A B C D E F G H I J L M N O P Q R S T U V W

A

AbstractRecordFileReader<T extends Model<?>> - Class in org.oncoblocks.centromere.core.dataimport.component

Simple abstract implementation of RecordReader, for reading input files.

AbstractRecordFileReader() - Constructor for class org.oncoblocks.centromere.core.dataimport.component.AbstractRecordFileReader

AbstractRecordFileWriter<T extends Model<?>> - Class in org.oncoblocks.centromere.core.dataimport.component

Basic abstract implementation of RecordWriter, for writing records to temp files.

AbstractRecordFileWriter() - Constructor for class org.oncoblocks.centromere.core.dataimport.component.AbstractRecordFileWriter

addDataSet(DataSetMetadata) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetManager

Adds or overwrites a DataSetMetadata record to the internal map.

addDataSets(Iterable<DataSetMetadata>) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetManager

Adds or overwrites multiple DataSetMetadata records to the map.

addDataType(DataType) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataTypeManager

Adds a data type mapping, overwriting existing ones with the same name.

addDataTypes(Iterable<DataType>) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataTypeManager

Adds multiple data type mappings at once.

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

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

checkImportOptions() - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

close() - Method in class org.oncoblocks.centromere.core.dataimport.component.AbstractRecordFileReader

Closes the target file, if a reader exists.

close() - Method in class org.oncoblocks.centromere.core.dataimport.component.AbstractRecordFileWriter

Flushes outstanding records to the output file and then closes the file and its writer object.

configurationCheck() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

Checks that all necessary configurations have taken place place before the import job runs.

configureDataSetManager() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

configureDataTypeManager() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

Creates and populates a DataTypeManager to handle mapping data types to RecordProcessor beans.

count() - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations

Returns a count of total records in the repository.

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.component

Defines basic connection information necessary for accessing a database.

DataImportException - Exception in org.oncoblocks.centromere.core.dataimport.component

Generic exception thrown when a data import component has an unresolvable problem.

DataImportException(String) - Constructor for exception org.oncoblocks.centromere.core.dataimport.component.DataImportException

DataSetAware - Interface in org.oncoblocks.centromere.core.dataimport.pipeline

Data import components that implement this interface are assumed to have the identifier of the currently processed data set assigned to them, for annotating processed records.

DataSetManager - Class in org.oncoblocks.centromere.core.dataimport.pipeline

Helper class for ImportJobRunner, which stores and retrieves references to DataSetMetadata for the current pipeline job.

DataSetManager() - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetManager

DataSetManager(Iterable<DataSetMetadata>) - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetManager

DataSetMetadata - Class in org.oncoblocks.centromere.core.dataimport.pipeline

Simple representation of a data set being processed and imported into the warehouse.

DataSetMetadata() - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetMetadata

DataType - Class in org.oncoblocks.centromere.core.dataimport.pipeline

Simple POJO that maps a user-defined data type name to a RecordProcessor bean and an instance of ImportOptions to dictate job parameters.

DataType() - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.DataType

DataType(String, String) - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.DataType

DataType(String, String, ImportOptions) - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.DataType

DataTypeManager - Class in org.oncoblocks.centromere.core.dataimport.pipeline

Simple object that handles mapping of user-defined data types to RecordProcessor beans, as defined by DataType instances.

DataTypeManager() - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.DataTypeManager

DataTypeManager(Iterable<DataType>) - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.DataTypeManager

DataTypeManager(DataType...) - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.DataTypeManager

DataTypes - Annotation Type in org.oncoblocks.centromere.core.dataimport.component

Identifies an annotated RecordProcessor as the primary handler of the specified data types.

delete(ID) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations

Deletes a record in the repository, identified by its ID.

deleteAll() - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations

Deletes every record in the repository.

