def test_source_headers_correct(self):
print 'testing source_headers_correct'
tsvfile1 = self.framework.tsvtest1
tsvfile2 = self.framework.tsvtest2
csvfile1 = self.framework.csvtest1
csvfile2 = self.framework.csvtest2
header = read_header(tsvfile1)
modelheader = []
modelheader.append('materialSampleID')
modelheader.append('principalInvestigator')
modelheader.append('locality')
modelheader.append('phylum')
modelheader.append('')
#print 'len(header)=%s len(model)=%s\nheader:\nmodel:%s\n%s' % (len(header), len(modelheader), header, modelheader)
self.assertEqual(len(header), 5,
'incorrect number of fields in header')
self.assertEqual(header, modelheader,
'header not equal to the model header')
header = read_header(tsvfile2)
modelheader = []
modelheader.append('materialSampleID')
modelheader.append('principalInvestigator')
modelheader.append('locality')
modelheader.append('phylum')
modelheader.append('decimalLatitude')
modelheader.append('decimalLongitude')
#print 'len(header)=%s len(model)=%s\nheader:\n%smodel:\n%s' % (len(header), len(modelheader), header, modelheader)
self.assertEqual(len(header), 6,
'incorrect number of fields in header')
self.assertEqual(header, modelheader,
'header not equal to the model header')
header = read_header(csvfile2)
modelheader = []
modelheader.append('materialSampleID')
modelheader.append('principalInvestigator')
modelheader.append('locality')
modelheader.append('phylum')
modelheader.append('decimalLatitude')
modelheader.append('decimalLongitude')
#print 'len(header)=%s len(model)=%s\nheader:\nmodel:%s\n%s' % (len(header), len(modelheader), header, modelheader)
self.assertEqual(len(header), 6,
'incorrect number of fields in header')
self.assertEqual(header, modelheader,
'header not equal to the model header')
header = read_header(csvfile1)
modelheader = []
modelheader.append('materialSampleID')
modelheader.append('principalInvestigator')
modelheader.append('locality')
modelheader.append('phylum')
modelheader.append('')
#print 'len(header)=%s len(model)=%s\nheader:\nmodel:%s\n%s' % (len(header), len(modelheader), header, modelheader)
self.assertEqual(len(header), 5,
'incorrect number of fields in header')
self.assertEqual(header, modelheader,
'header not equal to the model header')
def test_vocab_appender(self):
print 'testing vocab_appender'
testvocabfile = self.framework.testvocabfile
geogkey = compose_key_from_list(geogkeytermlist)
g1 = 'Oceania|United States|US|Hawaii|Honolulu|Honolulu|'
g1 += 'North Pacific Ocean|Hawaiian Islands|Oahu'
g2 = '|United States||WA|Chelan Co.||||'
n = [g1, g2]
inputs = {}
inputs['vocabfile'] = testvocabfile
inputs['key'] = geogkey
inputs['checkvaluelist'] = n
# print 'inputs:\n%s' % inputs
# Add new vocab to new vocab file
response = vocab_appender(inputs)
# print 'response1:\n%s' % response
writtenlist = response['addedvalues']
#print 'writtenlist1: %s' % writtenlist
self.assertEqual(writtenlist, n,
'values not written to new testvocabfile')
header = read_header(testvocabfile)
#print 'vocab file header:\n%s' % header
# Attempt to add same vocabs to the same vocabs file
response = vocab_appender(inputs)
#print 'response2:\n%s' % response
writtenlist = response['addedvalues']
#print 'writtenlist2: %s' % writtenlist
self.assertIsNone(writtenlist,
'duplicate value written to testvocabfile')
header = read_header(testvocabfile)
#print 'vocab file header:\n%s' % header
self.assertEquals(header[0], geogkey,
'key field not correct in testvocabfile')
def test_term_exists(self):
print 'testing term_exists'
testfile = self.framework.testfile1
header = read_header(testfile)
term = 'year'
present = term in header
s = 'test file %s does not contain "%s" field' % (testfile, term)
self.assertTrue(present, s)
term = 'fieldNumber '
present = term in header
s = 'test file %s does not contain "%s" field' % (testfile, term)
self.assertTrue(present, s)
testfile = self.framework.testfile2
header = read_header(testfile)
term = 'month'
present = term in header
s = 'test file %s does not contain "%s" field' % (testfile, term)
self.assertTrue(present, s)
def test_text_file_filter(self):
print 'testing text_file_filter'
testinputfile = self.framework.testinputfile
