Package ubic.gemma.persistence.service.expression.experiment

Interface FactorValueMigratorService

All Known Implementing Classes:

FactorValueMigratorServiceImpl

public interface FactorValueMigratorService

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	FactorValueMigratorService.Migration
static class	FactorValueMigratorService.MigrationFailedException	Keep track of the first failed migration when multiple migrations are performed in a single transaction.
static class	FactorValueMigratorService.MigrationResult

Method Summary

Modifier and Type	Method	Description
FactorValueMigratorService.MigrationResult	performMigration(FactorValueMigratorService.Migration migration, boolean noop)	Perform the given migration.
Map<Long,List<FactorValueMigratorService.MigrationResult>>	performMigrationOfRemainingFactorValues(Set<Long> migratedFactorValueIds, boolean migrateNonTrivialCases, boolean noop)	Migrate all remaining factor values that have not been migrated yet.
List<FactorValueMigratorService.MigrationResult>	performMigrationOfRemainingOldStyleCharacteristics(Long fvId, Set<Long> migratedOldStyleCharacteristicIds, boolean noop)	Migrate all the old-style characteristics of a given factor value to subject-only statements.
List<FactorValueMigratorService.MigrationResult>	performMultipleMigrations(List<FactorValueMigratorService.Migration> migrations, boolean noop)	Perform multiple migrations in a single transaction.

Method Detail

performMigration

FactorValueMigratorService.MigrationResult performMigration(FactorValueMigratorService.Migration migration,
                                                            boolean noop)

Perform the given migration.

Parameters:

migration - a migration to perform

noop - if true, do not save the resulting statement

Returns:

the created or updated statement

performMultipleMigrations

List<FactorValueMigratorService.MigrationResult> performMultipleMigrations(List<FactorValueMigratorService.Migration> migrations,
                                                                           boolean noop)
                                                                    throws FactorValueMigratorService.MigrationFailedException

Perform multiple migrations in a single transaction.

Parameters:

migrations - a list of migrations to perform

Returns:

a list of created or updated statements

Throws:

FactorValueMigratorService.MigrationFailedException - if any of the migrations fail, the first failed migration is stored in the exception wrapper

performMigrationOfRemainingOldStyleCharacteristics

List<FactorValueMigratorService.MigrationResult> performMigrationOfRemainingOldStyleCharacteristics(Long fvId,
                                                                                                    Set<Long> migratedOldStyleCharacteristicIds,
                                                                                                    boolean noop)

Migrate all the old-style characteristics of a given factor value to subject-only statements.

The FV will be marked as troubled.

Parameters:

fvId - ID of the factor value to migrate

migratedOldStyleCharacteristicIds - a set of already migrated old-style characteristic IDs, if null the Characteristic.isMigratedToStatement() flag will be used to determine if a characteristic has already been migrated

noop - if true, do not save the resulting statements

Returns:

list of created or updated statements from the given factor value

performMigrationOfRemainingFactorValues

Map<Long,List<FactorValueMigratorService.MigrationResult>> performMigrationOfRemainingFactorValues(Set<Long> migratedFactorValueIds,
                                                                                                         boolean migrateNonTrivialCases,
                                                                                                         boolean noop)

Migrate all remaining factor values that have not been migrated yet.

All the FVs with zero or one characteristics will be migrated automatically unless migratedToSubjectOnly is set, in which case all the old-style characteristics will be migrated to subject-only statements.

Parameters:

migratedFactorValueIds - IDs of already migrated FVs

migrateNonTrivialCases - allow migration to subject-only statements for FVs with more than one old-style characteristics; those FVs will be marked as troubled.

noop - if true, do not save the resulting statements

Returns:

created of updated statements organized by factor value ID