Beispiel #1
0
    def testRequiredFields(self):
        required = Annotation.required_fields()

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

        self.assertTrue(len(required) > 0,
                        "required_field() did not return empty value.")
Beispiel #2
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username = "test"
password = "test"

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)

session = iHMPSession(username, password)

print("Required fields: ")
print(Annotation.required_fields())

annot = Annotation()

annot.annotation_pipeline = "the annotation pipeline"
annot.checksums = { "md5": "72bdc024d83226ccc90fbd2177e78d56" }
annot.format = "gff3"
annot.format_doc = "the format url"
annot.orf_process = "the orf process"
annot.study = "prediabetes"
annot.size = 131313

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