Package de.julielab.gene.candidateretrieval

Class NameCentricRetrieval

java.lang.Object

de.julielab.gene.candidateretrieval.NameCentricRetrieval

All Implemented Interfaces:

CandidateRetrieval, de.julielab.geneexpbase.candidateretrieval.CandidateRetrieval, Closeable, AutoCloseable

public class NameCentricRetrieval
extends Object
implements CandidateRetrieval

Field Summary

Fields

Modifier and Type	Field	Description
static org.slf4j.Logger	candidateLog
static de.julielab.geneexpbase.candidateretrieval.QueryGenerator	CONJUNCTION
static de.julielab.geneexpbase.candidateretrieval.QueryGenerator	DISJUNCTION
static de.julielab.geneexpbase.candidateretrieval.QueryGenerator	DISJUNCTION_MINUS_1
static de.julielab.geneexpbase.candidateretrieval.QueryGenerator	DISJUNCTION_MINUS_2
static int	JAROWINKLER_SCORER
static int	LEVENSHTEIN_SCORER
static String	LOGGER_NAME_CANDIDATES
static int	LUCENE_MAX_HITS	the maximal number of hits lucene returns for a query
static int	LUCENE_SCORER
static int	MAXENT_SCORER
static String	MAXENT_SCORER_MODEL	default model for MaxEntScorer
static String	NAME_PRIO_DELIMITER
static de.julielab.geneexpbase.candidateretrieval.QueryGenerator	NGRAM_2_3
static int	SIMPLE_SCORER
static int	TFIDF
static int	TOKEN_JAROWINKLER_SCORER

Constructor Summary

Constructors

Constructor	Description
NameCentricRetrieval(Configuration config, de.julielab.geneexpbase.services.CacheService cacheService)

Method Summary

Modifier and Type	Method	Description
void	close()
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention, String organism, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention, Collection<String> organisms, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention gm, Collection<String> taxId, de.julielab.geneexpbase.configuration.Parameters parameters, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention, Collection<String> geneIdsFilter, Collection<String> organisms, boolean loadFields, de.julielab.geneexpbase.configuration.Parameters parameters, int numReturnedHits, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention, Collection<String> geneIdsFilter, Collection<String> organisms, boolean loadFields, de.julielab.geneexpbase.configuration.Parameters parameters, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention, Collection<String> geneIdsFilter, Collection<String> organisms, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(String originalSearchTerm, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(String geneMentionText, String organism, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(String geneMentionText, Collection<String> organism, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(String geneMentionText, Collection<String> geneIdsFilter, Collection<String> organism, boolean loadFields, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(String geneMentionText, Collection<String> geneIdsFilter, Collection<String> organism, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getFamilyNames(de.julielab.geneexpbase.genemodel.GeneMention gm, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)	Searches the index for the given gene mention filtered for family names.
Set<GeneRecordHit>	getGeneRecords(Collection<String> ids)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getIndexEntries(List<String> ids)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getIndexRecords(Collection<String> ids)	The record-index equivalent to getIndexEntries(List).
de.julielab.geneexpbase.TermNormalizer	getNormalizer()
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getOriginalNamesIndexRecords(Collection<String> geneIds)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getOriginalNamesIndexRecords(Collection<String> geneIds, de.julielab.geneexpbase.genemodel.GeneName geneName)
List<String>	getPriorityNames(String id, int priority)
List<String>	getPriorityNames(Collection<String> ids, int priority)
Map<String,String>	getPriorityNamesMap(Collection<String> ids, int priority)
de.julielab.geneexpbase.scoring.Scorer	getScorer()
String	getScorerInfo()
int	getScorerType()
org.apache.lucene.search.spell.SpellChecker	getSpellingChecker()
List<String>	getSynonyms(String id)
de.julielab.geneexpbase.scoring.TFIDFScorer	getTFIDFOnGeneRecordNames()
static AtomicLong	getTotalCacheGettime()
static AtomicLong	getTotalCachePuttime()
static AtomicLong	getTotalLuceneQueryTime()
String	mapGeneIdToTaxId(String geneId)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	scoreIdsByBoWSynonyms(Collection<String> allSynonyms, Set<String> ids, de.julielab.geneexpbase.candidateretrieval.QueryGenerator qg)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	scoreIdsByExactSynonyms(Collection<String> allSynonyms, Set<String> geneIds)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	scoreIdsByNGramSynonyms(String synonymsString, Set<String> geneIds)
org.apache.commons.lang3.tuple.Pair<Map<String,Double>,Map<String,Set<String>>>	scoreSynonymsRecordIndex(String queryType, Map<String,Collection<de.julielab.geneexpbase.genemodel.GeneName>> ids2entities, Function<GeneRecordHit,String[]> synhit2namesFunc, de.julielab.geneexpbase.candidateretrieval.QueryGenerator qg)
org.apache.commons.lang3.tuple.Pair<Map<String,Double>,Map<String,List<String>>>	scoreSynonymsRecordIndex(Collection<de.julielab.geneexpbase.genemodel.GeneName> allSynonyms, Set<String> ids, Function<GeneRecordHit,String[]> synhit2namesFunc, de.julielab.geneexpbase.candidateretrieval.QueryGenerator qg)	Scores each synonym in allSynonym against the IDs in ids.
void	setFulltextFieldsToRecordHits(Collection<? extends de.julielab.geneexpbase.candidateretrieval.SynHit> recordHits, Collection<String> recordContextFieldNames)
void	setNormalizer(de.julielab.geneexpbase.TermNormalizer normalizer)
de.julielab.geneexpbase.scoring.Scorer	setScorerType(int type)
static void	shutdownExecutor()

