def list_files(name=None):
"""
Returns a list of all files in the user's staging area. It uses the 'name' as a case-insensitive
search string to filter the files. E.g., looking for files named "foo" will return files named
"Foo.txt", "FOO", "myfoobar", etc.
If name is None, returns all files.
This simply returns a list of strings, where each string is the file path that the App can use.
"""
staging = StagingHelper()
files = staging.list()
if not name:
return files
filter_files = list()
name = name.lower()
filter_files = [f for f in files if name in f.lower()]
return filter_files
# Using Workspace Metadata
# from https://kbase.github.io/kb_sdk_docs/howtos/workspace.html
#Import KBase app manager
from biokbase.narrative.jobs.appmanager import AppManager
#List all files in Staging Area
#Set up the link to the staging area helper class
from biokbase.narrative.staging.helper import Helper as StagingHelper
staging_helper = StagingHelper()
#list root directory files and all subdirectory files (default)
file_list = staging_helper.list()
print 'All files:'
print '\n'.join(file_list)
#Import FASTA File as Assembly from Staging Area
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app(
"kb_uploadmethods/import_fasta_as_assembly_from_staging",
{
"staging_file_subdir_path": "_Test/TARA_ANE_MAG_00002.fna",
"type": "mag",
class StagingHelperTest(unittest.TestCase):
def setUp(self):
self.good_fake_token = 'good_fake_token'
os.environ['KB_AUTH_TOKEN'] = self.good_fake_token
self.staging_helper = Helper()
def test_missing_token(self):
os.environ['KB_AUTH_TOKEN'] = ''
with self.assertRaises(ValueError) as context:
Helper()
self.assertEqual('Cannot retrieve auth token', str(context.exception))
def test_token(self):
self.assertEqual(self.good_fake_token, self.staging_helper._token)
def test_staging_url(self):
self.assertTrue('kbase.us/services/staging_service' in
self.staging_helper._staging_url)
def test_unauthorized_token(self):
with self.assertRaises(ValueError) as context:
self.staging_helper.list()
self.assertTrue('Reason: Unauthorized' in str(context.exception))
self.assertTrue('Error code: 401' in str(context.exception))
def mock_fetch_url(end_point,
values=None,
headers=None,
method='GET',
save_path=None):
if 'list' in end_point:
print('mocking __fetch_url list endpoint')
return '[{"path": "tgu/test_file_1", "isFolder": false},\
{"path": "tgu/test_dir", "isFolder": true},\
{"path": "tgu/test_dir/test_file_2", "isFolder": false}]'
elif 'jgi-metadata' in end_point:
print('mocking __fetch_url jgi-metadata endpoint')
return '{"file_name": "test_file", "file_status": "BACKUP_COMPLETE"}'
elif 'metadata' in end_point:
print('mocking __fetch_url metadata endpoint')
return '{"head": "head_line", "tail": "tail_line", "lineCount": 10}'
elif 'search' in end_point:
print('mocking __fetch_url search endpoint')
return '[{"isFolder": false, "mtime": 1515526154896, "name": "LMS-PROC-315.pdf"}]'
elif 'delete' in end_point:
print('mocking __fetch_url delete endpoint')
return "successfully deleted tgu2/test.pdf"
elif 'download' in end_point:
print('mocking __fetch_url download endpoint')
elif 'mv' in end_point:
print('mocking __fetch_url mv endpoint')
return "successfully moved tgu2/test.pdf to tgu2/test_1.pdf"
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_list(self, _fetch_url):
file_list = self.staging_helper.list()
self.assertTrue('tgu/test_file_1' in file_list)
self.assertTrue('tgu/test_dir/test_file_2' in file_list)
self.assertTrue('tgu/test_dir' not in file_list)
def test_missing_path(self):
with self.assertRaises(ValueError) as context:
self.staging_helper.metadata()
self.assertEqual('Must provide path argument', str(context.exception))
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_metadata(self, _fetch_url):
