uk.ac.ebi.intact.application.dataConversion.dao.ExperimentListGeneratorDao.getSession java code examples

/**
 * 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();
}

/**
 * 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();
}

/**
 * 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();
}

/**
 * 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();
}

/**
 * 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();
}

/**
 * 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();
}

public static Map<String, List<String>> getExperimentAcAndTaxids( String shortLabelLike ) {
  List<Object[]> expsAndTaxidResults = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .createAlias( "xrefs", "xref" )
      .createAlias( "xref.cvXrefQualifier", "cvXrefQual" )
      .add( Restrictions.eq( "cvXrefQual.shortLabel", CvXrefQualifier.TARGET_SPECIES ) )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.property( "xref.primaryId" ) ) ).list();
  Map<String, List<String>> expAndTaxid = new HashMap<String, List<String>>();
  for ( Object[] expAndTaxidResult : expsAndTaxidResults ) {
    String expAc = (String) expAndTaxidResult[ 0 ];
    String taxId = (String) expAndTaxidResult[ 1 ];
    if ( expAndTaxid.containsKey( expAc ) ) {
      expAndTaxid.get( expAc ).add( taxId );
    } else {
      List<String> taxIds = new ArrayList<String>();
      taxIds.add( taxId );
      expAndTaxid.put( expAc, taxIds );
    }
  }
  return expAndTaxid;
}

public static Map<String, List<String>> getExperimentAcAndTaxids( String shortLabelLike ) {
  List<Object[]> expsAndTaxidResults = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .createAlias( "xrefs", "xref" )
      .createAlias( "xref.cvXrefQualifier", "cvXrefQual" )
      .add( Restrictions.eq( "cvXrefQual.shortLabel", CvXrefQualifier.TARGET_SPECIES ) )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.property( "xref.primaryId" ) ) ).list();
  Map<String, List<String>> expAndTaxid = new HashMap<String, List<String>>();
  for ( Object[] expAndTaxidResult : expsAndTaxidResults ) {
    String expAc = (String) expAndTaxidResult[ 0 ];
    String taxId = (String) expAndTaxidResult[ 1 ];
    if ( expAndTaxid.containsKey( expAc ) ) {
      expAndTaxid.get( expAc ).add( taxId );
    } else {
      List<String> taxIds = new ArrayList<String>();
      taxIds.add( taxId );
      expAndTaxid.put( expAc, taxIds );
    }
  }
  return expAndTaxid;
}

public static Map<String, List<String>> getExperimentAcAndTaxids( String shortLabelLike ) {
  List<Object[]> expsAndTaxidResults = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .createAlias( "xrefs", "xref" )
      .createAlias( "xref.cvXrefQualifier", "cvXrefQual" )
      .add( Restrictions.eq( "cvXrefQual.shortLabel", CvXrefQualifier.TARGET_SPECIES ) )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.property( "xref.primaryId" ) ) ).list();
  Map<String, List<String>> expAndTaxid = new HashMap<String, List<String>>();
  for ( Object[] expAndTaxidResult : expsAndTaxidResults ) {
    String expAc = (String) expAndTaxidResult[ 0 ];
    String taxId = (String) expAndTaxidResult[ 1 ];
    if ( expAndTaxid.containsKey( expAc ) ) {
      expAndTaxid.get( expAc ).add( taxId );
    } else {
      List<String> taxIds = new ArrayList<String>();
      taxIds.add( taxId );
      expAndTaxid.put( expAc, taxIds );
    }
  }
  return expAndTaxid;
}

