public static Document generatePsiData(Collection<Interaction> interactions, PsiVersion psiVersion, CvMapping cvMapping) { UserSessionDownload session = new UserSessionDownload(psiVersion); if (cvMapping != null) { session.setReverseCvMapping(cvMapping); } return generatePsiData(interactions, session); }
private Element createConfidenceElement(UserSessionDownload session, CvObject unit, Object value) { Element confidenceElement = session.createElement(CONFIDENCE_TAG_NAME); // 2. Generating Unit... Element unitElement = session.createElement(CONFIDENCE_UNIT_TAG_NAME); createNames(session, unitElement, unit); confidenceElement.appendChild(unitElement); // TODO check if it has MI reference, if so export them as xref of the confidence.unit. // 3. Generating value... Element valueElement = session.createElement(CONFIDENCE_VALUE_TAG_NAME); Text valueTextElement = session.createTextNode((String)value); valueElement.appendChild(valueTextElement); confidenceElement.appendChild(valueElement); return confidenceElement; } }
/** * Return the source element under the entry of the PSI document. If the element doesn't exist, it is created. * * @return the source Element. */ public Element getSourceElement() { if ( sourceElement == null ) { Document document = getPsiDocument(); sourceElement = document.createElement( "source" ); Element entry = getEntryElement(); entry.appendChild( sourceElement ); } return sourceElement; }
Element element = session.createElement( PROTEIN_PARTICIPANT_TAG_NAME ); if ( false == session.isAlreadyDefined( protein ) ) { Element interactorList = session.getInteractorListElement(); session.declareAlreadyDefined( protein ); Element featureListElement = session.createElement( "featureList" ); Element role = session.createElement( "role" ); Text roleText = session.createTextNode( theRole ); role.appendChild( roleText ); element.appendChild( role );
Element element = session.createElement( INTERACTION_TAG_NAME ); element.setAttribute( "id", "" + session.getInteractionIdentifier( interaction ) ); Element experimentList = session.getExperimentListElement(); Element localExperimentList = null; for ( Iterator iterator = experiments.iterator(); iterator.hasNext(); ) { if ( false == session.isAlreadyDefined( experiment ) ) { session.declareAlreadyDefined( experiment ); localExperimentList = session.createElement( "experimentList" ); element.appendChild( localExperimentList ); Element participantListElement = session.createElement( "participantList" ); Element experimentalFormListElement = session.createElement( "experimentalFormList" ); inferredInteractionListElement = session.createElement( "inferredInteractionList" ); Element inferredInteractionElement = session.createElement( "inferredInteraction" );
System.out.println( version ); UserSessionDownload session = new UserSessionDownload( version ); session.filterObsoleteAnnotationTopic(); session.getExperimentListElement(); session.getInteractorListElement(); Interaction interaction = (Interaction) iterator1.next(); interaction2xml.create( session, session.getInteractionListElement(), interaction ); if ( ( count % 50 ) == 0 ) { System.out.println( "" ); write( session.getPsiDocument().getDocumentElement(), file ); builder.writeData( file.getAbsolutePath(), session.getPsiDocument() ); } catch ( DataConversionException e ) { e.printStackTrace();
session.addMessage( "WARNING: could not generate PSI-MI content for interaction (" + interaction.getAc() + " / " + interaction.getShortLabel() + ") as PSI-MI v1.0 requires" + "at least 2 participants, that interaction contains " + stoichiometrySum + "." ); Element element = session.createElement( INTERACTION_TAG_NAME ); Element experimentList = session.getExperimentListElement(); Element localExperimentList = null; for ( Iterator iterator = experiments.iterator(); iterator.hasNext(); ) { if ( false == session.isAlreadyDefined( experiment ) ) { session.declareAlreadyDefined( experiment ); localExperimentList = session.createElement( "experimentList" ); element.appendChild( localExperimentList ); Element participantListElement = session.createElement( "participantList" );
UserSessionDownload session = new UserSessionDownload( version ); if ( mapping != null ) { session.setReverseCvMapping( mapping ); session.getExperimentListElement(); session.getInteractorListElement(); Interaction interaction = (Interaction) itemsToProcess.get( i ); interaction2xml.create( session, session.getInteractionListElement(), interaction ); write( session.getPsiDocument().getDocumentElement(), new File( mainFileName ) ); System.out.println();
if ( session.hasCvMapping() ) { CvObject toCvObject = session.getReverseCvMapping().getPSI2toPSI1( cv ); if ( toCvObject != null && ! toCvObject.equals( cv ) ) { String msg = "NOTE: '" + cv.getShortLabel() + "' remapped to '" + toCvObject.getShortLabel() + "'."; session.addMessage( msg ); cv = toCvObject; element = session.createElement( tagName ); Element xrefElement = session.createElement( "xref" );
Element element = session.createElement( PARTICIPANT_FEATURE_REF_NAME ); Text refText = session.createTextNode( "" + session.getFeatureIdentifier( feature ) ); element.appendChild( refText );