metadata = self.staging_helper.metadata('test_fake_file')
self.assertTrue('head' in metadata)
self.assertEqual(metadata.get('head'), 'head_line')
self.assertTrue('tail' in metadata)
self.assertEqual(metadata.get('tail'), 'tail_line')
self.assertTrue('lineCount' in metadata)
self.assertEqual(metadata.get('lineCount'), 10)
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_jgi_metadata(self, _fetch_url):
metadata = self.staging_helper.jgi_metadata('test_fake_file')
self.assertTrue('file_name' in metadata)
self.assertEqual(metadata.get('file_name'), 'test_file')
self.assertTrue('file_status' in metadata)
self.assertEqual(metadata.get('file_status'), 'BACKUP_COMPLETE')
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_search(self, _fetch_url):
search_ret = self.staging_helper.search('test_fake_file')
self.assertTrue(isinstance(search_ret, (list)))
element = search_ret[0]
self.assertTrue('isFolder' in element)
self.assertFalse(element.get('isFolder'))
self.assertTrue('name' in element)
self.assertEqual(element.get('name'), 'LMS-PROC-315.pdf')
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_delete(self, _fetch_url):
delete_ret = self.staging_helper.delete('test_fake_file')
self.assertTrue('server_response' in delete_ret)
self.assertEqual(delete_ret.get('server_response'),
'successfully deleted tgu2/test.pdf')
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_download(self, _fetch_url):
download_ret = self.staging_helper.download('test_fake_file')
self.assertTrue('test_fake_file' in download_ret)
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_mv(self, _fetch_url):
mv_ret = self.staging_helper.mv('test.pdf ', 'test_1.pdf')
self.assertTrue('server_response' in mv_ret)
self.assertEqual(
mv_ret.get('server_response'),
'successfully moved tgu2/test.pdf to tgu2/test_1.pdf')
def setUp(self):
self.good_fake_token = 'good_fake_token'
os.environ['KB_AUTH_TOKEN'] = self.good_fake_token
self.staging_helper = Helper()
def test_missing_token(self):
os.environ['KB_AUTH_TOKEN'] = ''
with self.assertRaises(ValueError) as context:
Helper()
self.assertEqual('Cannot retrieve auth token', str(context.exception))
def setUp(self):
self.good_fake_token = 'good_fake_token'
os.environ['KB_AUTH_TOKEN'] = self.good_fake_token
self.staging_helper = Helper()
class StagingHelperTest(unittest.TestCase):
def setUp(self):
self.good_fake_token = 'good_fake_token'
os.environ['KB_AUTH_TOKEN'] = self.good_fake_token
self.staging_helper = Helper()
def test_missing_token(self):
os.environ['KB_AUTH_TOKEN'] = ''
with self.assertRaises(ValueError) as context:
Helper()
self.assertEqual('Cannot retrieve auth token', str(context.exception.message))
def test_token(self):
self.assertEqual(self.good_fake_token, self.staging_helper._token)
def test_staging_url(self):
self.assertTrue('kbase.us/services/staging_service' in
self.staging_helper._staging_url)
def test_unauthorized_token(self):
with self.assertRaises(ValueError) as context:
self.staging_helper.list()
self.assertTrue('Reason: Unauthorized' in str(context.exception.message))
self.assertTrue('Error code: 401' in str(context.exception.message))
def mock_fetch_url(end_point, values=None, headers=None, method='GET', save_path=None):
if 'list' in end_point:
print 'mocking __fetch_url list endpoint'
return '[{"path": "tgu/test_file_1", "isFolder": false},\
{"path": "tgu/test_dir", "isFolder": true},\
{"path": "tgu/test_dir/test_file_2", "isFolder": false}]'
elif 'jgi-metadata' in end_point:
print 'mocking __fetch_url jgi-metadata endpoint'
return '{"file_name": "test_file", "file_status": "BACKUP_COMPLETE"}'
elif 'metadata' in end_point:
print 'mocking __fetch_url metadata endpoint'
return '{"head": "head_line", "tail": "tail_line", "lineCount": 10}'
