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A

AbstractComponentRegistry<T> - Class in org.oncoblocks.centromere.core.util
Abstract ComponentRegistry implementation that uses a HashMap to register and reference target objects.
AbstractComponentRegistry() - Constructor for class org.oncoblocks.centromere.core.util.AbstractComponentRegistry
 
AbstractRecordFileReader<T extends Model<?>> - Class in org.oncoblocks.centromere.core.dataimport
Simple abstract implementation of RecordReader, for reading input files.
AbstractRecordFileReader() - Constructor for class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileReader
 
AbstractRecordFileWriter<T extends Model<?>> - Class in org.oncoblocks.centromere.core.dataimport
Basic abstract implementation of RecordWriter, for writing records to temp files.
AbstractRecordFileWriter() - Constructor for class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileWriter
 
add(String, T) - Method in class org.oncoblocks.centromere.core.util.AbstractComponentRegistry
 
add(T) - Method in interface org.oncoblocks.centromere.core.util.ComponentRegistry
Adds a new mapping in the registry for the given object.
add(String, T) - Method in interface org.oncoblocks.centromere.core.util.ComponentRegistry
Adds a new mapping in theregistry, with the given keyword and object value.
add(RecordProcessor) - Method in class org.oncoblocks.centromere.core.util.DataTypeProcessorRegistry
Adds a new data type processor mapping, if the submitted processor has a DataTypes annotation or implements the DataTypeSupport interface.
add(Class<? extends RecordProcessor>) - Method in class org.oncoblocks.centromere.core.util.DataTypeProcessorRegistry
Searches the ApplicationContext for RecordProcessor beans and attempts to register them.
add(Class<? extends Model>) - Method in class org.oncoblocks.centromere.core.util.ModelRegistry
 
add(RepositoryOperations) - Method in class org.oncoblocks.centromere.core.util.ModelRepositoryRegistry
Adds a new model repository mapping.
add(String, RepositoryOperations) - Method in class org.oncoblocks.centromere.core.util.ModelRepositoryRegistry
 
add(Class<? extends RepositoryOperations>) - Method in class org.oncoblocks.centromere.core.util.ModelRepositoryRegistry
Searches the ApplicationContext for RecordProcessor beans and attempts to register them.
addClasspathModels(String) - Method in class org.oncoblocks.centromere.core.util.ModelRegistry
 
Alias - Annotation Type in org.oncoblocks.centromere.core.model
Allows the use of query string parameters, other than the model field's name to be used in web API query operations.
Aliases - Annotation Type in org.oncoblocks.centromere.core.model
Allows for a field to have multiple Alias annotations applied to it.
and(String) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
Attribute - Class in org.oncoblocks.centromere.core.model.support
Simple class for representing key-value attributes in other entity classes.
Attribute() - Constructor for class org.oncoblocks.centromere.core.model.support.Attribute
 
Attribute(String, String) - Constructor for class org.oncoblocks.centromere.core.model.support.Attribute
 
Attributes - Interface in org.oncoblocks.centromere.core.model.support
Interface for adding controller query methods to entity classes with key-value attributes.

B

BasicDataFileMetadata - Class in org.oncoblocks.centromere.core.model.support
Deprecated.
BasicDataFileMetadata() - Constructor for class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
BasicDataSetMetadata - Class in org.oncoblocks.centromere.core.model.support
Deprecated.
BasicDataSetMetadata() - Constructor for class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
BasicImportOptions - Class in org.oncoblocks.centromere.core.dataimport
Captures basic parameters required for a data import pipeline.
BasicImportOptions() - Constructor for class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
BasicImportOptions(Map<String, String>) - Constructor for class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
BasicImportOptions(ImportOptions) - Constructor for class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
between(Object, Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
betweenIncluding(Object, Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
build() - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 

