Package psidev.psi.mi.jami.xml.model.extension.datasource

Class AbstractPsiXmlStream<T extends Interaction>

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.datasource.AbstractPsiXmlStream<T>

All Implemented Interfaces:

ErrorHandler, InteractionStream<T>, MIDataSource, MIFileDataSource, MIFileParserListener, PsiXmlParserListener, PsiXmlStreamSource<T>

Direct Known Subclasses:

AbstractPsiXmlBinaryStream, AbstractPsiXmlSource, LightXmlStreamSource, XmlComplexStreamSource, XmlEvidenceStreamSource, XmlModelledStreamSource, XmlStreamSource

public abstract class AbstractPsiXmlStream<T extends Interaction>
extends Object
implements PsiXmlStreamSource<T>

Abstract class for psiXml data source

Since:

16/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	SCHEMA_FEATURE	Constant SCHEMA_FEATURE="http://apache.org/xml/features/validati"{trunked}
static String	VALIDATION_FEATURE	Constant VALIDATION_FEATURE="http://xml.org/sax/features/validation"

Fields inherited from interface psidev.psi.mi.jami.datasource.MIFileDataSource

FILE_URI_PREFIX, URL_PREFIX_REGEXP

Constructor Summary

Constructors

Constructor	Description
AbstractPsiXmlStream()	Constructor for AbstractPsiXmlStream.
AbstractPsiXmlStream(File file)	Constructor for AbstractPsiXmlStream.
AbstractPsiXmlStream(InputStream input)	Constructor for AbstractPsiXmlStream.
AbstractPsiXmlStream(Reader reader)	Constructor for AbstractPsiXmlStream.
AbstractPsiXmlStream(URL url)	Constructor for AbstractPsiXmlStream.