elif 'search' in end_point:
print 'mocking __fetch_url search endpoint'
return '[{"isFolder": false, "mtime": 1515526154896, "name": "LMS-PROC-315.pdf"}]'
elif 'delete' in end_point:
print 'mocking __fetch_url delete endpoint'
return "successfully deleted tgu2/test.pdf"
elif 'download' in end_point:
print 'mocking __fetch_url download endpoint'
elif 'mv' in end_point:
print 'mocking __fetch_url mv endpoint'
return "successfully moved tgu2/test.pdf to tgu2/test_1.pdf"
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_list(self, _fetch_url):
file_list = self.staging_helper.list()
self.assertTrue('tgu/test_file_1' in file_list)
self.assertTrue('tgu/test_dir/test_file_2' in file_list)
self.assertTrue('tgu/test_dir' not in file_list)
def test_missing_path(self):
with self.assertRaises(ValueError) as context:
self.staging_helper.metadata()
self.assertEqual('Must provide path argument', str(context.exception.message))
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_metadata(self, _fetch_url):
metadata = self.staging_helper.metadata('test_fake_file')
self.assertTrue('head' in metadata)
self.assertEqual(metadata.get('head'), 'head_line')
self.assertTrue('tail' in metadata)
self.assertEqual(metadata.get('tail'), 'tail_line')
self.assertTrue('lineCount' in metadata)
self.assertEqual(metadata.get('lineCount'), 10)
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_jgi_metadata(self, _fetch_url):
metadata = self.staging_helper.jgi_metadata('test_fake_file')
self.assertTrue('file_name' in metadata)
self.assertEqual(metadata.get('file_name'), 'test_file')
self.assertTrue('file_status' in metadata)
self.assertEqual(metadata.get('file_status'), 'BACKUP_COMPLETE')
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_search(self, _fetch_url):
search_ret = self.staging_helper.search('test_fake_file')
self.assertTrue(isinstance(search_ret, (list)))
element = search_ret[0]
self.assertTrue('isFolder' in element)
self.assertFalse(element.get('isFolder'))
self.assertTrue('name' in element)
self.assertEqual(element.get('name'), 'LMS-PROC-315.pdf')
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_delete(self, _fetch_url):
delete_ret = self.staging_helper.delete('test_fake_file')
self.assertTrue('server_response' in delete_ret)
self.assertEqual(delete_ret.get('server_response'), 'successfully deleted tgu2/test.pdf')
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_download(self, _fetch_url):
download_ret = self.staging_helper.download('test_fake_file')
self.assertTrue('test_fake_file' in download_ret)
@patch.object(Helper, '_Helper__fetch_url', side_effect=mock_fetch_url)
def test_mv(self, _fetch_url):
mv_ret = self.staging_helper.mv('test.pdf ', 'test_1.pdf')
self.assertTrue('server_response' in mv_ret)
self.assertEqual(mv_ret.get('server_response'),
'successfully moved tgu2/test.pdf to tgu2/test_1.pdf')
def setUp(self):
self.good_fake_token = "good_fake_token"
os.environ["KB_AUTH_TOKEN"] = self.good_fake_token
self.staging_helper = Helper()
class StagingHelperTest(unittest.TestCase):
def setUp(self):
self.good_fake_token = "good_fake_token"
os.environ["KB_AUTH_TOKEN"] = self.good_fake_token
self.staging_helper = Helper()
def test_missing_token(self):
os.environ["KB_AUTH_TOKEN"] = ""
with self.assertRaises(ValueError) as context:
Helper()
self.assertEqual("Cannot retrieve auth token", str(context.exception))
def test_token(self):
self.assertEqual(self.good_fake_token, self.staging_helper._token)
def test_staging_url(self):
self.assertTrue(
"kbase.us/services/staging_service" in self.staging_helper._staging_url
)
def test_unauthorized_token(self):
with self.assertRaises(ValueError) as context:
self.staging_helper.list()
