def setup_module():
"""Create a fresh db (once) for all tests in this module"""
configure_logging(verbosity=2, logfile='unittest.log')
c = Config()
if c.get('general', 'in_production'): # pragma: no cover
raise RuntimeError("DO NOT run destructive test on production system")
create_tables(enable_delete=True, **db_params(CONFIG_SECTION))
# create a "test_region" and a couple bogus facilities
f1 = Facility(county='KING',
npi=10987,
zip='12345',
organization_name='Reason Medical Center',
local_code='RMC')
f2 = Facility(county='POND',
npi=65432,
zip='67890',
organization_name='No-Reason Medical Center',
local_code='NMC')
conn = db_connection(CONFIG_SECTION)
conn.session.add(f1)
conn.session.add(f2)
conn.session.commit()
rr1 = ReportableRegion(region_name='test_region', dim_facility_pk=10987)
conn.session.add(rr1)
conn.session.commit()
conn.disconnect()
def setup_module():
"""Create a fresh db (once) for all tests in this module"""
configure_logging(verbosity=2, logfile='unittest.log')
c = Config()
if c.get('general', 'in_production'): # pragma: no cover
raise RuntimeError("DO NOT run destructive test on production system")
create_tables(enable_delete=True, **db_params(CONFIG_SECTION))
def setup_module():
"""Create a fresh db (once) for all tests in this module"""
configure_logging(verbosity=2, logfile='unittest.log')
c = Config()
if c.get('general', 'in_production'): # pragma: no cover
raise RuntimeError("DO NOT run destructive test on production system")
create_tables(enable_delete=True, **db_params(CONFIG_SECTION))
def execute(self):
"""Use the collected info to launch execution"""
configure_logging(verbosity=self.verbosity,
logfile="%s.log" % self.criteria.report_method)
gr = GenerateReport(user=self.user,
password=self.password,
report_criteria=self.criteria,
datefile=self.datefile)
gr.execute(save_report=self.save_report,
transmit_report=self.transmit_report,
transmit_differences=self.transmit_differences)
def execute(self):
"""Use the collected info to launch execution"""
configure_logging(verbosity=self.verbosity,
logfile="%s.log" % self.criteria.report_method)
gr = GenerateReport(user=self.user,
password=self.password,
report_criteria=self.criteria,
datefile=self.datefile)
gr.execute(save_report=self.save_report,
transmit_report=self.transmit_report,
transmit_differences=self.transmit_differences)
def setup_module():
"""Create a fresh db (once) for all tests in this module"""
configure_logging(verbosity=2, logfile='unittest.log')
c = Config()
if c.get('general', 'in_production'): # pragma: no cover
raise RuntimeError("DO NOT run destructive test on production system")
create_tables(enable_delete=True, **db_params(CONFIG_SECTION))
# Load in all the static data in anonymized form
static_data_file = open(os.path.join(os.path.dirname(
os.path.abspath(__file__)), 'anon_static_db_data.yaml'), 'r')
load_file(static_data_file)
def setup_module():
"""Create a fresh db (once) for all tests in this module"""
configure_logging(verbosity=2, logfile='unittest.log')
c = Config()
if c.get('general', 'in_production'): # pragma: no cover
raise RuntimeError("DO NOT run destructive test on production system")
create_tables(enable_delete=True, **db_params(CONFIG_SECTION))
# Load in all the static data in anonymized form
static_data_file = open(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'anon_static_db_data.yaml'), 'r')
load_file(static_data_file)
def processArgs(self):
""" Process any optional arguments and possitional parameters
"""
parser = OptionParser(usage=usage)
parser.add_option("-v",
"--verbose",
dest="verbosity",
action="count",
default=self.verbosity,
help="increase output verbosity")
parser.add_option("-b",
"--backwards",
dest="progression",
default=self.progression,
help="Progress backwards in time through "
"available batch files (default is forwards)")
parser.add_option("-f",
"--file",
dest="namedfiles",
default=self.files,
action='store_true',
help="only process named file(s)")
parser.add_option("--copy-to-tempdir",
dest="tempdir",
default=None,
action='store',
help="Don't upload or track, just copy files "
"to named directory")
(options, args) = parser.parse_args()
if not parser.values.namedfiles:
if len(args) != 0:
parser.error("incorrect number of arguments")
else:
# User says they're feeding us files. Gobble up the list
self.daemon_mode = False
if not len(args):
parser.error("must supply at least one filename with"
"the files(-f) option")
self.files = []
for filename in args:
self.files.append(filename)
self.copy_tempdir = parser.values.tempdir
self.verbosity = parser.values.verbosity
configure_logging(verbosity=self.verbosity, logfile='stderr')
self.execute()
def test_configure_logging():
logfile = configure_logging(verbosity=2, logfile='unittest.log',
append=False)
logging.debug("just testing")
