aliby.io.omero.BridgeOmero

class BridgeOmero(host=None, username=None, password=None, ome_id=None)

Bases: object

Core to interact with OMERO, using credentials or fetching them from h5 file (temporary trick). See https://docs.openmicroscopy.org/omero/5.6.0/developers/Python.html

Attributes

file_annotations

ome_class

Methods

add_file_as_annotation(file_to_upload, **kwargs)	Upload annotation to object on OMERO server.
server_info_from_h5(filepath)	Return server info from hdf5 file.

create_gate
set_id

Parameters

hoststring

web address of OMERO host

username: string

passwordstring

ome_id: Optional int

Unique identifier on Omero database. Used to fetch specific objects.

Attributes

file_annotations

ome_class

Methods

add_file_as_annotation(file_to_upload, **kwargs)	Upload annotation to object on OMERO server.
server_info_from_h5(filepath)	Return server info from hdf5 file.

create_gate
set_id

__init__(host=None, username=None, password=None, ome_id=None)

Parameters

hoststring

web address of OMERO host

username: string

passwordstring

ome_id: Optional int

Unique identifier on Omero database. Used to fetch specific objects.

Methods

__init__([host, username, password, ome_id])	Parameters
add_file_as_annotation(file_to_upload, **kwargs)	Upload annotation to object on OMERO server.
create_gate()	rtype bool
server_info_from_h5(filepath)	Return server info from hdf5 file.
set_id(ome_id)

Attributes

file_annotations
ome_class

add_file_as_annotation(file_to_upload, **kwargs)

Upload annotation to object on OMERO server. Only valid in subclasses.

Parameters

file_to_upload: File to upload

**kwargs: Additional keyword arguments passed on

to BlitzGateway.createFileAnnfromLocalFile

classmethod server_info_from_h5(filepath)

Return server info from hdf5 file.

Parameters

clsBridgeOmero

BridgeOmero class

filepatht.Union[str, PosixPath]

Location of hdf5 file.

Examples

FIXME: Add docs.