Index (Corpus Storage System 1.6.2 API)

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

A

addFieldConfiguration(FieldConfig) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Classes for query()
addPKAdaptedFieldConfiguration(List<Map<String, String>>, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
addPKAdaptedFieldConfiguration(List<Map<String, String>>, String, String, List<Map<String, String>>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
addXmiAnnotationFieldConfiguration(List<Map<String, String>>, boolean) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Deprecated.
JeDIS does not store annotations in columns to the primary document table.
addXmiDocumentFieldConfiguration(List<Map<String, String>>, boolean) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Adds an auto-generated field configuration that exhibits the given primary key and all the fields required to store complete XMI document data (i.e.
addXmiTextFieldConfiguration(List<Map<String, String>>, List<Map<String, String>>, boolean) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Adds an auto-generated field configuration that exhibits the given primary key and all the fields required to store XMI base document data (i.e.
assureColumnsExist(String, List<String>, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Checks if the given columns exist with the given data type.
AUTO_ID_FIELD_NAME - Static variable in class de.julielab.costosys.Constants

B

backgroundThread - Variable in class de.julielab.costosys.dbconnection.DBCThreadedIterator
baseOutDirStr - Variable in class de.julielab.costosys.cli.QueryOptions
batchSizeStr - Variable in class de.julielab.costosys.cli.QueryOptions
BinaryDataHandler - Class in de.julielab.costosys.cli
BinaryDataHandler(DataBaseConnector, String, Set<String>, List<File>) - Constructor for class de.julielab.costosys.cli.BinaryDataHandler

