def test_import_bii_s_7(self):
test_case = 'BII-S-7'
json_expected = json.load(
open(
os.path.join(utils.JSON_DATA_DIR, test_case,
test_case + '.json')))
from isatools.sampledata import bii_s_7
utils.assert_json_equal(json_expected, bii_s_7.json)
def test_isatab2json_convert_charac_param_factor(self):
test_case = 'TEST-ISA-charac-param-factor'
actual_json = isatab2json.convert(
os.path.join(self._tab_data_dir, test_case), self.identifier_type)
expected_json = json.load(
open(os.path.join(self._json_data_dir, test_case + '.json')))
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_isatab2json_convert_sample_pool(self):
test_case = 'TEST-ISA-sample-pool'
actual_json = isatab2json.convert(
os.path.join(self._tab_data_dir, test_case), self.identifier_type)
expected_json = json.load(
open(os.path.join(self._json_data_dir, test_case + '.json')))
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_isatab2json_convert_source_split_with_error(self):
test_case = 'TEST-ISA-source-split-with-error'
actual_json = isatab2json.convert(
os.path.join(self._tab_data_dir, test_case), self.identifier_type)
expected_json = json.load(
open(os.path.join(self._json_data_dir, test_case + '.json')))
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_json2isatab_isatab2json_2way_convert_sample_pool(self):
test_case = 'TEST-ISA-sample-pool'
test_json = open(os.path.join(self._json_data_dir, test_case + '.json'))
json2isatab.convert(test_json, self._tmp_dir, validate_first=False)
test_json.seek(0) # reset pointer
expected_json = json.load(test_json)
actual_json = isatab2json.convert(self._tmp_dir, validate_first=False)
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_json2isatab_isatab2json_2way_convert_sample_pool(self):
test_case = 'TEST-ISA-sample-pool'
test_json = open(os.path.join(self._json_data_dir, test_case + '.json'))
json2isatab.convert(test_json, self._tmp_dir)
test_json.seek(0) # reset pointer
expected_json = json.load(test_json)
actual_json = isatab2json.convert(self._tmp_dir)
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_isatab2cedar_convert_mtbls3(self):
test_case = 'MTBLS3'
isa2cedar = ISATab2CEDAR("http://www.isa-tools.org/")
isa2cedar.createCEDARjson(os.path.join(self._tab_data_dir, test_case), self._tmp_dir, True)
expected_json = json.load(open(os.path.join(self._json_data_dir, 'cedar', test_case + '.json')))
actual_json = json.load(open(os.path.join(self._tmp_dir, test_case + '.json')))
utils.strip_ids(expected_json)
utils.strip_ids(actual_json)
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_isatab2json_convert_mtbls1(self):
test_case = 'MTBLS1'
actual_json = isatab2json.convert(
os.path.join(self._tab_data_dir, test_case), self.identifier_type)
expected_json = json.load(
open(
os.path.join(self._json_data_dir, test_case,
test_case + '.json')))
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_isatab2json_convert_sample_pool(self):
test_case = 'TEST-ISA-sample-pool'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir,
test_case),
validate_first=False)
with open(os.path.join(self._json_data_dir,
test_case + '.json')) as expected_file:
expected_json = json.load(expected_file)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2json_convert_charac_param_factor(self):
test_case = 'TEST-ISA-charac-param-factor'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir,
test_case),
validate_first=False)
with open(os.path.join(self._json_data_dir,
test_case + '.json')) as expected_file:
expected_json = json.load(expected_file)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2json_convert_source_split_with_error(self):
test_case = 'TEST-ISA-source-split-with-error'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir,
test_case),
validate_first=False)
with open(os.path.join(self._json_data_dir,
test_case + '.json')) as expected_file:
expected_json = json.load(expected_file)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2json_convert_bii_s_7(self):
test_case = 'BII-S-7'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir,
test_case),
validate_first=False)
with open(
os.path.join(self._json_data_dir, test_case,
test_case + '.json')) as expected_file:
expected_json = json.load(expected_file)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2cedar_convert_mtbls1(self):
test_case = 'MTBLS1'
isa2cedar = ISATab2CEDAR("http://www.isa-tools.org/")
isa2cedar.createCEDARjson(os.path.join(self._tab_data_dir, test_case),
