public static String getDoiId(Experiment exp){ if (exp == null){ return null; } else if (exp.getPublication() == null){ return null; } else{ return exp.getPublication().getDoi(); } }
public static String getPubmedId(Experiment exp){ if (exp == null){ return null; } else if (exp.getPublication() == null){ return null; } else{ return exp.getPublication().getPubmedId(); } }
public void onPublicationUpdate(Experiment experiment, Publication oldPublication) { if (oldPublication == null){ experimentChangeLogger.log(Level.INFO, "The publication has been initialised for the experiment " + experiment.toString()); } else if (experiment.getPublication() == null){ experimentChangeLogger.log(Level.INFO, "The publication has been reset for the experiment " + experiment.toString()); } else { experimentChangeLogger.log(Level.INFO, "The publication " + oldPublication + " has been updated with " + experiment.getPublication() + " in the experiment " + experiment.toString()); } }
public static Xref getDoiReference(Experiment exp){ if (exp == null){ return null; } else{ return PublicationUtils.getDoiReference(exp.getPublication()); } }
public static Xref getPubmedReference(Experiment exp){ if (exp == null){ return null; } else{ return PublicationUtils.getPubmedReference(exp.getPublication()); } }
@Override public Collection<ValidatorMessage> check(Experiment experiment) throws ValidatorException { if (experiment.getPublication() == null){ // list of messages to return MiContext experimentContext = RuleUtils.buildContext(experiment, "experiment"); return Collections.singletonList(new ValidatorMessage( "Experiment must have a publication.'", MessageLevel.ERROR, experimentContext, this ) ); } return Collections.EMPTY_LIST; }
protected void initialiseInteractionAnnotations(Collection<MitabAnnotation> annots, T interaction){ Iterator<MitabAnnotation> annotsIterator = annots.iterator(); while (annotsIterator.hasNext()){ MitabAnnotation annot = annotsIterator.next(); // add curation depth if (AnnotationUtils.doesAnnotationHaveTopic(annot, Annotation.IMEX_CURATION_MI, Annotation.IMEX_CURATION)){ interaction.getExperiment().getPublication().setCurationDepth(CurationDepth.IMEx); } else if (AnnotationUtils.doesAnnotationHaveTopic(annot, Annotation.MIMIX_CURATION_MI, Annotation.MIMIX_CURATION)){ interaction.getExperiment().getPublication().setCurationDepth(CurationDepth.MIMIx); } else if (AnnotationUtils.doesAnnotationHaveTopic(annot, Annotation.RAPID_CURATION_MI, Annotation.RAPID_CURATION)){ interaction.getExperiment().getPublication().setCurationDepth(CurationDepth.rapid_curation); } else{ interaction.getAnnotations().add(annot); } } }
public void writeSource(BinaryInteractionEvidence interaction) throws IOException { Experiment experiment = interaction.getExperiment(); if (experiment != null){ Publication pub = experiment.getPublication(); if (pub != null){ writeCvTerm(pub.getSource()); } else { getWriter().write(MitabUtils.EMPTY_COLUMN); } } else{ getWriter().write(MitabUtils.EMPTY_COLUMN); } }
public void writeInteractionAnnotations(BinaryInteractionEvidence interaction) throws IOException { // writes interaction annotations first if (!interaction.getAnnotations().isEmpty()){ Iterator<Annotation> interactorAnnotationIterator = interaction.getAnnotations().iterator(); while (interactorAnnotationIterator.hasNext()){ Annotation annot = interactorAnnotationIterator.next(); writeAnnotation(annot); if(interactorAnnotationIterator.hasNext()){ getWriter().write(MitabUtils.FIELD_SEPARATOR); } } if (interaction.getExperiment() != null){ Publication pub = interaction.getExperiment().getPublication(); if (pub != null){ getWriter().write(MitabUtils.FIELD_SEPARATOR); writeInteractionAnnotationTagsFrom(pub); } } } else if (interaction.getExperiment() != null){ Publication pub = interaction.getExperiment().getPublication(); if (pub != null){ // writes curation depth first writeInteractionAnnotationTagsFrom(pub); } } else{ getWriter().write(MitabUtils.EMPTY_COLUMN); } }
Publication pub = interaction.getExperiment().getPublication(); Publication pub = interaction.getExperiment().getPublication();
Publication pub1 = experiment1.getPublication(); Publication pub2 = experiment2.getPublication();
Publication pub = experiment.getPublication();
public void writeFirstAuthor(BinaryInteractionEvidence interaction) throws IOException { Experiment experiment = interaction.getExperiment(); if (experiment != null){ Publication pub = experiment.getPublication();
/*** * This method will copy properties of experiment source in experiment target and will override all the other properties of Target experiment. * This method will ignore interaction evidences * It will set the publication but will not add this experiment to the list of experiments of the publication reported in the source experiment * It will fully clone all the VariableParameters and set their experiment to the current experiment target * @param source * @param target */ public static void copyAndOverrideExperimentProperties(Experiment source, Experiment target){ if (source != null && target != null){ target.setHostOrganism(source.getHostOrganism()); target.setInteractionDetectionMethod(source.getInteractionDetectionMethod()); target.setPublication(source.getPublication()); // copy collections target.getAnnotations().clear(); target.getAnnotations().addAll(source.getAnnotations()); target.getXrefs().clear(); target.getXrefs().addAll(source.getXrefs()); target.getConfidences().clear(); target.getConfidences().addAll(source.getConfidences()); target.getVariableParameters().clear(); target.addAllVariableParameters(source.getVariableParameters()); } }
/*** * This method will copy properties of experiment source in experiment target and will override all the other properties of Target experiment. * This method will also move interaction evidences from source to target * It will set the publication but will not add this experiment to the list of experiments of the publication reported in the source experiment * It will fully clone all the VariableParameters and set their experiment to the current experiment target * @param source * @param target */ public static void copyAndOverrideExperimentPropertiesAndInteractionEvidences(Experiment source, Experiment target){ if (source != null && target != null){ target.setHostOrganism(source.getHostOrganism()); target.setInteractionDetectionMethod(source.getInteractionDetectionMethod()); target.setPublication(source.getPublication()); // copy collections target.getAnnotations().clear(); target.getAnnotations().addAll(source.getAnnotations()); target.getXrefs().clear(); target.getXrefs().addAll(source.getXrefs()); target.getConfidences().clear(); target.getConfidences().addAll(source.getConfidences()); target.getVariableParameters().clear(); target.addAllVariableParameters(source.getVariableParameters()); target.getInteractionEvidences().clear(); target.addAllInteractionEvidences(source.getInteractionEvidences()); } } }
Publication pub = exp.getPublication(); hashcode = 31*hashcode + UnambiguousCuratedPublicationComparator.hashCode(pub);
Publication pub = exp.getPublication(); hashcode = 31*hashcode + UnambiguousPublicationComparator.hashCode(pub);
if (interaction.getExperiment() != null){ Experiment exp = interaction.getExperiment(); if (exp.getPublication() != null){ Publication pub = exp.getPublication(); if (pub.getSource() != null){ return pub.getSource().getShortName();
Publication publication = experiment.getPublication(); if (publication != null){ checkPublication(messages, publication, experiment);
if (experiment.getPublication() != null){ MIJsonUtils.writeSeparator(this.writer); getPublicationWriter().write(experiment.getPublication());