public static Map<String, String> getExperimentAcAndPmid( String shortLabelLike ) {
  List<Object[]> expsAndPmidResults = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .createAlias( "xrefs", "xref" )
      .createAlias( "xref.cvDatabase", "cvDb" )
      .createAlias( "xref.cvXrefQualifier", "cvXrefQual" )
      .add( Restrictions.eq( "cvDb.shortLabel", CvDatabase.PUBMED ) )
      .add( Restrictions.eq( "cvXrefQual.shortLabel", CvXrefQualifier.PRIMARY_REFERENCE ) )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.property( "xref.primaryId" ) ) ).list();
  Map<String, String> expAndPmids = new HashMap<String, String>();
  for ( Object[] expAndPmid : expsAndPmidResults ) {
    String pmid = (String) expAndPmid[ 1 ];
    if ( pmid != null ) {
      expAndPmids.put( (String) expAndPmid[ 0 ], pmid );
    }
  }
  return expAndPmids;
}

public static Map<String, String> getExperimentAcAndPmid( String shortLabelLike ) {
  List<Object[]> expsAndPmidResults = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .createAlias( "xrefs", "xref" )
      .createAlias( "xref.cvDatabase", "cvDb" )
      .createAlias( "xref.cvXrefQualifier", "cvXrefQual" )
      .add( Restrictions.eq( "cvDb.shortLabel", CvDatabase.PUBMED ) )
      .add( Restrictions.eq( "cvXrefQual.shortLabel", CvXrefQualifier.PRIMARY_REFERENCE ) )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.property( "xref.primaryId" ) ) ).list();
  Map<String, String> expAndPmids = new HashMap<String, String>();
  for ( Object[] expAndPmid : expsAndPmidResults ) {
    String pmid = (String) expAndPmid[ 1 ];
    if ( pmid != null ) {
      expAndPmids.put( (String) expAndPmid[ 0 ], pmid );
    }
  }
  return expAndPmids;
}

public static Map<String, String> getExperimentAcAndPmid( String shortLabelLike ) {
  List<Object[]> expsAndPmidResults = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .createAlias( "xrefs", "xref" )
      .createAlias( "xref.cvDatabase", "cvDb" )
      .createAlias( "xref.cvXrefQualifier", "cvXrefQual" )
      .add( Restrictions.eq( "cvDb.shortLabel", CvDatabase.PUBMED ) )
      .add( Restrictions.eq( "cvXrefQual.shortLabel", CvXrefQualifier.PRIMARY_REFERENCE ) )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.property( "xref.primaryId" ) ) ).list();
  Map<String, String> expAndPmids = new HashMap<String, String>();
  for ( Object[] expAndPmid : expsAndPmidResults ) {
    String pmid = (String) expAndPmid[ 1 ];
    if ( pmid != null ) {
      expAndPmids.put( (String) expAndPmid[ 0 ], pmid );
    }
  }
  return expAndPmids;
}

public static Map<String, String> getExperimentAcAndLabelWithoutPubmedId( String shortLabelLike ) {
  List<Object[]> allExps = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.property( "shortLabel" ) ) ).list();
  Map<String, String> filteredExpsMap = new HashMap<String, String>();
  for ( Object[] exp : allExps ) {
    filteredExpsMap.put( (String) exp[ 0 ], (String) exp[ 1 ] );
  }
  Map<String, String> expsAndPmid = getExperimentAcAndPmid( shortLabelLike );
  for ( String expWithPmid : expsAndPmid.keySet() ) {
    filteredExpsMap.remove( expWithPmid );
  }
  return filteredExpsMap;
}

List<Object[]> expWithDataset = getSession().createCriteria( Experiment.class )
    .add( Restrictions.like( "shortLabel", shortLabelLike ) )
    .createAlias( "annotations", "annot" )

public static Map<String, String> getExperimentAcAndLabelWithoutPubmedId( String shortLabelLike ) {
  List<Object[]> allExps = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.property( "shortLabel" ) ) ).list();
  Map<String, String> filteredExpsMap = new HashMap<String, String>();
  for ( Object[] exp : allExps ) {
    filteredExpsMap.put( (String) exp[ 0 ], (String) exp[ 1 ] );
  }
  Map<String, String> expsAndPmid = getExperimentAcAndPmid( shortLabelLike );
  for ( String expWithPmid : expsAndPmid.keySet() ) {
    filteredExpsMap.remove( expWithPmid );
  }
  return filteredExpsMap;
}

