Package org.incenp.obofoundry.sssom.util

Class ExtendedPrefixMap

java.lang.Object
org.incenp.obofoundry.sssom.util.ExtendedPrefixMap
public class ExtendedPrefixMap extends Object
A basic implementation of the “Extended Prefix Map” concept promoted by the Bioregistry.

The implementation is basic because it is never intended to actually be used to manage prefixes. The only purpose here is to be able to perform a single “reconciliation” operation, to force a mapping set to use the “canonical” prefixes set forth in a given extended prefix map.

This is another case of “the usual bioinformatics paradigm of ignoring the specs and inferring a format from a few examples”, but then again, the entire “spec” is nothing more than a single example, so we don’t have much choice.

See Also:

  • Constructor Details

    • ExtendedPrefixMap

      public ExtendedPrefixMap(File file) throws IOException
      Creates a new extended prefix map from the specified file.
      Parameters:
      file - The file to read the map from.
      Throws:
      IOException - If any error occurs when reading the file (including a format error).

    • ExtendedPrefixMap

      public ExtendedPrefixMap(String filename) throws IOException
      Creates a new extended prefix map from the specified filename.
      Parameters:
      filename - The name of the file to read the map from.
      Throws:
      IOException - If any error occurs when reading the file (including a format error).

    • ExtendedPrefixMap

      public ExtendedPrefixMap(InputStream stream) throws IOException
      Creates a new extended prefix map from the specified stream.
      Parameters:
      stream - The stream to read the map from.
      Throws:
      IOException - If any error occurs when reading the file (including a format error).

  • Method Details

    • getSimplePrefixMap

      public Map<String,String> getSimplePrefixMap()
      Gets a simple prefix map associating the canonical prefix name to the canonical URL prefix.
      Returns:
      The simple, canonical prefix map.

    • getFullPrefixMap

      public Map<String,String> getFullPrefixMap()
      Gets the full prefix map, associating every known prefix names to the canonical URL prefix.
      Returns:
      The full prefix map.

    • canonicalise

      public String canonicalise(String iri)
      Canonicalises an IRI. This method checks whether the specified IRI uses a prefix that is a synonym of a canonical prefix, and returns a new IRI using the corresponding canonical prefix.
      Parameters:
      iri - The IRI to canonicalise.
      Returns:
      The canonical form of the IRI; may be identical to the original IRI if (1) that URI was already using the canonical prefix, or (2) no matching prefix was found in the extended map.

    • canonicalise

      public List<String> canonicalise(List<String> iris, boolean inPlace)
      Canonicalises a list of IRIs.
      Parameters:
      iris - The IRIs to canonicalise.
      inPlace - If true, the original list will be modified and returned; otherwise a new list with canonicalised IRIs will be returned.
      Returns:
      A list with canonicalised IRIs.

    • canonicalise

      public void canonicalise(List<Mapping> mappings)
      Canonicalises a list of mappings. This method performs a canonicalisation on the values of all slots of type EntityReference.
      Parameters:
      mappings - The mappings of canonicalise.

    • canonicalise

      public void canonicalise(MappingSet set)
      Canonicalises a mapping set. This performs a canonicalisation on the values of all slots of type EntityReference in the set itself, then in the individual mappings. The original prefix map of the set is updated with the canonical prefix map.
      Parameters:
      set - The mapping set to canonicalise.