def getFromMOBEDAC(cls, id, source, sess_obj):
conn = None
complete_url = ""
try:
# dev mode?
my_remote_objects_are_local = get_parm("remote_objects_are_local")
if get_parm("remote_objects_are_local").lower() == 'true':
new_obj = cls.get_instance(id, sess_obj)
if new_obj == None:
raise ObjectRetrievalException(
"Unable to retrieve object: " + id + " from db")
else:
headers = {'content-type': 'application/json'}
conn = httplib.HTTPConnection(get_parm("mobedac_host"))
object_path = cls.get_REST_sub_path()
# complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_key")
# complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_ 38 key")
complete_url = get_parm(
"mobedac_base_path") + "r/" + object_path + "/" + id
if (conn.host == "localhost"
or conn.host == "api.metagenomics.anl.gov"):
complete_url = get_parm(
"mobedac_base_path"
) + object_path + "/" + id + "?auth=" + get_parm(
"mobedac_auth_key")
complete_url += "&template=1"
conn.request("GET", complete_url)
response = conn.getresponse()
data = response.read()
# if all went ok then build an object
if response.status != httplib.OK:
raise ObjectRetrievalException(
"Unable to retrieve object: " + id + " from host: " +
get_parm('mobedac_host') + " url: " + complete_url)
new_obj = cls({})
decoded_data = unidecode(data).strip()
mobedac_logger.info("complete_url: " + complete_url)
mobedac_logger.info("json string for object id_1: " + id +
" json: " + decoded_data)
json_obj = json.loads(decoded_data)
#mobedac_logger.info("json obj: " + str(json_obj))
new_obj.from_json(True, json_obj, sess_obj)
return new_obj
except ObjectRetrievalException as ore:
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type, exc_value, exc_traceback)
raise ore
except Exception as e:
raise ObjectRetrievalException("Unable to retrieve object: " + id +
" from host: " +
get_parm('mobedac_host') +
" url: " + complete_url +
" error: " + str(e))
finally:
if conn != None:
conn.close()
def getFromMOBEDAC(cls, id, source, sess_obj):
conn = None
complete_url = ""
try:
# dev mode?
my_remote_objects_are_local = get_parm("remote_objects_are_local")
if get_parm("remote_objects_are_local").lower() == 'true':
new_obj = cls.get_instance(id, sess_obj)
if new_obj == None:
raise ObjectRetrievalException("Unable to retrieve object: " + id + " from db");
else:
headers = {'content-type': 'application/json'}
conn = httplib.HTTPConnection(get_parm("mobedac_host"))
object_path = cls.get_REST_sub_path()
# complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_key")
# complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_ 38 key")
complete_url = get_parm("mobedac_base_path") + "r/" + object_path + "/" + id
if (conn.host == "localhost" or conn.host == "api.metagenomics.anl.gov"):
complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_key")
complete_url += "&template=1"
conn.request("GET", complete_url)
response = conn.getresponse()
data = response.read()
# if all went ok then build an object
if response.status != httplib.OK:
raise ObjectRetrievalException("Unable to retrieve object: " + id + " from host: " + get_parm('mobedac_host') + " url: " + complete_url)
new_obj = cls({})
decoded_data = unidecode(data).strip()
mobedac_logger.info("complete_url: "+complete_url)
mobedac_logger.info("json string for object id_1: " + id + " json: " + decoded_data)
json_obj = json.loads(decoded_data)
#mobedac_logger.info("json obj: " + str(json_obj))
new_obj.from_json(True, json_obj, sess_obj)
return new_obj
except ObjectRetrievalException as ore:
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type, exc_value, exc_traceback)
raise ore
except Exception as e:
raise ObjectRetrievalException("Unable to retrieve object: " + id + " from host: " + get_parm('mobedac_host') + " url: " + complete_url + " error: " + str(e))
finally:
if conn != None:
conn.close()
# -*- coding: utf-8 -*-
#
# Copyright (C) 2011, Marine Biological Laboratory
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# Please read the COPYING file.
#
import MySQLdb
import sys
import traceback
from sqlalchemy import *
from sqlalchemy.orm import scoped_session, sessionmaker
from initparms import get_parm
test_engine = create_engine(get_parm("ws_connection_url"), echo=False)
Session = scoped_session(sessionmaker(bind=test_engine))
vamps_engine = create_engine(get_parm("vamps_connection_url"), echo=False)
vampsSession = scoped_session(sessionmaker(bind=vamps_engine))
def set_error_file_logging_debug():
global mobedac_logger
mobedac_logger.setLevel(logging.DEBUG)
def set_error_file_logging_info():
global mobedac_logger
mobedac_logger.setLevel(logging.INFO)
# Remove the default FileHandlers if present.
log.error_file = ""
log.access_file = ""
maxBytes = getattr(log, "rot_maxBytes", 10000000)
backupCount = getattr(log, "rot_backupCount", 10)
# Make a new RotatingFileHandler for the error log.
fname = getattr(log, "rot_error_file", get_parm("error_log_path"))
h = RotatingFileHandler(fname, 'a', maxBytes, backupCount)
h.doRollover()
h.setFormatter(logging.Formatter("%(asctime)s - %(levelname)s - %(message)s"))
log.error_log.addHandler(h)
# Make a new RotatingFileHandler for the access log.
fname = getattr(log, "rot_access_file", get_parm("access_log_path"))
h = RotatingFileHandler(fname, 'a', maxBytes, backupCount)
h.setFormatter(cherrypy._cplogging.logfmt)
log.access_log.addHandler(h)
# this is to be what is visible
mobedac_logger = log.error_log
mobedac_logger.setLevel(logging.DEBUG)
# wait here for the processor to stop
self.submission_processor_thread.join(20.0)
# did it stop? do we need to to whack it?
if self.submission_processor_thread.is_alive():
self.submission_processor_thread.stop_processing()
except:
mobedac_logger.exception("Got error trying to stop submission processor thread")
cherrypy.engine.exit()
if __name__ == '__main__':
import argparse
the_root = None
try:
from initparms import get_parm
port = get_parm('port')
logicalpath = get_parm('logicalpath')
workingfiledir = get_parm('workingfiledir')
mobedac_logger.debug("in main of mobedac_server")
submission_processor_thread = Submission_Processor(10, get_parm('vamps_data_post_url'), get_parm('vamps_data_gast_url'), workingfiledir)
# do we want to not start listening to requests on startup
disable_processor_flag = get_parm("processor_disabled_on_startup")
if disable_processor_flag != None and disable_processor_flag.lower() == 'true':
submission_processor_thread.disable_processing()
submission_processor_thread.start()
# force cherrypy to use the port WE want
cherrypy.config.update({'server.socket_port': int(port),})
the_root = Root(submission_processor_thread)