Public:BWmeta service/Transformers

From YaddaWiki

Background and motivation

As of 2010Q4, three versions of BWmeta format and at least three Java models of BWmeta are used in YADDA. See here for details. Serialization and deserialization is implemented for the following pairs:

	Repo	DL	Y	…
1.0.5
1.2.0
2.0.0
2.1.0

There are also converters between selected models:

• Y ↔ DL

Serialization of Y model to BWmeta 1.0.5 is therefore possible through the following chain of transformations:

• Y model → DL model → BWmeta 1.0.5

Conversion from DL model to Repo model is possible through:

• DL model → BWmeta 1.0.5 → Repo model

Unfortunately, many mutually-incompatible transformation interfaces are present. It is difficult to understand which transformations are possible, how to combine them, which classes should be used for that end and how to instantiate the classes.

A unified interface to all the transformations would be very helpful.

Unified interface

Four different transformer types are present: readers, writers and model converters and format converters. Each type has a corresponding interface:

• IMetadataReader<T> deserializes an object of type T from a String or a Reader
• IMetadataWriter<T> serializes an object of type T to a String or a Writer
• IMetadataModelConverter<S, T> converts an object of type S to an object of type T
• IMetadataFormatConverter converts serialized metadata from one format to another one

See detailed description of transformers interface below.

Existing transformers in YADDA

Existing transformers are located in the pl.edu.icm.yadda.bwmeta.transformers package.

Readers:

Writers:

Model converters:

MetadataTransformerFactory

MetadataTransformerFactory maintains a list of available "atomic" transformers and is able to combine the atomic transformers into more complex ones.

MetadataTransformerFactory in YADDA

pl.edu.icm.yadda.bwmeta.transformers.BwmetaTransformers contains a static instance of MetadataTransformerFactory (BTF), which can be used to obtain a transformer (reader, writer, model or format converter) between given formats and/or models. All new transformers should be added to the factory.

Repo transformers (reader and writer) are currently not included in BTF. However, there is a simple way to add new transformers to an existing factory without changing it: all you have to do is build a new factory from an existing one and additional transformers using MetadataTransformerFactory constructor. For example, to build a factory including BTF and Repo readers and writers:

 IMetadataTransformerFactory myFactory = new MetadataTransformerFactory(
   (MetadataTransformerFactory) BwmetaTransformers.BTF,
   Arrays.<IMetadataReader<?>>asList(new Bwmeta1_0ToRepoTransformer()),
   Arrays.<IMetadataWriter<?>>asList(new RepoToBwmeta1_0Transformer()),
   Arrays.<IMetadataModelConverter<?, ?>>asList(),
   Arrays.<IMetadataFormatConverter>asList());

For factory usage, see detailed description of MetadataTransformerFactory below.

Hints

Hints are objects that can be passed to transformers to change their internal behaviour.

Hints can be either passed directly to transformers methods (in the form of Object... hints methods argument, see transformers interface below), or set in the factory as "global hints" (through factory constructor, see factory interface below). Global hints set in factory are passed automatically to all transformation methods in transformers obtained from the factory.

Hints can be either simple flags declared as static String instances in pl.edu.icm.yadda.bwmeta.transformers.BwmetaTransformers, or objects needed by transformers.

Currently there are two supported flag hints:

• FAST_TRANSFORMER - no validation

Normally writers try to validate the input. With this hint passed, they will skip the validation stage to make transformation faster.

• NO_BWMETA_ROOT - when possible, skip "bwmeta" root in output XML documents

This hint applies to writers only. Normally, regardless of the amount of model objects passed to a writer, they are all surrounded by a <bwmeta></bwmeta> root element. With this hint passed, the <bwmeta></bwmeta> root element will not be included if possible, that is, if there is only one model object passed to the writer.

There are also two supported object hints:

• Ancestor - element Ancestor data
• CategoryCodeMapper - mapping between category extId and (classificationId, code)

Transformers interface

Classes listed in Unified interface section provide following methods:

IMetadataReader<T> (T is a model class)

• MetadataFormat getSourceFormat() -- returns the source format
• MetadataModel<T> getTargetModel() -- returns the target model
• List<T> read(String string, Object... hints) throws TransformationException -- deserializes metadata from string; returns a list of model objects.
• List<T> read(Reader reader, Object... hints) throws TransformationException -- deserializes metadata from reader stream; returns a list of model objects.

IMetadataWriter<T>

• MetadataModel<T> getSourceModel() -- returns the source model
• MetadataFormat getTargetFormat() -- returns the target format
• String write(List<T> objects, Object... hints) throws TransformationException -- serializes metadata model objects given in objects list; returns a string contains all metadata
• void write(Writer writer, List<T> objects, Object... hints) throws TransformationException -- serializes metadata model objects given in objects list; the result is written into writer stream.

