private List<String> taxIdsForExperiment( String experimentAc ) { if ( expAcToTaxid == null ) { expAcToTaxid = ExperimentListGeneratorDao.getExperimentAcAndTaxids( searchPattern ); } return expAcToTaxid.get( experimentAc ); }
private Collection<SimpleDataset> datasetForExperiment( String experimentAc ) { if ( experiment2dataset == null ) { experiment2dataset = ExperimentListGeneratorDao.datasetForExperiments( searchPattern ); } if ( experimentAc == null ) { throw new NullPointerException( "Experiment AC is null" ); } if ( experiment2dataset.containsKey( experimentAc ) ) { return experiment2dataset.get( experimentAc ); } return null; }
private int interactionsForExperiment( String experimentAc ) { if ( interactionCount == null ) { interactionCount = ExperimentListGeneratorDao.countInteractionCountsForExperiments( searchPattern ); } if ( experimentAc == null ) { throw new NullPointerException( "Experiment AC is null" ); } if ( interactionCount.containsKey( experimentAc ) ) { return interactionCount.get( experimentAc ); } return 0; }
/** * Query to obtain annotated objects by searching for an Annotation with the cvTopic label provided */ public static <T extends AnnotatedObjectImpl> List<T> getContainingAnnotation( Class<T> annObject, String cvshortLabel, String shortLabelLike ) { return getSession().createCriteria( annObject.getClass() ) .add( Restrictions.like( "shortLabel", shortLabelLike ) ) .createCriteria( "annotations" ) .createCriteria( "cvTopic" ) .add( Restrictions.eq( "shortLabel", cvshortLabel ) ).list(); }
/** * Fetch publication primaryId from experiment. * * @param experimentAc the experiment AC for which we want the primary pubmed ID. * * @return a pubmed Id or null if none found. */ private String getPubmedId( String experimentAc ) { if ( expAcToPmid == null ) { // map all exps to pmid expAcToPmid = ExperimentListGeneratorDao.getExperimentAcAndPmid( searchPattern ); } String pubmedId = expAcToPmid.get( experimentAc ); if ( pubmedId == null ) { experimentsWithErrors.put( experimentAc, "Null pubmed Id" ); } try { Integer.parseInt( pubmedId ); } catch ( NumberFormatException e ) { experimentsWithErrors.put( experimentAc, "Not a number pubmedId" ); } return pubmedId; }
private Collection<SimpleDataset> datasetForExperiment( String experimentAc ) { if ( experiment2dataset == null ) { experiment2dataset = ExperimentListGeneratorDao.datasetForExperiments( searchPattern ); } if ( experimentAc == null ) { throw new NullPointerException( "Experiment AC is null" ); } if ( experiment2dataset.containsKey( experimentAc ) ) { return experiment2dataset.get( experimentAc ); } return null; }
/** * Query to obtain annotated objects by searching for an Annotation with the cvTopic label provided */ public static <T extends AnnotatedObjectImpl> List<T> getContainingAnnotation( Class<T> annObject, String cvshortLabel, String shortLabelLike ) { return getSession().createCriteria( annObject.getClass() ) .add( Restrictions.like( "shortLabel", shortLabelLike ) ) .createCriteria( "annotations" ) .createCriteria( "cvTopic" ) .add( Restrictions.eq( "shortLabel", cvshortLabel ) ).list(); }
private List<String> taxIdsForExperiment( String experimentAc ) { if ( expAcToTaxid == null ) { expAcToTaxid = ExperimentListGeneratorDao.getExperimentAcAndTaxids( searchPattern ); } return expAcToTaxid.get( experimentAc ); }
private int interactionsForExperiment( String experimentAc ) { if ( interactionCount == null ) { interactionCount = ExperimentListGeneratorDao.countInteractionCountsForExperiments( searchPattern ); } if ( experimentAc == null ) { throw new NullPointerException( "Experiment AC is null" ); } if ( interactionCount.containsKey( experimentAc ) ) { return interactionCount.get( experimentAc ); } return 0; }
/** * Fetch publication primaryId from experiment. * * @param experimentAc the experiment AC for which we want the primary pubmed ID. * * @return a pubmed Id or null if none found. */ private String getPubmedId( String experimentAc ) { if ( expAcToPmid == null ) { // map all exps to pmid expAcToPmid = ExperimentListGeneratorDao.getExperimentAcAndPmid( searchPattern ); } String pubmedId = expAcToPmid.get( experimentAc ); if ( pubmedId == null ) { experimentsWithErrors.put( experimentAc, "Null pubmed Id" ); } try { Integer.parseInt( pubmedId ); } catch ( NumberFormatException e ) { experimentsWithErrors.put( experimentAc, "Not a number pubmedId" ); } return pubmedId; }
