def test_parseDate():
assert(parseDate('20090131') == date(2009, 1, 31))
assert(parseDate('2009-01-31') == date(2009, 1, 31))
try:
parseDate('20093101')
except ValueError:
pass # desired as month & day are inverted
else: # pragma: no cover
assert(not "inverted month & day should raise")
def test_parseDate():
assert (parseDate('20090131') == date(2009, 1, 31))
assert (parseDate('2009-01-31') == date(2009, 1, 31))
try:
parseDate('20093101')
except ValueError:
pass # desired as month & day are inverted
else: # pragma: no cover
assert (not "inverted month & day should raise")
def __init__(self, data_warehouse=None, data_mart=None,
reportDate=None, database_user=None,
database_password=None, verbosity=0):
self.data_warehouse = data_warehouse
self.warehouse_port = 5432 # postgres default
self.data_mart = data_mart
self.mart_port = 5432 # postgres default
self.reportDate = reportDate and parseDate(reportDate) or None
self.database_user = database_user
self.database_password = database_password
self.dir, thisFile = os.path.split(__file__)
self.verbosity = verbosity
self.queue = JoinableQueue()
self.datefile = "/tmp/longitudinal_datefile"
self.datePersistence = Datefile(initial_date=self.reportDate)
self.lock = FileLock(LOCKFILE)
self.skip_prep = False
def processArgs(self):
""" Process any optional arguments and possitional parameters
"""
parser = OptionParser(usage=usage)
parser.add_option("-c", "--countdown", dest="countdown",
default=None,
help="count {down,up} date using date string in "\
"%s - set to 'forwards' or 'backwards' "\
"if desired" % self.datefile)
parser.add_option("-d", "--date", dest="date", default=None,
help="single admission date to dedup "\
"(by default, checks the entire database)")
parser.add_option("-s", "--skip-prep", dest="skip_prep",
default=False, action="store_true",
help="skip the expense of looking for new "\
"messages")
parser.add_option("-v", "--verbose", dest="verbosity",
action="count", default=self.verbosity,
help="increase output verbosity")
parser.add_option("-m", "--mart-port", dest="mart_port",
default=self.mart_port, type="int",
help="alternate port number for data mart")
parser.add_option("-w", "--warehouse-port", dest="warehouse_port",
default=self.warehouse_port, type="int",
help="alternate port number for data warehouse")
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error("incorrect number of arguments")
self.data_warehouse = args[0]
self.data_mart = args[1]
self.warehouse_port = parser.values.warehouse_port
self.mart_port = parser.values.mart_port
self.verbosity = parser.values.verbosity
self.skip_prep = parser.values.skip_prep
initial_date = parser.values.date and \
parseDate(parser.values.date) or None
self.datePersistence = Datefile(initial_date=initial_date,
persistence_file=self.datefile,
direction=parser.values.countdown)
self.reportDate = self.datePersistence.get_date()
def __init__(
self,
data_warehouse=None,
data_mart=None,
reportDate=None,
database_user=None,
database_password=None,
verbosity=0,
):
self.data_warehouse = data_warehouse
self.warehouse_port = 5432 # postgres default
self.data_mart = data_mart
self.mart_port = 5432 # postgres default
self.reportDate = reportDate and parseDate(reportDate) or None
self.database_user = database_user
self.database_password = database_password
self.dir, thisFile = os.path.split(__file__)
self.verbosity = verbosity
self.queue = JoinableQueue()
self.datefile = "/tmp/longitudinal_datefile"
self.datePersistence = Datefile(initial_date=self.reportDate)
self.lock = FileLock(LOCKFILE)
self.skip_prep = False
def process_args(self):
"""Process any optional arguments and possitional parameters
Using the values provided, assemble ReportCriteria and
Datefile instances to control report generation.
"""
parser = OptionParser(usage=usage)
