def setUp(self):
self._json_data_dir = utils.JSON_DATA_DIR
self._sra_data_dir = utils.SRA_DATA_DIR
self._tmp_dir = tempfile.mkdtemp()
study_id = 'BII-S-7'
self._inv_obj = isajson.load(open(os.path.join(self._json_data_dir, study_id, study_id + '.json')))
self._study_sra_data_dir = os.path.join(self._sra_data_dir, study_id)
self._expected_submission_xml_obj = etree.fromstring(open(os.path.join(self._study_sra_data_dir, 'submission.xml'), 'rb').read())
self._expected_project_set_xml_obj = etree.fromstring(open(os.path.join(self._study_sra_data_dir, 'project_set.xml'),
'rb').read())
self._expected_sample_set_xml_obj = etree.fromstring(open(os.path.join(self._study_sra_data_dir, 'sample_set.xml'),
'rb').read())
self._expected_exp_set_xml_obj = etree.fromstring(open(os.path.join(self._study_sra_data_dir, 'experiment_set.xml'),
'rb').read())
self._expected_run_set_xml_obj = etree.fromstring(open(os.path.join(self._study_sra_data_dir, 'run_set.xml'),
'rb').read())
self._sra_default_config = {
"sra_broker": "",
"sra_center": "OXFORD",
"sra_project": "OXFORD",
"sra_lab": "Oxford e-Research Centre",
"sra_broker_inform_on_status": "*****@*****.**",
"sra_broker_inform_on_error": "*****@*****.**",
"sra_broker_contact_name": "PRS"
}
def convert(json_fp,
path,
config_dir=None,
sra_settings=None,
datafilehashes=None,
validate_first=True):
""" Converter for ISA-JSON to SRA.
:param json_fp: File pointer to ISA JSON input
:param path: Directory for output SRA XMLs to be written
:param config_dir: path to JSON configuration. If none, uses default
embedded in API
:param sra_settings: SRA settings dict
:param datafilehashes: Data files with hashes, in a dict
"""
if validate_first:
log.info("Validating input JSON before conversion")
report = isajson.validate(fp=json_fp,
config_dir=config_dir,
log_level=logging.ERROR)
if len(report.get('errors')) > 0:
log.fatal("Could not proceed with conversion as there are some "
"validation errors. Check log.")
return
log.info("Loading isajson {}".format(json_fp.name))
isa = isajson.load(fp=json_fp)
log.info("Exporting SRA to {}".format(path))
log.debug("Using SRA settings ".format(sra_settings))
sra.export(isa,
path,
sra_settings=sra_settings,
datafilehashes=datafilehashes)
def _make_investigation_instance(self, filename):
# Parse JSON file
fp = utf8_text_file_open(filename)
isa = isajson.load(fp)
return isa
def _make_investigation_instance(self, filename):
# Parse JSON file
with open(filename, newline='', encoding='utf8') as fp:
isa = isajson.load(fp)
return isa
def _make_investigation_instance(self, filename):
# Parse JSON file
fp = utf8_text_file_open(filename)
isa = isajson.load(fp)
return isa
def convert(source_json_fp, out_path):
""" Converter for ISA-JSON to MAGE-Tab.
