Commit 7ea05268 authored by nanahira's avatar nanahira

finish

parent 32e878e7
Pipeline #1189 canceled with stages
# Logs
logs
*.log
npm-debug.log*
yarn-debug.log*
yarn-error.log*
lerna-debug.log*
# Diagnostic reports (https://nodejs.org/api/report.html)
report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
# Runtime data
pids
*.pid
*.seed
*.pid.lock
# Directory for instrumented libs generated by jscoverage/JSCover
lib-cov
# Coverage directory used by tools like istanbul
coverage
*.lcov
# nyc test coverage
.nyc_output
# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
.grunt
# Bower dependency directory (https://bower.io/)
bower_components
# node-waf configuration
.lock-wscript
# Compiled binary addons (https://nodejs.org/api/addons.html)
build/Release
# Dependency directories
node_modules/
jspm_packages/
# TypeScript v1 declaration files
typings/
# TypeScript cache
*.tsbuildinfo
# Optional npm cache directory
.npm
# Optional eslint cache
.eslintcache
# Microbundle cache
.rpt2_cache/
.rts2_cache_cjs/
.rts2_cache_es/
.rts2_cache_umd/
# Optional REPL history
.node_repl_history
# Output of 'npm pack'
*.tgz
# Yarn Integrity file
.yarn-integrity
# dotenv environment variables file
.env
.env.test
# parcel-bundler cache (https://parceljs.org/)
.cache
# Next.js build output
.next
# Nuxt.js build / generate output
.nuxt
dist
# Gatsby files
.cache/
# Comment in the public line in if your project uses Gatsby and *not* Next.js
# https://nextjs.org/blog/next-9-1#public-directory-support
# public
# vuepress build output
.vuepress/dist
# Serverless directories
.serverless/
# FuseBox cache
.fusebox/
# DynamoDB Local files
.dynamodb/
# TernJS port file
.tern-port
/build
/output
/config
/config.yaml
__pycache__
*.pyc
/ansible/inventory.yaml
/data
.git*
.dockerignore
Dockerfile
.gitlab-ci.yml
/config.yaml
# Logs
logs
*.log
npm-debug.log*
yarn-debug.log*
yarn-error.log*
lerna-debug.log*
# Diagnostic reports (https://nodejs.org/api/report.html)
report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
# Runtime data
pids
*.pid
*.seed
*.pid.lock
# Directory for instrumented libs generated by jscoverage/JSCover
lib-cov
# Coverage directory used by tools like istanbul
coverage
*.lcov
# nyc test coverage
.nyc_output
# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
.grunt
# Bower dependency directory (https://bower.io/)
bower_components
# node-waf configuration
.lock-wscript
# Compiled binary addons (https://nodejs.org/api/addons.html)
build/Release
# Dependency directories
node_modules/
jspm_packages/
# TypeScript v1 declaration files
typings/
# TypeScript cache
*.tsbuildinfo
# Optional npm cache directory
.npm
# Optional eslint cache
.eslintcache
# Microbundle cache
.rpt2_cache/
.rts2_cache_cjs/
.rts2_cache_es/
.rts2_cache_umd/
# Optional REPL history
.node_repl_history
# Output of 'npm pack'
*.tgz
# Yarn Integrity file
.yarn-integrity
# dotenv environment variables file
.env
.env.test
# parcel-bundler cache (https://parceljs.org/)
.cache
# Next.js build output
.next
# Nuxt.js build / generate output
.nuxt
dist
# Gatsby files
.cache/
# Comment in the public line in if your project uses Gatsby and *not* Next.js
# https://nextjs.org/blog/next-9-1#public-directory-support
# public
# vuepress build output
.vuepress/dist
# Serverless directories
.serverless/
# FuseBox cache
.fusebox/
# DynamoDB Local files
.dynamodb/
# TernJS port file
.tern-port
/build
/output
/config
/config.yaml
__pycache__
*.pyc
/ansible/inventory.yaml
/data