Method Summary

Modifier and Type	Method	Description
void	close()	This method close the file data source and all opened streams and readers
protected abstract Iterator<T>	createXmlIterator()	createXmlIterator.
void	error(SAXParseException exception)
void	fatalError(SAXParseException exception)
protected PsiXmlIdCache	getElementCache()	Getter for the field elementCache.
MIFileParserListener	getFileParserListener()	The MIFileParserListener can be null if not initialised
Iterator<T>	getInteractionsIterator()	The iterator of Interactions for this datasource
XmlInteractorFactory	getInteractorFactory()	Getter for the field interactorFactory.
protected PsiXmlParser<T>	getParser()	Getter for the field parser.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the MIDataSource given a map of options
protected abstract void	initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected abstract void	initialiseXmlParser(File file)	initialiseXmlParser.
protected abstract void	initialiseXmlParser(InputStream input)	initialiseXmlParser.
protected abstract void	initialiseXmlParser(Reader reader)	initialiseXmlParser.
protected abstract void	initialiseXmlParser(URL url)	initialiseXmlParser.
protected boolean	isInitialised()	isInitialised.
void	onAliasWithoutName(FileSourceContext context)	Listen to an event fired when an alias does not have a name
void	onAnnotationWithoutTopic(FileSourceContext context)	Listen to an event fired when an annotation does not have a topic
void	onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)	Listen to an event fired when an interaction is read and does not have any participants.
void	onInvalidOrganismTaxid(String taxid, FileSourceContext context)	Listen to an event fired when an organism does not have a valid taxid (positive integer or -1, -2, -3, -4, -5)
void	onInvalidPosition(String message, FileSourceContext context)	Listen to an event fired when a position is not valid
void	onInvalidRange(String message, FileSourceContext context)	Listen to an event fired when a range is not valid
void	onInvalidStoichiometry(String message, FileSourceContext context)	Listen to an event fired when a stoichiometry is not valid
void	onInvalidSyntax(FileSourceContext context, Exception e)	Listen to an invalid syntax causing an Exception
void	onMissingChecksumMethod(FileSourceContext context)	Listen to an event fired when a checksum does not have a method
void	onMissingChecksumValue(FileSourceContext context)	Listen to an event fired when a checksum does not have a value
void	onMissingConfidenceType(FileSourceContext context)	Listen to an event fired when a confidence does not have a confidence type
void	onMissingConfidenceValue(FileSourceContext context)	Listen to an event fired when a confidence does not have a value
void	onMissingCvTermName(CvTerm term, FileSourceContext context, String message)	Listen to an event fired when a CvTerm is read and does not have any names.
void	onMissingInteractorName(Interactor interactor, FileSourceContext context)	Listen to an event fired when an interactor is read and does not have any names.
void	onMissingParameterType(FileSourceContext context)	Listen to an event fired when a parameter does not have a type
void	onMissingParameterValue(FileSourceContext context)	Listen to an event fired when a parameter does not have a value
void	onParticipantWithoutInteractor(Participant participant, FileSourceContext context)	Listen to en event fired when a Participant is read and no interactor details has been provided.
void	onSeveralExperimentalRolesFound(Collection<CvTerm> roles, FileSourceLocator locator)	onSeveralExperimentalRolesFound.
void	onSeveralExperimentsFound(Collection<Experiment> experiments, FileSourceLocator locator)	onSeveralExperimentsFound.
void	onSeveralExpressedInOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)	onSeveralExpressedInOrganismFound.
void	onSeveralHostOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)	onSeveralHostOrganismFound.
void	onSyntaxWarning(FileSourceContext context, String message)	Listen to an event fired when the syntax of the file is valid but the content is not expected or some information may be lost.
void	onUnresolvedReference(XmlIdReference ref, String message)	onUnresolvedReference.
void	onXrefWithoutDatabase(FileSourceContext context)	Listen to an event fired when a xref does not have a database
void	onXrefWithoutId(FileSourceContext context)	Listen to an event fired when a xref does not have an id
protected void	reInit()	reInit.
void	reset()	This method will reset the data sources from all loaded options.
void	setFileParserListener(MIFileParserListener listener)	setFileParserListener
void	setInteractorFactory(XmlInteractorFactory interactorFactory)	Setter for the field interactorFactory.
protected void	setMIFileParserListener(MIFileParserListener listener)	setMIFileParserListener.
protected void	setParser(PsiXmlParser<T> parser)	Setter for the field parser.
protected void	setXmlFileParserListener(PsiXmlParserListener listener)	setXmlFileParserListener.
boolean	validateSyntax()	Validate the syntax of this MIFileDataSource.
boolean	validateSyntax(MIFileParserListener listener)	Validate the syntax of this MIFileDataSource and uses the provided MIFileParserListener to listen to the events.
void	warning(SAXParseException exception)

Methods inherited from class java.lang.Object

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

Field Detail

VALIDATION_FEATURE

public static final String VALIDATION_FEATURE

Constant VALIDATION_FEATURE="http://xml.org/sax/features/validation"

See Also:

Constant Field Values

SCHEMA_FEATURE

public static final String SCHEMA_FEATURE

Constant SCHEMA_FEATURE="http://apache.org/xml/features/validati"{trunked}

See Also:

Constant Field Values

Constructor Detail

AbstractPsiXmlStream

public AbstractPsiXmlStream()

Constructor for AbstractPsiXmlStream.

AbstractPsiXmlStream

public AbstractPsiXmlStream(File file)

Constructor for AbstractPsiXmlStream.

Parameters:

file - a File object.

AbstractPsiXmlStream

public AbstractPsiXmlStream(InputStream input)

Constructor for AbstractPsiXmlStream.

Parameters:

input - a InputStream object.

AbstractPsiXmlStream

public AbstractPsiXmlStream(Reader reader)

Constructor for AbstractPsiXmlStream.

Parameters:

reader - a Reader object.

AbstractPsiXmlStream

public AbstractPsiXmlStream(URL url)

Constructor for AbstractPsiXmlStream.

Parameters:

url - a URL object.

