def test_ftp_download():
"""Test downloading an Entity that points to a file on an FTP server. """
# Another test with an external reference. This is because we only need to test FTP download; not upload. Also so we don't have to maintain an FTP server just for this purpose.
# Make an entity that points to an FTP server file.
entity = File(parent=project['id'], name='1KB.zip')
fileHandle = {}
fileHandle['externalURL'] = 'ftp://speedtest.tele2.net/1KB.zip'
fileHandle["fileName"] = entity.name
fileHandle["contentType"] = "application/zip"
fileHandle["contentMd5"] = '0f343b0931126a20f133d67c2b018a3b'
fileHandle["contentSize"] = 1024
fileHandle[
"concreteType"] = "org.sagebionetworks.repo.model.file.ExternalFileHandle"
fileHandle = syn.restPOST('/externalFileHandle', json.dumps(fileHandle),
syn.fileHandleEndpoint)
entity.dataFileHandleId = fileHandle['id']
entity = syn.store(entity)
# Download the entity and check that MD5 matches expected
FTPfile = syn.get(entity.id,
downloadLocation=os.getcwd(),
downloadFile=True)
assert FTPfile.md5 == utils.md5_for_file(FTPfile.path).hexdigest()
schedule_for_cleanup(entity)
os.remove(FTPfile.path)
def test_download_file_entity__correct_local_state(syn):
mock_cache_path = utils.normalize_path("/i/will/show/you/the/path/yi.txt")
file_entity = File(parentId="syn123")
file_entity.dataFileHandleId = 123
with patch.object(syn.cache, 'get', return_value=mock_cache_path):
syn._download_file_entity(downloadLocation=None, entity=file_entity, ifcollision="overwrite.local",
submission=None)
assert mock_cache_path == file_entity.path
assert os.path.dirname(mock_cache_path) == file_entity.cacheDir
assert 1 == len(file_entity.files)
assert os.path.basename(mock_cache_path) == file_entity.files[0]
def init(self, syn, schedule_for_cleanup):
self.syn = syn
# create external file handles for https://www.synapse.org/images/logo.svg,
project = Project(str(uuid.uuid4()))
project = self.syn.store(project)
schedule_for_cleanup(project)
# create file entity from externalFileHandle
external_file_handle_request_1 = {
"concreteType": "org.sagebionetworks.repo.model.file.ExternalFileHandle",
"externalURL": "https://www.synapse.org/images/logo.svg",
"fileName": "testExternalFileHandle"
}
external_response_1 = self.syn.restPOST('/externalFileHandle', body=json.dumps(external_file_handle_request_1),
endpoint=self.syn.fileHandleEndpoint)
self.file_handle_id_1 = external_response_1['id']
test_entity_1 = File(parent=project)
test_entity_1.dataFileHandleId = self.file_handle_id_1
test_entity_1 = self.syn.store(test_entity_1)
self.obj_id_1 = str(test_entity_1['id'][3:])
def _copyFile(syn, entity, destinationId, version=None, update=False, setProvenance="traceback"):
"""
Copies most recent version of a file to a specified synapse ID.
:param entity: A synapse ID of a File entity
:param destinationId: Synapse ID of a folder/project that the file wants to be copied to
:param version: Can specify version of a file.
Default to None
:param update: Can choose to update files that have the same name
Default to False
:param setProvenance: Has three values to set the provenance of the copied entity:
traceback: Sets to the source entity
existing: Sets to source entity's original provenance (if it exists)
None: No provenance is set
"""
ent = syn.get(entity, downloadFile=False, version=version, followLink=False)
#CHECK: If File is in the same parent directory (throw an error) (Can choose to update files)
if not update:
search = syn.query('select name from entity where parentId =="%s"'%destinationId)
for i in search['results']:
if i['entity.name'] == ent.name:
raise ValueError('An item named "%s" already exists in this location. File could not be copied'%ent.name)
profile = syn.getUserProfile()
# get provenance earlier to prevent errors from being called in the end
# If traceback, set activity to old entity
if setProvenance == "traceback":
act = Activity("Copied file", used=ent)
# if existing, check if provenance exists
elif setProvenance == "existing":
try:
act = syn.getProvenance(ent.id)
except SynapseHTTPError as e:
# Should catch the 404
act = None
elif setProvenance is None or setProvenance.lower() == 'none':
act = None
else:
raise ValueError('setProvenance must be one of None, existing, or traceback')
#Grab file handle createdBy annotation to see the user that created fileHandle
fileHandleList = syn.restGET('/entity/%s/version/%s/filehandles'%(ent.id,ent.versionNumber))
#NOTE: May not always be the first index (need to filter to make sure not PreviewFileHandle)
#Loop through to check which dataFileHandles match and return createdBy
# Look at convenience function
for fileHandle in fileHandleList['list']:
if fileHandle['id'] == ent.dataFileHandleId:
createdBy = fileHandle['createdBy']
break
else:
createdBy = None
#CHECK: If the user created the file, copy the file by using fileHandleId else hard copy
if profile.ownerId == createdBy:
new_ent = File(name=ent.name, parentId=destinationId)
new_ent.dataFileHandleId = ent.dataFileHandleId
else:
#CHECK: If the synapse entity is an external URL, change path and store
if ent.externalURL is None: #and ent.path == None:
#####If you have never downloaded the file before, the path is None
store = True
#This needs to be here, because if the file has never been downloaded before
#there wont be a ent.path
ent = syn.get(entity,downloadFile=store,version=version)
path = ent.path
else:
store = False
ent = syn.get(entity,downloadFile=store,version=version)
path = ent.externalURL
new_ent = File(path, name=ent.name, parentId=destinationId, synapseStore=store)
#Set annotations here
new_ent.annotations = ent.annotations
#Store provenance if act is not None
if act is not None:
new_ent = syn.store(new_ent, activity=act)
else:
new_ent = syn.store(new_ent)
#Leave this return statement for test
return new_ent['id']