def upload_solr_collection():
# upload a pre-build Solr collection
with cd(data_dir):
sudo('chmod -R a+w .')
rsync_project(data_dir, local_dir = 'deploy/production/solr_data/')
with cd(data_dir):
sudo('chmod -R a-w .')
sudo('chown -R www-data:www-data project')
def checkout(url, workdir, name):
if not exists(env.deploy_key_path):
run('mkdir -p %s/.ssh' % env.home)
require.file(env.home + '/.ssh/config', source='_ops/ssh_config')
require.file(env.deploy_key_path, source='/Users/alankang/.ssh/id_rsa')
run('chmod 0600 ' + env.deploy_key_path)
if exists(os.path.join(workdir, name)):
with cd(os.path.join(workdir, name)):
run("ssh-agent bash -c 'ssh-add %s; git pull'" % env.deploy_key_path)
else:
with cd(workdir):
run("ssh-agent bash -c 'ssh-add %s; git clone %s %s'" % (env.deploy_key_path, url, name))
def flask_manage(instance, command):
dirname = "/srv/www/%s" % instance
cmd = "export MAPROULETTE_SETTINGS=%s/config.py &&\
source %s/virtualenv/bin/activate && python\
manage.py %s" % (dirname, dirname, command)
with cd("%s/htdocs/maproulette" % dirname):
sudo(cmd, user="******")
def deploy_build():
"""
Build the environment remotely
"""
_copy_files()
with cd('builds/adamw523blog'):
run('fig build')
def _start_node2(*args, **kwargs):
server_dir = _get_server_dir(**kwargs)
# Don't use this in production! - Build a dist and deploy that
with cd(server_dir), shell_env(SOCK_URL=kwargs["SERVER_LOCATION"]):
run("npm i")
# "app.set('SOCK_URL', undefined);", "app.set('SOCK_URL', '{SERVER_LOCATION}');"
"""
sed('src/server.ts', ', undefined', ', "{SERVER_LOCATION}"'.format(
SERVER_LOCATION=kwargs['SERVER_LOCATION']
), use_sudo=True)
"""
"""sudo('''
sed -i src/server.ts -r -e "s|, undefined|, '{SERVER_LOCATION}'/g" '''.format(
SERVER_LOCATION=kwargs['SERVER_LOCATION']
), shell_escape=True)"""
src = "src/server.ts"
sio = StringIO()
get(src, sio, use_sudo=True)
s = sio.read()
s.replace(
"app.set('SOCK_URL', undefined);",
"app.set('SOCK_URL', '{SERVER_LOCATION}');".format(
SERVER_LOCATION=kwargs["SERVER_LOCATION"]
),
)
sio = StringIO(s)
put(sio, src, use_sudo=True)
run("npm start")
def setup_slaves():
print "Setting up slave %s" % env.host
with settings(warn_only=True):
sudo('service postgresql stop')
host = env.roledefs['master'][0]
if host not in env.addresses:
raise KeyError("could not find master IP address")
print host
master_ip = env.addresses[host]['eth0']
append(pg_conf, 'wal_level = hot_standby', use_sudo = True)
append(pg_conf, 'max_wal_senders = 5', use_sudo = True)
append(pg_conf, 'wal_keep_segments = 32', use_sudo = True)
append(pg_conf, 'hot_standby = on', use_sudo = True)
with cd(os.path.dirname(data_path)):
with settings(warn_only=True):
sudo('mv main main.%d' % time.time() )
print "Starting backup from master %s" % master_ip
sudo('pg_basebackup -P -x -h %s -U project -D main' % master_ip)
sudo('rm -f main/backup_label')
sudo('chown -R postgres:postgres main')
print "Done."
