def get_isa_json(self, study_id, api_key, study_location=None):
"""
Get an ISA-API Investigation object reading directly from the ISA-Tab files
:param study_id: MTBLS study identifier
:param api_key: User API key for accession check
:param study_location: The filesystem location of the study
:return: an ISA-API Investigation object
"""
start = time.time()
if study_location is None:
logger.info("Study location is not set, will have load study from filesystem")
path = self.wsc.get_study_location(study_id, api_key)
else:
logger.info("Study location is: " + study_location)
path = study_location
# try the new parser first
isa_json = None
try:
isa_json = isatab2json.convert(path, validate_first=False, use_new_parser=True)
except Exception: # on failure, use the old one
try:
isa_json = isatab2json.convert(path, validate_first=False, use_new_parser=False)
except Exception:
# if it fails too
if isa_json is None:
abort(500)
else:
logger.info('... get_isa_json() processing (I): %s sec.', time.time() - start)
return isa_json
else:
logger.info('... get_isa_json() processing (II): %s sec.', time.time() - start)
return isa_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_isatab2json_convert_sample_pool_with_error(self):
test_case = 'TEST-ISA-sample-pool-with-error'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir, test_case),
validate_first=False,
use_new_parser=True)
json.dump(actual_json, open(os.path.join(self._tmp_dir, 'isa.json'), 'w'))
with open(os.path.join(self._tmp_dir, 'isa.json')) as actual_json:
report = isajson.validate(actual_json)
self.assertEqual(len(report['errors']), 0)
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_isatab2json_convert_mtbls3(self):
test_case = 'MTBLS3'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir, test_case),
validate_first=False,
use_new_parser=True)
json.dump(actual_json, open(os.path.join(self._tmp_dir, 'isa.json'), 'w'))
with open(os.path.join(self._tmp_dir, 'isa.json')) as actual_json:
report = isajson.validate(actual_json)
self.assertEqual(len(report['errors']), 0)
def test_isatab2json_convert_bii_s_3(self):
test_case = 'BII-S-3'
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_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_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_repeated_measure(self):
test_case = 'TEST-ISA-repeated-measure'
actual_json = isatab2json.convert(
os.path.join(self._tab_data_dir, test_case), validate_first=False,
use_new_parser=True)
with open(os.path.join(self._tmp_dir, 'isa.json'), 'w') as out_fp:
json.dump(actual_json, out_fp)
with open(os.path.join(self._tmp_dir, 'isa.json')) as actual_json:
report = isajson.validate(actual_json)
self.assertEqual(len(report['errors']), 0)
def get_isa_json(self, study_id, api_key, study_location=None):
"""
Get an ISA-API Investigation object reading directly from the ISA-Tab files
:param study_id: MTBLS study identifier
:param api_key: User API key for accession check
:param study_location: The filesystem location of the study
:return: an ISA-API Investigation object
"""
start = time.time()
if study_location is None:
logger.info(
"Study location is not set, will have load study from filesystem"
)
path = self.wsc.get_study_location(study_id, api_key)
else:
logger.info("Study location is: " + study_location)
path = study_location
# try the new parser first
isa_json = None
try:
isa_json = isatab2json.convert(path,
validate_first=False,
use_new_parser=True)
except Exception: # on failure, use the old one
try:
isa_json = isatab2json.convert(path,
validate_first=False,
use_new_parser=False)
except Exception:
# if it fails too
if isa_json is None:
abort(500)
else:
logger.info('... get_isa_json() processing (I): %s sec.',
time.time() - start)
return isa_json
else:
logger.info('... get_isa_json() processing (II): %s sec.',
time.time() - start)
return isa_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 post(self):
response = Response(status=415)
if request.mimetype == "application/zip":
tmp_dir = None
tmp_file = None
combined_json = None
try:
# Write request data to file
tmp_file = str(uuid.uuid4()) + ".zip"
file_path = _write_request_data(request, config.UPLOAD_FOLDER, tmp_file)
if file_path is None:
return Response(500)
# Extract ISArchive files
with zipfile.ZipFile(file_path, 'r') as z:
# Create temporary directory
tmp_dir = _create_temp_dir()
if tmp_dir is None:
return Response(500)
z.extractall(tmp_dir)
# Convert
src_dir = os.path.normpath(os.path.join(tmp_dir, z.filelist[0].filename))
isatab2json.convert(src_dir, src_dir)
# return just the combined JSON
files = [f for f in os.listdir(src_dir) if f.endswith('.json')]
if len(files) == 1: # current assumption is that only one JSON should exist to know what to return
combined_json_file = os.path.join(src_dir, files[0])
combined_json = json.load(open(combined_json_file))
else:
raise IOError("More than one .json was output - cannot disambiguate what to return")
except Exception as e:
print(e)
return Response(status=500)
finally:
# cleanup generated directories
try:
shutil.rmtree(tmp_dir, ignore_errors=True)
os.remove(os.path.join(config.UPLOAD_FOLDER, tmp_file))
except:
pass
response = jsonify(combined_json)
return response
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,
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_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 getj(mtbls_study_id):
"""
This function downloads the specified MetaboLights study and returns an ISA JSON representation of it
:param mtbls_study_id: Study identifier for MetaboLights study to get, as a str (e.g. MTBLS1)
:return: ISA JSON representation of the MetaboLights study
Example usage:
isa_json = MTBLS.load('MTBLS1')
"""
tmp_dir = get(mtbls_study_id)
if tmp_dir is None:
raise IOError("There was a problem retrieving the study ", mtbls_study_id)
isa_json = isatab2json.convert(tmp_dir, identifier_type=isatab2json.IdentifierType.name, validate_first=False)
shutil.rmtree(tmp_dir)
return isa_json
def getj(mtbls_study_id):
"""
This function downloads the specified MetaboLights study and returns an ISA JSON representation of it
:param mtbls_study_id: Study identifier for MetaboLights study to get, as a str (e.g. MTBLS1)
:return: ISA JSON representation of the MetaboLights study
Example usage:
isa_json = MTBLS.load('MTBLS1')
"""
tmp_dir = get(mtbls_study_id)
if tmp_dir is None:
raise IOError("There was a problem retrieving the study ", mtbls_study_id)
isa_json = isatab2json.convert(tmp_dir, identifier_type=isatab2json.IdentifierType.name,
validate_first=False,
use_new_parser=True)
shutil.rmtree(tmp_dir)
return isa_json
def convert(source_path, dest_path, sra_settings=None, validate_first=True):
from isatools.convert import isatab2json, json2sra
isa_json = isatab2json.convert(source_path, validate_first=validate_first)
isa_json_fp = StringIO(json.dumps(isa_json))
isa_json_fp.name = "BII-S-3.json"
json2sra.convert2(isa_json_fp, dest_path, sra_settings=sra_settings, validate_first=False)
logging.info("Conversion complete...")
buffer = BytesIO()
if os.path.isdir(dest_path):
with ZipFile(buffer, 'w') as zip_file:
# use relative dir_name to avoid absolute path on file names
zipdir(dest_path, zip_file)
print(zip_file.namelist())
# clean up the target directory after the ZIP file has been closed
# rmtree(sra_dir)
buffer.seek(0)
return buffer
def convert(source_path, dest_path, sra_settings=None, validate_first=True):
log.info("Converting ISA-Tab to JSON for %s", source_path)
isa_json = isatab2json.convert(source_path, validate_first=validate_first)
log.debug("Writing JSON to memory file")
isa_json_fp = StringIO(json.dumps(isa_json))
isa_json_fp.name = "BII-S-3.json"
log.info("Converting JSON to SRA, writing to %s", dest_path)
log.info("Using SRA settings %s", sra_settings)
json2sra.convert(isa_json_fp, dest_path, sra_settings=sra_settings, validate_first=False)
log.info("Conversion from ISA-Tab to SRA complete")
buffer = BytesIO()
if os.path.isdir(dest_path):
log.info("Zipping SRA files")
with ZipFile(buffer, 'w') as zip_file:
zipdir(dest_path, zip_file)
log.debug("Zipped %s", zip_file.namelist())
buffer.seek(0)
log.info("Returning zipped files as memory file")
return buffer
def convert(source_path, dest_path, sra_settings=None, validate_first=True):
isa_json = isatab2json.convert(source_path, validate_first=validate_first)
isa_json_fp = StringIO(json.dumps(isa_json))
isa_json_fp.name = "BII-S-3.json"
json2sra.convert(isa_json_fp,
dest_path,
sra_settings=sra_settings,
validate_first=False)
logging.info("Conversion complete...")
