def test_json2isatab_convert_sample_pool_assay_table(self):
json2isatab.convert(open(os.path.join(self._json_data_dir, 'TEST-ISA-sample-pool.json')), self._tmp_dir,
validate_first=False)
self.assertTrue(assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 'a_test-template3-splitting_transcription_profiling_DNA_microarray.txt')),
open(os.path.join(self._tab_data_dir, 'TEST-ISA-sample-pool',
'a_test-template3-splitting_transcription_profiling_DNA_microarray.txt'))))
def test_assert_tab_content_equal_assay_table(self):
with open(os.path.join(utils.TAB_DATA_DIR, 'BII-I-1',
's_BII-S-1.txt')) as s_tab1:
with open(
os.path.join(utils.TAB_DATA_DIR, 'BII-I-1',
's_BII-S-1.txt')) as s_tab2:
self.assertTrue(utils.assert_tab_content_equal(s_tab1, s_tab2))
def test_mzml2isa_convert_investigation(self):
study_id = 'MTBLS267'
report = mzml2isa.convert(os.path.join(self._mzml_data_dir,
study_id + '-partial'),
self._tmp_dir,
study_id,
validate_output=True)
self.assertTrue(report['validation_finished'])
self.assertEqual(len(report['errors']), 0)
# Strip out the line with Comment[Created With Tool] to avoid changes in version number generated by mzml2isa
with open(os.path.join(self._tmp_dir, study_id, 'i_Investigation.txt')
) as in_fp, StringIO() as stripped_actual_file:
stripped_actual_file.name = 'i_Investigation.txt'
for row in in_fp:
if row.startswith('Comment[Created With Tool]'):
pass
else:
stripped_actual_file.write(row)
stripped_actual_file.seek(0)
with open(
os.path.join(self._tab_data_dir, study_id + '-partial',
'i_Investigation.txt')) as reference_fp:
self.assertTrue(
assert_tab_content_equal(stripped_actual_file,
reference_fp))
def test_assert_tab_content_equal_investigation(self):
with open(
os.path.join(utils.TAB_DATA_DIR, 'BII-I-1',
'i_investigation.txt')) as i_tab1:
with open(
os.path.join(utils.TAB_DATA_DIR, 'BII-I-1',
'i_investigation.txt')) as i_tab2:
self.assertTrue(utils.assert_tab_content_equal(i_tab1, i_tab2))
def test_json2isatab_convert_bii_i_1_study2_table(self):
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir)
with open(os.path.join(self._tmp_dir, 's_BII-S-2.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-I-1',
's_BII-S-2.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_s_7_study_table(self):
with open(os.path.join(self._json_data_dir, 'BII-S-7',
'BII-S-7.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir, validate_first=False)
with open(os.path.join(self._tmp_dir, 's_BII-S-7.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-S-7',
's_BII-S-7.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_study2_table(self):
json2isatab.convert(
open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')),
self._tmp_dir)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 's_BII-S-2.txt')),
open(
os.path.join(self._tab_data_dir, 'BII-I-1',
's_BII-S-2.txt'))))
def test_json2isatab_convert_source_split_study_table(self):
with open(
os.path.join(self._json_data_dir,
'TEST-ISA-source-split.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir, validate_first=False)
with open(os.path.join(self._tmp_dir,
's_TEST-Template1-Splitting.txt')) as out_fp:
with open(os.path.join(self._tab_data_dir, 'TEST-ISA-source-split', 's_TEST-Template1-Splitting.txt')) \
as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_assay_table_metabolome(self):
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir)
with open(os.path.join(self._tmp_dir, 'a_metabolome.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_metabolome.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_s_3_assay_table_Gx(self):
with open(os.path.join(self._json_data_dir, 'BII-S-3',
'BII-S-3.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir, validate_first=False)
with open(os.path.join(self._tmp_dir,
'a_gilbert-assay-Gx.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-S-3',
'a_gilbert-assay-Gx.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_s_3_study_table(self):
