def test_store_with_create_or_update_flag():
project = create_project()
filepath = utils.make_bogus_binary_file()
bogus1 = File(filepath, name='Bogus Test File', parent=project)
bogus1 = syn.store(bogus1, createOrUpdate=True)
# Create a different file with the same name and parent
new_filepath = utils.make_bogus_binary_file()
bogus1.path = new_filepath
# Expected behavior is that a new version of the first File will be created
bogus2 = syn.store(bogus1, createOrUpdate=True)
assert bogus2.id == bogus1.id
assert bogus2.versionNumber == 2
assert not filecmp.cmp(bogus2.path, filepath)
bogus2a = syn.get(bogus2.id)
assert bogus2a.id == bogus1.id
assert bogus2a.versionNumber == 2
assert filecmp.cmp(bogus2.path, bogus2a.path)
# Create yet another file with the same name and parent
newer_filepath = utils.make_bogus_binary_file()
bogus3 = File(newer_filepath, name='Bogus Test File', parent=project)
# Expected behavior is raising an exception with a 409 error
assert_raises(requests.exceptions.HTTPError, syn.store, bogus3, createOrUpdate=False)
def test_store_with_create_or_update_flag():
project = create_project()
filepath = utils.make_bogus_binary_file()
bogus1 = File(filepath, name='Bogus Test File', parent=project)
bogus1 = syn.store(bogus1, createOrUpdate=True)
# Create a different file with the same name and parent
new_filepath = utils.make_bogus_binary_file()
bogus1.path = new_filepath
# Expected behavior is that a new version of the first File will be created
bogus2 = syn.store(bogus1, createOrUpdate=True)
assert bogus2.id == bogus1.id
assert bogus2.versionNumber == 2
assert not filecmp.cmp(bogus2.path, filepath)
bogus2a = syn.get(bogus2.id)
assert bogus2a.id == bogus1.id
assert bogus2a.versionNumber == 2
assert filecmp.cmp(bogus2.path, bogus2a.path)
# Create yet another file with the same name and parent
newer_filepath = utils.make_bogus_binary_file()
bogus3 = File(newer_filepath, name='Bogus Test File', parent=project)
# Expected behavior is raising an exception with a 409 error
assert_raises(requests.exceptions.HTTPError,
syn.store,
bogus3,
createOrUpdate=False)
def test_uploadFileEntity(syn, project, schedule_for_cleanup):
# Create a FileEntity
# Dictionaries default to FileEntity as a type
fname = utils.make_bogus_data_file()
schedule_for_cleanup(fname)
entity = File(name='fooUploadFileEntity',
path=fname,
parentId=project['id'],
description='A test file entity')
entity = syn.store(entity)
# Download and verify
entity = syn.get(entity)
assert entity['files'][0] == os.path.basename(fname)
assert filecmp.cmp(fname, entity['path'])
# Check if we upload the wrong type of file handle
fh = syn.restGET('/entity/%s/filehandles' % entity.id)['list'][0]
assert fh[
'concreteType'] == 'org.sagebionetworks.repo.model.file.S3FileHandle'
# Create a different temporary file
fname = utils.make_bogus_data_file()
schedule_for_cleanup(fname)
# Update existing FileEntity
entity.path = fname
entity = syn.store(entity)
# Download and verify that it is the same file
entity = syn.get(entity)
assert entity['files'][0] == os.path.basename(fname)
assert filecmp.cmp(fname, entity['path'])
def test_download_file_URL_false():
# Upload an external file handle
fileThatExists = 'http://dev-versions.synapse.sagebase.org/synapsePythonClient'
reupload = File(fileThatExists, synapseStore=False, parent=project)
reupload = syn.store(reupload)
reupload = syn.get(reupload, downloadFile=False)
originalVersion = reupload.versionNumber
# Reupload and check that the URL and version does not get mangled
reupload = syn.store(reupload, forceVersion=False)
assert_equals(reupload.path, fileThatExists,
"Entity should still be pointing at a URL")
assert_equals(originalVersion, reupload.versionNumber)
# Try a URL with an extra slash at the end
fileThatDoesntExist = 'http://dev-versions.synapse.sagebase.org/synapsePythonClient/'
reupload.synapseStore = False
reupload.path = fileThatDoesntExist
reupload = syn.store(reupload)
reupload = syn.get(reupload, downloadFile=False)
originalVersion = reupload.versionNumber
reupload = syn.store(reupload, forceVersion=False)
assert_equals(reupload.path, fileThatDoesntExist,
"Entity should still be pointing at a URL")
assert_equals(originalVersion, reupload.versionNumber)
def test_Entity():
# Test CRUD on Entity objects, Project, Folder, File with createEntity/getEntity/updateEntity
project_name = str(uuid.uuid4())
project = Project(project_name, description='Bogus testing project')
project = syn.createEntity(project)
schedule_for_cleanup(project)
folder = Folder('Test Folder', parent=project, description='A place to put my junk', foo=1000)
folder = syn.createEntity(folder)
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(path, parent=folder, description='Random data for testing', foo='An arbitrary value', bar=[33,44,55], bday=Datetime(2013,3,15))
a_file = syn._createFileEntity(a_file)
## local object state should be preserved
assert a_file.path == path
## check the project entity
project = syn.getEntity(project)
assert project.name == project_name
## check the folder entity
folder = syn.getEntity(folder.id)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.foo[0] == 1000
## check the file entity
a_file = syn.getEntity(a_file)
assert a_file['foo'][0] == 'An arbitrary value'
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
## make sure file comes back intact
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(path, a_file.path)
#TODO We're forgotten the local file path
a_file.path = path
## update the file entity
a_file['foo'] = 'Another arbitrary chunk of text data'
a_file['new_key'] = 'A newly created value'
a_file = syn.updateEntity(a_file)
assert a_file['foo'][0] == 'Another arbitrary chunk of text data'
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
assert a_file.new_key[0] == 'A newly created value'
assert a_file.path == path
## upload a new file
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file = syn.uploadFile(a_file, new_path)
## make sure file comes back intact
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(new_path, a_file.path)
def test_download_file_URL_false():
# Upload an external file handle
fileThatExists = 'http://dev-versions.synapse.sagebase.org/synapsePythonClient'
reupload = File(fileThatExists, synapseStore=False, parent=project)
reupload = syn.store(reupload)
reupload = syn.get(reupload, downloadFile=False)
originalVersion = reupload.versionNumber