C

checkTableDefinition(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Checks whether the given table matches the active table schema.
checkTableDefinition(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Compares the actual table in the database with its definition in the xml configuration
Note: This method currently does not check other then primary key columns for tables that reference another table, even if those should actually be data tables.
checkTableHasSchemaColumns(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Checks if the given table has at least the columns defined in the given schema.
checkTableSchemaCompatibility(String...) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
checkTableSchemaCompatibility(String, String[]) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
CLI - Class in de.julielab.costosys.cli: Command line interface for interaction with a databases holding e.g.
CLI() - Constructor for class de.julielab.costosys.cli.CLI
CliOptionsProvider - Class in de.julielab.costosys.cli
CliOptionsProvider() - Constructor for class de.julielab.costosys.cli.CliOptionsProvider
close() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
close() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
close() - Method in class de.julielab.costosys.dbconnection.DBCIterator: Frees resources occupied by this iterator (e.g.
close() - Method in class de.julielab.costosys.dbconnection.DBCThreadedIterator
close() - Method in class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
close() - Method in class de.julielab.costosys.dbconnection.ThreadedColumnsToRetrieveIterator
closeConnection() - Method in interface de.julielab.costosys.dbconnection.ConnectionClosable
closeConnection() - Method in class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
COLUMN_FILENAME - Static variable in class de.julielab.costosys.medline.PMCUpdater
COLUMN_FILENAME - Static variable in class de.julielab.costosys.medline.PubmedUpdater
COLUMN_IS_IMPORTED - Static variable in class de.julielab.costosys.medline.PMCUpdater
COLUMN_IS_IMPORTED - Static variable in class de.julielab.costosys.medline.PubmedUpdater
COLUMN_TIMESTAMP - Static variable in class de.julielab.costosys.medline.PMCUpdater
COLUMN_TIMESTAMP - Static variable in class de.julielab.costosys.medline.PubmedUpdater
commit() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
ConfigBase - Class in de.julielab.costosys.configuration
ConfigBase() - Constructor for class de.julielab.costosys.configuration.ConfigBase
ConfigReader - Class in de.julielab.costosys.configuration: This class reads an xml configuration file, containing the definition of a database connection and the fields used in the database.
ConfigReader(InputStream) - Constructor for class de.julielab.costosys.configuration.ConfigReader
ConfigurationConstants - Class in de.julielab.costosys.medline
ConfigurationNotFoundException - Exception in de.julielab.costosys.cli
ConfigurationNotFoundException() - Constructor for exception de.julielab.costosys.cli.ConfigurationNotFoundException
ConfigurationNotFoundException(String) - Constructor for exception de.julielab.costosys.cli.ConfigurationNotFoundException
ConfigurationNotFoundException(String, Throwable) - Constructor for exception de.julielab.costosys.cli.ConfigurationNotFoundException
ConfigurationNotFoundException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.costosys.cli.ConfigurationNotFoundException
ConfigurationNotFoundException(Throwable) - Constructor for exception de.julielab.costosys.cli.ConfigurationNotFoundException
configure(HierarchicalConfiguration<ImmutableNode>) - Method in class de.julielab.costosys.medline.ElasticSearchDocumentDeleter
configure(HierarchicalConfiguration<ImmutableNode>) - Method in interface de.julielab.costosys.medline.IDocumentDeleter: Passes the XML contents of the deletion element.
configure(HierarchicalConfiguration<ImmutableNode>) - Method in class de.julielab.costosys.medline.SimplePKDataTableDocumentDeleter
ConnectionClosable - Interface in de.julielab.costosys.dbconnection
Constants - Class in de.julielab.costosys: This class provides Constants useful for common tasks.
Constants() - Constructor for class de.julielab.costosys.Constants
COSTOSYS_CONFIG_FILE - Static variable in class de.julielab.costosys.Constants
CoStoSysConnection - Class in de.julielab.costosys.dbconnection
CoStoSysConnection(DataBaseConnector, Connection, boolean) - Constructor for class de.julielab.costosys.dbconnection.CoStoSysConnection
CoStoSysException - Exception in de.julielab.costosys.dbconnection.util
CoStoSysException() - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysException
CoStoSysException(String) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysException
CoStoSysException(String, Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysException
CoStoSysException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysException
CoStoSysException(Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysException
CoStoSysJedisTools - Class in de.julielab.costosys.dbconnection.util
CoStoSysJedisTools() - Constructor for class de.julielab.costosys.dbconnection.util.CoStoSysJedisTools
CoStoSysJedisTools.JedisDataFormat - Class in de.julielab.costosys.dbconnection.util
CoStoSysRuntimeException - Exception in de.julielab.costosys.dbconnection.util
CoStoSysRuntimeException() - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysRuntimeException
CoStoSysRuntimeException(String) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysRuntimeException
CoStoSysRuntimeException(String, Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysRuntimeException
CoStoSysRuntimeException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysRuntimeException
CoStoSysRuntimeException(Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysRuntimeException
CoStoSysSQLRuntimeException - Exception in de.julielab.costosys.dbconnection.util
CoStoSysSQLRuntimeException() - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysSQLRuntimeException
CoStoSysSQLRuntimeException(String) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysSQLRuntimeException
CoStoSysSQLRuntimeException(String, Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysSQLRuntimeException
CoStoSysSQLRuntimeException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysSQLRuntimeException
CoStoSysSQLRuntimeException(Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.CoStoSysSQLRuntimeException
countRowsOfDataTable(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
countRowsOfDataTable(String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
countUnprocessed(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
countUnprocessed(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Counts the unprocessed rows in a subset table
createField(String...) - Static method in class de.julielab.costosys.configuration.FieldConfig
createIndex(String, String...) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Creates an index for table table on the given columns.
createSchema(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Creates the PostgreSQL schema schemaName in the active database.
createStatement() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
createSubsetTable(String, String, Integer, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Does the same as DataBaseConnector.createSubsetTable(String, String, Integer, String, String) with the exception that the assumed table schema is that of the active schema defined in the configuration file.
createSubsetTable(String, String, Integer, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Creates an empty table referencing the primary key of the data table given by superSetTable or, if this is a subset table itself, the data table referenced by that table.
createSubsetTable(String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Does the same as DataBaseConnector.createSubsetTable(String, String, Integer, String, String) with the exception that the assumed table schema is that of the active schema defined in the configuration file and the first referenced data table is used as data table.
createTable(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Creates a new table according to the field schema definition corresponding to the active schema name determined in the configuration.
createTable(String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Creates a new table according to the field schema definition corresponding to the name schemaName given in the configuration file.
createTable(String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Creates a new table according to the field schema definition corresponding to the name schemaName and with foreign key references to the primary key of referenceTableName.