testreportfile = self.framework.testreportfile
workspace = self.framework.testdatapath
outputfile = '%s/%s' % (workspace.rstrip('/'), testreportfile)
termname = 'year'
matchingvalue = '1990'
inputs = {}
inputs['inputfile'] = testinputfile
inputs['termname'] = termname
inputs['matchingvalue'] = matchingvalue
inputs['workspace'] = workspace
inputs['outputfile'] = testreportfile
# Create the report
#print 'inputs:\n%s' % inputs
response = text_file_filter(inputs)
#print 'response:\n%s' % response
success = response['success']
s = 'text file filter failed: %s' % response['message']
self.assertTrue(success, s)
outputfile = response['outputfile']
#print 'response:\n%s' % response
s = 'Output file %s not created' % outputfile
self.assertTrue(os.path.isfile(outputfile), s)
header = read_header(outputfile)
dialect = csv_file_dialect(outputfile)
encoding = csv_file_encoding(outputfile)
matches = 0
# Iterate through all rows in the input file
for row in read_csv_row(outputfile,
dialect=dialect,
encoding=encoding,
header=True,
fieldnames=header):
#print 'row: %s' % row
if row[termname] == matchingvalue:
matches += 1
expected = 5
s = 'Number of matches in output (%s) not as expected (%s)' % (
matches, expected)
self.assertEqual(matches, expected, s)
matches = count_rows(outputfile)
expected = 7
s = 'Number of matches of %s in %s ' % (matchingvalue, outputfile)
s += 'was %s, not as expected (%s) ' % (matches, expected)
self.assertEqual(matches, expected, s)
def test_writevocabheader(self):
print 'testing writevocabheader'
writevocabheadertestfile = self.framework.writevocabheadertestfile
fieldnames = ['country|stateprovince|county', 'standard', 'vetted', 'error',
'misplaced', 'unresolved', 'source', 'comment']
dialect = vocab_dialect()
success = writevocabheader(writevocabheadertestfile, fieldnames, dialect)
self.assertTrue(success,'vocab header not written')
header = read_header(writevocabheadertestfile)
expected = ['country|stateprovince|county', 'standard', 'vetted', 'error',
'misplaced', 'unresolved', 'source', 'comment']
s = 'header:\n%s\nfrom file: %s\nnot as expected:\n%s' \
% (header,writevocabheadertestfile,expected)
self.assertEqual(header, expected, s)
def test_read_vocab_header(self):
print 'testing read_vocab_header'
vocabdialect = vocab_dialect()
vocabencoding = 'utf-8'
monthvocabfile = self.framework.monthvocabfile
header = read_header(monthvocabfile, vocabdialect, vocabencoding)
found = len(header)
expected = 3
s = 'Found %s fields in header. Expected %s' % (found, expected)
self.assertEqual(found, expected, s)
expected = ['month'] + vocabfieldlist
s = 'File: %s\nheader: %s\n' % (monthvocabfile, header)
s += 'not as expected: %s' % expected
self.assertEqual(header, expected, s)
def test_vocab_headers_correct(self):
print 'testing vocab_headers_correct'
vocabpath = self.framework.vocabpath
vocabdialect = vocab_dialect()
vocabencoding = 'utf-8'
for field in controlledtermlist:
vocabfile = vocabpath + field + '.txt'
if not os.path.isfile(vocabfile):
success = writevocabheader(vocabfile, vocabfieldlist, vocabdialect,
vocabencoding)
header = read_header(vocabfile, vocabdialect, vocabencoding)
expected = [field.lower()] + vocabfieldlist
s = 'File: %s\nheader: %s\n' % (vocabfile, header)
s += 'not as expected: %s' % expected
self.assertEqual(header, expected, s)
def test_term_standardizer_report(self):
print 'testing term_standardizer_report'
testcorrectioninputfile = self.framework.testcorrectioninputfile
testcorrectionreportfile = self.framework.testcorrectionreportfile
testmonthvocabfile = self.framework.testmonthvocabfile
key = 'month'
result = term_standardizer_report(testcorrectioninputfile, \
testcorrectionreportfile, testmonthvocabfile, key)
s = 'term_standardizer_report() result not True '
s += 'with inputfile: %s ' % testcorrectioninputfile
s += 'outpufile: %s' % testcorrectionreportfile
s += 'and vocabfile: %s' % testmonthvocabfile
self.assertTrue(result, s)
outputheader = read_header(testcorrectionreportfile)
expected = ['ID', 'month', 'country', 'month_orig']
s = 'outputheader: %s not as expected: %s' % (outputheader, expected)
self.assertEqual(outputheader, expected, s)