C

cleanFilePath(String) - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileWriter
 
close() - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileReader
Closes the target file, if a reader exists.
close() - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileWriter
Flushes outstanding records to the output file and then closes the file and its writer object.
ComponentRegistry<T> - Interface in org.oncoblocks.centromere.core.util
API for a bean object that allows registering and looking-up beans with String aliases.
configure() - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
Performs configuration steps after bean creation.
configure() - Method in class org.oncoblocks.centromere.core.util.DataTypeProcessorRegistry
Configures the registry object and builds the object mappings.
configure() - Method in class org.oncoblocks.centromere.core.util.ModelRepositoryRegistry
Configures the registry object and builds the object mappings.
configureComponents() - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
Assigns options and metadata objects to the individual processing components that are expecting them.
configureComponents() - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
Performs any necessary component configuration steps before the processor executes the run method.
convert(String) - Method in class org.oncoblocks.centromere.core.util.JsonModelConverter
 
convert(Map<String, String>) - Method in class org.oncoblocks.centromere.core.util.KeyValueMapModelConverter
 
count(Iterable<QueryCriteria>) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Returns a count of all records that satify the requested criteria.
createQueryCriteria(Object) - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 

D

DatabaseCredentials - Interface in org.oncoblocks.centromere.core.dataimport
Defines basic connection information necessary for accessing a database.
DataFileMetadata<ID extends Serializable> - Interface in org.oncoblocks.centromere.core.model.support
Deprecated.
DataFileMetadataRepository<T extends DataFileMetadata<ID>,ID extends Serializable> - Interface in org.oncoblocks.centromere.core.repository.support
Deprecated.
DataImportComponent - Interface in org.oncoblocks.centromere.core.dataimport
Ensures that data import component classes have flexible setup and teardown methods that run before and after the main import methods.
DataImportException - Exception in org.oncoblocks.centromere.core.dataimport
Generic exception thrown when a data import component has an unresolvable problem.
DataImportException(String) - Constructor for exception org.oncoblocks.centromere.core.dataimport.DataImportException
 
DataSetMetadata<ID extends Serializable> - Interface in org.oncoblocks.centromere.core.model.support
Deprecated.
DataSetMetadataRepository<T extends DataSetMetadata<ID>,ID extends Serializable> - Interface in org.oncoblocks.centromere.core.repository.support
Deprecated.
DataTypeProcessorRegistry - Class in org.oncoblocks.centromere.core.util
Implementation of ComponentRegistry for mapping input file data types to their appropriate RecordProcessor beans.
DataTypeProcessorRegistry() - Constructor for class org.oncoblocks.centromere.core.util.DataTypeProcessorRegistry
 
DataTypeProcessorRegistry(ApplicationContext) - Constructor for class org.oncoblocks.centromere.core.util.DataTypeProcessorRegistry
 
DataTypes - Annotation Type in org.oncoblocks.centromere.core.dataimport
Identifies an annotated RecordProcessor as the primary handler of the specified data types.
DataTypeSupport - Interface in org.oncoblocks.centromere.core.dataimport
Implementing classes are expected to support specific data types, which can be defined in the class declaration with a DataTypes annotation, or at runtime with the defined methods.
distinct(String) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Returns a unsorted list of distinct values of the requested field.
distinct(String, Iterable<QueryCriteria>) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Returns a unsorted list of distinct values of the requested field, filtered using a QueryCriteria based query.
doAfter(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileReader
Calls the close method on the reader.
doAfter(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileWriter
Closes the open file writer.
doAfter(Object...) - Method in interface org.oncoblocks.centromere.core.dataimport.DataImportComponent
To be executed after the main component method is called for the last time.
doAfter(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
To be executed after the main component method is called for the last time.
doAfter(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.RecordCollectionReader
 
doAfter(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.RepositoryRecordUpdater
Deprecated.
To be executed after the main component method is called for the last time.
doAfter(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter
To be executed after the main component method is called for the last time.
doBefore(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileReader
Closes any open readers and opens the new target file.
doBefore(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileWriter
Opens a new output file for writing.
doBefore(Object...) - Method in interface org.oncoblocks.centromere.core.dataimport.DataImportComponent
To be executed before the main component method is first called.
doBefore(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
To be executed before the main component method is first called.
doBefore(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.RecordCollectionReader
 
doBefore(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.RepositoryRecordUpdater
Deprecated.
To be executed before the main component method is first called.
doBefore(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter
To be executed before the main component method is first called.

