org.sbml.jsbml.xml.parsers

Class SBMLRDFAnnotationParser

java.lang.Object

org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser

All Implemented Interfaces:

AnnotationReader, AnnotationWriter

public class SBMLRDFAnnotationParser
extends java.lang.Object
implements AnnotationReader, AnnotationWriter

Parses the RDF annotations as defined in the SBML specifications and put them into objects. TODO - extends a lot the doc to describe the whole process of validation, reading and writing.

Since:

1.0

Author:

Nicolas Rodriguez

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static class	SBMLRDFAnnotationParser.NODE_COLOR

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CUSTOM_RDF A Constant String that is used to store any remaining children or attributes after having removed the standard SBML RDF elements and attributes.
private static org.apache.log4j.Logger	logger Logger to be able to send informative, debug, warning or error messages.
static java.lang.String	RDF_NODE_COLOR A Constant String that is used to store a XMLNode color in the user objects map.

Constructor Summary

Constructors

Constructor and Description
SBMLRDFAnnotationParser()

Method Summary

Modifier and Type	Method and Description
private SBMLRDFAnnotationParser.NODE_COLOR	addColor(SBMLRDFAnnotationParser.NODE_COLOR color1, SBMLRDFAnnotationParser.NODE_COLOR color2) Adds the given colors and return the resulting color.
private SBMLRDFAnnotationParser.NODE_COLOR	areValidModifiedDates(java.util.List<XMLNode> modifiedNodes) Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the modified Dates.
private void	checkAbout(SBase contextObject) Checks and Sets about String, that correspond to the value of the rdf:about attribute.
private int	findFirstNonEmptyTextElementIndex(XMLNode xmlNode) Return the first child element of type text that is not empty.
private int	getLastIndexOf(XMLNode xmlNode, java.lang.String elementName, java.lang.String elementURI)
int	getNumberOfNonEmptyChildElement(XMLNode xmlNode) Returns the number of child XMLNode, excluding text XMLNode that contains only spaces.
private XMLNode	getOrCreate(XMLNode parent, int index, java.lang.String elementName, java.lang.String elementNamespaceURI, java.lang.String prefix)
private XMLNode	getOrCreate(XMLNode parent, java.lang.String elementName, java.lang.String elementNamespaceURI, java.lang.String prefix)
private XMLNode	getOrCreateAfter(XMLNode parent, java.lang.String elementName, java.lang.String elementNamespaceURI, java.lang.String prefix, java.lang.String precedingElementName, java.lang.String precedingElementNamespaceURI)
private XMLNode	getOrCreateDescription(XMLNode rdfNode)
private XMLNode	getOrCreateWithCustomRDF(XMLNode parent, int precedingTermIndex, java.lang.String elementName, java.lang.String cvtermURI, java.lang.String cvtermPrefix, java.lang.Object customRDFXMLNode)
private int	getTrueIndexOf(XMLNode xmlNode, java.lang.String elementName, java.lang.String elementURI, int index)
private SBMLRDFAnnotationParser.NODE_COLOR	isValidCreatedDate(XMLNode createdNode) Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the created Date.
private SBMLRDFAnnotationParser.NODE_COLOR	isValidCreator(XMLNode creatorNode) Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the Creator elements compared to the SBML specifications.
private SBMLRDFAnnotationParser.NODE_COLOR	isValidRDF(XMLNode annotationXMLNode) Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the RDF block compared to the SBML specifications.
private SBMLRDFAnnotationParser.NODE_COLOR	isValidRDFDescription(XMLNode rdfNode) Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the RDF Description element compared to the SBML specifications.
private SBMLRDFAnnotationParser.NODE_COLOR	isValidRDFHistory(XMLNode xmlNode) Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the History elements compared to the SBML specifications.
private SBMLRDFAnnotationParser.NODE_COLOR	isValidRDFURIs(XMLNode rdfNode) Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the first bqmodel and bqbiol CVTerm.
private boolean	isValidSBMLRDF(SBase contextObject) Returns true if the SBML RDF block is recognized as valid or partially valid.
private SBMLRDFAnnotationParser.NODE_COLOR	isValidVCard(XMLNode xmlNode) Returns SBMLRDFAnnotationParser.NODE_COLOR.GREEN if at least one of these three nodes is present: vCard:N, vCard:EMAIL or vCard:ORG, meaning that we consider that the VCard is at least partially defined.
void	processAnnotation(SBase contextObject) Process the annotation of the given SBase object.
private void	readCreatedDate(SBase contextSBase, XMLNode createdNode) Reads the 'dcterms:created' part of the SBML RDF annotation into a java Date.
private void	readCreator(SBase contextSBase, XMLNode creatorNode) Reads the 'dc:creator' part of the SBML RDF annotation into Creators.
private void	readModifiedDate(SBase contextSBase, XMLNode modifiedNode) Reads the 'dcterms:modified' part of the SBML RDF annotation into java Date(s).
private void	readRDFHistory(SBase contextSBase, XMLNode descriptionNode) Reads the 'rdf:Description' to extract the History part of the SBML RDF annotation.
private void	readRDFURIs(java.lang.Object contextSBase, XMLNode descriptionNode) Reads the relation elements part of the SBML RDF annotation into CVTerms.
private void	readSBMLRDF(SBase contextObject) Reads the 'rdf:RDF' block, if present in the Annotation, to extract the History and the CVTerm(s) as defined in the SBML specifications, section 6: 'A standard format for the annotation element'.
private boolean	removeXmlNodeIfEmpty(XMLNode xmlNode) Removes an XMLNode from its parent if it has no child elements, no attributes and no namespaces declared any more.
XMLNode	writeAnnotation(SBase contextObject, XMLNode xmlNode) Writes the annotation of the given SBase object into the given XMLNode.
private void	writeCreators(History history, XMLNode descriptionNode)
private void	writeCVTerm(CVTerm cvterm, XMLNode parentNode, java.lang.String precedingElementName, java.lang.String precedingElementNamespaceURI)
private void	writeDates(History history, XMLNode descriptionNode)
private void	writeHistory(SBase contextObject, XMLNode descriptionNode)
private XMLNode	writeSBMLRDF(SBase contextObject, XMLNode annotationXMLNode)
private void	writeURIs(CVTerm currentCVTerm, XMLNode parentNode)
private void	writeURIs(SBase contextObject, XMLNode descriptionNode)

