def reconciliation_step_3(rec_list_1=[], rec_list_2=[], unparsed_meds_1=[], unparsed_meds_2=[], rec=[], stats={}):
"""Helper function to handle matching by brand names."""
print "********** RECONCILIATION STEP 3 **********"
print
# Unpack the lists produced by the regular expression.findall,
# and restore missing meds if they couldn't be parsed
# rec_bn is a MatchResult object with the results of matching by brand name
rec_bn = match_by_brand_name(rec_list_1, rec_list_2)
pb1, pb2, bnrec = rec_bn.list1, rec_bn.list2, rec_bn.reconciled
left1 = pb1 + unparsed_meds_1
left2 = pb2 + unparsed_meds_2
print "List 1 after brand name matching=\n", '\n'.join([str(x) for x in left1])
print
print "List 2 after brand name matching=\n", '\n'.join([str(x) for x in left2])
print
print "Reconciled after brand name matching=\n", '\n'.join([str(x) for x in bnrec])
print
if stats is not None:
stats['reconciled_brand_name'] = len(bnrec)
already_reconciled = [x for x in bnrec] + rec
print "All reconciled=\n", '\n'.join([str(x) for x in already_reconciled])
print "********** END OF STEP 3 **********"
return dict(
pb1=pb1,
pb2=pb2,
unparsed_meds_1=unparsed_meds_1,
unparsed_meds_2=unparsed_meds_2,
already_reconciled=already_reconciled,
stats=stats
)
def reconciliation_step_2(rec_list_1=[], rec_list_2=[], rec=[], stats={}):
"""Helper function to handle matching by brand names."""
print "********** RECONCILIATION STEP 2 **********"
print
# Separate parsed and unparsed medications
parsed_meds_1, unparsed_meds_1 = separate_parsed_from_unparsed(rec_list_1)
parsed_meds_2, unparsed_meds_2 = separate_parsed_from_unparsed(rec_list_2)
# Unpack the lists produced by the regular expression.findall,
# and restore missing meds if they couldn't be parsed
print
# rec_bn is a MatchResult object with the results of matching by brand name
rec_bn = match_by_brand_name(parsed_meds_1, parsed_meds_2)
pb1, pb2, bnrec = rec_bn.list1, rec_bn.list2, rec_bn.reconciled
left1 = pb1 + unparsed_meds_1
left2 = pb2 + unparsed_meds_2
print "List 1 after brand name matching=\n", '\n'.join([str(x) for x in left1])
print
print "List 2 after brand name matching=\n", '\n'.join([str(x) for x in left2])
print
print "Reconciled after brand name matching=\n", '\n'.join([str(x) for x in bnrec])
print
if stats is not None:
stats['reconciled_brand_name'] = len(bnrec)
already_reconciled = [x for x in bnrec] + rec.reconciled
print "All reconciled=\n", '\n'.join([str(x) for x in already_reconciled])
print "********** END OF STEP 2 **********"
return dict(
pb1=pb1,
pb2=pb2,
unparsed_meds_1=unparsed_meds_1,
unparsed_meds_2=unparsed_meds_2,
already_reconciled=already_reconciled,
stats=stats
)
class TestFunctions(unittest.TestCase):
"""A set of unit tests to exercise the functions in the 'match' module.
