gov.usda.gdpc
Interface DBConnection

All Known Implementing Classes:

AbstractDBConnection, AbstractJDBCConnection, DBConnectionProxy

public interface DBConnection

Defines the low level interaction with a database.

Author:

terryc

Method Summary

void	close() This method is used to tell the connection to close or generally release any resources and shutdown.
java.lang.String	getDataSource() Returns the data source of this connection.
java.lang.String	getDescription() Returns a description of this connection.
DistinctPropertyValues	getDistinctProperties(java.util.List properties) Returns list(s) of distinct property values for the given properties.
EnvironmentExperimentGroup	getEnvironmentExperimentGroup(EnvironmentExperimentFilter filter) Gets an environment experiment group based on the given environment experiment filter.
GenotypeExperimentGroup	getGenotypeExperimentGroup(GenotypeExperimentFilter filter) Gets a genotype experiment group based on the given genotype experiment filter.
GenericTable	getGenotypeGenericTable(GenotypeExperimentGroup experimentGroup, TaxonGroup taxonGroup) Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
GenotypeGroup	getGenotypeGroup(GenotypeExperimentGroup experimentGroup, TaxonGroup taxonGroup) Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
LocalityGroup	getLocalityGroup(LocalityFilter filter) Gets a locality group based on the given locality filter.
LocusGroup	getLocusGroup(LocusFilter filter) Gets a locus group based on the given locus filter.
PhenotypeGroup	getPhenotypeGroup(EnvironmentExperimentGroup experimentGroup, TaxonGroup taxonGroup, PhenotypeOntologyGroup ontologyGroup) Gets the phenotypes for all combinations of environment experiments, taxa, and phenotype ontologys defined by the respective groups.
PhenotypeOntologyGroup	getPhenotypeOntologyGroup(PhenotypeOntologyFilter filter) Get a phenotype ontology group based on the given pheotype ontology filter.
TaxonGroup	getTaxonGroup(TaxonFilter filter) Gets a taxon group based on the given taxon filter.

Method Detail

getDataSource

public java.lang.String getDataSource()

Returns the data source of this connection. Typically, a URI.

Returns:

data source

getDescription

public java.lang.String getDescription()

Returns a description of this connection.

Returns:

description

getLocusGroup

public LocusGroup getLocusGroup(LocusFilter filter)

Gets a locus group based on the given locus filter.

Parameters:

filter - filter containing criteria to build locus group.

Returns:

the locus group

getGenotypeExperimentGroup

public GenotypeExperimentGroup getGenotypeExperimentGroup(GenotypeExperimentFilter filter)

Gets a genotype experiment group based on the given genotype experiment filter.

Parameters:

filter - filter containing criteria.

Returns:

the genotype experiment group

getTaxonGroup

public TaxonGroup getTaxonGroup(TaxonFilter filter)

Gets a taxon group based on the given taxon filter.

Parameters:

filter - filter containing criteria.

Returns:

the taxon group

getPhenotypeOntologyGroup

public PhenotypeOntologyGroup getPhenotypeOntologyGroup(PhenotypeOntologyFilter filter)

Get a phenotype ontology group based on the given pheotype ontology filter.

Parameters:

filter - phenotype ontology filter

Returns:

phenotype ontology group

getPhenotypeGroup

public PhenotypeGroup getPhenotypeGroup(EnvironmentExperimentGroup experimentGroup,
                                        TaxonGroup taxonGroup,
                                        PhenotypeOntologyGroup ontologyGroup)

Gets the phenotypes for all combinations of environment experiments, taxa, and phenotype ontologys defined by the respective groups.

Parameters:

experimentGroup - environment experiment group

taxonGroup - taxon group

ontologyGroup - phenotype ontology group

Returns:

phenotype group

getEnvironmentExperimentGroup

public EnvironmentExperimentGroup getEnvironmentExperimentGroup(EnvironmentExperimentFilter filter)

Gets an environment experiment group based on the given environment experiment filter.

Parameters:

filter - filter containing criteria.

Returns:

the environment experiment group

getLocalityGroup

public LocalityGroup getLocalityGroup(LocalityFilter filter)

Gets a locality group based on the given locality filter.

Parameters:

filter - filter containing criteria.

Returns:

the locality group

getGenotypeGroup

public GenotypeGroup getGenotypeGroup(GenotypeExperimentGroup experimentGroup,
                                      TaxonGroup taxonGroup)

Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.

Parameters:

experimentGroup - genotype experiment group

taxonGroup - taxon group

Returns:

genotype group

getGenotypeGenericTable

public GenericTable getGenotypeGenericTable(GenotypeExperimentGroup experimentGroup,
                                            TaxonGroup taxonGroup)

Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups. Since the return type of this method does not include experiment or taxon information, neither input parameter can be empty or null. This method returns an empty table in that event.

Parameters:

experimentGroup - genotype experiment group

taxonGroup - taxon group

Returns:

generic table

getDistinctProperties

public DistinctPropertyValues getDistinctProperties(java.util.List properties)

Returns list(s) of distinct property values for the given properties. The list(s) are values retrieved from this database connection. If null returned, this connection does not support the properties or the values could not be retrieved.

Parameters:

properties - list of properties

Returns:

list(s) of distinct property values

close

public void close()

This method is used to tell the connection to close or generally release any resources and shutdown. The connection may choice to not support this method if end users are not allowed to close the connection.