def test_entity_version():
# Test the ability to get specific versions of Synapse Entities
#Create a new project
project = create_project()
entity = create_data_entity(project['id'])
syn.setAnnotations(entity, {'fizzbuzz':111222})
#Get new entity and check that it is same
entity = syn.getEntity(entity)
assert entity.versionNumber == 1
entity.description = 'Changed something'
entity.foo = 998877
entity = syn.updateEntity(entity, incrementVersion=True)
assert entity.versionNumber == 2
annotations = syn.getAnnotations(entity, version=1)
assert annotations['fizzbuzz'][0] == 111222
returnEntity = syn.getEntity(entity, version=1)
assert returnEntity.versionNumber == 1
assert returnEntity['fizzbuzz'][0] == 111222
assert 'foo' not in returnEntity
returnEntity = syn.getEntity(entity)
assert returnEntity.versionNumber == 2
assert returnEntity['description'] == 'Changed something'
assert returnEntity['foo'][0] == 998877
returnEntity = syn.get(entity, version=1)
assert returnEntity.versionNumber == 1
assert returnEntity['fizzbuzz'][0] == 111222
assert 'foo' not in returnEntity
def test_annotations():
## create a new project
project = create_project()
entity = create_data_entity(project['id'])
a = syn.getAnnotations(entity)
assert 'etag' in a
print a
a['bogosity'] = 'total'
print a
syn.setAnnotations(entity, a)
a2 = syn.getAnnotations(entity)
assert a2['bogosity'] == ['total']
a2['primes'] = [2, 3, 5, 7, 11, 13, 17, 19, 23, 29]
a2['phat_numbers'] = [1234.5678, 8888.3333, 1212.3434, 6677.8899]
a2['goobers'] = ['chris', 'jen', 'jane']
a2['present_time'] = datetime.now()
syn.setAnnotations(entity, a2)
a3 = syn.getAnnotations(entity)
assert a3['primes'] == [2, 3, 5, 7, 11, 13, 17, 19, 23, 29]
assert a3['phat_numbers'] == [1234.5678, 8888.3333, 1212.3434, 6677.8899]
assert a3['goobers'] == ['chris', 'jen', 'jane']
## only accurate to within a second 'cause synapse strips off the fractional part
assert a3['present_time'][0].strftime('%Y-%m-%d %H:%M:%S') == a2[
'present_time'].strftime('%Y-%m-%d %H:%M:%S')
def test_annotations():
## create a new project
project = create_project()
entity = create_data_entity(project['id'])
a = syn.getAnnotations(entity)
assert 'etag' in a
print a
a['bogosity'] = 'total'
print a
syn.setAnnotations(entity, a)
a2 = syn.getAnnotations(entity)
assert a2['bogosity'] == ['total']
a2['primes'] = [2,3,5,7,11,13,17,19,23,29]
a2['phat_numbers'] = [1234.5678, 8888.3333, 1212.3434, 6677.8899]
a2['goobers'] = ['chris', 'jen', 'jane']
a2['present_time'] = datetime.now()
syn.setAnnotations(entity, a2)
a3 = syn.getAnnotations(entity)
assert a3['primes'] == [2,3,5,7,11,13,17,19,23,29]
assert a3['phat_numbers'] == [1234.5678, 8888.3333, 1212.3434, 6677.8899]
assert a3['goobers'] == ['chris', 'jen', 'jane']
## only accurate to within a second 'cause synapse strips off the fractional part
assert a3['present_time'][0].strftime('%Y-%m-%d %H:%M:%S') == a2['present_time'].strftime('%Y-%m-%d %H:%M:%S')
def test_entity_version():
# Test the ability to get specific versions of Synapse Entities
#Create a new project
project = create_project()
entity = create_data_entity(project['id'])
syn.setAnnotations(entity, {'fizzbuzz': 111222})
#Get new entity and check that it is same
entity = syn.getEntity(entity)
assert entity.versionNumber == 1
entity.description = 'Changed something'
entity.foo = 998877
entity = syn.updateEntity(entity, incrementVersion=True)
assert entity.versionNumber == 2
annotations = syn.getAnnotations(entity, version=1)
assert annotations['fizzbuzz'][0] == 111222
returnEntity = syn.getEntity(entity, version=1)
assert returnEntity.versionNumber == 1
assert returnEntity['fizzbuzz'][0] == 111222
assert 'foo' not in returnEntity
returnEntity = syn.getEntity(entity)
assert returnEntity.versionNumber == 2
assert returnEntity['description'] == 'Changed something'
assert returnEntity['foo'][0] == 998877
returnEntity = syn.get(entity, version=1)
assert returnEntity.versionNumber == 1
assert returnEntity['fizzbuzz'][0] == 111222
assert 'foo' not in returnEntity
def test_query():
#Create a project then add entities and verify that I can find them with a query
project = create_project()
for i in range(2):
try:
entity = create_data_entity(project['id'])
except Exception as ex:
print ex
print ex.response.text
qry= syn.query("select id, name from entity where entity.parentId=='%s'" % project['id'])
assert qry['totalNumberOfResults']==(i+1)
def test_keyword_annotations():
"""
Test setting annotations using keyword arguments
"""
## create a new project and data entity
project = create_project()
entity = create_data_entity(project['id'])
annos = syn.setAnnotations(entity, wazoo='Frank', label='Barking Pumpkin', shark=16776960)
assert annos['wazoo'] == ['Frank']
assert annos['label'] == ['Barking Pumpkin']
assert annos['shark'] == [16776960]
def test_updateEntity_version():
project = create_project()
entity = create_data_entity(project['id'])
entity['name'] = 'foobarbat'
entity['description'] = 'This is a test entity...'
