omero.gateway.facility

Class TablesFacility

java.lang.Object

omero.gateway.facility.Facility

omero.gateway.facility.TablesFacility

public class TablesFacility
extends Facility

Facility to interact with OMERO.tables

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_MAX_ROWS_TO_FETCH Maximum number of rows to fetch if not specified otherwise
static java.lang.String	TABLES_MIMETYPE The mimetype of an omero tables file

Method Summary

Modifier and Type	Method and Description
TableData	addTable(SecurityContext ctx, DataObject target, java.lang.String name, java.lang.String ns, TableData data) Adds a new table with the provided data
TableData	addTable(SecurityContext ctx, DataObject target, java.lang.String name, TableData data) Adds a new table with the provided data
java.util.Collection<FileAnnotationData>	getAvailableTables(SecurityContext ctx, DataObject parent) Get all available tables for a the specified object
TableData	getTable(SecurityContext ctx, long fileId) Load the data from a table (Note: limited to DEFAULT_MAX_ROWS_TO_FETCH number of rows)
TableData	getTable(SecurityContext ctx, long fileId, java.util.List<java.lang.Long> rows) Load data from a table
TableData	getTable(SecurityContext ctx, long fileId, long... rows) Load data from a table
TableData	getTable(SecurityContext ctx, long fileId, long rowFrom, long rowTo, int... columns) Load data from a table
TableData	getTable(SecurityContext ctx, long fileId, long rowFrom, long rowTo, long... columns) Load data from a table
TableData	getTableInfo(SecurityContext ctx, long fileId) Get basic information about a table.
long[]	query(SecurityContext ctx, long fileId, java.lang.String condition) Perform a query on the table
long[]	query(SecurityContext ctx, long fileId, java.lang.String condition, long start, long stop, long step) Perform a query on the table
void	updateTable(SecurityContext ctx, TableData data) Deprecated. This method is not reliable and might be removed/replaced in future.

Methods inherited from class omero.gateway.facility.Facility

addPropertyChangeListener, clear, firePropertyChanged, firePropertyChanged, getFacility, logDebug, logError, logInfo, logWarn, removePropertyChangeListener

Methods inherited from class java.lang.Object

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

Field Detail

TABLES_MIMETYPE

public static final java.lang.String TABLES_MIMETYPE

The mimetype of an omero tables file

See Also:

Constant Field Values

DEFAULT_MAX_ROWS_TO_FETCH

public static final int DEFAULT_MAX_ROWS_TO_FETCH

Maximum number of rows to fetch if not specified otherwise

See Also:

Constant Field Values

Method Detail

addTable

public TableData addTable(SecurityContext ctx,
                          DataObject target,
                          java.lang.String name,
                          TableData data)
                   throws DSOutOfServiceException,
                          DSAccessException

Adds a new table with the provided data

Parameters:

ctx - The SecurityContext

target - The object to attach the table to

name - A name for the table (can be null)

data - The data

Returns:

The TableData

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

addTable

public TableData addTable(SecurityContext ctx,
                          DataObject target,
                          java.lang.String name,
                          java.lang.String ns,
                          TableData data)
                   throws DSOutOfServiceException,
                          DSAccessException

Adds a new table with the provided data

Parameters:

ctx - The SecurityContext

target - The object to attach the table to

name - A name for the table (can be null)

ns - An optional namespace for the file annotation

data - The data

Returns:

The TableData

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getTableInfo

public TableData getTableInfo(SecurityContext ctx,
                              long fileId)
                       throws DSOutOfServiceException,
                              DSAccessException

Get basic information about a table.

Parameters:

ctx - The SecurityContext

fileId - The id of the OriginalFile which stores the table

Returns:

An 'empty' TableData object without the actual table data loaded; which only contains information about the columns and the size of the table.