# Reupload and check that the URL and version does not get mangled
reupload = syn.store(reupload, forceVersion=False)
assert reupload.path == fileThatExists, "Entity should still be pointing at a URL"
assert originalVersion == reupload.versionNumber
# Try a URL with an extra slash at the end
fileThatDoesntExist = 'http://dev-versions.synapse.sagebase.org/synapsePythonClient/'
reupload.synapseStore = False
reupload.path = fileThatDoesntExist
reupload = syn.store(reupload)
reupload = syn.get(reupload, downloadFile=False)
originalVersion = reupload.versionNumber
reupload = syn.store(reupload, forceVersion=False)
assert reupload.path == fileThatDoesntExist, "Entity should still be pointing at a URL"
assert originalVersion == reupload.versionNumber
def test_Entity():
# Update the project
project_name = str(uuid.uuid4())
project = Project(name=project_name)
project = syn.store(project)
schedule_for_cleanup(project)
project = syn.getEntity(project)
assert project.name == project_name
# Create and get a Folder
folder = Folder('Test Folder', parent=project, description='A place to put my junk', foo=1000)
folder = syn.createEntity(folder)
folder = syn.getEntity(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'A place to put my junk'
assert folder.foo[0] == 1000
# Update and get the Folder
folder.pi = 3.14159265359
folder.description = 'The rejects from the other folder'
folder = syn.store(folder)
folder = syn.get(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other folder'
assert folder.pi[0] == 3.14159265359
# Test CRUD on Files
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(path, parent=folder, description='Random data for testing',
contentType='text/flapdoodle',
foo='An arbitrary value', bar=[33,44,55], bday=Datetime(2013,3,15))
a_file = syn._createFileEntity(a_file)
assert a_file.path == path
a_file = syn.getEntity(a_file)
assert a_file['foo'][0] == 'An arbitrary value'
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
assert a_file.contentType == 'text/flapdoodle'
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(path, a_file.path)
# Update the File
a_file.path = path
a_file['foo'] = 'Another arbitrary chunk of text data'
a_file['new_key'] = 'A newly created value'
a_file = syn.updateEntity(a_file)
assert a_file['foo'][0] == 'Another arbitrary chunk of text data'
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
assert a_file.new_key[0] == 'A newly created value'
assert a_file.path == path
assert a_file.versionNumber == 1
# Upload a new File and verify
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file = syn.uploadFile(a_file, new_path)
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(new_path, a_file.path)
assert a_file.versionNumber == 2
# Make sure we can still get the older version of file
old_random_data = syn.get(a_file.id, version=1)
assert filecmp.cmp(old_random_data.path, path)
def test_Entity():
# Update the project
project_name = str(uuid.uuid4())
project = Project(name=project_name)
project = syn.store(project)
schedule_for_cleanup(project)
project = syn.getEntity(project)
assert project.name == project_name
# Create and get a Folder
folder = Folder('Test Folder',
parent=project,
description='A place to put my junk',
foo=1000)
folder = syn.createEntity(folder)
folder = syn.getEntity(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'A place to put my junk'
assert folder.foo[0] == 1000
# Update and get the Folder
folder.pi = 3.14159265359
folder.description = 'The rejects from the other folder'
folder = syn.store(folder)
folder = syn.get(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other folder'
assert folder.pi[0] == 3.14159265359
# Test CRUD on Files, check unicode
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(path,
parent=folder,
description=
u'Description with funny characters: Déjà vu, ประเทศไทย, 中国',
contentType='text/flapdoodle',
foo='An arbitrary value',
bar=[33, 44, 55],
bday=Datetime(2013, 3, 15),
band=u"Motörhead",
lunch=u"すし")
a_file = syn.store(a_file)
assert a_file.path == path
a_file = syn.getEntity(a_file)
assert a_file.description == u'Description with funny characters: Déjà vu, ประเทศไทย, 中国', u'description= %s' % a_file.description
assert a_file['foo'][
0] == 'An arbitrary value', u'foo= %s' % a_file['foo'][0]
assert a_file['bar'] == [33, 44, 55]
assert a_file['bday'][0] == Datetime(2013, 3, 15)
assert a_file.contentType == 'text/flapdoodle', u'contentType= %s' % a_file.contentType
assert a_file['band'][0] == u"Motörhead", u'band= %s' % a_file['band'][0]
assert a_file['lunch'][0] == u"すし", u'lunch= %s' % a_file['lunch'][0]
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(path, a_file.path)
# Update the File
a_file.path = path
a_file['foo'] = 'Another arbitrary chunk of text data'
a_file['new_key'] = 'A newly created value'
a_file = syn.updateEntity(a_file)
assert a_file['foo'][0] == 'Another arbitrary chunk of text data'
assert a_file['bar'] == [33, 44, 55]
assert a_file['bday'][0] == Datetime(2013, 3, 15)
assert a_file.new_key[0] == 'A newly created value'
assert a_file.path == path
assert a_file.versionNumber == 1, "unexpected version number: " + str(
a_file.versionNumber)
#Test create, store, get Links
link = Link(a_file['id'],
targetVersion=a_file.versionNumber,
parent=project)
link = syn.store(link)
assert link['linksTo']['targetId'] == a_file['id']
assert link['linksTo']['targetVersionNumber'] == a_file.versionNumber
assert link['linksToClassName'] == a_file['concreteType']
testLink = syn.get(link, followLink=False)
assert testLink == link
link = syn.getEntity(link)
assert link['foo'][0] == 'Another arbitrary chunk of text data'
assert link['bar'] == [33, 44, 55]
assert link['bday'][0] == Datetime(2013, 3, 15)
assert link.new_key[0] == 'A newly created value'
assert utils.equal_paths(link.path, path)
assert link.versionNumber == 1, "unexpected version number: " + str(
a_file.versionNumber)
# Upload a new File and verify
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file = syn.uploadFile(a_file, new_path)
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(new_path, a_file.path)
assert a_file.versionNumber == 2
# Make sure we can still get the older version of file
old_random_data = syn.get(a_file.id, version=1)
assert filecmp.cmp(old_random_data.path, path)
tmpdir = tempfile.mkdtemp()
schedule_for_cleanup(tmpdir)
## test file name override
a_file.fileNameOverride = "peaches_en_regalia.zoinks"
syn.store(a_file)
