def data_download_test_xml(self, xml_file_name, uuids,
client_options='', server_options='', check_sha1=True):
server = None
# delete the bams so we can download them
for uuid in uuids:
if os.path.isfile(self.client_bam(uuid)):
os.remove(self.client_bam(uuid))
if TestConfig.MOCKHUB:
# prepare server
server = GeneTorrentInstance(
'-s server%sroot -q server%sworkdir -c %s ' \
'--security-api %s %s' \
% (
os.path.sep,
os.path.sep,
self.cred_filename,
TestConfig.SECURITY_API,
server_options,
), instance_type=InstanceType.GT_SERVER)
# add new download GTO to server work queue
# add gt_download_mode flag to server gto
for uuid in uuids:
gtodict = read_gto(self.client_gto(uuid))
gtodict['gt_download_mode'] = 'true'
expiry = time.time() + (1 * 3600 * 24) # expire in 1 day
set_key(gtodict, 'expires on', int(expiry))
emit_gto(gtodict, self.server_gto(uuid), True)
else:
self.upload_sleep(3)
# prepare download client
client = GeneTorrentInstance('-d %s ' \
'-p client2 -c %s %s' \
% (
xml_file_name,
self.cred_filename,
client_options,
), instance_type=InstanceType.GT_DOWNLOAD)
# wait for download client to exit
client_sout, client_serr = client.communicate()
if server:
self.terminate_server(server)
# check download client return code
self.assertEqual(client.returncode, 0)
self.assertTrue('Downloaded' in client_serr)
self.assertTrue('state changed to: finished' in client_sout)
# check file hashes on both sides of transfer
for uuid in uuids:
if check_sha1 and TestConfig.MOCKHUB:
self.assertTrue(self.compare_hashes(
self.client_bam2(uuid), self.server_bam(uuid)))
return client.returncode
def data_download_test_uuid(self, uuid, client_options='', server_options='',
check_sha1=True, assert_rc=0, assert_serr='', server_ct=1):
# delete the bam so we can download it
if os.path.isfile(self.client_bam(uuid)):
os.remove(self.client_bam(uuid))
servers = []
if TestConfig.MOCKHUB:
# prepare server(s)
for i in range(0, server_ct):
server = GeneTorrentInstance(
'-s server%sroot -q server%sworkdir -c %s ' \
'--security-api %s %s' \
% (
os.path.sep,
os.path.sep,
self.cred_filename,
TestConfig.SECURITY_API,
server_options,
), instance_type=InstanceType.GT_SERVER,
client_num=i)
servers.append(server)
# add new download GTO to server work queue
# add gt_download_mode flag to server gto
gtodict = read_gto(self.client_gto(uuid))
gtodict['gt_download_mode'] = 'true'
expiry = time.time() + (1 * 3600 * 24) # expire in 1 day
set_key(gtodict, 'expires on', int(expiry))
emit_gto(gtodict, self.server_gto(uuid), True)
else:
self.upload_sleep(3)
# prepare download client
client = GeneTorrentInstance('-d %s/cghub/data/analysis/download/%s ' \
'-p client2 %s %s' \
% (
TestConfig.HUB_SERVER,
str(uuid),
'-c ' + self.cred_filename if not '-c ' in client_options else '',
client_options,
), instance_type=InstanceType.GT_DOWNLOAD)
# wait for download client to exit
client_sout, client_serr = client.communicate()
if servers:
for server in servers:
self.terminate_server(server)
# check download client return code
self.assertEqual(client.returncode, assert_rc)
# caller-passed client_serr contains assert
if assert_serr:
self.assertTrue(assert_serr in client_serr)
# only continue checking if assert_rc == 0
if assert_rc == 0:
# check download client
self.assertTrue('Downloaded' in client_serr)
self.assertTrue('state changed to: finished' in client_sout)
# check file hashes on both sides of transfer
if servers and check_sha1:
self.assertTrue(self.compare_hashes(
self.client_bam2(uuid), self.server_bam(uuid)))
return client.returncode