"""
medString1 = 'Lisinopril 5 MG Tablet;TAKE TABLET TWICE DAILY; Rx'
pMed1 = ParsedMedication(medString1, mappings)
pMed1CUIs = set(['C0065374'])
pMed1Tradenames = [
'C0591228', 'C0591229', 'C0678140', 'C0701176', 'C0722805', 'C1602677',
'C2368718', 'C2368722', 'C2368725'
]
medString2 = 'Pramipexole 0.5 MG Tablet;TAKE 1 TABLET 3 TIMES DAILY.; Rx'
pMed2 = ParsedMedication(medString2, mappings)
pMed2CUIs = set(['C0074710'])
pMed2Tradenames = ['C0721754']
medString2a = 'PRAMIPEXOLE 0.5 MG TABLET;take 1 tablet 3 times daily.; rx'
pMed2a = ParsedMedication(medString2a, mappings)
pMed2aCUIs = set(['C0074710'])
pMed2aTradenames = ['C0721754']
medString2b = 'Mirapex 0.5 MG Tablet;TAKE 1 TABLET 3 TIMES DAILY.; Rx'
pMed2b = ParsedMedication(medString2b, mappings)
pMed2bCUIs = set(['C0721754'])
pMed2bTradenames = []
medString3 = 'Warfarin Sodium 2.5 MG Tablet;TAKE AS DIRECTED.; Rx'
pMed3 = ParsedMedication(medString3, mappings)
pMed3CUIs = set(['C0376218'])
pMed3Tradenames = []
medString4 = 'Protonix 40 MG Tablet Delayed Release;TAKE 1 TABLET DAILY.; Rx'
pMed4 = ParsedMedication(medString4, mappings)
medString5 = 'Pantoprazole Sodium 40 MG Tablet Delayed Release;TAKE 1 TABLET DAILY.; Rx'
pMed5 = ParsedMedication(medString5, mappings)
medString6 = 'Paroxetine 20 MG Tablet; TAKE 1 TABLET DAILY.; Rx'
pMed6 = ParsedMedication(medString6, mappings)
medString7 = 'Sertraline 50 MG Tablet;TAKE 1 TABLET BY MOUTH EVERY DAY; Rx'
pMed7 = ParsedMedication(medString7, mappings)
medString8 = 'Razadyne 16 MG Capsule Extended Release 24 Hour;TAKE 1 CAPSULE DAILY IN THE MORNING take with meal daily; Rx.'
pMed8 = ParsedMedication(medString8, mappings)
medString9 = 'Cyclandelate 16 MG Capsule Extended Release 24 Hour;TAKE 1 CAPSULE DAILY IN THE MORNING take with meal daily; Rx.'
pMed9 = ParsedMedication(medString9, mappings)
medString10 = 'docosahexaenoic acid 200 mg capsules; one cap BID'
pMed10 = ParsedMedication(medString10, mappings)
medString11 = 'Exelon 4.6 MG/24HR Transdermal Patch 24 Hour;APPLY 1 PATCH DAILY AS DIRECTED.; Rx'
pMed11 = ParsedMedication(medString11, mappings)
list1 = [pMed1, pMed2]
list1rev = [pMed2, pMed1]
list2 = [pMed2a, pMed3]
list2rev = [pMed3, pMed2a]
list3 = [pMed2b, pMed3]
list3rev = [pMed3, pMed2b]
medication_list_test_CUIs = [
pMed1CUIs, pMed2CUIs, pMed2aCUIs, pMed3CUIs, pMed2bCUIs, pMed3CUIs
]
medication_list_test_tradenames = [
pMed1Tradenames, pMed2Tradenames, pMed2aTradenames, pMed3Tradenames,
pMed2bTradenames, pMed3Tradenames
]
test_objects = None
if test_match_objects:
test_objects = test_match_objects['TestFunctions']
matched_by_strings = match.match_by_strings(list1, list2)
matched_by_strings_rev = match.match_by_strings(list1rev, list2rev)
if mappings:
matched_by_brand_name1 = match.match_by_brand_name(list1, list3)
matched_by_brand_name1_rev = match.match_by_brand_name(
list1rev, list3rev)
matched_by_brand_name2 = match.match_by_brand_name(list3, list1)
matched_by_ingredients_above = match.match_by_ingredients(
[pMed4], [pMed5], min_match_threshold=0.6)
matched_by_ingredients_below = match.match_by_ingredients(
[pMed4], [pMed5], min_match_threshold=0.7)
matched_by_ingredients_rev_above = match.match_by_ingredients(
[pMed5], [pMed4], min_match_threshold=0.6)
matched_by_ingredients_rev_below = match.match_by_ingredients(
[pMed5], [pMed4], min_match_threshold=0.7)
if mappings.treatment:
matched_by_treatment_above = match.match_by_treatment(
[pMed6], [pMed7], mappings, match_acceptance_threshold=0.3)
matched_by_treatment_below = match.match_by_treatment([pMed6],
