "--bare", action="store_true", dest="bare_clone", help="clone bare repositories"
    )
    parser.add_argument(
        "--no-prune",
        action="store_true",
        dest="no_prune",
        help="disable prune option for git fetch",
    )
    parser.add_argument(
        "--lfs",
        action="store_true",
        dest="lfs_clone",
        help="clone LFS repositories (requires Git LFS to be installed, https://git-lfs.github.com) [*]",
    )
    parser.add_argument(
        "--wikis",
        action="store_true",
        dest="include_wiki",
        help="include wiki clone in backup",
    )
    parser.add_argument(
        "--gists",
        action="store_true",
        dest="include_gists",
        help="include gists in backup [*]",
    )
    parser.add_argument(
        "--starred-gists",
        action="store_true",
        dest="include_starred_gists",
        help="include starred gists in backup [*]",
    )
    parser.add_argument(
        "--skip-archived",
        action="store_true",
        dest="skip_archived",
        help="skip project if it is archived",
    )
    parser.add_argument(
        "--skip-existing",
        action="store_true",
        dest="skip_existing",
        help="skip project if a backup directory exists",
    )
    parser.add_argument(
        "-L",
        "--languages",
        dest="languages",
        help="only allow these languages",
        nargs="*",
    )
    parser.add_argument(
        "-N",
        "--name-regex",
        dest="name_regex",
        help="python regex to match names against",
    )
    parser.add_argument(
        "-H", "--github-host", dest="github_host", help="GitHub Enterprise hostname"
    )
    parser.add_argument(
        "-O",
        "--organization",
        action="store_true",
        dest="organization",
        help="whether or not this is an organization user",
    )
    parser.add_argument(
        "-R",
        "--repository",
        dest="repository",
        help="name of repository to limit backup to",
    )
    parser.add_argument(
        "-P",
        "--private",
        action="store_true",
        dest="private",
        help="include private repositories [*]",
    )
    parser.add_argument(
        "-F",
        "--fork",
        action="store_true",
        dest="fork",
        help="include forked repositories [*]",
    )
    parser.add_argument(
        "--prefer-ssh",
        action="store_true",
        help="Clone repositories using SSH instead of HTTPS",
    )
    parser.add_argument(
        "-v", "--version", action="version", version="%(prog)s " + VERSION
    )
    parser.add_argument(
        "--keychain-name",
        dest="osx_keychain_item_name",
        help="OSX ONLY: name field of password item in OSX keychain that holds the personal access or OAuth token",
    )
    parser.add_argument(
        "--keychain-account",
        dest="osx_keychain_item_account",
        help="OSX ONLY: account field of password item in OSX keychain that holds the personal access or OAuth token",
    )
    parser.add_argument(
        "--releases",
        action="store_true",
        dest="include_releases",
        help="include release information, not including assets or binaries",
    )
    parser.add_argument(
        "--latest-releases",
        type=int,
        default=0,
        dest="number_of_latest_releases",
        help="include certain number of the latest releases; only applies if including releases",
    )
    parser.add_argument(
        "--skip-prerelease",
        action="store_true",
        dest="skip_prerelease",
        help="skip prerelease and draft versions; only applies if including releases",
    )
    parser.add_argument(
        "--assets",
        action="store_true",
        dest="include_assets",
        help="include assets alongside release information; only applies if including releases",
    )
    parser.add_argument(
        "--throttle-limit",
        dest="throttle_limit",
        type=int,
        default=0,
        help="start throttling of GitHub API requests after this amount of API requests remain",
    )
    parser.add_argument(
        "--throttle-pause",
        dest="throttle_pause",
        type=float,
        default=30.0,
        help="wait this amount of seconds when API request throttling is active (default: 30.0, requires --throttle-limit to be set)",
    )
    parser.add_argument(
        "--exclude", dest="exclude", help="names of repositories to exclude", nargs="*"
    )
    return parser.parse_args(args)


def get_auth(args, encode=True, for_git_cli=False):
    auth = None

    if args.osx_keychain_item_name:
        if not args.osx_keychain_item_account:
            raise Exception(
                "You must specify both name and account fields for osx keychain password items"
            )
        else:
            if platform.system() != "Darwin":
                raise Exception("Keychain arguments are only supported on Mac OSX")
            try:
                with open(os.devnull, "w") as devnull:
                    token = subprocess.check_output(
                        [
                            "security",
                            "find-generic-password",
                            "-s",
                            args.osx_keychain_item_name,
                            "-a",
                            args.osx_keychain_item_account,
                            "-w",
                        ],
                        stderr=devnull,
                    ).strip()
                token = token.decode("utf-8")
                auth = token + ":" + "x-oauth-basic"
            except subprocess.SubprocessError:
                raise Exception(
                    "No password item matching the provided name and account could be found in the osx keychain."
                )
    elif args.osx_keychain_item_account:
        raise Exception(
            "You must specify both name and account fields for osx keychain password items"
        )
    elif args.token_fine:
        if args.token_fine.startswith(FILE_URI_PREFIX):
            args.token_fine = read_file_contents(args.token_fine)