:param source_json_fp: File descriptor of input ISA JSON file
:param out_path: Output path to write output MAGE-Tab to
"""
ISA = isajson.load(source_json_fp)
magetab.dump(ISA, out_path)
def test_json_load_and_dump_bii_s_3(self):
# Load into ISA objects
with open(os.path.join(utils.JSON_DATA_DIR, 'BII-S-3', 'BII-S-3.json')) as isajson_fp:
ISA = isajson.load(isajson_fp)
# Dump into ISA JSON from ISA objects
ISA_J = json.loads(json.dumps(ISA, cls=isajson.ISAJSONEncoder))
self.assertListEqual([s['filename'] for s in ISA_J['studies']], ['s_BII-S-3.txt']) # 1 studies in i_gilbert.txt
study_bii_s_3 = [s for s in ISA_J['studies'] if s['filename'] == 's_BII-S-3.txt'][0]
self.assertEqual(len(study_bii_s_3['materials']['sources']), 4) # 4 sources in s_BII-S-1.txt
self.assertEqual(len(study_bii_s_3['materials']['samples']), 4) # 4 study samples in s_BII-S-1.txt
self.assertEqual(len(study_bii_s_3['processSequence']), 4) # 4 study processes in s_BII-S-1.txt
self.assertListEqual([a['filename'] for a in study_bii_s_3['assays']], ['a_gilbert-assay-Gx.txt', 'a_gilbert-assay-Tx.txt']) # 2 assays in s_BII-S-1.txt
assay_gx = [a for a in study_bii_s_3['assays'] if a['filename'] == 'a_gilbert-assay-Gx.txt'][0]
self.assertEqual(len(assay_gx['materials']['samples']), 4) # 4 assay samples in a_gilbert-assay-Gx.txt
self.assertEqual(len(assay_gx['materials']['otherMaterials']), 4) # 4 other materials in a_gilbert-assay-Gx.txt
self.assertEqual(len(assay_gx['dataFiles']), 6) # 6 data files in a_gilbert-assay-Gx.txt
self.assertEqual(len(assay_gx['processSequence']), 18) # 18 processes in in a_gilbert-assay-Gx.txt
assay_tx = [a for a in study_bii_s_3['assays'] if a['filename'] == 'a_gilbert-assay-Tx.txt'][0]
self.assertEqual(len(assay_tx['materials']['samples']), 4) # 4 assay samples in a_gilbert-assay-Tx.txt
self.assertEqual(len(assay_tx['materials']['otherMaterials']), 4) # 4 other materials in a_gilbert-assay-Tx.txt
self.assertEqual(len(assay_tx['dataFiles']), 24) # 24 data files in a_gilbert-assay-Tx.txt
self.assertEqual(len(assay_tx['processSequence']), 36) # 36 processes in in a_gilbert-assay-Tx.txt
def test_json_load_and_dump_bii_s_3(self):
with open(os.path.join(self._json_data_dir, 'BII-S-3',
'BII-S-3.json')) as isajson_fp:
ISA = isajson.load(isajson_fp)
ISA_J = json.loads(json.dumps(ISA, cls=isajson.ISAJSONEncoder))
self.assertListEqual([s['filename'] for s in ISA_J['studies']],
['s_BII-S-3.txt'])
study_bii_s_3 = \
[s for s in ISA_J['studies'] if s['filename'] == 's_BII-S-3.txt'][0]
self.assertEqual(len(study_bii_s_3['materials']['sources']), 4)
self.assertEqual(len(study_bii_s_3['materials']['samples']), 4)
self.assertEqual(len(study_bii_s_3['processSequence']), 4)
self.assertListEqual(
[a['filename'] for a in study_bii_s_3['assays']],
['a_gilbert-assay-Gx.txt', 'a_gilbert-assay-Tx.txt'])
assay_gx = [
a for a in study_bii_s_3['assays']
if a['filename'] == 'a_gilbert-assay-Gx.txt'
][0]
self.assertEqual(len(assay_gx['materials']['samples']), 4)
self.assertEqual(len(assay_gx['materials']['otherMaterials']), 4)
self.assertEqual(len(assay_gx['dataFiles']), 6)
self.assertEqual(len(assay_gx['processSequence']), 18)
assay_tx = [
a for a in study_bii_s_3['assays']
if a['filename'] == 'a_gilbert-assay-Tx.txt'
][0]
self.assertEqual(len(assay_tx['materials']['samples']), 4)
self.assertEqual(len(assay_tx['materials']['otherMaterials']), 4)
self.assertEqual(len(assay_tx['dataFiles']), 24)
self.assertEqual(len(assay_tx['processSequence']), 36)
def convert(source_json_fp, target_fp):
""" Converter for ISA-JSON to SampleTab.
:param source_json_fp: File descriptor of input ISA JSON file
:param target_fp: File descriptor to write output SampleTab to (must be writeable)
"""
ISA = isajson.load(source_json_fp)
sampletab.dump(ISA, target_fp)
def convert(source_json_fp, out_path):
""" Converter for ISA-JSON to MAGE-Tab.
:param source_json_fp: File descriptor of input ISA JSON file
:param out_path: Output path to write output MAGE-Tab to
"""
log.info("loading isajson %s", source_json_fp.name)
ISA = isajson.load(source_json_fp)
log.info("dumping magetab %s", out_path)
magetab.dump(ISA, out_path)
def convert(source_json_fp, target_fp):
""" Converter for ISA-JSON to SampleTab.
