Package org.incenp.obofoundry.sssom

Class SSSOMWriter

java.lang.Object
org.incenp.obofoundry.sssom.SSSOMWriter
Direct Known Subclasses:
JSONWriter, RDFWriter, TSVWriter
public abstract class SSSOMWriter extends Object
Base class to serialise a mapping set.

This class should be derived into specialised classes that implement a precise serialisation format.

  • Field Details

  • Constructor Details

    • SSSOMWriter

      public SSSOMWriter()

  • Method Details

    • setCurieMap

      public void setCurieMap(Map<String,String> map)
      Sets the Curie map to use to shorten identifiers. The Curie map associated with the mapping set (MappingSet.getCurieMap()) will then be completely ignored in favour of the specified map.
      Parameters:
      map - A map associating prefix names to prefixes.

    • setExtraMetadataPolicy

      public void setExtraMetadataPolicy(ExtraMetadataPolicy policy)
      Sets the policy to deal with non-standard metadata in the mapping set to write.
      Parameters:
      policy - The policy instructing the writer about what to do with any non-standard metadata. The default policy is ExtraMetadataPolicy.NONE, meaning that no non-standard metadata is ever written.

    • setCondensationEnabled

      public void setCondensationEnabled(boolean enabled)
      Enables or disables the condensation of "propagatable slots".
      Parameters:
      enabled - False to disable condensation; it is enabled by default.

    • setSortingEnabled

      public void setSortingEnabled(boolean enabled)
      Enables or disables sorting the mappings when writing them.
      Parameters:
      enabled - False to disable sorting; it is enabled by default.

    • write

      public void write(MappingSet mappingSet) throws IOException
      Serialises a mapping set into the underlying file. This method performs some prelimiary steps that are common to all serialisers, then delegates the actual serialisation task to doWrite(MappingSet).
      Parameters:
      mappingSet - The mapping set to serialise.
      Throws:
      IOException - If an I/O error occurs.

    • doWrite

      protected abstract void doWrite(MappingSet mappingSet) throws IOException
      Actually serialises a mapping set. This method should be overridden by derived classes to implement the serialisation in a specific format.
      Parameters:
      mappingSet - The mapping set to serialise.
      Throws:
      IOException - If an I/O error occurs.

    • getUsedPrefixes

      protected Set<String> getUsedPrefixes(MappingSet mappingSet)
      Gets the prefix names that are actually used in the given set. This excludes prefix names that are considered builtin.
      Parameters:
      mappingSet - The mapping set to query for used prefix names.
      Returns:
      A set of all prefix names that are effectively needed to condense all identifiers in the mapping set.

    • getUsedPrefixes

      protected Set<String> getUsedPrefixes(MappingSet mappingSet, boolean includeBuiltin)
      Gets the prefix names that are actually used in the given set, possibly including the builtin prefix names.
      Parameters:
      mappingSet - The mapping set to query for used prefix names.
      includeBuiltin - If true, builtin prefix names will be included.
      Returns:
      A set of all prefix names that are effectively needed to condense all identifiers in the mapping set.

    • condenseSet

      protected Set<String> condenseSet(MappingSet mappingSet)
      Performs condensation of "propagatable slots" in a mapping set.

      If condensation is disabled (see setCondensationEnabled(boolean)), this is merely a no-op.

      Parameters:
      mappingSet - The mapping set whose slots should be condensed.
      Returns:
      A set of all mapping slot names that have been effectively condensed (may be empty if no slots have been condensed at all).