Method Detail

getInteractionsIterator

public Iterator<T> getInteractionsIterator()
                                    throws MIIOException

The iterator of Interactions for this datasource

Specified by:

getInteractionsIterator in interface InteractionStream<T extends Interaction>

Returns:

iterator of Interactions for this datasource

Throws:

MIIOException - exception thrown when it cannot iterate MI data

getFileParserListener

public MIFileParserListener getFileParserListener()

The MIFileParserListener can be null if not initialised

Specified by:

getFileParserListener in interface MIFileDataSource

Returns:

the file parser listener that listen to the different parsing events

setFileParserListener

public void setFileParserListener(MIFileParserListener listener)

setFileParserListener

Specified by:

setFileParserListener in interface MIFileDataSource

Parameters:

listener - a MIFileParserListener object.

validateSyntax

public boolean validateSyntax()
                       throws MIIOException

Validate the syntax of this MIFileDataSource. It returns true if the file syntax is valid, false otherwise. When the file syntax is invalid, the syntax errors are fired and should be retrieved using a proper MIFileParserListener

Specified by:

validateSyntax in interface MIFileDataSource

Returns:

a boolean.

Throws:

MIIOException - if any.

validateSyntax

public boolean validateSyntax(MIFileParserListener listener)
                       throws MIIOException

Validate the syntax of this MIFileDataSource and uses the provided MIFileParserListener to listen to the events. The provided listener will be set as the MIFileParserListener of this datasource

Specified by:

validateSyntax in interface MIFileDataSource

Parameters:

listener - : the listener for parsing events

Returns:

true if the file syntax is valid

Throws:

MIIOException - : if some severe syntax errors are found in the file and it stops the parsing

getInteractorFactory

public XmlInteractorFactory getInteractorFactory()

Getter for the field interactorFactory.

Returns:

a XmlInteractorFactory object.

setInteractorFactory

public void setInteractorFactory(XmlInteractorFactory interactorFactory)

Setter for the field interactorFactory.

Parameters:

interactorFactory - a XmlInteractorFactory object.

initialiseContext

public void initialiseContext(Map<String,Object> options)

Initialise the context of the MIDataSource given a map of options

Specified by:

initialiseContext in interface MIDataSource

Parameters:

options - : the options provided by the user

close

public void close()
           throws MIIOException

This method close the file data source and all opened streams and readers

Specified by:

close in interface MIDataSource

Throws:

MIIOException - if the dataSource cannot be closed

reset

public void reset()
           throws MIIOException

This method will reset the data sources from all loaded options. The data source will be back to what is was before the initialiseContext was called. To re-use the data source after calling the reset() method, the data source needs to be re-initialised with initialiseContext. Any provided inputStream or reader will not be closed and will have to be closed separately.

Specified by:

reset in interface MIDataSource

Throws:

MIIOException - if the dataSource cannot be reset

onUnresolvedReference

public void onUnresolvedReference(XmlIdReference ref,
                                  String message)

onUnresolvedReference.

Specified by:

onUnresolvedReference in interface PsiXmlParserListener

Parameters:

ref - a XmlIdReference object.

message - a String object.

onSeveralHostOrganismFound

public void onSeveralHostOrganismFound(Collection<Organism> organisms,
                                       FileSourceLocator locator)

onSeveralHostOrganismFound.

Specified by:

onSeveralHostOrganismFound in interface PsiXmlParserListener

Parameters:

organisms - a Collection object.

locator - a FileSourceLocator object.

onSeveralExpressedInOrganismFound

public void onSeveralExpressedInOrganismFound(Collection<Organism> organisms,
                                              FileSourceLocator locator)

onSeveralExpressedInOrganismFound.

Specified by:

onSeveralExpressedInOrganismFound in interface PsiXmlParserListener

Parameters:

organisms - a Collection object.

locator - a FileSourceLocator object.

onSeveralExperimentalRolesFound

public void onSeveralExperimentalRolesFound(Collection<CvTerm> roles,
                                            FileSourceLocator locator)

onSeveralExperimentalRolesFound.

Specified by:

onSeveralExperimentalRolesFound in interface PsiXmlParserListener

Parameters:

roles - a Collection object.

locator - a FileSourceLocator object.

onSeveralExperimentsFound

public void onSeveralExperimentsFound(Collection<Experiment> experiments,
                                      FileSourceLocator locator)

onSeveralExperimentsFound.