Methods inherited from class java.lang.Object

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

Field Detail

RDF_NODE_COLOR

public static final java.lang.String RDF_NODE_COLOR

A Constant String that is used to store a XMLNode color in the user objects map.

See Also:

Constant Field Values

CUSTOM_RDF

public static final java.lang.String CUSTOM_RDF

A Constant String that is used to store any remaining children or attributes after having removed the standard SBML RDF elements and attributes.

It is stored as an XMLNode in the user objects map.

See Also:

Constant Field Values

logger

private static final transient org.apache.log4j.Logger logger

Logger to be able to send informative, debug, warning or error messages.

Constructor Detail

SBMLRDFAnnotationParser

public SBMLRDFAnnotationParser()

Method Detail

writeAnnotation

public XMLNode writeAnnotation(SBase contextObject,
                               XMLNode xmlNode)

Description copied from interface: AnnotationWriter

Writes the annotation of the given SBase object into the given XMLNode.

This method can change the content of the XMLNode by removing or adding nodes.

Specified by:

writeAnnotation in interface AnnotationWriter

Returns:

processAnnotation

public void processAnnotation(SBase contextObject)

Description copied from interface: AnnotationReader

Process the annotation of the given SBase object. This method can change the content of the annotation XMLNode by removing or adding nodes.

Specified by:

processAnnotation in interface AnnotationReader

isValidSBMLRDF

private boolean isValidSBMLRDF(SBase contextObject)

Returns true if the SBML RDF block is recognized as valid or partially valid.

Additional elements are allowed but what is defined in the SBML specifications should be there as well. It means that the RDF element needs to have the color SBMLRDFAnnotationParser.NODE_COLOR.GREEN or SBMLRDFAnnotationParser.NODE_COLOR.ORANGE.