FROM node:buster-slim
RUN apt update && apt -y install python3 build-essential && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
WORKDIR /usr/src/app
COPY ./package*.json ./
RUN npm ci
COPY . ./
RUN npm run build
CMD ["npm", "run", "start"]
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[defaults]
inventory = ./inventory.yaml
host_key_checking = False
strategy_plugins = mitogen-0.2.9/ansible_mitogen/plugins/strategy
strategy = mitogen_linear
- hosts: jupyter
remote_user: root
tasks:
- name: load data
include_vars:
name: instancesData
file: '{{data_file}}'
- name: load instances var
set_fact:
instances: '{{instancesData.instances}}'
- name: directories
file:
path: '{{item}}'
state: directory
with_items:
- '{{jupyter_root}}'
- '{{jupyter_root}}/certs'
- '{{jupyter_root}}/nginx'
- '{{jupyter_root}}/nginx/conf.d'
- '{{jupyter_root}}/instances'
- '{{jupyter_root}}/instances/config'
- name: docker-compose file
template:
src: './docker-compose.yml.j2'
dest: '{{jupyter_root}}/docker-compose.yml'
- name: nginx files
synchronize:
src: './nginx-conf/'
dest: '{{ jupyter_root }}/nginx/conf.d'
delete: yes
copy_links: yes
recursive: yes
verify_host: no
checksum: yes
archive: no
perms: yes
notify: restart_nginx
- name: certs
synchronize:
src: '{{certs_path}}/'
dest: '{{ jupyter_root }}/certs'
delete: yes
copy_links: yes
recursive: yes
verify_host: no
checksum: yes
archive: no
perms: yes
notify: restart_nginx
- name: instance configs
copy:
content: '{{ item.notebookConfig | to_json }}'
dest: '{{jupyter_root}}/instances/config/{{item.name}}.json'
with_items: '{{instances}}'
notify: restart_all
- name: docker-compose up -d
docker_compose:
project_src: '{{ jupyter_root }}'
remove_orphans: true
pull: true
handlers:
- name: restart_nginx
docker_compose:
project_src: '{{ jupyter_root }}'
services:
- nginx
restarted: true
- name: restart_all
docker_compose:
project_src: '{{ jupyter_root }}'
restarted: true
version: '2'
services:
nginx:
restart: always
image: {{nginx_image}}
ports:
- '80:80'
- '443:443'
- '444:443'
volumes:
- ./nginx/conf.d:/etc/nginx/conf.d:ro
- ./certs:/etc/nginx/certs:ro
- ./nginx/cache:/etc/nginx/cache
- ./nginx/log:/var/log/nginx
{% for instance in instances %}
{{instance.name}}:
restart: always
image: {{ jupyter_image }}
volumes:
- ./instances/config/{{ instance.name }}.json:/home/jovyan/.jupyter/jupyter_notebook_config.json:ro
- ./instances/data/{{ instance.name }}:/home/jovyan/work
environment:
GRANT_SUDO: 'yes'
{% endfor %}
Copyright 2019, David Wilson
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors
may be used to endorse or promote products derived from this software without
specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Metadata-Version: 1.1
Name: mitogen
Version: 0.2.9
Summary: Library for writing distributed self-replicating programs.
Home-page: https://github.com/dw/mitogen/
Author: David Wilson
Author-email: UNKNOWN
License: New BSD
Description: UNKNOWN
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Intended Audience :: System Administrators
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.4
Classifier: Programming Language :: Python :: 2.5
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: System :: Distributed Computing
Classifier: Topic :: System :: Systems Administration
# Mitogen
<!-- [![Build Status](https://travis-ci.org/dw/mitogen.png?branch=master)](https://travis-ci.org/dw/mitogen}) -->
<a href="https://mitogen.networkgenomics.com/">Please see the documentation</a>.