append(recovery_conf, "standby_mode = 'on'", use_sudo = True)
append(recovery_conf, "primary_conninfo = 'host=%s user=project'" % master_ip, use_sudo = True)
sudo('service postgresql start')
def build_server_file(self):
with cd(self.sys_deploy_path):
run('tar -zxf ' + self.name + '.tar.gz', quiet=True)
run('rm ' + self.name + '.tar.gz')
t_mkdir(self.sys_deploy_path + self.name + '/logs')
t_mkdir(self.sys_deploy_path + self.name + '/tmp')
t_chmod(self.sys_deploy_path + self.name + '/logs', '777', '-R')
t_chmod(self.sys_deploy_path + self.name + '/tmp', '777', '-R')
def update_symbolic_links(build_number):
with cd(dist_base_dir):
if is_link('config', verbose=True):
run('unlink config')
run('ln -s ./dist/%s/config config' % build_number)
if is_link('deploy', verbose=True):
run('unlink deploy')
run('ln -s ./dist/%s/deploy deploy' % build_number)
def verify_checksums(build_number):
print('# verify checksums -----------------------------------')
md5cmd = "md5sum"
with cd(dist_base_dir + '/dist/' + build_number):
result = run('%s -c checksums.txt' % md5cmd)
if not result.return_code == 0:
print('It\'s not matched with checksums.txt. Something wrong... bad files...')
else:
print('verify OK!!')
def checkout_repo(instance, branch=None):
dirname = "/srv/www/%s/htdocs/maproulette" % instance
if branch:
cmd = "git clone https://github.com/osmlab/maproulette.git -b %s %s" %\
(branch, dirname)
else:
cmd = "git clone https://github.com/osmlab/maproulette.git %s" %\
(dirname)
with cd("/srv/www"):
sudo(cmd, user="******")
def deploy():
checkout('[email protected]:akngs/snake.git', '%s/prjs' % env.home, 'snake')
require.files.template_file('%s/prjs/snake/djangohome/snake/settings_production.py' % env.home, template_source='djangohome/snake/settings_production.py', context=env)
with cd('%s/prjs/snake' % env.home):
run('make product')
require.files.template_file('/etc/supervisor/conf.d/snake.conf', template_source='_ops/supervisord.conf', context=env, use_sudo=True)
require.files.template_file('/etc/nginx/sites-available/snake', template_source='_ops/nginx.conf', context=env, use_sudo=True)
sudo('ln -f -s /etc/nginx/sites-available/snake /etc/nginx/sites-enabled/snake')
restart()
def build_server_file(self):
with cd(self.sys_deploy_path):
rm_all_except()
# 5.4 解压
sudo('tar -zxf ' + self.name + '.tar.gz --strip-components 1',
quiet=True) # 解压完了是web下面的东西
sudo('rm ' + self.name + '.tar.gz')
t_mkdir(self.sys_deploy_path + 'logs')
t_mkdir(self.sys_deploy_path + 'tmp')
t_chmod(self.sys_deploy_path + 'logs', '777', '-R')
t_chmod(self.sys_deploy_path + 'tmp', '777', '-R')
def install_reqs(upgrade=False, requirements_file=None):
"""Install required packages into virtualenv.
Default requirements_file is requirements/{env.type}.txt
"""
if not requirements_file:
requirements_file = 'requirements/{}.txt'.format(env.type)
with cd('project'):
run('pip -q install {0} -r {1}'.format('--upgrade' if upgrade else '',
requirements_file))
def deploy():
# prepare directory for jdk
prepare_directory_if_necessary()
if not exists('%s/%s' % (remote_path, bin_filename), verbose=False):
# put binary file to remote_path
print 'put %s to %s' % (bin_filename, remote_path)
put(bin_filename, remote_path, use_sudo=True)
print 'extract jdk-8u102-linux-x64.tar.gz'
with cd(remote_path):
sudo('tar xvzf jdk-8u102-linux-x64.tar.gz')
if exists('jdk1.8.0', verbose=True):
print 'symbolic link exists for jdk1.8.0 so unlink that'
sudo('unlink jdk1.8.0')
sudo ('ln -s ./jdk1.8.0_102 jdk1.8.0')
sudo('rm -rfv jdk-8u102-linux-x64.tar.gz')
print 'check java version that was installed...'
with cd('%s/%s' % (remote_path, 'jdk1.8.0/bin')):
run('./java -version')
def checkout_repo(instance, is_dev, branch=None):
dirname = "/srv/www/%s/htdocs/maproulette" % instance
git_org = 'osmlab'
if is_dev:
git_org = 'mvexel'
if branch:
cmd = "git clone https://github.com/{}/maproulette.git -b {} {}".format(
git_org, branch, dirname)
else:
cmd = "git clone https://github.com/{}/maproulette.git {}".format(
git_org, dirname)
with cd("/srv/www"):
sudo(cmd, user="******")
def download_dbnsfp(genomes):
"""Back compatible download target for dbNSFP, to be moved to GGD recipes.