dialect = csv_file_dialect(testcorrectionreportfile)
encoding = csv_file_encoding(testcorrectionreportfile)
rows = read_rows(testcorrectionreportfile,
1,
dialect=dialect,
encoding=encoding,
header=True,
fieldnames=outputheader)
firstrow = rows[0]
field = 'month_orig'
value = firstrow[field]
expected = 'vi'
s = 'Field %s value %s not as expected (%s)' % (field, value, expected)
self.assertEqual(value, expected, s)
field = 'month'
value = firstrow[field]
expected = '6'
s = 'Field %s value %s not as expected (%s)' % (field, value, expected)
self.assertEqual(value, expected, s)
def test_text_file_field_stripper(self):
print 'testing text_file_field_stripper'
testinputfile = self.framework.testinputfile
testreportfile = self.framework.testreportfile
workspace = self.framework.testdatapath
outputfile = '%s/%s' % (workspace.rstrip('/'), testreportfile)
termlist = 'country|stateProvince'
inputs = {}
inputs['inputfile'] = testinputfile
inputs['termlist'] = termlist
inputs['workspace'] = workspace
inputs['outputfile'] = testreportfile
inputs['separator'] = '|'
# Create the report
#print 'inputs:\n%s' % inputs
response = text_file_field_stripper(inputs)
#print 'response:\n%s' % response
success = response['success']
s = 'text file filter failed: %s' % response['message']
self.assertTrue(success, s)
outputfile = response['outputfile']
#print 'response:\n%s' % response
s = 'Output file %s not created' % outputfile
self.assertTrue(os.path.isfile(outputfile), s)
header = read_header(outputfile)
dialect = csv_file_dialect(outputfile)
encoding = csv_file_encoding(outputfile)
rows = count_rows(outputfile)
expected = 10
s = 'Number of rows in %s ' % outputfile
s += 'was %s, not as expected (%s) ' % (rows, expected)
self.assertEqual(rows, expected, s)
expected = ['country', 'stateprovince']
s = 'Header: %s, not as expected: %s' % (header, expected)
self.assertEqual(header, expected, s)
def test_aggregate_tsvs(self):
print 'testing aggregate_tsvs'
tsvfile = self.framework.tsvfile
tsvcompositepath = self.framework.tsvcompositepath
workspace = self.framework.testdatapath
inputs = {}
inputs['inputpath'] = tsvcompositepath
inputs['outputfile'] = tsvfile
inputs['inputdialect'] = 'tsv'
inputs['workspace'] = workspace
#print 'inputs:\n%s' % (inputs)
# Aggregate text file
response = text_file_aggregator(inputs)
#print 'inputs:\n%s\nresponse:\n%s' % (inputs, response)
outputfile = response['outputfile']
self.assertTrue(os.path.isfile(outputfile),
outputfile + ' does not exist')
self.assertEqual(response['aggregaterowcount'], 6,
'incorrect number of rows')
header = read_header(outputfile)
modelheader = []
modelheader.append('decimalLatitude')
modelheader.append('decimalLongitude')
modelheader.append('locality')
modelheader.append('materialSampleID')
modelheader.append('phylum')
modelheader.append('principalInvestigator')
#print 'len(header)=%s len(model)=%s\nheader:\n%smodel:\n\n%s' % (len(header), len(modelheader), header, modelheader)
self.assertEqual(len(header), 6,
'incorrect number of fields in header')
self.assertEqual(header, modelheader,
'header not equal to the model header')
def test_term_completeness_reporter(self):
print 'testing term_completeness_reporter'
testinputfile = self.framework.testinputfile
testreportfile = self.framework.testreportfile
workspace = self.framework.testdatapath
outputfile = '%s/%s' % (workspace.rstrip('/'), testreportfile)
inputs = {}
inputs['inputfile'] = testinputfile
inputs['workspace'] = workspace
inputs['outputfile'] = testreportfile
# Create the report
#print 'inputs:\n%s' % inputs
response = term_completeness_reporter(inputs)
#print 'response:\n%s' % response
success = response['success']
s = 'Term completeness counter failed: %s' % response['message']
self.assertTrue(success, s)
outputfile = response['outputfile']
#print 'response:\n%s' % response
s = 'Output file %s not created' % outputfile
self.assertTrue(os.path.isfile(outputfile), s)
header = read_header(outputfile)
rows = count_rows(outputfile)
expected = 24
s = 'Number of rows in %s ' % outputfile
s += 'was %s, not as expected (%s) ' % (rows, expected)
self.assertEqual(rows, expected, s)