entity = syn.updateEntity(entity, incrementVersion=True, versionLabel="Prada remix")
returnEntity = syn.getEntity(entity)
# syn.printEntity(returnEntity)
assert returnEntity['name'] == 'foobarbat'
assert returnEntity['description'] == 'This is a test entity...'
assert returnEntity['versionNumber'] == 2
assert returnEntity['versionLabel'] == 'Prada remix'
def test_query():
#Create a project then add entities and verify that I can find them with a query
project = create_project()
for i in range(2):
try:
entity = create_data_entity(project['id'])
except Exception as ex:
print ex
print ex.response.text
qry = syn.query(
"select id, name from entity where entity.parentId=='%s'" %
project['id'])
assert qry['totalNumberOfResults'] == (i + 1)
def test_updateEntity_version():
project = create_project()
entity = create_data_entity(project['id'])
entity['name'] = 'foobarbat'
entity['description'] = 'This is a test entity...'
entity = syn.updateEntity(entity,
incrementVersion=True,
versionLabel="Prada remix")
returnEntity = syn.getEntity(entity)
# syn.printEntity(returnEntity)
assert returnEntity['name'] == 'foobarbat'
assert returnEntity['description'] == 'This is a test entity...'
assert returnEntity['versionNumber'] == 2
assert returnEntity['versionLabel'] == 'Prada remix'
def test_keyword_annotations():
"""
Test setting annotations using keyword arguments
"""
## create a new project and data entity
project = create_project()
entity = create_data_entity(project['id'])
annos = syn.setAnnotations(entity,
wazoo='Frank',
label='Barking Pumpkin',
shark=16776960)
assert annos['wazoo'] == ['Frank']
assert annos['label'] == ['Barking Pumpkin']
assert annos['shark'] == [16776960]
def test_uploadFile():
project = create_project()
## here, entity has been saved to Synapse and entity is an Entity object
entity = create_data_entity(project['id'])
#create a temporary file
fname = utils.make_bogus_data_file()
syn.uploadFile(entity, fname)
#Download and verify that it is the same filename
entity = syn.downloadEntity(entity)
assert entity['files'][0]==os.path.basename(fname)
assert filecmp.cmp(fname, os.path.join(entity['cacheDir'],entity['files'][0]))
os.remove(fname)
def test_uploadFile():
project = create_project()
## here, entity has been saved to Synapse and entity is an Entity object
entity = create_data_entity(project['id'])
#create a temporary file
fname = utils.make_bogus_data_file()
syn.uploadFile(entity, fname)
#Download and verify that it is the same filename
entity = syn.downloadEntity(entity)
assert entity['files'][0] == os.path.basename(fname)
assert filecmp.cmp(fname,
os.path.join(entity['cacheDir'], entity['files'][0]))
os.remove(fname)
def test_chunked_query():
# Change the size of the query limit
oldLimit = client.QUERY_LIMIT
client.QUERY_LIMIT = 3
# Create a project to dump a bunch of Entities into
project = create_project()
for i in range(client.QUERY_LIMIT * 5):
try:
entity = create_data_entity(project['id'])
except Exception as ex:
print ex
print ex.response.text
iter = syn.chunkedQuery("select * from entity where entity.parentId=='%s'" % project['id'])
count = 0
for res in iter:
count += 1
assert count == (client.QUERY_LIMIT * 5)
# Restore the size of the query limit
client.QUERY_LIMIT = oldLimit
def test_chunked_query():
# Change the size of the query limit
oldLimit = client.QUERY_LIMIT
client.QUERY_LIMIT = 3
# Create a project to dump a bunch of Entities into
project = create_project()
for i in range(client.QUERY_LIMIT * 5):
try:
entity = create_data_entity(project['id'])
except Exception as ex:
print ex
print ex.response.text
iter = syn.chunkedQuery(
"select * from entity where entity.parentId=='%s'" % project['id'])
count = 0
for res in iter:
count += 1
assert count == (client.QUERY_LIMIT * 5)
# Restore the size of the query limit
client.QUERY_LIMIT = oldLimit
def test_provenance():
"""
test provenance features
"""
## create a new project
project = create_project()
## create a data entity
try:
filename = utils.make_bogus_data_file()
data_entity = create_data_entity(project['id'])