self.assertTrue("Reason: Unauthorized" in str(context.exception))
self.assertTrue("Error code: 401" in str(context.exception))
def mock_fetch_url(
end_point, values=None, headers=None, method="GET", save_path=None
):
if "list" in end_point:
print("mocking __fetch_url list endpoint")
return '[{"path": "tgu/test_file_1", "isFolder": false},\
{"path": "tgu/test_dir", "isFolder": true},\
{"path": "tgu/test_dir/test_file_2", "isFolder": false}]'
elif "jgi-metadata" in end_point:
print("mocking __fetch_url jgi-metadata endpoint")
return '{"file_name": "test_file", "file_status": "BACKUP_COMPLETE"}'
elif "metadata" in end_point:
print("mocking __fetch_url metadata endpoint")
return '{"head": "head_line", "tail": "tail_line", "lineCount": 10}'
elif "search" in end_point:
print("mocking __fetch_url search endpoint")
return '[{"isFolder": false, "mtime": 1515526154896, "name": "LMS-PROC-315.pdf"}]'
elif "delete" in end_point:
print("mocking __fetch_url delete endpoint")
return "successfully deleted tgu2/test.pdf"
elif "download" in end_point:
print("mocking __fetch_url download endpoint")
elif "mv" in end_point:
print("mocking __fetch_url mv endpoint")
return "successfully moved tgu2/test.pdf to tgu2/test_1.pdf"
@patch.object(Helper, "_Helper__fetch_url", side_effect=mock_fetch_url)
def test_list(self, _fetch_url):
file_list = self.staging_helper.list()
self.assertTrue("tgu/test_file_1" in file_list)
self.assertTrue("tgu/test_dir/test_file_2" in file_list)
self.assertTrue("tgu/test_dir" not in file_list)
def test_missing_path(self):
with self.assertRaises(ValueError) as context:
self.staging_helper.metadata()
self.assertEqual("Must provide path argument", str(context.exception))
@patch.object(Helper, "_Helper__fetch_url", side_effect=mock_fetch_url)
def test_metadata(self, _fetch_url):
metadata = self.staging_helper.metadata("test_fake_file")
self.assertTrue("head" in metadata)
self.assertEqual(metadata.get("head"), "head_line")
self.assertTrue("tail" in metadata)
self.assertEqual(metadata.get("tail"), "tail_line")
self.assertTrue("lineCount" in metadata)
self.assertEqual(metadata.get("lineCount"), 10)
@patch.object(Helper, "_Helper__fetch_url", side_effect=mock_fetch_url)
def test_jgi_metadata(self, _fetch_url):
metadata = self.staging_helper.jgi_metadata("test_fake_file")
self.assertTrue("file_name" in metadata)
self.assertEqual(metadata.get("file_name"), "test_file")
self.assertTrue("file_status" in metadata)
self.assertEqual(metadata.get("file_status"), "BACKUP_COMPLETE")
@patch.object(Helper, "_Helper__fetch_url", side_effect=mock_fetch_url)
def test_search(self, _fetch_url):
search_ret = self.staging_helper.search("test_fake_file")
self.assertTrue(isinstance(search_ret, (list)))
element = search_ret[0]
self.assertTrue("isFolder" in element)
self.assertFalse(element.get("isFolder"))
self.assertTrue("name" in element)
self.assertEqual(element.get("name"), "LMS-PROC-315.pdf")
@patch.object(Helper, "_Helper__fetch_url", side_effect=mock_fetch_url)
def test_delete(self, _fetch_url):
delete_ret = self.staging_helper.delete("test_fake_file")
self.assertTrue("server_response" in delete_ret)
self.assertEqual(
delete_ret.get("server_response"), "successfully deleted tgu2/test.pdf"
)
@patch.object(Helper, "_Helper__fetch_url", side_effect=mock_fetch_url)
def test_download(self, _fetch_url):
download_ret = self.staging_helper.download("test_fake_file")
self.assertTrue("test_fake_file" in download_ret)
@patch.object(Helper, "_Helper__fetch_url", side_effect=mock_fetch_url)
def test_mv(self, _fetch_url):
mv_ret = self.staging_helper.mv("test.pdf ", "test_1.pdf")
self.assertTrue("server_response" in mv_ret)
self.assertEqual(
mv_ret.get("server_response"),
"successfully moved tgu2/test.pdf to tgu2/test_1.pdf",
)
