Package org.incenp.obofoundry.sssom

Class SSSOMReader

java.lang.Object

org.incenp.obofoundry.sssom.SSSOMReader

Direct Known Subclasses:

JSONReader, RDFReader, TSVReader

public abstract class SSSOMReader
extends Object

Base class to read a mapping set from any of the supported serialisation formats.

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

Field Summary

Fields

Modifier and Type	Field	Description
protected Version	assumedVersion
protected ExtraMetadataPolicy	extraPolicy
protected PropagationPolicy	propagationPolicy

Constructor Summary

Constructors

Constructor	Description
SSSOMReader()

Method Summary

Modifier and Type	Method	Description
void	fillPrefixMap(Map<String,String> map)	Declares all prefix names in the specified map.
abstract MappingSet	read()	Reads a mapping set from the source file.
void	setAssumedVersion(Version version)	Sets the version of the SSSOM specification that the reader should assume the set is compliant with, if the set does not have a sssom_version slot.
void	setExtraMetadataPolicy(ExtraMetadataPolicy policy)	Sets the policy to deal with non-standard metadata in the input file.
void	setPropagationEnabled(boolean enabled)	Enables or disables the propagation of "propagatable slots".
void	setValidation(ValidationLevel validationType)	Controls whether a mapping set should be validated after it has been parsed, and how.
void	setValidationEnabled(boolean enabled)	Enables or disables post-parsing validation of mappings.
protected void	validate(MappingSet mappingSet)	Validates a mapping set.

Methods inherited from class java.lang.Object

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

Field Detail

extraPolicy

protected ExtraMetadataPolicy extraPolicy

propagationPolicy

protected PropagationPolicy propagationPolicy

assumedVersion

protected Version assumedVersion

Constructor Detail

SSSOMReader

public SSSOMReader()

Method Detail

setExtraMetadataPolicy

public void setExtraMetadataPolicy(ExtraMetadataPolicy policy)

Sets the policy to deal with non-standard metadata in the input file.

Parameters:

policy - The policy instructing the parser about what to do when encountering non-standard metadata. The default policy is ExtraMetadataPolicy.NONE.

setPropagationEnabled

public void setPropagationEnabled(boolean enabled)

Enables or disables the propagation of "propagatable slots".

Parameters:

enabled - False to disable propagation; it is enabled by default.

setAssumedVersion

public void setAssumedVersion(Version version)

Sets the version of the SSSOM specification that the reader should assume the set is compliant with, if the set does not have a sssom_version slot. The default is to assume that the set is compliant with version 1.0, as mandated by the specification.

This parameter has no effect if the set does have a sssom_version slot: in that case, the set will be expected to be compliant with the version indicated in that slot.

Parameters:

version - The SSSOM version a set is assumed to be compliant with.

setValidationEnabled

public void setValidationEnabled(boolean enabled)

Enables or disables post-parsing validation of mappings.

Parameters:

enabled - False to disable validation; it is enabled by default.

setValidation

public void setValidation(ValidationLevel validationType)

Controls whether a mapping set should be validated after it has been parsed, and how.

This method provides a finer control than setValidationEnabled(boolean), which simply enables full validation or disables validation entirely.

Parameters:

validationType - The level of validation to use; set to ValidationLevel.DISABLED to disable validation entirely; the default is ValidationLevel.FULL.

fillPrefixMap

public void fillPrefixMap(Map<String,String> map)

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.

Parameters:

map - The prefix map to use.

read

public abstract MappingSet read()
                         throws SSSOMFormatException,
                                IOException

Reads a mapping set from the source file.

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.

validate

protected void validate(MappingSet mappingSet)
                 throws SSSOMFormatException

Validates a mapping set. This method performs all post-parsing checks to ensure the mapping set is valid according to the SSSOM specification.

Parameters:

mappingSet - The set to validate. It should be called by the read method in concrete derived classes.

Throws:

SSSOMFormatException - If the mapping set is invalid.