loci.formats.meta

Class MetadataConverter

java.lang.Object

loci.formats.meta.MetadataConverter

public final class MetadataConverter
extends Object

A utility class containing a method for piping a source MetadataRetrieve object into a destination MetadataStore.

This technique allows conversion between two different storage media. For example, it can be used to convert an OMEROMetadataStore (OMERO's metadata store implementation) into an OMEXMLMetadata, thus generating OME-XML from information in an OMERO database.

Author:

Curtis Rueden ctrueden at wisc.edu

Constructor Summary

Constructors

Modifier	Constructor and Description
private	MetadataConverter() Private constructor; all methods in MetadataConverter are static, so this should not be called.

Method Summary

Methods

Modifier and Type	Method and Description
private static void	convertBooleanAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all BooleanAnnotation attributes.
private static void	convertCommentAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all CommentAnnotation attributes.
private static void	convertDatasets(MetadataRetrieve src, MetadataStore dest) Convert all Dataset attributes.
private static void	convertDoubleAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all DoubleAnnotation attributes.
private static void	convertExperimenterGroups(MetadataRetrieve src, MetadataStore dest) Convert all ExperimenterGroup attributes.
private static void	convertExperimenters(MetadataRetrieve src, MetadataStore dest) Convert all Experimenter attributes.
private static void	convertExperiments(MetadataRetrieve src, MetadataStore dest) Convert all Experiment attributes.
private static void	convertFileAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all FileAnnotation attributes.
private static void	convertFolders(MetadataRetrieve src, MetadataStore dest) Convert all Folder attributes.
private static void	convertImages(MetadataRetrieve src, MetadataStore dest, List<String> lightSourceIds) Convert all Image attributes.
private static List<String>	convertInstruments(MetadataRetrieve src, MetadataStore dest) Convert all Instrument attributes.
private static void	convertLightSources(MetadataRetrieve src, MetadataStore dest, int instrumentIndex, List<String> lightSourceIds) Convert all LightSource attributes for the given instrument.
private static void	convertListAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all ListAnnotation attributes.
private static void	convertLongAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all LongAnnotation attributes.
private static void	convertMapAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all MapAnnotation attributes.
static void	convertMetadata(MetadataRetrieve src, MetadataStore dest) Copies information from a metadata retrieval object (source) into a metadata store (destination).
private static void	convertPlates(MetadataRetrieve src, MetadataStore dest) Convert all Plate attributes.
private static void	convertProjects(MetadataRetrieve src, MetadataStore dest) Convert all Project attributes.
private static void	convertROIs(MetadataRetrieve src, MetadataStore dest) Convert all ROI attributes.
private static void	convertRootAttributes(MetadataRetrieve src, MetadataStore dest) Convert all top-level attributes.
private static void	convertScreens(MetadataRetrieve src, MetadataStore dest) Convert all Screen attributes.
private static void	convertTagAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all TagAnnotation attributes.
private static void	convertTermAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all TermAnnotation attributes.
private static void	convertTimestampAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all TimestampAnnotation attributes.
private static void	convertXMLAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all XMLAnnotation attributes.

Methods inherited from class java.lang.Object

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

Constructor Detail

MetadataConverter

private MetadataConverter()

Private constructor; all methods in MetadataConverter are static, so this should not be called.

Method Detail

convertMetadata

public static void convertMetadata(MetadataRetrieve src,
                   MetadataStore dest)

Copies information from a metadata retrieval object (source) into a metadata store (destination).

convertBooleanAnnotations

private static void convertBooleanAnnotations(MetadataRetrieve src,
                             MetadataStore dest)

Convert all BooleanAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertCommentAnnotations

private static void convertCommentAnnotations(MetadataRetrieve src,
                             MetadataStore dest)

Convert all CommentAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertDatasets

private static void convertDatasets(MetadataRetrieve src,
                   MetadataStore dest)

Convert all Dataset attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertDoubleAnnotations

private static void convertDoubleAnnotations(MetadataRetrieve src,
                            MetadataStore dest)

Convert all DoubleAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertExperiments

private static void convertExperiments(MetadataRetrieve src,
                      MetadataStore dest)

Convert all Experiment attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertExperimenters

private static void convertExperimenters(MetadataRetrieve src,
                        MetadataStore dest)

Convert all Experimenter attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertExperimenterGroups

private static void convertExperimenterGroups(MetadataRetrieve src,
                             MetadataStore dest)

Convert all ExperimenterGroup attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertFileAnnotations

private static void convertFileAnnotations(MetadataRetrieve src,
                          MetadataStore dest)

Convert all FileAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertFolders

private static void convertFolders(MetadataRetrieve src,
                  MetadataStore dest)

Convert all Folder attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertImages

private static void convertImages(MetadataRetrieve src,
                 MetadataStore dest,
                 List<String> lightSourceIds)

Convert all Image attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

lightSourceIds - the collection of light source identifiers.

convertInstruments

private static List<String> convertInstruments(MetadataRetrieve src,
                              MetadataStore dest)

Convert all Instrument attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

Returns:

Collection of light source identifiers.

convertListAnnotations

private static void convertListAnnotations(MetadataRetrieve src,
                          MetadataStore dest)

Convert all ListAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertLongAnnotations

private static void convertLongAnnotations(MetadataRetrieve src,
                          MetadataStore dest)

Convert all LongAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertMapAnnotations

private static void convertMapAnnotations(MetadataRetrieve src,
                         MetadataStore dest)

Convert all MapAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertPlates

private static void convertPlates(MetadataRetrieve src,
                 MetadataStore dest)

Convert all Plate attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertProjects

private static void convertProjects(MetadataRetrieve src,
                   MetadataStore dest)

Convert all Project attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertROIs

private static void convertROIs(MetadataRetrieve src,
               MetadataStore dest)

Convert all ROI attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertScreens

private static void convertScreens(MetadataRetrieve src,
                  MetadataStore dest)

Convert all Screen attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertTagAnnotations

private static void convertTagAnnotations(MetadataRetrieve src,
                         MetadataStore dest)

Convert all TagAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertTermAnnotations

private static void convertTermAnnotations(MetadataRetrieve src,
                          MetadataStore dest)

Convert all TermAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertTimestampAnnotations

private static void convertTimestampAnnotations(MetadataRetrieve src,
                               MetadataStore dest)

Convert all TimestampAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertXMLAnnotations

private static void convertXMLAnnotations(MetadataRetrieve src,
                         MetadataStore dest)

Convert all XMLAnnotation attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

convertLightSources

private static void convertLightSources(MetadataRetrieve src,
                       MetadataStore dest,
                       int instrumentIndex,
                       List<String> lightSourceIds)

Convert all LightSource attributes for the given instrument.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy

instrumentIndex - the index of the Instrument to convert

lightSourceIds - the collection of light source to populate

convertRootAttributes

private static void convertRootAttributes(MetadataRetrieve src,
                         MetadataStore dest)

Convert all top-level attributes.

Parameters:

src - the MetadataRetrieve from which to copy

dest - the MetadataStore to which to copy