## TODO We haven't defined how filename override interacts with
## TODO previously cached files so, side-step that for now by
## TODO making sure the file is not in the cache!
syn.cache.remove(a_file.dataFileHandleId, delete=True)
a_file_retreived = syn.get(a_file, downloadLocation=tmpdir)
assert os.path.basename(
a_file_retreived.path) == a_file.fileNameOverride, os.path.basename(
a_file_retreived.path)
## test getting the file from the cache with downloadLocation parameter (SYNPY-330)
a_file_cached = syn.get(a_file.id, downloadLocation=tmpdir)
assert a_file_cached.path is not None
assert os.path.basename(
a_file_cached.path) == a_file.fileNameOverride, a_file_cached.path
print("\n\nList of files in project:\n")
syn._list(project, recursive=True)
def test_Entity():
# Test CRUD on Entity objects, Project, Folder, File with createEntity/getEntity/updateEntity
project_name = str(uuid.uuid4())
project = Project(project_name, description='Bogus testing project')
project = syn.createEntity(project)
schedule_for_cleanup(project)
folder = Folder('Test Folder',
parent=project,
description='A place to put my junk',
foo=1000)
folder = syn.createEntity(folder)
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(path,
parent=folder,
description='Random data for testing',
foo='An arbitrary value',
bar=[33, 44, 55],
bday=Datetime(2013, 3, 15))
a_file = syn._createFileEntity(a_file)
## local object state should be preserved
assert a_file.path == path
## check the project entity
project = syn.getEntity(project)
assert project.name == project_name
## check the folder entity
folder = syn.getEntity(folder.id)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.foo[0] == 1000
## check the file entity
a_file = syn.getEntity(a_file)
assert a_file['foo'][0] == 'An arbitrary value'
assert a_file['bar'] == [33, 44, 55]
assert a_file['bday'][0] == Datetime(2013, 3, 15)
## make sure file comes back intact
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(path, a_file.path)
#TODO We're forgotten the local file path
a_file.path = path
## update the file entity
a_file['foo'] = 'Another arbitrary chunk of text data'
a_file['new_key'] = 'A newly created value'
a_file = syn.updateEntity(a_file)
assert a_file['foo'][0] == 'Another arbitrary chunk of text data'
assert a_file['bar'] == [33, 44, 55]
assert a_file['bday'][0] == Datetime(2013, 3, 15)
assert a_file.new_key[0] == 'A newly created value'
assert a_file.path == path
## upload a new file
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file = syn.uploadFile(a_file, new_path)
## make sure file comes back intact
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(new_path, a_file.path)
def test_get_and_store():
"""Test synapse.get and synapse.store in Project, Folder and File"""
## create project
project = Project(name=str(uuid.uuid4()),
description='A bogus test project')
project = syn.store(project)
schedule_for_cleanup(project)
## create folder
folder = Folder('Bad stuff',
parent=project,
description='The rejects from the other fauxldurr',
pi=3)
folder = syn.store(folder)
## get folder
folder = syn.get(folder.id)
assert folder.name == 'Bad stuff'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other fauxldurr'
assert folder.pi[0] == 3
## update folder
folder.pi = 3.14159265359
folder.description = 'The rejects from the other folder'
syn.store(folder)
## verify that the updates stuck
folder = syn.get(folder)
assert folder.name == 'Bad stuff'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other folder'
assert folder.pi[0] == 3.14159265359
## upload a File
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
random_data = File(path,
parent=folder,
description='Random data',
foo=9844)
random_data = syn.store(random_data)
## make sure file comes back intact
random_data_2 = syn.downloadEntity(random_data)
assert filecmp.cmp(path, random_data_2.path)
assert random_data.foo[0] == 9844
## update with a new File
new_file_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_file_path)
random_data.path = new_file_path
random_data.foo = 1266
random_data = syn.store(random_data)
## should be version 2
assert random_data.versionNumber == 2
## make sure the updates stuck
random_data_2 = syn.get(random_data)
assert random_data_2.path is not None
assert filecmp.cmp(new_file_path, random_data_2.path)
assert random_data_2.foo[0] == 1266
assert random_data_2.versionNumber == 2
## make sure we can still get the older version of file
old_random_data = syn.get(random_data.id, version=1)
assert filecmp.cmp(old_random_data.path, path)
def test_Entity():
# Update the project
project_name = str(uuid.uuid4())
project = Project(name=project_name)
project = syn.store(project)
schedule_for_cleanup(project)
project = syn.getEntity(project)
assert project.name == project_name
# Create and get a Folder
folder = Folder('Test Folder', parent=project, description='A place to put my junk', foo=1000)
folder = syn.createEntity(folder)
folder = syn.getEntity(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'A place to put my junk'
assert folder.foo[0] == 1000
# Update and get the Folder
folder.pi = 3.14159265359
folder.description = 'The rejects from the other folder'
folder = syn.store(folder)
folder = syn.get(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other folder'
