def start(config_file,
shock_url=None,
mongo_host=None,
mongo_port=None,
rabbit_host=None,
rabbit_port=None,
deploy_config=None):
logger.info("============================================")
logger.info(" Starting Assembly Service Control Server")
logger.info("============================================")
# Read config file
cparser = SafeConfigParser()
if deploy_config:
cparser.read(deploy_config)
logger.info("[.] Found Deployment Config: {}".format(deploy_config))
else:
cparser.read(config_file)
if not shock_url:
shock_host = cparser.get('shock', 'host')
shock_url = shock.verify_shock_url(shock_host)
if not mongo_host:
mongo_host = cparser.get('assembly', 'mongo_host')
if not mongo_port:
mongo_port = int(cparser.get('assembly', 'mongo_port'))
if not rabbit_host:
rabbit_host = cparser.get('assembly', 'rabbitmq_host')
if not rabbit_port:
rabbit_port = int(cparser.get('assembly', 'rabbitmq_port'))
logger.info("[.] Shock URL: {}".format(shock_url))
logger.info("[.] MongoDB host: {}".format(mongo_host))
logger.info("[.] MongoDB port: {}".format(mongo_port))
logger.info("[.] RabbitMQ host: {}".format(rabbit_host))
logger.info("[.] RabbitMQ port: {}".format(rabbit_port))
# Check MongoDB status
try:
connection = pymongo.mongo_client.MongoClient(mongo_host, mongo_port)
logging.debug("MongoDB Info: %s" % connection.server_info())
except pymongo.errors.PyMongoError as e:
logger.error("MongoDB connection error: {}".format(e))
sys.exit('MongoDB error: {}'.format(e))
logger.info("[.] MongoDB connection successful.")
router_kwargs = {
'shock_url': shock_url,
'mongo_host': mongo_host,
'mongo_port': mongo_port,
'rabbit_host': rabbit_host,
'rabbit_port': rabbit_port
}
router_process = multiprocessing.Process(name='router',
target=start_router,
args=(config_file, ),
kwargs=router_kwargs)
router_process.start()
def start(config_file, shock_url=None, mongo_host=None, mongo_port=None,
rabbit_host=None, rabbit_port=None, deploy_config=None):
logger.info("============================================")
logger.info(" Starting Assembly Service Control Server")
logger.info("============================================")
# Read config file
cparser = SafeConfigParser()
if deploy_config:
cparser.read(deploy_config)
logger.info("[.] Found Deployment Config: {}".format(deploy_config))
else:
cparser.read(config_file)
if not shock_url:
shock_host = cparser.get('shock', 'host')
shock_url = shock.verify_shock_url(shock_host)
if not mongo_host:
mongo_host = cparser.get('assembly', 'mongo_host')
if not mongo_port:
mongo_port = int(cparser.get('assembly', 'mongo_port'))
if not rabbit_host:
rabbit_host = cparser.get('assembly', 'rabbitmq_host')
if not rabbit_port:
rabbit_port = int(cparser.get('assembly', 'rabbitmq_port'))
logger.info("[.] Shock URL: {}".format(shock_url))
logger.info("[.] MongoDB host: {}".format(mongo_host))
logger.info("[.] MongoDB port: {}".format(mongo_port))
logger.info("[.] RabbitMQ host: {}".format(rabbit_host))
logger.info("[.] RabbitMQ port: {}".format(rabbit_port))
# Check MongoDB status
try:
connection = pymongo.mongo_client.MongoClient(mongo_host, mongo_port)
logging.debug("MongoDB Info: %s" % connection.server_info())
except pymongo.errors.PyMongoError as e:
logger.error("MongoDB connection error: {}".format(e))
sys.exit('MongoDB error: {}'.format(e))
logger.info("[.] MongoDB connection successful.")