self._tmp_dir, True)
with open(os.path.join(self._json_data_dir, 'cedar', test_case + '.json')) as expected_file, \
open(os.path.join(self._tmp_dir, '1425901783014' + '.json')) as actual_file:
expected_json = json.load(expected_file)
actual_json = json.load(actual_file)
utils.strip_ids(expected_json)
utils.strip_ids(actual_json)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2cedar_convert_charac_param_factor(self):
test_case = 'TEST-ISA-charac-param-factor'
isa2cedar = ISATab2CEDAR("http://www.isa-tools.org/")
isa2cedar.createCEDARjson(os.path.join(self._tab_data_dir, test_case),
self._tmp_dir, True)
with open(os.path.join(self._json_data_dir, 'cedar', test_case + '.json')) as expected_file, \
open(os.path.join(self._tmp_dir, test_case + '.json')) as actual_file:
expected_json = json.load(expected_file)
actual_json = json.load(actual_file)
utils.strip_ids(expected_json)
utils.strip_ids(actual_json)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_json2isatab_isatab2json_2way_convert_source_split(self):
test_case = 'TEST-ISA-source-split'
test_json = open(os.path.join(self._json_data_dir, test_case + '.json'))
json2isatab.convert(test_json, self._tmp_dir)
test_json.seek(0) # reset pointer
expected_json = json.load(test_json)
actual_json = isatab2json.convert(self._tmp_dir)
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
# def test_json2isatab_isatab2json_2way_convert_bii_i_1(self):
# # FIXME: Get error in isatab2json.createUnitsCategories
# # json_item.update(self.createOntologyAnnotation(value_attributes.Unit, value_attributes.Term_Source_REF, value_attributes.Term_Accession_Number))
# # AttributeError: 'Attrs' object has no attribute 'Term_Source_REF'
# # Are Units always OntologyAnnotations? (i.e. Unit column alway accompanied by Term Accession and
# # Term Source REF?
# test_case = 'BII-I-1'
# test_json = open(os.path.join(self._json_data_dir, test_case, test_case + '.json'))
# json2isatab.convert(test_json, self._tmp_dir)
# test_json.seek(0) # reset pointer
# expected_json = json.load(test_json)
# actual_json = isatab2json.convert(self._tmp_dir)
# self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
#
# def test_json2isatab_isatab2json_2way_convert_bii_s_3(self):
# # FIXME: Get error in isatab2json.createUnitsCategories
# # json_item.update(self.createOntologyAnnotation(value_attributes.Unit, value_attributes.Term_Source_REF, value_attributes.Term_Accession_Number))
# # AttributeError: 'Attrs' object has no attribute 'Term_Source_REF'
# # Are Units always OntologyAnnotations? (i.e. Unit column alway accompanied by Term Accession and
# # Term Source REF? If so, related to below bii_s_7 error
# test_case = 'BII-S-3'
# test_json = open(os.path.join(self._json_data_dir, test_case, test_case + '.json'))
# json2isatab.convert(test_json, self._tmp_dir)
# test_json.seek(0) # reset pointer
# expected_json = json.load(test_json)
# actual_json = isatab2json.convert(self._tmp_dir)
# self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
#
# def test_json2isatab_isatab2json_2way_convert_bii_s_7(self):
# # FIXME: It reports a big diff because when doing json2isatab, if Term Accession and Term Source REF columns
# # are empty it strips them out. When going back from isatab2json, it converts as string and not
# # OntologyAnnotation since there is no extra info to be able to cast back to original
# test_case = 'BII-S-7'
# test_json = open(os.path.join(self._json_data_dir, test_case, test_case + '.json'))
# json2isatab.convert(test_json, self._tmp_dir)
# test_json.seek(0) # reset pointer
# expected_json = json.load(test_json)
# actual_json = isatab2json.convert(self._tmp_dir)
# self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_json2isatab_isatab2json_2way_convert_source_split(self):
test_case = 'TEST-ISA-source-split'
test_json = open(os.path.join(self._json_data_dir, test_case + '.json'))
json2isatab.convert(test_json, self._tmp_dir, validate_first=False)
test_json.seek(0) # reset pointer
expected_json = json.load(test_json)
actual_json = isatab2json.convert(self._tmp_dir, validate_first=False)
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
# def test_json2isatab_isatab2json_2way_convert_bii_i_1(self):
# # FIXME: Get error in isatab2json.createUnitsCategories
# # json_item.update(self.createOntologyAnnotation(value_attributes.Unit, value_attributes.Term_Source_REF, value_attributes.Term_Accession_Number))