IMetadataModelConverter<S, T>

• MetadataModel<S> getSourceModel() -- returns the source model
• MetadataModel<T> -- returns the target model
• T convert(S source, Object... hints) throws TransformationException; -- converts a metadata object of type S into objects of type T

IMetadataFormatConverter

• MetadataFormat getSourceFormat() -- returns the source format
• MetadataFormat getTargetFormat() -- returns the target format
• String convert(String source, Object... hints) throws TransformationException -- converts serialized metadata given in source string; returns a string containing metadata in target format
• void convert(Reader from, Writer to, Object... hints) throws TransformationException -- converts serialized metadata read from a stream from; metadata in target format is written into a to stream.

MetadataTransformerFactory interface

Public constructors provided by MetadataTransformerFactory:

• constructor that builds a MetadataTransformerFactory from given lists of atomic transformers:

   MetadataTransformerFactory(List<IMetadataReaders>, List<IMetadataWriters>, List<IMetadataModelConverters>,
                              List<IMetadataFormatConverters>)

• constructor that builds a MetadataTransformerFactory from given lists of atomic transformers and global hints:

   MetadataTransformerFactory(List<IMetadataReader>, List<IMetadataWriter>, List<IMetadataModelConverter>,
                              List<IMetadataFormatConverter>, Object[])

• constructor that creates a new MetadataTransformerFactory from an existing one, which contains joined lists of atomic transformers:

   MetadataTransformerFactory(MetadataTransformerFactory, List<IMetadataReaders>, List<IMetadataWriters>,
                              List<IMetadataModelConverters>, List<IMetadataFormatConverters>)

• contructor that creates a new MetadataTransformerFactory from an existing one and global hints

   MetadataTransformerFactory(MetadataTransformerFactory, Object[])

• constructor that build a new MetadataTransformerFactory from an existing one, list of transformers and global hints:

   MetadataTransformerFactory(MetadataTransformerFactory, List<IMetadataReader>, List<IMetadataWriter>, 
                              List<IMetadataModelConverter>, List<IMetadataFormatConverter>, Object[]) {

Public methods of MetadataTransformerFactory, that returns transformer built from atomic transformers given in object constructor:

• <T> IMetadataReader<T> getReader(MetadataModel<T>, MetadataFormat)
• <T> IMetadataWriter<T> getWriter(MetadataModel<T>, MetadataFormat)
• <S, T> IMetadataModelConverter<S, T> getModelConverter(MetadataModel<S>, MetadataModel<T>)
• IMetadataFormatConverter getFormatConverter(MetadataFormat, MetadataFormat)

MetadataTransformerFactory also contains a set of static methods compose(), that return a complex transformer built from two given transformers. These methods are not part of IMetadataTransformerFactory interface.

• IMetadataReader compose(IMetadataFormatConverter, IMetadataReader)
• IMetadataReader compose(IMetadataReader, IMetadataModelConverter)
• IMetadataWriter compose(IMetadataWriter, IMetadataFormatConverter)
• IMetadataWriter compose(IMetadataModelConverter, IMetadataWriter)
• IMetadataFormatConverter compose(IMetadataFormatConverter, IMetadataFormatConverter)
• IMetadataFormatConverter compose(IMetadataReader, IMetadataWriter)
• IMetadataModelConverter compose(IMetadataModelConverter, IMetadataModelConverter)
• IMetadataModelConverter compose(IMetadataWriter, IMetadataReader)

Old transformers usage in the YADDA source

BwmetaReader105:

• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/transformers/Bwmeta1_0ToDLTransformer.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/desklight/serialization/BwmetaReader105.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/desklight/serialization/BwmetaSerializer105.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/Bwmeta20ConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterCategorizationNewToDLTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterDLTo20Test.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterDLToNewTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterNewToDLTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/desklight/serialization/BwmetaReader105Test.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/desklight/model/importer/DLMObjectsCreator.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/tools/BasicPackImporter.java
• ./DeskLight/trunk/src/main/java/pl/edu/icm/yadda/desklight/model/importer/AbstractDLMImporter.java
• ./DeskLight/trunk/src/main/java/pl/edu/icm/yadda/desklight/model/importer/DLMMultithreadImporter.java
• ./yadda-content/trunk/src/main/java/pl/edu/icm/yadda/tools/relations/RelationshipStorageFeeder.java
• ./yadda-oaiserver/trunk/src/main/java/pl/edu/icm/yadda/oaiserver/catalog/BwmetaCatalog.java

BwmetaReader120:

• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/dublincore/BWMeta120ToDCConverter.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/serialization/BwmetaReader120.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/transformers/Bwmeta1_2ToYTransformer.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/serialization/Bwmeta120SerializationTest.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/cejsh/CEJSHPackCreator.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/medline/MedlinePackCreator.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/psjc/PSJCPackCreator.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/springer/SpringerPackCreator.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/tools/BasicPackImporter.java
• ./bwmeta-import/trunk/src/test/java/pl/edu/icm/yadda/imports/springer/SpringerParserTest.java
• ./yadda-analysis-impl/trunk/src/test/java/pl/edu/icm/yadda/analysis/bibref/YToBibEntryTransformerTest.java
• ./yadda-analysis/trunk/src/test/java/pl/edu/icm/yadda/analysis/bibref/YToBibEntryTransformerTest.java
• ./yadda-content/trunk/src/test/java/pl/edu/icm/yadda/parsing/AbstractCitationParserTest.java
• ./yadda-content/trunk/src/test/java/pl/edu/icm/yadda/tools/relations/RelationshipFeederTest.java
• ./yadda-content/trunk/src/test/java/pl/edu/icm/yadda/tools/relations/RelationshipStatementBuilderExportTest.java
• ./yadda-content/trunk/src/test/java/pl/edu/icm/yadda/tools/relations/RelationshipStatementsBuilderTest.java

BwmetaReader2:

• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/serialization/BwmetaReader2.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/transformers/Bwmeta2_0ToYTransformer.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/Bwmeta20ConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterCategorizationNewToDLTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterNewToDLTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/serialization/Bwmeta20SerializationTest.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/export/PackCreatorBasedExporter.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/commons/impl/PackCreator.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/springer/SpringerNewMetadataSource.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/tools/BasicPackImporter.java
• ./yadda-content/trunk/src/test/java/pl/edu/icm/yadda/tools/relations/persons/BasicAbstractTest.java
• ./yadda-content/trunk/src/test/java/pl/edu/icm/yadda/tools/relations/RelationshipStatementBuilderExportTest.java

BwmetaWriter105:

• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/transformers/DLToBwmeta1_0Transformer.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/desklight/serialization/BwmetaSerializer105.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/desklight/serialization/BwmetaWriter105.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/Bwmeta20ConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterCategorizationNewToDLTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterNewToDLTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/desklight/serialization/BwmetaReader105Test.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/desklight/model/serialization/BwmetaExporter.java
• ./bwmeta-import/trunk/src/test/java/pl/edu/icm/yadda/imports/springer/SpringerParserTest.java
• ./DeskLight/trunk/src/main/java/pl/edu/icm/yadda/desklight/exporter/SimpleBwmetaExporter.java
• ./DeskLight/trunk/src/main/java/pl/edu/icm/yadda/desklight/util/FlatCategoryParser.java

BwmetaWriter120:

• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/serialization/BwmetaWriter120.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/transformers/YToBwmeta1_2Transformer.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterDLToNewTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/serialization/Bwmeta120SerializationTest.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/cejsh/CEJSHPackCreator.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/medline/MedlinePackCreator.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/psjc/PSJCPackCreator.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/springer/SpringerPackCreator.java
• ./bwmeta-import/trunk/src/test/java/pl/edu/icm/yadda/imports/springer/SpringerParserTest.java
• ./bwmeta-import/trunk/test/integration/pl/edu/icm/yadda/imports/springer/SpringerNewMetadataSourceTest.java
• ./yadda-content/trunk/src/main/java/pl/edu/icm/yadda/tools/relations/RelationshipStorageFeeder.java
• ./yadda-oaiserver/trunk/src/main/java/pl/edu/icm/yadda/oaiserver/catalog/BwmetaCatalog.java

BwmetaWriter20:

• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/serialization/BwmetaWriter20.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/transformers/YToBwmeta2_0Transformer.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/Bwmeta20ConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterDLTo20Test.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/serialization/Bwmeta20SerializationTest.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/export/PackCreatorBasedExporter.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/tools/BasicPackImporter.java

BwmetaConverterDLToNew:

• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterDLToNew.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/transformers/DLToYTransformer.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/Bwmeta20ConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterDLTo20Test.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterDLToNewTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterTest.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/tools/BasicPackImporter.java
• ./yadda-content/trunk/src/main/java/pl/edu/icm/yadda/tools/relations/RelationshipStorageFeeder.java
• ./yadda-oaiserver/trunk/src/main/java/pl/edu/icm/yadda/oaiserver/catalog/BwmetaCatalog.java

BwmetaConverterNewToDL:

• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterNewToDL.java
• ./bwmeta-core/trunk/src/main/java/pl/edu/icm/yadda/bwmeta/transformers/YToDLTransformer.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/Bwmeta20ConverterTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterCategorizationNewToDLTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterNewToDLTest.java
• ./bwmeta-core/trunk/src/test/java/pl/edu/icm/yadda/bwmeta/converters/BwmetaConverterTest.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/cejsh/CEJSHMetadataSource.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/imports/psjc/PSJCMetadataSource.java
• ./bwmeta-import/trunk/src/main/java/pl/edu/icm/yadda/tools/BasicPackImporter.java
• ./bwmeta-import/trunk/src/test/java/pl/edu/icm/yadda/imports/springer/SpringerParserTest.java