buffer = BytesIO()
if os.path.isdir(dest_path):
with ZipFile(buffer, 'w') as zip_file:
# use relative dir_name to avoid absolute path on file names
zipdir(dest_path, zip_file)
print(zip_file.namelist())
# clean up the target directory after the ZIP file has been closed
# rmtree(sra_dir)
buffer.seek(0)
return buffer
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)
#!/usr/bin/env python3
import json
import sys
input_path = sys.argv[1]
output_file_path = sys.argv[2]
try:
from isatools.convert import isatab2json
except ImportError as e:
raise RuntimeError('Could not import isatools package')
isatab_dir = input_path
my_json = isatab2json.convert(work_dir=isatab_dir,
validate_first=False,
use_new_parser=True)
with open(output_file_path, 'w') as out_fp:
json.dump(my_json, out_fp, indent=4)
import sys
import os
src_dir = sys.argv[1]
target_dir = sys.argv[2]
try:
from isatools.convert import isatab2json
except ImportError as e:
raise RuntimeError("Could not import isatools package")
isatab2json.convert(src_dir, target_dir)
def test_bii_i_1_conversion(self):
isatab2json.convert(os.path.join(self._dir, "./data/BII-I-1/"), self._tmp)
isa_json = json.load(open("../isatools/sampledata/BII-I-1.json"))
self.assertEqual(isa_json["identifier"], "BII-I-1")
self.assertEqual(isa_json["title"], "Growth control of the eukaryote cell: a systems biology study in yeast")
self.assertEqual(
isa_json["description"],
"Background Cell growth underlies many key cellular and "
"developmental processes, yet a limited number of studies have been "
"carried out on cell-growth regulation. Comprehensive studies at "
"the transcriptional, proteomic and metabolic levels under defined "
"controlled conditions are currently lacking. Results Metabolic "
"control analysis is being exploited in a systems biology study of "
"the eukaryotic cell. Using chemostat culture, we have measured the "
"impact of changes in flux (growth rate) on the transcriptome, "
"proteome, endometabolome and exometabolome of the yeast "
"Saccharomyces cerevisiae. Each functional genomic level shows clear "
"growth-rate-associated trends and discriminates between "
"carbon-sufficient and carbon-limited conditions. Genes consistently "
"and significantly upregulated with increasing growth rate are "
"frequently essential and encode evolutionarily conserved proteins "
"of known function that participate in many protein-protein "
"interactions. In contrast, more unknown, and fewer essential, genes "
"are downregulated with increasing growth rate; their protein "
"products rarely interact with one another. A large proportion of "
"yeast genes under positive growth-rate control share orthologs with "
"other eukaryotes, including humans. Significantly, transcription of "
"genes encoding components of the TOR complex (a major controller of "
"eukaryotic cell growth) is not subject to growth-rate regulation. "
"Moreover, integrative studies reveal the extent and importance of "
"post-transcriptional control, patterns of control of metabolic "
"fluxes at the level of enzyme synthesis, and the relevance of "
"specific enzymatic reactions in the control of metabolic fluxes "
"during cell growth. Conclusion This work constitutes a first "
"comprehensive systems biology study on growth-rate control in the "
"eukaryotic cell. The results have direct implications for advanced "
"studies on cell growth, in vivo regulation of metabolic fluxes for "