        if args.token_fine.startswith("github_pat_"):
            auth = args.token_fine
        else:
            raise Exception(
                "Fine-grained token supplied does not look like a GitHub PAT"
            )
    elif args.token_classic:
        if args.token_classic.startswith(FILE_URI_PREFIX):
            args.token_classic = read_file_contents(args.token_classic)

        if not args.as_app:
            auth = args.token_classic + ":" + "x-oauth-basic"
        else:
            if not for_git_cli:
                auth = args.token_classic
            else:
                auth = "x-access-token:" + args.token_classic
    elif args.username:
        if not args.password:
            args.password = getpass.getpass()
        if encode:
            password = args.password
        else:
            password = urlquote(args.password)
        auth = args.username + ":" + password
    elif args.password:
        raise Exception("You must specify a username for basic auth")

    if not auth:
        return None

    if not encode or args.token_fine is not None:
        return auth

    return base64.b64encode(auth.encode("ascii"))


def get_github_api_host(args):
    if args.github_host:
        host = args.github_host + "/api/v3"
    else:
        host = "api.github.com"

    return host


def get_github_host(args):
    if args.github_host:
        host = args.github_host
    else:
        host = "github.com"

    return host


def read_file_contents(file_uri):
    return open(file_uri[len(FILE_URI_PREFIX) :], "rt").readline().strip()


def get_github_repo_url(args, repository):
    if repository.get("is_gist"):
        if args.prefer_ssh:
            # The git_pull_url value is always https for gists, so we need to transform it to ssh form
            repo_url = re.sub(
                r"^https?:\/\/(.+)\/(.+)\.git$",
                r"git@\1:\2.git",
                repository["git_pull_url"],
            )
            repo_url = re.sub(
                r"^git@gist\.", "git@", repo_url
            )  # strip gist subdomain for better hostkey compatibility
        else:
            repo_url = repository["git_pull_url"]
        return repo_url

    if args.prefer_ssh:
        return repository["ssh_url"]

    auth = get_auth(args, encode=False, for_git_cli=True)
    if auth:
        repo_url = "https://{0}@{1}/{2}/{3}.git".format(
            auth if args.token_fine is None else "oauth2:" + auth,
            get_github_host(args),
            repository["owner"]["login"],
            repository["name"],
        )
    else:
        repo_url = repository["clone_url"]

    return repo_url


def retrieve_data_gen(args, template, query_args=None, single_request=False):
    auth = get_auth(args, encode=not args.as_app)
    query_args = get_query_args(query_args)
    per_page = 100
    page = 0

    while True:
        page = page + 1
        request = _construct_request(
            per_page,
            page,
            query_args,
            template,
            auth,
            as_app=args.as_app,
            fine=True if args.token_fine is not None else False,
        )  # noqa
        r, errors = _get_response(request, auth, template)

        status_code = int(r.getcode())
        # Check if we got correct data
        try:
            response = json.loads(r.read().decode("utf-8"))
        except IncompleteRead:
            logger.warning("Incomplete read error detected")
            read_error = True
        except json.decoder.JSONDecodeError:
            logger.warning("JSON decode error detected")
            read_error = True
        except TimeoutError:
            logger.warning("Tiemout error detected")
            read_error = True
        else:
            read_error = False

        # be gentle with API request limit and throttle requests if remaining requests getting low
        limit_remaining = int(r.headers.get("x-ratelimit-remaining", 0))
        if args.throttle_limit and limit_remaining <= args.throttle_limit:
            logger.info(
                "API request limit hit: {} requests left, pausing further requests for {}s".format(
                    limit_remaining, args.throttle_pause
                )
            )
            time.sleep(args.throttle_pause)

        retries = 0
        while retries < 3 and (status_code == 502 or read_error):
            logger.warning("API request failed. Retrying in 5 seconds")
            retries += 1
            time.sleep(5)
            request = _construct_request(
                per_page,
                page,
                query_args,
                template,
                auth,
                as_app=args.as_app,
                fine=True if args.token_fine is not None else False,
            )  # noqa
            r, errors = _get_response(request, auth, template)

