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380 lines (287 loc) · 14.3 KB
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# =============================================================================
# lookupTest.py - Test module for lookup.py
#
# Freely extensible biomedical record linkage (Febrl) Version 0.2.2
# See http://datamining.anu.edu.au/projects/linkage.html
#
# =============================================================================
# AUSTRALIAN NATIONAL UNIVERSITY OPEN SOURCE LICENSE (ANUOS LICENSE)
# VERSION 1.1
#
# The contents of this file are subject to the ANUOS License Version 1.1 (the
# "License"); you may not use this file except in compliance with the License.
# Software distributed under the License is distributed on an "AS IS" basis,
# WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
# the specific language governing rights and limitations under the License.
# The Original Software is "lookupTest.py".
# The Initial Developers of the Original Software are Dr Peter Christen
# (Department of Computer Science, Australian National University) and Dr Tim
# Churches (Centre for Epidemiology and Research, New South Wales Department
# of Health). Copyright (C) 2002, 2003 the Australian National University and
# others. All Rights Reserved.
# Contributors:
#
# =============================================================================
"""Module lookupTest.py - Test module for lookup.py.
Define file names for various look-up table files in 'setUp'.
"""
# -----------------------------------------------------------------------------
import unittest
import lookup
# -----------------------------------------------------------------------------
class TestCase(unittest.TestCase):
# Initialise test case - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
def setUp(self):
self.tag_lookup_files = ['./data/post_address.tbl',
'./data/postcode_nsw.tbl',
'./data/address_misc.tbl',
'./data/saints.tbl',
'./data/givenname_f.tbl',
'./data/surname.tbl']
self.frequency_lookup_files = ['./data/givenname_f_freq.csv',
'./data/surname_nsw_freq.csv',
'./data/postcode_act_freq.csv']
self.geocode_lookup_files = ['./data/postcode_nsw_geocode.csv']
self.correction_list_files = ['./data/address_corr.lst',
'./data/name_corr.lst']
# Clean up test case - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
def tearDown(self):
pass # Nothing to clean up
# ---------------------------------------------------------------------------
#
# Start test cases
def testTagLookupTables(self): # - - - - - - - - - - - - - - - - - - - - - -
"""Test tag look-up tables"""
# First load all files separately
#
for f in self.tag_lookup_files:
lookup_table = lookup.TagLookupTable(name=f, default = '')
assert (lookup_table.name == f), \
'Look-up table "'+f+'" does not have correct name: "'+ \
lookup_table.name+'"'
assert (lookup_table.file_names == []), \
'Look-up table "'+f+'" has non-empty file list: '+ \
str(lookup_table.file_names)
assert (isinstance(lookup_table,dict)), \
'Look-up table "'+f+'" is not a dictionary'
lookup_table.load(f) # Load the table
assert (len(lookup_table) > 0), \
'Look-up table "'+f+'" is empty after load'
assert (lookup_table['xyz1234zyx'] == lookup_table.default), \
'Look-up table "'+f+'" returns wrond default: '+ \
lookup_table.default
assert (lookup_table.get('xyz1234zyx') == lookup_table.default), \
'Look-up table "'+f+'" returns wrond default: '+ \
lookup_table.default
assert (lookup_table.max_key_length > 0), \
'Look-up table "'+f+'" has illegal key length: '+ \
str(lookup_table.max_key_length)
for (key,value) in lookup_table.items():
assert (isinstance(key,tuple)), \
'Key in look-up table "'+f+'" is not a tuple: '+str(key)
assert (len(value) == 2), \
'Value in look-up table "'+f+'" does not contain two '+ \
'elements: '+str(values)
# Now load all files into one look-up table
#
lookup_table = lookup.TagLookupTable(name=self.tag_lookup_files[0], \
default = '')
assert (lookup_table.name == self.tag_lookup_files[0]), \
'Combined look-up table does not have correct name: "'+ \
str(self.tag_lookup_files[0])+'"'
