def test_isatab_parse_bii_s_1_proteome(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.AssayTableParser(investigation_parser.isa)
self.parser.parse(
os.path.join(self._tab_data_dir, 'BII-I-1', 'a_proteome.txt'))
self.assertEqual(len(self.parser.samples), 8)
self.assertEqual(len(self.parser.data_files), 7)
self.assertEqual(len(self.parser.other_material), 19)
self.assertEqual(len(self.parser.process_sequence), 16)
def test_isatab_parse_bii_s_7_Gx(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.AssayTableParser(investigation_parser.isa)
self.parser.parse(
os.path.join(self._tab_data_dir, 'BII-S-7',
'a_matteo-assay-Gx.txt'))
self.assertEqual(len(self.parser.samples), 29)
self.assertEqual(len(self.parser.data_files), 29)
self.assertEqual(len(self.parser.other_material), 29)
self.assertEqual(len(self.parser.process_sequence), 116)
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 setUp(self):
self._tab_data_dir = os.path.join(os.path.dirname(__file__), 'data',
'tab')
self.parser = isatab.InvestigationParser()
def setUp(self):
self.parser = isatab.InvestigationParser()
self.ontology_source_ref_section = \
u'ONTOLOGY SOURCE REFERENCE\n' \
u'Term Source Name\t"A"\t"B"\n' \
u'Term Source File\t"f1"\t"f2"\n' \
u'Term Source Version\t"1"\t"2"\n' \
u'Term Source Description\t"d1"\t"d2"'
self.os1 = OntologySource('A', 'f1', '1', 'd1')
self.os2 = OntologySource('B', 'f2', '2', 'd2')
self.investigation_section = \
u'INVESTIGATION\n' \
u'Investigation Identifier\t"ID"\n' \
u'Investigation Title\t"T"\n' \
u'Investigation Description\t"D"\n' \
u'Investigation Submission Date\t"2017-10-24"\n' \
u'Investigation Public Release Date\t"2017-10-25"'
self.i = Investigation(identifier='ID',
title='T',
description='D',
submission_date='2017-10-24',
public_release_date='2017-10-25')
self.investigation_section_with_comment_lines = \
u'# This line is a comment\n' \
u'INVESTIGATION\n' \
u'Investigation Identifier\t"ID"\n' \
u'Investigation Title\t"T"\n' \
u'# This line is another comment\n' \
u'Investigation Description\t"D"\n' \
u'Investigation Submission Date\t"2017-10-24"\n' \
u'Investigation Public Release Date\t"2017-10-25"'
self.investigation_publications_section = \
u'INVESTIGATION PUBLICATIONS\n' \
u'Investigation PubMed ID\t"0"\t"1"\n' \
u'Investigation Publication DOI\t"doi1"\t"doi2"\n' \
u'Investigation Publication Author List\t"AL1"\t"AL2"\n' \
u'Investigation Publication Title\t"T1"\t"T2"\n' \
u'Investigation Publication Status\t"S1"\t"S2"\n' \
u'Investigation Publication Status Term Accession Number\t"acc1"\t"acc2"\n' \
u'Investigation Publication Status Term Source REF\t"src1"\t"src2"'
publication_status1 = OntologyAnnotation('S1', 'src1', 'acc1')
publication_status2 = OntologyAnnotation('S2', 'src2', 'acc2')
self.publication1 = Publication('0', 'doi1', 'AL1', 'T1',