expected = ['field', 'count']
s = 'Header: %s, not as expected: %s' % (header, expected)
self.assertEqual(header, expected, s)
def test_source_headers_correct(self):
print 'testing source_headers_correct'
dwca = self.framework.dwca
workspace = self.framework.testdatapath
outputfile = self.framework.outputfile
archivetype = self.framework.archivetype
inputs = {}
inputs['inputfile'] = dwca
inputs['outputfile'] = outputfile
inputs['workspace'] = workspace
inputs['archivetype'] = archivetype
response = dwca_core_to_tsv(inputs)
#print 'response:\n%s' % response
outputfilefullpath = response['outputfile']
header = read_header(outputfilefullpath, tsv_dialect())
modelheader = []
modelheader.append('type')
modelheader.append('modified')
modelheader.append('language')
modelheader.append('accessRights')
modelheader.append('references')
modelheader.append('institutionCode')
modelheader.append('collectionCode')
modelheader.append('basisOfRecord')
modelheader.append('informationWithheld')
modelheader.append('dynamicProperties')
modelheader.append('occurrenceID')
modelheader.append('catalogNumber')
modelheader.append('recordNumber')
modelheader.append('recordedBy')
modelheader.append('individualCount')
modelheader.append('sex')
modelheader.append('lifeStage')
modelheader.append('establishmentMeans')
modelheader.append('preparations')
modelheader.append('associatedMedia')
modelheader.append('associatedSequences')
modelheader.append('associatedTaxa')
modelheader.append('otherCatalogNumbers')
modelheader.append('occurrenceRemarks')
modelheader.append('associatedOccurrences')
modelheader.append('previousIdentifications')
modelheader.append('fieldNumber')
modelheader.append('eventDate')
modelheader.append('eventTime')
modelheader.append('endDayOfYear')
modelheader.append('year')
modelheader.append('month')
modelheader.append('day')
modelheader.append('verbatimEventDate')
modelheader.append('habitat')
modelheader.append('samplingProtocol')
modelheader.append('eventRemarks')
modelheader.append('higherGeography')
modelheader.append('continent')
modelheader.append('waterBody')
modelheader.append('islandGroup')
modelheader.append('island')
modelheader.append('country')
modelheader.append('stateProvince')
modelheader.append('county')
modelheader.append('locality')
modelheader.append('verbatimLocality')
modelheader.append('minimumElevationInMeters')
modelheader.append('maximumElevationInMeters')
modelheader.append('minimumDepthInMeters')
modelheader.append('maximumDepthInMeters')
modelheader.append('locationAccordingTo')
modelheader.append('locationRemarks')
modelheader.append('decimalLatitude')
modelheader.append('decimalLongitude')
modelheader.append('geodeticDatum')
modelheader.append('coordinateUncertaintyInMeters')
modelheader.append('verbatimCoordinates')
modelheader.append('verbatimCoordinateSystem')
modelheader.append('georeferencedBy')
modelheader.append('georeferencedDate')
modelheader.append('georeferenceProtocol')
modelheader.append('georeferenceSources')
modelheader.append('georeferenceVerificationStatus')
modelheader.append('identificationQualifier')
modelheader.append('typeStatus')
modelheader.append('identifiedBy')
modelheader.append('dateIdentified')
modelheader.append('identificationReferences')
modelheader.append('identificationVerificationStatus')
modelheader.append('identificationRemarks')
modelheader.append('scientificName')
modelheader.append('higherClassification')
modelheader.append('kingdom')
modelheader.append('phylum')
modelheader.append('class')
modelheader.append('order')
modelheader.append('family')
modelheader.append('genus')
modelheader.append('specificEpithet')
modelheader.append('infraspecificEpithet')
modelheader.append('taxonRank')
modelheader.append('nomenclaturalCode')
modelheader.append('individualID')
modelheader.append('rights')
self.assertEqual(len(header), 85,
'incorrect number of fields in header')
s = 'Header:\n%s\nnot equal to the model header:\n%s' % (header,
modelheader)
self.assertEqual(header, modelheader, s)
def test_term_setter_report(self):
print 'testing term_setter_report'
testsetterinputfile = self.framework.testsetterinputfile