            status_code = int(r.getcode())
            try:
                response = json.loads(r.read().decode("utf-8"))
                read_error = False
            except IncompleteRead:
                logger.warning("Incomplete read error detected")
                read_error = True
            except json.decoder.JSONDecodeError:
                logger.warning("JSON decode error detected")
                read_error = True
            except TimeoutError:
                logger.warning("Tiemout error detected")
                read_error = True

        if status_code != 200:
            template = "API request returned HTTP {0}: {1}"
            errors.append(template.format(status_code, r.reason))
            raise Exception(", ".join(errors))

        if read_error:
            template = "API request problem reading response for {0}"
            errors.append(template.format(request))
            raise Exception(", ".join(errors))

        if len(errors) == 0:
            if type(response) is list:
                for resp in response:
                    yield resp
                if len(response) < per_page:
                    break
            elif type(response) is dict and single_request:
                yield response

        if len(errors) > 0:
            raise Exception(", ".join(errors))

        if single_request:
            break


def retrieve_data(args, template, query_args=None, single_request=False):
    return list(retrieve_data_gen(args, template, query_args, single_request))


def get_query_args(query_args=None):
    if not query_args:
        query_args = {}
    return query_args


def _get_response(request, auth, template):
    retry_timeout = 3
    errors = []
    # We'll make requests in a loop so we can
    # delay and retry in the case of rate-limiting
    while True:
        should_continue = False
        try:
            r = urlopen(request, context=https_ctx)
        except HTTPError as exc:
            errors, should_continue = _request_http_error(exc, auth, errors)  # noqa
            r = exc
        except URLError as e:
            logger.warning(e.reason)
            should_continue, retry_timeout = _request_url_error(template, retry_timeout)
            if not should_continue:
                raise
        except socket.error as e:
            logger.warning(e.strerror)
            should_continue, retry_timeout = _request_url_error(template, retry_timeout)
            if not should_continue:
                raise

        if should_continue:
            continue

        break
    return r, errors


def _construct_request(
    per_page, page, query_args, template, auth, as_app=None, fine=False
):
    querystring = urlencode(
        dict(
            list({"per_page": per_page, "page": page}.items())
            + list(query_args.items())
        )
    )

    request = Request(template + "?" + querystring)
    if auth is not None:
        if not as_app:
            if fine:
                request.add_header("Authorization", "token " + auth)
            else:
                request.add_header("Authorization", "Basic ".encode("ascii") + auth)
        else:
            auth = auth.encode("ascii")
            request.add_header("Authorization", "token ".encode("ascii") + auth)
            request.add_header(
                "Accept", "application/vnd.github.machine-man-preview+json"
            )
    logger.info("Requesting {}?{}".format(template, querystring))
    return request


def _request_http_error(exc, auth, errors):
    # HTTPError behaves like a Response so we can
    # check the status code and headers to see exactly
    # what failed.

    should_continue = False
    headers = exc.headers
    limit_remaining = int(headers.get("x-ratelimit-remaining", 0))

    if exc.code == 403 and limit_remaining < 1:
        # The X-RateLimit-Reset header includes a
        # timestamp telling us when the limit will reset
        # so we can calculate how long to wait rather
        # than inefficiently polling:
        gm_now = calendar.timegm(time.gmtime())
        reset = int(headers.get("x-ratelimit-reset", 0)) or gm_now
        # We'll never sleep for less than 10 seconds:
        delta = max(10, reset - gm_now)

        limit = headers.get("x-ratelimit-limit")
        logger.warning(
            "Exceeded rate limit of {} requests; waiting {} seconds to reset".format(
                limit, delta
            )
        )  # noqa

        if auth is None:
            logger.info("Hint: Authenticate to raise your GitHub rate limit")

        time.sleep(delta)
        should_continue = True
    return errors, should_continue


def _request_url_error(template, retry_timeout):
    # In case of a connection timing out, we can retry a few time
    # But we won't crash and not back-up the rest now
    logger.info("'{}' timed out".format(template))
    retry_timeout -= 1

    if retry_timeout >= 0:
        return True, retry_timeout

    raise Exception("'{}' timed out to much, skipping!".format(template))


class S3HTTPRedirectHandler(HTTPRedirectHandler):
    """
    A subclassed redirect handler for downloading Github assets from S3.