[pMed7],
mappings)
matched_by_treatment_05_yes = match.match_by_treatment(
[pMed8], [pMed9], mappings, match_acceptance_threshold=0.5)
matched_by_treatment_05_no = match.match_by_treatment(
[pMed8], [pMed9], mappings, match_acceptance_threshold=0.51)
matched_by_treatment_04_yes = match.match_by_treatment(
[pMed10], [pMed11], mappings, match_acceptance_threshold=0.4)
matched_by_treatment_04_no = match.match_by_treatment(
[pMed10], [pMed11], mappings, match_acceptance_threshold=0.43)
# Use the demo lists for testing; this code was previously in TestMatchResult
demo_list_1 = [
pm for pm in [
make_medication(x, mappings, "List 1")
for x in constants.demo_list_1
] if isinstance(pm, ParsedMedication)
]
demo_list_2 = [
pm for pm in [
make_medication(x, mappings, "List 2")
for x in constants.demo_list_2
] if isinstance(pm, ParsedMedication)
]
demo_matched_by_strings = match.match_by_strings(demo_list_1, demo_list_2)
demo_matched_by_strings_rev = match.match_by_strings(
demo_list_2, demo_list_1)
if mappings:
demo_matched_by_brand_name = match.match_by_brand_name(
demo_list_1, demo_list_2)
demo_matched_by_brand_name_rev = match.match_by_brand_name(
demo_list_2, demo_list_1)
demo_matched_by_ingredients = match.match_by_ingredients(
demo_list_1, demo_list_2)
demo_matched_by_ingredients_rev = match.match_by_ingredients(
demo_list_2, demo_list_1)
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_match_by_strings(self):
"Test that the MatchResult from a by-string match contains the lists we expect."
self.assertEqual(self.matched_by_strings,
self.test_objects['matched_by_strings'])
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_match_by_strings_rev(self):
"""Test that the MatchResult from a by-string match is order-independent
with respect to the order the medication lists are passed in."""
self.assertEqual(self.matched_by_strings_rev,
self.test_objects['matched_by_strings_rev'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
def test_medication_list_CUIs(self):
"Test the operation of match.medication_list_CUIs()"
cuis = match.medication_list_CUIs(self.list1 + self.list2 + self.list3)
self.assertEqual(cuis, self.medication_list_test_CUIs)
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_medication_list_tradenames(self):
"Test the operation of match.medication_list_tradenames()"
tradenames = match.medication_list_tradenames(self.list1 + self.list2 +
self.list3)
self.assertEqual(tradenames, self.medication_list_test_tradenames)
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_match_by_brand_name1(self):
"""Test that the MatchResult from a by-brand-name match contains the
lists we expect."""
self.assertEqual(self.matched_by_brand_name1,
self.test_objects['matched_by_brand_name1'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_match_by_brand_name1_rev(self):
"""Test that the MatchResult from a by-brand-name match is order-independent
with respect to the order the medication lists are passed in."""
self.assertEqual(self.matched_by_brand_name1_rev,
self.test_objects['matched_by_brand_name1_rev'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_match_by_brand_name2(self):
"""Test that the MatchResult from a by-brand-name match contains the
lists we expect."""
self.assertEqual(self.matched_by_brand_name2,
self.test_objects['matched_by_brand_name2'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_match_by_ingredients_above(self):
"""Test reconcilation of medications by treatment intent that should
match at a threshold of 0.6."""
