This is an automated email from the git hooks/post-receive script. osallou pushed a commit to branch master in repository biomaj3-process.
commit 9e65114ec39faa32004f241d4c11c829ce26a4cd Author: Olivier Sallou <[email protected]> Date: Thu Aug 17 11:59:48 2017 +0000 New upstream version 3.0.7 --- .gitignore | 72 ++++ .travis.yml | 30 ++ CHANGES.txt | 19 + LICENSE | 662 ++++++++++++++++++++++++++++++++++ MANIFEST.in | 2 + README.md | 41 +++ bin/biomaj_process_consumer.py | 44 +++ biomaj_process/__init__.py | 0 biomaj_process/biomaj_process_web.py | 124 +++++++ biomaj_process/message/__init__.py | 0 biomaj_process/message/message.proto | 46 +++ biomaj_process/message/message_pb2.py | 356 ++++++++++++++++++ biomaj_process/process.py | 358 ++++++++++++++++++ biomaj_process/process_client.py | 107 ++++++ biomaj_process/process_service.py | 259 +++++++++++++ biomaj_process/wsgi.py | 4 + config.yml | 54 +++ gunicorn_conf.py | 3 + requirements.txt | 12 + setup.cfg | 2 + setup.py | 64 ++++ tests/biomaj_tests.py | 50 +++ tests/config.yml | 50 +++ tests/test.sh | 5 + 24 files changed, 2364 insertions(+) diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..754c2a7 --- /dev/null +++ b/.gitignore @@ -0,0 +1,72 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] + +# Coveralls +.coveralls.yml + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.cache +nosetests.xml +coverage.xml + +# Translations +*.mo +*.pot + +# Django stuff: +*.log + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# PyCharm +.idea + +# Vim +.viminfo +# Less history +.lesshst + +.dbshell +.emacs* +.ipython +.mongo* +#*.properties + diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..48f0648 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,30 @@ +language: python +sudo: false +python: + - "2.7" + - "3.4" + - "3.5" +services: + - redis +# Apply only on main branches +branches: + except: + - /^feature.*$/ +# command to install dependencies +#before_install: +# - "sudo apt-get update -qq" +# - "sudo apt-get install -qq libldap2-dev libsasl2-dev" +install: + - "pip install flake8" + - "pip install -r requirements.txt" + - "pip install coverage" + - "pip install python-coveralls" + - "python setup.py -q install" +# - "echo data_file=$TRAVIS_BUILD_DIR/.coverage >> .coveragerc" +# command to run tests +script: + - python setup.py test + - flake8 --ignore E501 biomaj_process/*.py +#after_success: +# - coveralls + diff --git a/CHANGES.txt b/CHANGES.txt new file mode 100644 index 0000000..162af9b --- /dev/null +++ b/CHANGES.txt @@ -0,0 +1,19 @@ +3.0.7: + fix case if process desc or type is missing in bank properties +3.0.6: + disable web thread logging +3.0.5: + retry in case of contact failure with proxy +3.0.4: + for docker, restrict directory to bank directory and dependencies + add host in prometheus stats +3.0.3: + fix prometheus + gunicorn multi process + add consul supervision +3.0.2: + add logging info + execute docker processes in biomaj micro service +3.0.1: + bug fixes +3.0.0: + move process management out of biomaj main package diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..cebe035 --- /dev/null +++ b/LICENSE @@ -0,0 +1,662 @@ +GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + <one line to give the program's name and a brief idea of what it does.> + Copyright (C) <year> <name of author> + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published + by the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +<http://www.gnu.org/licenses/>. + diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..2052e1d --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,2 @@ +include *.txt *.md +recursive-include biomaj_process *.txt diff --git a/README.md b/README.md new file mode 100644 index 0000000..35cca55 --- /dev/null +++ b/README.md @@ -0,0 +1,41 @@ +# About + +Microservice to manage the process execution of biomaj. + +A protobuf interface is available in biomaj_process/message/message_pb2.py to exchange messages between BioMAJ and the download service. +Messages go through RabbitMQ (to be installed). + +# Protobuf + +To compile protobuf, in biomaj_process/message: + + protoc --python_out=. message.proto + +# Development + + flake8 biomaj_process + +# Run + +## Message consumer: +export BIOMAJ_CONFIG=path_to_config.yml +python bin/biomaj_process_consumer.py + +## Web server + +If package is installed via pip, you need a file named *gunicorn_conf.py* containing somehwhere on local server: + + def worker_exit(server, worker): + from prometheus_client import multiprocess + multiprocess.mark_process_dead(worker.pid) + +If you cloned the repository and installed it via python setup.py install, just refer to the *gunicorn_conf.py* in the cloned repository. + + + export BIOMAJ_CONFIG=path_to_config.yml + rm -rf ..path_to/godocker-prometheus-multiproc + mkdir -p ..path_to/godocker-prometheus-multiproc + export prometheus_multiproc_dir=..path_to/godocker-prometheus-multiproc + gunicorn biomaj_download.biomaj_process_web:app + +Web processes should be behind a proxy/load balancer, API base url /api/download diff --git a/bin/biomaj_process_consumer.py b/bin/biomaj_process_consumer.py new file mode 100644 index 0000000..b2ee4e2 --- /dev/null +++ b/bin/biomaj_process_consumer.py @@ -0,0 +1,44 @@ +import os +import logging + +import requests +import yaml +import consul + +from biomaj_process.process_service import ProcessService +from biomaj_core.utils import Utils + +config_file = 'config.yml' +if 'BIOMAJ_CONFIG' in os.environ: + config_file = os.environ['BIOMAJ_CONFIG'] + +config = None +with open(config_file, 'r') as ymlfile: + config = yaml.load(ymlfile) + Utils.service_config_override(config) + + +def on_executed(bank, procs): + if 'prometheus' in config and not config['prometheus']: + return + metrics = [] + if not procs: + metric = {'bank': bank, 'error': 1} + metrics.append(metrics) + else: + for proc in procs: + metric = {'bank': bank} + if 'error' in proc and proc['error']: + metric['error'] = 1 + else: + metric['execution_time'] = proc['execution_time'] + if 'hostname' in config['web']: + metric['host'] = config['web']['hostname'] + metrics.append(metric) + r = requests.post(config['web']['local_endpoint'] + '/api/process/metrics', json = metrics) + + +process = ProcessService(config_file) +process.on_executed_callback(on_executed) +process.supervise() +process.wait_for_messages() diff --git a/biomaj_process/__init__.py