Specified by:

onSeveralExperimentsFound in interface PsiXmlParserListener

Parameters:

experiments - a Collection object.

locator - a FileSourceLocator object.

onInvalidSyntax

public void onInvalidSyntax(FileSourceContext context,
                            Exception e)

Listen to an invalid syntax causing an Exception

Specified by:

onInvalidSyntax in interface MIFileParserListener

Parameters:

context - : file context

e - a Exception object.

onSyntaxWarning

public void onSyntaxWarning(FileSourceContext context,
                            String message)

Listen to an event fired when the syntax of the file is valid but the content is not expected or some information may be lost.

Specified by:

onSyntaxWarning in interface MIFileParserListener

Parameters:

context - : file context

message - : warning message

onMissingCvTermName

public void onMissingCvTermName(CvTerm term,
                                FileSourceContext context,
                                String message)

Listen to an event fired when a CvTerm is read and does not have any names. At least a shortname is expected for each CvTerm so such a term may be loaded with an automatically generated shortname.

Specified by:

onMissingCvTermName in interface MIFileParserListener

Parameters:

term - : cv without name

context - : file context

message - : error message

onMissingInteractorName

public void onMissingInteractorName(Interactor interactor,
                                    FileSourceContext context)

Listen to an event fired when an interactor is read and does not have any names. At least a shortname is expected for each interactor so such an interactor may be loaded with an automatically generated shortname.

Specified by:

onMissingInteractorName in interface MIFileParserListener

Parameters:

interactor - : interactor without name

context - : file context

onParticipantWithoutInteractor

public void onParticipantWithoutInteractor(Participant participant,
                                           FileSourceContext context)

Listen to en event fired when a Participant is read and no interactor details has been provided. In such a case, the interactor can be automatically generated as an unknown interactor

Specified by:

onParticipantWithoutInteractor in interface MIFileParserListener

Parameters:

participant - : participant without interactor

context - : file context

onInteractionWithoutParticipants

public void onInteractionWithoutParticipants(Interaction interaction,
                                             FileSourceContext context)

Listen to an event fired when an interaction is read and does not have any participants. The interaction may be loaded as an empty interaction.

Specified by:

onInteractionWithoutParticipants in interface MIFileParserListener

Parameters:

interaction - : interaction without participants

context - : file context

warning

public void warning(SAXParseException exception)
             throws SAXException

Specified by:

warning in interface ErrorHandler

Throws:

SAXException

error

public void error(SAXParseException exception)
           throws SAXException

Specified by:

error in interface ErrorHandler

Throws:

SAXException

fatalError

public void fatalError(SAXParseException exception)
                throws SAXException

Specified by:

fatalError in interface ErrorHandler

Throws:

SAXException

onInvalidOrganismTaxid

public void onInvalidOrganismTaxid(String taxid,
                                   FileSourceContext context)

Listen to an event fired when an organism does not have a valid taxid (positive integer or -1, -2, -3, -4, -5)

Specified by:

onInvalidOrganismTaxid in interface MIFileParserListener

Parameters:

taxid - : invalid taxid

context - : file context

onMissingParameterValue

public void onMissingParameterValue(FileSourceContext context)

Listen to an event fired when a parameter does not have a value

Specified by:

onMissingParameterValue in interface MIFileParserListener

Parameters:

context - : file context

onMissingParameterType

public void onMissingParameterType(FileSourceContext context)

Listen to an event fired when a parameter does not have a type

Specified by:

onMissingParameterType in interface MIFileParserListener

Parameters:

context - : file context

onMissingConfidenceValue

public void onMissingConfidenceValue(FileSourceContext context)

Listen to an event fired when a confidence does not have a value

Specified by:

onMissingConfidenceValue in interface MIFileParserListener

Parameters:

context - : file context

onMissingConfidenceType

public void onMissingConfidenceType(FileSourceContext context)