    urllib will add the Authorization header to the redirected request to S3, which will result in a 400,
    so we should remove said header on redirect.
    """

    def redirect_request(self, req, fp, code, msg, headers, newurl):
        request = super(S3HTTPRedirectHandler, self).redirect_request(
            req, fp, code, msg, headers, newurl
        )
        del request.headers["Authorization"]
        return request


def download_file(url, path, auth, as_app=False, fine=False):
    # Skip downloading release assets if they already exist on disk so we don't redownload on every sync
    if os.path.exists(path):
        return

    request = _construct_request(
        per_page=100,
        page=1,
        query_args={},
        template=url,
        auth=auth,
        as_app=as_app,
        fine=fine,
    )
    request.add_header("Accept", "application/octet-stream")
    opener = build_opener(S3HTTPRedirectHandler)

    try:
        response = opener.open(request)

        chunk_size = 16 * 1024
        with open(path, "wb") as f:
            while True:
                chunk = response.read(chunk_size)
                if not chunk:
                    break
                f.write(chunk)
    except HTTPError as exc:
        # Gracefully handle 404 responses (and others) when downloading from S3
        logger.warning(
            "Skipping download of asset {0} due to HTTPError: {1}".format(
                url, exc.reason
            )
        )
    except URLError as e:
        # Gracefully handle other URL errors
        logger.warning(
            "Skipping download of asset {0} due to URLError: {1}".format(url, e.reason)
        )
    except socket.error as e:
        # Gracefully handle socket errors
        # TODO: Implement retry logic
        logger.warning(
            "Skipping download of asset {0} due to socker error: {1}".format(
                url, e.strerror
            )
        )


def get_authenticated_user(args):
    template = "https://{0}/user".format(get_github_api_host(args))
    data = retrieve_data(args, template, single_request=True)
    return data[0]


def check_git_lfs_install():
    exit_code = subprocess.call(["git", "lfs", "version"])
    if exit_code != 0:
        raise Exception(
            "The argument --lfs requires you to have Git LFS installed.\nYou can get it from https://git-lfs.github.com."
        )


def retrieve_repositories(args, authenticated_user):
    logger.info("Retrieving repositories")
    single_request = False
    if args.user == authenticated_user["login"]:
        # we must use the /user/repos API to be able to access private repos
        template = "https://{0}/user/repos".format(get_github_api_host(args))
    else:
        if args.private and not args.organization:
            logger.warning(
                "Authenticated user is different from user being backed up, thus private repositories cannot be accessed"
            )
        template = "https://{0}/users/{1}/repos".format(
            get_github_api_host(args), args.user
        )

    if args.organization:
        template = "https://{0}/orgs/{1}/repos".format(
            get_github_api_host(args), args.user
        )

    if args.repository:
        single_request = True
        template = "https://{0}/repos/{1}/{2}".format(
            get_github_api_host(args), args.user, args.repository
        )

    repos = retrieve_data(args, template, single_request=single_request)

    if args.all_starred:
        starred_template = "https://{0}/users/{1}/starred".format(
            get_github_api_host(args), args.user
        )
        starred_repos = retrieve_data(args, starred_template, single_request=False)
        # flag each repo as starred for downstream processing
        for item in starred_repos:
            item.update({"is_starred": True})
        repos.extend(starred_repos)

    if args.include_gists:
        gists_template = "https://{0}/users/{1}/gists".format(
            get_github_api_host(args), args.user
        )
        gists = retrieve_data(args, gists_template, single_request=False)
        # flag each repo as a gist for downstream processing
        for item in gists:
            item.update({"is_gist": True})
        repos.extend(gists)

    if args.include_starred_gists:
        starred_gists_template = "https://{0}/gists/starred".format(
            get_github_api_host(args)
        )
        starred_gists = retrieve_data(
            args, starred_gists_template, single_request=False
        )
        # flag each repo as a starred gist for downstream processing
        for item in starred_gists:
            item.update({"is_gist": True, "is_starred": True})
        repos.extend(starred_gists)

    return repos


def filter_repositories(args, unfiltered_repositories):
    logger.info("Filtering repositories")

    repositories = []
    for r in unfiltered_repositories:
        # gists can be anonymous, so need to safely check owner
        if r.get("owner", {}).get("login") == args.user or r.get("is_starred"):
            repositories.append(r)

    name_regex = None
    if args.name_regex:
        name_regex = re.compile(args.name_regex)

    languages = None
    if args.languages:
        languages = [x.lower() for x in args.languages]