public static Map<String, Integer> countInteractionCountsForExperiments( String shortLabelLike ) {
  List<Object[]> expWithInteractionsCount = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .createAlias( "interactions", "int" )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.count( "int.ac" ) )
          .add( Projections.groupProperty( "ac" ) ) ).list();
  Map<String, Integer> interactionCountByExpAc = new HashMap<String, Integer>();
  for ( Object[] expAndIntCount : expWithInteractionsCount ) {
    interactionCountByExpAc.put( (String) expAndIntCount[ 0 ], (Integer) expAndIntCount[ 1 ] );
  }
  return interactionCountByExpAc;
}

public static Map<String, String> getExperimentAcAndLabelWithoutPubmedId( String shortLabelLike ) {
  List<Object[]> allExps = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.property( "shortLabel" ) ) ).list();
  Map<String, String> filteredExpsMap = new HashMap<String, String>();
  for ( Object[] exp : allExps ) {
    filteredExpsMap.put( (String) exp[ 0 ], (String) exp[ 1 ] );
  }
  Map<String, String> expsAndPmid = getExperimentAcAndPmid( shortLabelLike );
  for ( String expWithPmid : expsAndPmid.keySet() ) {
    filteredExpsMap.remove( expWithPmid );
  }
  return filteredExpsMap;
}

List<Object[]> expWithDataset = getSession().createCriteria( Experiment.class )
    .add( Restrictions.like( "shortLabel", shortLabelLike ) )
    .createAlias( "annotations", "annot" )

public static Map<String, Integer> countInteractionCountsForExperiments( String shortLabelLike ) {
  List<Object[]> expWithInteractionsCount = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .createAlias( "interactions", "int" )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.count( "int.ac" ) )
          .add( Projections.groupProperty( "ac" ) ) ).list();
  Map<String, Integer> interactionCountByExpAc = new HashMap<String, Integer>();
  for ( Object[] expAndIntCount : expWithInteractionsCount ) {
    interactionCountByExpAc.put( (String) expAndIntCount[ 0 ], (Integer) expAndIntCount[ 1 ] );
  }
  return interactionCountByExpAc;
}

public static Map<String, Integer> countInteractionCountsForExperiments( String shortLabelLike ) {
  List<Object[]> expWithInteractionsCount = getSession().createCriteria( Experiment.class )
      .add( Restrictions.like( "shortLabel", shortLabelLike ) )
      .createAlias( "interactions", "int" )
      .setProjection( Projections.projectionList()
          .add( Projections.distinct( Projections.property( "ac" ) ) )
          .add( Projections.count( "int.ac" ) )
          .add( Projections.groupProperty( "ac" ) ) ).list();
  Map<String, Integer> interactionCountByExpAc = new HashMap<String, Integer>();
  for ( Object[] expAndIntCount : expWithInteractionsCount ) {
    interactionCountByExpAc.put( (String) expAndIntCount[ 0 ], (Integer) expAndIntCount[ 1 ] );
  }
  return interactionCountByExpAc;
}

Popular methods of ExperimentListGeneratorDao

countInteractionCountsForExperiments
datasetForExperiments
Retreives experiment ahving assiciated dataset annotation.
getContainingAnnotation
Query to obtain annotated objects by searching for an Annotation with the cvTopic label provided
getExpWithInteractionsContainingAnnotation
Query to get at the Experiment ACs containing negative interaction annotations
getExperimentAcAndLabelWithoutPubmedId
getExperimentAcAndPmid
getExperimentAcAndTaxids

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How to use getSessionmethodin uk.ac.ebi.intact.application.dataConversion.dao.ExperimentListGeneratorDao

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How to use
getSession
method
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uk.ac.ebi.intact.application.dataConversion.dao.ExperimentListGeneratorDao