gov.nih.nci.caarray.services.arraydesign
Interface ArrayDesignDataSource

All Known Implementing Classes:
DbArrayDesignDataSource

public interface ArrayDesignDataSource

Retrieves various MAGE objects needed to populate array designs.

Author:
ETavela

Method Summary
 void addCompositeSequence(CompositeGroup compositeGroup, CompositeSequence compositeSequence)
           
 void create(PhysicalArrayDesign arrayDesign, java.lang.String username)
          Saves a new array design to the database.
 void disableIndexesAndConstraints()
          Disables constraints and drops indexes in order to faster load array design data.
 void enableIndexesAndConstraints()
          Re-enables constraints and adds indexes after array design loading.
 PhysicalArrayDesign[] getAllArrayDesigns()
          Returns all array designs in the system
 PhysicalArrayDesign getArrayDesign(long id)
          Returns the array design requested.
 PhysicalArrayDesign getArrayDesign(java.lang.String identifier)
          Returns the existing array design matching the given identifier or null if none exists yet.
 ArrayDesignFileUploadEntry getArrayDesignFileUploadEntry(PhysicalArrayDesign design)
          Returns the upload entry associated with the array design, or null if there is none.
 OntologyEntry getOntologyEntry(java.lang.String category, java.lang.String value)
          Returns the entry corresponding to the data given or null if not found.
 Organization getOrganization(OrganizationDescriptor descriptor)
          Returns the Organization corresponding to the descriptor given, creating if necessary.
 void makePublic(PhysicalArrayDesign arrayDesign, java.lang.String username)
          Makes an array design public.
 void removeExistingDesignElements(PhysicalArrayDesign newArrayDesign)
          Clears all existing associated array design objects from the system, leaving only the top level PhysicalArrayDesign object.
 void save(PhysicalArrayDesign newArrayDesign)
          Saves an existing array design to the database.
 DesignElementRetrievalSettings setEfficientDesignElementRetrieval()
          Changes OJB auto-retrieval for design elements to false for all objects associated with design elements.
 void setNormalDesignElementRetrieval(DesignElementRetrievalSettings originalSettings)
          Restores OJB design element auto-retrieve settings to their original values.
 

Method Detail

getOntologyEntry

OntologyEntry getOntologyEntry(java.lang.String category,
                               java.lang.String value)
                               throws ArrayDesignDataSourceException
Returns the entry corresponding to the data given or null if not found.

Parameters:
category - the category
value - the value
Returns:
the matching entry or null.
Throws:
ArrayDesignDataSourceException

getOrganization

Organization getOrganization(OrganizationDescriptor descriptor)
                             throws ArrayDesignDataSourceException
Returns the Organization corresponding to the descriptor given, creating if necessary.

Parameters:
descriptor - the organization's descriptor
Returns:
the matching organization or null.
Throws:
ArrayDesignDataSourceException

makePublic

void makePublic(PhysicalArrayDesign arrayDesign,
                java.lang.String username)
                throws ArrayDesignDataSourceException
Makes an array design public.

Parameters:
arrayDesign - the array design to make public.
username - the owner of the design.
Throws:
ArrayDesignDataSourceException

create

void create(PhysicalArrayDesign arrayDesign,
            java.lang.String username)
            throws ArrayDesignDataSourceException
Saves a new array design to the database.

Parameters:
arrayDesign - the array design to create.
username - the user creating the design.
Throws:
ArrayDesignDataSourceException

getArrayDesign

PhysicalArrayDesign getArrayDesign(java.lang.String identifier)
                                   throws ArrayDesignDataSourceException
Returns the existing array design matching the given identifier or null if none exists yet.

Parameters:
identifier - identifier to match
Returns:
the matching design or null;
Throws:
ArrayDesignDataSourceException

getAllArrayDesigns

PhysicalArrayDesign[] getAllArrayDesigns()
                                         throws ArrayDesignDataSourceException
Returns all array designs in the system

Returns:
all array designs.
Throws:
ArrayDesignDataSourceException

removeExistingDesignElements

void removeExistingDesignElements(PhysicalArrayDesign newArrayDesign)
                                  throws ArrayDesignDataSourceException
Clears all existing associated array design objects from the system, leaving only the top level PhysicalArrayDesign object.

Parameters:
newArrayDesign -
Throws:
ArrayDesignDataSourceException

save

void save(PhysicalArrayDesign newArrayDesign)
          throws ArrayDesignDataSourceException
Saves an existing array design to the database.

Parameters:
newArrayDesign -
Throws:
ArrayDesignDataSourceException

getArrayDesignFileUploadEntry

ArrayDesignFileUploadEntry getArrayDesignFileUploadEntry(PhysicalArrayDesign design)
                                                         throws ArrayDesignDataSourceException
Returns the upload entry associated with the array design, or null if there is none.

Parameters:
design - get upload entry for this design
Returns:
the upload entry.
Throws:
ArrayDesignDataSourceException

getArrayDesign

PhysicalArrayDesign getArrayDesign(long id)
                                   throws ArrayDesignDataSourceException
Returns the array design requested.

Parameters:
id -
Returns:
Throws:
ArrayDesignDataSourceException

disableIndexesAndConstraints

void disableIndexesAndConstraints()
                                  throws ArrayDesignDataSourceException
Disables constraints and drops indexes in order to faster load array design data.

Throws:
ArrayDesignDataSourceException

enableIndexesAndConstraints

void enableIndexesAndConstraints()
                                 throws ArrayDesignDataSourceException
Re-enables constraints and adds indexes after array design loading.

Throws:
ArrayDesignDataSourceException

setEfficientDesignElementRetrieval

DesignElementRetrievalSettings setEfficientDesignElementRetrieval()
Changes OJB auto-retrieval for design elements to false for all objects associated with design elements.

Returns:
the original settings for later restoration
Throws:
ArrayDesignDataSourceException

setNormalDesignElementRetrieval

void setNormalDesignElementRetrieval(DesignElementRetrievalSettings originalSettings)
Restores OJB design element auto-retrieve settings to their original values.

Parameters:
originalSettings -
Throws:
ArrayDesignDataSourceException

addCompositeSequence

void addCompositeSequence(CompositeGroup compositeGroup,
                          CompositeSequence compositeSequence)
Parameters:
compositeGroup -
compositeSequence -