def test_annotations():
# Get the annotations of an Entity
entity = syn.store(Folder(parent=project['id']))
anno = syn.getAnnotations(entity)
assert hasattr(anno, 'id')
assert hasattr(anno, 'etag')
assert anno.id == entity.id
assert anno.etag == entity.etag
# Set the annotations, with keywords too
anno['bogosity'] = 'total'
syn.setAnnotations(entity, anno, wazoo='Frank', label='Barking Pumpkin', shark=16776960)
# Check the update
annote = syn.getAnnotations(entity)
assert annote['bogosity'] == ['total']
assert annote['wazoo'] == ['Frank']
assert annote['label'] == ['Barking Pumpkin']
assert annote['shark'] == [16776960]
# More annotation setting
annote['primes'] = [2,3,5,7,11,13,17,19,23,29]
annote['phat_numbers'] = [1234.5678, 8888.3333, 1212.3434, 6677.8899]
annote['goobers'] = ['chris', 'jen', 'jane']
annote['present_time'] = datetime.now()
syn.setAnnotations(entity, annote)
# Check it again
annotation = syn.getAnnotations(entity)
assert annotation['primes'] == [2,3,5,7,11,13,17,19,23,29]
assert annotation['phat_numbers'] == [1234.5678, 8888.3333, 1212.3434, 6677.8899]
assert annotation['goobers'] == ['chris', 'jen', 'jane']
assert annotation['present_time'][0].strftime('%Y-%m-%d %H:%M:%S') == annote['present_time'].strftime('%Y-%m-%d %H:%M:%S')
def test_chunked_query():
oldLimit = synapseclient.client.QUERY_LIMIT
try:
synapseclient.client.QUERY_LIMIT = 3
time.sleep(3)
# Remove all the Entities that are in the project
iter = syn.chunkedQuery("select id from entity where entity.parentId=='%s'" % project['id'])
for res in iter:
syn.delete(res['entity.id'])
# Dump a bunch of Entities into the project
for i in range(synapseclient.client.QUERY_LIMIT * 5):
syn.store(Folder(parent=project['id']))
time.sleep(3)
# Give a bunch of limits/offsets to be ignored (except for the first ones)
queryString = "select * from entity where entity.parentId=='%s' offset 1 limit 9999999999999 offset 2345 limit 6789 offset 3456 limit 5689" % project['id']
count = 0
start_time = time.time()
while count != (synapseclient.client.QUERY_LIMIT * 5):
assert_less(time.time() - start_time, QUERY_TIMEOUT_SEC)
time.sleep(2)
iter = syn.chunkedQuery(queryString)
count = 0
for res in iter:
count += 1
assert count == (synapseclient.client.QUERY_LIMIT * 5)
finally:
synapseclient.client.QUERY_LIMIT = oldLimit
def test_getChildren():
# setup a hierarchy for folders
# PROJECT
# | \
# File Folder
# |
# File
project_name = str(uuid.uuid1())
test_project = syn.store(Project(name=project_name))
folder = syn.store(Folder(name="firstFolder", parent=test_project))
syn.store(
File(path="~/doesntMatter.txt",
name="file inside folders",
parent=folder,
synapseStore=False))
project_file = syn.store(
File(path="~/doesntMatterAgain.txt",
name="file inside project",
parent=test_project,
synapseStore=False))
schedule_for_cleanup(test_project)
expected_id_set = {project_file.id, folder.id}
children_id_set = {x['id'] for x in syn.getChildren(test_project.id)}
assert_equals(expected_id_set, children_id_set)
def test_chunked_query_giant_row():
import synapseclient.utils as utils
absurdly_long_desription = 'This is an absurdly long description!' + '~'*512000
normal = syn.store(Folder('normal', description='A file with a normal length description', parentId=project['id']))
absurd = syn.store(Folder('absurd', description=absurdly_long_desription, parentId=project['id']))
## the expected behavior is that the absurdly long row will be skipped
## but the normal row will be returned
start_time = time.time()
ids = []
while normal.id not in ids:
assert_less(time.time() - start_time, QUERY_TIMEOUT_SEC)
time.sleep(2)
resultgen = syn.chunkedQuery('select * from entity where parentId=="%s"' % project['id'])
ids = [result['entity.id'] for result in resultgen]
def test_entity_constructors():
project = Project(name=str(uuid.uuid4()), description='Testing 123')
folder = Folder(name='Musicians',
parent=project,
genre='Jazz',
datatype='personnel')
personnel_file = File(fname,
parentId=folder.id,
group='Miles Davis Quintet',
album='Stockholm 1960 Complete')
def test_query():
## TODO: replace this test with the one below when query() is replaced
# Remove all the Entities that are in the project
qry = syn.query("select id from entity where entity.parentId=='%s'" %