Parameters:

contextObject - - the SBase where we want to check the Annotation.

Returns:

true if the SBML RDF block is recognized as valid or partially valid..

isValidRDF

private SBMLRDFAnnotationParser.NODE_COLOR isValidRDF(XMLNode annotationXMLNode)

Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the RDF block compared to the SBML specifications.

Parameters:

annotationXMLNode - - the top level XMLNode from the Annotation.

Returns:

a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the RDF block.

isValidRDFDescription

private SBMLRDFAnnotationParser.NODE_COLOR isValidRDFDescription(XMLNode rdfNode)

Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the RDF Description element compared to the SBML specifications.

Parameters:

rdfNode - - the rdf:RDF XMLNode from the Annotation.

Returns:

a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the RDF Description element.

addColor

private SBMLRDFAnnotationParser.NODE_COLOR addColor(SBMLRDFAnnotationParser.NODE_COLOR color1,
                                                    SBMLRDFAnnotationParser.NODE_COLOR color2)

Adds the given colors and return the resulting color.

Parameters:

color1 - - the first SBMLRDFAnnotationParser.NODE_COLOR

color2 - - the second SBMLRDFAnnotationParser.NODE_COLOR

Returns:

the resulting color.

isValidRDFHistory

private SBMLRDFAnnotationParser.NODE_COLOR isValidRDFHistory(XMLNode xmlNode)

Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the History elements compared to the SBML specifications.

Parameters:

xmlNode - - the rdf:RDF XMLNode from the Annotation.

Returns:

a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the History elements.

isValidCreator

private SBMLRDFAnnotationParser.NODE_COLOR isValidCreator(XMLNode creatorNode)

Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the Creator elements compared to the SBML specifications.

Parameters:

creatorNode - - the dc:Creator XMLNode from the RDF block.

Returns:

a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the Creator elements.

isValidVCard

private SBMLRDFAnnotationParser.NODE_COLOR isValidVCard(XMLNode xmlNode)

Returns SBMLRDFAnnotationParser.NODE_COLOR.GREEN if at least one of these three nodes is present: vCard:N, vCard:EMAIL or vCard:ORG, meaning that we consider that the VCard is at least partially defined.

The color is never SBMLRDFAnnotationParser.NODE_COLOR.ORANGE as we do not check at the moment for any additional elements or attributes or for the proper structure of the vCard:N or vCard:ORG elements. The reading and writing should work fine whatever the content of the rdf:li element.

Parameters:

xmlNode - - the rdf:li XMLNode from the dc:creator block.

Returns:

SBMLRDFAnnotationParser.NODE_COLOR.GREEN if at least one of these three nodes is present: vCard:N, vCard:EMAIL or vCard:ORG.

areValidModifiedDates

private SBMLRDFAnnotationParser.NODE_COLOR areValidModifiedDates(java.util.List<XMLNode> modifiedNodes)

Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the modified Dates.

The color of one dcterms:modified element is never SBMLRDFAnnotationParser.NODE_COLOR.ORANGE as we do not check at the moment for any additional elements or attributes. If the dcterms:modified element contain the dcterms:W3CDTF child element then it's color is SBMLRDFAnnotationParser.NODE_COLOR.GREEN, otherwise it is SBMLRDFAnnotationParser.NODE_COLOR.WHITE. The reading and writing should work fine whatever the content of the dcterms:modified elements.

Parameters:

modifiedNodes - - the dcterms:modified XMLNodes from the rdf:Description block.

Returns:

a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the modified Dates.

isValidCreatedDate

private SBMLRDFAnnotationParser.NODE_COLOR isValidCreatedDate(XMLNode createdNode)

Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the created Date.

The color of the dcterms:created element is never SBMLRDFAnnotationParser.NODE_COLOR.ORANGE as we do not check at the moment for any additional elements or attributes. If the dcterms:created element contain the dcterms:W3CDTF child element then it's color is SBMLRDFAnnotationParser.NODE_COLOR.GREEN, otherwise it is SBMLRDFAnnotationParser.NODE_COLOR.WHITE. The reading and writing should work fine whatever the content of the dcterms:created element.