# # AttributeError: 'Attrs' object has no attribute 'Term_Source_REF'
# # Are Units always OntologyAnnotations? (i.e. Unit column alway accompanied by Term Accession and
# # Term Source REF?
# test_case = 'BII-I-1'
# test_json = open(os.path.join(self._json_data_dir, test_case, test_case + '.json'))
# json2isatab.convert(test_json, self._tmp_dir)
# test_json.seek(0) # reset pointer
# expected_json = json.load(test_json)
# actual_json = isatab2json.convert(self._tmp_dir)
# self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
#
# def test_json2isatab_isatab2json_2way_convert_bii_s_3(self):
# # FIXME: Get error in isatab2json.createUnitsCategories
# # json_item.update(self.createOntologyAnnotation(value_attributes.Unit, value_attributes.Term_Source_REF, value_attributes.Term_Accession_Number))
# # AttributeError: 'Attrs' object has no attribute 'Term_Source_REF'
# # Are Units always OntologyAnnotations? (i.e. Unit column alway accompanied by Term Accession and
# # Term Source REF? If so, related to below bii_s_7 error
# test_case = 'BII-S-3'
# test_json = open(os.path.join(self._json_data_dir, test_case, test_case + '.json'))
# json2isatab.convert(test_json, self._tmp_dir)
# test_json.seek(0) # reset pointer
# expected_json = json.load(test_json)
# actual_json = isatab2json.convert(self._tmp_dir)
# self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
#
# def test_json2isatab_isatab2json_2way_convert_bii_s_7(self):
# # FIXME: It reports a big diff because when doing json2isatab, if Term Accession and Term Source REF columns
# # are empty it strips them out. When going back from isatab2json, it converts as string and not
# # OntologyAnnotation since there is no extra info to be able to cast back to original
# test_case = 'BII-S-7'
# test_json = open(os.path.join(self._json_data_dir, test_case, test_case + '.json'))
# json2isatab.convert(test_json, self._tmp_dir)
# test_json.seek(0) # reset pointer
# expected_json = json.load(test_json)
# actual_json = isatab2json.convert(self._tmp_dir)
# self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_import_bii_s_7(self):
test_case = "BII-S-7"
json_expected = json.load(open(os.path.join(utils.JSON_DATA_DIR, test_case, test_case + ".json")))
from isatools.sampledata import bii_s_7
utils.assert_json_equal(json_expected, bii_s_7.json)
def test_isatab2json_convert_mtbls1(self):
test_case = "MTBLS1"
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir, test_case), self.identifier_type)
expected_json = json.load(open(os.path.join(self._json_data_dir, test_case, test_case + ".json")))
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_isatab2json_convert_source_split_with_error(self):
test_case = "TEST-ISA-source-split-with-error"
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir, test_case), self.identifier_type)
expected_json = json.load(open(os.path.join(self._json_data_dir, test_case + ".json")))
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_isatab2json_convert_sample_pool(self):
test_case = "TEST-ISA-sample-pool"
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir, test_case), self.identifier_type)
expected_json = json.load(open(os.path.join(self._json_data_dir, test_case + ".json")))
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_isatab2json_convert_charac_param_factor(self):
test_case = "TEST-ISA-charac-param-factor"
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir, test_case), self.identifier_type)
expected_json = json.load(open(os.path.join(self._json_data_dir, test_case + ".json")))
self.assertTrue(utils.assert_json_equal(expected_json, actual_json))
def test_assert_json_equal(self):
self.assertTrue(utils.assert_json_equal(self.j1, self.j2))
self.assertFalse(utils.assert_json_equal(self.j1, self.j3))