json2isatab.convert(open(
os.path.join(self._json_data_dir, 'BII-S-3', 'BII-S-3.json')),
self._tmp_dir,
validate_first=False)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 's_BII-S-3.txt')),
open(
os.path.join(self._tab_data_dir, 'BII-S-3',
's_BII-S-3.txt'))))
def test_json2isatab_convert_bii_s_7_assay_table_Gx(self):
json2isatab.convert(open(
os.path.join(self._json_data_dir, 'BII-S-7', 'BII-S-7.json')),
self._tmp_dir,
validate_first=False)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 'a_matteo-assay-Gx.txt')),
open(
os.path.join(self._tab_data_dir, 'BII-S-7',
'a_matteo-assay-Gx.txt'))))
def test_json2isatab_convert_bii_i_1_investigation(self):
json2isatab.convert(
open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')),
self._tmp_dir)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 'i_investigation.txt')),
open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'i_investigation.txt'))))
def test_json2isatab_convert_bii_i_1_assay_table_proteome(
self): # FIXME: Same duplication problem as above
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir)
with open(os.path.join(self._tmp_dir, 'a_proteome.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_proteome.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_assay_table_metabolome(self):
json2isatab.convert(
open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')),
self._tmp_dir)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 'a_metabolome.txt')),
open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_metabolome.txt'))))
def test_json2isatab_convert_bii_s_3_investigation(self):
json2isatab.convert(open(
os.path.join(self._json_data_dir, 'BII-S-3', 'BII-S-3.json')),
self._tmp_dir,
i_file_name='i_gilbert.txt',
validate_first=False)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 'i_gilbert.txt')),
open(
os.path.join(self._tab_data_dir, 'BII-S-3',
'i_gilbert.txt'))))
def test_json2isatab_convert_bii_i_1_assay_table_microarray(
self
): # FIXME: ArrayExpress comments come out twice (on Assay AND Derived Data File output from assay), missing Data Transformation Name and Factor Values
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir)
with open(os.path.join(self._tmp_dir, 'a_microarray.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_microarray.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_assay_table_proteome(
self): # FIXME: Same duplication problem as above
json2isatab.convert(
open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')),
self._tmp_dir)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 'a_proteome.txt')),
open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_proteome.txt'))))
def test_json2isatab_convert_bii_s_3_investigation(self):
with open(os.path.join(self._json_data_dir, 'BII-S-3',
'BII-S-3.json')) as json_fp:
json2isatab.convert(json_fp,
self._tmp_dir,
i_file_name='i_gilbert.txt',
validate_first=False)
with open(os.path.join(self._tmp_dir, 'i_gilbert.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-S-3',
'i_gilbert.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_assay_table_transcriptome(
self
): # FIXME: Has inserted Protocol REFs but Array Design REF, Scan Name, Factor Values
json2isatab.convert(
open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')),
self._tmp_dir)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 'a_transcriptome.txt')),
open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_transcriptome.txt'))))
def test_json2isatab_convert_sample_pool_study_table(self):
json2isatab.convert(open(
os.path.join(self._json_data_dir, 'TEST-ISA-sample-pool.json')),
self._tmp_dir,
validate_first=False)
self.assertTrue(
assert_tab_content_equal(
open(
os.path.join(self._tmp_dir,
's_TEST-Template3-Splitting.txt')),
open(
os.path.join(self._tab_data_dir, 'TEST-ISA-sample-pool',
's_TEST-Template3-Splitting.txt'))))
def test_mzml2isa_convert_study_table(self):
study_id = 'MTBLS267'