publication_status1)
self.publication2 = Publication('1', 'doi2', 'AL2', 'T2',
publication_status2)
self.study_publications_section = \
u'STUDY\n' \
u'STUDY PUBLICATIONS\n' \
u'Study PubMed ID\t"0"\n' \
u'Study Publication DOI\t"doi1"\n' \
u'Study Publication Author List\t"AL1"\n' \
u'Study Publication Title\t"T1"\n' \
u'Study Publication Status\t"S1"\n' \
u'Study Publication Status Term Accession Number\t"acc1"\n' \
u'Study Publication Status Term Source REF\t"src1"\n' \
u'STUDY\n' \
u'STUDY PUBLICATIONS\n' \
u'Study PubMed ID\t"0b"\t"1b"\n' \
u'Study Publication DOI\t"doi1b"\t"doi2b"\n' \
u'Study Publication Author List\t"AL1b"\t"AL2b"\n' \
u'Study Publication Title\t"T1b"\t"T2b"\n' \
u'Study Publication Status\t"S1b"\t"S2b"\n' \
u'Study Publication Status Term Accession Number\t"acc1b"\t"acc2b"\n' \
u'Study Publication Status Term Source REF\t"src1b"\t"src2b"'
publication_status1b = OntologyAnnotation('S1b', 'src1b', 'acc1b')
publication_status2b = OntologyAnnotation('S2b', 'src2b', 'acc2b')
self.publication1b = Publication('0b', 'doi1b', 'AL1b', 'T1b',
publication_status1b)
self.publication2b = Publication('1b', 'doi2b', 'AL2b', 'T2b',
publication_status2b)
self.investigation_contacts_section = \
u'INVESTIGATION CONTACTS\n' \
u'Investigation Person Last Name\t"ln1"\t"ln2"\n' \
u'Investigation Person First Name\t"fn1"\t"fn2"\n' \
u'Investigation Person Mid Initials\t"mi1"\t"mi2"\n' \
u'Investigation Person Email\t"e1"\t"e2"\n' \
u'Investigation Person Phone\t"ph1"\t"ph2"\n' \
u'Investigation Person Fax\t"fax1"\t"fax2"\n' \
u'Investigation Person Address\t"ad1"\t"ad2"\n' \
u'Investigation Person Affiliation\t"af1"\t"af2"\n' \
u'Investigation Person Roles\t"r1"\t"r2"\n' \
u'Investigation Person Roles Term Accession Number\t"r_acc1"\t"r_acc2"\n' \
u'Investigation Person Roles Term Source REF\t"r_src1"\t"r_src2"'
self.study_contacts_section = \
u'STUDY\n'\
u'STUDY CONTACTS\n' \
u'Study Person Last Name\t"ln1"\t"ln2"\n' \
u'Study Person First Name\t"fn1"\t"fn2"\n' \
u'Study Person Mid Initials\t"mi1"\t"mi2"\n' \
u'Study Person Email\t"e1"\t"e2"\n' \
u'Study Person Phone\t"ph1"\t"ph2"\n' \
u'Study Person Fax\t"fax1"\t"fax2"\n' \
u'Study Person Address\t"ad1"\t"ad2"\n' \
u'Study Person Affiliation\t"af1"\t"af2"\n' \
u'Study Person Roles\t"r1"\t"r2"\n' \
u'Study Person Roles Term Accession Number\t"r_acc1"\t"r_acc2"\n' \
u'Study Person Roles Term Source REF\t"r_src1"\t"r_src2"\n' \
u'STUDY\n' \
u'STUDY CONTACTS\n' \
u'Study Person Last Name\t"ln1b"\t"ln2b"\n' \
u'Study Person First Name\t"fn1b"\t"fn2b"\n' \
u'Study Person Mid Initials\t"mi1b"\t"mi2b"\n' \
u'Study Person Email\t"e1b"\t"e2b"\n' \
u'Study Person Phone\t"ph1b"\t"ph2b"\n' \
u'Study Person Fax\t"fax1b"\t"fax2b"\n' \
u'Study Person Address\t"ad1b"\t"ad2b"\n' \
u'Study Person Affiliation\t"af1b"\t"af2b"\n' \
u'Study Person Roles\t"r1b"\t"r2b"\n' \