Methods inherited from class java.lang.Object

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

Field Detail

CONJUNCTION

public static final de.julielab.geneexpbase.candidateretrieval.QueryGenerator CONJUNCTION

DISJUNCTION

public static final de.julielab.geneexpbase.candidateretrieval.QueryGenerator DISJUNCTION

DISJUNCTION_MINUS_1

public static final de.julielab.geneexpbase.candidateretrieval.QueryGenerator DISJUNCTION_MINUS_1

DISJUNCTION_MINUS_2

public static final de.julielab.geneexpbase.candidateretrieval.QueryGenerator DISJUNCTION_MINUS_2

NGRAM_2_3

public static final de.julielab.geneexpbase.candidateretrieval.QueryGenerator NGRAM_2_3

NAME_PRIO_DELIMITER

public static final String NAME_PRIO_DELIMITER

See Also:

Constant Field Values

LOGGER_NAME_CANDIDATES

public static final String LOGGER_NAME_CANDIDATES

See Also:

Constant Field Values

SIMPLE_SCORER

public static final int SIMPLE_SCORER

See Also:

Constant Field Values

TOKEN_JAROWINKLER_SCORER

public static final int TOKEN_JAROWINKLER_SCORER

See Also:

Constant Field Values

MAXENT_SCORER

public static final int MAXENT_SCORER

See Also:

Constant Field Values

JAROWINKLER_SCORER

public static final int JAROWINKLER_SCORER

See Also:

Constant Field Values

LEVENSHTEIN_SCORER

public static final int LEVENSHTEIN_SCORER

See Also:

Constant Field Values

TFIDF

public static final int TFIDF

See Also:

Constant Field Values

LUCENE_SCORER

public static final int LUCENE_SCORER

See Also:

Constant Field Values

MAXENT_SCORER_MODEL

public static final String MAXENT_SCORER_MODEL

default model for MaxEntScorer

See Also:

Constant Field Values

candidateLog

public static final org.slf4j.Logger candidateLog

LUCENE_MAX_HITS

public static final int LUCENE_MAX_HITS

the maximal number of hits lucene returns for a query

See Also:

Constant Field Values

Constructor Detail

NameCentricRetrieval

@Inject
public NameCentricRetrieval(Configuration config,
                            de.julielab.geneexpbase.services.CacheService cacheService)
                     throws de.julielab.geneexpbase.candidateretrieval.GeneCandidateRetrievalException

Throws:

de.julielab.geneexpbase.candidateretrieval.GeneCandidateRetrievalException

Method Detail

getTotalCacheGettime

public static AtomicLong getTotalCacheGettime()

getTotalCachePuttime

public static AtomicLong getTotalCachePuttime()

getTotalLuceneQueryTime

public static AtomicLong getTotalLuceneQueryTime()

shutdownExecutor

public static void shutdownExecutor()

getNormalizer

public de.julielab.geneexpbase.TermNormalizer getNormalizer()

setNormalizer

public void setNormalizer(de.julielab.geneexpbase.TermNormalizer normalizer)

getScorer

public de.julielab.geneexpbase.scoring.Scorer getScorer()

getSpellingChecker

public org.apache.lucene.search.spell.SpellChecker getSpellingChecker()

Specified by:

getSpellingChecker in interface CandidateRetrieval

setScorerType

public de.julielab.geneexpbase.scoring.Scorer setScorerType(int type)
                                                     throws de.julielab.geneexpbase.candidateretrieval.GeneCandidateRetrievalException

Throws:

de.julielab.geneexpbase.candidateretrieval.GeneCandidateRetrievalException

getScorerInfo

public String getScorerInfo()

getScorerType

public int getScorerType()

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(String originalSearchTerm,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface CandidateRetrieval

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface de.julielab.geneexpbase.candidateretrieval.CandidateRetrieval

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention,
                                                                             Collection<String> organisms,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface de.julielab.geneexpbase.candidateretrieval.CandidateRetrieval

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention,
                                                                             Collection<String> geneIdsFilter,
                                                                             Collection<String> organisms,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface de.julielab.geneexpbase.candidateretrieval.CandidateRetrieval

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention,
                                                                             Collection<String> geneIdsFilter,
                                                                             Collection<String> organisms,
                                                                             boolean loadFields,
                                                                             de.julielab.geneexpbase.configuration.Parameters parameters,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface CandidateRetrieval

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention,
                                                                             Collection<String> geneIdsFilter,
                                                                             Collection<String> organisms,
                                                                             boolean loadFields,
                                                                             de.julielab.geneexpbase.configuration.Parameters parameters,
                                                                             int numReturnedHits,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(String geneMentionText,
                                                                             Collection<String> geneIdsFilter,
                                                                             Collection<String> organism,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface CandidateRetrieval

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(String geneMentionText,
                                                                             Collection<String> geneIdsFilter,
                                                                             Collection<String> organism,
                                                                             boolean loadFields,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention,
                                                                             String organism,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface CandidateRetrieval

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(String geneMentionText,
                                                                             String organism,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface CandidateRetrieval

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(String geneMentionText,
                                                                             Collection<String> organism,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface CandidateRetrieval

mapGeneIdToTaxId

public String mapGeneIdToTaxId(String geneId)

Specified by:

mapGeneIdToTaxId in interface de.julielab.geneexpbase.candidateretrieval.CandidateRetrieval

getIndexEntries

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getIndexEntries(List<String> ids)
                                                                        throws IOException

Throws:

IOException

getIndexRecords

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getIndexRecords(Collection<String> ids)
                                                                        throws IOException

The record-index equivalent to getIndexEntries(List). Returns GeneRecordHit instances with all fields loaded.