:param source_json_fp: File descriptor of input ISA JSON file
:param target_fp: File descriptor to write output SampleTab to (must be writeable)
"""
log.info("loading isajson %s", source_json_fp.name)
ISA = isajson.load(source_json_fp)
log.info("dumping sampletab %s", target_fp.name)
sampletab.dump(ISA, target_fp)
def test_json_load_and_dump_bii_i_1(self):
# Load into ISA objects
with open(os.path.join(utils.JSON_DATA_DIR, 'BII-I-1', 'BII-I-1.json')) as isajson_fp:
ISA = isajson.load(isajson_fp)
# Dump into ISA JSON from ISA objects
ISA_J = json.loads(json.dumps(ISA, cls=isajson.ISAJSONEncoder))
self.assertListEqual([s['filename'] for s in ISA_J['studies']], ['s_BII-S-1.txt', 's_BII-S-2.txt']) # 2 studies in i_investigation.txt
study_bii_s_1 = [s for s in ISA_J['studies'] if s['filename'] == 's_BII-S-1.txt'][0]
self.assertEqual(len(study_bii_s_1['materials']['sources']), 18) # 18 sources in s_BII-S-1.txt
self.assertEqual(len(study_bii_s_1['materials']['samples']), 164) # 164 study samples in s_BII-S-1.txt
self.assertEqual(len(study_bii_s_1['processSequence']), 18) # 18 study processes in s_BII-S-1.txt
self.assertListEqual([a['filename'] for a in study_bii_s_1['assays']], ['a_proteome.txt', 'a_metabolome.txt', 'a_transcriptome.txt']) # 2 assays in s_BII-S-1.txt
assay_proteome = [a for a in study_bii_s_1['assays'] if a['filename'] == 'a_proteome.txt'][0]
self.assertEqual(len(assay_proteome['materials']['samples']), 8) # 8 assay samples in a_proteome.txt
self.assertEqual(len(assay_proteome['materials']['otherMaterials']), 19) # 19 other materials in a_proteome.txt
self.assertEqual(len(assay_proteome['dataFiles']), 7) # 7 data files in a_proteome.txt
self.assertEqual(len(assay_proteome['processSequence']), 25) # 25 processes in in a_proteome.txt
assay_metabolome = [a for a in study_bii_s_1['assays'] if a['filename'] == 'a_metabolome.txt'][0]
self.assertEqual(len(assay_metabolome['materials']['samples']), 92) # 92 assay samples in a_metabolome.txt
self.assertEqual(len(assay_metabolome['materials']['otherMaterials']), 92) # 92 other materials in a_metabolome.txt
self.assertEqual(len(assay_metabolome['dataFiles']), 111) # 111 data files in a_metabolome.txt
self.assertEqual(len(assay_metabolome['processSequence']), 203) # 203 processes in in a_metabolome.txt
assay_transcriptome = [a for a in study_bii_s_1['assays'] if a['filename'] == 'a_transcriptome.txt'][0]
self.assertEqual(len(assay_transcriptome['materials']['samples']), 48) # 48 assay samples in a_transcriptome.txt
self.assertEqual(len(assay_transcriptome['materials']['otherMaterials']), 96) # 96 other materials in a_transcriptome.txt
self.assertEqual(len(assay_transcriptome['dataFiles']), 49) # 49 data files in a_transcriptome.txt
self.assertEqual(len(assay_transcriptome['processSequence']), 193) # 203 processes in in a_transcriptome.txt
study_bii_s_2 = [s for s in ISA_J['studies'] if s['filename'] == 's_BII-S-2.txt'][0]
self.assertEqual(len(study_bii_s_2['materials']['sources']), 1) # 1 sources in s_BII-S-2.txt
self.assertEqual(len(study_bii_s_2['materials']['samples']), 2) # 2 study samples in s_BII-S-2.txt
self.assertEqual(len(study_bii_s_2['processSequence']), 1) # 1 study processes in s_BII-S-2.txt
self.assertEqual(len(study_bii_s_2['assays']), 1) # 1 assays in s_BII-S-2.txt
self.assertListEqual([a['filename'] for a in study_bii_s_2['assays']], ['a_microarray.txt']) # 1 assays in s_BII-S-2.txt
assay_microarray = [a for a in study_bii_s_2['assays'] if a['filename'] == 'a_microarray.txt'][0]
self.assertEqual(len(assay_microarray['materials']['samples']), 2) # 2 assay samples in a_microarray.txt
self.assertEqual(len(assay_microarray['materials']['otherMaterials']), 28) # 28 other materials in a_microarray.txt
self.assertEqual(len(assay_microarray['dataFiles']), 15) # 15 data files in a_microarray.txt
self.assertEqual(len(assay_microarray['processSequence']), 45) # 45 processes in in a_microarray.txt
def test_detect_graph_process_pooling(self):