assert (lookup_table.file_names == []), \
'Combined look-up table has non-empty file list: '+ \
str(lookup_table.file_names)
assert (isinstance(lookup_table,dict)), \
'Combined lookup-table is not a '+'dictionary'
lookup_table.load(self.tag_lookup_files) # Load the table
assert (len(lookup_table) > 0), \
'Combined look-up table is empty after load'
assert (lookup_table['xyz1234zyx'] == lookup_table.default), \
'Combined look-up table returns wrond default: '+ \
lookup_table.default
assert (lookup_table.get('xyz1234zyx') == lookup_table.default), \
'Combined look-up table returns wrond default: '+ \
lookup_table.default
assert (lookup_table.max_key_length > 0), \
'Combined look-up table has illegal key length: '+ \
str(lookup_table.max_key_length)
for (key,value) in lookup_table.items():
assert (isinstance(key,tuple)), \
'Key in combined look-up table is not a tuple: '+str(key)
assert (len(value) == 2), \
'Value in combined look-up table does not contain two '+ \
'elements: '+str(values)
def testFrequencyLookupTables(self): # - - - - - - - - - - - - - - - - - - -
"""Test frequency look-up tables"""
# First load all files separately
#
for f in self.frequency_lookup_files:
lookup_table = lookup.FrequencyLookupTable(name=f, default = '')
assert (lookup_table.name == f), \
'Look-up table "'+f+'" does not have correct name: "'+ \
lookup_table.name+'"'
assert (lookup_table.file_names == []), \
'Look-up table "'+f+'" has non-empty file list: '+ \
str(lookup_table.file_names)
assert (isinstance(lookup_table,dict)), \
'Look-up table "'+f+'" is not a dictionary'
assert (lookup_table.sum == None), \
'Look-up table "'+f+'" has non-None sum'
lookup_table.load(f) # Load the table
assert (len(lookup_table) > 0), \
'Look-up table "'+f+'" is empty after load'
assert (lookup_table.sum > 0), \
'Look-up table "'+f+'" has zero sum'
assert (lookup_table.sum > lookup_table.length), \
'Look-up table "'+f+'" has sum smaller than number of entries: '+\
str(self.length)
assert (lookup_table['xyz1234zyx'] == lookup_table.default), \
'Look-up table "'+f+'" returns wrond default: '+ \
lookup_table.default
assert (lookup_table.get('xyz1234zyx') == lookup_table.default), \
'Look-up table "'+f+'" returns wrond default: '+ \
lookup_table.default
for (key,value) in lookup_table.items():
assert (isinstance(key,str)), \
'Key in look-up table "'+f+'" is not a string: '+str(key)
assert (isinstance(value,int) and (value > 0)), \
'Value in look-up table "'+f+'" is not an integer: '+str(value)
# Now load all files into one look-up table
#
lookup_table = lookup.FrequencyLookupTable( \
name=self.frequency_lookup_files[0], \
default = '')
assert (lookup_table.name == self.frequency_lookup_files[0]), \
'Combined look-up table does not have correct name: "'+ \
str(self.frequency_lookup_files[0])+'"'
assert (lookup_table.file_names == []), \
'Combined look-up table has non-empty file list: '+ \
str(lookup_table.file_names)
assert (isinstance(lookup_table,dict)), \
'Combined lookup-table is not a '+'dictionary'
assert (lookup_table.sum == None), \
'Combined look-up table has non-None sum'
lookup_table.load(self.frequency_lookup_files) # Load the table
assert (len(lookup_table) > 0), \
'Combined look-up table is empty after load'
assert (lookup_table.sum > 0), \
'Combined look-up table has zero sum'
assert (lookup_table['xyz1234zyx'] == lookup_table.default), \
'Combined look-up table returns wrond default: '+ \
lookup_table.default
assert (lookup_table.get('xyz1234zyx') == lookup_table.default), \
'Combined look-up table returns wrond default: '+ \
lookup_table.default
for (key,value) in lookup_table.items():
assert (isinstance(key,str)), \
'Key in combined look-up table is not a string: '+str(key)
assert (isinstance(value,int) and (value > 0)), \
'Value in combined look-up table is not an integer: '+str(value)
def testGeocodeLookupTables(self): # - - - - - - - - - - - - - - - - - - - -
"""Test geocode look-up tables"""
# First load all files separately
#
for f in self.geocode_lookup_files:
lookup_table = lookup.GeocodeLookupTable(name=f, default = '')
assert (lookup_table.name == f), \