# Provide the ReportCriteria instance an error callback so any
# command line errors provoke the standard graceful exit with
# warning text.
self.criteria.error_callback = parser.error
parser.add_option("-u",
"--user",
dest="user",
default=self.user,
help="database user")
parser.add_option("-p", "--password", dest="password",
default=self.password,
help="database password, or file containing "\
"just the password")
parser.add_option("-c", "--countdown", dest="countdown",
default=None,
help="count {down,up} the start and end dates "\
"set to 'forwards' or 'backwards' "\
"if desired")
parser.add_option("-i", "--include-updates",
action='store_true', dest="includeUpdates",
default=False, help="include "\
"visits updated since last similar report")
parser.add_option("--include-vitals",
action='store_true', dest="includeVitals",
default=False, help="include "\
"vitals (measured temperature, O2 "\
"saturation, influenza and H1N1 vaccine "\
"data) as additional columns in the "\
"report")
parser.add_option("-k", "--patient-class",
dest="patient_class",
default=None, help="use "\
"to filter report on a specific patient "\
"class [E,I,O]")
parser.add_option("-r", "--region", dest="region",
default=None,
help="reportable region defining limited set "\
"of facilities to include, by default "\
"all facilities are included")
parser.add_option("-s", "--save-and-upload",
action='store_true', dest="save_upload",
default=False, help="save file and upload to "\
"DOH")
parser.add_option("-x",
"--save-without-upload",
action='store_true',
dest="save_only",
default=False,
help="save file but don't upload")
parser.add_option("-d", "--upload-diff",
action='store_true', dest="upload_diff",
default=False, help="upload differences only "\
"(from yesterdays like report) to DOH")
parser.add_option("-t", "--thirty-days",
action='store_true', dest="thirty_days",
default=False, help="include 30 days up to "\
"requested date ")
parser.add_option("-v",
"--verbose",
dest="verbosity",
action="count",
default=self.verbosity,
help="increase output verbosity")
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error("incorrect number of arguments")
# Database to query
self.criteria.database = args[0]
self.user = options.user
self.password = options.password
self.criteria.credentials(user=self.user, password=self.password)
# Potential region restriction
self.criteria.reportable_region = options.region
# Potential patient class restriction
self.criteria.patient_class = options.patient_class
# Potential to include vitals (not tied to gipse format)
self.criteria.include_vitals = options.includeVitals
# Potential inclusion of updates
self.criteria.include_updates = options.includeUpdates
# Report date(s) and potential step direction.
# NB - several options affect report_method and must be set
# first!
initial_date = parseDate(args[1])
config = Config()
ps_file = os.path.join(
config.get('general', 'tmp_dir', default='/tmp'),
self.criteria.report_method)
step = options.thirty_days and 30 or None
direction = options.countdown
self.datefile = Datefile(initial_date=initial_date,
persistence_file=ps_file,
direction=direction,
step=step)
self.criteria.start_date, self.criteria.end_date =\
self.datefile.get_date_range()
# What to do once report is completed. Complicated, protect
# user from themselves!
self.save_report = options.save_upload or \
options.save_only or options.upload_diff
self.transmit_report = options.save_upload
self.transmit_differences = options.upload_diff
if options.save_only and options.save_upload:
parser.error("save-without-upload and save-and-upload "\
"are mutually exclusive")
if options.save_only and options.upload_diff:
parser.error("save-without-upload and upload-diff "\
"are mutually exclusive")
if options.upload_diff and options.save_upload:
parser.error("upload-diff and save-and-upload"\
"are mutually exclusive")
# Can't transmit w/o saving
if options.save_upload or options.upload_diff:
assert (self.save_report)
# Sanity check
if options.save_only:
assert (self.save_report and not self.transmit_report
and not self.transmit_differences)
# How verbosely to log
self.verbosity = options.verbosity
def end_date(self, value):
if 'end_date' in self._lock_attrs:
raise AttributeError("can't set attribute")
if isinstance(value, basestring):
value = parseDate(value)
self._crit['end_date'] = value
def process_args(self):
"""Process any optional arguments and possitional parameters
Using the values provided, assemble ReportCriteria and
Datefile instances to control report generation.
"""
parser = OptionParser(usage=usage)
