def upload_csv_to_omero(ctx,
file,
tablename,
target_id,
target_type="Project"):
"""Upload the CSV file and attach it to the specified object"""
print file
print file.name
svc = gateway.getFacility(DataManagerFacility)
file_size = os.path.getsize(file.name)
original_file = OriginalFileI()
original_file.setName(rstring(tablename))
original_file.setPath(rstring(file.name))
original_file.setSize(rlong(file_size))
checksum_algorithm = ChecksumAlgorithmI()
checksum_algorithm.setValue(rstring(ChecksumAlgorithmSHA1160.value))
original_file.setHasher(checksum_algorithm)
original_file.setMimetype(rstring("text/csv"))
original_file = svc.saveAndReturnObject(ctx, original_file)
store = gateway.getRawFileService(ctx)
# Open file and read stream
store.setFileId(original_file.getId().getValue())
print original_file.getId().getValue()
try:
store.setFileId(original_file.getId().getValue())
with open(file.name, 'rb') as stream:
buf = 10000
for pos in range(0, long(file_size), buf):
block = None
if file_size - pos < buf:
block_size = file_size - pos
else:
block_size = buf
stream.seek(pos)
block = stream.read(block_size)
store.write(block, pos, block_size)
original_file = store.save()
finally:
store.close()
# create the file annotation
namespace = "training.demo"
fa = FileAnnotationI()
fa.setFile(original_file)
fa.setNs(rstring(namespace))
if target_type == "Project":
target_obj = ProjectData(ProjectI(target_id, False))
elif target_type == "Dataset":
target_obj = DatasetData(DatasetI(target_id, False))
elif target_type == "Image":
target_obj = ImageData(ImageI(target_id, False))
svc.attachAnnotation(ctx, FileAnnotationData(fa), target_obj)
def make_file_annotation(self,
name=None,
binary=None,
format=None,
client=None,
ns=None):
"""
Creates a new DatasetI instance and returns the persisted object.
If no name has been provided, a UUID string shall be used.
:param name: the name of the project
:param client: The client to use to create the object
:param ns: The namespace for the annotation
"""
if client is None:
client = self.client
update = client.sf.getUpdateService()
# file
if format is None:
format = "application/octet-stream"
if binary is None:
binary = "12345678910"
if name is None:
name = str(self.uuid())
oFile = OriginalFileI()
oFile.setName(rstring(name))
oFile.setPath(rstring(str(self.uuid())))
oFile.setSize(rlong(len(binary)))
oFile.hasher = ChecksumAlgorithmI()
oFile.hasher.value = rstring("SHA1-160")
oFile.setMimetype(rstring(str(format)))
oFile = update.saveAndReturnObject(oFile)
# save binary
store = client.sf.createRawFileStore()
store.setFileId(oFile.id.val)
store.write(binary, 0, 0)
oFile = store.save() # See ticket:1501
store.close()
fa = FileAnnotationI()
fa.setFile(oFile)
if ns is not None:
fa.setNs(rstring(ns))
return update.saveAndReturnObject(fa)
def make_file_annotation(self, name=None, binary=None, format=None, client=None, ns=None):
"""
Creates a new DatasetI instance and returns the persisted object.
If no name has been provided, a UUID string shall be used.
:param name: the name of the project
:param client: The client to use to create the object
:param ns: The namespace for the annotation
"""
if client is None:
client = self.client
update = client.sf.getUpdateService()
# file
if format is None:
format = "application/octet-stream"
if binary is None:
binary = "12345678910"
if name is None:
name = str(self.uuid())
oFile = OriginalFileI()
oFile.setName(rstring(name))
oFile.setPath(rstring(str(self.uuid())))
oFile.setSize(rlong(len(binary)))
oFile.hasher = ChecksumAlgorithmI()
oFile.hasher.value = rstring("SHA1-160")
oFile.setMimetype(rstring(str(format)))
oFile = update.saveAndReturnObject(oFile)
# save binary
store = client.sf.createRawFileStore()
store.setFileId(oFile.id.val)
store.write(binary, 0, 0)
oFile = store.save() # See ticket:1501
store.close()
fa = FileAnnotationI()
fa.setFile(oFile)
if ns is not None:
fa.setNs(rstring(ns))
return update.saveAndReturnObject(fa)