u'Study Person Roles Term Accession Number\t"r_acc1b"\t"r_acc2b"\n' \
u'Study Person Roles Term Source REF\t"r_src1b"\t"r_src2b"'
role1 = OntologyAnnotation('r1', 'r_src1', 'r_acc1')
role2 = OntologyAnnotation('r2', 'r_src2', 'r_acc2')
self.person1 = Person('ln1', 'fn1', 'mi1', 'e1', 'ph1', 'fax1', 'ad1',
'af1', [role1])
self.person2 = Person('ln2', 'fn2', 'mi2', 'e2', 'ph2', 'fax2', 'ad2',
'af2', [role2])
role1b = OntologyAnnotation('r1b', 'r_src1b', 'r_acc1b')
role2b = OntologyAnnotation('r2b', 'r_src2b', 'r_acc2b')
self.person1b = Person('ln1b', 'fn1b', 'mi1b', 'e1b', 'ph1b', 'fax1b',
'ad1b', 'af1b', [role1b])
self.person2b = Person('ln2b', 'fn2b', 'mi2b', 'e2b', 'ph2b', 'fax2b',
'ad2b', 'af2b', [role2b])
self.study_section = \
u'STUDY\n' \
u'Study Identifier\t"ID"\n' \
u'Study Title\t"T"\n' \
u'Study Description\t"D"\n' \
u'Study Submission Date\t"2017-10-24"\n' \
u'Study Public Release Date\t"2017-10-25"\n' \
u'Study File Name\t"f"'
self.s = Study(identifier='ID',
title='T',
description='D',
submission_date='2017-10-24',
public_release_date='2017-10-25',
filename='f')
self.study_design_descriptors_section = \
u'STUDY\n' \
u'STUDY DESIGN DESCRIPTORS\n' \
u'Study Design Type\t"d1"\t"d2"\n' \
u'Study Design Type Term Accession Number\t"acc1"\t"acc2"\n' \
u'Study Design Type Term Source REF\t"src1"\t"src2"'
self.study_design = [
OntologyAnnotation('d1', 'src1', 'acc1'),
OntologyAnnotation('d2', 'src2', 'acc2')
]
self.study_factors_section = \
u'STUDY\n' \
u'STUDY FACTORS\n' \
u'Study Factor Name\t"f1"\t"f2"\n' \
u'Study Factor Type\t"t1"\t"t2"\n' \
u'Study Factor Type Term Accession Number\t"acc1"\t"acc2"\n' \
u'Study Factor Type Term Source REF\t"src1"\t"src2"'
self.study_factors = [
StudyFactor(name='f1',
factor_type=OntologyAnnotation('t1', 'src1', 'acc1')),
StudyFactor(name='f2',
factor_type=OntologyAnnotation('t2', 'src2', 'acc2'))
]
self.study_assays_section = \
u'STUDY\n' \
u'STUDY ASSAYS\n' \
u'Study Assay Measurement Type\t"mt1"\t"mt2"\n' \
u'Study Assay Measurement Type Term Accession Number\t"mt_acc1"\t"mt_acc2"\n' \
u'Study Assay Measurement Type Term Source REF\t"mt_src1"\t"mt_src2"\n' \
u'Study Assay Technology Type\t"tt1"\t"tt2"\n' \
u'Study Assay Technology Type Term Accession Number\t"tt_acc1"\t"tt_acc2"\n' \
u'Study Assay Technology Type Term Source REF\t"tt_src1"\t"tt_src2"\n' \
u'Study Assay Technology Platform\t"tp1"\t"tp2"\n' \
u'Study Assay File Name\t"f1"\t"f2"'
self.study_assay1 = Assay(
measurement_type=OntologyAnnotation('mt1', 'mt_src1', 'mt_acc1'),
technology_type=OntologyAnnotation('tt1', 'tt_src1', 'tt_acc1'),
technology_platform='tp1',
filename='f1')
self.study_assay2 = Assay(
measurement_type=OntologyAnnotation('mt2', 'mt_src2', 'mt_acc2'),
technology_type=OntologyAnnotation('tt2', 'tt_src2', 'tt_acc2'),
technology_platform='tp2',