router_kwargs = {'shock_url': shock_url,
'mongo_host': mongo_host, 'mongo_port': mongo_port,
'rabbit_host' :rabbit_host, 'rabbit_port' : rabbit_port}
router_process = multiprocessing.Process(name='router', target=start_router,
args=(config_file,), kwargs=router_kwargs)
router_process.start()
def compute(self, body):
self.job_list_lock.acquire()
try:
job_data = self.prepare_job_data(body)
self.job_list.append(job_data)
except:
logger.error("Error in adding new job to job_list")
raise
finally:
self.job_list_lock.release()
status = ''
logger.debug('job_data = {}'.format(job_data))
params = json.loads(body)
job_id = params['job_id']
data_id = params['data_id']
uid = params['_id']
user = params['ARASTUSER']
token = params['oauth_token']
pipelines = params.get('pipeline')
recipe = params.get('recipe')
wasp_in = params.get('wasp')
jobpath = os.path.join(self.datapath, user, str(data_id), str(job_id))
url = shock.verify_shock_url(self.shockurl)
self.start_time = time.time()
timer_thread = UpdateTimer(self.metadata, 29, time.time(), uid, self.done_flag)
timer_thread.start()
#### Parse pipeline to wasp exp
reload(recipes)
if recipe:
try: wasp_exp = recipes.get(recipe[0], job_id)
except AttributeError: raise Exception('"{}" recipe not found.'.format(recipe[0]))
elif wasp_in:
wasp_exp = wasp_in[0]
elif not pipelines:
wasp_exp = recipes.get('auto', job_id)
elif pipelines:
## Legacy client
if pipelines[0] == 'auto':
wasp_exp = recipes.get('auto', job_id)
##########
else:
if type(pipelines[0]) is not list: # --assemblers
pipelines = [pipelines]
all_pipes = []
for p in pipelines:
all_pipes += self.pmanager.parse_input(p)
logger.debug("pipelines = {}".format(all_pipes))
wasp_exp = wasp.pipelines_to_exp(all_pipes, params['job_id'])
else:
raise asmtypes.ArastClientRequestError('Malformed job request.')
logger.debug('Wasp Expression: {}'.format(wasp_exp))
w_engine = wasp.WaspEngine(self.pmanager, job_data, self.metadata)
###### Run Job
try:
w_engine.run_expression(wasp_exp, job_data)
###### Upload all result files and place them into appropriate tags
uploaded_fsets = job_data.upload_results(url, token)
# Format report
new_report = open('{}.tmp'.format(self.out_report_name), 'w')
### Log errors
if len(job_data['errors']) > 0:
new_report.write('PIPELINE ERRORS\n')
for i,e in enumerate(job_data['errors']):
new_report.write('{}: {}\n'.format(i, e))
try: ## Get Quast output
quast_report = job_data['wasp_chain'].find_module('quast')['data'].find_type('report')[0].files[0]
with open(quast_report) as q:
new_report.write(q.read())
except:
new_report.write('No Summary File Generated!\n\n\n')
self.out_report.close()
with open(self.out_report_name) as old:
new_report.write(old.read())
for log in job_data['logfiles']:
new_report.write('\n{1} {0} {1}\n'.format(os.path.basename(log), '='*20))
with open(log) as l:
new_report.write(l.read())
### Log tracebacks
if len(job_data['tracebacks']) > 0:
new_report.write('EXCEPTION TRACEBACKS\n')
for i,e in enumerate(job_data['tracebacks']):
new_report.write('{}: {}\n'.format(i, e))
new_report.close()
os.remove(self.out_report_name)
shutil.move(new_report.name, self.out_report_name)
res = self.upload(url, user, token, self.out_report_name)
report_info = asmtypes.FileInfo(self.out_report_name, shock_url=url, shock_id=res['data']['id'])
self.metadata.update_job(uid, 'report', [asmtypes.set_factory('report', [report_info])])
status = 'Complete with errors' if job_data.get('errors') else 'Complete'
## Make compatible with JSON dumps()
del job_data['out_report']
del job_data['initial_reads']
del job_data['raw_reads']
self.metadata.update_job(uid, 'data', job_data)
self.metadata.update_job(uid, 'result_data', uploaded_fsets)
###### Legacy Support #######
filesets = uploaded_fsets.append(asmtypes.set_factory('report', [report_info]))
contigsets = [fset for fset in uploaded_fsets if fset.type == 'contigs' or fset.type == 'scaffolds']
download_ids = {fi['filename']: fi['shock_id'] for fset in uploaded_fsets for fi in fset['file_infos']}
contig_ids = {fi['filename']: fi['shock_id'] for fset in contigsets for fi in fset['file_infos']}
self.metadata.update_job(uid, 'result_data_legacy', [download_ids])
self.metadata.update_job(uid, 'contig_ids', [contig_ids])
###################
sys.stdout.flush()
touch(os.path.join(jobpath, "_DONE_"))
logger.info('============== JOB COMPLETE ===============')
except asmtypes.ArastUserInterrupt:
status = 'Terminated by user'
sys.stdout.flush()
touch(os.path.join(jobpath, "_CANCELLED__"))
logger.info('============== JOB KILLED ===============')
finally:
self.remove_job_from_lists(job_data)