Annotation annotation ) { Element parent = session.getAvailabilityListElement(); element = session.createElement( AVAILABILITY_NODE_NAME ); Text text = session.createTextNode( sText ); element.appendChild( text );
UserSessionDownload session = new UserSessionDownload( version ); if ( mapping != null ) { session.setReverseCvMapping( mapping ); session.printMessageReport( System.err );
/** * Store in the cache the XML representation related to the given CvObject instance. * * @param session the user session in which the cache is stored. * @param cvObject the cvObject we wanted to comvert to XML. * @param element The DOM root (as an Element) of the XML representation of the given CvObject. */ private void updateCache( UserSessionDownload session, Element parent, CvObject cvObject, Element element ) { Map cache = session.getCvObjectCache(); CvObject2xmlCommons.getInstance().updateCache( cache, new Cv2Source( cvObject, parent.getNodeName() ), element ); }
private Element createStatus( UserSessionDownload session, Element parent, CvFuzzyType fuzzyType, String tagName ) { Element element = session.createElement( tagName ); // 1. Generating names... createNames( session, element, fuzzyType ); // 2. generating xref... Element xrefElement = session.createElement( "xref" ); createCvObjectXrefs( session, xrefElement, fuzzyType ); if ( xrefElement.hasChildNodes() ) { element.appendChild( xrefElement ); } parent.appendChild( element ); return element; }
/** * get the value what will be used as ID of the experiment. * * @param experiment the experiment for which we need an ID. * * @return the ID of the experiment. */ private String getExperimentId( UserSessionDownload session, Experiment experiment ) { long id = session.getExperimentIdentifier( experiment ); return "" + id; }
/** * Return the entry element of the PSI document. If the element doesn't exist, it is created. * * @return the source Element. */ public Element getEntryElement() { return getEntryElement( false ); }
session.addMessage( "NOTE: CvExperimentalRole( '" + expRole + "' ) has been renamed '" + role + "'." + "(Component: " + component.getAc() + " - " + "Interaction: " + component.getInteraction().getAc() + ")" ); session.addMessage( "NOTE: CvBiologicalRole( '" + bio.getShortLabel() + "' ) has been renamed '" + role + "'." + "(Component: " + component.getAc() + " - " + "Interaction: " + component.getInteraction().getAc() + ")" ); session.addMessage( "NOTE: Failed to select a single role when given " + "CvExperimentalRole( '" + ( exp == null ? "null" : exp.getShortLabel() ) + "' ) and " + "CvBiologicalRole( '" + ( bio == null ? "null" : bio.getShortLabel() ) + "' ). " +
Element element = session.createElement( PROTEIN_PARTICIPANT_TAG_NAME ); if ( false == session.isAlreadyDefined( protein ) ) { Element interactorList = session.getInteractorListElement(); session.declareAlreadyDefined( protein ); Element featureListElement = session.createElement( "featureList" ); Element role = session.createElement( "role" ); session.addMessage( "NOTE: CvComponentRole( '" + theRole + "' ) has been renamed '" + newRole + "'." + "(Component: " + component.getAc() + " - " + "Interaction: " + component.getInteraction().getAc() + ")" ); session.addMessage( "NOTE: CvComponentRole( '" + theRole + "' ) is nont allowed in PSI 1, it has been " + "set to the default '" + newRole + "'.(Component: " + component.getAc() + " - " + "Interaction: " + component.getInteraction().getAc() + ")" ); Text roleText = session.createTextNode( theRole ); role.appendChild( roleText ); element.appendChild( role );
Element element = session.createElement( INTERACTION_TAG_NAME ); element.setAttribute( "id", "" + session.getInteractionIdentifier( interaction ) ); Element experimentList = session.getExperimentListElement(); Element localExperimentList = null; for ( Iterator iterator = experiments.iterator(); iterator.hasNext(); ) { if ( false == session.isAlreadyDefined( experiment ) ) { session.declareAlreadyDefined( experiment ); localExperimentList = session.createElement( "experimentList" ); element.appendChild( localExperimentList ); Element participantListElement = session.createElement( "participantList" ); Element experimentalFormListElement = session.createElement( "experimentalFormList" ); inferredInteractionListElement = session.createElement( "inferredInteractionList" ); Element inferredInteractionElement = session.createElement( "inferredInteraction" );
System.out.println( version ); UserSessionDownload session = new UserSessionDownload( version ); session.filterObsoleteAnnotationTopic(); session.getExperimentListElement(); session.getInteractorListElement(); Interaction interaction = (Interaction) iterator1.next(); interaction2xml.create( session, session.getInteractionListElement(), interaction ); if ( ( count % 50 ) == 0 ) { System.out.println( "" ); write( session.getPsiDocument().getDocumentElement(), file ); builder.writeData( file.getAbsolutePath(), session.getPsiDocument() ); } catch ( DataConversionException e ) { e.printStackTrace();