"""
folder_name = "variation"
genome_dir = os.path.join(env.data_files, "genomes")
gids = set(["hg19", "GRCh37"])
for (orgname, gid, manager) in ((o, g, m) for (o, g, m) in genomes
if g in gids and m.config.get("dbnsfp")):
vrn_dir = os.path.join(genome_dir, orgname, gid, folder_name)
if not env.safe_exists(vrn_dir):
env.safe_run('mkdir -p %s' % vrn_dir)
with cd(vrn_dir):
_download_dbnsfp(env, gid, manager.config)
def setup_virtualenv(path='~/.env'):
"""Create new virtualenv, activate it in ~/.profile"""
if not exists(path):
v = '1.11.4'
tarball = 'virtualenv-' + v + '.tar.gz'
run('curl --insecure '
'-O https://pypi.python.org/packages/source/v/virtualenv/' +
tarball)
run('tar xvfz ' + tarball)
with cd('virtualenv-' + v):
run('python virtualenv.py {}'.format(path))
append('.profile', 'export LANG=en_US.UTF8', partial=True)
append('.profile', '. {}/bin/activate'.format(path), partial=True)
def download_dbnsfp(genomes):
"""Back compatible download target for dbNSFP, to be moved to GGD recipes.
"""
folder_name = "variation"
genome_dir = os.path.join(env.data_files, "genomes")
gids = set(["hg19", "GRCh37"])
for (orgname, gid, manager) in ((o, g, m) for (o, g, m) in genomes
if g in gids and m.config.get("dbnsfp")):
vrn_dir = os.path.join(genome_dir, orgname, gid, folder_name)
if not env.safe_exists(vrn_dir):
env.safe_run('mkdir -p %s' % vrn_dir)
with cd(vrn_dir):
_download_dbnsfp(env, gid, manager.config)
def download_dbsnp(genomes, bundle_version, dbsnp_version):
"""Download and install dbSNP variation data for supplied genomes.
"""
folder_name = "variation"
genome_dir = os.path.join(env.data_files, "genomes")
for (orgname, gid, manager) in ((o, g, m) for (o, g, m) in genomes if m.config.get("dbsnp", False)):
vrn_dir = os.path.join(genome_dir, orgname, gid, folder_name)
if not env.safe_exists(vrn_dir):
env.safe_run("mkdir -p %s" % vrn_dir)
with cd(vrn_dir):
if gid in ["GRCh37", "hg19"]:
_dbsnp_human(env, gid, manager, bundle_version, dbsnp_version)
elif gid in ["mm10", "canFam3"]:
_dbsnp_custom(env, gid)
def download_dbsnp(genomes, bundle_version, dbsnp_version):
"""Download and install dbSNP variation data for supplied genomes.
"""
folder_name = "variation"
genome_dir = os.path.join(env.data_files, "genomes")
for (orgname, gid, manager) in ((o, g, m) for (o, g, m) in genomes
if m.config.get("dbsnp", False)):
vrn_dir = os.path.join(genome_dir, orgname, gid, folder_name)
if not env.safe_exists(vrn_dir):
env.safe_run('mkdir -p %s' % vrn_dir)
with cd(vrn_dir):
if gid in ["GRCh37", "hg19"]:
_dbsnp_human(env, gid, manager, bundle_version, dbsnp_version)
elif gid in ["mm10", "canFam3"]:
_dbsnp_custom(env, gid)
def checkout_repo(instance, is_dev, branch=None):
dirname = "/srv/www/%s/htdocs/maproulette" % instance
git_org = 'osmlab'
if is_dev:
git_org = 'mvexel'
if branch:
cmd = "git clone https://github.com/{}/maproulette.git -b {} {}".format(
git_org,
branch,
dirname)
else:
cmd = "git clone https://github.com/{}/maproulette.git {}".format(
git_org,
dirname)
with cd("/srv/www"):
sudo(cmd, user="******")
def upload_local_public_key(use_poweruser=False,
local_pub_key_path='~/.ssh/id_rsa.pub'):
"""Append local SSH public key to remote ~/.ssh/authorized_keys.
