def getObject(self, identifier):
''' DRS formatted details of an EGA file '''
display_file_name, file_name, file_size, check_sum = ega.get_file_name_size_md5(
self.token, identifier)
response = {
"access_methods": [{
"access_id": "ega",
"region": "",
"type": "pyega3"
}],
"checksums": [{
"checksum": check_sum,
"type": "md5"
}],
"created_time":
"2020-02-26T18:01:43.252269",
"id":
identifier,
"mime_type":
"application/json",
"description":
file_name,
"name":
display_file_name,
"self_uri":
"drs://egasim/{}".format(identifier),
"size":
file_size,
"updated_time":
"2020-02-26T18:01:43.252275"
}
return response
def testhtsget(self, identifier, ref, start, end, type, saveTo):
display_file_name, file_name, file_size, check_sum = ega.get_file_name_size_md5(
self.token, identifier)
genomic_range_args = (ref, check_sum, start, end, type)
print(display_file_name)
ega.download_file_retry(self.credentials, identifier,
display_file_name, file_name, file_size,
check_sum, 3, self.key, saveTo,
genomic_range_args, -1, 10)
def test_get_file_name_size_md5(self):
good_file_id = "EGAF00000000001"
file_size = 4804928
file_name = "EGAZ00000000001/ENCFF000001.bam"
display_file_name = "ENCFF000001.bam"
check_sum = "3b89b96387db5199fef6ba613f70e27c"
good_token = rand_str()
def request_callback(request):
auth_hdr = request.headers['Authorization']
if auth_hdr is not None and auth_hdr == 'Bearer ' + good_token:
return (200, {},
json.dumps({
"fileName": file_name,
"displayFileName": display_file_name,
"fileSize": file_size,
"unencryptedChecksum": check_sum
}))
else:
return (400, {},
json.dumps({"error_description": "invalid token"}))
responses.add_callback(
responses.GET,
"https://ega.ebi.ac.uk:8052/elixir/data/metadata/files/{}".format(
good_file_id),
callback=request_callback,
content_type='application/json',
)
rv = pyega3.get_file_name_size_md5(good_token, good_file_id)
self.assertEqual(len(rv), 3)
self.assertEqual(rv[0], display_file_name)
self.assertEqual(rv[1], file_size)
self.assertEqual(rv[2], check_sum)
bad_token = rand_str()
with self.assertRaises(requests.exceptions.HTTPError):
pyega3.get_file_name_size_md5(bad_token, good_file_id)
bad_file_id = "EGAF00000000000"
with self.assertRaises(requests.exceptions.ConnectionError):
pyega3.get_file_name_size_md5(good_token, bad_file_id)
bad_file_id_2 = "EGAF00000000666"
responses.add(
responses.GET,
"https://ega.ebi.ac.uk:8052/elixir/data/metadata/files/{}".format(
bad_file_id_2),
json={
"fileName": None,
"displayFileName": None,
"unencryptedChecksum": None
},
status=200)
with self.assertRaises(RuntimeError):
pyega3.get_file_name_size_md5(good_token, bad_file_id_2)
def getSize(self, identifier):
display_file_name, file_name, file_size, check_sum = ega.get_file_name_size_md5(
self.token, identifier)
return file_size