with open(os.path.join(
test_utils.JSON_DATA_DIR, 'MTBLS1', 'MTBLS1.json')) as \
isajson_fp:
ISA = isajson.load(isajson_fp)
for study in ISA.studies:
utils.detect_graph_process_pooling(study.graph)
for assay in study.assays:
pooling_list = utils.detect_graph_process_pooling(
assay.graph)
self.assertListEqual(
sorted(pooling_list),
sorted(['#process/Extraction1', '#process/NMR_assay1']))
def convert(json_fp,
path,
i_file_name='i_investigation.txt',
config_dir=isajson.default_config_dir,
validate_first=True):
"""
Converter for ISA JSON to ISA Tab. Currently only converts
investigation file contents
:param json_fp: File pointer to ISA JSON input
:param path: Directory to ISA tab output
:param i_file_name: Investigation file name, default is
i_investigation.txt
:param config_dir: Directory to config directory
:param validate_first: Validate JSON before conversion, default is True
Example usage:
Read from a JSON and write to an investigation file, make sure to
create/open relevant Python file objects.
from isatools.convert import json2isatab
json_file = open('BII-I-1.json', 'r')
tab_file = open('i_investigation.txt', 'w')
json2isatab.convert(json_file, path)
"""
if validate_first:
log.info("Validating input JSON before conversion")
report = isajson.validate(fp=json_fp,
config_dir=config_dir,
log_level=logging.ERROR)
if len(report['errors']) > 0:
log.fatal("Could not proceed with conversion as there are some "
"fatal validation errors. Check log.")
return
json_fp.seek(0) # reset file pointer after validation
log.info("Loading ISA-JSON from %s", json_fp.name)
isa_obj = isajson.load(fp=json_fp)
log.info("Dumping ISA-Tab to %s", path)
log.debug("Using configuration from %s", config_dir)
isatab.dump(isa_obj=isa_obj, output_path=path, i_file_name=i_file_name)
# copy data files across from source directory where JSON is located
log.info("Copying data files from source to target")
for file in [
f for f in os.listdir(os.path.dirname(json_fp.name))
if not (f.endswith('.txt') and (f.startswith('i_') or f.startswith(
's_') or f.startswith('a_'))) and not (f.endswith('.json'))
]:
filepath = os.path.join(os.path.dirname(json_fp.name), file)
if os.path.isfile(filepath):
log.debug("Copying %s to %s", filepath, path)
shutil.copy(filepath, path)
def convert2(json_fp, path, config_dir=None, sra_settings=None, datafilehashes=None, validate_first=True):
""" (New) 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. If none, uses default embedded in API
:param sra_settings: SRA settings dict
:param datafilehashes: Data files with hashes, in a dict
"""
if validate_first:
log_msg_stream = isajson.validate(fp=json_fp, config_dir=config_dir, log_level=logging.WARNING)
if '(E)' in log_msg_stream.getvalue():
logger.fatal("Could not proceed with conversion as there are some validation errors. Check log.")
return
i = isajson.load(fp=json_fp)
sra.export(i, path, sra_settings=sra_settings, datafilehashes=datafilehashes)
def convert(json_fp, path, config_dir=None, sra_settings=None, datafilehashes=None, validate_first=True):
""" (New) 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. If none, uses default embedded in API
:param sra_settings: SRA settings dict
:param datafilehashes: Data files with hashes, in a dict
"""
if validate_first:
log_msg_stream = isajson.validate(fp=json_fp, config_dir=config_dir, log_level=logging.WARNING)
if '(E)' in log_msg_stream.getvalue():
logger.fatal("Could not proceed with conversion as there are some validation errors. Check log.")
return
i = isajson.load(fp=json_fp)
sra.export(i, path, sra_settings=sra_settings, datafilehashes=datafilehashes)
def test_detect_graph_process_pooling_batch_on_mtbls(self):
for i in range(1, 1):
try:
J = MTBLS.getj('MTBLS{}'.format(i))
ISA = isajson.load(StringIO(json.dumps(J)))
for study in ISA.studies:
utils.detect_graph_process_pooling(study.graph)
for assay in study.assays:
utils.detect_graph_process_pooling(assay.graph)
except IOError:
log.error('IO Error, skipping...')
