public class MongoDBAdaptorFactory extends DBAdaptorFactory
cellBaseConfiguration, logger
Constructor and Description |
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MongoDBAdaptorFactory(CellBaseConfiguration cellBaseConfiguration) |
getAssembly, getCellBaseConfiguration, getSpecies, setConfiguration
public MongoDBAdaptorFactory(CellBaseConfiguration cellBaseConfiguration)
public org.opencb.commons.datastore.mongodb.MongoDataStore getMongoDBDatastore(String species, String assembly)
species
- Species nameassembly
- Assembly versionpublic org.opencb.commons.datastore.mongodb.MongoDataStore getMongoDBDatastore(String databaseName)
databaseName
- name of databasepublic void open(String species, String assembly)
open
in class DBAdaptorFactory
public void close()
close
in class DBAdaptorFactory
public Map<String,HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus> getDatabaseStatus(String species, String assembly)
getDatabaseStatus
in class DBAdaptorFactory
public GenomeDBAdaptor getGenomeDBAdaptor(String species)
getGenomeDBAdaptor
in class DBAdaptorFactory
public GenomeDBAdaptor getGenomeDBAdaptor(String species, String assembly)
getGenomeDBAdaptor
in class DBAdaptorFactory
public CellBaseDBAdaptor<org.bson.Document> getMetaDBAdaptor(String species)
getMetaDBAdaptor
in class DBAdaptorFactory
public CellBaseDBAdaptor<org.bson.Document> getMetaDBAdaptor(String species, String assembly)
getMetaDBAdaptor
in class DBAdaptorFactory
public GeneDBAdaptor getGeneDBAdaptor(String species)
getGeneDBAdaptor
in class DBAdaptorFactory
public GeneDBAdaptor getGeneDBAdaptor(String species, String assembly)
getGeneDBAdaptor
in class DBAdaptorFactory
public TranscriptDBAdaptor getTranscriptDBAdaptor(String species)
getTranscriptDBAdaptor
in class DBAdaptorFactory
public TranscriptDBAdaptor getTranscriptDBAdaptor(String species, String assembly)
getTranscriptDBAdaptor
in class DBAdaptorFactory
public ConservationDBAdaptor getConservationDBAdaptor(String species)
getConservationDBAdaptor
in class DBAdaptorFactory
public ConservationDBAdaptor getConservationDBAdaptor(String species, String assembly)
getConservationDBAdaptor
in class DBAdaptorFactory
public XRefDBAdaptor getXRefDBAdaptor(String species)
getXRefDBAdaptor
in class DBAdaptorFactory
public XRefDBAdaptor getXRefDBAdaptor(String species, String assembly)
getXRefDBAdaptor
in class DBAdaptorFactory
public VariantDBAdaptor getVariationDBAdaptor(String species)
getVariationDBAdaptor
in class DBAdaptorFactory
public VariantDBAdaptor getVariationDBAdaptor(String species, String assembly)
getVariationDBAdaptor
in class DBAdaptorFactory
public ClinicalDBAdaptor getClinicalLegacyDBAdaptor(String species)
getClinicalLegacyDBAdaptor
in class DBAdaptorFactory
public ClinicalDBAdaptor getClinicalLegacyDBAdaptor(String species, String assembly)
getClinicalLegacyDBAdaptor
in class DBAdaptorFactory
public ClinicalDBAdaptor getClinicalDBAdaptor(String species)
getClinicalDBAdaptor
in class DBAdaptorFactory
public ClinicalDBAdaptor getClinicalDBAdaptor(String species, String assembly)
getClinicalDBAdaptor
in class DBAdaptorFactory
public RepeatsDBAdaptor getRepeatsDBAdaptor(String species, String assembly)
getRepeatsDBAdaptor
in class DBAdaptorFactory
public ProteinDBAdaptor getProteinDBAdaptor(String species)
getProteinDBAdaptor
in class DBAdaptorFactory
public ProteinDBAdaptor getProteinDBAdaptor(String species, String assembly)
getProteinDBAdaptor
in class DBAdaptorFactory
public ProteinProteinInteractionDBAdaptor getProteinProteinInteractionDBAdaptor(String species)
getProteinProteinInteractionDBAdaptor
in class DBAdaptorFactory
public ProteinProteinInteractionDBAdaptor getProteinProteinInteractionDBAdaptor(String species, String assembly)
getProteinProteinInteractionDBAdaptor
in class DBAdaptorFactory
public RegulationDBAdaptor getRegulationDBAdaptor(String species)
getRegulationDBAdaptor
in class DBAdaptorFactory
public RegulationDBAdaptor getRegulationDBAdaptor(String species, String assembly)
getRegulationDBAdaptor
in class DBAdaptorFactory
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