testsetterreportfile = self.framework.testsetterreportfile
# Test field addition
key = 'institutionCode'
result = term_setter_report(testsetterinputfile,
testsetterreportfile,
key,
constantvalues='CAS')
s = 'term_setter_report() result not True '
s += 'with inputfile: %s ' % testsetterinputfile
s += 'and outputfile: %s' % testsetterreportfile
self.assertTrue(result, s)
outputheader = read_header(testsetterreportfile)
expected = ['ID', 'month', 'country', 'institutionCode']
s = 'outputheader: %s not as expected: %s' % (outputheader, expected)
self.assertEqual(outputheader, expected, s)
dialect = csv_file_dialect(testsetterreportfile)
encoding = csv_file_encoding(testsetterreportfile)
rows = read_rows(testsetterreportfile,
1,
dialect=dialect,
encoding=encoding,
header=True,
fieldnames=outputheader)
firstrow = rows[0]
field = 'institutionCode'
value = firstrow[field]
expected = 'CAS'
s = 'Field %s value %s not as expected (%s)' % (field, value, expected)
self.assertEqual(value, expected, s)
# Test field list addition
key = 'institutionCode|license'
result = term_setter_report(testsetterinputfile,
testsetterreportfile,
key,
constantvalues='CAS|CC0')
s = 'term_setter_report() result not True '
s += 'with inputfile: %s ' % testsetterinputfile
s += 'and outputfile: %s' % testsetterreportfile
self.assertTrue(result, s)
outputheader = read_header(testsetterreportfile)
expected = ['ID', 'month', 'country', 'institutionCode', 'license']
s = 'outputheader: %s not as expected: %s' % (outputheader, expected)
self.assertEqual(outputheader, expected, s)
dialect = csv_file_dialect(testsetterreportfile)
encoding = csv_file_encoding(testsetterreportfile)
rows = read_rows(testsetterreportfile,
1,
dialect=dialect,
encoding=encoding,
header=True,
fieldnames=outputheader)
firstrow = rows[0]
field = 'institutionCode'
value = firstrow[field]
expected = 'CAS'
s = 'Field %s value %s not as expected (%s)' % (field, value, expected)
self.assertEqual(value, expected, s)
field = 'license'
value = firstrow[field]
expected = 'CC0'
s = 'Field %s value %s not as expected (%s)' % (field, value, expected)
self.assertEqual(value, expected, s)
# Test field replacement
key = 'country'
result = term_setter_report(testsetterinputfile,
testsetterreportfile,
key,
constantvalues='Argentina')
s = 'term_setter_report() result not True '
s += 'with inputfile: %s ' % testsetterinputfile
s += 'and outputfile: %s' % testsetterreportfile
self.assertTrue(result, s)
outputheader = read_header(testsetterreportfile)
expected = ['ID', 'month', 'country']
s = 'outputheader: %s not as expected: %s' % (outputheader, expected)
self.assertEqual(outputheader, expected, s)
dialect = csv_file_dialect(testsetterreportfile)
encoding = csv_file_encoding(testsetterreportfile)
rows = read_rows(testsetterreportfile,
1,
dialect=dialect,
encoding=encoding,
header=True,
fieldnames=outputheader)
firstrow = rows[0]
field = 'country'
value = firstrow[field]
expected = 'Argentina'
s = 'Field %s value %s not as expected (%s)' % (field, value, expected)
self.assertEqual(value, expected, s)
def test_darwinize_header(self):
print 'testing darwinize_header'
testfile1 = self.framework.testfile1
testfile2 = self.framework.testfile2
testfile3 = self.framework.testfile3
testdatapath = self.framework.testdatapath
dwccloudfile = self.framework.dwccloudfile
outputfile = self.framework.outputfile
inputs = {}
inputs['inputfile'] = testfile1
inputs['dwccloudfile'] = dwccloudfile
inputs['outputfile'] = outputfile
inputs['workspace'] = testdatapath
# Darwinize the header
response = darwinize_header(inputs)
outfilelocation = '%s/%s' % (testdatapath, outputfile)
header = read_header(outfilelocation)
#print 'inputs1:\n%s' % inputs
#print 'response1:\n%s' % response
expected = [
'catalogNumber', 'recordedBy', 'fieldNumber', 'year', 'month',
'day', 'decimalLatitude', 'decimalLongitude', 'geodeticDatum',
'country', 'stateProvince', 'county', 'locality', 'family',
'scientificName', 'scientificNameAuthorship',
'reproductiveCondition', 'institutionCode', 'collectionCode',
'datasetName', 'Id'
]
s = 'From input: %s\nFound:\n%s\nExpected:\n%s' % (testfile1, header,
expected)
self.assertEqual(header, expected, s)