report = mzml2isa.convert(os.path.join(self._mzml_data_dir,
study_id + '-partial'),
self._tmp_dir,
study_id,
validate_output=True)
self.assertTrue(report['validation_finished'])
self.assertEqual(len(report['errors']), 0)
with open(
os.path.join(self._tmp_dir, study_id,
's_{}.txt'.format(study_id))) as out_fp:
with open(
os.path.join(self._tab_data_dir, study_id + '-partial',
's_{}.txt'.format(study_id))) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_source_split_assay_table(self):
with open(
os.path.join(self._json_data_dir,
'TEST-ISA-source-split.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir, validate_first=False)
with open(
os.path.join(
self._tmp_dir,
'a_test-template1-splitting_transcription_profiling_DNA_microarray.txt'
)) as out_fp:
with open(
os.path.join(
self._tab_data_dir, 'TEST-ISA-source-split',
'a_test-template1-splitting_transcription_profiling_DNA_microarray.txt'
)) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_s_7_assay_table_Gx(self):
json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-S-7', 'BII-S-7.json')), self._tmp_dir)
self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 'a_matteo-assay-Gx.txt')),
open(os.path.join(self._tab_data_dir, 'BII-S-7',
'a_matteo-assay-Gx.txt'))))
# def test_json2isatab_convert_bii_i_1_investigation(self):
# json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')), self._tmp_dir)
# self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 'i_investigation.txt')),
# open(os.path.join(self._tab_data_dir, 'BII-I-1', 'i_investigation.txt'))))
#
# def test_json2isatab_convert_bii_i_1_study_table(self):
# json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')), self._tmp_dir)
# self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 's_BII-S-1.txt')),
# open(os.path.join(self._tab_data_dir, 'BII-I-1', 's_BII-S-1.txt'))))
#
# def test_json2isatab_convert_bii_i_1_study2_table(self):
# json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')), self._tmp_dir)
# self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 's_BII-S-2.txt')),
# open(os.path.join(self._tab_data_dir, 'BII-I-1', 's_BII-S-2.txt'))))
#
# def test_json2isatab_convert_bii_i_1_assay_table_metabolome(self):
# json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')), self._tmp_dir)
# self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 'a_metabolome.txt')),
# open(os.path.join(self._tab_data_dir, 'BII-I-1',
# 'a_metabolome.txt'))))
#
# def test_json2isatab_convert_bii_i_1_assay_table_microarray(self):
# json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')), self._tmp_dir)
# self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 'a_microarray.txt')),
# open(os.path.join(self._tab_data_dir, 'BII-I-1',
# 'a_microarray.txt'))))
#
# def test_json2isatab_convert_bii_i_1_assay_table_proteome(self):
# json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')), self._tmp_dir)
# self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 'a_proteome.txt')),
# open(os.path.join(self._tab_data_dir, 'BII-I-1',
# 'a_proteome.txt'))))
#
# def test_json2isatab_convert_bii_i_1_assay_table_transcriptome(self):
# json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-I-1', 'BII-I-1.json')), self._tmp_dir)
# self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 'a_transcriptome.txt')),
# open(os.path.join(self._tab_data_dir, 'BII-I-1',
# 'a_transcriptome.txt'))))
def test_mzml2isa_convert_assay_table(self):
study_id = 'MTBLS267'
report = mzml2isa.convert(os.path.join(self._mzml_data_dir,
study_id + '-partial'),
self._tmp_dir,
study_id,
validate_output=True)
self.assertTrue(report['validation_finished'])
self.assertEqual(len(report['errors']), 0)
self.assertTrue(
assert_tab_content_equal(
open(
os.path.join(
self._tmp_dir, study_id,
'a_{}_metabolite_profiling_mass_spectrometry.txt'.
format(study_id))),
open(
os.path.join(
self._tab_data_dir, study_id + '-partial',
'a_{}_metabolite_profiling_mass_spectrometry.txt'.