    if not args.fork:
        repositories = [r for r in repositories if not r.get("fork")]
    if not args.private:
        repositories = [
            r for r in repositories if not r.get("private") or r.get("public")
        ]
    if languages:
        repositories = [
            r
            for r in repositories
            if r.get("language") and r.get("language").lower() in languages
        ]  # noqa
    if name_regex:
        repositories = [
            r for r in repositories if "name" not in r or name_regex.match(r["name"])
        ]
    if args.skip_archived:
        repositories = [r for r in repositories if not r.get("archived")]
    if args.exclude:
        repositories = [
            r for r in repositories if "name" not in r or r["name"] not in args.exclude
        ]

    return repositories


def backup_repositories(args, output_directory, repositories):
    logger.info("Backing up repositories")
    repos_template = "https://{0}/repos".format(get_github_api_host(args))

    if args.incremental:
        last_update_path = os.path.join(output_directory, "last_update")
        if os.path.exists(last_update_path):
            args.since = open(last_update_path).read().strip()
        else:
            args.since = None
    else:
        args.since = None

    last_update = "0000-00-00T00:00:00Z"
    for repository in repositories:
        if "updated_at" in repository and repository["updated_at"] > last_update:
            last_update = repository["updated_at"]
        elif "pushed_at" in repository and repository["pushed_at"] > last_update:
            last_update = repository["pushed_at"]

        if repository.get("is_gist"):
            repo_cwd = os.path.join(output_directory, "gists", repository["id"])
        elif repository.get("is_starred"):
            # put starred repos in -o/starred/${owner}/${repo} to prevent collision of
            # any repositories with the same name
            repo_cwd = os.path.join(
                output_directory,
                "starred",
                repository["owner"]["login"],
                repository["name"],
            )
        else:
            repo_cwd = os.path.join(
                output_directory, "repositories", repository["name"]
            )

        repo_dir = os.path.join(repo_cwd, "repository")
        repo_url = get_github_repo_url(args, repository)

        include_gists = args.include_gists or args.include_starred_gists
        if (args.include_repository or args.include_everything) or (
            include_gists and repository.get("is_gist")
        ):
            repo_name = (
                repository.get("name")
                if not repository.get("is_gist")
                else repository.get("id")
            )
            fetch_repository(
                repo_name,
                repo_url,
                repo_dir,
                skip_existing=args.skip_existing,
                bare_clone=args.bare_clone,
                lfs_clone=args.lfs_clone,
                no_prune=args.no_prune,
            )

            if repository.get("is_gist"):
                # dump gist information to a file as well
                output_file = "{0}/gist.json".format(repo_cwd)
                with codecs.open(output_file, "w", encoding="utf-8") as f:
                    json_dump(repository, f)

                continue  # don't try to back anything else for a gist; it doesn't exist

        download_wiki = args.include_wiki or args.include_everything
        if repository["has_wiki"] and download_wiki:
            fetch_repository(
                repository["name"],
                repo_url.replace(".git", ".wiki.git"),
                os.path.join(repo_cwd, "wiki"),
                skip_existing=args.skip_existing,
                bare_clone=args.bare_clone,
                lfs_clone=args.lfs_clone,
                no_prune=args.no_prune,
            )
        if args.include_issues or args.include_everything:
            backup_issues(args, repo_cwd, repository, repos_template)

        if args.include_pulls or args.include_everything:
            backup_pulls(args, repo_cwd, repository, repos_template)

        if args.include_milestones or args.include_everything:
            backup_milestones(args, repo_cwd, repository, repos_template)

        if args.include_labels or args.include_everything:
            backup_labels(args, repo_cwd, repository, repos_template)

        if args.include_hooks or args.include_everything:
            backup_hooks(args, repo_cwd, repository, repos_template)

        if args.include_releases or args.include_everything:
            backup_releases(
                args,
                repo_cwd,
                repository,
                repos_template,
                include_assets=args.include_assets or args.include_everything,
            )

    if args.incremental:
        if last_update == "0000-00-00T00:00:00Z":
            last_update = time.strftime("%Y-%m-%dT%H:%M:%SZ", time.localtime())

        open(last_update_path, "w").write(last_update)


def backup_issues(args, repo_cwd, repository, repos_template):
    has_issues_dir = os.path.isdir("{0}/issues/.git".format(repo_cwd))
    if args.skip_existing and has_issues_dir:
        return

    logger.info("Retrieving {0} issues".format(repository["full_name"]))
    issue_cwd = os.path.join(repo_cwd, "issues")
    mkdir_p(repo_cwd, issue_cwd)

    issues = {}
    issues_skipped = 0
    issues_skipped_message = ""
    _issue_template = "{0}/{1}/issues".format(repos_template, repository["full_name"])

    should_include_pulls = args.include_pulls or args.include_everything
    issue_states = ["open", "closed"]
    for issue_state in issue_states:
        query_args = {"filter": "all", "state": issue_state}
        if args.since:
            query_args["since"] = args.since