# What is not Darwin Core?
casesensitive = True
notdwc = terms_not_in_dwc(header, casesensitive)
expected = ['Id']
s = 'From input: %s\nFound:\n%s\nExpected:\n%s' % (testfile1, notdwc,
expected)
self.assertEqual(notdwc, expected, s)
inputs['inputfile'] = testfile2
# Darwinize the header
response = darwinize_header(inputs)
header = read_header(outfilelocation)
#print 'response2:\n%s' % response
expected = [
'materialSampleID', 'principalInvestigator', 'locality', 'phylum',
'decimalLatitude', 'decimalLongitude',
'coordinateUncertaintyInMeters', 'georeferenceProtocol', 'year',
'month', 'day', 'genus', 'specificEpithet', 'permitInformation',
'basisOfIdentification', 'taxonID', 'country', 'stateProvince',
'island', 'islandGroup', 'sampleOwnerInstitutionCode',
'fundingSource', 'occurrenceID', 'associatedMedia',
'associatedReferences', 'preservative', 'previousIdentifications',
'lifeStage', 'weight', 'length', 'sex', 'establishmentMeans',
'associatedSequences', 'occurrenceRemarks', 'habitat',
'microHabitat', 'substratum', 'samplingProtocol',
'minimumDepthInMeters', 'maximumDepthInMeters',
'minimumDistanceAboveSurfaceInMeters',
'maximumDistanceAboveSurfaceInMeters', 'associatedTaxa',
'fieldNotes', 'eventRemarks', 'recordedBy', 'identifiedBy',
'yearIdentified', 'monthIdentified', 'dayIdentified', 'class',
'order', 'family', 'infraspecificEpithet', 'vernacularName',
'taxonRemarks', 'geneticTissueType', 'plateID', 'wellID',
'extractionID', 'otherCatalogNumbers', 'tissueStorageID', 'BCID',
'UNNAMED_COLUMN_1'
]
s = 'From input: %s\nFound:\n%s\nExpected:\n%s' % (testfile2, header,
expected)
self.assertEqual(header, expected, s)
# What is not Darwin Core?
casesensitive = True
notdwc = terms_not_in_dwc(header, casesensitive)
expected = [
'BCID', 'UNNAMED_COLUMN_1', 'basisOfIdentification',
'dayIdentified', 'extractionID', 'fundingSource',
'geneticTissueType', 'length', 'microHabitat', 'monthIdentified',
'permitInformation', 'plateID', 'preservative',
'principalInvestigator', 'sampleOwnerInstitutionCode',
'substratum', 'tissueStorageID', 'weight', 'wellID',
'yearIdentified'
]
s = 'From input: %s\nFound:\n%s\nExpected:\n%s' % (testfile1, notdwc,
expected)
self.assertEqual(notdwc, expected, s)
inputs['inputfile'] = testfile3
# Darwinize the header
response = darwinize_header(inputs)
header = read_header(outfilelocation)
#print 'response2:\n%s' % response
expected = [
'id', 'institutionCode', 'collectionCode', 'basisOfRecord',
'occurrenceID', 'catalogNumber', 'otherCatalogNumbers', 'kingdom',
'phylum', 'class', 'order', 'family', 'scientificName',
'scientificNameAuthorship', 'genus', 'specificEpithet',
'taxonRank', 'infraspecificEpithet', 'identifiedBy',
'dateIdentified', 'identificationReferences',
'identificationRemarks', 'taxonRemarks', 'identificationQualifier',
'typeStatus', 'recordedBy', 'recordedByID', 'associatedCollectors',
'recordNumber', 'eventDate', 'year', 'month', 'day',
'startDayOfYear', 'endDayOfYear', 'verbatimEventDate',
'occurrenceRemarks', 'habitat', 'substrate', 'verbatimAttributes',
'fieldNumber', 'informationWithheld', 'dataGeneralizations',
'dynamicProperties', 'associatedTaxa', 'reproductiveCondition',
'establishmentMeans', 'cultivationStatus', 'lifeStage', 'sex',
'individualCount', 'samplingProtocol', 'samplingEffort',
'preparations', 'country', 'stateProvince', 'county',
'municipality', 'locality', 'locationRemarks', 'localitySecurity',
'localitySecurityReason', 'decimalLatitude', 'decimalLongitude',
'geodeticDatum', 'coordinateUncertaintyInMeters',
'verbatimCoordinates', 'georeferencedBy', 'georeferenceProtocol',
'georeferenceSources', 'georeferenceVerificationStatus',
'georeferenceRemarks', 'minimumElevationInMeters',
'maximumElevationInMeters', 'minimumDepthInMeters',
'maximumDepthInMeters', 'verbatimDepth', 'verbatimElevation',
'disposition', 'language', 'recordEnteredBy', 'modified',
'sourcePrimaryKey', 'collId', 'recordId', 'references'
]
s = 'From input: %s\nFound:\n%s\nExpected:\n%s' % (testfile3, header,
expected)
self.maxDiff = None
self.assertEqual(header, expected, s)