assert folder.pi[0] == 3.14159265359
# Test CRUD on Files, check unicode
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(path, parent=folder, description=u'Description with funny characters: Déjà vu, ประเทศไทย, 中国',
contentType='text/flapdoodle',
foo='An arbitrary value',
bar=[33,44,55],
bday=Datetime(2013,3,15),
band=u"Motörhead",
lunch=u"すし")
a_file = syn.store(a_file)
assert a_file.path == path
a_file = syn.getEntity(a_file)
assert a_file.description == u'Description with funny characters: Déjà vu, ประเทศไทย, 中国', u'description= %s' % a_file.description
assert a_file['foo'][0] == 'An arbitrary value', u'foo= %s' % a_file['foo'][0]
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
assert a_file.contentType == 'text/flapdoodle', u'contentType= %s' % a_file.contentType
assert a_file['band'][0] == u"Motörhead", u'band= %s' % a_file['band'][0]
assert a_file['lunch'][0] == u"すし", u'lunch= %s' % a_file['lunch'][0]
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(path, a_file.path)
# Update the File
a_file.path = path
a_file['foo'] = 'Another arbitrary chunk of text data'
a_file['new_key'] = 'A newly created value'
a_file = syn.updateEntity(a_file)
assert a_file['foo'][0] == 'Another arbitrary chunk of text data'
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
assert a_file.new_key[0] == 'A newly created value'
assert a_file.path == path
assert a_file.versionNumber == 1, "unexpected version number: " + str(a_file.versionNumber)
# Upload a new File and verify
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file = syn.uploadFile(a_file, new_path)
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(new_path, a_file.path)
assert a_file.versionNumber == 2
# Make sure we can still get the older version of file
old_random_data = syn.get(a_file.id, version=1)
assert filecmp.cmp(old_random_data.path, path)
def test_Entity(syn, project, schedule_for_cleanup):
# Update the project
project_name = str(uuid.uuid4())
project = Project(name=project_name)
project = syn.store(project)
schedule_for_cleanup(project)
project = syn.get(project)
assert project.name == project_name
# Create and get a Folder
folder = Folder('Test Folder', parent=project, description='A place to put my junk', foo=1000)
folder = syn.store(folder)
folder = syn.get(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'A place to put my junk'
assert folder.foo[0] == 1000
# Update and get the Folder
folder.pi = 3.14159265359
folder.description = 'The rejects from the other folder'
folder = syn.store(folder)
folder = syn.get(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other folder'
assert folder.pi[0] == 3.14159265359
# Test CRUD on Files, check unicode
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(path, parent=folder, description=u'Description with funny characters: Déjà vu, ประเทศไทย, 中国',
contentType='text/flapdoodle',
foo='An arbitrary value',
bar=[33, 44, 55],
bday=Datetime(2013, 3, 15),
band=u"Motörhead",
lunch=u"すし")
a_file = syn.store(a_file)
assert a_file.path == path
a_file = syn.get(a_file)
assert a_file.description ==\
u'Description with funny characters: Déjà vu, ประเทศไทย, 中国', \
u'description= %s' % a_file.description
assert a_file['foo'][0] == 'An arbitrary value', u'foo= %s' % a_file['foo'][0]
assert a_file['bar'] == [33, 44, 55]
assert a_file['bday'][0] == Datetime(2013, 3, 15)
assert a_file.contentType == 'text/flapdoodle', u'contentType= %s' % a_file.contentType
assert a_file['band'][0] == u"Motörhead", u'band= %s' % a_file['band'][0]
assert a_file['lunch'][0] == u"すし", u'lunch= %s' % a_file['lunch'][0]
a_file = syn.get(a_file)
assert filecmp.cmp(path, a_file.path)
b_file = File(name="blah", parent=folder, dataFileHandleId=a_file.dataFileHandleId)
b_file = syn.store(b_file)
assert b_file.dataFileHandleId == a_file.dataFileHandleId
# Update the File
a_file.path = path
a_file['foo'] = 'Another arbitrary chunk of text data'
a_file['new_key'] = 'A newly created value'
a_file = syn.store(a_file, forceVersion=False)
assert a_file['foo'][0] == 'Another arbitrary chunk of text data'
assert a_file['bar'] == [33, 44, 55]
assert a_file['bday'][0] == Datetime(2013, 3, 15)
assert a_file.new_key[0] == 'A newly created value'
assert a_file.path == path
assert a_file.versionNumber == 1, "unexpected version number: " + str(a_file.versionNumber)
# Test create, store, get Links
# If version isn't specified, targetVersionNumber should not be set
link = Link(a_file['id'],
parent=project)
link = syn.store(link)
assert link['linksTo']['targetId'] == a_file['id']
assert link['linksTo'].get('targetVersionNumber') is None
assert link['linksToClassName'] == a_file['concreteType']
link = Link(a_file['id'],
targetVersion=a_file.versionNumber,
parent=project)
link = syn.store(link)
assert link['linksTo']['targetId'] == a_file['id']
assert link['linksTo']['targetVersionNumber'] == a_file.versionNumber
assert link['linksToClassName'] == a_file['concreteType']
testLink = syn.get(link)
assert testLink == link
link = syn.get(link, followLink=True)
assert link['foo'][0] == 'Another arbitrary chunk of text data'
assert link['bar'] == [33, 44, 55]
assert link['bday'][0] == Datetime(2013, 3, 15)
assert link.new_key[0] == 'A newly created value'
assert utils.equal_paths(link.path, path)