D

DataBaseConnector - Class in de.julielab.costosys.dbconnection: This class creates a connection with a database and allows for convenient queries and commands.
DataBaseConnector(InputStream) - Constructor for class de.julielab.costosys.dbconnection.DataBaseConnector: This class creates a connection with a database and allows for convenient queries and commands.
DataBaseConnector(InputStream, int) - Constructor for class de.julielab.costosys.dbconnection.DataBaseConnector: This class creates a connection with a database and allows for convenient queries and commands.
DataBaseConnector(String) - Constructor for class de.julielab.costosys.dbconnection.DataBaseConnector: Constructors ********************************
DataBaseConnector(String, String, String) - Constructor for class de.julielab.costosys.dbconnection.DataBaseConnector: This class creates a connection with a database and allows for convenient queries and commands.
DataBaseConnector(String, String, String, String, int, InputStream) - Constructor for class de.julielab.costosys.dbconnection.DataBaseConnector: This class creates a connection with a database and allows for convenient queries and commands.
DataBaseConnector(String, String, String, String, InputStream) - Constructor for class de.julielab.costosys.dbconnection.DataBaseConnector: This class creates a connection with a database and allows for convenient queries and commands.
DataBaseConnector(String, String, String, String, String, int, InputStream) - Constructor for class de.julielab.costosys.dbconnection.DataBaseConnector
DataBaseConnector(String, String, String, String, String, InputStream) - Constructor for class de.julielab.costosys.dbconnection.DataBaseConnector
DataBaseConnector.StatusElement - Enum in de.julielab.costosys.dbconnection
DATE_FIELD_NAME - Static variable in class de.julielab.costosys.Constants
DbcExecution - Interface in de.julielab.costosys.dbconnection
DBCIterator<E> - Class in de.julielab.costosys.dbconnection: Abstract class for iterators returned by the DataBaseConnector which hold JDBC Connection objects.
DBCIterator() - Constructor for class de.julielab.costosys.dbconnection.DBCIterator
DBCMedlineUtilities - Class in de.julielab.costosys.medline
DBCMedlineUtilities() - Constructor for class de.julielab.costosys.medline.DBCMedlineUtilities
DBConfig - Class in de.julielab.costosys.configuration
DBConfig(byte[]) - Constructor for class de.julielab.costosys.configuration.DBConfig
DbcQuery<T> - Interface in de.julielab.costosys.dbconnection
DBCThreadedIterator<E> - Class in de.julielab.costosys.dbconnection: This iterator class employs multiple Threads for database queries.
DBCThreadedIterator() - Constructor for class de.julielab.costosys.dbconnection.DBCThreadedIterator
de.julielab.costosys - package de.julielab.costosys
de.julielab.costosys.cli - package de.julielab.costosys.cli
de.julielab.costosys.configuration - package de.julielab.costosys.configuration
de.julielab.costosys.dbconnection - package de.julielab.costosys.dbconnection
de.julielab.costosys.dbconnection.util - package de.julielab.costosys.dbconnection.util
de.julielab.costosys.medline - package de.julielab.costosys.medline
decodeBinaryXmiData(byte[][], boolean) - Method in class de.julielab.costosys.cli.BinaryDataHandler
DEFAULT_DATA_SCHEMA - Static variable in class de.julielab.costosys.Constants: The default PostgreSQL schema in which all data related tables are stored.
DEFAULT_DATA_TABLE_NAME - Static variable in class de.julielab.costosys.Constants: Constant for the name of a database table holding at least document ID and document data (e.g.
DEFAULT_PIPELINE_STATE - Static variable in class de.julielab.costosys.dbconnection.DataBaseConnector
defineMirrorSubset(String, String, boolean, Integer, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineMirrorSubset(String, String, boolean, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineMirrorSubset(String, String, boolean, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineRandomSubset(int, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineRandomSubset(int, String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineSubset(String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineSubset(String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineSubset(List<String>, String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineSubset(List<String>, String, String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineSubsetWithWhereClause(String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
defineSubsetWithWhereClause(String, String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Convenience method for creating and initializing a subset in one step.
deleteDocuments(List<String>) - Method in class de.julielab.costosys.medline.ElasticSearchDocumentDeleter
deleteDocuments(List<String>) - Method in interface de.julielab.costosys.medline.IDocumentDeleter
deleteDocuments(List<String>) - Method in class de.julielab.costosys.medline.SimplePKDataTableDocumentDeleter
deleteFromTable(String, List<Object[]>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Deletes entries from a table
deleteFromTableSimplePK(String, List<T>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Deletes entries from a table where the primary key of this table must consist of exactly one column.
DELETER - Static variable in class de.julielab.costosys.medline.ConfigurationConstants
DELETION - Static variable in class de.julielab.costosys.medline.ConfigurationConstants
determineDataFormat(DataBaseConnector, String, String) - Static method in class de.julielab.costosys.dbconnection.util.CoStoSysJedisTools: Reads the first row of the given table and returns information about whether the data is in GZIP format and/or the JeDIS binary format.
determineExistingSubsetRows(CoStoSysConnection, String, List<Object[]>, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
DIRECTORY - Static variable in class de.julielab.costosys.medline.ConfigurationConstants
DOC_ID_FIELD_NAME - Static variable in class de.julielab.costosys.Constants: Deprecated.
DocumentDeletionException - Exception in de.julielab.costosys.medline
DocumentDeletionException() - Constructor for exception de.julielab.costosys.medline.DocumentDeletionException
DocumentDeletionException(String) - Constructor for exception de.julielab.costosys.medline.DocumentDeletionException
DocumentDeletionException(String, Throwable) - Constructor for exception de.julielab.costosys.medline.DocumentDeletionException
DocumentDeletionException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.costosys.medline.DocumentDeletionException
DocumentDeletionException(Throwable) - Constructor for exception de.julielab.costosys.medline.DocumentDeletionException
dropSchema(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Drops the empty Postgres schema with given name.
dropTable(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Drops the table with the given name.

