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.

Field Summary

Fields inherited from class org.incenp.obofoundry.sssom.SSSOMReader

assumedVersion, extraPolicy, propagationPolicy

Constructor Summary

Constructors

Constructor	Description
JSONReader(File file)	Creates a new instance that will read data from the specified file.
JSONReader(InputStream stream)	Creates a new instance that will read data from the specified stream.
JSONReader(Reader reader)	Creates a new instance that will read data from the specified reader.
JSONReader(String filename)	Creates a new instance that will read data from a file with the specified name.

Method Summary

Modifier and Type	Method	Description
void	fillPrefixMap(Map<String,String> map)	Declares all prefix names in the specified map.
MappingSet	read()	Reads a mapping set from the source file.

Methods inherited from class org.incenp.obofoundry.sssom.SSSOMReader

setAssumedVersion, setExtraMetadataPolicy, setPropagationEnabled, setValidation, setValidationEnabled, validate

Methods inherited from class java.lang.Object

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

Constructor Detail

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 Detail

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.