logger.debug('Reinitialize plugin manager...') # Reinitialize to get live changes
self.pmanager = ModuleManager(self.threads, self.kill_list, self.kill_list_lock, self.job_list, self.binpath, self.modulebin)
self.metadata.update_job(uid, 'status', status)
def compute(self, body):
self.job_list_lock.acquire()
try:
job_data = self.prepare_job_data(body)
self.job_list.append(job_data)
except:
logger.error("Error in adding new job to job_list")
raise
finally:
self.job_list_lock.release()
status = ''
logger.debug('job_data = {}'.format(job_data))
params = json.loads(body)
job_id = params['job_id']
data_id = params['data_id']
uid = params['_id']
user = params['ARASTUSER']
token = params['oauth_token']
pipelines = params.get('pipeline')
recipe = params.get('recipe')
wasp_in = params.get('wasp')
jobpath = os.path.join(self.datapath, user, str(data_id), str(job_id))
url = shock.verify_shock_url(self.shockurl)
self.start_time = time.time()
timer_thread = UpdateTimer(self.metadata, 29, time.time(), uid,
self.done_flag)
timer_thread.start()
#### Parse pipeline to wasp exp
reload(recipes)
if recipe:
try:
wasp_exp = recipes.get(recipe[0], job_id)
except AttributeError:
raise Exception('"{}" recipe not found.'.format(recipe[0]))
elif wasp_in:
wasp_exp = wasp_in[0]
elif not pipelines:
wasp_exp = recipes.get('auto', job_id)
elif pipelines:
## Legacy client
if pipelines[0] == 'auto':
wasp_exp = recipes.get('auto', job_id)
##########
else:
if type(pipelines[0]) is not list: # --assemblers
pipelines = [pipelines]
all_pipes = []
for p in pipelines:
all_pipes += self.pmanager.parse_input(p)
logger.debug("pipelines = {}".format(all_pipes))
wasp_exp = wasp.pipelines_to_exp(all_pipes, params['job_id'])
else:
raise asmtypes.ArastClientRequestError('Malformed job request.')
logger.debug('Wasp Expression: {}'.format(wasp_exp))
w_engine = wasp.WaspEngine(self.pmanager, job_data, self.metadata)
###### Run Job
try:
w_engine.run_expression(wasp_exp, job_data)
###### Upload all result files and place them into appropriate tags
uploaded_fsets = job_data.upload_results(url, token)
# Format report
new_report = open('{}.tmp'.format(self.out_report_name), 'w')
### Log errors
if len(job_data['errors']) > 0:
new_report.write('PIPELINE ERRORS\n')
for i, e in enumerate(job_data['errors']):
new_report.write('{}: {}\n'.format(i, e))
try: ## Get Quast output
quast_report = job_data['wasp_chain'].find_module(
'quast')['data'].find_type('report')[0].files[0]
with open(quast_report) as q:
new_report.write(q.read())
except:
new_report.write('No Summary File Generated!\n\n\n')
self.out_report.close()
with open(self.out_report_name) as old:
new_report.write(old.read())
for log in job_data['logfiles']:
new_report.write('\n{1} {0} {1}\n'.format(
os.path.basename(log), '=' * 20))
with open(log) as l:
new_report.write(l.read())
### Log tracebacks
if len(job_data['tracebacks']) > 0:
new_report.write('EXCEPTION TRACEBACKS\n')
for i, e in enumerate(job_data['tracebacks']):
new_report.write('{}: {}\n'.format(i, e))
new_report.close()
os.remove(self.out_report_name)
shutil.move(new_report.name, self.out_report_name)
res = self.upload(url, user, token, self.out_report_name)
report_info = asmtypes.FileInfo(self.out_report_name,
shock_url=url,
shock_id=res['data']['id'])
self.metadata.update_job(
uid, 'report', [asmtypes.set_factory('report', [report_info])])
status = 'Complete with errors' if job_data.get(
'errors') else 'Complete'
## Make compatible with JSON dumps()
del job_data['out_report']
del job_data['initial_reads']
del job_data['raw_reads']
self.metadata.update_job(uid, 'data', job_data)
self.metadata.update_job(uid, 'result_data', uploaded_fsets)
###### Legacy Support #######
filesets = uploaded_fsets.append(
asmtypes.set_factory('report', [report_info]))
contigsets = [
fset for fset in uploaded_fsets
if fset.type == 'contigs' or fset.type == 'scaffolds'
]
download_ids = {
fi['filename']: fi['shock_id']
for fset in uploaded_fsets for fi in fset['file_infos']
}
contig_ids = {
fi['filename']: fi['shock_id']
for fset in contigsets for fi in fset['file_infos']
}
self.metadata.update_job(uid, 'result_data_legacy', [download_ids])
self.metadata.update_job(uid, 'contig_ids', [contig_ids])
###################
sys.stdout.flush()
touch(os.path.join(jobpath, "_DONE_"))
logger.info('============== JOB COMPLETE ===============')
except asmtypes.ArastUserInterrupt:
status = 'Terminated by user'
sys.stdout.flush()
touch(os.path.join(jobpath, "_CANCELLED__"))
logger.info('============== JOB KILLED ===============')
finally:
self.remove_job_from_lists(job_data)
logger.debug('Reinitialize plugin manager...'
