def main_sortResults(argv):
mod = SQLQueryDataFile()
subargv = ["SQLQueryDataFile.py", "-q", DATA_QUERY]
subargv.extend([
BASE_RESULT_DIR + FORMATTED_FILENAME, BASE_RESULT_DIR + SORTED_FILENAME
])
mod.main(subargv)
def main_filter(argv):
mod = SQLQueryDataFile()
for resultDir in RESULT_DIRS:
subargv = ["SQLQueryDataFile.py", "-q", DATA_QUERY]
subargv.extend(
[resultDir + CONCATENATE_FILENAME, resultDir + FILTERED_FILENAME])
mod.main(subargv)
def setUp(self):
"""Prepare state for test cases"""
BaseTestAnalysis.setUp(self)
# Instance to test on
self.analyzer = SQLQueryDataFile()
class TestSQLQueryDataFile(BaseTestAnalysis):
def setUp(self):
"""Prepare state for test cases"""
BaseTestAnalysis.setUp(self)
# Instance to test on
self.analyzer = SQLQueryDataFile()
def tearDown(self):
"""Restore state from any setUp or test steps"""
BaseTestAnalysis.tearDown(self)
def test_main(self):
# Simulate data files
inputFileStr = \
"""# {"argv": ["medinfo\\\\ConcatenateDataFiles.py", "test.out"]}
patient_id\tnumQueryItems\tnumVerifyItems\tnumRecommendedItems\trecall\tprecision\torder_set_id\t-s\t-R\t-p
-111\t8\t10\t20\t0.3\t0.6\t0\tOR\tItemAssociationRecommender\tpatient_
-111\t13\t15\t13\t0.6\t0.6\t1\tOR\tItemAssociationRecommender\tpatient_
-111\t8\t13\t11\t0.3\t0.9\t2\tOR\tItemAssociationRecommender\tpatient_
-111\t7\t13\t28\t0.8\t0\t3\tOR\tItemAssociationRecommender\tpatient_
-111\t15\t15\t12\t0.6\t0.9\t4\tOR\tItemAssociationRecommender\tpatient_
-111\t5\t13\t23\t0.6\t0.4\t5\tOR\tItemAssociationRecommender\tpatient_
-222\t15\t7\t19\t0.7\t0.9\t0\tOR\tItemAssociationRecommender\tpatient_
-222\t7\t6\t28\t0.2\t0.5\t1\tOR\tItemAssociationRecommender\tpatient_
-222\t10\t5\t20\t0.1\t0.5\t2\tOR\tItemAssociationRecommender\tpatient_
-222\t5\t5\t0\t0.7\t0.9\t3\tOR\tItemAssociationRecommender\tpatient_
-222\t8\t0\t16\t0.9\t0.7\t4\tOR\tItemAssociationRecommender\tpatient_
-222\t0\t6\t19\t0\t0.9\t5\tOR\tItemAssociationRecommender\tpatient_
-333\t12\t10\t28\t0.1\t0.7\t0\tOR\tItemAssociationRecommender\tpatient_
-333\t7\t10\t24\t0.3\t0.4\t1\tOR\tItemAssociationRecommender\tpatient_
-333\t15\t7\t21\t0\t0.8\t2\tOR\tItemAssociationRecommender\tpatient_
-333\t9\t10\t11\t0.9\t0.7\t3\tOR\tItemAssociationRecommender\tpatient_
-333\t11\t10\t26\t0.8\tNone\t4\tOR\tItemAssociationRecommender\tpatient_
-333\t11\t10\t12\tNone\t0.1\t5\tOR\tItemAssociationRecommender\tpatient_
-111\t8\t10\t20\t0.4\t0.2\t0\tPPV\tItemAssociationRecommender\tpatient_
-111\t13\t15\t13\t0.9\t0.5\t1\tPPV\tItemAssociationRecommender\tpatient_
-111\t8\t13\t11\t0.4\t0.9\t2\tPPV\tItemAssociationRecommender\tpatient_
-111\t7\t13\t28\t0.3\t0.1\t3\tPPV\tItemAssociationRecommender\tpatient_
-111\t15\t15\t12\t0.7\t0\t4\tPPV\tItemAssociationRecommender\tpatient_
-111\t5\t13\t23\t0.1\t0.3\t5\tPPV\tItemAssociationRecommender\tpatient_
-222\t15\t7\t19\t0.9\t0.9\t0\tPPV\tItemAssociationRecommender\tpatient_
-222\t7\t6\t28\t0.6\t0.4\t1\tPPV\tItemAssociationRecommender\tpatient_
-222\t10\t5\t20\t0.1\t0.3\t2\tPPV\tItemAssociationRecommender\tpatient_
-222\t5\t5\t0\t0.9\t0.9\t3\tPPV\tItemAssociationRecommender\tpatient_
-222\t8\t0\t16\t0.9\t0.1\t4\tPPV\tItemAssociationRecommender\tpatient_
-222\t0\t6\t19\t0.4\t0.6\t5\tPPV\tItemAssociationRecommender\tpatient_