E

Evaluation - Enum in org.oncoblocks.centromere.core.repository
List of constants, representing database query evaluations, to be supported by each repository implementation.
exists(String) - Method in class org.oncoblocks.centromere.core.util.AbstractComponentRegistry
 
exists(T) - Method in class org.oncoblocks.centromere.core.util.AbstractComponentRegistry
 
exists(String) - Method in interface org.oncoblocks.centromere.core.util.ComponentRegistry
Tests to see if a mapping exists for the given keyword.
exists(T) - Method in interface org.oncoblocks.centromere.core.util.ComponentRegistry
Tests to see if a given object is mapped in the registry.
exists(Class<? extends Model>) - Method in class org.oncoblocks.centromere.core.util.ModelRepositoryRegistry
Tests to see if a Model has an RepositoryOperations bean registered.

F

Filterable - Annotation Type in org.oncoblocks.centromere.core.model
Allows field filtering during JSON serialization, XML marshalling, etc.
find(Iterable<QueryCriteria>) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Searches for all records that satisfy the requested criteria.
find(Iterable<QueryCriteria>, Sort) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Searches for all records that satisfy the requested criteria, and returns them in the requested order.
find(Iterable<QueryCriteria>, Pageable) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Searches for all records that satisfy the requested criteria, and returns them as a paged collection.
find(String) - Method in class org.oncoblocks.centromere.core.util.AbstractComponentRegistry
 
find(String) - Method in interface org.oncoblocks.centromere.core.util.ComponentRegistry
Returns the mapped object, given a keyword alias.
findByDataType(String) - Method in interface org.oncoblocks.centromere.core.repository.support.DataFileMetadataRepository
Deprecated.
 
findByFilePath(String) - Method in interface org.oncoblocks.centromere.core.repository.support.DataFileMetadataRepository
Deprecated.
 
findByLabel(String) - Method in interface org.oncoblocks.centromere.core.repository.support.DataSetMetadataRepository
Deprecated.
 
findByModel(Class<? extends Model>) - Method in class org.oncoblocks.centromere.core.util.ModelRepositoryRegistry
Returns all instances of RepositoryOperations beans that are associated with a particular Model class.
findByName(String) - Method in interface org.oncoblocks.centromere.core.repository.support.DataSetMetadataRepository
Deprecated.
 
findBySource(String) - Method in interface org.oncoblocks.centromere.core.repository.support.DataSetMetadataRepository
Deprecated.
 
ForeignKey - Annotation Type in org.oncoblocks.centromere.core.model
Marks a Model class field as being a foreign key identifier of another class.
ForeignKey.Relationship - Enum in org.oncoblocks.centromere.core.model
 
fromModelScan(ModelScan) - Static method in class org.oncoblocks.centromere.core.util.ModelRegistry
Creates a ModelRegistry instance, using a ModelScan annotation to supply Model classes or classpath locations to be registered.

G

GenericRecordProcessor<T extends Model<?>> - Class in org.oncoblocks.centromere.core.dataimport
Basic RecordProcessor implementation, which can be used to handle most file import jobs.
GenericRecordProcessor() - Constructor for class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
getAvailableQueryParameters(Class<? extends Model<?>>, boolean) - Static method in class org.oncoblocks.centromere.core.util.QueryParameterUtil
Returns all available query parameters for a given model, optionally including parameters of any related models, as inferred by the presence of ForeignKey annotations.
getAvailableQueryParameters(Class<? extends Model<?>>) - Static method in class org.oncoblocks.centromere.core.util.QueryParameterUtil
 
getBoolean(String) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
getDatabase() - Method in interface org.oncoblocks.centromere.core.dataimport.DatabaseCredentials
 
getDataFileId() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
getDataSet() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
getDataSetId() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
getDataType() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
getDataType() - Method in interface org.oncoblocks.centromere.core.model.support.DataFileMetadata
Deprecated.
 