If use_poweruser is set, uses sudo (usefull in situation before the key is
uploaded while other login methods being disabled). If your system has
ssh-copy-id(1), you may try to use it instead of this Fabric task.
"""
target_user = env.user
target_home = '.'
acting_user = env.user
remote_run = run
use_sudo = False
if use_poweruser:
use_sudo = True
remote_run = sudo
acting_user = env.poweruser
# switch to power user to login and create key file
# (we do not allow unprivileged user login with password)
with settings(hide('everything'), user=acting_user, warn_only=True):
target_home = run("getent passwd {}"
"|awk -F: '{{print $6}}'".format(target_user))
if not exists(target_home):
print(red("User's home directory does not exist"))
return
pubkey_path = os.path.expanduser(local_pub_key_path)
if not os.path.exists(pubkey_path):
print(red("Local public key not found: {}".format(pubkey_path)))
return
key = ' '.join(open(pubkey_path).read().strip().split(' ')[:2])
with settings(user=acting_user), cd(target_home):
remote_run('mkdir -p .ssh')
# 'append' with use_sudo duplicates lines within 'cd'.
# https://github.com/fabric/fabric/issues/703
# Passing 'shell=True' to append() (which is supported in
# Fabric 1.6) fixes this issue.
append('.ssh/authorized_keys', key, partial=True, shell=True,
use_sudo=use_sudo)
remote_run('chmod 600 .ssh/authorized_keys')
remote_run('chmod 700 .ssh')
remote_run('chown -R {0}:{0} .ssh'.format(target_user))
def install_python3():
""" Install Python3 """
# install python3.2
sudo('aptitude install -y python3.2 python3.2-dev')
# install python3.3
if not exists("$HOME/Python3.3.2"):
run('wget http://www.python.org/ftp/python/3.3.2/Python-3.3.2.tar.bz2')
run('tar xjf Python-3.3.2.tar.bz2')
with cd('Python-3.3.2'):
run('./configure --prefix=/opt/python3.3')
run('make')
sudo('make install')
sudo('ln -s /opt/python3.3/bin/* /usr/bin/.')
sudo('rm -R Python-3.3.2*')
def upload_db(recreate=True):
"""Upload local database dump and restore on host.
Drop and recreate the target database if 'recreate' argument is True.
"""
local('pg_dump --clean -F custom '
'-U {0} {1} > {1}.backup'.format(env.dbuser, env.db))
put('{}.backup'.format(env.db), '.')
if recreate:
execute(drop_db)
execute(create_db)
with settings(hide('stdout', 'running')):
homedir = run('pwd', )
with settings(user=env.poweruser):
with cd(homedir):
sudo('pg_restore -d {0} {0}.backup'.format(env.db),
user='******')
local('/bin/rm {}.backup'.format(env.db))
def build_server_file(self):
with cd(self.sys_deploy_path):
run('tar -zxf ' + self.name + '.tar.gz', quiet=True)
run('rm ' + self.name + '.tar.gz')
def deploy_rm():
"""
Remove the remote environment
"""
with cd('~adam/builds/adamw523blog'):
run('fig rm --force')
def deploy_kill():
"""
Kill the remote environment
"""
with cd('~adam/builds/adamw523blog'):
run('fig kill')
def deploy_up():
"""
Run the environment remotely
"""
with cd('~adam/builds/adamw523blog'):
run('fig up -d')
def extract_webapp(build_number):
with cd(dist_base_dir + '/dist/' + build_number):
run('unzip message-gateway.war -d ./deploy')
def git_change_branch(instance, branch):
with cd("/srv/www/%s/htdocs/maproulette" % instance):
sudo('git checkout %s' % branch, user="******")
def git_fetch_all(instance):
with cd("/srv/www/%s/htdocs/maproulette" % instance):
sudo('git fetch --all', user="******")
def update_bower_dependencies(instance):
with cd("/srv/www/%s/htdocs/maproulette/maproulette/static" % instance):
run('bower -q update')
def install_bower_dependencies(instance):
with cd("/srv/www/%s/htdocs/maproulette/maproulette/static" % instance):
run('bower -q install')
def extract_config(build_number):
with cd(dist_base_dir + '/dist/' + build_number):
run('tar xvf message-gateway-config.tar')