-333\t12\t10\t28\t0.8\t0.5\t0\tPPV\tItemAssociationRecommender\tpatient_
-333\t7\t10\t24\t0\t0\t1\tPPV\tItemAssociationRecommender\tpatient_
-333\t15\t7\t21\t0.3\t0.7\t2\tPPV\tItemAssociationRecommender\tpatient_
-333\t9\t10\t11\t0.9\t0.5\t3\tPPV\tItemAssociationRecommender\tpatient_
-333\t11\t10\t26\t0.3\t0.9\t4\tPPV\tItemAssociationRecommender\tpatient_
-333\t11\t10\t12\t0.4\t0.1\t5\tPPV\tItemAssociationRecommender\tpatient_
-111\t7\t13\t28\t0\t0.7\t3\tNone\tOrderSetUsage\tNone
-111\t15\t15\t12\t0.1\t0.8\t4\tNone\tOrderSetUsage\tNone
-111\t5\t13\t23\t0.9\t0.1\t5\tNone\tOrderSetUsage\tNone
-111\t8\t10\t20\t0.7\t0.9\t0\tNone\tOrderSetUsage\tNone
-111\t13\t15\t13\t0.3\t0.8\t1\tNone\tOrderSetUsage\tNone
-111\t8\t13\t11\t0.5\t0.7\t2\tNone\tOrderSetUsage\tNone
-222\t5\t5\t0\t0.2\t0.5\t3\tNone\tOrderSetUsage\tNone
-222\t8\t0\t16\t0.9\t0.1\t4\tNone\tOrderSetUsage\tNone
-222\t0\t6\t19\t0.5\t0.9\t5\tNone\tOrderSetUsage\tNone
-222\t15\t7\t19\t0.7\t0.3\t0\tNone\tOrderSetUsage\tNone
-222\t7\t6\t28\t0.1\t0.1\t1\tNone\tOrderSetUsage\tNone
-222\t10\t5\t20\t0.6\t0.4\t2\tNone\tOrderSetUsage\tNone
-333\t12\t10\t28\t0.4\t0\t0\tNone\tOrderSetUsage\tNone
-333\t7\t10\t24\t0.1\t0.7\t1\tNone\tOrderSetUsage\tNone
-333\t15\t7\t21\t0.9\t0.8\t2\tNone\tOrderSetUsage\tNone
-333\t9\t10\t11\t0.7\t0.2\t3\tNone\tOrderSetUsage\tNone
-333\t11\t10\t26\t0.5\t0\t4\tNone\tOrderSetUsage\tNone
-333\t11\t10\t12\t0.7\t0.7\t5\tNone\tOrderSetUsage\tNone
"""
# Analysis via prepared validation data file
sqlQuery = "select * from data where numVerifyItems = 0"
verifyOutput = StringIO(
"""patient_id\tnumqueryitems\tnumverifyitems\tnumrecommendeditems\trecall\tprecision\torder_set_id\t_s\t_r\t_p
-222\t8\t0\t16\t0.9\t0.7\t4\tOR\tItemAssociationRecommender\tpatient_
-222\t8\t0\t16\t0.9\t0.1\t4\tPPV\tItemAssociationRecommender\tpatient_
-222\t8\t0\t16\t0.9\t0.1\t4\tNone\tOrderSetUsage\tNone
""")
self.verifyQueryResult(sqlQuery, StringIO(inputFileStr), verifyOutput)
# Analysis via prepared validation data file
sqlQuery = "select patient_id, sum(precision), count(distinct order_set_id) from data where numVerifyItems <> 0 group by patient_id"
verifyOutput = StringIO(
"""patient_id\tsum(precision)\tcount(distinct order_set_id)
-333\t7.8\t6
-222\t9.0\t5
-111\t9.4\t6
""")
self.verifyQueryResult(sqlQuery, StringIO(inputFileStr), verifyOutput)
sqlQuery = "select * from data where patient_id = -333 and numQueryItems = 11 and _s = 'OR'"
verifyOutput = StringIO(
"""patient_id\tnumqueryitems\tnumverifyitems\tnumrecommendeditems\trecall\tprecision\torder_set_id\t_s\t_r\t_p
-333\t11\t10\t26\t0.8\tNone\t4\tOR\tItemAssociationRecommender\tpatient_
-333\t11\t10\t12\tNone\t0.1\t5\tOR\tItemAssociationRecommender\tpatient_
""")
self.verifyQueryResult(sqlQuery, StringIO(inputFileStr), verifyOutput)
def verifyQueryResult(self, sqlQuery, inputFile, verifyOutputFile):
verifyDF = pandas_read_table(verifyOutputFile)
sys.stdin = inputFile
sys.stdout = StringIO()
argv = ["SQLQueryDataFile.py", "-q", sqlQuery, "-", "-"]
self.analyzer.main(argv)
textOutput = StringIO(sys.stdout.getvalue())
sampleDF = pandas_read_table(textOutput)
#print >> sys.stderr, sampleDF[verifyDF.columns];
pdt.assert_frame_equal(verifyDF, sampleDF[verifyDF.columns])