Package org.incenp.obofoundry.sssom

Class JSONReader

java.lang.Object
org.incenp.obofoundry.sssom.SSSOMReader
org.incenp.obofoundry.sssom.JSONReader
public class JSONReader extends SSSOMReader
A parser to read a SSSOM mapping set from a JSON serialisation format.

The JSON format expected by this reader is not the JSON format used by SSSOM-Py, which is based on JSON-LD and is currently unspecified. Instead, this reader expects a “pure” JSON format that is merely a direct JSON rendering of the internal SSSOM data model.

  • Constructor Details

    • JSONReader

      public JSONReader(File file) throws FileNotFoundException
      Creates a new instance that will read data from the specified file.
      Parameters:
      file - The file to read the mapping set from.
      Throws:
      FileNotFoundException - If the file cannot be found.

    • JSONReader

      public JSONReader(InputStream stream)
      Creates a new instance that will read data from the specified stream.
      Parameters:
      stream - The stream to read the mapping set from.

    • JSONReader

      public JSONReader(Reader reader)
      Creates a new instance that will read data from the specified reader.
      Parameters:
      reader - The reader object to read the mapping set from.

    • JSONReader

      public JSONReader(String filename) throws FileNotFoundException
      Creates a new instance that will read data from a file with the specified name.
      Parameters:
      filename - The name of the file to read the mapping set from.
      Throws:
      FileNotFoundException - If the file cannot be found.

  • Method Details

    • fillPrefixMap

      public void fillPrefixMap(Map<String,String> map)
      Description copied from class: SSSOMReader
      Declares all prefix names in the specified map. Prefix names declared here complement the declarations from the file’s own prefix map, allowing the reader to parse a file with an incomplete prefix map.

      It is up to concrete implementations to actually do something with that map. Some of them may ignore it.

      Overrides:
      fillPrefixMap in class SSSOMReader
      Parameters:
      map - The prefix map to use.

    • read

      public MappingSet read() throws SSSOMFormatException, IOException
      Description copied from class: SSSOMReader
      Reads a mapping set from the source file.
      Specified by:
      read in class SSSOMReader
      Returns:
      A complete SSSOM mapping set.
      Throws:
      SSSOMFormatException - If encountering invalid SSSOM data.
      IOException - If any kind of non-SSSOM-related I/O error occurs.