endrov.ioOMERO
Class OMEROConnection

java.lang.Object
  endrov.ioOMERO.OMEROConnection

public class OMEROConnection
extends java.lang.Object

Connection to an OMERO database

Constructor Summary

OMEROConnection()

Method Summary

void	connect(java.lang.String hostName, int port, java.lang.String userName, java.lang.String password, boolean encrypted)
void	disconnect()
void	downloadFile(java.util.List<omero.model.Annotation> annotations, java.io.File file)
omero.client	getClient()
java.util.Set<pojos.DatasetData>	getDatasetsForUser(long userId) Retrieve the Datasets for a user
omero.api.ServiceFactoryPrx	getEntry()
omero.model.Image	getImage(java.lang.Long imageId)
java.util.Set<pojos.ImageData>	getImagesForDataset(java.lang.Long datasetId) Retrieve the Images contained in a Dataset.
java.lang.Long	getMyGroupId()
java.lang.Long	getMyUserId()
java.util.Set<pojos.ProjectData>	getProjectsForUser(long userId) Get projects for a user
java.util.Set<java.lang.Long>	getUserIDs() Get all users this connection has access to(?) not tested
java.util.List<omero.model.Annotation>	loadAllAnnotationsInNamespace(long userId, java.lang.String namespace)
void	uploadFile(pojos.ImageData image, java.io.File file, java.lang.String generatedSha1, java.lang.String fileMimeType, java.lang.String description, java.lang.String namespace) there are many more examples for wells etc.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OMEROConnection

public OMEROConnection()

Method Detail

connect

public void connect(java.lang.String hostName,
                    int port,
                    java.lang.String userName,
                    java.lang.String password,
                    boolean encrypted)
             throws Glacier2.CannotCreateSessionException,
                    Glacier2.PermissionDeniedException,
                    omero.ServerError

Throws:

Glacier2.CannotCreateSessionException

Glacier2.PermissionDeniedException

omero.ServerError

getMyUserId

public java.lang.Long getMyUserId()
                           throws omero.ServerError

Throws:

omero.ServerError

getUserIDs

public java.util.Set<java.lang.Long> getUserIDs()
                                         throws omero.ServerError

Get all users this connection has access to(?) not tested

Throws:

omero.ServerError

getMyGroupId

public java.lang.Long getMyGroupId()
                            throws omero.ServerError

Throws:

omero.ServerError

disconnect

public void disconnect()

getProjectsForUser

public java.util.Set<pojos.ProjectData> getProjectsForUser(long userId)
                                                    throws omero.ServerError

Get projects for a user

Throws:

omero.ServerError

getDatasetsForUser

public java.util.Set<pojos.DatasetData> getDatasetsForUser(long userId)
                                                    throws omero.ServerError

Retrieve the Datasets for a user

Throws:

omero.ServerError

getImagesForDataset

public java.util.Set<pojos.ImageData> getImagesForDataset(java.lang.Long datasetId)
                                                   throws omero.ServerError

Retrieve the Images contained in a Dataset.

Throws:

omero.ServerError

getImage

public omero.model.Image getImage(java.lang.Long imageId)
                           throws omero.ServerError

Throws:

omero.ServerError

uploadFile

public void uploadFile(pojos.ImageData image,
                       java.io.File file,
                       java.lang.String generatedSha1,
                       java.lang.String fileMimeType,
                       java.lang.String description,
                       java.lang.String namespace)
                throws omero.ServerError,
                       java.io.FileNotFoundException,
                       java.io.IOException

there are many more examples for wells etc. see http://trac.openmicroscopy.org.uk/ome/wiki/OmeroJava Image img = set.iterator().next(); ImageData test = new ImageData( img ); and there are many writing examples ROIs deleting stuff server-side rendering & thumbnails

Throws:

omero.ServerError

java.io.FileNotFoundException

java.io.IOException

loadAllAnnotationsInNamespace

public java.util.List<omero.model.Annotation> loadAllAnnotationsInNamespace(long userId,
                                                                            java.lang.String namespace)
                                                                     throws omero.ServerError

Throws:

omero.ServerError

downloadFile

public void downloadFile(java.util.List<omero.model.Annotation> annotations,
                         java.io.File file)
                  throws omero.ServerError,
                         java.io.IOException

Throws:

omero.ServerError

java.io.IOException

getClient

public omero.client getClient()

getEntry

public omero.api.ServiceFactoryPrx getEntry()