def testRequiredFields(self):
required = AbundanceMatrix.required_fields()
self.assertEqual(type(required), tuple,
"required_fields() returns a tuple.")
self.assertTrue(len(required) > 0,
"required_fields() did not return empty value.")
def testRequiredFields(self):
""" Test the required_fields() static method. """
required = AbundanceMatrix.required_fields()
self.assertEqual(type(required), tuple,
"required_fields() returns a tuple.")
self.assertTrue(
len(required) > 0, "required_fields() did not return empty value.")
ch = logging.StreamHandler(sys.stdout)
ch.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
root.addHandler(ch)
set_logging()
session = iHMPSession(username, password)
print("Creating a temp file for example/testing purposes.")
temp_file = tempfile.NamedTemporaryFile(delete=False).name
print("Local file: %s" % temp_file)
print("Required fields: ")
print(AbundanceMatrix.required_fields())
matrix = AbundanceMatrix()
matrix.comment = "test comment"
matrix.checksums = { "md5": "72bdc024d83226ccc90fbd2177e78d56" }
matrix.format = "fastq"
matrix.format_doc = "http://format.url"
matrix.matrix_type = "host_cytokine"
matrix.study = "prediabetes"
matrix.size = 1000
matrix.local_file = temp_file
# Optional properties
matrix.sop = "the SOP"
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
root.addHandler(ch)
set_logging()
session = iHMPSession(username, password)
print("Creating a temp file for example/testing purposes.")
temp_file = tempfile.NamedTemporaryFile(delete=False).name
print("Local file: %s" % temp_file)
print("Required fields: ")
print(AbundanceMatrix.required_fields())
matrix = AbundanceMatrix()
matrix.comment = "test comment"
matrix.checksums = {"md5": "72bdc024d83226ccc90fbd2177e78d56"}
matrix.format = "csv"
matrix.format_doc = "http://format.url"
matrix.matrix_type = "host_cytokine"
matrix.study = "prediabetes"
matrix.size = 1000
matrix.local_file = temp_file
matrix.private_files = False
# Optional properties
matrix.sop = "the SOP"
