[med-svn] [biomaj3-process] 01/02: New upstream version 3.0.7
Olivier Sallou
osallou at debian.org
Thu Aug 17 14:44:23 UTC 2017
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 <osallou at debian.org>
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 @@
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+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Remote Network Interaction; Use with the GNU General Public License.
+
+ Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
+supports such interaction) an opportunity to receive the Corresponding
+Source of your version by providing access to the Corresponding Source
+from a network server at no charge, through some standard or customary
+means of facilitating copying of software. This Corresponding Source
+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. 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)
+
+
+ at app.route('/api/process', methods=['GET'])
+def ping():
+ return jsonify({'msg': 'pong'})
+
+
+ at app.route('/metrics', methods=['GET'])
+def metrics():
+ registry = CollectorRegistry()
+ multiprocess.MultiProcessCollector(registry)
+ return generate_latest(registry)
+
+
+ at app.route('/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'})
+
+
+ at app.route('/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})
+
+
+ at app.route('/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'})
+
+
+ at app.route('/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)
+
+
+ at app.route('/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': 'olivier.sallou at irisa.fr',
+ '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
--
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