'Look-up table "'+f+'" does not have correct name: "'+ \
lookup_table.name+'"'
assert (lookup_table.file_names == []), \
'Look-up table "'+f+'" has non-empty file list: '+ \
str(lookup_table.file_names)
assert (isinstance(lookup_table,dict)), \
'Look-up table "'+f+'" is not a dictionary'
lookup_table.load(f) # Load the table
assert (len(lookup_table) > 0), \
'Look-up table "'+f+'" is empty after load'
assert (lookup_table['xyz1234zyx'] == lookup_table.default), \
'Look-up table "'+f+'" returns wrond default: '+ \
lookup_table.default
assert (lookup_table.get('xyz1234zyx') == lookup_table.default), \
'Look-up table "'+f+'" returns wrond default: '+ \
lookup_table.default
for (key,value) in lookup_table.items():
assert (isinstance(key,str)), \
'Key in look-up table "'+f+'" is not a string: '+str(key)
assert (len(value) == 2) and \
isinstance(value[0],float) and isinstance(value[1],float), \
'Value in look-up table "'+f+'" is not an location: '+str(value)
assert (value[0] >= -180.0) and (value[0] <= 180.0), \
'Location in look-up table "'+f+'" has illegal longitude: '+ \
str(value[0])
assert (value[1] >= -90.0) and (value[1] <= 90.0), \
'Location in look-up table "'+f+'" has illegal latitude: '+ \
str(value[1])
# Now load all files into one look-up table
#
lookup_table = lookup.GeocodeLookupTable( \
name=self.geocode_lookup_files[0], \
default = '')
assert (lookup_table.name == self.geocode_lookup_files[0]), \
'Combined look-up table does not have correct name: "'+ \
str(self.geocode_lookup_files[0])+'"'
assert (lookup_table.file_names == []), \
'Combined look-up table has non-empty file list: '+ \
str(lookup_table.file_names)
assert (isinstance(lookup_table,dict)), \
'Combined lookup-table is not a '+'dictionary'
lookup_table.load(self.geocode_lookup_files) # Load the table
assert (len(lookup_table) > 0), \
'Combined look-up table is empty after load'
assert (lookup_table['xyz1234zyx'] == lookup_table.default), \
'Combined look-up table returns wrond default: '+ \
lookup_table.default
assert (lookup_table.get('xyz1234zyx') == lookup_table.default), \
'Combined look-up table returns wrond default: '+ \
lookup_table.default
for (key,value) in lookup_table.items():
assert (isinstance(key,str)), \
'Key in combined look-up table is not a string: '+str(key)
assert (len(value) == 2) and \
isinstance(value[0],float) and isinstance(value[1],float), \
'Value in combined look-up table is not an location: '+str(value)
assert (value[0] >= -180.0) and (value[0] <= 180.0), \
'Location in combined look-up table has illegal longitude: '+ \
str(value[0])
assert (value[1] >= -90.0) and (value[1] <= 90.0), \
'Location in combined look-up table has illegal latitude: '+ \
str(value[1])
def testCorrectionLists(self): # - - - - - - - - - - - - - - - - - - - - - -
"""Test correction lists"""
for f in self.correction_list_files:
corr_list = lookup.CorrectionList(name=f)
assert (corr_list.name == f), \
'Correction list "'+f+'" does not have correct name: "'+ \
corr_list.name+'"'
assert (corr_list.file_name == ''), \
'Correction list "'+f+'" has non-empty file name: '+ \
str(lookup_table.file_name)
assert (isinstance(corr_list,list)), \
'Correction list "'+f+'" is not a list'
corr_list.load(f) # Load the table
assert (len(corr_list) > 0), \
'Correction list "'+f+'" is empty after load'
elem_len = 9999 # Long elements first
old_key = ''
for (key,value) in corr_list:
assert (isinstance(key,str)), \
'Key in correction list "'+f+'" is not a string: '+str(key)
assert (isinstance(value,str)), \
'Value in correction list "'+f+'" is not a string: '+str(value)
assert (len(key) <= elem_len), \
'Correction list "'+f+'" element key "'+value+ \
'" is longer than previous key: "'+old_key+'"'
old_key = key
elem_len = len(key)
# -----------------------------------------------------------------------------
# Start tests when called from command line
if (__name__ == "__main__"):
unittest.main() # Run all test
# The following code does the same as 'unittest.main()'
#
# mysuite = unittest.makeSuite(TestCase,'test')
# testrunner = unittest.TextTestRunner(verbosity=1)
# testrunner.run(mysuite)