data_entity = syn.uploadFile(data_entity, filename)
finally:
os.remove(filename)
## create a code entity, source of the data above
code = """
## Chris's fabulous random data generator
############################################################
import random
random.seed(12345)
data = [random.gauss(mu=0.0, sigma=1.0) for i in range(100)]
"""
try:
try:
f = tempfile.NamedTemporaryFile(suffix=".py", delete=False)
f.write(code)
f.write("\n")
finally:
f.close()
CODE_JSON['parentId'] = project['id']
code_entity = syn.createEntity(CODE_JSON)
code_entity = syn.uploadFile(code_entity, f.name)
finally:
os.remove(f.name)
## create a new activity asserting that the code entity was used to
## make the data entity
activity = Activity(name='random.gauss',
description='Generate some random numbers')
activity.used(code_entity, wasExecuted=True)
activity.used(
{
'name': 'Superhack',
'url': 'https://github.com/joe_coder/Superhack'
},
wasExecuted=True)
activity = syn.setProvenance(data_entity, activity)
## retrieve the saved provenance record
retrieved_activity = syn.getProvenance(data_entity)
## does it match what we expect?
assert retrieved_activity == activity
## test update
new_description = 'Generate random numbers like a gangsta'
retrieved_activity['description'] = new_description
updated_activity = syn.updateActivity(retrieved_activity)
## did the update stick?
assert updated_activity['name'] == retrieved_activity['name']
assert updated_activity['description'] == new_description
## test delete
syn.deleteProvenance(data_entity)
try:
## provenance should be gone now
## decided this should throw exception with a 404
deleted_activity = syn.getProvenance(data_entity['id'])
except Exception as ex:
assert ex.response.status_code == 404
else:
assert False, 'Should throw 404 exception'
def test_download_empty_entity():
project = create_project()
entity = create_data_entity(project['id'])
entity = syn.downloadEntity(entity)
def test_download_empty_entity():
project = create_project()
entity = create_data_entity(project['id'])
entity = syn.downloadEntity(entity)
def test_provenance():
"""
test provenance features
"""
## create a new project
project = create_project()
## create a data entity
try:
filename = utils.make_bogus_data_file()
data_entity = create_data_entity(project['id'])
data_entity = syn.uploadFile(data_entity, filename)
finally:
os.remove(filename)
## create a code entity, source of the data above
code = """
## Chris's fabulous random data generator
############################################################
import random
random.seed(12345)
data = [random.gauss(mu=0.0, sigma=1.0) for i in range(100)]
"""
try:
try:
f = tempfile.NamedTemporaryFile(suffix=".py", delete=False)
f.write(code)
f.write("\n")
finally:
f.close()
CODE_JSON['parentId']= project['id']
code_entity = syn.createEntity(CODE_JSON)
code_entity = syn.uploadFile(code_entity, f.name)
finally:
os.remove(f.name)
## create a new activity asserting that the code entity was used to
## make the data entity
activity = Activity(name='random.gauss', description='Generate some random numbers')
activity.used(code_entity, wasExecuted=True)
activity.used({'name':'Superhack', 'url':'https://github.com/joe_coder/Superhack'}, wasExecuted=True)
activity = syn.setProvenance(data_entity, activity)
## retrieve the saved provenance record
retrieved_activity = syn.getProvenance(data_entity)
## does it match what we expect?
assert retrieved_activity == activity
## test update
new_description = 'Generate random numbers like a gangsta'
retrieved_activity['description'] = new_description
updated_activity = syn.updateActivity(retrieved_activity)
## did the update stick?
assert updated_activity['name'] == retrieved_activity['name']
assert updated_activity['description'] == new_description
## test delete
syn.deleteProvenance(data_entity)
try:
## provenance should be gone now
## decided this should throw exception with a 404
deleted_activity = syn.getProvenance(data_entity['id'])
except Exception as ex:
assert ex.response.status_code == 404
else:
assert False, 'Should throw 404 exception'