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getTable

public TableData getTable(SecurityContext ctx,
                          long fileId)
                   throws DSOutOfServiceException,
                          DSAccessException

Load the data from a table (Note: limited to DEFAULT_MAX_ROWS_TO_FETCH number of rows)

Parameters:

ctx - The SecurityContext

fileId - The id of the OriginalFile which stores the table

Returns:

The data which the table contains

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getTable

public TableData getTable(SecurityContext ctx,
                          long fileId,
                          long rowFrom,
                          long rowTo,
                          int... columns)
                   throws DSOutOfServiceException,
                          DSAccessException

Load data from a table

Parameters:

ctx - The SecurityContext

fileId - The id of the OriginalFile which stores the table

rowFrom - The start row (inclusive)

rowTo - The end row (inclusive) (can be -1 in which case DEFAULT_MAX_ROWS_TO_FETCH rows will be fetched)

columns - The columns to take into account (can be left unspecified, in which case all columns will used)

Returns:

The specified data

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

query

public long[] query(SecurityContext ctx,
                    long fileId,
                    java.lang.String condition)
             throws DSOutOfServiceException,
                    DSAccessException

Perform a query on the table

Parameters:

ctx - The SecurityContext

fileId - The id of the OriginalFile which stores the table

condition - The query string

Returns:

A list of row indices matching the condition

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

query

public long[] query(SecurityContext ctx,
                    long fileId,
                    java.lang.String condition,
                    long start,
                    long stop,
                    long step)
             throws DSOutOfServiceException,
                    DSAccessException

Perform a query on the table

Parameters:

ctx - The SecurityContext

fileId - The id of the OriginalFile which stores the table

condition - The query string

start - The index of the first row to consider (optional, default: 0)

stop - The index of the last+1 row to consider (optional, default: number of rows of the table)

step - The stepping interval between the start and stop rows to consider (optional, default: no stepping)

Returns:

A list of row indices matching the condition

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getTable

public TableData getTable(SecurityContext ctx,
                          long fileId,
                          java.util.List<java.lang.Long> rows)
                   throws DSOutOfServiceException,
                          DSAccessException

Load data from a table

Parameters:

ctx - The SecurityContext

fileId - The id of the OriginalFile which stores the table

rows - The rows to get

Returns:

The specified data

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getTable

public TableData getTable(SecurityContext ctx,
                          long fileId,
                          long... rows)
                   throws DSOutOfServiceException,
                          DSAccessException

Load data from a table

Parameters:

ctx - The SecurityContext

fileId - The id of the OriginalFile which stores the table

rows - The rows to get

Returns:

The specified data

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getTable

public TableData getTable(SecurityContext ctx,
                          long fileId,
                          long rowFrom,
                          long rowTo,
                          long... columns)
                   throws DSOutOfServiceException,
                          DSAccessException

Load data from a table

Parameters:

ctx - The SecurityContext

fileId - The id of the OriginalFile which stores the table

rowFrom - The start row (inclusive)

rowTo - The end row (inclusive) (can be -1 in which case DEFAULT_MAX_ROWS_TO_FETCH rows will be fetched)

columns - The columns to take into account (can be left unspecified, in which case all columns will used)

Returns:

The specified data

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getAvailableTables

public java.util.Collection<FileAnnotationData> getAvailableTables(SecurityContext ctx,
                                                                   DataObject parent)
                                                            throws DSOutOfServiceException,
                                                                   DSAccessException

Get all available tables for a the specified object

Parameters:

ctx - The SecurityContext

parent - The DataObject

Returns:

See above

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

updateTable

@Deprecated
public void updateTable(SecurityContext ctx,
                                    TableData data)
                             throws DSOutOfServiceException,
                                    DSAccessException

Deprecated. This method is not reliable and might be removed/replaced in future.

Saves the (modified) TableData back to the server. Note: - Addition/Removal of columns/rows is not supported, only modification of the values. - The size of Double/Float/Long arrays can't be changed!

Parameters:

ctx - The SecurityContext

data - The TableData to save

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.