Package ubic.gemma.core.loader.util.mapper

Class AbstractBioAssayMapper

java.lang.Object

ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper

All Implemented Interfaces:

BioAssayMapper, EntityMapper<BioAssay>

Direct Known Subclasses:

GeoBioAssayMapper, SimpleBioAssayMapper

public abstract class AbstractBioAssayMapper
extends Object
implements BioAssayMapper

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.core.loader.util.mapper.EntityMapper

EntityMapper.MappingStatistics, EntityMapper.StatefulEntityMapper<T extends Identifiable>

Constructor Summary

Constructors

Constructor	Description
AbstractBioAssayMapper()

Method Summary

Modifier and Type	Method	Description
boolean	contains(Collection<BioAssay> candidates, String identifier)	Check if any of the candidates can be mapped to the identifier.
boolean	containsAny(Collection<BioAssay> candidates, Collection<String> identifiers)	Check if any of the candidates can be mapped to any of the identifiers.
EntityMapper.StatefulEntityMapper<BioAssay>	forCandidates(Collection<BioAssay> candidates)	Create a stateful mapper for a set of candidates.
Set<BioAssay>	matchAll(Collection<BioAssay> candidates, String identifier)	Match the identifier to all the candidates.
Map<String,Set<BioAssay>>	matchAll(Collection<BioAssay> candidates, Collection<String> identifiers)	Match each identifier to all the candidates.
protected abstract Set<BioAssay>	matchAllInternal(Collection<BioAssay> candidates, String identifier)
protected boolean	matchDescriptionIgnoreCase(String a, String b)
protected boolean	matchId(Long a, String b)
protected boolean	matchName(String a, String b)
protected boolean	matchNameIgnoreCase(String a, String b)
Optional<BioAssay>	matchOne(Collection<BioAssay> candidates, String identifier)	Map the identifier to a single candidate.
Map<String,BioAssay>	matchOne(Collection<BioAssay> candidates, Collection<String> identifiers)	Match each identifier to a single candidate.
protected <T> boolean	matchWithFunction(Collection<BioAssay> bas, Function<BioAssay,T> extractor, BiFunction<T,String,Boolean> func, String sampleName, Collection<BioAssay> results)
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.loader.util.mapper.BioAssayMapper

forCandidates

Methods inherited from interface ubic.gemma.core.loader.util.mapper.EntityMapper

getMappingStatistics, getName

Constructor Detail

AbstractBioAssayMapper

public AbstractBioAssayMapper()

Method Detail

forCandidates

public EntityMapper.StatefulEntityMapper<BioAssay> forCandidates(Collection<BioAssay> candidates)

Description copied from interface: EntityMapper

Create a stateful mapper for a set of candidates.

Specified by:

forCandidates in interface EntityMapper<BioAssay>

contains

public boolean contains(Collection<BioAssay> candidates,
                        String identifier)

Description copied from interface: EntityMapper

Check if any of the candidates can be mapped to the identifier.

Specified by:

contains in interface EntityMapper<BioAssay>

containsAny

public boolean containsAny(Collection<BioAssay> candidates,
                           Collection<String> identifiers)

Description copied from interface: EntityMapper

Check if any of the candidates can be mapped to any of the identifiers.

Specified by:

containsAny in interface EntityMapper<BioAssay>

matchOne

public Optional<BioAssay> matchOne(Collection<BioAssay> candidates,
                                   String identifier)

Description copied from interface: EntityMapper

Map the identifier to a single candidate.

If more than one candidate matches the identifier, Optional.empty() is returned.

Specified by:

matchOne in interface EntityMapper<BioAssay>

matchOne

public Map<String,BioAssay> matchOne(Collection<BioAssay> candidates,
                                           Collection<String> identifiers)

Description copied from interface: EntityMapper

Match each identifier to a single candidate.

Specified by:

matchOne in interface EntityMapper<BioAssay>

matchAll

public Set<BioAssay> matchAll(Collection<BioAssay> candidates,
                              String identifier)

Description copied from interface: EntityMapper

Match the identifier to all the candidates.

Specified by:

matchAll in interface EntityMapper<BioAssay>

matchAll

public Map<String,Set<BioAssay>> matchAll(Collection<BioAssay> candidates,
                                                Collection<String> identifiers)

Description copied from interface: EntityMapper

Match each identifier to all the candidates.

Specified by:

matchAll in interface EntityMapper<BioAssay>

toString

public String toString()

Overrides:

toString in class Object

matchAllInternal

protected abstract Set<BioAssay> matchAllInternal(Collection<BioAssay> candidates,
                                                  String identifier)

matchWithFunction

protected <T> boolean matchWithFunction(Collection<BioAssay> bas,
                                        Function<BioAssay,T> extractor,
                                        BiFunction<T,String,Boolean> func,
                                        String sampleName,
                                        Collection<BioAssay> results)

matchId

protected boolean matchId(@Nullable
                          Long a,
                          String b)

matchName

protected boolean matchName(String a,
                            String b)

matchNameIgnoreCase

protected boolean matchNameIgnoreCase(String a,
                                      String b)

matchDescriptionIgnoreCase

protected boolean matchDescriptionIgnoreCase(String a,
                                             String b)