        _issues = retrieve_data(args, _issue_template, query_args=query_args)
        for issue in _issues:
            # skip pull requests which are also returned as issues
            # if retrieving pull requests is requested as well
            if "pull_request" in issue and should_include_pulls:
                issues_skipped += 1
                continue

            issues[issue["number"]] = issue

    if issues_skipped:
        issues_skipped_message = " (skipped {0} pull requests)".format(issues_skipped)

    logger.info(
        "Saving {0} issues to disk{1}".format(
            len(list(issues.keys())), issues_skipped_message
        )
    )
    comments_template = _issue_template + "/{0}/comments"
    events_template = _issue_template + "/{0}/events"
    for number, issue in list(issues.items()):
        issue_file = "{0}/{1}.json".format(issue_cwd, number)
        if args.incremental_by_files and os.path.isfile(issue_file):
            modified = os.path.getmtime(issue_file)
            modified = datetime.fromtimestamp(modified).strftime("%Y-%m-%dT%H:%M:%SZ")
            if modified > issue["updated_at"]:
                logger.info("Skipping issue {0} because it wasn't modified since last backup".format(number))
                continue

        if args.include_issue_comments or args.include_everything:
            template = comments_template.format(number)
            issues[number]["comment_data"] = retrieve_data(args, template)
        if args.include_issue_events or args.include_everything:
            template = events_template.format(number)
            issues[number]["event_data"] = retrieve_data(args, template)

        with codecs.open(issue_file + ".temp", "w", encoding="utf-8") as f:
            json_dump(issue, f)
            os.rename(issue_file + ".temp", issue_file)  # Unlike json_dump, this is atomic


def backup_pulls(args, repo_cwd, repository, repos_template):
    has_pulls_dir = os.path.isdir("{0}/pulls/.git".format(repo_cwd))
    if args.skip_existing and has_pulls_dir:
        return

    logger.info("Retrieving {0} pull requests".format(repository["full_name"]))  # noqa
    pulls_cwd = os.path.join(repo_cwd, "pulls")
    mkdir_p(repo_cwd, pulls_cwd)

    pulls = {}
    _pulls_template = "{0}/{1}/pulls".format(repos_template, repository["full_name"])
    _issue_template = "{0}/{1}/issues".format(repos_template, repository["full_name"])
    query_args = {
        "filter": "all",
        "state": "all",
        "sort": "updated",
        "direction": "desc",
    }

    if not args.include_pull_details:
        pull_states = ["open", "closed"]
        for pull_state in pull_states:
            query_args["state"] = pull_state
            _pulls = retrieve_data_gen(args, _pulls_template, query_args=query_args)
            for pull in _pulls:
                if args.since and pull["updated_at"] < args.since:
                    break
                if not args.since or pull["updated_at"] >= args.since:
                    pulls[pull["number"]] = pull
    else:
        _pulls = retrieve_data_gen(args, _pulls_template, query_args=query_args)
        for pull in _pulls:
            if args.since and pull["updated_at"] < args.since:
                break
            if not args.since or pull["updated_at"] >= args.since:
                pulls[pull["number"]] = retrieve_data(
                    args,
                    _pulls_template + "/{}".format(pull["number"]),
                    single_request=True,
                )[0]

    logger.info("Saving {0} pull requests to disk".format(len(list(pulls.keys()))))
    # Comments from pulls API are only _review_ comments
    # regular comments need to be fetched via issue API.
    # For backwards compatibility with versions <= 0.41.0
    # keep name "comment_data" for review comments
    comments_regular_template = _issue_template + "/{0}/comments"
    comments_template = _pulls_template + "/{0}/comments"
    commits_template = _pulls_template + "/{0}/commits"
    for number, pull in list(pulls.items()):
        pull_file = "{0}/{1}.json".format(pulls_cwd, number)
        if args.incremental_by_files and os.path.isfile(pull_file):
            modified = os.path.getmtime(pull_file)
            modified = datetime.fromtimestamp(modified).strftime("%Y-%m-%dT%H:%M:%SZ")
            if modified > pull["updated_at"]:
                logger.info("Skipping pull request {0} because it wasn't modified since last backup".format(number))
                continue
        if args.include_pull_comments or args.include_everything:
            template = comments_regular_template.format(number)
            pulls[number]["comment_regular_data"] = retrieve_data(args, template)
            template = comments_template.format(number)
            pulls[number]["comment_data"] = retrieve_data(args, template)
        if args.include_pull_commits or args.include_everything:
            template = commits_template.format(number)
            pulls[number]["commit_data"] = retrieve_data(args, template)

