ubic.gemma.persistence.util

Class BusinessKey

java.lang.Object

ubic.gemma.persistence.util.BusinessKey

public class BusinessKey
extends Object

Methods to test business-key-related issues on objects. The 'checkValidKey' methods can be used to check whether an object has the required business key values filled in. An exception is thrown if they don't. This class contains some important code that determines our rules for how entities are detected as being the same as another (in queries from the database; this is on top of basic 'equals', but should be compatible).

Author:

pavlidis

Constructor Summary

Constructors

Constructor and Description
BusinessKey()

Method Summary

Modifier and Type	Method and Description
static void	addRestrictions(Criteria queryObject, ArrayDesign arrayDesign)
static void	addRestrictions(Criteria queryObject, BioAssay bioAssay)
static void	addRestrictions(Criteria queryObject, BioMaterial bioMaterial)
static void	addRestrictions(Criteria queryObject, BioSequence bioSequence) Note: The finder has to do the additional checking for equality of sequence and/or database entry - we don't know until we get the sequences.
static void	addRestrictions(Criteria queryObject, Characteristic characteristic)
static void	addRestrictions(Criteria queryObject, Chromosome chromosome)
static void	addRestrictions(Criteria queryObject, Contact contact)
static void	addRestrictions(Criteria queryObject, ExperimentalFactor experimentalFactor)
static void	addRestrictions(Criteria queryObject, Gene2GOAssociation gene2GOAssociation)
static void	addRestrictions(Criteria queryObject, Gene gene, boolean stricter)
static void	addRestrictions(Criteria queryObject, QuantitationType quantitationType)
static void	addRestrictions(Criteria queryObject, Taxon taxon)
static void	addRestrictions(DetachedCriteria queryObject, DatabaseEntry databaseEntry)
static void	attachCriteria(Criteria queryObject, BioSequence bioSequence, String propertyName) Restricts the query to the provided BioSequence.
static void	attachCriteria(Criteria queryObject, Characteristic ontologyEntry, String propertyName) Restricts the query to the provided OntologyEntry.
static void	attachCriteria(Criteria queryObject, DatabaseEntry databaseEntry, String propertyName) Restricts query to the given DatabaseEntry association
static void	attachCriteria(Criteria queryObject, Gene gene, String propertyName) Restricts the query to the provided Gene.
static void	attachCriteria(Criteria queryObject, PhysicalLocation physicalLocation, String attributeName)
static void	attachCriteria(Criteria queryObject, Taxon taxon, String propertyName) Restricts query to the given Taxon.
static void	attachCriteria(DetachedCriteria queryObject, DatabaseEntry databaseEntry, String attributeName)
static void	checkKey(BibliographicReference bibliographicReference)
static void	checkKey(Characteristic ontologyEntry)
static void	checkKey(Contact contact)
static void	checkKey(DatabaseEntry accession)
static void	checkKey(DesignElementDataVector designElementDataVector)
static void	checkKey(ExpressionExperimentSubSet entity)
static void	checkKey(ExternalDatabase externalDatabase)
static void	checkKey(FactorValue factorValue)
static void	checkKey(Gene gene)
static void	checkKey(User user)
static void	checkValidKey(ArrayDesign arrayDesign)
static void	checkValidKey(BioSequence bioSequence)
static void	checkValidKey(Chromosome chromosome)
static void	checkValidKey(DatabaseEntry databaseEntry)
static void	checkValidKey(ExperimentalFactor experimentalFactor)
static void	checkValidKey(Gene gene)
static void	checkValidKey(Gene2GOAssociation gene2GOAssociation)
static void	checkValidKey(GeneProduct geneProduct)
static void	checkValidKey(LocalFile localFile)
static void	checkValidKey(Taxon taxon)
static void	checkValidKey(Unit unit)
static void	createQueryObject(Criteria queryObject, ExpressionExperimentSubSet entity)
static void	createQueryObject(Criteria queryObject, FactorValue factorValue)
static void	createQueryObject(Criteria queryObject, Gene gene)
static void	createQueryObject(Criteria queryObject, GeneProduct geneProduct)
static Criteria	createQueryObject(Session session, ArrayDesign arrayDesign)
static Criteria	createQueryObject(Session session, BioAssay bioAssay)
static Criteria	createQueryObject(Session session, BioSequence bioSequence)
static Criteria	createQueryObject(Session session, Characteristic ontologyEntry)
static Criteria	createQueryObject(Session session, Unit unit)

Methods inherited from class java.lang.Object

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

Constructor Detail

BusinessKey

public BusinessKey()

Method Detail

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   ArrayDesign arrayDesign)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   BioAssay bioAssay)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   BioMaterial bioMaterial)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   BioSequence bioSequence)

Note: The finder has to do the additional checking for equality of sequence and/or database entry - we don't know until we get the sequences. Due to the following issues:

• Sometimes the sequence in the database lacks the DatabaseEntry
• Sometimes the old entry lacks the actual sequence (ATCG..)