getDescriptorFromAlias(Alias, Field) - Static method in class org.oncoblocks.centromere.core.util.QueryParameterUtil
Accepts an Alias annotation and a Field reference and returns a single QueryParameterDescriptor instance describing an acceptable query parameter.
getDescriptorsFromAliases(Aliases, Field) - Static method in class org.oncoblocks.centromere.core.util.QueryParameterUtil
Accepts an Aliases annotation and a Field reference and returns all of the QueryParameterDescriptor instances associated with the embedded Alias annotations.
getDescriptorsFromAliases(Aliases) - Static method in class org.oncoblocks.centromere.core.util.QueryParameterUtil
 
getEvaluation() - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria
 
getEvaluation() - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
getFieldDescriptors(Field) - Static method in class org.oncoblocks.centromere.core.util.QueryParameterUtil
Returns all valid query parameter descriptors from a given field, as defined by the default field name and available Alias and Aliases annotations.
getFieldName() - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
getFilePath() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
getFilePath() - Method in interface org.oncoblocks.centromere.core.model.support.DataFileMetadata
Deprecated.
 
getForeignKeyModelParameters(Class<? extends Model<?>>) - Static method in class org.oncoblocks.centromere.core.util.QueryParameterUtil
Returns a map of QueryParameterDescriptor instances for models related to the given Model, inferred by the presence of ForeignKey annotations.
getHost() - Method in interface org.oncoblocks.centromere.core.dataimport.DatabaseCredentials
 
getId() - Method in interface org.oncoblocks.centromere.core.model.Model
 
getId() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
getId() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
getImporter() - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
getImporter() - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
 
getImportOptions() - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
getKey() - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria
 
getLabel() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
getLabel() - Method in interface org.oncoblocks.centromere.core.model.support.DataSetMetadata
Deprecated.
 
getModel() - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
getModel() - Method in interface org.oncoblocks.centromere.core.model.ModelSupport
Returns the model class reference.
getModelQueryParameters(Class<? extends Model<?>>) - Static method in class org.oncoblocks.centromere.core.util.QueryParameterUtil
Returns a mapping of all of a given Model class's available query parameters.
getName() - Method in class org.oncoblocks.centromere.core.model.support.Attribute
 
getName() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
getName() - Method in interface org.oncoblocks.centromere.core.model.support.DataSetMetadata
Deprecated.
 
getName() - Method in class org.oncoblocks.centromere.core.model.support.SourcedAlias
 
getNotes() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
getOption(String) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
getOption(String) - Method in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
Returns the string value of the given option, if it exists.
getOptions() - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
getOptions() - Method in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
Returns all of the key-value option pairs in the object.
getParamName() - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
getPassword() - Method in interface org.oncoblocks.centromere.core.dataimport.DatabaseCredentials
 
getPort() - Method in interface org.oncoblocks.centromere.core.dataimport.DatabaseCredentials
 
getQueryableFieldType(Field) - Static method in class org.oncoblocks.centromere.core.util.QueryParameterUtil
Returns the type of the model field that the parameter argument will be converted to from a string.
getReader() - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileReader
 
getReader() - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
getReader() - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
 
getRegisteredComponents() - Method in class org.oncoblocks.centromere.core.util.AbstractComponentRegistry
 
getRegisteredComponents() - Method in interface org.oncoblocks.centromere.core.util.ComponentRegistry
Returns only the registered objects, without their keyword aliases.
getRegisteredComponents() - Method in class org.oncoblocks.centromere.core.util.ModelRegistry
 
getRegistry() - Method in class org.oncoblocks.centromere.core.util.AbstractComponentRegistry
 
getRegistry() - Method in interface org.oncoblocks.centromere.core.util.ComponentRegistry
Returns the entire Map of registered items.
getRepository() - Method in class org.oncoblocks.centromere.core.dataimport.RepositoryRecordUpdater
Deprecated.
 
getRepository() - Method in class org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter
 
getSource() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
getSource() - Method in interface org.oncoblocks.centromere.core.model.support.DataSetMetadata
Deprecated.
 