project['id'])
for res in qry['results']:
syn.delete(res['entity.id'])
# Add entities and verify that I can find them with a query
for i in range(2):
syn.store(Folder(parent=project['id']))
qry = syn.query(
"select id, name from entity where entity.parentId=='%s'" %
project['id'])
assert qry['totalNumberOfResults'] == i + 1
def test_entity_constructors():
project = Project('TestProject', id='syn1001', foo='bar')
assert project.name == 'TestProject'
assert project['foo'] == 'bar'
folder = Folder('MyFolder', parent=project, foo='bat', id='syn1002')
assert folder.name == 'MyFolder'
assert folder.foo == 'bat'
assert folder.parentId == 'syn1001'
a_file = File('/path/to/fabulous_things.zzz', parent=folder, foo='biz')
#assert a_file.name == 'fabulous_things.zzz'
assert a_file.entityType == 'org.sagebionetworks.repo.model.FileEntity'
assert a_file.path == '/path/to/fabulous_things.zzz'
assert a_file.foo == 'biz'
assert a_file.parentId == 'syn1002'
def test_entity_constructors():
project = Project('TestProject', id='syn1001', foo='bar')
assert project.name == 'TestProject'
assert project['foo'] == 'bar'
folder = Folder('MyFolder', parent=project, foo='bat', id='syn1002')
assert folder.name == 'MyFolder'
assert folder.foo == 'bat'
assert folder.parentId == 'syn1001'
a_file = File('/path/to/fabulous_things.zzz',
parent=folder,
foo='biz',
contentType='application/cattywampus')
#assert a_file.name == 'fabulous_things.zzz'
assert a_file.concreteType == 'org.sagebionetworks.repo.model.FileEntity'
assert a_file.path == '/path/to/fabulous_things.zzz'
assert a_file.foo == 'biz'
assert a_file.parentId == 'syn1002'
assert a_file.contentType == 'application/cattywampus'
assert 'contentType' in a_file.__dict__
def test_entity_constructors():
project = Project('TestProject', id='syn1001', foo='bar')
assert_equals(project.name, 'TestProject')
assert_equals(project['foo'], 'bar')
folder = Folder('MyFolder', parent=project, foo='bat', id='syn1002')
assert_equals(folder.name, 'MyFolder')
assert_equals(folder.foo, 'bat')
assert_equals(folder.parentId, 'syn1001')
a_file = File('/path/to/fabulous_things.zzz',
parent=folder,
foo='biz',
contentType='application/cattywampus')
assert_equals(a_file.concreteType,
'org.sagebionetworks.repo.model.FileEntity')
assert_equals(a_file.path, '/path/to/fabulous_things.zzz')
assert_equals(a_file.foo, 'biz')
assert_equals(a_file.parentId, 'syn1002')
assert_equals(a_file.contentType, 'application/cattywampus')
assert_in('contentType', a_file._file_handle)
def test_query():
## TODO: replace this test with the one below when query() is replaced
query_str = "select id from entity where entity.parentId=='%s'" % project['id']
# Remove all the Entities that are in the project
qry = syn.query(query_str)
while len(qry['results']) > 0:
for res in qry['results']:
syn.delete(res['entity.id'])
qry = syn.query(query_str)
# Add entities and verify that I can find them with a query
for i in range(2):
syn.store(Folder(parent=project['id']))
start_time = time.time()
qry = syn.query(query_str)
while len(qry['results']) != i + 1:
assert_less(time.time() - start_time, QUERY_TIMEOUT_SEC)
time.sleep(2)
qry = syn.query(query_str)
assert len(qry['results']) == i + 1
def test_is_container():
## result from a Synapse entity annotation query
## Note: prefix may be capitalized or not, depending on the from clause of the query
result = {
'entity.versionNumber': 1,
'entity.nodeType': 'project',
'entity.concreteType': ['org.sagebionetworks.repo.model.Project'],
'entity.createdOn': 1451512703905,
'entity.id': 'syn5570912',
'entity.name': 'blah'
}
assert is_container(result)
result = {
'Entity.nodeType': 'project',
'Entity.id': 'syn5570912',
'Entity.name': 'blah'
}
assert is_container(result)
result = {
'entity.concreteType': ['org.sagebionetworks.repo.model.Folder'],
'entity.id': 'syn5570914',
'entity.name': 'flapdoodle'
}
assert is_container(result)
result = {
'File.concreteType': ['org.sagebionetworks.repo.model.FileEntity'],
'File.id': 'syn5570914',
'File.name': 'flapdoodle'
}
assert not is_container(result)
assert is_container(Folder("Stuff", parentId="syn12345"))
assert is_container(Project("My Project", parentId="syn12345"))
assert not is_container(File("asdf.png", parentId="syn12345"))