# Thanks to nose working so hard to capture logging, it's quite
# difficult to test - hand verified.
assert(logfile == os.path.join(Config().get('general', 'log_dir'),
'unittest.log'))
def test_configure_logging():
logfile = configure_logging(verbosity=2,
logfile='unittest.log',
append=False)
logging.debug("just testing")
# Thanks to nose working so hard to capture logging, it's quite
# difficult to test - hand verified.
assert (logfile == os.path.join(Config().get('general', 'log_dir'),
'unittest.log'))
def processArgs(self):
""" Process any optional arguments and possitional parameters
"""
parser = OptionParser(usage=usage)
parser.add_option("-v", "--verbose", dest="verbosity",
action="count", default=self.verbosity,
help="increase output verbosity")
parser.add_option("-b", "--backwards", dest="progression",
default=self.progression,
help="Progress backwards in time through "
"available batch files (default is forwards)")
parser.add_option("-f", "--file", dest="namedfiles",
default=self.files, action='store_true',
help="only process named file(s)")
parser.add_option("--copy-to-tempdir", dest="tempdir",
default=None, action='store',
help="Don't upload or track, just copy files "
"to named directory")
(options, args) = parser.parse_args()
if not parser.values.namedfiles:
if len(args) != 0:
parser.error("incorrect number of arguments")
else:
# User says they're feeding us files. Gobble up the list
self.daemon_mode = False
if not len(args):
parser.error("must supply at least one filename with"
"the files(-f) option")
self.files = []
for filename in args:
self.files.append(filename)
self.copy_tempdir = parser.values.tempdir
self.verbosity = parser.values.verbosity
configure_logging(verbosity=self.verbosity, logfile='stderr')
self.execute()
def setup_module():
"""Create a fresh db (once) for all tests in this module"""
configure_logging(verbosity=2, logfile='unittest.log')
c = Config()
if c.get('general', 'in_production'): # pragma: no cover
raise RuntimeError("DO NOT run destructive test on production system")
create_tables(enable_delete=True, **db_params(CONFIG_SECTION))
# create a "test_region" and a couple bogus facilities
f1 = Facility(county='KING', npi=10987, zip='12345',
organization_name='Reason Medical Center',
local_code='RMC')
f2 = Facility(county='POND', npi=65432, zip='67890',
organization_name='No-Reason Medical Center',
local_code='NMC')
conn = db_connection(CONFIG_SECTION)
conn.session.add(f1)
conn.session.add(f2)
conn.session.commit()
rr1 = ReportableRegion(region_name='test_region',
dim_facility_pk=10987)
conn.session.add(rr1)
conn.session.commit()
conn.disconnect()
def execute(self):
""" Start the process """
# Initialize logging now (verbosity is now set regardless of
# invocation method)
configure_logging(verbosity=self.verbosity, logfile="longitudinal-manager.log")
logging.info("Initiate deduplication for %s", (self.reportDate and self.reportDate or "whole database"))
# Only allow one instance of the manager to run at a time.
if self.lock.is_locked():
logging.warn("Can't continue, %s is locked ", LOCKFILE)
return
if systemUnderLoad():
logging.warn("system under load - continue anyhow")
try:
self.lock.acquire()
self.access = DirectAccess(
database=self.data_warehouse,
port=self.warehouse_port,
user=self.database_user,
password=self.database_password,
)
self.data_warehouse_access = AlchemyAccess(
database=self.data_warehouse,
port=self.warehouse_port,
user=self.database_user,
password=self.database_password,
)
self.data_mart_access = AlchemyAccess(
database=self.data_mart, port=self.mart_port, user=self.database_user, password=self.database_password
)
startTime = time.time()
if not self.skip_prep:
self._prepDeduplicateTables()
visits_to_process = self._visitsToProcess()
# Now done with db access needs at the manager level
# free up resources:
self.data_mart_access.disconnect()
self.data_warehouse_access.disconnect()
self.access.close()