format(study_id)))))
def test_isatab_dump_source_sample_split(self):
i = Investigation()
uberon = OntologySource(
name="UBERON",
description="Uber Anatomy Ontology",
version="216",
file="http://data.bioontology.org/ontologies/UBERON",
)
ncbitaxon = OntologySource(
name="NCBITAXON",
description="National Center for Biotechnology Information (NCBI) Organismal Classification",
version="2",
file="http://data.bioontology.org/ontologies/NCBITAXON",
)
i.ontology_source_references.append(uberon)
i.ontology_source_references.append(ncbitaxon)
s = Study(filename="s_pool.txt")
sample_collection_protocol = Protocol(
name="sample collection", protocol_type=OntologyAnnotation(term="sample collection")
)
s.protocols.append(sample_collection_protocol)
reference_descriptor_category = OntologyAnnotation(term="reference descriptor")
material_type_category = OntologyAnnotation(term="material type")
organism_category = OntologyAnnotation(term="organism")
source1 = Source(name="source1")
source1.characteristics = [
Characteristic(category=reference_descriptor_category, value="not applicable"),
Characteristic(category=material_type_category, value="specimen"),
Characteristic(
category=organism_category,
value=OntologyAnnotation(
term="Human", term_source=ncbitaxon, term_accession="http://purl.bioontology.org/ontology/STY/T016"
),
),
]
sample1 = Sample(name="sample1")
organism_part = OntologyAnnotation(term="organism part")
sample1.characteristics.append(
Characteristic(
category=organism_part,
value=OntologyAnnotation(
term="liver", term_source=uberon, term_accession="http://purl.obolibrary.org/obo/UBERON_0002107"
),
)
)
sample2 = Sample(name="sample2")
sample2.characteristics.append(
Characteristic(
category=organism_part,
value=OntologyAnnotation(
term="heart", term_source=uberon, term_accession="http://purl.obolibrary.org/obo/UBERON_0000948"
),
)
)
sample3 = Sample(name="sample3")
sample3.characteristics.append(
Characteristic(
category=organism_part,
value=OntologyAnnotation(
term="blood", term_source=uberon, term_accession="http://purl.obolibrary.org/obo/UBERON_0000178"
),
)
)
sample4 = Sample(name="sample4")
sample4.characteristics.append(
Characteristic(
category=organism_part,
value=OntologyAnnotation(
term="blood", term_source=uberon, term_accession="http://purl.obolibrary.org/obo/UBERON_0000178"
),
)
)
sample_collection_process = Process(executes_protocol=sample_collection_protocol)
sample_collection_process.inputs = [source1]
sample_collection_process.outputs = [sample1, sample2, sample3, sample4]
s.process_sequence = [sample_collection_process]
from isatools.model.v1 import _build_assay_graph
s.graph = _build_assay_graph(s.process_sequence)
i.studies = [s]
isatab.dump(i, self._tmp_dir)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, "s_pool.txt")),
open(os.path.join(self._tab_data_dir, "TEST-ISA-source-split", "s_TEST-Template1-Splitting.txt")),
)
)
def test_isatab_dump_source_sample_split(self):
i = Investigation()
uberon = OntologySource(
name='UBERON',
description="Uber Anatomy Ontology",
version='216',
file='http://data.bioontology.org/ontologies/UBERON')
ncbitaxon = OntologySource(
name='NCBITAXON',
description=
"National Center for Biotechnology Information (NCBI) Organismal Classification",
version='2',
file='http://data.bioontology.org/ontologies/NCBITAXON')
i.ontology_source_references.append(uberon)
i.ontology_source_references.append(ncbitaxon)
s = Study(filename='s_pool.txt')
sample_collection_protocol = Protocol(
name='sample collection',
protocol_type=OntologyAnnotation(term='sample collection'))
s.protocols.append(sample_collection_protocol)
reference_descriptor_category = OntologyAnnotation(
term='reference descriptor')
material_type_category = OntologyAnnotation(term='material type')
organism_category = OntologyAnnotation(term='organism')
source1 = Source(name='source1')
source1.characteristics = [
Characteristic(category=reference_descriptor_category,
value='not applicable'),
Characteristic(category=material_type_category, value='specimen'),
Characteristic(
category=organism_category,
value=OntologyAnnotation(