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() - Method in class org.oncoblocks.centromere.core.dataimport.component.AbstractRecordFileReader

Calls the close method on the reader.

doAfter() - Method in class org.oncoblocks.centromere.core.dataimport.component.AbstractRecordFileWriter

Closes the open file writer.

doAfter() - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

RecordProcessor.doAfter()

doAfter() - Method in interface org.oncoblocks.centromere.core.dataimport.component.RecordProcessor

Executes after the run method.

doAfter() - Method in interface org.oncoblocks.centromere.core.dataimport.component.RecordReader

To be executed after the last readRecord call.

doAfter() - Method in interface org.oncoblocks.centromere.core.dataimport.component.RecordWriter

Executes after the last writeRecord call.

doAfter() - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordUpdater

Performs no action.

doAfter() - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordWriter

Performs no action.

doBefore(String) - Method in class org.oncoblocks.centromere.core.dataimport.component.AbstractRecordFileReader

Closes any open readers and opens the new target file.

doBefore(String) - Method in class org.oncoblocks.centromere.core.dataimport.component.AbstractRecordFileWriter

Opens a new output file for writing.

doBefore() - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

RecordProcessor.doBefore()

doBefore() - Method in interface org.oncoblocks.centromere.core.dataimport.component.RecordProcessor

Executes before the run method.

doBefore(String) - Method in interface org.oncoblocks.centromere.core.dataimport.component.RecordReader

To be executed before the readRecord method is called.

doBefore(String) - Method in interface org.oncoblocks.centromere.core.dataimport.component.RecordWriter

Executes before the first writeRecord method call.

doBefore(String) - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordUpdater

Performs no action.

doBefore(String) - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordWriter

Performs no action.

E

Evaluation - Enum in org.oncoblocks.centromere.core.repository

List of constants, representing database query evaluations, to be supported by each repository implementation.

exists(ID) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations

Tests whether or not a record with the given ID exists in the repository.

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.

findAll() - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations

Retrieves all records from the repository.

findAll(Sort) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations

Retrieves all records from the repository, sorted into the desired order.

findAll(Pageable) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations

Retrieves a paged representation of every records in the repository.

findOne(ID) - Method in interface org.oncoblocks.centromere.core.repository.RepositoryOperations

Retrieves a single record by it's ID.

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

G

GenericRecordProcessor<T extends Model<?>> - Class in org.oncoblocks.centromere.core.dataimport.component

Basic RecordProcessor implementation, which can be used to handle most file import jobs.

GenericRecordProcessor() - Constructor for class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

GenericRecordProcessor(RecordReader<T>, Validator, RecordWriter<T>, RecordImporter, ImportOptions) - Constructor for class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

getApplicationContext() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

getBoolean(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportOptions

getDatabase() - Method in interface org.oncoblocks.centromere.core.dataimport.component.DatabaseCredentials

getDataSet() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.InputFile

getDataSetByName(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetManager

Retireves a DataSetMetadata record by name, as stored in the internal map.

getDataSetId() - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

getDataSetId(DataSetMetadata, InputFile) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

Returns a data set identifier based upon its DataSetMetadata reference.

getDataSetManager() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

getDataSets() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

getDataType() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.InputFile

getDataTypeManager() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

getDataTypes() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

getEvaluation() - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria

getEvaluation() - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor

getFieldName() - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor

getFiles() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

getHost() - Method in interface org.oncoblocks.centromere.core.dataimport.component.DatabaseCredentials

getId() - Method in interface org.oncoblocks.centromere.core.model.Model

getImporter() - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

getImportJob() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

getImportOptions() - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

getKey() - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria

getLogger() - Static method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

getName() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetMetadata

getName() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataType

getName() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

getName() - Method in class org.oncoblocks.centromere.core.model.support.Attribute

getName() - Method in class org.oncoblocks.centromere.core.model.support.SourcedAlias

getNotes() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetMetadata

getNotes() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

getOptions() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataType

getOptions() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

getOptions() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.InputFile

getOptionsMap() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportOptions

getParamName() - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor

getPassword() - Method in interface org.oncoblocks.centromere.core.dataimport.component.DatabaseCredentials

getPath() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.InputFile

getPort() - Method in interface org.oncoblocks.centromere.core.dataimport.component.DatabaseCredentials

getProcessor() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataType

getProcessorByDataType(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataTypeManager

Returns reference to a RecordProcessor bean class, if one of that type has been mapped to a data set.

getProcessorInstanceByDataType(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

Returns reference to existing RecordProcessor bean, given an associated data type.

getReader() - Method in class org.oncoblocks.centromere.core.dataimport.component.AbstractRecordFileReader

getReader() - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

getRepository() - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordUpdater

getRepository() - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordWriter

getSource() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetMetadata

getSource() - Method in class org.oncoblocks.centromere.core.model.support.SourcedAlias

getString(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportOptions

getType() - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor

getUsername() - Method in interface org.oncoblocks.centromere.core.dataimport.component.DatabaseCredentials

getValidator() - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

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.component.AbstractRecordFileWriter

getWriter() - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

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.pipeline.ImportOptions

I

Ignored - Annotation Type in org.oncoblocks.centromere.core.model

Marks a Model field as ignored when mapping query string parameters from HTTP requests.

importFile(String) - Method in interface org.oncoblocks.centromere.core.dataimport.component.RecordImporter

Runs the data import on the specified temp file.

ImportJob - Class in org.oncoblocks.centromere.core.dataimport.pipeline

Simple POJO representation of an import job configuration.

ImportJob() - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

ImportJobRunner - Class in org.oncoblocks.centromere.core.dataimport.pipeline

Configures and runs a data import job, as defined by a ImportJob object.

ImportJobRunner() - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

ImportJobRunner(ApplicationContext) - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

ImportOptions - Class in org.oncoblocks.centromere.core.dataimport.pipeline

Captures basic parameters required for a data import pipeline.

ImportOptions() - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.ImportOptions

ImportOptions(Map<String, String>) - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.ImportOptions

ImportOptionsAware - Interface in org.oncoblocks.centromere.core.dataimport.pipeline

Data import components that implement this interface are assumed to reference the ImportOptions for the containing data file or data set processing components.

in(Collection<Object>) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder

InputFile - Class in org.oncoblocks.centromere.core.dataimport.pipeline

Simple representation of a file to be imported.

InputFile() - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.InputFile

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

isSupportedDataType(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataTypeManager

Tests whether a data type mapping has been registered.

isTrue(Boolean) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder

J

JobFileParser - Interface in org.oncoblocks.centromere.core.dataimport.pipeline

Interface for classes that parse a job-description file and output an ImportJob object.

jobSetup() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

Runs the required configuration before the import job executes.

JsonJobFileParser - Class in org.oncoblocks.centromere.core.dataimport.pipeline

Converts a JSON-formatted job description file and returns an ImportJob object.

JsonJobFileParser() - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.JsonJobFileParser

JsonJobFileParser(ObjectMapper) - Constructor for class org.oncoblocks.centromere.core.dataimport.pipeline.JsonJobFileParser

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

mergeImportOptions(ImportOptions, ImportOptions) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

Merges the data set-level ImportOptions with the file-level options.

Model<ID extends Serializable> - Interface in org.oncoblocks.centromere.core.model

Basic entity interface to ensure that model objects have identifiable attributes.

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.

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.component.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.component.AbstractRecordFileWriter

Creates or overwrites an output file, creates a FileWriter for writing records to the file.

org.oncoblocks.centromere.core.dataimport.component - package org.oncoblocks.centromere.core.dataimport.component

org.oncoblocks.centromere.core.dataimport.pipeline - package org.oncoblocks.centromere.core.dataimport.pipeline

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

outside(Object, Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder

outsideIncluding(Object, Object) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteriaBuilder

P

parseJobFile(String) - Method in interface org.oncoblocks.centromere.core.dataimport.pipeline.JobFileParser

Reads an input file and converts its contents to an ImportJob object.

parseJobFile(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.JsonJobFileParser

JobFileParser.parseJobFile(String)

processDataSet(DataSetMetadata, InputFile) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

Processes the current data set record.

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

R

readRecord() - Method in interface org.oncoblocks.centromere.core.dataimport.component.RecordReader

Generates and returns a single Model entity from the input data source.

