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A

and(Condition...) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
and(Conditions...) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 

C

ComplexTableDescription - Class in org.oncoblocks.centromere.sql.sqlbuilder
Based on TableDescription, with some modifications and additions.
ComplexTableDescription(String, List<String>, String, String, String) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
ComplexTableDescription(String, List<String>, String, String) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
ComplexTableDescription(String, List<String>, String) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
ComplexTableDescription(String, List<String>) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
ComplexTableDescription(String) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
Condition - Class in org.oncoblocks.centromere.sql.sqlbuilder
Maps a QueryCriteria to SQL operations.
Condition(String, Object, Evaluation) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.Condition
 
Conditions - Class in org.oncoblocks.centromere.sql.sqlbuilder
Wraps a series of conditions and joins them with AND/OR operators
Conditions(Conditions.Operation, Condition...) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.Conditions
 
Conditions(Conditions.Operation, Conditions...) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.Conditions
 
Conditions.Operation - Enum in org.oncoblocks.centromere.sql.sqlbuilder
 
count() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
count(Iterable<QueryCriteria>) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository

D

delete(Iterable<? extends T>) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
CrudRepository.delete(Iterable)
delete(T) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
CrudRepository.delete(Object)
delete(ID) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
CrudRepository.delete(ID)
delete() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
deleteAll() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
CrudRepository.deleteAll()
distinct(String) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
TODO
distinct(String, Iterable<QueryCriteria>) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
TODO
doAfter(Object...) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileImporter
 
doBefore(Object...) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileImporter
 

E

equal(String, Object) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
exists(ID) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
CrudRepository.exists(ID)

F

find(Iterable<QueryCriteria>) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
PagingAndSortingRepository.findAll(org.springframework.data.domain.Sort)
find(Iterable<QueryCriteria>, Sort) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
PagingAndSortingRepository.findAll(org.springframework.data.domain.Sort)
find(Iterable<QueryCriteria>, Pageable) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
PagingAndSortingRepository.findAll(org.springframework.data.domain.Sort)
findAll() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
PagingAndSortingRepository.findAll(org.springframework.data.domain.Sort)
findAll(Sort) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
PagingAndSortingRepository.findAll(org.springframework.data.domain.Sort)
findAll(Pageable) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
PagingAndSortingRepository.findAll(org.springframework.data.domain.Sort)
findAll(Iterable<ID>) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
CrudRepository.findAll(Iterable)
findOne(ID) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
CrudRepository.findOne(ID)
from(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 

G

GenericJdbcRepository<T extends Model<ID>,ID extends Serializable> - Class in org.oncoblocks.centromere.sql
Generic implementation of RepositoryOperations, designed for use with a SqlBuilder that generates SQL queries to be executed in a JdbcTemplate.
GenericJdbcRepository(DataSource, ComplexTableDescription, RowMapper<T>, RowUnmapper<T>) - Constructor for class org.oncoblocks.centromere.sql.GenericJdbcRepository
Creates a new repository instance using a DataSource to generate a new JdbcTemplate, a ComplexTableDescription used to create a SqlBuilder for query generation, a RowMapper for mapping database records to Model objects, and a RowUnmapper for mapping model objects back to database records.
GenericJdbcRepository(DataSource, ComplexTableDescription, RowMapper<T>, RowUnmapper<T>, Class<T>) - Constructor for class org.oncoblocks.centromere.sql.GenericJdbcRepository
 