Parameters:

createdNode - - the dcterms:created XMLNode from the rdf:Description block.

Returns:

a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the created Date

isValidRDFURIs

private SBMLRDFAnnotationParser.NODE_COLOR isValidRDFURIs(XMLNode rdfNode)

Returns a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the first bqmodel and bqbiol CVTerm.

The color of the relation elements is never SBMLRDFAnnotationParser.NODE_COLOR.ORANGE as we do not check at the moment for any additional elements or attributes. If the bqmodel:* or bqbiol:* elements contain a rdf:Bag that contain at least one rdf:li, then we consider the XMLNode to be at least partially valid and return SBMLRDFAnnotationParser.NODE_COLOR.GREEN. Otherwise we return SBMLRDFAnnotationParser.NODE_COLOR.WHITE. The reading and writing should work fine whatever the content of the bqmodel:* or bqbiol:* element.

Parameters:

rdfNode - - the rdf:Description XMLNode from the RDF block.

Returns:

a SBMLRDFAnnotationParser.NODE_COLOR corresponding to the validity of the first bqmodel and bqbiol CVTerm.

readSBMLRDF

private void readSBMLRDF(SBase contextObject)

Reads the 'rdf:RDF' block, if present in the Annotation, to extract the History and the CVTerm(s) as defined in the SBML specifications, section 6: 'A standard format for the annotation element'.

This method will remove, from the XMLNode tree, all known elements and attributes. Any additional attributes or elements inside the RDF block are stored as a userObject with the key CUSTOM_RDF.
Different parts of the XMLNode tree are stored in different objects. The additional XML from dc:creator/rdf:Bag/rdf:li are stored in each corresponding Creator. The additional XML from any of the relation elements (bqmodel:* and bqbiol:*) are stored in each corresponding CVTerm. All the rest is stored on the Annotation object.

Parameters:

contextObject - the SBase in which we will store the History and the CVTerm(s).

readRDFHistory

private void readRDFHistory(SBase contextSBase,
                            XMLNode descriptionNode)

Reads the 'rdf:Description' to extract the History part of the SBML RDF annotation.

Parameters:

contextSBase - the SBase in which we will store the History.

descriptionNode - the 'rdf:Description' XMLNode that contain the definition of the created and modified dates and the creators.

readModifiedDate

private void readModifiedDate(SBase contextSBase,
                              XMLNode modifiedNode)

Reads the 'dcterms:modified' part of the SBML RDF annotation into java Date(s).

Parameters:

contextSBase - the SBase in which we will add the modified Date(s).

modifiedNode - the 'dcterms:modified' XMLNode that contain the definition of the modified dates.

findFirstNonEmptyTextElementIndex

private int findFirstNonEmptyTextElementIndex(XMLNode xmlNode)

Return the first child element of type text that is not empty.

Parameters:

xmlNode -

Returns:

the first child element of type text that is not empty.

readCreatedDate

private void readCreatedDate(SBase contextSBase,
                             XMLNode createdNode)

Reads the 'dcterms:created' part of the SBML RDF annotation into a java Date.

Parameters:

contextSBase - the SBase in which we will add the created Date.

createdNode - the 'dcterms:created' XMLNode that contain the definition of the created date.

readCreator

private void readCreator(SBase contextSBase,
                         XMLNode creatorNode)

Reads the 'dc:creator' part of the SBML RDF annotation into Creators.

Parameters:

contextSBase - the SBase in which we will add the Creators.

creatorNode - the 'dc:creator' XMLNode that contain the definition of the creator vCards.

readRDFURIs

private void readRDFURIs(java.lang.Object contextSBase,
                         XMLNode descriptionNode)

Reads the relation elements part of the SBML RDF annotation into CVTerms.

Parameters:

contextSBase - the SBase in which we will add the created CVTerms.

descriptionNode - the rdf:Description XMLNode that contain the qualifiers and URIs.

removeXmlNodeIfEmpty

private boolean removeXmlNodeIfEmpty(XMLNode xmlNode)

Removes an XMLNode from its parent if it has no child elements, no attributes and no namespaces declared any more.