filename='f2')
self.study_protocols_section = \
u'STUDY\n' \
u'STUDY PROTOCOLS\n' \
u'Study Protocol Name\t"p1"\t"p2"\n' \
u'Study Protocol Type\t"pt1"\t"pt2"\n' \
u'Study Protocol Type Term Accession Number\t"pt1_acc"\t"pt2_acc"\n' \
u'Study Protocol Type Term Source REF\t"pt1_src"\t"pt2_src"\n' \
u'Study Protocol Description\t"d1"\t"d2"\n' \
u'Study Protocol URI\t"u1"\t"u2"\n' \
u'Study Protocol Version\t"v1"\t"v2"\n' \
u'Study Protocol Parameters Name\t"ppn1a;ppn1b"\t"ppn2"\n' \
u'Study Protocol Parameters Name Term Accession Number\t"ppn1a_acc;ppn1b_acc"\t"ppn2_acc"\n' \
u'Study Protocol Parameters Name Term Source REF\t"ppn1a_src;ppn1b_src"\t"ppn2_src"\n' \
u'Study Protocol Components Name\t"cn1a;cn1b"\t"cn2"\n' \
u'Study Protocol Components Type\t"ct1a;ct1b"\t"ct2"\n' \
u'Study Protocol Components Type Term Accession Number\t"ct1a_acc;ct1b_acc"\t"ct2_acc"\n' \
u'Study Protocol Components Type Term Source REF\t"ct1a_src;ct1b_src"\t"ct2_src"\n' \
u'STUDY\n' \
u'STUDY PROTOCOLS\n' \
u'Study Protocol Name\t"p1b"\n' \
u'Study Protocol Type\t"pt1b"\n' \
u'Study Protocol Type Term Accession Number\t"pt1b_acc"\n' \
u'Study Protocol Type Term Source REF\t"pt1b_src"\n' \
u'Study Protocol Description\t"d1b"\n' \
u'Study Protocol URI\t"u1b"\n' \
u'Study Protocol Version\t"v1b"\n' \
u'Study Protocol Parameters Name\t"ppn1b"\n' \
u'Study Protocol Parameters Name Term Accession Number\t"ppn1b_acc"\n' \
u'Study Protocol Parameters Name Term Source REF\t"ppn1b_src"\n' \
u'Study Protocol Components Name\t"cn1b"\n' \
u'Study Protocol Components Type\t"ct1b"\n' \
u'Study Protocol Components Type Term Accession Number\t"ct1b_acc"\n' \
u'Study Protocol Components Type Term Source REF\t"ct1b_src"'
self.study_protocol1 = Protocol(
'', 'p1', OntologyAnnotation('pt1', 'pt1_src', 'pt1_acc'), 'u1',
'd1', 'v1', [
ProtocolParameter(parameter_name=OntologyAnnotation(
'ppn1a', 'ppn1a_src', 'ppn1a_acc')),
ProtocolParameter(parameter_name=OntologyAnnotation(
'ppn1b', 'ppn1b_src', 'ppn1b_acc'))
], [
ProtocolComponent(name='cn1a',
component_type=OntologyAnnotation(
'ct1a', 'ct1a_src', 'ct1a_acc')),
ProtocolComponent(name='cn1b',
component_type=OntologyAnnotation(
'ct1b', 'ct1b_src', 'ct1b_acc'))
])
self.study_protocol2 = Protocol(
'', 'p2', OntologyAnnotation('pt2', 'pt2_src', 'pt2_acc'), 'u2',
'd2', 'v2', [
ProtocolParameter(parameter_name=OntologyAnnotation(
'ppn2', 'ppn2_src', 'ppn2_acc'))
], [
ProtocolComponent(name='cn2',
component_type=OntologyAnnotation(
'ct2', 'ct2_src', 'ct2_acc'))
])
self.study_protocol1b = Protocol(
'', 'p1b', OntologyAnnotation('pt1b', 'pt1b_src', 'pt1b_acc'),
'u1b', 'd1b', 'v1b', [
ProtocolParameter(parameter_name=OntologyAnnotation(
'ppn1b', 'ppn1b_src', 'ppn1b_acc'))
], [
ProtocolComponent(name='cn1b',
component_type=OntologyAnnotation(
'ct1b', 'ct1b_src', 'ct1b_acc'))
])