b/biomaj_process/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/biomaj_process/biomaj_process_web.py b/biomaj_process/biomaj_process_web.py new file mode 100644 index 0000000..8903792 --- /dev/null +++ b/biomaj_process/biomaj_process_web.py @@ -0,0 +1,124 @@ +''' +Web interface to query list/download status +Manage sessions and metrics +''' + +import ssl +import os + +import yaml +from flask import Flask +from flask import jsonify +from flask import request +from prometheus_client import Counter +from prometheus_client.exposition import generate_latest +from prometheus_client import multiprocess +from prometheus_client import CollectorRegistry +import consul +import redis + +from biomaj_process.message import message_pb2 +from biomaj_process.process_service import ProcessService +from biomaj_core.utils import Utils + +app = Flask(__name__) + +process_metric = Counter("biomaj_process_total", "Bank total process execution.", ['bank']) +process_error_metric = Counter("biomaj_process_errors", "Bank total process errors.", ['bank']) +process_time_metric = Counter("biomaj_process_time", "Bank process execution time in seconds.", ['bank', 'host']) + +config_file = 'config.yml' +if 'BIOMAJ_CONFIG' in os.environ: + config_file = os.environ['BIOMAJ_CONFIG'] + +config = None +with open(config_file, 'r') as ymlfile: + config = yaml.load(ymlfile) + Utils.service_config_override(config) + + +redis_client = redis.StrictRedis( + host=config['redis']['host'], + port=config['redis']['port'], + db=config['redis']['db'], + decode_responses=True +) + + +def consul_declare(config): + if config['consul']['host']: + consul_agent = consul.Consul(host=config['consul']['host']) + consul_agent.agent.service.register('biomaj-process', service_id=config['consul']['id'], address=config['web']['hostname'], port=config['web']['port'], tags=['biomaj']) + check = consul.Check.http(url='http://' + config['web']['hostname'] + ':' + str(config['web']['port']) + '/api/process', interval=20) + consul_agent.agent.check.register(config['consul']['id'] + '_check', check=check, service_id=config['consul']['id']) + + +consul_declare(config) + + [email protected]('/api/process', methods=['GET']) +def ping(): + return jsonify({'msg': 'pong'}) + + [email protected]('/metrics', methods=['GET']) +def metrics(): + registry = CollectorRegistry() + multiprocess.MultiProcessCollector(registry) + return generate_latest(registry) + + [email protected]('/api/process/metrics', methods=['POST']) +def add_metrics(): + ''' + Expects a JSON request with an array of {'bank': 'bank_name', 'error': 'error_message', 'execution_time': seconds_to_execute} + ''' + + procs = request.get_json() + for proc in procs: + host = 'na' + if 'host' in proc: + host = proc['host'] + if 'error' in proc and proc['error']: + process_error_metric.labels(proc['bank']).inc() + else: + process_metric.labels(proc['bank']).inc() + process_time_metric.labels(proc['bank'], host).inc(proc['execution_time']) + return jsonify({'msg': 'OK'}) + + [email protected]('/api/process/session/<bank>', methods=['POST']) +def create_session(bank): + dserv = ProcessService(config_file, rabbitmq=False) + session = dserv._create_session(bank) + return jsonify({'session': session}) + + [email protected]('/api/process/session/<bank>/<session>', methods=['DELETE']) +def clean_session(bank, session): + dserv = ProcessService(config_file, rabbitmq=False) + biomaj_file_info = message_pb2.Process() + biomaj_file_info.bank = bank + biomaj_file_info.session = session + dserv.clean(biomaj_file_info) + return jsonify({'msg': 'session cleared'}) + + [email protected]('/api/process/session/<bank>/<session>', methods=['GET']) +def get_session(bank, session): + error = redis_client.get(config['redis']['prefix'] + ':' + bank + ':session:' + session + ':error') + exitcode = redis_client.get(config['redis']['prefix'] + ':' + bank + ':session:' + session + ':exitcode') + info = redis_client.get(config['redis']['prefix'] + ':' + bank + ':session:' + session + ':error:info') + if exitcode: + exitcode = int(exitcode) + else: + exitcode = -1 + return jsonify({'error': error, 'exitcode': exitcode, 'info': info}) + + +if __name__ == "__main__": + context = None + if config['tls']['cert']: + context = ssl.SSLContext(ssl.PROTOCOL_TLSv1_2) + context.load_cert_chain(config['tls']['cert'], config['tls']['key']) + app.run(host='0.0.0.0', port=config['web']['port'], ssl_context=context, threaded=True, debug=config['web']['debug']) diff --git a/biomaj_process/message/__init__.py b/biomaj_process/message/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/biomaj_process/message/message.proto b/biomaj_process/message/message.proto new file mode 100644 index 0000000..234acfe --- /dev/null +++ b/biomaj_process/message/message.proto @@ -0,0 +1,46 @@ +package biomaj; + +message Process { + + message EnvVar { + required string name = 1; + required string value = 2; + } + // Name of the bank + required string bank = 1; + required string session = 2; + required string log_dir = 3; + required string exe = 4; + repeated string args = 5; + repeated EnvVar env_vars = 6; + optional bool shell_expand = 7 [default=false]; + optional string name = 8; + optional string description = 9; + optional string proc_type = 10; + + message Docker { + required string image = 1; + optional bool use_sudo = 2 [default=false]; + } + optional bool is_docker = 11 [default=false]; + optional Docker docker = 12; +} + + +message Operation { + + enum OPERATION { + EXECUTE = 1; + } + + optional Process process = 1; + + required OPERATION type = 2 [default=EXECUTE]; + + message Trace { + required string trace_id = 1; + required string span_id = 2; + } + + optional Trace trace = 3; +} diff --git a/biomaj_process/message/message_pb2.py b/biomaj_process/message/message_pb2.py new file mode 100644 index 0000000..d0183d1 --- /dev/null +++ b/biomaj_process/message/message_pb2.py @@ -0,0 +1,356 @@ +# Generated by the protocol buffer compiler. DO NOT EDIT! +# source: message.proto + +import sys +_b=sys.version_info[0]<3 and (lambda x:x) or (lambda x:x.encode('latin1')) +from google.protobuf import descriptor as _descriptor +from google.protobuf import message as _message +from google.protobuf import reflection as _reflection +from google.protobuf import symbol_database as _symbol_database +from google.protobuf import descriptor_pb2 +# @@protoc_insertion_point(imports) + +_sym_db = _symbol_database.Default() + + + + +DESCRIPTOR = _descriptor.FileDescriptor( + name='message.proto', + package='biomaj', + serialized_pb=_b('\n\rmessage.proto\x12\x06\x62iomaj\"\xec\x02\n\x07Process\x12\x0c\n\x04\x62\x61nk\x18\x01 \x02(\t\x12\x0f\n\x07session\x18\x02 \x02(\t\x12\x0f\n\x07log_dir\x18\x03 \x02(\t\x12\x0b\n\x03\x65xe\x18\x04 \x02(\t\x12\x0c\n\x04\x61rgs\x18\x05 \x03(\t\x12(\n\x08\x65nv_vars\x18\x06 \x03(\x0b\x32\x16.biomaj.Process.EnvVar\x12\x1b\n\x0cshell_expand\x18\x07 \x01(\x08:\x05\x66\x61lse\x12\x0c\n\x04name\x18\x08 \x01(\t\x12\x13\n\x0b\x64\x65scription\x18\t \x01(\t\x12\x11\n\tproc_ty [...] +) +_sym_db.RegisterFileDescriptor(DESCRIPTOR) + + + +_OPERATION_OPERATION = _descriptor.EnumDescriptor( + name='OPERATION', + full_name='biomaj.Operation.OPERATION', + filename=None, + file=DESCRIPTOR, + values=[ + _descriptor.EnumValueDescriptor( + name='EXECUTE', index=0, number=1, + options=None, + type=None), + ], + containing_type=None, + options=None, + serialized_start=576, + serialized_end=600, +) +_sym_db.RegisterEnumDescriptor(_OPERATION_OPERATION) + + +_PROCESS_ENVVAR = _descriptor.Descriptor( + name='EnvVar', + full_name='biomaj.Process.EnvVar', + filename=None, + file=DESCRIPTOR, + containing_type=None, + fields=[ + _descriptor.FieldDescriptor( + name='name', full_name='biomaj.Process.EnvVar.name', index=0, + number=1, type=9, cpp_type=9, label=2, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='value', full_name='biomaj.Process.EnvVar.value', index=1, + number=2, type=9, cpp_type=9, label=2, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + ], + extensions=[ + ], + nested_types=[], + enum_types=[ + ], + options=None, + is_extendable=False, + extension_ranges=[], + oneofs=[ + ], + serialized_start=303, + serialized_end=340, +) + +_PROCESS_DOCKER = _descriptor.Descriptor( + name='Docker', + full_name='biomaj.Process.Docker', + filename=None, + file=DESCRIPTOR, + containing_type=None, + fields=[ + _descriptor.FieldDescriptor( + name='image', full_name='biomaj.Process.Docker.image', index=0, + number=1, type=9, cpp_type=9, label=2, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='use_sudo', full_name='biomaj.Process.Docker.use_sudo', index=1, + number=2, type=8, cpp_type=7, label=1, + has_default_value=True, default_value=False, + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + ], + extensions=[ + ], + nested_types=[], + enum_types=[ + ], + options=None, + is_extendable=False, + extension_ranges=[], + oneofs=[ + ], + serialized_start=342, + serialized_end=390, +) + +_PROCESS = _descriptor.Descriptor( + name='Process', + full_name='biomaj.Process', + filename=None, + file=DESCRIPTOR, + containing_type=None, + fields=[ + _descriptor.FieldDescriptor( + name='bank', full_name='biomaj.Process.bank', index=0, + number=1, type=9, cpp_type=9, label=2, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='session', full_name='biomaj.Process.session', index=1, + number=2, type=9, cpp_type=9, label=2, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='log_dir', full_name='biomaj.Process.log_dir', index=2, + number=3, type=9, cpp_type=9, label=2, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='exe', full_name='biomaj.Process.exe', index=3, + number=4, type=9, cpp_type=9, label=2, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='args', full_name='biomaj.Process.args', index=4, + number=5, type=9, cpp_type=9, label=3, + has_default_value=False, default_value=[], + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='env_vars', full_name='biomaj.Process.env_vars', index=5, + number=6, type=11, cpp_type=10, label=3, + has_default_value=False, default_value=[], + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='shell_expand', full_name='biomaj.Process.shell_expand', index=6, + number=7, type=8, cpp_type=7, label=1, + has_default_value=True, default_value=False, + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='name', full_name='biomaj.Process.name', index=7, + number=8, type=9, cpp_type=9, label=1, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='description', full_name='biomaj.Process.description', index=8, + number=9, type=9, cpp_type=9, label=1, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='proc_type', full_name='biomaj.Process.proc_type', index=9, + number=10, type=9, cpp_type=9, label=1, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='is_docker', full_name='biomaj.Process.is_docker', index=10, + number=11, type=8, cpp_type=7, label=1, + has_default_value=True, default_value=False, + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='docker', full_name='biomaj.Process.docker', index=11, + number=12, type=11, cpp_type=10, label=1, + has_default_value=False, default_value=None, + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + ], + extensions=[ + ], + nested_types=[_PROCESS_ENVVAR, _PROCESS_DOCKER, ], + enum_types=[ + ], + options=None, + is_extendable=False, + extension_ranges=[], + oneofs=[ + ], + serialized_start=26, + serialized_end=390, +) + + +_OPERATION_TRACE = _descriptor.Descriptor( + name='Trace', + full_name='biomaj.Operation.Trace', + filename=None, + file=DESCRIPTOR, + containing_type=None, + fields=[ + _descriptor.FieldDescriptor( + name='trace_id', full_name='biomaj.Operation.Trace.trace_id', index=0, + number=1, type=9, cpp_type=9, label=2, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='span_id', full_name='biomaj.Operation.Trace.span_id', index=1, + number=2, type=9, cpp_type=9, label=2, + has_default_value=False, default_value=_b("").decode('utf-8'), + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + ], + extensions=[ + ], + nested_types=[], + enum_types=[ + ], + options=None, + is_extendable=False, + extension_ranges=[], + oneofs=[ + ], + serialized_start=532, + serialized_end=574, +) + +_OPERATION = _descriptor.Descriptor( + name='Operation', + full_name='biomaj.Operation', + filename=None, + file=DESCRIPTOR, + containing_type=None, + fields=[ + _descriptor.FieldDescriptor( + name='process', full_name='biomaj.Operation.process', index=0, + number=1, type=11, cpp_type=10, label=1, + has_default_value=False, default_value=None, + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='type', full_name='biomaj.Operation.type', index=1, + number=2, type=14, cpp_type=8, label=2, + has_default_value=True, default_value=1, + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + _descriptor.FieldDescriptor( + name='trace', full_name='biomaj.Operation.trace', index=2, + number=3, type=11, cpp_type=10, label=1, + has_default_value=False, default_value=None, + message_type=None, enum_type=None, containing_type=None, + is_extension=False, extension_scope=None, + options=None), + ], + extensions=[ + ], + nested_types=[_OPERATION_TRACE, ], + enum_types=[ + _OPERATION_OPERATION, + ], + options=None, + is_extendable=False, + extension_ranges=[], + oneofs=[ + ], + serialized_start=393, + serialized_end=600, +) + +_PROCESS_ENVVAR.containing_type = _PROCESS +_PROCESS_DOCKER.containing_type = _PROCESS +_PROCESS.fields_by_name['env_vars'].message_type = _PROCESS_ENVVAR +_PROCESS.fields_by_name['docker'].message_type = _PROCESS_DOCKER +_OPERATION_TRACE.containing_type = _OPERATION +_OPERATION.fields_by_name['process'].message_type = _PROCESS +_OPERATION.fields_by_name['type'].enum_type = _OPERATION_OPERATION +_OPERATION.fields_by_name['trace'].message_type = _OPERATION_TRACE +_OPERATION_OPERATION.containing_type = _OPERATION +DESCRIPTOR.message_types_by_name['Process'] = _PROCESS +DESCRIPTOR.message_types_by_name['Operation'] = _OPERATION + +Process = _reflection.GeneratedProtocolMessageType('Process', (_message.Message,), dict( + + EnvVar = _reflection.GeneratedProtocolMessageType('EnvVar', (_message.Message,), dict( + DESCRIPTOR = _PROCESS_ENVVAR, + __module__ = 'message_pb2' + # @@protoc_insertion_point(class_scope:biomaj.Process.EnvVar) + )) + , + + Docker = _reflection.GeneratedProtocolMessageType('Docker', (_message.Message,), dict( + DESCRIPTOR = _PROCESS_DOCKER, + __module__ = 'message_pb2' + # @@protoc_insertion_point(class_scope:biomaj.Process.Docker) + )) + , + DESCRIPTOR = _PROCESS, + __module__ = 'message_pb2' + # @@protoc_insertion_point(class_scope:biomaj.Process) + )) +_sym_db.RegisterMessage(Process) +_sym_db.RegisterMessage(Process.EnvVar) +_sym_db.RegisterMessage(Process.Docker) + +Operation = _reflection.GeneratedProtocolMessageType('Operation', (_message.Message,), dict( + + Trace = _reflection.GeneratedProtocolMessageType('Trace', (_message.Message,), dict( + DESCRIPTOR = _OPERATION_TRACE, + __module__ = 'message_pb2' + # @@protoc_insertion_point(class_scope:biomaj.Operation.Trace) + )) + , + DESCRIPTOR = _OPERATION, + __module__ = 'message_pb2' + # @@protoc_insertion_point(class_scope:biomaj.Operation) + )) +_sym_db.RegisterMessage(Operation) +_sym_db.RegisterMessage(Operation.Trace) + + +# @@protoc_insertion_point(module_scope) diff --git a/biomaj_process/process.py b/biomaj_process/process.py new file mode 100644 index 0000000..a040714 --- /dev/null +++ b/biomaj_process/process.py @@ -0,0 +1,358 @@ +from builtins import str +from builtins import object +import logging +import os +import subprocess +import tempfile +import datetime +import time +import sys + +from biomaj_process.process_client import ProcessServiceClient + + +class Process(object): + ''' + Define a process to execute + ''' + + def __init__(self, name, exe, args, desc=None, proc_type=None, expand=True, bank_env=None, log_dir=None): + ''' + Define one process + + :param name: name of the process (descriptive) + :type name: str + :param exe: path to the executable (relative to process.dir or full path) + :type exe: str + :param args: arguments + :type args: str + :param desc: process description + :type desc: str + :param proc_type: types of data generated by process + :type proc_type: str + :param expand: allow shell expansion on command line + :type expand: bool + :param bank_env: environnement variables to set + :type bank_env: list + :param log_dir: directroy to place process stdout and stderr + :type log_dir: str + ''' + # Replace env vars in args + if args: + for key, value in bank_env.items(): + if value is not None: + args = args.replace('${' + key + '}', value) + + self.name = name + self.exe = exe + self.desc = desc + if args is not None: + self.args = args.split() + else: + self.args = [] + self.bank_env = bank_env + self.type = proc_type + self.expand = expand + self.log_dir = log_dir + if log_dir is not None: + self.output_file = os.path.join(log_dir, name + '.out') + self.error_file = os.path.join(log_dir, name + '.err') + else: + self.output_file = name + '.out' + self.error_file = name + '.err' + + self.types = '' + self.format = '' + self.tags = '' + self.files = '' + self.exitcode = -1 + self.exec_time = 0 + self.proc_type = proc_type + self.trace_id = None + self.parent_id = None + + def set_trace(self, trace_id, parent_id): + ''' + Set span info for zipkin integration, optional + ''' + self.trace_id = trace_id + self.parent_id = parent_id + + def run(self, simulate=False): + ''' + Execute process + + :param simulate: does not execute process + :type simulate: bool + :return: exit code of process + ''' + args = [self.exe] + self.args + logging.debug('PROCESS:EXEC:' + str(self.args)) + err = False + if not simulate: + logging.info('PROCESS:RUN:' + self.name) + with open(self.output_file, 'w') as fout: + with open(self.error_file, 'w') as ferr: + start_time = datetime.datetime.now() + start_time = time.mktime(start_time.timetuple()) + + if self.expand: + args = " ".join(args) + proc = subprocess.Popen(args, stdout=fout, stderr=ferr, env=self.bank_env, shell=True) + else: + proc = subprocess.Popen(args, stdout=fout, stderr=ferr, env=self.bank_env, shell=False) + proc.wait() + end_time = datetime.datetime.now() + end_time = time.mktime(end_time.timetuple()) + + self.exec_time = end_time - start_time + + self.exitcode = proc.returncode + + if proc.returncode == 0: + err = True + else: + logging.error('PROCESS:ERROR:' + self.name) + fout.flush() + ferr.flush() + else: + err = True + logging.info('PROCESS:EXEC:' + self.name + ':' + str(err)) + + return err + + +class RemoteProcess(Process): + def __init__(self, name, exe, args, desc=None, proc_type=None, docker=None, docker_sudo=False, expand=True, bank_env=None, log_dir=None, rabbit_mq=None, rabbit_mq_port=5672, rabbit_mq_user=None, rabbit_mq_password=None, rabbit_mq_virtualhost=None, proxy=None, bank=None): + Process.__init__(self, name, exe, args, desc, proc_type, expand, bank_env, log_dir) + self.proxy = proxy + self.rabbit_mq = rabbit_mq + self.rabbit_mq_port = rabbit_mq_port + self.rabbit_mq_user = rabbit_mq_user + self.rabbit_mq_password = rabbit_mq_password + self.rabbit_mq_virtualhost = rabbit_mq_virtualhost + self.bank = bank + self.trace_id = None + self.parent_id = None + self.docker = docker + self.docker_sudo = docker_sudo + # Process.