private Collection<SimpleDataset> datasetForExperiment( String experimentAc ) { if ( experiment2dataset == null ) { experiment2dataset = ExperimentListGeneratorDao.datasetForExperiments( searchPattern ); } if ( experimentAc == null ) { throw new NullPointerException( "Experiment AC is null" ); } if ( experiment2dataset.containsKey( experimentAc ) ) { return experiment2dataset.get( experimentAc ); } return null; }
/** * Query to get at the Experiment ACs containing negative interaction annotations */ public static List<Experiment> getExpWithInteractionsContainingAnnotation( String cvshortLabel, String shortLabelLike ) { return getSession().createCriteria( Experiment.class ) .add( Restrictions.like( "shortLabel", shortLabelLike ) ) .createCriteria( "interactions" ) .createCriteria( "annotations" ) .createCriteria( "cvTopic" ) .add( Restrictions.eq( "shortLabel", cvshortLabel ) ).list(); }
private List<String> taxIdsForExperiment( String experimentAc ) { if ( expAcToTaxid == null ) { expAcToTaxid = ExperimentListGeneratorDao.getExperimentAcAndTaxids( searchPattern ); } return expAcToTaxid.get( experimentAc ); }
private int interactionsForExperiment( String experimentAc ) { if ( interactionCount == null ) { interactionCount = ExperimentListGeneratorDao.countInteractionCountsForExperiments( searchPattern ); } if ( experimentAc == null ) { throw new NullPointerException( "Experiment AC is null" ); } if ( interactionCount.containsKey( experimentAc ) ) { return interactionCount.get( experimentAc ); } return 0; }
/** * Fetch dataset information (if any) from experiment. * * @param experimentAc the experiment AC for which we want the primary pubmed ID. * * @return a dataset or null. */ private Collection<SimpleDataset> getDatasets( String experimentAc ) { if ( experiment2dataset == null ) { // map all exps to pmid experiment2dataset = ExperimentListGeneratorDao.datasetForExperiments( searchPattern ); log.info( "Loaded " + experiment2dataset.size() + " experiments having datasets information." ); } Collection<SimpleDataset> datasets = experiment2dataset.get( experimentAc ); return datasets; }
/** * Query to obtain annotated objects by searching for an Annotation with the cvTopic label provided */ public static <T extends AnnotatedObjectImpl> List<T> getContainingAnnotation( Class<T> annObject, String cvshortLabel, String shortLabelLike ) { return getSession().createCriteria( annObject.getClass() ) .add( Restrictions.like( "shortLabel", shortLabelLike ) ) .createCriteria( "annotations" ) .createCriteria( "cvTopic" ) .add( Restrictions.eq( "shortLabel", cvshortLabel ) ).list(); }
/** * Fetch dataset information (if any) from experiment. * * @param experimentAc the experiment AC for which we want the primary pubmed ID. * * @return a dataset or null. */ private Collection<SimpleDataset> getDatasets( String experimentAc ) { if ( experiment2dataset == null ) { // map all exps to pmid experiment2dataset = ExperimentListGeneratorDao.datasetForExperiments( searchPattern ); output.println( "Loaded " + experiment2dataset.size() + " experiments having datasets information." ); } Collection<SimpleDataset> datasets = experiment2dataset.get( experimentAc ); return datasets; }
/** * Query to get at the Experiment ACs containing negative interaction annotations */ public static List<Experiment> getExpWithInteractionsContainingAnnotation( String cvshortLabel, String shortLabelLike ) { return getSession().createCriteria( Experiment.class ) .add( Restrictions.like( "shortLabel", shortLabelLike ) ) .createCriteria( "interactions" ) .createCriteria( "annotations" ) .createCriteria( "cvTopic" ) .add( Restrictions.eq( "shortLabel", cvshortLabel ) ).list(); }
/** * Fetch dataset information (if any) from experiment. * * @param experimentAc the experiment AC for which we want the primary pubmed ID. * * @return a dataset or null. */ private Collection<SimpleDataset> getDatasets( String experimentAc ) { if ( experiment2dataset == null ) { // map all exps to pmid experiment2dataset = ExperimentListGeneratorDao.datasetForExperiments( searchPattern ); output.println( "Loaded " + experiment2dataset.size() + " experiments having datasets information." ); } Collection<SimpleDataset> datasets = experiment2dataset.get( experimentAc ); return datasets; }
/** * Query to get at the Experiment ACs containing negative interaction annotations */ public static List<Experiment> getExpWithInteractionsContainingAnnotation( String cvshortLabel, String shortLabelLike ) { return getSession().createCriteria( Experiment.class ) .add( Restrictions.like( "shortLabel", shortLabelLike ) ) .createCriteria( "interactions" ) .createCriteria( "annotations" ) .createCriteria( "cvTopic" ) .add( Restrictions.eq( "shortLabel", cvshortLabel ) ).list(); }