# Provide the ReportCriteria instance an error callback so any
# command line errors provoke the standard graceful exit with
# warning text.
self.criteria.error_callback = parser.error
parser.add_option("-u", "--user", dest="user",
default=self.user, help="database user")
parser.add_option("-p", "--password", dest="password",
default=self.password,
help="database password, or file containing "\
"just the password")
parser.add_option("-c", "--countdown", dest="countdown",
default=None,
help="count {down,up} the start and end dates "\
"set to 'forwards' or 'backwards' "\
"if desired")
parser.add_option("-i", "--include-updates",
action='store_true', dest="includeUpdates",
default=False, help="include "\
"visits updated since last similar report")
parser.add_option("--include-vitals",
action='store_true', dest="includeVitals",
default=False, help="include "\
"vitals (measured temperature, O2 "\
"saturation, influenza and H1N1 vaccine "\
"data) as additional columns in the "\
"report")
parser.add_option("-k", "--patient-class",
dest="patient_class",
default=None, help="use "\
"to filter report on a specific patient "\
"class [E,I,O]")
parser.add_option("-r", "--region", dest="region",
default=None,
help="reportable region defining limited set "\
"of facilities to include, by default "\
"all facilities are included")
parser.add_option("-s", "--save-and-upload",
action='store_true', dest="save_upload",
default=False, help="save file and upload to "\
"DOH")
parser.add_option("-x", "--save-without-upload",
action='store_true', dest="save_only",
default=False, help="save file but don't upload")
parser.add_option("-d", "--upload-diff",
action='store_true', dest="upload_diff",
default=False, help="upload differences only "\
"(from yesterdays like report) to DOH")
parser.add_option("-t", "--thirty-days",
action='store_true', dest="thirty_days",
default=False, help="include 30 days up to "\
"requested date ")
parser.add_option("-v", "--verbose", dest="verbosity",
action="count", default=self.verbosity,
help="increase output verbosity")
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error("incorrect number of arguments")
# Database to query
self.criteria.database = args[0]
self.user = options.user
self.password = options.password
self.criteria.credentials(user=self.user,
password=self.password)
# Potential region restriction
self.criteria.reportable_region = options.region
# Potential patient class restriction
self.criteria.patient_class = options.patient_class
# Potential to include vitals (not tied to gipse format)
self.criteria.include_vitals = options.includeVitals
# Potential inclusion of updates
self.criteria.include_updates = options.includeUpdates
# Report date(s) and potential step direction.
# NB - several options affect report_method and must be set
# first!
initial_date = parseDate(args[1])
config = Config()
ps_file = os.path.join(config.get('general', 'tmp_dir',
default='/tmp'),
self.criteria.report_method)
step = options.thirty_days and 30 or None
direction = options.countdown
self.datefile = Datefile(initial_date=initial_date,
persistence_file=ps_file,
direction=direction,
step=step)
self.criteria.start_date, self.criteria.end_date =\
self.datefile.get_date_range()
# What to do once report is completed. Complicated, protect
# user from themselves!
self.save_report = options.save_upload or \
options.save_only or options.upload_diff
self.transmit_report = options.save_upload
self.transmit_differences = options.upload_diff
if options.save_only and options.save_upload:
parser.error("save-without-upload and save-and-upload "\
"are mutually exclusive")
if options.save_only and options.upload_diff:
parser.error("save-without-upload and upload-diff "\
"are mutually exclusive")
if options.upload_diff and options.save_upload:
parser.error("upload-diff and save-and-upload"\
"are mutually exclusive")
# Can't transmit w/o saving
if options.save_upload or options.upload_diff:
assert(self.save_report)
# Sanity check
if options.save_only:
assert(self.save_report and not self.transmit_report and
not self.transmit_differences)
# How verbosely to log
self.verbosity = options.verbosity
def end_date(self, value):
if 'end_date' in self._lock_attrs:
raise AttributeError("can't set attribute")
if isinstance(value, basestring):
value = parseDate(value)
self._crit['end_date'] = value
def processArgs(self):
""" Process any optional arguments and possitional parameters
"""
parser = OptionParser(usage=usage)
parser.add_option(
"-c",
"--countdown",
dest="countdown",
default=None,
help="count {down,up} date using date string in "
"%s - set to 'forwards' or 'backwards' "
"if desired" % self.datefile,
)
parser.add_option(
"-d",
"--date",
dest="date",
default=None,
help="single admission date to dedup " "(by default, checks the entire database)",
)
parser.add_option(
"-s",
"--skip-prep",
dest="skip_prep",
default=False,
action="store_true",
help="skip the expense of looking for new " "messages",
)
parser.add_option(
"-v",
"--verbose",
dest="verbosity",
action="count",
default=self.verbosity,
help="increase output verbosity",
)
parser.add_option(
"-m",
"--mart-port",
dest="mart_port",
default=self.mart_port,
type="int",
help="alternate port number for data mart",
)
parser.add_option(
"-w",
"--warehouse-port",
dest="warehouse_port",
default=self.warehouse_port,
type="int",
help="alternate port number for data warehouse",
)
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error("incorrect number of arguments")
self.data_warehouse = args[0]
self.data_mart = args[1]
self.warehouse_port = parser.values.warehouse_port
self.mart_port = parser.values.mart_port
self.verbosity = parser.values.verbosity
self.skip_prep = parser.values.skip_prep
initial_date = parser.values.date and parseDate(parser.values.date) or None
self.datePersistence = Datefile(
initial_date=initial_date, persistence_file=self.datefile, direction=parser.values.countdown
)
self.reportDate = self.datePersistence.get_date()