getSource() - Method in class org.oncoblocks.centromere.core.model.support.SourcedAlias
 
getSupportedDataTypes() - Method in interface org.oncoblocks.centromere.core.dataimport.DataTypeSupport
Returns all of the supported data type identifiers.
getSupportedDataTypes() - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
getTempDirectoryPath() - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
getType() - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
getUsername() - Method in interface org.oncoblocks.centromere.core.dataimport.DatabaseCredentials
 
getValidator() - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
getValidator() - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
 
getValue() - Method in class org.oncoblocks.centromere.core.model.support.Attribute
 
getValue() - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria
 
getWriter() - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileWriter
 
getWriter() - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
getWriter() - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
 
greaterThan(Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
greaterThanOrEqual(Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 

H

hasOption(String) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
hasOption(String) - Method in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
Tests whether the option is present in the object's key-value map.

I

Ignored - Annotation Type in org.oncoblocks.centromere.core.model
Marks a Model field as ignored when mapping query string parameters from HTTP requests and when documenting web services.
importFile(String) - Method in interface org.oncoblocks.centromere.core.dataimport.RecordImporter
Runs the data import on the specified temp file.
ImportOptions - Interface in org.oncoblocks.centromere.core.dataimport
Simple interface for allowing the passing of key-value string parameters between data import components.
ImportOptionsAware - Interface in org.oncoblocks.centromere.core.dataimport
Data import components that implement this interface are assumed to reference the BasicImportOptions for the containing data file or data set processing components.
in(Collection<Object>) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
insert(S) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Creates a new record in the repository and returns the updated model object.
insert(Iterable<S>) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Creates multiple new records and returns their updated representations.
is(Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
isFalse(Boolean) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
isNot(Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
isNull(Boolean) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
isSkipExistingFiles() - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
isSkipInvalidDataSets() - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
isSkipInvalidGenes() - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
isSkipInvalidMetadata() - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
isSkipInvalidRecords() - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
isSkipInvalidSamples() - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
isSupportedDataType(String) - Method in interface org.oncoblocks.centromere.core.dataimport.DataTypeSupport
Returns true if the implementing class supports the input data type identifier.
isSupportedDataType(String) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
isTrue(Boolean) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 

J

JsonModelConverter - Class in org.oncoblocks.centromere.core.util
Simple utility class for converting JSON into Model objects using Jackson.
JsonModelConverter(Class<? extends Model>) - Constructor for class org.oncoblocks.centromere.core.util.JsonModelConverter
 
JsonModelConverter(ObjectMapper, Class<? extends Model>) - Constructor for class org.oncoblocks.centromere.core.util.JsonModelConverter
 

K

KeyValueMapModelConverter - Class in org.oncoblocks.centromere.core.util
Simple utility class for converting key-value String maps into Model objects through a JSON intermediary, using Jackson.
KeyValueMapModelConverter(Class<? extends Model>) - Constructor for class org.oncoblocks.centromere.core.util.KeyValueMapModelConverter
 
KeyValueMapModelConverter(ObjectMapper, Class<? extends Model>) - Constructor for class org.oncoblocks.centromere.core.util.KeyValueMapModelConverter
 

L

lessThan(Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
lessThanOrEqual(Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
like(String) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 

M

Model<ID extends Serializable> - Interface in org.oncoblocks.centromere.core.model
Basic entity interface to ensure that model objects have identifiable attributes.
ModelRegistry - Class in org.oncoblocks.centromere.core.util
ComponentRegistry implementation for tracking all instances of Model classes in a given project.
ModelRegistry() - Constructor for class org.oncoblocks.centromere.core.util.ModelRegistry
 
ModelRepository - Annotation Type in org.oncoblocks.centromere.core.repository
Identifies the annotated class as a Repository and allows it to be referenced as the primary interface for the provided Model instance.
ModelRepositoryRegistry - Class in org.oncoblocks.centromere.core.util
Registers RepositoryOperations beans and associates them with their respective Model classes.
ModelRepositoryRegistry() - Constructor for class org.oncoblocks.centromere.core.util.ModelRepositoryRegistry
 
ModelRepositoryRegistry(ApplicationContext) - Constructor for class org.oncoblocks.centromere.core.util.ModelRepositoryRegistry
 
ModelScan - Annotation Type in org.oncoblocks.centromere.core.util
Annotation intended to be used in configuration classes to identify individual Model classes, or classpath locations of model classes, that will be used to generate a ModelRegistry instance that identifies and maps valid persisted models in the current context.
ModelSupport<T extends Model<?>> - Interface in org.oncoblocks.centromere.core.model
Ensures that component classes that support Model classes have accessible type definitions.