__init__(self, name, exe, args, desc, proc_type, expand, bank_env, log_dir) + # (self, name, exe, args, desc=None, proc_type=None, expand=True, bank_env=None, log_dir=None) + + def run(self, simulate=False): + psc = ProcessServiceClient(self.rabbit_mq, self.rabbit_mq_port, self.rabbit_mq_virtualhost, self.rabbit_mq_user, self.rabbit_mq_password) + session = psc.create_session(self.bank, self.proxy) + from biomaj_process.message import message_pb2 + biomaj_process = message_pb2.Operation() + biomaj_process.type = 1 + process = message_pb2.Process() + process.bank = self.bank + process.session = session + process.log_dir = self.log_dir + process.exe = self.exe + for arg in self.args: + process.args.append(arg) + + for envvar in list(self.bank_env.keys()): + proc_env_var = process.env_vars.add() + proc_env_var.name = envvar + proc_env_var.value = self.bank_env[envvar] + process.shell_expand = self.expand + process.name = self.name + process.description = str(self.desc) + process.proc_type = str(self.proc_type) + if self.docker: + process.is_docker = True + docker_info = message_pb2.Process.Docker() + docker_info.image = self.docker + docker_info.use_sudo = self.docker_sudo + process.docker.MergeFrom(docker_info) + biomaj_process.process.MergeFrom(process) + if self.trace_id: + trace = message_pb2.Operation.Trace() + trace.trace_id = self.trace_id + trace.span_id = self.parent_id + biomaj_process.trace.MergeFrom(trace) + psc.execute_process(biomaj_process) + (exitcode, info) = psc.wait_for_process() + psc.clean() + if exitcode > 0: + return False + else: + return True + + +class DockerProcess(Process): + def __init__(self, name, exe, args, desc=None, proc_type=None, docker=None, expand=True, bank_env=None, log_dir=None, use_sudo=True, docker_url=None, run_as_root=False): + Process.__init__(self, name, exe, args, desc, proc_type, expand, bank_env, log_dir) + self.docker = docker + self.docker_url = docker_url + self.use_sudo = use_sudo + self.run_as_root = run_as_root + + def run(self, simulate=False): + ''' + Execute process in docker container + + :param simulate: does not execute process + :type simulate: bool + :return: exit code of process + ''' + use_sudo = '' + docker_url = '' + if self.docker_url: + docker_url = '-H ' + self.docker_url + if self.use_sudo: + use_sudo = 'sudo' + release_dir = self.bank_env['datadir'] + '/' + self.bank_env['dirversion'] + '/' + self.bank_env['localrelease'] + env = '' + depends = [] + if self.bank_env: + for key, value in self.bank_env.items(): + env += ' -e "{0}={1}"'.format(key, value) + # Bank dependency production directory + if key.endswith('source'): + depends.append(value) + # docker run with data.dir env as shared volume + # forwarded env variables + data_dir = self.bank_env['datadir'] + '/' + self.bank_env['dirversion'] + if 'BIOMAJ_DIR' in os.environ and os.environ['BIOMAJ_DIR'] and not os.environ['BIOMAJ_DIR'].startswith('local'): + data_dir = os.environ['BIOMAJ_DIR'] + '/' + self.bank_env['dirversion'] + + depends_vol = '' + for vol in depends_vol: + depends_vol += '-v %s:%s:ro' % (vol, vol) + + if not self.run_as_root: + cmd = '''uid={uid} + gid={gid} + {sudo} docker {docker_url} pull {container_id} + {sudo} docker {docker_url} run --rm -w {bank_dir} {depends_vol} -v {data_dir}:{data_dir} {env} {container_id} \ + bash -c "groupadd --gid {gid} {group_biomaj} && useradd --uid {uid} --gid {gid} {user_biomaj}; \ + {exe} {args}; \ + chown -R {uid}:{gid} {bank_dir}"'''.format( + uid=os.getuid(), + gid=os.getgid(), + data_dir=data_dir, + env=env, + container_id=self.docker, + group_biomaj='biomaj', + user_biomaj='biomaj', + exe=self.exe, + args=' '.join(self.args), + bank_dir=release_dir, + sudo=use_sudo, + docker_url=docker_url, + depends_vol=depends_vol + ) + else: + cmd = ''' + {sudo} docker {docker_url} pull {container_id} + {sudo} docker {docker_url} run --rm -w {bank_dir} -v {data_dir}:{data_dir} {env} {container_id} \ + {exe} {args} \ + '''.format( + uid=os.getuid(), + gid=os.getgid(), + data_dir=data_dir, + env=env, + container_id=self.docker, + group_biomaj='biomaj', + user_biomaj='biomaj', + exe=self.exe, + args=' '.join(self.args), + bank_dir=release_dir, + sudo=use_sudo, + docker_url=docker_url, + depends_vol=depends_vol + ) + + (handler, tmpfile) = tempfile.mkstemp('biomaj') + if sys.version_info[0] < 3: + os.write(handler, cmd) + else: + os.write(handler, bytes(cmd, 'UTF-8')) + os.close(handler) + os.chmod(tmpfile, 0o755) + args = [tmpfile] + logging.debug('PROCESS:EXEC:Docker:' + str(self.args)) + logging.debug('PROCESS:EXEC:Docker:Tmpfile:' + tmpfile) + err = False + if not simulate: + logging.info('PROCESS:RUN:Docker:' + self.docker + ':' + self.name) + with open(self.output_file, 'w') as fout: + with open(self.error_file, 'w') as ferr: + start_time = datetime.datetime.now() + start_time = time.mktime(start_time.timetuple()) + if self.expand: + args = " ".join(args) + proc = subprocess.Popen(args, stdout=fout, stderr=ferr, env=self.bank_env, shell=True) + else: + proc = subprocess.Popen(args, stdout=fout, stderr=ferr, env=self.bank_env, shell=False) + proc.wait() + end_time = datetime.datetime.now() + end_time = time.mktime(end_time.timetuple()) + + self.exec_time = end_time - start_time + + self.exitcode = proc.returncode + if proc.returncode == 0: + err = True + else: + logging.error('PROCESS:ERROR:' + self.name) + fout.flush() + ferr.flush() + else: + err = True + logging.info('PROCESS:EXEC:' + self.name + ':' + str(err)) + os.remove(tmpfile) + return err + + +class DrmaaProcess(Process): + def __init__(self, name, exe, args, desc=None, proc_type=None, native=None, expand=True, bank_env=None, log_dir=None): + Process.