def test_isatab_load_bii_s_7(self):
with io.open(
os.path.join(self._tab_data_dir, 'BII-S-7',
'i_matteo.txt')) as fp:
investigation_parser = isatab.InvestigationParser()
investigation_parser.parse(fp)
self.parser = isatab.StudySampleTableParser(
investigation_parser.isa)
self.parser.parse(
os.path.join(self._tab_data_dir, 'BII-S-7',
investigation_parser.isa.studies[-1].filename))
self.assertEqual(len(self.parser.sources), 29)
self.assertEqual(len(self.parser.samples), 29)
self.assertEqual(len(self.parser.process_sequence), 29)
def test_isatab_parse_study_table_bii_s_1(self):
with io.open(
os.path.join(self._tab_data_dir, 'BII-I-1',
'i_investigation.txt')) as fp:
investigation_parser = isatab.InvestigationParser()
investigation_parser.parse(fp)
self.parser = isatab.StudySampleTableParser(
investigation_parser.isa)
self.parser.parse(
os.path.join(self._tab_data_dir, 'BII-I-1',
investigation_parser.isa.studies[0].filename))
self.assertEqual(len(self.parser.sources), 18)
self.assertEqual(len(self.parser.samples), 164)
self.assertEqual(len(self.parser.process_sequence), 18)
def test_isatab_parse_study_no_investigation_object(self):
with self.assertRaises(IOError):
isatab.StudySampleTableParser()
with self.assertRaises(IOError):
isatab.StudySampleTableParser(isa=object())
def setUp(self):
self.isa = Investigation()
self.isa.ontology_source_references = [
OntologySource('A', 'f1', '1', 'd1'),
OntologySource('B', 'f2', '2', 'd2')
]
self.parser = isatab.StudySampleTableParser(self.isa)
self.study_sample_table = \
u'Source Name\tSample Name\n' \
u'source1\tsample1\n' \
u'source2\tsample2'
self.study_sample_table_with_two_sample_names_columns = \
u'Source Name\tSample Name\tSample Name\n' \
u'source1\tsample1\tsample2\n'
self.study_sample_table_with_numbers_as_ids = \
u'Source Name\tSample Name\tSample Name\n' \
u'source1\t1\t2\n'
self.study_sample_table_with_process = \
u'Source Name\tProtocol REF\tSample Name\n' \
u'source1\tsample collection\tsample1\n' \
u'source2\tsample collection\tsample2'
self.study_sample_table_with_process_split = \
u'Source Name\tProtocol REF\tSample Name\n' \
u'source1\tsample collection\tsample1\n' \
u'source1\tsample collection\tsample2'
self.study_sample_table_with_process_pool = \
u'Source Name\tProtocol REF\tSample Name\n' \
u'source1\tsample collection\tsample1\n' \
u'source2\tsample collection\tsample1'
self.study_sample_table_source_characteristics_fragment = \
u'Source Name\tCharacteristics[c1]\tCharacteristics[c2]\n' \
u'source1\tsource1-c1\tsource1-c2\n' \
u'source2\tsource2-c1\tsource2-c2'
self.study_sample_table_sample_characteristics_fragment = \
u'Sample Name\tCharacteristics[c1]\tCharacteristics[c2]\n' \
u'sample1\tsample1-c1\tsample1-c2\n' \
u'sample2\tsample2-c1\tsample2-c2'
self.study_sample_table_source_comments_fragment = \
u'Source Name\tComment[c1]\tComment[c2]\n' \
u'source1\tsource1-c1\tsource1-c2\n' \
u'source2\tsource2-c1\tsource2-c2'
self.study_sample_table_sample_comments_fragment = \
u'Sample Name\tComment[c1]\tComment[c2]\n' \
u'sample1\tsample1-c1\tsample1-c2\n' \
u'sample2\tsample2-c1\tsample2-c2'
self.source_list = [Source(name='source1'), Source(name='source2')]
self.sample_list = [Sample(name='sample1'), Sample(name='sample2')]
self.sample_list_with_numbers_as_ids = [
Sample(name='1'), Sample(name='2')
]
characteristic_category_c1 = OntologyAnnotation(term='c1')
characteristic_category_c2 = OntologyAnnotation(term='c2')
self.source_list_with_characteristics = [
Source(name='source1',
characteristics=[
Characteristic(category=characteristic_category_c1,
value='source1-c1'),
Characteristic(category=characteristic_category_c2,
value='source1-c2')
]),
Source(name='source2',
characteristics=[
Characteristic(characteristic_category_c1,
value='source2-c1'),
Characteristic(category=characteristic_category_c2,
value='source2-c2')
])
]
self.sample_list_with_characteristics = [
Sample(name='sample1',
characteristics=[
Characteristic(category=characteristic_category_c1,
value='sample1-c1'),
Characteristic(category=characteristic_category_c2,
value='sample1-c2')
]),
Sample(name='sample2',
characteristics=[
Characteristic(characteristic_category_c1,
value='sample2-c1'),
Characteristic(category=characteristic_category_c2,
value='sample2-c2')
])
]
self.source_list_with_comments = [
Source(name='source1',
comments=[
Comment(name='c1', value='source1-c1'),
Comment(name='c2', value='source1-c2')
]),
Source(name='source2',
comments=[
Comment(name='c1', value='source2-c1'),
Comment(name='c2', value='source2-c2')
])
]
self.sample_list_with_comments = [
Sample(name='sample1',
comments=[
Comment(name='c1', value='sample1-c1'),
Comment(name='c2', value='sample1-c2')
]),
Sample(name='sample2',
comments=[
Comment(name='c1', value='sample2-c1'),
Comment(name='c2', value='sample2-c2')
])
]