# Set of locks used, one for each table needing protection
# from asynchronous inserts. Names should match table
# minus 'dim_' prefix, plus '_lock' suffix
# i.e. dim_location -> 'location_lock'
table_locks = {
"admission_source_lock": Lock(),
"admission_o2sat_lock": Lock(),
"admission_temp_lock": Lock(),
"assigned_location_lock": Lock(),
"admit_reason_lock": Lock(),
"chief_complaint_lock": Lock(),
"diagnosis_lock": Lock(),
"disposition_lock": Lock(),
"flu_vaccine_lock": Lock(),
"h1n1_vaccine_lock": Lock(),
"lab_flag_lock": Lock(),
"lab_result_lock": Lock(),
"location_lock": Lock(),
"note_lock": Lock(),
"order_number_lock": Lock(),
"performing_lab_lock": Lock(),
"pregnancy_lock": Lock(),
"race_lock": Lock(),
"reference_range_lock": Lock(),
"service_area_lock": Lock(),
"specimen_source_lock": Lock(),
}
# If we have visits to process, fire up the workers...
if len(visits_to_process) > 1:
for i in range(self.NUM_PROCS):
dw = Process(
target=LongitudinalWorker,
kwargs={
"queue": self.queue,
"procNumber": i,
"data_warehouse": self.data_warehouse,
"warehouse_port": self.warehouse_port,
"data_mart": self.data_mart,
"mart_port": self.mart_port,
"dbUser": self.database_user,
"dbPass": self.database_password,
"table_locks": table_locks,
"verbosity": self.verbosity,
},
)
dw.daemon = True
dw.start()
# Populate the queue
for v in visits_to_process:
self.queue.put(v)
# Wait on the queue until empty
self.queue.join()
# Common cleanup
self.tearDown()
self.datePersistence.bump_date()
logging.info("Queue is empty - done in %s", time.time() - startTime)
finally:
self.lock.release()
def execute(self):
""" Start the process """
# Initialize logging now (verbosity is now set regardless of
# invocation method)
configure_logging(verbosity=self.verbosity,
logfile="longitudinal-manager.log")
logging.info("Initiate deduplication for %s",
(self.reportDate and self.reportDate or
"whole database"))
# Only allow one instance of the manager to run at a time.
if self.lock.is_locked():
logging.warn("Can't continue, %s is locked ", LOCKFILE)
return
if systemUnderLoad():
logging.warn("system under load - continue anyhow")
try:
self.lock.acquire()
self.access = DirectAccess(database=self.data_warehouse,
port=self.warehouse_port,
user=self.database_user,
password=self.database_password)
self.data_warehouse_access = AlchemyAccess(
database=self.data_warehouse,
port=self.warehouse_port,
user=self.database_user, password=self.database_password)
self.data_mart_access = AlchemyAccess(
database=self.data_mart, port=self.mart_port,
user=self.database_user, password=self.database_password)
startTime = time.time()
if not self.skip_prep:
self._prepDeduplicateTables()
visits_to_process = self._visitsToProcess()
# Now done with db access needs at the manager level
# free up resources:
self.data_mart_access.disconnect()
self.data_warehouse_access.disconnect()
self.access.close()
# Set of locks used, one for each table needing protection
# from asynchronous inserts. Names should match table
# minus 'dim_' prefix, plus '_lock' suffix
# i.e. dim_location -> 'location_lock'
table_locks = {'admission_source_lock': Lock(),
'admission_o2sat_lock': Lock(),
'admission_temp_lock': Lock(),
'assigned_location_lock': Lock(),
'admit_reason_lock': Lock(),
'chief_complaint_lock': Lock(),
'diagnosis_lock': Lock(),
'disposition_lock': Lock(),
'flu_vaccine_lock': Lock(),
'h1n1_vaccine_lock': Lock(),
'lab_flag_lock': Lock(),
'lab_result_lock': Lock(),
'location_lock': Lock(),
'note_lock': Lock(),
'order_number_lock': Lock(),
'performing_lab_lock': Lock(),
'pregnancy_lock': Lock(),
'race_lock': Lock(),
'reference_range_lock': Lock(),
'service_area_lock': Lock(),
'specimen_source_lock': Lock(),
}
# If we have visits to process, fire up the workers...
if len(visits_to_process) > 1:
for i in range(self.NUM_PROCS):
dw = Process(target=LongitudinalWorker,
kwargs={'queue': self.queue,
'procNumber': i,
'data_warehouse': self.data_warehouse,
'warehouse_port': self.warehouse_port,
'data_mart': self.data_mart,
'mart_port': self.mart_port,
'dbUser': self.database_user,
'dbPass': self.database_password,
'table_locks': table_locks,
'verbosity': self.verbosity})
dw.daemon = True
dw.start()
# Populate the queue
for v in visits_to_process:
self.queue.put(v)
# Wait on the queue until empty
self.queue.join()
# Common cleanup
self.tearDown()
self.datePersistence.bump_date()
logging.info("Queue is empty - done in %s", time.time() -
startTime)
finally:
self.lock.release()