"comprehensive metabolic engineering, and for the design of "
"genome-scale systems biology models of the eukaryotic cell.",
)
self.assertEqual(isa_json["submissionDate"], "2007-04-30")
self.assertEqual(isa_json["publicReleaseDate"], "2009-03-10")
self.assertEqual(isa_json["commentCreatedWithConfiguration"]["name"], "Created With Configuration")
self.assertEqual(isa_json["commentCreatedWithConfiguration"]["value"], "")
self.assertEqual(isa_json["commentLastOpenedWithConfiguration"]["name"], "Last Opened With Configuration")
self.assertEqual(isa_json["commentLastOpenedWithConfiguration"]["value"], "isaconfig-default_v2013-02-13")
self.assertEqual(len(isa_json["ontologySourceReferences"]), 7)
self.assertEqual(len(isa_json["publications"]), 1)
self.assertEqual(isa_json["publications"][0]["pubMedID"], "17439666")
self.assertEqual(isa_json["publications"][0]["doi"], "doi:10.1186/jbiol54")
self.assertEqual(
isa_json["publications"][0]["authorList"],
"Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes "
"A, Gardner DC, Cornell MJ, Petty J, Hakes L, "
"Wardleworth L, Rash B, Brown M, Dunn WB, "
"Broadhurst D, O'Donoghue K, Hester SS, Dunkley "
"TP, Hart SR, Swainston N, Li P, Gaskell SJ, Paton "
"NW, Lilley KS, Kell DB, Oliver SG.",
)
self.assertEqual(
isa_json["publications"][0]["title"],
"Growth control of the eukaryote cell: a systems " "biology study in yeast.",
)
self.assertEqual(isa_json["publications"][0]["status"]["name"], "indexed in Pubmed")
self.assertEqual(len(isa_json["people"]), 3)
self.assertEqual(isa_json["people"][0]["firstName"], "Oliver")
self.assertEqual(isa_json["people"][1]["firstName"], "Juan")
self.assertEqual(isa_json["people"][2]["firstName"], "Leo")
self.assertEqual(isa_json["people"][0]["lastName"], "Stephen")
self.assertEqual(isa_json["people"][1]["lastName"], "Castrillo")
self.assertEqual(isa_json["people"][2]["lastName"], "Zeef")
self.assertEqual(isa_json["people"][0]["midInitials"], "G")
self.assertEqual(isa_json["people"][1]["midInitials"], "I")
self.assertEqual(isa_json["people"][2]["midInitials"], "A")
self.assertEqual(isa_json["people"][0]["address"], "Oxford Road, Manchester M13 9PT, UK")
self.assertEqual(isa_json["people"][1]["address"], "Oxford Road, Manchester M13 9PT, UK")
self.assertEqual(isa_json["people"][2]["address"], "Oxford Road, Manchester M13 9PT, UK")
self.assertEqual(
isa_json["people"][0]["affiliation"],
"Faculty of Life Sciences, Michael Smith Building, " "University of Manchester",
)
self.assertEqual(
isa_json["people"][1]["affiliation"],
"Faculty of Life Sciences, Michael Smith Building, " "University of Manchester",
)
self.assertEqual(
isa_json["people"][2]["affiliation"],
"Faculty of Life Sciences, Michael Smith Building, " "University of Manchester",
)
self.assertEqual(len(isa_json["studies"]), 2)
self.assertEqual(isa_json["studies"][0]["identifier"], "BII-S-1")
self.assertEqual(isa_json["studies"][1]["identifier"], "BII-S-2")
self.assertEqual(len(isa_json["studies"][0]["factors"]), 2)
self.assertEqual(isa_json["studies"][0]["factors"][0]["factorName"], "limiting nutrient")
self.assertEqual(isa_json["studies"][0]["factors"][1]["factorName"], "rate")
self.assertEqual(isa_json["studies"][0]["factors"][0]["factorType"]["name"], "chemical compound")
self.assertEqual(isa_json["studies"][0]["factors"][1]["factorType"]["name"], "rate")
self.assertEqual(len(isa_json["studies"][0]["sources"]), 18)
self.assertEqual(len(isa_json["studies"][0]["samples"]), 163)