        with codecs.open(pull_file + ".temp", "w", encoding="utf-8") as f:
            json_dump(pull, f)
            os.rename(pull_file + ".temp", pull_file)  # Unlike json_dump, this is atomic


def backup_milestones(args, repo_cwd, repository, repos_template):
    milestone_cwd = os.path.join(repo_cwd, "milestones")
    if args.skip_existing and os.path.isdir(milestone_cwd):
        return

    logger.info("Retrieving {0} milestones".format(repository["full_name"]))
    mkdir_p(repo_cwd, milestone_cwd)

    template = "{0}/{1}/milestones".format(repos_template, repository["full_name"])

    query_args = {"state": "all"}

    _milestones = retrieve_data(args, template, query_args=query_args)

    milestones = {}
    for milestone in _milestones:
        milestones[milestone["number"]] = milestone

    logger.info("Saving {0} milestones to disk".format(len(list(milestones.keys()))))
    for number, milestone in list(milestones.items()):
        milestone_file = "{0}/{1}.json".format(milestone_cwd, number)
        with codecs.open(milestone_file, "w", encoding="utf-8") as f:
            json_dump(milestone, f)


def backup_labels(args, repo_cwd, repository, repos_template):
    label_cwd = os.path.join(repo_cwd, "labels")
    output_file = "{0}/labels.json".format(label_cwd)
    template = "{0}/{1}/labels".format(repos_template, repository["full_name"])
    _backup_data(args, "labels", template, output_file, label_cwd)


def backup_hooks(args, repo_cwd, repository, repos_template):
    auth = get_auth(args)
    if not auth:
        logger.info("Skipping hooks since no authentication provided")
        return
    hook_cwd = os.path.join(repo_cwd, "hooks")
    output_file = "{0}/hooks.json".format(hook_cwd)
    template = "{0}/{1}/hooks".format(repos_template, repository["full_name"])
    try:
        _backup_data(args, "hooks", template, output_file, hook_cwd)
    except Exception as e:
        if "404" in str(e):
            logger.info("Unable to read hooks, skipping")
        else:
            raise e


def backup_releases(args, repo_cwd, repository, repos_template, include_assets=False):
    repository_fullname = repository["full_name"]

    # give release files somewhere to live & log intent
    release_cwd = os.path.join(repo_cwd, "releases")
    logger.info("Retrieving {0} releases".format(repository_fullname))
    mkdir_p(repo_cwd, release_cwd)

    query_args = {}

    release_template = "{0}/{1}/releases".format(repos_template, repository_fullname)
    releases = retrieve_data(args, release_template, query_args=query_args)

    if args.skip_prerelease:
        releases = [r for r in releases if not r["prerelease"] and not r["draft"]]

    if args.number_of_latest_releases and args.number_of_latest_releases < len(
        releases
    ):
        releases.sort(
            key=lambda item: datetime.strptime(
                item["created_at"], "%Y-%m-%dT%H:%M:%SZ"
            ),
            reverse=True,
        )
        releases = releases[: args.number_of_latest_releases]
        logger.info("Saving the latest {0} releases to disk".format(len(releases)))
    else:
        logger.info("Saving {0} releases to disk".format(len(releases)))

    # for each release, store it
    for release in releases:
        release_name = release["tag_name"]
        release_name_safe = release_name.replace("/", "__")
        output_filepath = os.path.join(
            release_cwd, "{0}.json".format(release_name_safe)
        )
        with codecs.open(output_filepath, "w+", encoding="utf-8") as f:
            json_dump(release, f)

        if include_assets:
            assets = retrieve_data(args, release["assets_url"])
            if len(assets) > 0:
                # give release asset files somewhere to live & download them (not including source archives)
                release_assets_cwd = os.path.join(release_cwd, release_name_safe)
                mkdir_p(release_assets_cwd)
                for asset in assets:
                    download_file(
                        asset["url"],
                        os.path.join(release_assets_cwd, asset["name"]),
                        get_auth(args, encode=not args.as_app),
                        as_app=args.as_app,
                        fine=True if args.token_fine is not None else False,
                    )