This means that we can't use those criteria up front. Instead we match by name and taxon. If those match, the caller has to sort through possible multiple results to find the correct one.

Parameters:

bioSequence - bio sequence

queryObject - query object

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   Characteristic characteristic)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   Chromosome chromosome)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   Contact contact)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   ExperimentalFactor experimentalFactor)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   Gene gene,
                                   boolean stricter)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   Gene2GOAssociation gene2GOAssociation)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   QuantitationType quantitationType)

addRestrictions

public static void addRestrictions(Criteria queryObject,
                                   Taxon taxon)

addRestrictions

public static void addRestrictions(DetachedCriteria queryObject,
                                   DatabaseEntry databaseEntry)

attachCriteria

public static void attachCriteria(Criteria queryObject,
                                  BioSequence bioSequence,
                                  String propertyName)

Restricts the query to the provided BioSequence.

Parameters:

bioSequence - The object used to create the criteria

propertyName - Often this will be 'bioSequence'

queryObject - query object

attachCriteria

public static void attachCriteria(Criteria queryObject,
                                  Characteristic ontologyEntry,
                                  String propertyName)

Restricts the query to the provided OntologyEntry.

Parameters:

ontologyEntry - The object used to create the criteria

propertyName - Often this will be 'ontologyEntry'

queryObject - query object

attachCriteria

public static void attachCriteria(Criteria queryObject,
                                  DatabaseEntry databaseEntry,
                                  String propertyName)

Restricts query to the given DatabaseEntry association

Parameters:

databaseEntry - to match

propertyName - often "accession"

queryObject - query object

attachCriteria

public static void attachCriteria(Criteria queryObject,
                                  Gene gene,
                                  String propertyName)

Restricts the query to the provided Gene.

Parameters:

queryObject - query object

gene - gene

propertyName - property name

attachCriteria

public static void attachCriteria(Criteria queryObject,
                                  PhysicalLocation physicalLocation,
                                  String attributeName)

attachCriteria

public static void attachCriteria(Criteria queryObject,
                                  Taxon taxon,
                                  String propertyName)

Restricts query to the given Taxon.

Parameters:

propertyName - often "taxon"

queryObject - query object

taxon - taxon

attachCriteria

public static void attachCriteria(DetachedCriteria queryObject,
                                  DatabaseEntry databaseEntry,
                                  String attributeName)

checkKey

public static void checkKey(BibliographicReference bibliographicReference)

checkKey

public static void checkKey(Characteristic ontologyEntry)

checkKey

public static void checkKey(Contact contact)

checkKey

public static void checkKey(DatabaseEntry accession)

checkKey

public static void checkKey(DesignElementDataVector designElementDataVector)

checkKey

public static void checkKey(ExternalDatabase externalDatabase)

checkKey

public static void checkKey(FactorValue factorValue)

checkKey

public static void checkKey(Gene gene)

checkKey

public static void checkKey(User user)

checkValidKey

public static void checkValidKey(ArrayDesign arrayDesign)

checkValidKey

public static void checkValidKey(BioSequence bioSequence)

checkValidKey

public static void checkValidKey(Chromosome chromosome)

checkValidKey

public static void checkValidKey(DatabaseEntry databaseEntry)

checkValidKey

public static void checkValidKey(ExperimentalFactor experimentalFactor)

checkValidKey

public static void checkValidKey(Gene gene)

checkValidKey

public static void checkValidKey(Gene2GOAssociation gene2GOAssociation)

checkValidKey

public static void checkValidKey(GeneProduct geneProduct)

checkValidKey

public static void checkValidKey(Taxon taxon)

checkValidKey

public static void checkValidKey(LocalFile localFile)

checkValidKey

public static void checkValidKey(Unit unit)

createQueryObject

public static void createQueryObject(Criteria queryObject,
                                     FactorValue factorValue)

createQueryObject

public static void createQueryObject(Criteria queryObject,
                                     Gene gene)

createQueryObject

public static void createQueryObject(Criteria queryObject,
                                     GeneProduct geneProduct)

createQueryObject

public static Criteria createQueryObject(Session session,
                                         ArrayDesign arrayDesign)

createQueryObject

public static Criteria createQueryObject(Session session,
                                         BioAssay bioAssay)

createQueryObject

public static Criteria createQueryObject(Session session,
                                         BioSequence bioSequence)

createQueryObject

public static Criteria createQueryObject(Session session,
                                         Characteristic ontologyEntry)

createQueryObject

public static Criteria createQueryObject(Session session,
                                         Unit unit)

checkKey

public static void checkKey(ExpressionExperimentSubSet entity)

createQueryObject

public static void createQueryObject(Criteria queryObject,
                                     ExpressionExperimentSubSet entity)