N

notIn(Collection<Object>) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
notLike(String) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
notNull(Boolean) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 

O

open(String) - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileReader
Opens the target file and creates a BufferedReader, which can be referenced via its getter method.
open(String) - Method in class org.oncoblocks.centromere.core.dataimport.AbstractRecordFileWriter
Creates or overwrites an output file, creates a FileWriter for writing records to the file.
org.oncoblocks.centromere.core.dataimport - package org.oncoblocks.centromere.core.dataimport
 
org.oncoblocks.centromere.core.model - package org.oncoblocks.centromere.core.model
 
org.oncoblocks.centromere.core.model.support - package org.oncoblocks.centromere.core.model.support
 
org.oncoblocks.centromere.core.repository - package org.oncoblocks.centromere.core.repository
 
org.oncoblocks.centromere.core.repository.support - package org.oncoblocks.centromere.core.repository.support
 
org.oncoblocks.centromere.core.util - package org.oncoblocks.centromere.core.util
 
outside(Object, Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
outsideIncluding(Object, Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 

Q

QueryCriteria - Class in org.oncoblocks.centromere.core.repository
Simple representation of a database query evaluation that can be passed to generic RepositoryOperations implementations.
QueryCriteria(String, Object, Evaluation) - Constructor for class org.oncoblocks.centromere.core.repository.QueryCriteria
 
QueryCriteria(String, Object) - Constructor for class org.oncoblocks.centromere.core.repository.QueryCriteria
 
QueryCriteriaBuilder - Class in org.oncoblocks.centromere.core.repository
TODO QueryCriteriaBuilder.where("symbol").is("AKT1").and("signal").between(3.0, 1.2).build();
QueryCriteriaBuilder(String) - Constructor for class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
QueryCriteriaBuilder() - Constructor for class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
QueryParameterDescriptor - Class in org.oncoblocks.centromere.core.repository
POJO that describes a model query parameter, used when reflecting Model classes and mapping HTTP requests to QueryCriteria.
QueryParameterDescriptor() - Constructor for class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
QueryParameterDescriptor(String, String, Class<?>, Evaluation) - Constructor for class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
QueryParameterException - Exception in org.oncoblocks.centromere.core.repository
Generic exception to alert mishandling of query parameter generation, mapping, conversion, or execution.
QueryParameterException() - Constructor for exception org.oncoblocks.centromere.core.repository.QueryParameterException
 
QueryParameterException(String) - Constructor for exception org.oncoblocks.centromere.core.repository.QueryParameterException
 
QueryParameterException(String, Throwable) - Constructor for exception org.oncoblocks.centromere.core.repository.QueryParameterException
 
QueryParameterException(Throwable) - Constructor for exception org.oncoblocks.centromere.core.repository.QueryParameterException
 
QueryParameterException(String, Throwable, boolean, boolean) - Constructor for exception org.oncoblocks.centromere.core.repository.QueryParameterException
 
QueryParameterUtil - Class in org.oncoblocks.centromere.core.util
TODO
QueryParameterUtil() - Constructor for class org.oncoblocks.centromere.core.util.QueryParameterUtil
 

R

readRecord() - Method in class org.oncoblocks.centromere.core.dataimport.RecordCollectionReader
 
readRecord() - Method in interface org.oncoblocks.centromere.core.dataimport.RecordReader
Generates and returns a single Model entity from the input data source.
RecordCollectionReader<T extends Model<?>> - Class in org.oncoblocks.centromere.core.dataimport
Simple RecordReader implementation that iterates through a collection if Model records, rather than reading from a data source.
RecordCollectionReader(List<T>) - Constructor for class org.oncoblocks.centromere.core.dataimport.RecordCollectionReader
 