![](https://i.imgur.com/eBM6LhJ.gif)
[![Total alerts](https://img.shields.io/lgtm/alerts/g/dw/mitogen.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/dw/mitogen/alerts/)
[![Build Status](https://travis-ci.org/dw/mitogen.svg?branch=master)](https://travis-ci.org/dw/mitogen)
[![Pipelines Status](https://dev.azure.com/dw-mitogen/Mitogen/_apis/build/status/dw.mitogen?branchName=master)](https://dev.azure.com/dw-mitogen/Mitogen/_build/latest?definitionId=1?branchName=master)
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"""JSON token scanner
"""
import re
try:
from simplejson._speedups import make_scanner as c_make_scanner
except ImportError:
c_make_scanner = None
__all__ = ['make_scanner']
NUMBER_RE = re.compile(
r'(-?(?:0|[1-9]\d*))(\.\d+)?([eE][-+]?\d+)?',
(re.VERBOSE | re.MULTILINE | re.DOTALL))
def py_make_scanner(context):
parse_object = context.parse_object
parse_array = context.parse_array
parse_string = context.parse_string
match_number = NUMBER_RE.match
encoding = context.encoding
strict = context.strict
parse_float = context.parse_float
parse_int = context.parse_int
parse_constant = context.parse_constant
object_hook = context.object_hook
def _scan_once(string, idx):
try:
nextchar = string[idx]
except IndexError:
raise StopIteration
if nextchar == '"':
return parse_string(string, idx + 1, encoding, strict)
elif nextchar == '{':
return parse_object((string, idx + 1), encoding, strict, _scan_once, object_hook)
elif nextchar == '[':
return parse_array((string, idx + 1), _scan_once)
elif nextchar == 'n' and string[idx:idx + 4] == 'null':
return None, idx + 4
elif nextchar == 't' and string[idx:idx + 4] == 'true':
return True, idx + 4
elif nextchar == 'f' and string[idx:idx + 5] == 'false':
return False, idx + 5
m = match_number(string, idx)
if m is not None:
integer, frac, exp = m.groups()
if frac or exp:
res = parse_float(integer + (frac or '') + (exp or ''))
else:
res = parse_int(integer)
return res, m.end()
elif nextchar == 'N' and string[idx:idx + 3] == 'NaN':
return parse_constant('NaN'), idx + 3
elif nextchar == 'I' and string[idx:idx + 8] == 'Infinity':
return parse_constant('Infinity'), idx + 8
elif nextchar == '-' and string[idx:idx + 9] == '-Infinity':
return parse_constant('-Infinity'), idx + 9
else:
raise StopIteration
return _scan_once
make_scanner = c_make_scanner or py_make_scanner
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# Copyright 2019, David Wilson
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software without
# specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""
Stable names for PluginLoader instances across Ansible versions.
"""
from __future__ import absolute_import
__all__ = [
'action_loader',
'connection_loader',
'module_loader',
'module_utils_loader',
'shell_loader',
'strategy_loader',
]
try:
from ansible.plugins.loader import action_loader
from ansible.plugins.loader import connection_loader
from ansible.plugins.loader import module_loader
from ansible.plugins.loader import module_utils_loader
from ansible.plugins.loader import shell_loader
from ansible.plugins.loader import strategy_loader
except ImportError: # Ansible <2.4
from ansible.plugins import action_loader
from ansible.plugins import connection_loader
from ansible.plugins import module_loader
from ansible.plugins import module_utils_loader
from ansible.plugins import shell_loader
from ansible.plugins import strategy_loader
# These are original, unwrapped implementations
action_loader__get = action_loader.get
connection_loader__get = connection_loader.get
# Copyright 2019, David Wilson
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software without
# specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
from __future__ import absolute_import
import logging
import os
import mitogen.core
import mitogen.utils
try:
from __main__ import display
except ImportError:
from ansible.utils.display import Display
display = Display()
#: The process name set via :func:`set_process_name`.
_process_name = None
#: The PID of the process that last called :func:`set_process_name`, so its
#: value can be ignored in unknown fork children.
_process_pid = None
def set_process_name(name):
"""
Set a name to adorn log messages with.
"""
global _process_name
_process_name = name
global _process_pid
_process_pid = os.getpid()
class Handler(logging.Handler):
"""
Use Mitogen's log format, but send the result to a Display method.
"""
def __init__(self, normal_method):
logging.Handler.__init__(self)
self.formatter = mitogen.utils.log_get_formatter()
self.normal_method = normal_method
#: Set of target loggers that produce warnings and errors that spam the
#: console needlessly. Their log level is forced to INFO. A better strategy
#: may simply be to bury all target logs in DEBUG output, but not by
#: overriding their log level as done here.