assert link.versionNumber == 1, "unexpected version number: " + str(a_file.versionNumber)
newfolder = Folder('Testing Folder', parent=project)
newfolder = syn.store(newfolder)
link = Link(newfolder, parent=folder.id)
link = syn.store(link)
assert link['linksTo']['targetId'] == newfolder.id
assert link['linksToClassName'] == newfolder['concreteType']
assert link['linksTo'].get('targetVersionNumber') is None
# Upload a new File and verify
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file.path = new_path
a_file = syn.store(a_file)
a_file = syn.get(a_file)
assert filecmp.cmp(new_path, a_file.path)
assert a_file.versionNumber == 2
# Make sure we can still get the older version of file
old_random_data = syn.get(a_file.id, version=1)
assert filecmp.cmp(old_random_data.path, path)
tmpdir = tempfile.mkdtemp()
schedule_for_cleanup(tmpdir)
# test getting the file from the cache with downloadLocation parameter (SYNPY-330)
a_file_cached = syn.get(a_file.id, downloadLocation=tmpdir)
assert a_file_cached.path is not None
assert os.path.basename(a_file_cached.path) == os.path.basename(a_file.path)
def test_Entity():
# Update the project
project_name = str(uuid.uuid4())
project = Project(name=project_name)
project = syn.store(project)
schedule_for_cleanup(project)
project = syn.getEntity(project)
assert project.name == project_name
# Create and get a Folder
folder = Folder("Test Folder", parent=project, description="A place to put my junk", foo=1000)
folder = syn.createEntity(folder)
folder = syn.getEntity(folder)
assert folder.name == "Test Folder"
assert folder.parentId == project.id
assert folder.description == "A place to put my junk"
assert folder.foo[0] == 1000
# Update and get the Folder
folder.pi = 3.14159265359
folder.description = "The rejects from the other folder"
folder = syn.store(folder)
folder = syn.get(folder)
assert folder.name == "Test Folder"
assert folder.parentId == project.id
assert folder.description == "The rejects from the other folder"
assert folder.pi[0] == 3.14159265359
# Test CRUD on Files, check unicode
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(
path,
parent=folder,
description="Description with funny characters: Déjà vu, ประเทศไทย, 中国",
contentType="text/flapdoodle",
foo="An arbitrary value",
bar=[33, 44, 55],
bday=Datetime(2013, 3, 15),
band="Motörhead",
lunch="すし",
)
a_file = syn.store(a_file)
assert a_file.path == path
a_file = syn.getEntity(a_file)
assert a_file.description == "Description with funny characters: Déjà vu, ประเทศไทย, 中国", (
"description= %s" % a_file.description
)
assert a_file["foo"][0] == "An arbitrary value", "foo= %s" % a_file["foo"][0]
assert a_file["bar"] == [33, 44, 55]
assert a_file["bday"][0] == Datetime(2013, 3, 15)
assert a_file.contentType == "text/flapdoodle", "contentType= %s" % a_file.contentType
assert a_file["band"][0] == "Motörhead", "band= %s" % a_file["band"][0]
assert a_file["lunch"][0] == "すし", "lunch= %s" % a_file["lunch"][0]
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(path, a_file.path)
# Update the File
a_file.path = path
a_file["foo"] = "Another arbitrary chunk of text data"
a_file["new_key"] = "A newly created value"
a_file = syn.updateEntity(a_file)
assert a_file["foo"][0] == "Another arbitrary chunk of text data"
assert a_file["bar"] == [33, 44, 55]
assert a_file["bday"][0] == Datetime(2013, 3, 15)
assert a_file.new_key[0] == "A newly created value"
assert a_file.path == path
assert a_file.versionNumber == 1
# Upload a new File and verify
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file = syn.uploadFile(a_file, new_path)
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(new_path, a_file.path)
assert a_file.versionNumber == 2
# Make sure we can still get the older version of file
old_random_data = syn.get(a_file.id, version=1)
assert filecmp.cmp(old_random_data.path, path)
def test_Entity():
# Update the project
project_name = str(uuid.uuid4())
project = Project(name=project_name)
project = syn.store(project)
schedule_for_cleanup(project)
project = syn.getEntity(project)
assert project.name == project_name
# Create and get a Folder
folder = Folder('Test Folder', parent=project, description='A place to put my junk', foo=1000)
folder = syn.createEntity(folder)
folder = syn.getEntity(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'A place to put my junk'
assert folder.foo[0] == 1000
# Update and get the Folder
folder.pi = 3.14159265359
folder.description = 'The rejects from the other folder'
folder = syn.store(folder)
folder = syn.get(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other folder'
assert folder.pi[0] == 3.14159265359
# Test CRUD on Files, check unicode
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(path, parent=folder, description=u'Description with funny characters: Déjà vu, ประเทศไทย, 中国',
contentType='text/flapdoodle',
foo='An arbitrary value',
bar=[33,44,55],
bday=Datetime(2013,3,15),
band=u"Motörhead",
lunch=u"すし")
a_file = syn.store(a_file)
assert a_file.path == path
a_file = syn.getEntity(a_file)
assert a_file.description == u'Description with funny characters: Déjà vu, ประเทศไทย, 中国', u'description= %s' % a_file.description
assert a_file['foo'][0] == 'An arbitrary value', u'foo= %s' % a_file['foo'][0]
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