except KeyError:
log.error('KeyError, skipping...')
except AttributeError:
log.error('AttributeError, skipping...')
except ValidationError:
log.error('jsonschema ValidationError, skipping...')
def test_json_load_and_dump_bii_s_7(self):
# Load into ISA objects
with open(os.path.join(utils.JSON_DATA_DIR, 'BII-S-7',
'BII-S-7.json')) as isajson_fp:
ISA = isajson.load(isajson_fp)
# Dump into ISA JSON from ISA objects
ISA_J = json.loads(json.dumps(ISA, cls=isajson.ISAJSONEncoder))
self.assertListEqual(
[s['filename'] for s in ISA_J['studies']],
['s_BII-S-7.txt']) # 1 studies in i_gilbert.txt
study_bii_s_7 = [
s for s in ISA_J['studies'] if s['filename'] == 's_BII-S-7.txt'
][0]
self.assertEqual(len(study_bii_s_7['materials']['sources']),
29) # 29 sources in s_BII-S-1.txt
self.assertEqual(len(study_bii_s_7['materials']['samples']),
29) # 29 study samples in s_BII-S-1.txt
self.assertEqual(len(study_bii_s_7['processSequence']),
29) # 29 study processes in s_BII-S-1.txt
self.assertListEqual(
[a['filename'] for a in study_bii_s_7['assays']],
['a_matteo-assay-Gx.txt']) # 1 assays in s_BII-S-1.txt
assay_gx = [
a for a in study_bii_s_7['assays']
if a['filename'] == 'a_matteo-assay-Gx.txt'
][0]
self.assertEqual(len(assay_gx['materials']['samples']),
29) # 29 assay samples in a_matteo-assay-Gx.txt
self.assertEqual(len(assay_gx['materials']['otherMaterials']),
29) # 29 other materials in a_matteo-assay-Gx.txt
self.assertEqual(len(assay_gx['dataFiles']),
29) # 29 data files in a_matteo-assay-Gx.txt
self.assertEqual(len(assay_gx['processSequence']),
116) # 116 processes in in a_matteo-assay-Gx.txt
def setUp(self):
self._json_data_dir = utils.JSON_DATA_DIR
self._sra_data_dir = utils.SRA_DATA_DIR
self._tmp_dir = tempfile.mkdtemp()
study_id = 'BII-S-7'
with open(
os.path.join(self._json_data_dir, study_id,
study_id + '.json')) as json_fp:
self._inv_obj = isajson.load(json_fp)
self._study_sra_data_dir = os.path.join(self._sra_data_dir, study_id)
with open(os.path.join(self._study_sra_data_dir, 'submission.xml'),
'rb') as sub_fp:
self._expected_submission_xml_obj = etree.fromstring(sub_fp.read())
with open(os.path.join(self._study_sra_data_dir, 'project_set.xml'),
'rb') as ps_fp:
self._expected_project_set_xml_obj = etree.fromstring(ps_fp.read())
with open(os.path.join(self._study_sra_data_dir, 'sample_set.xml'),
'rb') as ss_fp:
self._expected_sample_set_xml_obj = etree.fromstring(ss_fp.read())
with open(os.path.join(self._study_sra_data_dir, 'experiment_set.xml'),
'rb') as es_fp:
self._expected_exp_set_xml_obj = etree.fromstring(es_fp.read())
with open(os.path.join(self._study_sra_data_dir, 'run_set.xml'),
'rb') as rs_fp:
self._expected_run_set_xml_obj = etree.fromstring(rs_fp.read())
self._sra_default_config = {
"sra_broker": "",
"sra_center": "OXFORD",
"sra_project": "OXFORD",
"sra_lab": "Oxford e-Research Centre",
"sra_broker_inform_on_status": "*****@*****.**",
"sra_broker_inform_on_error": "*****@*****.**",
"sra_broker_contact_name": "PRS"
}
def test_json_load_and_dump_bii_s_7(self):
# Load into ISA objects
with open(os.path.join(self._json_data_dir, 'BII-S-7',
'BII-S-7.json')) as isajson_fp:
ISA = isajson.load(isajson_fp)
ISA_J = json.loads(json.dumps(ISA, cls=isajson.ISAJSONEncoder))
self.assertListEqual([s['filename'] for s in ISA_J['studies']],
['s_BII-S-7.txt'])
