Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix Google drive upload tests #83

Merged
merged 1 commit into from
Mar 20, 2024
Merged

Fix Google drive upload tests #83

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
47 changes: 13 additions & 34 deletions test/ReadsUtils_server_test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,8 @@ class ReadsUtilsTest(unittest.TestCase):

@classmethod
def setUpClass(cls):
cls.nodes_to_delete = []
cls.handles_to_delete = []
cls.token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
Expand Down Expand Up @@ -78,8 +80,6 @@ def setUpClass(cls):
cls.ws_info = cls.ws.create_workspace({'workspace': wsName})
cls.dfu = DataFileUtil(os.environ['SDK_CALLBACK_URL'], token=cls.token)
cls.staged = {}
cls.nodes_to_delete = []
cls.handles_to_delete = []
cls.setupTestData()
cls.ftp_domain = socket.gethostbyname(socket.gethostname())
cls.ftp_port = 21
Expand Down Expand Up @@ -112,7 +112,7 @@ def tearDownClass(cls):
if hasattr(cls, 'nodes_to_delete'):
for node in cls.nodes_to_delete:
cls.delete_shock_node(node)
if hasattr(cls, 'handles_to_delete'):
if cls.handles_to_delete:
cls.hs.delete_handles(cls.hs.hids_to_handles(cls.handles_to_delete))
print('Deleted handles ' + str(cls.handles_to_delete))

Expand Down Expand Up @@ -1234,7 +1234,8 @@ def check_lib(self, lib, size, filename, md5):
print("File Input: {}".format(str(fileinput)))
files = self.dfu.shock_to_file_mass(fileinput)
path = files[0]["file_path"]
file_md5 = hashlib.md5(open(path, 'rb').read()).hexdigest()
with open(path, 'rb') as f:
file_md5 = hashlib.md5(f.read()).hexdigest()
libfile = lib['file']
self.assertEqual(file_md5, md5)
self.assertEqual(lib['size'], size)
Expand Down Expand Up @@ -3144,40 +3145,18 @@ def test_upload_reads_from_web_ftp_gz_file(self):
node = d['lib']['file']['id']
self.delete_shock_node(node)

@unittest.skip("Google downloads currently fail")
def test_upload_reads_from_web_google_drive(self):
url = 'https://drive.google.com/file/d/1kDyuUrupB86arXbculE-gOkmZxtNRWtH/'
# in kbase org -> Testing/PublicTestData/ReadsUtils
url = 'https://drive.google.com/file/d/1X4pEdEhiHtQM0-8m6Nkqi82Kqkeo2_fX/'
url += 'view?usp=sharing'
self._upload_reads_from_web_google_drive(url)

params = {
'download_type': 'Google Drive',
'fwd_file_url': url,
'sequencing_tech': 'Unknown',
'name': 'test_reads_file_name.reads',
'wsname': self.getWsName()
}

ref = self.impl.upload_reads(self.ctx, params)
self.assertTrue('obj_ref' in ref[0])
obj = self.dfu.get_objects(
{'object_refs': [self.ws_info[1] + '/test_reads_file_name.reads']})['data'][0]
self.assertEqual(ref[0]['obj_ref'], self.make_ref(obj['info']))
self.assertEqual(obj['info'][2].startswith(
'KBaseFile.SingleEndLibrary'), True)
d = obj['data']
self.assertEqual(d['sequencing_tech'], 'Unknown')
self.assertEqual(d['single_genome'], 1)
self.assertEqual('source' not in d, True)
self.assertEqual('strain' not in d, True)
self.check_lib(d['lib'], 2966, 'Sample1.fastq.gz',
'f118ee769a5e1b40ec44629994dfc3cd')
node = d['lib']['file']['id']
self.delete_shock_node(node)

@unittest.skip("Google downloads currently fail")
def test_upload_reads_from_web_google_drive_different_format(self):
url = 'https://drive.google.com/open?id='
url += '1kDyuUrupB86arXbculE-gOkmZxtNRWtH'
# in kbase org -> Testing/PublicTestData/ReadsUtils
url = 'https://drive.google.com/open?id=1X4pEdEhiHtQM0-8m6Nkqi82Kqkeo2_fX'
self._upload_reads_from_web_google_drive(url)

def _upload_reads_from_web_google_drive(self, url):
params = {
'download_type': 'Google Drive',
'fwd_file_url': url,
Expand Down
Loading