GenericJdbcRepository(DataSource, ComplexTableDescription, RowMapper<T>) - Constructor for class org.oncoblocks.centromere.sql.GenericJdbcRepository
Creates a new repository instance using the default constructor, but with a MissingRowUnmapper to enforce read-only functionality.
getClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.Condition
 
getConditionFromQueryCriteria(QueryCriteria) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
Creates a Condition instance from a QueryCriteria search parameter for use in SQL query generation.
getDeleteClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
getDelimiter() - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
getEnclosedBy() - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
getEscapedBy() - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
getFromClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
getFromClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
getGroupByClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
getGroupByClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
getIdColumns() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
getIgnoredFields() - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
getInsertClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
getJdbcTemplate() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
 
getLimitClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
getModel() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
Returns the model class reference.
getOperation() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.Conditions
 
getOrderByClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
getQueryParameterValues() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
getRowMapper() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
 
getRowUnmapper() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
 
getSelectClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
getSelectClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
getSql() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.Conditions
 
getSqlBuilder() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
Creates a new SqlBuilder instance.
getTableDescription() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
 
getTableName() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
getTerminatedBy() - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
getUpdateClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
getValue() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.Condition
 
getValues() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.Conditions
 
getWhereClause() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
groupBy(String...) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 

I

idToObjectList(ID) - Static method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
Converts an ID instance into a collection of objects.
importFile(String) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileImporter
 
in(String, Object[]) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
insert(S) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
insert(Iterable<S>) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
insert(Map<String, Object>) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
isNull(String) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 

L

limit(Integer, Integer) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
limit(Integer) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
limit(Pageable) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 

M

MySqlImportTempFileImporter - Class in org.oncoblocks.centromere.sql
 
MySqlImportTempFileImporter(DatabaseCredentials, String) - Constructor for class org.oncoblocks.centromere.sql.MySqlImportTempFileImporter
 
MySqlImportTempFileImporter(DatabaseCredentials) - Constructor for class org.oncoblocks.centromere.sql.MySqlImportTempFileImporter
 
MySqlImportTempFileWriter<T extends Model<?>> - Class in org.oncoblocks.centromere.sql
Writes entities to a delimited-text file for import via mysqlimport utility.
MySqlImportTempFileWriter() - Constructor for class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 

N

notEqual(String, Object) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
notIn(String, Object[]) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
notNull(String) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 

O

or(Condition...) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
or(Conditions...) - Static method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
orderBy(Sort) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
orderBy(Sort.Order...) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
orderBy(String, Sort.Direction) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
orderBy(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
org.oncoblocks.centromere.sql - package org.oncoblocks.centromere.sql
 
org.oncoblocks.centromere.sql.sqlbuilder - package org.oncoblocks.centromere.sql.sqlbuilder
 

S

save(Iterable<S>) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
CrudRepository.save(Iterable)
save(S) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
CrudRepository.save(Object) )}
select(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
setDelimiter(String) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
setDropCollection(boolean) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileImporter
 
setEnclosedBy(String) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
setEscapedBy(String) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
setFromClause(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
setFromClause(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
setGroupByClause(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
setGroupByClause(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
setIdColumns(List<String>) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
setIgnoredFields(List<String>) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
setLimitClause(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
setOrderByClause(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
setSelectClause(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
setSelectClause(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
setStopOnError(boolean) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileImporter
 
setTableName(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.ComplexTableDescription
 
setTerminatedBy(String) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
setWhereClause(String) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
SqlBuilder - Class in org.oncoblocks.centromere.sql.sqlbuilder
Uses basic table and query definitions set in ComplexTableDescription to generate SQL queries that can be executed in a JdbcTemplate, or by another SQL execution method.
SqlBuilder(ComplexTableDescription) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
SqlBuilder(String) - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
SqlBuilder() - Constructor for class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 

T

toSql() - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
truncateTable() - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
Truncates the target table, dropping all records.

U

update(S) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
update(Iterable<S>) - Method in class org.oncoblocks.centromere.sql.GenericJdbcRepository
update(Map<String, Object>) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 

V

valueOf(String) - Static method in enum org.oncoblocks.centromere.sql.sqlbuilder.Conditions.Operation
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.oncoblocks.centromere.sql.sqlbuilder.Conditions.Operation
Returns an array containing the constants of this enum type, in the order they are declared.

W

where(Conditions) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
where(Condition) - Method in class org.oncoblocks.centromere.sql.sqlbuilder.SqlBuilder
 
writeRecord(T) - Method in class org.oncoblocks.centromere.sql.MySqlImportTempFileWriter
 
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