assert a_file.contentType == 'text/flapdoodle', u'contentType= %s' % a_file.contentType
assert a_file['band'][0] == u"Motörhead", u'band= %s' % a_file['band'][0]
assert a_file['lunch'][0] == u"すし", u'lunch= %s' % a_file['lunch'][0]
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(path, a_file.path)
assert_raises(ValueError,File,a_file.path,parent=folder,dataFileHandleId=56456)
b_file = File(name="blah",parent=folder,dataFileHandleId=a_file.dataFileHandleId)
b_file = syn.store(b_file)
assert b_file.dataFileHandleId == a_file.dataFileHandleId
# Update the File
a_file.path = path
a_file['foo'] = 'Another arbitrary chunk of text data'
a_file['new_key'] = 'A newly created value'
a_file = syn.updateEntity(a_file)
assert a_file['foo'][0] == 'Another arbitrary chunk of text data'
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
assert a_file.new_key[0] == 'A newly created value'
assert a_file.path == path
assert a_file.versionNumber == 1, "unexpected version number: " + str(a_file.versionNumber)
#Test create, store, get Links
link = Link(a_file['id'],
targetVersion=a_file.versionNumber,
parent=project)
link = syn.store(link)
assert link['linksTo']['targetId'] == a_file['id']
assert link['linksTo']['targetVersionNumber'] == a_file.versionNumber
assert link['linksToClassName'] == a_file['concreteType']
testLink = syn.get(link)
assert testLink == link
link = syn.get(link,followLink= True)
assert link['foo'][0] == 'Another arbitrary chunk of text data'
assert link['bar'] == [33,44,55]
assert link['bday'][0] == Datetime(2013,3,15)
assert link.new_key[0] == 'A newly created value'
assert utils.equal_paths(link.path, path)
assert link.versionNumber == 1, "unexpected version number: " + str(a_file.versionNumber)
# Upload a new File and verify
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file = syn.uploadFile(a_file, new_path)
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(new_path, a_file.path)
assert a_file.versionNumber == 2
# Make sure we can still get the older version of file
old_random_data = syn.get(a_file.id, version=1)
assert filecmp.cmp(old_random_data.path, path)
tmpdir = tempfile.mkdtemp()
schedule_for_cleanup(tmpdir)
## test file name override
a_file.fileNameOverride = "peaches_en_regalia.zoinks"
syn.store(a_file)
## TODO We haven't defined how filename override interacts with
## TODO previously cached files so, side-step that for now by
## TODO making sure the file is not in the cache!
syn.cache.remove(a_file.dataFileHandleId, delete=True)
a_file_retreived = syn.get(a_file, downloadLocation=tmpdir)
assert os.path.basename(a_file_retreived.path) == a_file.fileNameOverride, os.path.basename(a_file_retreived.path)
## test getting the file from the cache with downloadLocation parameter (SYNPY-330)
a_file_cached = syn.get(a_file.id, downloadLocation=tmpdir)
assert a_file_cached.path is not None
assert os.path.basename(a_file_cached.path) == a_file.fileNameOverride, a_file_cached.path
print("\n\nList of files in project:\n")
syn._list(project, recursive=True)
def test_Entity():
# Update the project
project_name = str(uuid.uuid4())
project = Project(name=project_name)
project = syn.store(project)
schedule_for_cleanup(project)
project = syn.getEntity(project)
assert_equals(project.name, project_name)
# Create and get a Folder
folder = Folder('Test Folder', parent=project, description='A place to put my junk', foo=1000)
folder = syn.createEntity(folder)
folder = syn.getEntity(folder)
assert_equals(folder.name, 'Test Folder')
assert_equals(folder.parentId, project.id)
assert_equals(folder.description, 'A place to put my junk')
assert_equals(folder.foo[0], 1000)
# Update and get the Folder
folder.pi = 3.14159265359
folder.description = 'The rejects from the other folder'
folder = syn.store(folder)
folder = syn.get(folder)
assert_equals(folder.name, 'Test Folder')
assert_equals(folder.parentId, project.id)
assert_equals(folder.description, 'The rejects from the other folder')
assert_equals(folder.pi[0], 3.14159265359)
# Test CRUD on Files, check unicode
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(path, parent=folder, description=u'Description with funny characters: Déjà vu, ประเทศไทย, 中国',
contentType='text/flapdoodle',
foo='An arbitrary value',
bar=[33, 44, 55],
bday=Datetime(2013, 3, 15),
band=u"Motörhead",
lunch=u"すし")
a_file = syn.store(a_file)
assert_equals(a_file.path, path)
a_file = syn.getEntity(a_file)
assert_equals(a_file.description,
u'Description with funny characters: Déjà vu, ประเทศไทย, 中国', u'description= %s'
% a_file.description)
assert_equals(a_file['foo'][0], 'An arbitrary value', u'foo= %s' % a_file['foo'][0])
assert_equals(a_file['bar'], [33, 44, 55])
assert_equals(a_file['bday'][0], Datetime(2013, 3, 15))
assert_equals(a_file.contentType, 'text/flapdoodle', u'contentType= %s' % a_file.contentType)
assert_equals(a_file['band'][0], u"Motörhead", u'band= %s' % a_file['band'][0])
assert_equals(a_file['lunch'][0], u"すし", u'lunch= %s' % a_file['lunch'][0])
a_file = syn.downloadEntity(a_file)
assert_true(filecmp.cmp(path, a_file.path))
b_file = File(name="blah", parent=folder, dataFileHandleId=a_file.dataFileHandleId)
b_file = syn.store(b_file)
assert_equals(b_file.dataFileHandleId, a_file.dataFileHandleId)