RecordImporter - Interface in org.oncoblocks.centromere.core.dataimport
Data import component designed to take a temporary record file and import it directly into the database, via a specified utility (eg.
RecordProcessor<T extends Model<?>> - Interface in org.oncoblocks.centromere.core.dataimport
Record processors take all of the individual data import components (reader, writer, validator, and importer), and combines them to handle a single data type's import
RecordReader<T extends Model<?>> - Interface in org.oncoblocks.centromere.core.dataimport
Data impoer component class.
RecordWriter<T extends Model<?>> - Interface in org.oncoblocks.centromere.core.dataimport
Data import component class for writing imported Model records to a temporary file or RepositoryOperations implementation.
RepositoryOperations<T extends Model<ID>,ID extends Serializable> - Interface in org.oncoblocks.centromere.core.repository
Basic operations that all repositories must implement, regardless database technology used.
RepositoryRecordUpdater<T extends Model<ID>,ID extends Serializable> - Class in org.oncoblocks.centromere.core.dataimport
Deprecated.
RepositoryRecordUpdater(RepositoryOperations<T, ID>) - Constructor for class org.oncoblocks.centromere.core.dataimport.RepositoryRecordUpdater
Deprecated.
 
RepositoryRecordWriter<T extends Model<?>> - Class in org.oncoblocks.centromere.core.dataimport
Simple implementation of RecordWriter, that writes all records directly to the database using a RepositoryOperations implementation.
RepositoryRecordWriter(RepositoryOperations<T, ?>) - Constructor for class org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter
 
RepositoryRecordWriter(RepositoryOperations<T, ?>, RepositoryRecordWriter.WriteMode) - Constructor for class org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter
 
RepositoryRecordWriter.WriteMode - Enum in org.oncoblocks.centromere.core.dataimport
 
run(Object...) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
run(Object...) - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
Executes the pipeline and processes the input through the individual components.

S

setAlias(String) - Method in interface org.oncoblocks.centromere.core.model.support.SimpleAliases
 
setAlias(SourcedAlias) - Method in interface org.oncoblocks.centromere.core.model.support.SourcedAliases
 
setAliasName(String) - Method in interface org.oncoblocks.centromere.core.model.support.SourcedAliases
 
setAliasSource(String) - Method in interface org.oncoblocks.centromere.core.model.support.SourcedAliases
 
setApplicationContext(ApplicationContext) - Method in class org.oncoblocks.centromere.core.util.DataTypeProcessorRegistry
 
setApplicationContext(ApplicationContext) - Method in class org.oncoblocks.centromere.core.util.ModelRepositoryRegistry
 
setAttribute(Attribute) - Method in interface org.oncoblocks.centromere.core.model.support.Attributes
 
setAttributeName(String) - Method in interface org.oncoblocks.centromere.core.model.support.Attributes
 
setAttributeValue(String) - Method in interface org.oncoblocks.centromere.core.model.support.Attributes
 
setDataFileId(Object) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
setDataSet(DataSetMetadata) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
setDataSetId(Object) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
setDataType(String) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
setEvaluation(Evaluation) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria
 
setEvaluation(Evaluation) - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
setFieldName(String) - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
setFilePath(String) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
setId(String) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
setId(String) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
setImporter(RecordImporter) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
setImporter(RecordImporter) - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
 
setImportOptions(ImportOptions) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
setImportOptions(BasicImportOptions) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
setImportOptions(ImportOptions) - Method in interface org.oncoblocks.centromere.core.dataimport.ImportOptionsAware
 
setKey(String) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria
 
setLabel(String) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
setModel(Class<T>) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
setName(String) - Method in class org.oncoblocks.centromere.core.model.support.Attribute
 
setName(String) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
setName(String) - Method in class org.oncoblocks.centromere.core.model.support.SourcedAlias
 
setNotes(String) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
setOption(String, String) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
setOptions(Map<String, String>) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
setParamName(String) - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
setReader(RecordReader<T>) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
setReader(RecordReader<T>) - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
 
setRegistry(Map<String, T>) - Method in class org.oncoblocks.centromere.core.util.AbstractComponentRegistry
 