Parameters:

xmlNode -

Returns:

true if the node was removed.

getNumberOfNonEmptyChildElement

public int getNumberOfNonEmptyChildElement(XMLNode xmlNode)

Returns the number of child XMLNode, excluding text XMLNode that contains only spaces.

Parameters:

xmlNode -

Returns:

the number of child XMLNode, excluding text XMLNode that contains only spaces.

writeSBMLRDF

private XMLNode writeSBMLRDF(SBase contextObject,
                             XMLNode annotationXMLNode)

Parameters:

contextObject -

annotationXMLNode -

Returns:

checkAbout

private void checkAbout(SBase contextObject)

Checks and Sets about String, that correspond to the value of the rdf:about attribute.

A metaid is created and set if it was not set before.

Parameters:

contextObject -

getOrCreateDescription

private XMLNode getOrCreateDescription(XMLNode rdfNode)

Parameters:

rdfNode -

Returns:

getOrCreate

private XMLNode getOrCreate(XMLNode parent,
                            java.lang.String elementName,
                            java.lang.String elementNamespaceURI,
                            java.lang.String prefix)

Parameters:

parent -

elementName -

elementNamespaceURI -

prefix -

Returns:

getOrCreateAfter

private XMLNode getOrCreateAfter(XMLNode parent,
                                 java.lang.String elementName,
                                 java.lang.String elementNamespaceURI,
                                 java.lang.String prefix,
                                 java.lang.String precedingElementName,
                                 java.lang.String precedingElementNamespaceURI)

Parameters:

parent -

elementName -

elementNamespaceURI -

prefix -

precedingElementName -

precedingElementNamespaceURI -

Returns:

getOrCreate

private XMLNode getOrCreate(XMLNode parent,
                            int index,
                            java.lang.String elementName,
                            java.lang.String elementNamespaceURI,
                            java.lang.String prefix)

Parameters:

parent -

index -

elementName -

elementNamespaceURI -

prefix -

Returns:

getOrCreateWithCustomRDF

private XMLNode getOrCreateWithCustomRDF(XMLNode parent,
                                         int precedingTermIndex,
                                         java.lang.String elementName,
                                         java.lang.String cvtermURI,
                                         java.lang.String cvtermPrefix,
                                         java.lang.Object customRDFXMLNode)

Parameters:

parent -

precedingTermIndex -

elementName -

cvtermURI -

cvtermPrefix -

customRDFXMLNode -

Returns:

getLastIndexOf

private int getLastIndexOf(XMLNode xmlNode,
                           java.lang.String elementName,
                           java.lang.String elementURI)

Parameters:

xmlNode -

elementName -

elementURI -

Returns:

getTrueIndexOf

private int getTrueIndexOf(XMLNode xmlNode,
                           java.lang.String elementName,
                           java.lang.String elementURI,
                           int index)

Parameters:

xmlNode -

elementName -

elementURI -

index -

Returns:

writeHistory

private void writeHistory(SBase contextObject,
                          XMLNode descriptionNode)

Parameters:

contextObject -

descriptionNode -

writeDates

private void writeDates(History history,
                        XMLNode descriptionNode)

Parameters:

history -

descriptionNode -

writeCreators

private void writeCreators(History history,
                           XMLNode descriptionNode)

Parameters:

history -

descriptionNode -

writeURIs

private void writeURIs(SBase contextObject,
                       XMLNode descriptionNode)

Parameters:

contextObject -

descriptionNode -

writeURIs

private void writeURIs(CVTerm currentCVTerm,
                       XMLNode parentNode)

Parameters:

currentCVTerm -

parentNode -

writeCVTerm

private void writeCVTerm(CVTerm cvterm,
                         XMLNode parentNode,
                         java.lang.String precedingElementName,
                         java.lang.String precedingElementNamespaceURI)

Parameters:

cvterm -

parentNode -

precedingElementName -

precedingElementNamespaceURI -