__init__(self, name, exe, args, desc, proc_type, expand, bank_env, log_dir) + self.native = native + + def run(self, simulate=False): + ''' + Execute process + + :param simulate: does not execute process + :type simulate: bool + :return: exit code of process + ''' + # args = [self.exe] + self.args + logging.debug('PROCESS:EXEC:' + str(self.args)) + err = False + if not simulate: + logging.info('Run process ' + self.name) + # Execute on DRMAA + try: + import drmaa + with drmaa.Session() as s: + jt = s.createJobTemplate() + jt.remoteCommand = self.exe + jt.args = self.args + jt.joinFiles = False + jt.workingDirectory = os.path.dirname(os.path.realpath(self.output_file)) + jt.jobEnvironment = self.bank_env + if self.native: + jt.nativeSpecification = " " + self.native + " " + jt.outputPath = self.output_file + jt.errorPath = self.error_file + jobid = s.runJob(jt) + retval = s.wait(jobid, drmaa.Session.TIMEOUT_WAIT_FOREVER) + if retval.hasExited > 0: + err = True + else: + logging.error('PROCESS:ERROR:' + self.name) + s.deleteJobTemplate(jt) + + except Exception as e: + logging.error('Drmaa process error: ' + str(e)) + return False + else: + err = True + logging.info('PROCESS:EXEC:' + self.name + ':' + str(err)) + + return err diff --git a/biomaj_process/process_client.py b/biomaj_process/process_client.py new file mode 100644 index 0000000..14d0dad --- /dev/null +++ b/biomaj_process/process_client.py @@ -0,0 +1,107 @@ +import logging +import logging.config +import uuid +import time + +import requests +import pika + + +class ProcessServiceClient(object): + + def __init__(self, rabbitmq_host=None, rabbitmq_port=5672, rabbitmq_vhost='/', rabbitmq_user=None, rabbitmq_password=None, logger=None): + self.rabbitmq = rabbitmq_host + self.remote = False + self.session = None + self.proxy = None + self.channel = None + self.biomaj_process = None + self.logger = logging + if logger: + self.logger = logger + if rabbitmq_host: + self.remote = True + connection = None + if rabbitmq_user: + credentials = pika.PlainCredentials(rabbitmq_user, rabbitmq_password) + connection = pika.BlockingConnection(pika.ConnectionParameters(rabbitmq_host, rabbitmq_port, rabbitmq_vhost, credentials, heartbeat_interval=0)) + else: + connection = pika.BlockingConnection(pika.ConnectionParameters(rabbitmq_host, rabbitmq_port, rabbitmq_vhost, heartbeat_interval=0)) + self.channel = connection.channel() + + def create_session(self, bank, proxy=None): + self.bank = bank + if not self.remote: + self.session = str(uuid.uuid4()) + return self.session + + for i in range(3): + try: + url = proxy + '/api/process/session/' + bank + r = requests.post(url) + if r.status_code == 200: + result = r.json() + self.session = result['session'] + self.proxy = proxy + return result['session'] + except Exception: + logging.exception('Failed to send create operation: %s' % (url)) + raise Exception('Failed to connect to the process proxy') + + def execute_process(self, biomaj_process): + if self.remote: + self.channel.basic_publish( + exchange='', + routing_key='biomajprocess', + body=biomaj_process.SerializeToString(), + properties=pika.BasicProperties( + # make message persistent + delivery_mode=2 + )) + else: + self.biomaj_process = biomaj_process + + def wait_for_process(self): + over = False + exitcode = -1 + info = None + logging.info("Process:RemoteProcess:Waiting") + errors = 0 + while not over: + if errors >= 3: + raise Exception('Failed to contact process proxy 3 times, stopping...') + result = {'exitcode': -1} + try: + r = requests.get(self.proxy + '/api/process/session/' + self.bank + '/' + self.session) + if not r.status_code == 200: + logging.error('Failed to connect to the process proxy') + errors += 1 + else: + result = r.json() + errors = 0 + except Exception: + logging.exception('Failed to get status from process proxy') + errors += 1 + + # {'error': error, 'exitcode': exitcode, 'info': info} + if result['exitcode'] > -1: + exitcode = result['exitcode'] + over = True + if result['exitcode'] > 0: + info = result['info'] + self.logger.error('Process:RemoteProcess:Error:' + str(result['info'])) + else: + time.sleep(10) + return (exitcode, info) + + def clean(self): + if self.remote: + for i in range(3): + try: + url = self.proxy + '/api/process/session/' + self.bank + '/' + self.session + r = requests.delete(url) + if r.status_code == 200: + return + except Exception: + logging.exception('Failed to send clean operation: %s' % (url)) + raise Exception('Failed to connect to the process proxy') diff --git a/biomaj_process/process_service.py b/biomaj_process/process_service.py new file mode 100644 index 0000000..ae9b296 --- /dev/null +++ b/biomaj_process/process_service.py @@ -0,0 +1,259 @@ +import logging +import logging.config +import yaml +import redis +import uuid +import traceback +import threading + +import pika +from flask import Flask +from flask import jsonify +import consul + +from biomaj_process.message import message_pb2 +from biomaj_process.process import Process +from biomaj_process.process import DockerProcess +from biomaj_core.utils import Utils + +from biomaj_zipkin.zipkin import Zipkin + + +app = Flask(__name__) +app_log = logging.getLogger('werkzeug') +app_log.setLevel(logging.ERROR) + + [email protected]('/api/process-message') +def ping(): + return jsonify({'msg': 'pong'}) + + +def start_web(config): + app.run(host='0.0.0.0', port=config['web']['port']) + + +def consul_declare(config): + if config['consul']['host']: + consul_agent = consul.Consul(host=config['consul']['host']) + consul_agent.agent.service.register( + 'biomaj-process-message', + service_id=config['consul']['id'], + address=config['web']['hostname'], + port=config['web']['port'], + tags=['biomaj'] + ) + check = consul.Check.http( + url='http://' + config['web']['hostname'] + ':' + str(config['web']['port']) + '/api/process-message', + interval=20 + ) + consul_agent.agent.check.register( + config['consul']['id'] + '_check', + check=check, + service_id=config['consul']['id'] + ) + return True + else: + return False + + +class ProcessService(object): + + channel = None + redis_client = None + + def supervise(self): + if consul_declare(self.config): + web_thread = threading.Thread(target=start_web, args=(self.config,)) + web_thread.start() + + def __init__(self, config_file, rabbitmq=True): + self.logger = logging + self.session = None + self.bank = None + self.executed_callback = None + with open(config_file, 'r') as ymlfile: + self.config = yaml.load(ymlfile) + Utils.service_config_override(self.config) + + Zipkin.set_config(self.config) + + if 'log_config' in self.config: + for handler in list(self.config['log_config']['handlers'].keys()): + self.config['log_config']['handlers'][handler] = dict(self.config['log_config']['handlers'][handler]) + logging.config.dictConfig(self.config['log_config']) + self.logger = logging.getLogger('biomaj') + + if not self.redis_client: + self.logger.debug('Init redis connection') + self.redis_client = redis.StrictRedis(host=self.config['redis']['host'], + port=self.config['redis']['port'], + db=self.config['redis']['db'], + decode_responses=True) + + if rabbitmq and not self.channel: + connection = None + rabbitmq_port = self.config['rabbitmq']['port'] + rabbitmq_user = self.config['rabbitmq']['user'] + rabbitmq_password = self.config['rabbitmq']['password'] + rabbitmq_vhost = self.config['rabbitmq']['virtual_host'] + if rabbitmq_user: + credentials = pika.PlainCredentials(rabbitmq_user, rabbitmq_password) + connection = pika.BlockingConnection(pika.ConnectionParameters(self.config['rabbitmq']['host'], rabbitmq_port, rabbitmq_vhost, credentials, heartbeat_interval=0)) + else: + connection = pika.BlockingConnection(pika.ConnectionParameters(self.config['rabbitmq']['host'], heartbeat_interval=0)) + self.channel = connection.channel() + self.logger.info('Process service started') + + def close(self): + if self.channel: + self.channel.close() + + def on_executed_callback(self, func): + self.executed_callback = func + + def clean(self, biomaj_file_info=None): + ''' + Clean session and download info + ''' + session = self.session + bank = self.bank + if biomaj_file_info: + session = biomaj_file_info.session + bank = biomaj_file_info.bank + self.logger.debug('Clean %s session %s' % (bank, session)) + self.redis_client.delete(self.config['redis']['prefix'] + ':' + bank + ':session:' + session) + self.redis_client.delete(self.config['redis']['prefix'] + ':' + bank + ':session:' + session + ':error') + self.redis_client.delete(self.config['redis']['prefix'] + ':' + bank + ':session:' + session + ':exitcode') + self.redis_client.delete(self.config['redis']['prefix'] + ':' + bank + ':session:' + session + ':error:info') + + def _create_session(self, bank): + ''' + Creates a unique session + ''' + self.session = str(uuid.uuid4()) + self.redis_client.set(self.config['redis']['prefix'] + ':' + bank + ':session:' + self.session, 1) + self.logger.debug('Create %s new session %s' % (bank, self.session)) + self.bank = bank + return self.session + + def execute(self, biomaj_file_info): + ''' + List remote content + ''' + self.logger.debug('New process request %s session %s, execute %s' % (biomaj_file_info.bank, biomaj_file_info.session, biomaj_file_info.exe)) + session = self.redis_client.get(self.config['redis']['prefix'] + ':' + biomaj_file_info.bank + ':session:' + biomaj_file_info.session) + if not session: + self.logger.debug('Session %s for bank %s has expired, skipping execution of %s' % (biomaj_file_info.session, biomaj_file_info.bank, biomaj_file_info.exe)) + proc = {'bank': self.bank} + proc['exitcode'] = 129 + proc['execution_time'] = 0 + return + + bank_env = {} + for env_var in biomaj_file_info.env_vars: + bank_env[env_var.name] = env_var.value + + args = ' '.join(biomaj_file_info.args) + + if biomaj_file_info.is_docker: + process = DockerProcess( + biomaj_file_info.name, + biomaj_file_info.exe, + args, + desc=biomaj_file_info.description, + proc_type=biomaj_file_info.proc_type, + expand=biomaj_file_info.shell_expand, + bank_env=bank_env, + log_dir=biomaj_file_info.log_dir, + docker_url=self.config['docker']['url'], + docker=biomaj_file_info.docker.image, + run_as_root=True, + use_sudo=biomaj_file_info.docker.use_sudo + ) + else: + process = Process( + biomaj_file_info.name, + biomaj_file_info.exe, + args, + desc=biomaj_file_info.description, + proc_type=biomaj_file_info.proc_type, + expand=biomaj_file_info.shell_expand, + bank_env=bank_env, + log_dir=biomaj_file_info.log_dir + ) + exitcode = -1 + proc = {'bank': self.bank} + + try: + process.run() + exitcode = process.exitcode + proc['exitcode'] = exitcode + proc['execution_time'] = process.exec_time + except Exception as e: + proc['exitcode'] = 129 + proc['execution_time'] = 0 + self.logger.error('Execution error:%s:%s:%s' % (biomaj_file_info.bank, biomaj_file_info.session, str(e))) + session = self.redis_client.get(self.config['redis']['prefix'] + ':' + biomaj_file_info.bank + ':session:' + biomaj_file_info.session) + if session: + # If session deleted, do not track + self.redis_client.set(self.config['redis']['prefix'] + ':' + biomaj_file_info.bank + ':session:' + biomaj_file_info.session + ':error', 1) + self.redis_client.set(self.config['redis']['prefix'] + ':' + biomaj_file_info.bank + ':session:' + biomaj_file_info.session + ':error:info', str(e)) + self.logger.debug('Execution result: %d' % (exitcode)) + if exitcode > 0: + proc['error'] = True + + session = self.redis_client.get(self.config['redis']['prefix'] + ':' + biomaj_file_info.bank + ':session:' + biomaj_file_info.session) + if session: + # If session deleted, do not track + self.redis_client.set(self.config['redis']['prefix'] + ':' + biomaj_file_info.bank + ':session:' + biomaj_file_info.session + ':exitcode', exitcode) + + return proc + + def ask_execute(self, biomaj_info_file): + self.channel.basic_publish( + exchange='', + routing_key='biomajprocess', + body=biomaj_info_file.SerializeToString(), + properties=pika.BasicProperties( + # make message persistent + delivery_mode=2 + )) + + def callback_messages(self, ch, method, properties, body): + ''' + Manage download and send ACK message + ''' + try: + operation = message_pb2.Operation() + operation.ParseFromString(body) + # self.logger.debug('Received message: %s' % (operation)) + if operation.type == 1: + message = operation.process + self.logger.debug('Execute operation %s, %s' % (message.bank, message.session)) + span = None + if operation.trace and operation.trace.trace_id: + span = Zipkin('biomaj-process-executor', message.exe, trace_id=operation.trace.trace_id, parent_id=operation.trace.span_id) + + proc = self.execute(message) + if span: + span.trace() + if proc: + self.executed_callback(message.bank, [proc]) + else: + self.logger.warn('Wrong message type, skipping') + except Exception as e: + self.logger.error('Error with message: %s' % (str(e))) + traceback.print_exc() + ch.basic_ack(delivery_tag=method.delivery_tag) + + def wait_for_messages(self): + ''' + Loop queue waiting for messages + ''' + self.channel.queue_declare(queue='biomajprocess', durable=True) + self.channel.basic_qos(prefetch_count=1) + self.channel.basic_consume( + self.callback_messages, + queue='biomajprocess') + self.channel.start_consuming() diff --git a/biomaj_process/wsgi.py b/biomaj_process/wsgi.py new file mode 100644 index 0000000..45d7604 --- /dev/null +++ b/biomaj_process/wsgi.py @@ -0,0 +1,4 @@ +from