self.assertEqual(len(isa_json["studies"][1]["sources"]), 1)
self.assertEqual(len(isa_json["studies"][1]["samples"]), 2)
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))
#parser.add_argument("-o", "--out", dest="outfile",
# help="output json ISA file, no extension", metavar="ISAjson")
#parser.add_argument("-q", "--quiet",
# action="store_false", dest="verbose", default=True,
# help="don't print status messages to stdout")
args = parser.parse_args()
print(args.indir)
#print (args.outfile)
output_file = args.indir + ".json"
output_path = "./jsondir/"
input_path = "./isatabs/" + args.indir
if not os.path.exists(output_path):
os.makedirs(output_path)
#print(output_path)
print("ISA json built in " + output_path + output_file + "\n")
# isa_json = isatab2json.convert('./isatabs/'args.indir, use_new_parser=True)
#isa_json = isatab2json.convert(join('./isatabs/'args.indir), use_new_parser=True)
isa_json = isatab2json.convert(input_path, use_new_parser=True)
try:
with open(join(output_path, output_file), 'w') as out_fp:
json.dump(isa_json, out_fp, indent=4)
except IOError as e:
print("something went wrong:", e)
import json
import requests
from isatools import isatab
from isatools.convert import isatab2json
directory_1 = '/Users/Philippe/Documents/Dropbox-Backup/Eurovis 2015 - Chronoglyph/ISATAB-datasets/BII-S-8_FP001RO-isatab-TEST'
inv_name_1 = 'i_fp001ro-investigation.txt'
isa_config_1 = '/Users/Philippe/Documents/git/Configuration-Files/isaconfig-default_v2014-01-16/'
directory_2 = '/Users/Philippe/Documents/git/ISAdatasets/tab/MTBLS404/'
inv_name_2 = 'i_sacurine.txt'
# isa_config_2 = '/Users/Philippe/Documents/git/Configuration-Files/isaconfig-seq_v2016-11-17-SRA1.5-august2014mod/'
try:
# my_isa_read = isatab.load(open(os.path.join('/Users/Philippe/Downloads/ISAcreator-1.7.11-all/isatab files/SRA_assembly_test', 'i_investigation.txt')))
my_isa_read = isatab.load(open(os.path.join(directory_1, inv_name_1)))
print("reading in:", my_isa_read.studies)
# my_json_report = isatab.validate(open(os.path.join('/Users/Philippe/Downloads/ISAcreator-1.7.11-all/isatab files/SRA_assembly_test', 'i_investigation.txt')), '/Users/Philippe/Documents/git/Configuration-Files/isaconfig-seq_v2016-11-17-SRA1.5-august2014mod/')
# my_json_report = isatab.validate(open(os.path.join(directory_1,inv_name_1)), isa_config_1)
# print(my_json_report)
try:
isa_json = isatab2json.convert(directory_2)
except Exception as excep:
print(excep)
except IOError as e:
print(e)
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_isa_source_split_with_error_conversion(self):
isatab2json.convert(os.path.join(self._dir, './data/TEST-ISA-source-split-with-error/'), self._dir, isatab2json.IdentifierType.name)
def test_isa_sample_pool_with_error_conversion(self):
isatab2json.convert(os.path.join(self._dir, './data/TEST-ISA-sample-pool-with-error/'), self._dir, isatab2json.IdentifierType.name)
def test_isa_repeated_measure_conversion(self):
isatab2json.convert(os.path.join(self._dir, './data/TEST-ISA-repeated-measure/'), self._dir, isatab2json.IdentifierType.name)
def test_isa_charac_param_factor(self):
isatab2json.convert(os.path.join(self._dir, './data/TEST-ISA-charax-param-factor/'), self._dir, isatab2json.IdentifierType.name)
isa_json = json.load(open(os.path.join(self._dir, 'TEST-ISA-charac-param-factor.json')))
self.assertEqual(isa_json["identifier"], "TEST-ISA-charac-param-factor")
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))