self.assertEqual(self.matched_by_ingredients_above,
self.test_objects['matched_by_ingredients_above'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_match_by_ingredients_below(self):
"""Test reconcilation of medications by treatment intent that should
not match at a threshold of 0.7."""
self.assertEqual(self.matched_by_ingredients_below,
self.test_objects['matched_by_ingredients_below'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_match_by_ingredients_rev_above(self):
"""Test order independence of the reconcilation of medications by
treatment intent that should match at a threshold of 0.6."""
self.assertEqual(self.matched_by_ingredients_rev_above,
self.test_objects['matched_by_ingredients_rev_above'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_match_by_ingredients_rev_below(self):
"""Test order independence of the reconcilation of medications by
treatment intent that should not match at a threshold of 0.7."""
self.assertEqual(self.matched_by_ingredients_rev_below,
self.test_objects['matched_by_ingredients_rev_below'])
@unittest.skipUnless(test_objects, 'missing test_objects data')
def test_demo_match_by_strings(self):
"""Use demo lists to test matching by strings."""
self.assertEqual(self.demo_matched_by_strings,
self.test_objects['demo_matched_by_strings'])
@unittest.skipUnless(test_objects, 'missing test_objects data')
def test_demo_match_by_strings_rev(self):
"""Use demo lists to test order independence of matching by strings."""
self.assertEqual(self.demo_matched_by_strings_rev,
self.test_objects['demo_matched_by_strings_rev'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(mappings and test_objects,
'missing MappingContext with RXNORM data')
def test_demo_match_by_brand_name(self):
"""Use demo lists to test matching by brand names."""
self.assertEqual(self.demo_matched_by_brand_name,
self.test_objects['demo_matched_by_brand_name'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(mappings and test_objects,
'missing MappingContext with RXNORM data')
def test_demo_match_by_brand_name_rev(self):
"""Use demo lists to test order independence of matching by brand names."""
self.assertEqual(self.demo_matched_by_brand_name_rev,
self.test_objects['demo_matched_by_brand_name_rev'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(mappings and test_objects,
'missing MappingContext with RXNORM data')
def test_demo_match_by_ingredients_list(self):
"""Use demo lists to test matching by ingredients."""
self.assertEqual(self.demo_matched_by_ingredients,
self.test_objects['demo_matched_by_ingredients'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(test_objects, 'missing test_match data')
def test_demo_match_by_ingredients_list_rev(self):
"""Use demo lists to test order independence of matching by ingredients."""
self.assertEqual(self.demo_matched_by_ingredients_rev,
self.test_objects['demo_matched_by_ingredients_rev'])
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(mappings and mappings.treatment,
'MappingContext lacks treatment data')
def test_match_by_treatment_above(self):
"""These two medications should match by treatment if the
match_acceptance_threshold is set to 0.3; note that this
behavior may change as the underlying 'treats' data change."""
self.assertEqual(len(self.matched_by_treatment_above.reconciled), 1)
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(mappings and mappings.treatment,
'MappingContext lacks treatment data')
def test_match_by_treatment_below(self):
"""These two medications should not match by treatment if the
match_acceptance_threshold is set to default (0.5); note that this
behavior may change as the underlying 'treats' data change."""
self.assertEqual(len(self.matched_by_treatment_below.reconciled), 0)
@unittest.skipUnless(mappings, 'missing MappingContext with RXNORM data')
@unittest.skipUnless(mappings and mappings.treatment,
'MappingContext lacks treatment data')
def test_match_by_treatment_varies(self):
"""Test matching by treatment intent, varying thresholds to induce
matches and non-matches on the same two sets of medication lists.
"""
self.assertEqual(len(self.matched_by_treatment_05_yes.reconciled), 1)
self.assertEqual(len(self.matched_by_treatment_05_no.reconciled), 0)
self.assertEqual(len(self.matched_by_treatment_04_yes.reconciled), 1)
self.assertEqual(len(self.matched_by_treatment_04_no.reconciled), 0)