Listen to an event fired when a confidence does not have a confidence type

Specified by:

onMissingConfidenceType in interface MIFileParserListener

Parameters:

context - : file context

onMissingChecksumValue

public void onMissingChecksumValue(FileSourceContext context)

Listen to an event fired when a checksum does not have a value

Specified by:

onMissingChecksumValue in interface MIFileParserListener

Parameters:

context - : file context

onMissingChecksumMethod

public void onMissingChecksumMethod(FileSourceContext context)

Listen to an event fired when a checksum does not have a method

Specified by:

onMissingChecksumMethod in interface MIFileParserListener

Parameters:

context - : file context

onInvalidPosition

public void onInvalidPosition(String message,
                              FileSourceContext context)

Listen to an event fired when a position is not valid

Specified by:

onInvalidPosition in interface MIFileParserListener

Parameters:

message - : error message

context - : file context

onInvalidRange

public void onInvalidRange(String message,
                           FileSourceContext context)

Listen to an event fired when a range is not valid

Specified by:

onInvalidRange in interface MIFileParserListener

Parameters:

message - : error message

context - : file context

onInvalidStoichiometry

public void onInvalidStoichiometry(String message,
                                   FileSourceContext context)

Listen to an event fired when a stoichiometry is not valid

Specified by:

onInvalidStoichiometry in interface MIFileParserListener

Parameters:

message - : : error message

context - : file context

onXrefWithoutDatabase

public void onXrefWithoutDatabase(FileSourceContext context)

Listen to an event fired when a xref does not have a database

Specified by:

onXrefWithoutDatabase in interface MIFileParserListener

Parameters:

context - : file context

onXrefWithoutId

public void onXrefWithoutId(FileSourceContext context)

Listen to an event fired when a xref does not have an id

Specified by:

onXrefWithoutId in interface MIFileParserListener

Parameters:

context - : file context

onAnnotationWithoutTopic

public void onAnnotationWithoutTopic(FileSourceContext context)

Listen to an event fired when an annotation does not have a topic

Specified by:

onAnnotationWithoutTopic in interface MIFileParserListener

Parameters:

context - : file context

onAliasWithoutName

public void onAliasWithoutName(FileSourceContext context)

Listen to an event fired when an alias does not have a name

Specified by:

onAliasWithoutName in interface MIFileParserListener

Parameters:

context - : file context

initialiseXmlParser

protected abstract void initialiseXmlParser(Reader reader)

initialiseXmlParser.

Parameters:

reader - a Reader object.

initialiseXmlParser

protected abstract void initialiseXmlParser(File file)

initialiseXmlParser.

Parameters:

file - a File object.

initialiseXmlParser

protected abstract void initialiseXmlParser(InputStream input)

initialiseXmlParser.

Parameters:

input - a InputStream object.

initialiseXmlParser

protected abstract void initialiseXmlParser(URL url)

initialiseXmlParser.

Parameters:

url - a URL object.

setXmlFileParserListener

protected void setXmlFileParserListener(PsiXmlParserListener listener)

setXmlFileParserListener.

Parameters:

listener - a PsiXmlParserListener object.

setMIFileParserListener

protected void setMIFileParserListener(MIFileParserListener listener)

setMIFileParserListener.

Parameters:

listener - a MIFileParserListener object.

reInit

protected void reInit()
               throws MIIOException

reInit.

Throws:

MIIOException - if any.

initialiseExpansionMethod

protected abstract void initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)

initialiseExpansionMethod.

Parameters:

expansionMethod - a ComplexExpansionMethod object.

createXmlIterator

protected abstract Iterator<T> createXmlIterator()

createXmlIterator.

Returns:

a Iterator object.

getParser

protected PsiXmlParser<T> getParser()

Getter for the field parser.

Returns:

a PsiXmlParser object.

setParser

protected void setParser(PsiXmlParser<T> parser)

Setter for the field parser.

Parameters:

parser - a PsiXmlParser object.

isInitialised

protected boolean isInitialised()

isInitialised.

Returns:

a boolean.

getElementCache

protected PsiXmlIdCache getElementCache()

Getter for the field elementCache.

Returns:

a PsiXmlIdCache object.