# What is not Darwin Core?
casesensitive = True
notdwc = terms_not_in_dwc(header, casesensitive)
expected = [
'associatedCollectors', 'collId', 'cultivationStatus', 'id',
'localitySecurity', 'localitySecurityReason', 'recordEnteredBy',
'recordId', 'recordedByID', 'sourcePrimaryKey', 'substrate',
'verbatimAttributes'
]
s = 'From input: %s\nFound:\n%s\nExpected:\n%s' % (testfile1, notdwc,
expected)
self.assertEqual(notdwc, expected, s)
def test_headers(self):
print 'testing headers'
testfile = self.framework.testfile1
header = read_header(testfile)
expected = [
'catalogNumber ', 'recordedBy', 'fieldNumber ', 'year', 'month',
'day', 'decimalLatitude ', 'decimalLongitude ', 'geodeticDatum ',
'country', 'stateProvince', 'county', 'locality', 'family ',
'scientificName ', 'scientificNameAuthorship ',
'reproductiveCondition ', 'InstitutionCode ', 'CollectionCode ',
'DatasetName ', 'Id'
]
s = 'test file %s header:\n%s does not match expected:\n%s' % (
testfile, header, expected)
self.assertEqual(header, expected)
testfile = self.framework.testfile2
header = read_header(testfile)
expected = [
'materialSampleID', 'principalInvestigator', 'locality', 'phylum',
'decimalLatitude', 'decimalLongitude',
'coordinateUncertaintyInMeters', 'georeferenceProtocol',
'yearCollected', 'monthCollected', 'dayCollected', 'genus',
'species', 'permitInformation', 'basisOfIdentification', 'wormsID',
'country', 'stateProvince', 'island', 'islandGroup',
'sampleOwnerInstitutionCode', 'fundingSource', 'occurrenceID',
'associatedMedia', 'associatedReferences', 'preservative',
'previousIdentifications', 'lifeStage', 'weight', 'length', 'sex',
'establishmentMeans', 'associatedSequences', 'occurrenceRemarks',
'habitat', 'microHabitat', 'substratum', 'samplingProtocol',
'minimumDepthInMeters', 'maximumDepthInMeters',
'minimumDistanceAboveSurfaceInMeters',
'maximumDistanceAboveSurfaceInMeters', 'associatedTaxa',
'fieldNotes', 'eventRemarks', 'recordedBy', 'identifiedBy',
'yearIdentified', 'monthIdentified', 'dayIdentified', 'class',
'order', 'family', 'subSpecies', 'vernacularName', 'taxonRemarks',
'geneticTissueType', 'plateID', 'wellID', 'extractionID',
'previousTissueID', 'tissueStorageID', 'BCID', ''
]
s = 'test file %s header:\n%s does not match expected:\n%s' % \
(testfile, header, expected)
self.assertEqual(header, expected)
testfile = self.framework.testfile3
header = read_header(testfile)
expected = [
'id', 'institutionCode', 'collectionCode', 'basisOfRecord',
'occurrenceID', 'catalogNumber', 'otherCatalogNumbers', 'kingdom',
'phylum', 'class', 'order', 'family', 'scientificName',
'scientificNameAuthorship', 'genus', 'specificEpithet',
'taxonRank', 'infraspecificEpithet', 'identifiedBy',
'dateIdentified', 'identificationReferences',
'identificationRemarks', 'taxonRemarks', 'identificationQualifier',
'typeStatus', 'recordedBy', 'recordedByID', 'associatedCollectors',
'recordNumber', 'eventDate', 'year', 'month', 'day',
'startDayOfYear', 'endDayOfYear', 'verbatimEventDate',
'occurrenceRemarks', 'habitat', 'substrate', 'verbatimAttributes',
'fieldNumber', 'informationWithheld', 'dataGeneralizations',
'dynamicProperties', 'associatedTaxa', 'reproductiveCondition',
'establishmentMeans', 'cultivationStatus', 'lifeStage', 'sex',
'individualCount', 'samplingProtocol', 'samplingEffort',
'preparations', 'country', 'stateProvince', 'county',
'municipality', 'locality', 'locationRemarks', 'localitySecurity',
'localitySecurityReason', 'decimalLatitude', 'decimalLongitude',
'geodeticDatum', 'coordinateUncertaintyInMeters',
'verbatimCoordinates', 'georeferencedBy', 'georeferenceProtocol',
'georeferenceSources', 'georeferenceVerificationStatus',
'georeferenceRemarks', 'minimumElevationInMeters',
'maximumElevationInMeters', 'minimumDepthInMeters',
'maximumDepthInMeters', 'verbatimDepth', 'verbatimElevation',
'disposition', 'language', 'recordEnteredBy', 'modified',