RecordImporter - Interface in org.oncoblocks.centromere.core.dataimport.component

Data import component designed to take a temporary record file and import it directly into the database, via a specified utility (eg.

RecordProcessor - Interface in org.oncoblocks.centromere.core.dataimport.component

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.component

Data impoer component class.

RecordWriter<T extends Model<?>> - Interface in org.oncoblocks.centromere.core.dataimport.component

Data import component class for writing imported Model records to a temporary file or RepositoryOperations implementation.

RepositoryOperations<T,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.component

Simple implementation of RecordWriter, that updates existing database records using a RepositoryOperations implementation.

RepositoryRecordUpdater() - Constructor for class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordUpdater

RepositoryRecordUpdater(RepositoryOperations<T, ID>) - Constructor for class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordUpdater

RepositoryRecordWriter<T extends Model<?>> - Class in org.oncoblocks.centromere.core.dataimport.component

Simple implementation of RecordWriter, that writes all records directly to the database using a RepositoryOperations implementation.

RepositoryRecordWriter() - Constructor for class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordWriter

RepositoryRecordWriter(RepositoryOperations<T, ?>) - Constructor for class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordWriter

run(String) - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

RecordProcessor.run(String)

run(String) - Method in interface org.oncoblocks.centromere.core.dataimport.component.RecordProcessor

Executes the pipeline and processes the input through the individual components.

runImport() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

Executes the import pipeline and processes all of the files in the ImportJob.

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.dataimport.pipeline.ImportJobRunner

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

setDataSet(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.InputFile

setDataSetId(Object) - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

setDataSetId(Object) - Method in interface org.oncoblocks.centromere.core.dataimport.pipeline.DataSetAware

setDataSets(List<DataSetMetadata>) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

setDataType(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.InputFile

setDataTypes(List<DataType>) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

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

setFiles(List<InputFile>) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

setImporter(RecordImporter) - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

setImportJob(ImportJob) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

setImportOptions(ImportOptions) - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

setImportOptions(ImportOptions) - Method in interface org.oncoblocks.centromere.core.dataimport.pipeline.ImportOptionsAware

setKey(String) - Method in class org.oncoblocks.centromere.core.repository.QueryCriteria

setName(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetMetadata

setName(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataType

setName(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

setName(String) - Method in class org.oncoblocks.centromere.core.model.support.Attribute

setName(String) - Method in class org.oncoblocks.centromere.core.model.support.SourcedAlias

setNotes(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetMetadata

setNotes(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

setObjectMapper(ObjectMapper) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.JsonJobFileParser

setOption(String, String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportOptions

setOptions(ImportOptions) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataType

setOptions(Map<String, String>) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJob

setOptions(Map<String, String>) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportOptions

setOptions(Map<String, String>) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.InputFile

setParamName(String) - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor

setPath(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.InputFile

setProcessor(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataType

setReader(RecordReader<T>) - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

setRepository(RepositoryOperations<T, ID>) - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordUpdater

setRepository(RepositoryOperations<T, ?>) - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordWriter

setSource(String) - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.DataSetMetadata

setSource(String) - Method in class org.oncoblocks.centromere.core.model.support.SourcedAlias

setType(Class<?>) - Method in class org.oncoblocks.centromere.core.repository.QueryParameterDescriptor

setValidator(Validator) - Method in class org.oncoblocks.centromere.core.dataimport.component.GenericRecordProcessor

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.component.GenericRecordProcessor

SimpleAliases - Interface in org.oncoblocks.centromere.core.model.support

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

toString() - Method in class org.oncoblocks.centromere.core.model.support.Attribute

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

validateImportJob() - Method in class org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

Checks that the submitted ImportJob object contains all the required components.

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.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.component.RecordWriter

Writes a single Model entity to the target destination.

writeRecord(T) - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordUpdater

Writes the input Model record to the target RepositoryOperations implementation, using an update operation.

writeRecord(T) - Method in class org.oncoblocks.centromere.core.dataimport.component.RepositoryRecordWriter

Writes the input Model record to the target RepositoryOperations implementation, using an insert operation.

A B C D E F G H I J L M N O P Q R S T U V W