term='Human',
term_source=ncbitaxon,
term_accession=
'http://purl.bioontology.org/ontology/STY/T016')),
]
sample1 = Sample(name='sample1')
organism_part = OntologyAnnotation(term='organism part')
sample1.characteristics.append(
Characteristic(category=organism_part,
value=OntologyAnnotation(
term='liver',
term_source=uberon,
term_accession=
'http://purl.obolibrary.org/obo/UBERON_0002107',
)))
sample2 = Sample(name='sample2')
sample2.characteristics.append(
Characteristic(category=organism_part,
value=OntologyAnnotation(
term='heart',
term_source=uberon,
term_accession=
'http://purl.obolibrary.org/obo/UBERON_0000948',
)))
sample3 = Sample(name='sample3')
sample3.characteristics.append(
Characteristic(category=organism_part,
value=OntologyAnnotation(
term='blood',
term_source=uberon,
term_accession=
'http://purl.obolibrary.org/obo/UBERON_0000178',
)))
sample4 = Sample(name='sample4')
sample4.characteristics.append(
Characteristic(category=organism_part,
value=OntologyAnnotation(
term='blood',
term_source=uberon,
term_accession=
'http://purl.obolibrary.org/obo/UBERON_0000178',
)))
sample_collection_process = Process(
executes_protocol=sample_collection_protocol)
sample_collection_process.inputs = [source1]
sample_collection_process.outputs = [
sample1, sample2, sample3, sample4
]
s.process_sequence = [sample_collection_process]
from isatools.model.v1 import _build_assay_graph
s.graph = _build_assay_graph(s.process_sequence)
i.studies = [s]
isatab.dump(i, self._tmp_dir)
self.assertTrue(
assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 's_pool.txt')),
open(
os.path.join(self._tab_data_dir, 'TEST-ISA-source-split',
's_TEST-Template1-Splitting.txt'))))
def test_json2isatab_convert_source_split_study_table(self):
json2isatab.convert(open(os.path.join(self._json_data_dir, 'TEST-ISA-source-split.json')), self._tmp_dir)
self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 's_TEST-Template1-Splitting.txt')),
open(os.path.join(self._tab_data_dir, 'TEST-ISA-source-split',
's_TEST-Template1-Splitting.txt'))))
def test_assert_tab_content_equal_assay_table(self):
self.assertTrue(utils.assert_tab_content_equal(self.s_tab1, self.s_tab2))
def test_assert_tab_content_equal_investigation(self):
self.assertTrue(utils.assert_tab_content_equal(self.i_tab1, self.i_tab2))
def test_json2isatab_convert_bii_s_7_study_table(self):
json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-S-7', 'BII-S-7.json')), self._tmp_dir)
self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 's_BII-S-7.txt')),
open(os.path.join(self._tab_data_dir, 'BII-S-7', 's_BII-S-7.txt'))))
def test_json2isatab_convert_bii_s_7_investigation(self):
json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-S-7', 'BII-S-7.json')), self._tmp_dir,
i_file_name='i_matteo.txt')
self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 'i_matteo.txt')),
open(os.path.join(self._tab_data_dir, 'BII-S-7', 'i_matteo.txt'))))
def test_json2isatab_convert_bii_s_3_assay_table_Gx(self):
json2isatab.convert(open(os.path.join(self._json_data_dir, 'BII-S-3', 'BII-S-3.json')), self._tmp_dir)
self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 'a_gilbert-assay-Gx.txt')),
open(os.path.join(self._tab_data_dir, 'BII-S-3',
'a_gilbert-assay-Gx.txt'))))
def test_json2isatab_convert_sample_pool_assay_table(self):
json2isatab.convert(open(os.path.join(self._json_data_dir, 'TEST-ISA-sample-pool.json')), self._tmp_dir)
self.assertTrue(assert_tab_content_equal(
open(os.path.join(self._tmp_dir, 'a_test-template3-splitting_transcription_profiling_DNA_microarray.txt')),
open(os.path.join(self._tab_data_dir, 'TEST-ISA-sample-pool',
'a_test-template3-splitting_transcription_profiling_DNA_microarray.txt'))))
def test_json2isatab_convert_sample_pool_study_table(self):
json2isatab.convert(open(os.path.join(self._json_data_dir, 'TEST-ISA-sample-pool.json')), self._tmp_dir)
self.assertTrue(assert_tab_content_equal(open(os.path.join(self._tmp_dir, 's_TEST-Template3-Splitting.txt')),
open(os.path.join(self._tab_data_dir, 'TEST-ISA-sample-pool',
's_TEST-Template3-Splitting.txt'))))