biomaj_process.biomaj_process_web import app + +if __name__ == "__main__": + app.run() diff --git a/config.yml b/config.yml new file mode 100644 index 0000000..6645d15 --- /dev/null +++ b/config.yml @@ -0,0 +1,54 @@ + + +redis: + host: '127.0.0.1' + #host: '131.254.17.40' + port: 6379 + db: 0 + prefix: 'biomaj' + +rabbitmq: + host: '127.0.0.1' + port: 5672 + user: null + password: null + virtual_host: '/' + +consul: + host: null + # Unique agent identifier name among biomaj downloaders + id: 'biomaj_process_agent' + +web: + debug: true + port: 5000 + local_endpoint: 'http://127.0.0.1:5000' + +docker: + # URL to connect to docker, use null if direct docker access, else put IP of the host (not localhost) + url: 'tcp://127.0.0.1:2375' + +tls: + key: null + cert: null + +log_config: + 'version': 1 + 'formatters': + 'generic': + 'format': '%(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s' + 'handlers': + 'console': + 'class': 'logging.StreamHandler' + 'formatter': 'generic' + 'level': 'DEBUG' + 'loggers': + 'root': + 'level': 'INFO' + 'handlers': + - 'console' + 'biomaj': + 'level': 'DEBUG' + 'handlers': + - 'console' + 'disable_existing_loggers': False diff --git a/gunicorn_conf.py b/gunicorn_conf.py new file mode 100644 index 0000000..b5a65b0 --- /dev/null +++ b/gunicorn_conf.py @@ -0,0 +1,3 @@ +def worker_exit(server, worker): + from prometheus_client import multiprocess + multiprocess.mark_process_dead(worker.pid) diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..791eb57 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,12 @@ +mock +nose +pika +redis +PyYAML +protobuf +flask +python-consul +prometheus_client>=0.0.18 +requests +biomaj_core +biomaj_zipkin diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..3c6e79c --- /dev/null +++ b/setup.cfg @@ -0,0 +1,2 @@ +[bdist_wheel] +universal=1 diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..16ff240 --- /dev/null +++ b/setup.py @@ -0,0 +1,64 @@ +try: + from setuptools import setup, find_packages +except ImportError: + from distutils.core import setup + +from distutils.command.install import install +import os + + +here = os.path.abspath(os.path.dirname(__file__)) +with open(os.path.join(here, 'README.md')) as f: + README = f.read() +with open(os.path.join(here, 'CHANGES.txt')) as f: + CHANGES = f.read() + + +config = { + 'description': 'BioMAJ process service', + 'long_description': README + '\n\n' + CHANGES, + 'author': 'Olivier Sallou', + 'url': 'http://biomaj.genouest.org', + 'download_url': 'http://biomaj.genouest.org', + 'author_email': '[email protected]', + 'version': '3.0.7', + 'classifiers': [ + # How mature is this project? Common values are + # 3 - Alpha + # 4 - Beta + # 5 - Production/Stable + 'Development Status :: 5 - Production/Stable', + 'Environment :: Console', + 'Natural Language :: English', + 'Operating System :: POSIX :: Linux', + # Indicate who your project is intended for + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + # Pick your license as you wish (should match "license" above) + 'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)', + # Specify the Python versions you support here. In particular, ensure + # that you indicate whether you support Python 2, Python 3 or both. + 'Programming Language :: Python :: 3', + 'Programming Language :: Python :: 3.4' + ], + 'install_requires': [ + 'biomaj_core', + 'biomaj_zipkin', + 'pika', + 'redis', + 'PyYAML', + 'flask', + 'python-consul', + 'prometheus_client>=0.0.18', + 'protobuf', + 'requests' + ], + 'tests_require': ['nose', 'mock'], + 'test_suite': 'nose.collector', + 'packages': find_packages(), + 'include_package_data': True, + 'scripts': ['bin/biomaj_process_consumer.py'], + 'name': 'biomaj_process' +} + +setup(**config) diff --git a/tests/biomaj_tests.py b/tests/biomaj_tests.py new file mode 100644 index 0000000..0b099f9 --- /dev/null +++ b/tests/biomaj_tests.py @@ -0,0 +1,50 @@ +from nose.tools import * +from nose.plugins.attrib import attr + +import json +import shutil +import os +import tempfile +import logging +import copy +import stat +import time + +from mock import patch + +from biomaj_process.message import message_pb2 +from biomaj_process.process_service import ProcessService + +import unittest + + +class TestBiomajProcess(unittest.TestCase): + + def setUp(self): + self.curdir = os.path.dirname(os.path.realpath(__file__)) + self.pserv = ProcessService(os.path.join(self.curdir, 'config.yml'),rabbitmq=False) + self.session = self.pserv._create_session('test') + self.test_dir = tempfile.mkdtemp('biomaj') + + def tearDown(self): + self.pserv.clean() + shutil.rmtree(self.test_dir) + + def test_execute(self): + """ + Checks bank init + """ + msg = message_pb2.Process() + msg.bank = 'test' + msg.session = self.session + msg.log_dir = self.test_dir + msg.exe = os.path.join(self.curdir, 'test.sh') + msg.args.append('arg1') + msg.args.append('arg2') + env_var = msg.env_vars.add() + env_var.name = 'BIOMAJ_RELEASE' + env_var.value = '1.2.3' + msg.shell_expand = False + print(msg) + proc = self.pserv.execute(msg) + self.assertTrue(proc['exitcode'] == 0) diff --git a/tests/config.yml b/tests/config.yml new file mode 100644 index 0000000..69d57f7 --- /dev/null +++ b/tests/config.yml @@ -0,0 +1,50 @@ + + +redis: + host: '127.0.0.1' + #host: '131.254.17.40' + port: 6379 + db: 0 + prefix: 'biomaj' + +rabbitmq: + host: '127.0.0.1' + port: 5672 + user: null + password: null + virtual_host: '/' + +consul: + host: null + # Unique agent identifier name among biomaj downloaders + id: 'biomaj_process_agent' + +web: + debug: true + port: 5000 + local_endpoint: 'http://127.0.0.1:5000' + +tls: + key: null + cert: null + +log_config: + 'version': 1 + 'formatters': + 'generic': + 'format': '%(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s' + 'handlers': + 'console': + 'class': 'logging.StreamHandler' + 'formatter': 'generic' + 'level': 'DEBUG' + 'loggers': + 'root': + 'level': 'INFO' + 'handlers': + - 'console' + 'biomaj': + 'level': 'DEBUG' + 'handlers': + - 'console' + 'disable_existing_loggers': False diff --git a/tests/test.sh b/tests/test.sh new file mode 100755 index 0000000..73a56fe --- /dev/null +++ b/tests/test.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +echo $BIOMAJ_RELEASE + +echo "TEST:$BIOMAJ_RELEASE:$1" > test.out -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/biomaj3-process.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