# Update the File
a_file.path = path
a_file['foo'] = 'Another arbitrary chunk of text data'
a_file['new_key'] = 'A newly created value'
a_file = syn.updateEntity(a_file)
assert_equals(a_file['foo'][0], 'Another arbitrary chunk of text data')
assert_equals(a_file['bar'], [33, 44, 55])
assert_equals(a_file['bday'][0], Datetime(2013, 3, 15))
assert_equals(a_file.new_key[0], 'A newly created value')
assert_equals(a_file.path, path)
assert_equals(a_file.versionNumber, 1, "unexpected version number: " + str(a_file.versionNumber))
# Test create, store, get Links
# If version isn't specified, targetVersionNumber should not be set
link = Link(a_file['id'],
parent=project)
link = syn.store(link)
assert_equals(link['linksTo']['targetId'], a_file['id'])
assert_is_none(link['linksTo'].get('targetVersionNumber'))
assert_equals(link['linksToClassName'], a_file['concreteType'])
link = Link(a_file['id'],
targetVersion=a_file.versionNumber,
parent=project)
link = syn.store(link)
assert_equals(link['linksTo']['targetId'], a_file['id'])
assert_equals(link['linksTo']['targetVersionNumber'], a_file.versionNumber)
assert_equals(link['linksToClassName'], a_file['concreteType'])
testLink = syn.get(link)
assert_equals(testLink, link)
link = syn.get(link, followLink=True)
assert_equals(link['foo'][0], 'Another arbitrary chunk of text data')
assert_equals(link['bar'], [33, 44, 55])
assert_equals(link['bday'][0], Datetime(2013, 3, 15))
assert_equals(link.new_key[0], 'A newly created value')
assert_true(utils.equal_paths(link.path, path))
assert_equals(link.versionNumber, 1, "unexpected version number: " + str(a_file.versionNumber))
newfolder = Folder('Testing Folder', parent=project)
newfolder = syn.store(newfolder)
link = Link(newfolder, parent=folder.id)
link = syn.store(link)
assert_equals(link['linksTo']['targetId'], newfolder.id)
assert_equals(link['linksToClassName'], newfolder['concreteType'])
assert_is_none(link['linksTo'].get('targetVersionNumber'))
# Upload a new File and verify
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file = syn.uploadFile(a_file, new_path)
a_file = syn.downloadEntity(a_file)
assert_true(filecmp.cmp(new_path, a_file.path))
assert_equals(a_file.versionNumber, 2)
# Make sure we can still get the older version of file
old_random_data = syn.get(a_file.id, version=1)
assert_true(filecmp.cmp(old_random_data.path, path))
tmpdir = tempfile.mkdtemp()
schedule_for_cleanup(tmpdir)
# test getting the file from the cache with downloadLocation parameter (SYNPY-330)
a_file_cached = syn.get(a_file.id, downloadLocation=tmpdir)
assert_is_not_none(a_file_cached.path)
assert_equal(os.path.basename(a_file_cached.path), os.path.basename(a_file.path))
def test_store_with_flags(syn, project, schedule_for_cleanup):
# -- CreateOrUpdate flag for Projects --
# If we store a project with the same name, it should become an update
projUpdate = Project(project.name)
projUpdate.updatedThing = 'Yep, sho\'nuf it\'s updated!'
projUpdate = syn.store(projUpdate, createOrUpdate=True)
assert project.id == projUpdate.id
assert projUpdate.updatedThing == ['Yep, sho\'nuf it\'s updated!']
# Store a File
filepath = utils.make_bogus_binary_file()
schedule_for_cleanup(filepath)
origBogus = File(filepath, name='Bogus Test File', parent=project)
origBogus = syn.store(origBogus, createOrUpdate=True)
assert origBogus.versionNumber == 1
# Modify existing annotations by createOrUpdate
del projUpdate['parentId']
del projUpdate['id']
projUpdate.updatedThing = 'Updated again'
projUpdate.addedThing = 'Something new'
projUpdate = syn.store(projUpdate, createOrUpdate=True)
assert project.id == projUpdate.id
assert projUpdate.updatedThing == ['Updated again']
# -- ForceVersion flag --
# Re-store the same thing and don't up the version
mutaBogus = syn.store(origBogus, forceVersion=False)
assert mutaBogus.versionNumber == 1
# Re-store again, essentially the same condition
mutaBogus = syn.store(mutaBogus, createOrUpdate=True, forceVersion=False)
assert mutaBogus.versionNumber == 1, "expected version 1 but got version %s" % mutaBogus.versionNumber
# And again, but up the version this time
mutaBogus = syn.store(mutaBogus, forceVersion=True)
assert mutaBogus.versionNumber == 2
# Create file with different contents and store it with force version false
# This should be ignored because contents (and md5) are different
different_filepath = utils.make_bogus_binary_file()
schedule_for_cleanup(different_filepath)
mutaBogus = File(different_filepath, name='Bogus Test File',
parent=project)
mutaBogus = syn.store(mutaBogus, forceVersion=False)
assert mutaBogus.versionNumber == 3
# -- CreateOrUpdate flag for files --
# Store a different file with the same name and parent
# Expected behavior is that a new version of the first File will be created
new_filepath = utils.make_bogus_binary_file()
schedule_for_cleanup(new_filepath)
mutaBogus.path = new_filepath
mutaBogus = syn.store(mutaBogus, createOrUpdate=True)
assert mutaBogus.id == origBogus.id
assert mutaBogus.versionNumber == 4
assert not filecmp.cmp(mutaBogus.path, filepath)
# Make doubly sure the File was uploaded
checkBogus = syn.get(mutaBogus.id)
assert checkBogus.id == origBogus.id
assert checkBogus.versionNumber == 4
assert filecmp.cmp(mutaBogus.path, checkBogus.path)