def fetch_repository(
    name,
    remote_url,
    local_dir,
    skip_existing=False,
    bare_clone=False,
    lfs_clone=False,
    no_prune=False,
):
    if bare_clone:
        if os.path.exists(local_dir):
            clone_exists = (
                subprocess.check_output(
                    ["git", "rev-parse", "--is-bare-repository"], cwd=local_dir
                )
                == b"true\n"
            )
        else:
            clone_exists = False
    else:
        clone_exists = os.path.exists(os.path.join(local_dir, ".git"))

    if clone_exists and skip_existing:
        return

    masked_remote_url = mask_password(remote_url)

    initialized = subprocess.call(
        "git ls-remote " + remote_url, stdout=FNULL, stderr=FNULL, shell=True
    )
    if initialized == 128:
        logger.info(
            "Skipping {0} ({1}) since it's not initialized".format(
                name, masked_remote_url
            )
        )
        return

    if clone_exists:
        logger.info("Updating {0} in {1}".format(name, local_dir))

        remotes = subprocess.check_output(["git", "remote", "show"], cwd=local_dir)
        remotes = [i.strip() for i in remotes.decode("utf-8").splitlines()]

        if "origin" not in remotes:
            git_command = ["git", "remote", "rm", "origin"]
            logging_subprocess(git_command, cwd=local_dir)
            git_command = ["git", "remote", "add", "origin", remote_url]
            logging_subprocess(git_command, cwd=local_dir)
        else:
            git_command = ["git", "remote", "set-url", "origin", remote_url]
            logging_subprocess(git_command, cwd=local_dir)

        git_command = ["git", "fetch", "--all", "--force", "--tags", "--prune"]
        if no_prune:
            git_command.pop()
        logging_subprocess(git_command, cwd=local_dir)
        if lfs_clone:
            git_command = ["git", "lfs", "fetch", "--all", "--prune"]
            if no_prune:
                git_command.pop()
            logging_subprocess(git_command, cwd=local_dir)
    else:
        logger.info(
            "Cloning {0} repository from {1} to {2}".format(
                name, masked_remote_url, local_dir
            )
        )
        if bare_clone:
            git_command = ["git", "clone", "--mirror", remote_url, local_dir]
            logging_subprocess(git_command)
            if lfs_clone:
                git_command = ["git", "lfs", "fetch", "--all", "--prune"]
                if no_prune:
                    git_command.pop()
                logging_subprocess(git_command, cwd=local_dir)
        else:
            if lfs_clone:
                git_command = ["git", "lfs", "clone", remote_url, local_dir]
            else:
                git_command = ["git", "clone", remote_url, local_dir]
            logging_subprocess(git_command)


def backup_account(args, output_directory):
    account_cwd = os.path.join(output_directory, "account")

    if args.include_starred or args.include_everything:
        output_file = "{0}/starred.json".format(account_cwd)
        template = "https://{0}/users/{1}/starred".format(
            get_github_api_host(args), args.user
        )
        _backup_data(args, "starred repositories", template, output_file, account_cwd)

    if args.include_watched or args.include_everything:
        output_file = "{0}/watched.json".format(account_cwd)
        template = "https://{0}/users/{1}/subscriptions".format(
            get_github_api_host(args), args.user
        )
        _backup_data(args, "watched repositories", template, output_file, account_cwd)

    if args.include_followers or args.include_everything:
        output_file = "{0}/followers.json".format(account_cwd)
        template = "https://{0}/users/{1}/followers".format(
            get_github_api_host(args), args.user
        )
        _backup_data(args, "followers", template, output_file, account_cwd)

    if args.include_following or args.include_everything:
        output_file = "{0}/following.json".format(account_cwd)
        template = "https://{0}/users/{1}/following".format(
            get_github_api_host(args), args.user
        )
        _backup_data(args, "following", template, output_file, account_cwd)


def _backup_data(args, name, template, output_file, output_directory):
    skip_existing = args.skip_existing
    if not skip_existing or not os.path.exists(output_file):
        logger.info("Retrieving {0} {1}".format(args.user, name))
        mkdir_p(output_directory)
        data = retrieve_data(args, template)

        logger.info("Writing {0} {1} to disk".format(len(data), name))
        with codecs.open(output_file, "w", encoding="utf-8") as f:
            json_dump(data, f)


def json_dump(data, output_file):
    json.dump(
        data,
        output_file,
        ensure_ascii=False,
        sort_keys=True,
        indent=4,
        separators=(",", ": "),
    )