def __init__(self, options):#dbname, outfile, save_dir, table, idcolumn, txtcolumn, doGraphs):
"""create an instance of a criticalFinder object associated with the SQLite
database.
dbname: name of SQLite database
"""
t = time.localtime()
self.doGraphs = options.doGraphs
self.allow_uncertainty = options.allow_uncertainty
self.proc_category = options.category
self.reports = Report.objects.filter(dataset=options.dataset)[:options.number]
#print "number of reports to process",len(self.reports)
#raw_input('continue')
# create context objects for each of the questions we want to be answering
self.context = {"disease":pyConText.pyConText()}
rsltsDB = options.odbname
alerts=Alert.objects.all()
alerts.delete()
rslts=Result.objects.all()
rslts.delete()
# Create the itemData object to store the modifiers for the analysis
# starts with definitions defined in pyConText and then adds
# definitions specific for peFinder
probableNegations = itemData('PROBABLE_NEGATED_EXISTENCE')
definiteNegations = itemData('DEFINITE_NEGATED_EXISTENCE')
pseudoNegations = itemData('PSEUDONEG')
indications = itemData('INDICATION')
historicals = itemData('HISTORICAL')
conjugates = itemData('CONJ')
probables = itemData('PROBABLE_EXISTENCE')
definites = itemData('DEFINITE_EXISTENCE')
future = itemData('FUTURE')
critItems = itemData('CRIT_ITEMS')
self.modifiers = {"disease":itemData('')}
self.modifiers["disease"].prepend(pseudoNegations)
self.modifiers["disease"].prepend(definiteNegations)
self.modifiers["disease"].prepend(probableNegations)
self.modifiers["disease"].prepend(probables)
self.modifiers["disease"].prepend(definites)
self.modifiers["disease"].prepend(indications)
self.modifiers["disease"].prepend(conjugates)
self.modifiers["disease"].prepend(future)
self.modifiers["disease"].prepend(historicals)
# Quality targets (generated from category parameter set by parser)
if( options.category.lower() == 'all'):
targetItems = critItems
else:
targetItems = itemData(options.category)
self.targets = {"disease":targetItems}
self.models = {}