NOISY_LOGGERS = frozenset([
'dnf', # issue #272; warns when a package is already installed.
'boto', # issue #541; normal boto retry logic can cause ERROR logs.
])
def emit(self, record):
mitogen_name = getattr(record, 'mitogen_name', '')
if mitogen_name == 'stderr':
record.levelno = logging.ERROR
if mitogen_name in self.NOISY_LOGGERS and record.levelno >= logging.WARNING:
record.levelno = logging.DEBUG
if _process_pid == os.getpid():
process_name = _process_name
else:
process_name = '?'
s = '[%-4s %d] %s' % (process_name, os.getpid(), self.format(record))
if record.levelno >= logging.ERROR:
display.error(s, wrap_text=False)
elif record.levelno >= logging.WARNING:
display.warning(s, formatted=True)
else:
self.normal_method(s)
def setup():
"""
Install handlers for Mitogen loggers to redirect them into the Ansible
display framework. Ansible installs its own logging framework handlers when
C.DEFAULT_LOG_PATH is set, therefore disable propagation for our handlers.
"""
l_mitogen = logging.getLogger('mitogen')
l_mitogen_io = logging.getLogger('mitogen.io')
l_ansible_mitogen = logging.getLogger('ansible_mitogen')
l_operon = logging.getLogger('operon')
for logger in l_mitogen, l_mitogen_io, l_ansible_mitogen, l_operon:
logger.handlers = [Handler(display.vvv)]
logger.propagate = False
if display.verbosity > 2:
l_ansible_mitogen.setLevel(logging.DEBUG)
l_mitogen.setLevel(logging.DEBUG)
else:
# Mitogen copies the active log level into new children, allowing them
# to filter tiny messages before they hit the network, and therefore
# before they wake the IO loop. Explicitly setting INFO saves ~4%
# running against just the local machine.
l_mitogen.setLevel(logging.ERROR)
l_ansible_mitogen.setLevel(logging.ERROR)
if display.verbosity > 3:
l_mitogen_io.setLevel(logging.DEBUG)
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# Copyright 2019, David Wilson
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software without
# specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
from __future__ import absolute_import
from __future__ import unicode_literals
import mitogen.core
def parse_script_interpreter(source):
"""
Parse the script interpreter portion of a UNIX hashbang using the rules
Linux uses.
:param str source: String like "/usr/bin/env python".
:returns:
Tuple of `(interpreter, arg)`, where `intepreter` is the script
interpreter and `arg` is its sole argument if present, otherwise
:py:data:`None`.
"""
# Find terminating newline. Assume last byte of binprm_buf if absent.
nl = source.find(b'\n', 0, 128)
if nl == -1:
nl = min(128, len(source))
# Split once on the first run of whitespace. If no whitespace exists,
# bits just contains the interpreter filename.
bits = source[0:nl].strip().split(None, 1)
if len(bits) == 1:
return mitogen.core.to_text(bits[0]), None
return mitogen.core.to_text(bits[0]), mitogen.core.to_text(bits[1])
def parse_hashbang(source):
"""
Parse a UNIX "hashbang line" using the syntax supported by Linux.
:param str source: String like "#!/usr/bin/env python".
:returns:
Tuple of `(interpreter, arg)`, where `intepreter` is the script
interpreter and `arg` is its sole argument if present, otherwise
:py:data:`None`.
"""
# Linux requires first 2 bytes with no whitespace, pretty sure it's the
# same everywhere. See binfmt_script.c.
if not source.startswith(b'#!'):
return None, None
return parse_script_interpreter(source[2:])
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Metadata-Version: 1.1
Name: mitogen
Version: 0.2.9
Summary: Library for writing distributed self-replicating programs.
Home-page: https://github.com/dw/mitogen/
Author: David Wilson
Author-email: UNKNOWN
License: New BSD
Description: UNKNOWN
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Intended Audience :: System Administrators
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.4
Classifier: Programming Language :: Python :: 2.5
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: System :: Distributed Computing
Classifier: Topic :: System :: Systems Administration
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