def testBackwards(self):
df = Datefile(datetime.strptime('2009-01-01', '%Y-%m-%d'),
persistence_file=self.persistence_file,
direction='backwards')
self.assertEquals(df.get_date().strftime('%Y-%m-%d'), '2009-01-01')
df.bump_date()
self.assertEquals(df.get_date().strftime('%Y-%m-%d'), '2008-12-31')
def testRangeSansStep(self):
"range w/o step"
df = Datefile(datetime.strptime('2009-10-31', '%Y-%m-%d'),
persistence_file=self.persistence_file,
direction='forwards')
start, end = df.get_date_range()
self.assertEquals(start.strftime('%Y-%m-%d'), '2009-10-31')
self.assertEquals(end.strftime('%Y-%m-%d'), '2009-10-31')
def testRangeStepSansDirection(self):
"give step and no directon"
df = Datefile(datetime.strptime('2009-10-31', '%Y-%m-%d'),
persistence_file=self.persistence_file,
step=30)
start, end = df.get_date_range()
self.assertEquals(start.strftime('%Y-%m-%d'), '2009-10-02')
self.assertEquals(end.strftime('%Y-%m-%d'), '2009-10-31')
def testNoDirection(self):
df = Datefile(datetime.now())
self.assert_(df.get_date(), "Even w/o direction, should get "
"initial date back")
datebefore = df.get_date()
df.bump_date()
dateafter = df.get_date()
self.assertEquals(datebefore, dateafter)
def testStepDatesBack(self):
"steping backward, end date should be step-1 days before start"
df = Datefile(datetime.strptime('2009-01-31', '%Y-%m-%d'),
persistence_file=self.persistence_file,
direction='backwards',
step=10)
start, end = df.get_date_range()
self.assertEquals(start.strftime('%Y-%m-%d'), '2009-01-22')
self.assertEquals(end.strftime('%Y-%m-%d'), '2009-01-31')
def testStepDatesFwd(self):
"steping forward, end date should be step-1 days after start"
df = Datefile(datetime.strptime('2009-02-01', '%Y-%m-%d'),
persistence_file=self.persistence_file,
direction='forwards',
step=10)
start, end = df.get_date_range()
self.assertEquals(start.strftime('%Y-%m-%d'), '2009-02-01')
self.assertEquals(end.strftime('%Y-%m-%d'), '2009-02-10')
def testInitialDate(self):
# write a date to the file, then call with a different initial
# date. should get the date from the file.
with open(self.persistence_file, 'w') as p_file:
p_file.write('2009-06-06')
df = Datefile(datetime.strptime('2009-01-01', '%Y-%m-%d'),
persistence_file=self.persistence_file,
direction='backwards')
self.assertEquals(df.get_date().strftime('%Y-%m-%d'), '2009-06-06')
df.bump_date()
self.assertEquals(df.get_date().strftime('%Y-%m-%d'), '2009-06-05')
def testStepDatesBackThrice(self):
"steping backward three times, duplication avoided?"
df = Datefile(datetime.strptime('2011-04-30', '%Y-%m-%d'),
persistence_file=self.persistence_file,
direction='backwards',
step=10)
start, end = df.get_date_range()
self.assertEquals(start.strftime('%Y-%m-%d'), '2011-04-21')
self.assertEquals(end.strftime('%Y-%m-%d'), '2011-04-30')
df.bump_date()
start, end = df.get_date_range()
self.assertEquals(start.strftime('%Y-%m-%d'), '2011-04-11')
self.assertEquals(end.strftime('%Y-%m-%d'), '2011-04-20')
df.bump_date()
start, end = df.get_date_range()
self.assertEquals(start.strftime('%Y-%m-%d'), '2011-04-01')
self.assertEquals(end.strftime('%Y-%m-%d'), '2011-04-10')
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 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 testDefaultAccess(self):
df = Datefile(initial_date=datetime.strptime('2009-01-01', '%Y-%m-%d'))
self.assertEquals(df.get_date().strftime('%Y-%m-%d'), '2009-01-01')
def testRangeSansFile(self):
"range w/o step"
df = Datefile(datetime.strptime('2009-10-31', '%Y-%m-%d'))
start, end = df.get_date_range()
self.assertEquals(start.strftime('%Y-%m-%d'), '2009-10-31')
self.assertEquals(end.strftime('%Y-%m-%d'), '2009-10-31')