예제 #1
0
    def testRequiredFields(self):
        required = Metabolome.required_fields()

        self.assertEqual(type(required), tuple,
                         "required_fields() returns a tuple.")

        self.assertTrue(len(required) > 0,
                        "required_field() did not return empty value.")
예제 #2
0
    def testRequiredFields(self):
        """ Test the required_fields() static method. """
        required = Metabolome.required_fields()

        self.assertEqual(type(required), tuple,
                         "required_fields() returns a tuple.")

        self.assertTrue(
            len(required) > 0, "required_field() did not return empty value.")
예제 #3
0
def set_logging():
    root = logging.getLogger()
    root.setLevel(logging.DEBUG)
    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("Required fields: ")
print(Metabolome.required_fields())

metabolome = Metabolome()

metabolome.checksums = { "md5": "72bdc024d83226ccc90fbd2177e78d56" }
metabolome.study = "prediabetes"
metabolome.subtype = "host"

print("Creating a temp file for example/testing purposes.")
temp_file = tempfile.NamedTemporaryFile(delete=False).name
print("Local file: %s" % temp_file)

# Optional properties
metabolome.comment = "test metabolome comment"
metabolome.format = "gff3"
metabolome.format_doc = "the format url"
예제 #4
0
    root = logging.getLogger()
    root.setLevel(logging.DEBUG)
    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("Required fields: ")
print(Metabolome.required_fields())

metabolome = Metabolome()

metabolome.checksums = {"md5": "72bdc024d83226ccc90fbd2177e78d56"}
metabolome.study = "prediabetes"
metabolome.subtype = "host"

print("Creating a temp file for example/testing purposes.")
temp_file = tempfile.NamedTemporaryFile(delete=False).name
print("Local file: %s" % temp_file)

# Optional properties
metabolome.comment = "test metabolome comment"
metabolome.format = "gff3"
metabolome.format_doc = "the format url"