'sourcePrimaryKey', 'collId', 'recordId', 'references'
]
s = 'test file %s header:\n%s does not match expected:\n%s' % (
testfile, header, expected)
self.assertEqual(header, expected)
def test_aggregate_mix(self):
print 'testing aggregate_mix'
tsvfile = self.framework.tsvfile
mixedcompositepath = self.framework.mixedcompositepath
workspace = self.framework.testdatapath
inputs = {}
inputs['inputpath'] = mixedcompositepath
inputs['outputfile'] = self.framework.tsvfile
inputs['workspace'] = workspace
inputs['format'] = 'txt'
# Aggregate text file
response = text_file_aggregator(inputs)
outputfile = response['outputfile']
self.assertTrue(os.path.isfile(outputfile),
outputfile + ' does not exist')
self.assertEqual(response['aggregaterowcount'], 19,
'incorrect number of rows')
header = read_header(outputfile)
modelheader = []
modelheader.append('BCID')
modelheader.append('CollectionCode')
modelheader.append('DatasetName')
modelheader.append('Id')
modelheader.append('InstitutionCode')
modelheader.append('associatedMedia')
modelheader.append('associatedReferences')
modelheader.append('associatedSequences')
modelheader.append('associatedTaxa')
modelheader.append('basisOfIdentification')
modelheader.append('catalogNumber')
modelheader.append('class')
modelheader.append('coordinateUncertaintyInMeters')
modelheader.append('country')
modelheader.append('county')
modelheader.append('day')
modelheader.append('dayCollected')
modelheader.append('dayIdentified')
modelheader.append('decimalLatitude')
modelheader.append('decimalLongitude')
modelheader.append('establishmentMeans')
modelheader.append('eventRemarks')
modelheader.append('extractionID')
modelheader.append('family')
modelheader.append('fieldNotes')
modelheader.append('fieldNumber')
modelheader.append('fundingSource')
modelheader.append('geneticTissueType')
modelheader.append('genus')
modelheader.append('geodeticDatum')
modelheader.append('georeferenceProtocol')
modelheader.append('habitat')
modelheader.append('identifiedBy')
modelheader.append('island')
modelheader.append('islandGroup')
modelheader.append('length')
modelheader.append('lifeStage')
modelheader.append('locality')
modelheader.append('materialSampleID')
modelheader.append('maximumDepthInMeters')
modelheader.append('maximumDistanceAboveSurfaceInMeters')
modelheader.append('microHabitat')
modelheader.append('minimumDepthInMeters')
modelheader.append('minimumDistanceAboveSurfaceInMeters')
modelheader.append('month')
modelheader.append('monthCollected')
modelheader.append('monthIdentified')
modelheader.append('occurrenceID')
modelheader.append('occurrenceRemarks')
modelheader.append('order')
modelheader.append('permitInformation')
modelheader.append('phylum')
modelheader.append('plateID')
modelheader.append('preservative')
modelheader.append('previousIdentifications')
modelheader.append('previousTissueID')
modelheader.append('principalInvestigator')
modelheader.append('recordedBy')
modelheader.append('reproductiveCondition')
modelheader.append('sampleOwnerInstitutionCode')
modelheader.append('samplingProtocol')
modelheader.append('scientificName')
modelheader.append('scientificNameAuthorship')
modelheader.append('sex')
modelheader.append('species')
modelheader.append('stateProvince')
modelheader.append('subSpecies')
modelheader.append('substratum')
modelheader.append('taxonRemarks')
modelheader.append('tissueStorageID')
modelheader.append('vernacularName')
modelheader.append('weight')
modelheader.append('wellID')
modelheader.append('wormsID')
modelheader.append('year')
modelheader.append('yearCollected')
modelheader.append('yearIdentified')
#print 'len(header)=%s len(model)=%s\nheader:\n%smodel:\n\n%s' % (len(header), len(modelheader), header, modelheader)
self.assertEqual(len(header), 77,
'incorrect number of fields in header')
self.assertEqual(header, modelheader,
'header not equal to the model header')