) # Reinitialize to get live changes
self.pmanager = ModuleManager(self.threads, self.kill_list,
self.kill_list_lock, self.job_list,
self.binpath, self.modulebin)
self.metadata.update_job(uid, 'status', status)
def start(config_file, shock_url=None,
mongo_host=None, mongo_port=None,
rabbit_host=None, rabbit_port=None):
global parser, metadata, rjobmon
# logging.basicConfig(level=logging.DEBUG)
parser = SafeConfigParser()
parser.read(config_file)
collections = {'jobs': parser.get('meta', 'mongo.collection'),
'auth': parser.get('meta', 'mongo.collection.auth'),
'data': parser.get('meta', 'mongo.collection.data'),
'running': parser.get('meta', 'mongo.collection.running')}
# Config precedence: args > config file
if shock_url:
parser.set('shock', 'host', shock.verify_shock_url(shock_url))
if mongo_host:
parser.set('assembly', 'mongo_host', mongo_host)
if mongo_port:
parser.set('assembly', 'mongo_port', str(mongo_port))
if rabbit_host:
parser.set('assembly', 'rabbitmq_host', rabbit_host)
if rabbit_port:
parser.set('assembly', 'rabbitmq_port', str(rabbit_port))
metadata = meta.MetadataConnection(parser.get('assembly', 'mongo_host'),
int(parser.get('assembly', 'mongo_port')),
parser.get('meta', 'mongo.db'),
collections)
##### Running Job Monitor #####
rjobmon = RunningJobsMonitor(metadata)
cherrypy.process.plugins.Monitor(cherrypy.engine, rjobmon.purge,
frequency=int(parser.get('monitor', 'running_job_freq'))).subscribe()
##### CherryPy ######
conf = {
'global': {
'server.socket_host': '0.0.0.0',
'server.socket_port': int(parser.get('assembly', 'cherrypy_port')),
'log.screen': True,
'ar_shock_url': parser.get('shock', 'host'),
'environment': 'production'
},
}
static_root = parser.get('web_serve', 'root')
root = Root()
root.user = UserResource()
root.module = ModuleResource()
root.recipe = RecipeResource()
root.shock = ShockResource({"shockurl": get_upload_url()})
root.static = StaticResource(static_root)
#### Admin Routes ####
rmq_host = parser.get('assembly', 'rabbitmq_host')
rmq_mp = parser.get('rabbitmq', 'management_port')
rmq_user = parser.get('rabbitmq', 'management_user')
rmq_pass = parser.get('rabbitmq', 'management_pass')
root.admin = SystemResource(rmq_host, rmq_mp, rmq_user, rmq_pass)
cherrypy.request.hooks.attach('before_finalize', CORS)
cherrypy.quickstart(root, '/', conf)
def start(config_file, shock_url=None, mongo_host=None, mongo_port=None, rabbit_host=None, rabbit_port=None):
global parser, metadata, rjobmon
logging.basicConfig(level=logging.DEBUG)
parser = SafeConfigParser()
parser.read(config_file)
collections = {
"jobs": parser.get("meta", "mongo.collection"),
"auth": parser.get("meta", "mongo.collection.auth"),
"data": parser.get("meta", "mongo.collection.data"),
"running": parser.get("meta", "mongo.collection.running"),
}
# Config precedence: args > config file
if shock_url:
parser.set("shock", "host", shock.verify_shock_url(shock_url))
if mongo_host:
parser.set("assembly", "mongo_host", mongo_host)
if mongo_port:
parser.set("assembly", "mongo_port", str(mongo_port))
if rabbit_host:
parser.set("assembly", "rabbitmq_host", rabbit_host)
if rabbit_port:
parser.set("assembly", "rabbitmq_port", str(rabbit_port))
metadata = meta.MetadataConnection(
parser.get("assembly", "mongo_host"),