study_bii_s_7 = \
[s for s in ISA_J['studies'] if s['filename'] == 's_BII-S-7.txt'][0]
self.assertEqual(len(study_bii_s_7['materials']['sources']), 29)
self.assertEqual(len(study_bii_s_7['materials']['samples']), 29)
self.assertEqual(len(study_bii_s_7['processSequence']), 29)
self.assertListEqual(
[a['filename'] for a in study_bii_s_7['assays']],
['a_matteo-assay-Gx.txt'])
assay_gx = [
a for a in study_bii_s_7['assays']
if a['filename'] == 'a_matteo-assay-Gx.txt'
][0]
self.assertEqual(len(assay_gx['materials']['samples']), 29)
self.assertEqual(len(assay_gx['materials']['otherMaterials']), 29)
self.assertEqual(len(assay_gx['dataFiles']), 29)
self.assertEqual(len(assay_gx['processSequence']), 116)
def test_json_load_and_dump_bii_i_1(self):
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as isajson_fp:
ISA = isajson.load(isajson_fp)
ISA_J = json.loads(json.dumps(ISA, cls=isajson.ISAJSONEncoder))
self.assertListEqual([s['filename'] for s in ISA_J['studies']],
['s_BII-S-1.txt', 's_BII-S-2.txt'])
study_bii_s_1 = \
[s for s in ISA_J['studies'] if s['filename'] == 's_BII-S-1.txt'][0]
self.assertEqual(len(study_bii_s_1['materials']['sources']), 18)
self.assertEqual(len(study_bii_s_1['materials']['samples']), 164)
self.assertEqual(len(study_bii_s_1['processSequence']), 18)
self.assertListEqual(
[a['filename'] for a in study_bii_s_1['assays']],
['a_proteome.txt', 'a_metabolome.txt', 'a_transcriptome.txt'])
assay_proteome = [
a for a in study_bii_s_1['assays']
if a['filename'] == 'a_proteome.txt'
][0]
self.assertEqual(len(assay_proteome['materials']['samples']), 8)
self.assertEqual(
len(assay_proteome['materials']['otherMaterials']), 19)
self.assertEqual(len(assay_proteome['dataFiles']), 7)
self.assertEqual(len(assay_proteome['processSequence']), 25)
assay_metabolome = [
a for a in study_bii_s_1['assays']
if a['filename'] == 'a_metabolome.txt'
][0]
self.assertEqual(len(assay_metabolome['materials']['samples']), 92)
self.assertEqual(
len(assay_metabolome['materials']['otherMaterials']), 92)
self.assertEqual(len(assay_metabolome['dataFiles']), 111)
self.assertEqual(len(assay_metabolome['processSequence']), 203)
assay_transcriptome = [
a for a in study_bii_s_1['assays']
if a['filename'] == 'a_transcriptome.txt'
][0]
self.assertEqual(len(assay_transcriptome['materials']['samples']),
48)
self.assertEqual(
len(assay_transcriptome['materials']['otherMaterials']), 96)
self.assertEqual(len(assay_transcriptome['dataFiles']), 49)
self.assertEqual(len(assay_transcriptome['processSequence']), 193)
study_bii_s_2 = \
[s for s in ISA_J['studies'] if s['filename'] == 's_BII-S-2.txt'][0]
self.assertEqual(len(study_bii_s_2['materials']['sources']), 1)
self.assertEqual(len(study_bii_s_2['materials']['samples']), 2)
self.assertEqual(len(study_bii_s_2['processSequence']), 1)
self.assertEqual(len(study_bii_s_2['assays']), 1)
self.assertListEqual(
[a['filename'] for a in study_bii_s_2['assays']],
['a_microarray.txt'])
assay_microarray = [
a for a in study_bii_s_2['assays']
if a['filename'] == 'a_microarray.txt'
][0]
self.assertEqual(len(assay_microarray['materials']['samples']), 2)
self.assertEqual(
len(assay_microarray['materials']['otherMaterials']), 28)
self.assertEqual(len(assay_microarray['dataFiles']), 15)
self.assertEqual(len(assay_microarray['processSequence']), 45)