setRegistry(Map<String, T>) - Method in interface org.oncoblocks.centromere.core.util.ComponentRegistry
Sets the registry mappings, given a supplied Map of keyword-object mappings.
setSkipExistingFiles(boolean) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
setSkipInvalidDataSets(boolean) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
setSkipInvalidGenes(boolean) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
setSkipInvalidMetadata(boolean) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
setSkipInvalidRecords(boolean) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
setSkipInvalidSamples(boolean) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
setSource(String) - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
setSource(String) - Method in class org.oncoblocks.centromere.core.model.support.SourcedAlias
 
setSupportedDataTypes(Iterable<String>) - Method in interface org.oncoblocks.centromere.core.dataimport.DataTypeSupport
Sets all of the supported data type identifiers.
setSupportedDataTypes(Iterable<String>) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
setTempDirectoryPath(String) - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
setType(Class<?>) - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 
setValidator(Validator) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
setValidator(Validator) - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
 
setValue(String) - Method in class org.oncoblocks.centromere.core.model.support.Attribute
 
setValue(Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria
 
setWriter(RecordWriter<T>) - Method in class org.oncoblocks.centromere.core.dataimport.GenericRecordProcessor
 
setWriter(RecordWriter<T>) - Method in interface org.oncoblocks.centromere.core.dataimport.RecordProcessor
 
SimpleAliases - Interface in org.oncoblocks.centromere.core.model.support
 
SKIP_EXISTING_FILES - Static variable in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
 
SKIP_INVALID_DATA_SETS - Static variable in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
 
SKIP_INVALID_GENES - Static variable in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
 
SKIP_INVALID_METADATA - Static variable in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
 
SKIP_INVALID_RECORDS - Static variable in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
 
SKIP_INVALID_SAMPLES - Static variable in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
 
SourcedAlias - Class in org.oncoblocks.centromere.core.model.support
Simple representation of alias names for embedding in other entities.
SourcedAlias() - Constructor for class org.oncoblocks.centromere.core.model.support.SourcedAlias
 
SourcedAlias(String, String) - Constructor for class org.oncoblocks.centromere.core.model.support.SourcedAlias
 
SourcedAliases - Interface in org.oncoblocks.centromere.core.model.support
Interface for adding controller query methods to entity classes with key-value aliases.

T

TEMP_DIRECTORY_PATH - Static variable in interface org.oncoblocks.centromere.core.dataimport.ImportOptions
 
toString() - Method in class org.oncoblocks.centromere.core.dataimport.BasicImportOptions
 
toString() - Method in class org.oncoblocks.centromere.core.model.support.Attribute
 
toString() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataFileMetadata
Deprecated.
 
toString() - Method in class org.oncoblocks.centromere.core.model.support.BasicDataSetMetadata
Deprecated.
 
toString() - Method in class org.oncoblocks.centromere.core.model.support.SourcedAlias
 
toString() - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria
 
toString() - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor
 

U

update(S) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Updates an existing record in the repository and returns its instance.
update(Iterable<S>) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations
Updates multiple records and returns their instances.

V

valueOf(String) - Static method in enum org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter.WriteMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.oncoblocks.centromere.core.model.ForeignKey.Relationship
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.oncoblocks.centromere.core.repository.Evaluation
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter.WriteMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.oncoblocks.centromere.core.model.ForeignKey.Relationship
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.oncoblocks.centromere.core.repository.Evaluation
Returns an array containing the constants of this enum type, in the order they are declared.

W

where(String) - Static method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder
 
writeRecord(T) - Method in interface org.oncoblocks.centromere.core.dataimport.RecordWriter
Writes a single Model entity to the target destination.
writeRecord(T) - Method in class org.oncoblocks.centromere.core.dataimport.RepositoryRecordUpdater
Deprecated.
Writes the input Model record to the target RepositoryOperations implementation, using an update operation.
writeRecord(T) - Method in class org.oncoblocks.centromere.core.dataimport.RepositoryRecordWriter
Writes the input Model record to the target RepositoryOperations implementation, using the appropriate operation.
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