int(parser.get("assembly", "mongo_port")),
parser.get("meta", "mongo.db"),
collections,
)
##### Running Job Monitor #####
rjobmon = RunningJobsMonitor(metadata)
cherrypy.process.plugins.Monitor(
cherrypy.engine, rjobmon.purge, frequency=int(parser.get("monitor", "running_job_freq"))
).subscribe()
##### CherryPy ######
conf = {
"global": {
"server.socket_host": "0.0.0.0",
"server.socket_port": int(parser.get("assembly", "cherrypy_port")),
"log.screen": True,
"ar_shock_url": parser.get("shock", "host"),
}
}
static_root = parser.get("web_serve", "root")
root = Root()
root.user = UserResource()
root.module = ModuleResource()
root.recipe = RecipeResource()
root.shock = ShockResource({"shockurl": get_upload_url()})
root.static = StaticResource(static_root)
#### Admin Routes ####
rmq_host = parser.get("assembly", "rabbitmq_host")
rmq_mp = parser.get("rabbitmq", "management_port")
rmq_user = parser.get("rabbitmq", "management_user")
rmq_pass = parser.get("rabbitmq", "management_pass")
root.admin = SystemResource(rmq_host, rmq_mp, rmq_user, rmq_pass)
cherrypy.request.hooks.attach("before_finalize", CORS)
cherrypy.quickstart(root, "/", conf)
def start(config_file,
shock_url=None,
mongo_host=None,
mongo_port=None,
rabbit_host=None,
rabbit_port=None):
global parser, metadata, rjobmon
# logging.basicConfig(level=logging.DEBUG)
parser = SafeConfigParser()
parser.read(config_file)
collections = {
'jobs': parser.get('meta', 'mongo.collection'),
'auth': parser.get('meta', 'mongo.collection.auth'),
'data': parser.get('meta', 'mongo.collection.data'),
'running': parser.get('meta', 'mongo.collection.running')
}
# Config precedence: args > config file
if shock_url:
parser.set('shock', 'host', shock.verify_shock_url(shock_url))
if mongo_host:
parser.set('assembly', 'mongo_host', mongo_host)
if mongo_port:
parser.set('assembly', 'mongo_port', str(mongo_port))
if rabbit_host:
parser.set('assembly', 'rabbitmq_host', rabbit_host)
if rabbit_port:
parser.set('assembly', 'rabbitmq_port', str(rabbit_port))
metadata = meta.MetadataConnection(
parser.get('assembly', 'mongo_host'),
int(parser.get('assembly', 'mongo_port')),
parser.get('meta', 'mongo.db'), collections)
##### Running Job Monitor #####
rjobmon = RunningJobsMonitor(metadata)
cherrypy.process.plugins.Monitor(
cherrypy.engine,
rjobmon.purge,
frequency=int(parser.get('monitor', 'running_job_freq'))).subscribe()
##### CherryPy ######
conf = {
'global': {
'server.socket_host': '0.0.0.0',
'server.socket_port': int(parser.get('assembly', 'cherrypy_port')),
'log.screen': True,
'ar_shock_url': parser.get('shock', 'host'),
'environment': 'production'
},
}
static_root = parser.get('web_serve', 'root')
root = Root()
root.user = UserResource()
root.module = ModuleResource()
root.recipe = RecipeResource()
root.shock = ShockResource({"shockurl": get_upload_url()})
root.static = StaticResource(static_root)
#### Admin Routes ####
rmq_host = parser.get('assembly', 'rabbitmq_host')
rmq_mp = parser.get('rabbitmq', 'management_port')
rmq_user = parser.get('rabbitmq', 'management_user')
rmq_pass = parser.get('rabbitmq', 'management_pass')
root.admin = SystemResource(rmq_host, rmq_mp, rmq_user, rmq_pass)
cherrypy.request.hooks.attach('before_finalize', CORS)
cherrypy.quickstart(root, '/', conf)