# Create yet another file with the same name and parent
# Expected behavior is raising an exception with a 409 error
newer_filepath = utils.make_bogus_binary_file()
schedule_for_cleanup(newer_filepath)
badBogus = File(newer_filepath, name='Bogus Test File', parent=project)
pytest.raises(SynapseHTTPError, syn.store, badBogus, createOrUpdate=False)
# -- Storing after syn.get(..., downloadFile=False) --
ephemeralBogus = syn.get(mutaBogus, downloadFile=False)
ephemeralBogus.description = 'Snorklewacker'
ephemeralBogus.shoe_size = 11.5
ephemeralBogus = syn.store(ephemeralBogus)
ephemeralBogus = syn.get(ephemeralBogus, downloadFile=False)
assert ephemeralBogus.description == 'Snorklewacker'
assert ephemeralBogus.shoe_size == [11.5]
def test_Entity():
# Update the project
project_name = str(uuid.uuid4())
project = Project(name=project_name)
project = syn.store(project)
schedule_for_cleanup(project)
project = syn.getEntity(project)
assert project.name == project_name
# Create and get a Folder
folder = Folder('Test Folder', parent=project, description='A place to put my junk', foo=1000)
folder = syn.createEntity(folder)
folder = syn.getEntity(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'A place to put my junk'
assert folder.foo[0] == 1000
# Update and get the Folder
folder.pi = 3.14159265359
folder.description = 'The rejects from the other folder'
folder = syn.store(folder)
folder = syn.get(folder)
assert folder.name == 'Test Folder'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other folder'
assert folder.pi[0] == 3.14159265359
# Test CRUD on Files, check unicode
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
a_file = File(path, parent=folder, description=u'Description with funny characters: Déjà vu, ประเทศไทย, 中国',
contentType='text/flapdoodle',
foo='An arbitrary value',
bar=[33,44,55],
bday=Datetime(2013,3,15),
band=u"Motörhead",
lunch=u"すし")
a_file = syn.store(a_file)
assert a_file.path == path
a_file = syn.getEntity(a_file)
assert a_file.description == u'Description with funny characters: Déjà vu, ประเทศไทย, 中国', u'description= %s' % a_file.description
assert a_file['foo'][0] == 'An arbitrary value', u'foo= %s' % a_file['foo'][0]
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
assert a_file.contentType == 'text/flapdoodle', u'contentType= %s' % a_file.contentType
assert a_file['band'][0] == u"Motörhead", u'band= %s' % a_file['band'][0]
assert a_file['lunch'][0] == u"すし", u'lunch= %s' % a_file['lunch'][0]
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(path, a_file.path)
# Update the File
a_file.path = path
a_file['foo'] = 'Another arbitrary chunk of text data'
a_file['new_key'] = 'A newly created value'
a_file = syn.updateEntity(a_file)
assert a_file['foo'][0] == 'Another arbitrary chunk of text data'
assert a_file['bar'] == [33,44,55]
assert a_file['bday'][0] == Datetime(2013,3,15)
assert a_file.new_key[0] == 'A newly created value'
assert a_file.path == path
assert a_file.versionNumber == 1
# Upload a new File and verify
new_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_path)
a_file = syn.uploadFile(a_file, new_path)
a_file = syn.downloadEntity(a_file)
assert filecmp.cmp(new_path, a_file.path)
assert a_file.versionNumber == 2
# Make sure we can still get the older version of file
old_random_data = syn.get(a_file.id, version=1)
assert filecmp.cmp(old_random_data.path, path)
def test_get_and_store():
"""Test synapse.get and synapse.store in Project, Folder and File"""
## create project
project = Project(name=str(uuid.uuid4()), description='A bogus test project')
project = syn.store(project)
schedule_for_cleanup(project)
## create folder
folder = Folder('Bad stuff', parent=project, description='The rejects from the other fauxldurr', pi=3)
folder = syn.store(folder)
## get folder
folder = syn.get(folder.id)
assert folder.name == 'Bad stuff'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other fauxldurr'
assert folder.pi[0] == 3
## update folder
folder.pi = 3.14159265359
folder.description = 'The rejects from the other folder'
syn.store(folder)
## verify that the updates stuck
folder = syn.get(folder)
assert folder.name == 'Bad stuff'
assert folder.parentId == project.id
assert folder.description == 'The rejects from the other folder'
assert folder.pi[0] == 3.14159265359
## upload a File
path = utils.make_bogus_data_file()
schedule_for_cleanup(path)
random_data = File(path, parent=folder, description='Random data', foo=9844)
random_data = syn.store(random_data)
## make sure file comes back intact
random_data_2 = syn.downloadEntity(random_data)
assert filecmp.cmp(path, random_data_2.path)
assert random_data.foo[0] == 9844
## update with a new File
new_file_path = utils.make_bogus_data_file()
schedule_for_cleanup(new_file_path)
random_data.path = new_file_path
random_data.foo = 1266
random_data = syn.store(random_data)
## should be version 2
assert random_data.versionNumber == 2
## make sure the updates stuck
random_data_2 = syn.get(random_data)
assert random_data_2.path is not None
assert filecmp.cmp(new_file_path, random_data_2.path)
assert random_data_2.foo[0] == 1266
assert random_data_2.versionNumber == 2
## make sure we can still get the older version of file
old_random_data = syn.get(random_data.id, version=1)
assert filecmp.cmp(old_random_data.path, path)