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_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_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_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_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_3_study_table(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, 's_BII-S-3.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-S-3',
's_BII-S-3.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):
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,
'a_matteo-assay-Gx.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-S-7',
'a_matteo-assay-Gx.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_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_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_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_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_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 convert(json_fp, path, config_dir=None):
""" Converter for ISA JSON to SRA.
:param json_fp: File pointer to ISA JSON input
:param path: Directory for output to be written
:param config_dir: path to JSON configuration
"""
from isatools.convert import json2isatab, isatab2sra
json2isatab.convert(json_fp=json_fp, path=path, config_dir=config_dir)
isatab2sra.create_sra(path, path)
for f in glob(path + '/*.txt'): # remove generated isatab files
os.remove(f)
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_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_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_transcriptome(self):
# FIXME: Has inserted Protocol REFs but Array Design REF, Scan Name, 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_transcriptome.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_transcriptome.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
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_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_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_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_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 post(self):
response = Response(status=415)
if request.mimetype == "application/json":
tmp_file = str(uuid.uuid4()) + ".json"
tmp_dir = _create_temp_dir()
try:
# Write request data to file
file_path = _write_request_data(request, tmp_dir, tmp_file)
if file_path is None:
return Response(500)
json2isatab.convert(open(file_path), tmp_dir)
os.remove(file_path)
memf = io.BytesIO()
with zipfile.ZipFile(memf, 'w') as zf:
for file in os.listdir(tmp_dir):
zf.write(os.path.join(tmp_dir, file), file)
memf.seek(0)
response = send_file(memf, mimetype='application/zip')
finally:
# cleanup generated directories
shutil.rmtree(tmp_dir, ignore_errors=True)
return response
import sys
import os
src_json = sys.argv[1]
target_dir = sys.argv[2]
try:
from isatools.convert import json2isatab
except ImportError as e:
raise RuntimeError("Could not import isatools package")
json2isatab.convert(open(src_json), target_dir)
#!/usr/bin/env python3
import sys
import os
src_json = sys.argv[1]
try:
from isatools.convert import json2isatab
except ImportError as e:
raise RuntimeError('Could not import isatools package')
if not os.path.exists(src_json):
print('File path to ISA-JSON file \'{}\' does not exist'.format(src_json))
sys.exit(0)
with open(src_json, encoding='utf-8') as in_fp:
json2isatab.convert(
json_fp=in_fp, path=os.path.dirname(src_json), validate_first=False)
def test_json2isatab_validate_first(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=True)
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_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'))))
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_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 main(argv=None):
"""Run **isatools** from the command line
Arguments
argv (list, optional): the list of arguments to run isatools
with (if None, then sys.argv is used) [default: None]
"""
p = argparse.ArgumentParser(
prog=__name__,
formatter_class=argparse.RawDescriptionHelpFormatter,
description=
'''Create, convert, and manipulate ISA-formatted metadata''',
usage='isatools -c COMMAND [options]',
)
p.add_argument('-c',
dest='cmd',
help='isatools API command to run',
required=True,
choices=[
'isatab2json', 'json2isatab', 'sampletab2isatab',
'sampletab2json'
])
p.add_argument('-i',
dest='in_path',
help='in (files or directory will be read from here)',
required=True)
p.add_argument(
'-o',
dest='out_path',
help=
'out (file will be written out here or written to directory if ISA-Tab '
'archive out)',
required=True)
p.add_argument('--version',
action='version',
version='isatools {}'.format("0.7"))
p.add_argument('-v',
dest='verbose',
help="show more output",
action='store_true',
default=False)
args = p.parse_args(argv or sys.argv[1:])
if args.verbose:
print("{} input: {}".format(os.linesep, args.in_path))
print("output: {}".format(args.out_path))
if args.cmd == 'isatab2json':
from isatools.convert import isatab2json
J = isatab2json.convert(args.in_path)
with open(args.out_path, 'w') as out_fp:
json.dump(J, out_fp)
elif args.cmd == 'json2isatab':
from isatools.convert import json2isatab
with open(args.in_path) as in_fp:
json2isatab.convert(in_fp, args.out_path)
elif args.cmd == 'sampletab2isatab':
from isatools.convert import sampletab2isatab
with open(args.in_path) as in_fp:
sampletab2isatab.convert(in_fp, args.out_path)
elif args.cmd == 'sampletab2json':
from isatools.convert import sampletab2json
with open(args.in_path) as in_fp:
with open(args.out_path, 'w') as out_fp:
sampletab2json.convert(in_fp, out_fp)
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'))))