Parameters:

ids -

Returns:

Throws:

IOException

getSynonyms

public List<String> getSynonyms(String id)

scoreIdsByNGramSynonyms

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> scoreIdsByNGramSynonyms(String synonymsString,
                                                                                       Set<String> geneIds)

scoreIdsByBoWSynonyms

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> scoreIdsByBoWSynonyms(Collection<String> allSynonyms,
                                                                                     Set<String> ids,
                                                                                     de.julielab.geneexpbase.candidateretrieval.QueryGenerator qg)

Specified by:

scoreIdsByBoWSynonyms in interface CandidateRetrieval

getCandidates

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention gm,
                                                                             Collection<String> taxId,
                                                                             de.julielab.geneexpbase.configuration.Parameters parameters,
                                                                             de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Specified by:

getCandidates in interface CandidateRetrieval

scoreSynonymsRecordIndex

public org.apache.commons.lang3.tuple.Pair<Map<String,Double>,Map<String,List<String>>> scoreSynonymsRecordIndex(Collection<de.julielab.geneexpbase.genemodel.GeneName> allSynonyms,
                                                                                                                                   Set<String> ids,
                                                                                                                                   Function<GeneRecordHit,String[]> synhit2namesFunc,
                                                                                                                                   de.julielab.geneexpbase.candidateretrieval.QueryGenerator qg)

Scores each synonym in allSynonym against the IDs in ids.

Each resulting SynHit adds its mention score to the ID represented by this SynHit.

Parameters:

allSynonyms -

ids -

qg -

Returns:

scoreIdsByExactSynonyms

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> scoreIdsByExactSynonyms(Collection<String> allSynonyms,
                                                                                       Set<String> geneIds)

getPriorityNames

public List<String> getPriorityNames(String id,
                                     int priority)

getPriorityNamesMap

public Map<String,String> getPriorityNamesMap(Collection<String> ids,
                                                    int priority)

getPriorityNames

public List<String> getPriorityNames(Collection<String> ids,
                                     int priority)
                              throws IOException

Throws:

IOException

close

public void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface CandidateRetrieval

Specified by:

close in interface Closeable

getFamilyNames

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getFamilyNames(de.julielab.geneexpbase.genemodel.GeneMention gm,
                                                                              de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Description copied from interface: CandidateRetrieval

Searches the index for the given gene mention filtered for family names.

Specified by:

getFamilyNames in interface CandidateRetrieval

Parameters:

gm - The gene mention to check for family names.

queryGenerator - The query generator to use.

Returns:

getOriginalNamesIndexRecords

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getOriginalNamesIndexRecords(Collection<String> geneIds,
                                                                                            de.julielab.geneexpbase.genemodel.GeneName geneName)

Specified by:

getOriginalNamesIndexRecords in interface CandidateRetrieval

getOriginalNamesIndexRecords

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getOriginalNamesIndexRecords(Collection<String> geneIds)

Specified by:

getOriginalNamesIndexRecords in interface CandidateRetrieval

getTFIDFOnGeneRecordNames

public de.julielab.geneexpbase.scoring.TFIDFScorer getTFIDFOnGeneRecordNames()

Specified by:

getTFIDFOnGeneRecordNames in interface CandidateRetrieval

setFulltextFieldsToRecordHits

public void setFulltextFieldsToRecordHits(Collection<? extends de.julielab.geneexpbase.candidateretrieval.SynHit> recordHits,
                                          Collection<String> recordContextFieldNames)

Specified by:

setFulltextFieldsToRecordHits in interface CandidateRetrieval

scoreSynonymsRecordIndex

public org.apache.commons.lang3.tuple.Pair<Map<String,Double>,Map<String,Set<String>>> scoreSynonymsRecordIndex(String queryType,
                                                                                                                                  Map<String,Collection<de.julielab.geneexpbase.genemodel.GeneName>> ids2entities,
                                                                                                                                  Function<GeneRecordHit,String[]> synhit2namesFunc,
                                                                                                                                  de.julielab.geneexpbase.candidateretrieval.QueryGenerator qg)

Specified by:

scoreSynonymsRecordIndex in interface CandidateRetrieval

getGeneRecords

public Set<GeneRecordHit> getGeneRecords(Collection<String> ids)