E

ElasticSearchDocumentDeleter - Class in de.julielab.costosys.medline
ElasticSearchDocumentDeleter() - Constructor for class de.julielab.costosys.medline.ElasticSearchDocumentDeleter
execute(DataBaseConnector) - Method in interface de.julielab.costosys.dbconnection.DbcExecution
expandPKNames(String) - Method in class de.julielab.costosys.configuration.FieldConfig: Applies each primary key element to the format string and returns the results as array.
expandPKNames(String[]) - Method in class de.julielab.costosys.configuration.FieldConfig: Takes an array of format strings according to String.format(String, Object...) with a single %s symbol.
ExtractDeleteCitations - Class in de.julielab.costosys.cli: Extracts PMIDs of deleted Medline documents from Medline Update XML batches.
ExtractDeleteCitations() - Constructor for class de.julielab.costosys.cli.ExtractDeleteCitations

F

FieldConfig - Class in de.julielab.costosys.configuration: This class holds the definition of fields for the database table to work with.
FieldConfig(byte[], String) - Constructor for class de.julielab.costosys.configuration.FieldConfig
FieldConfig(List<Map<String, String>>, String, String) - Constructor for class de.julielab.costosys.configuration.FieldConfig
FieldConfigurationManager - Class in de.julielab.costosys.configuration: This class is essentially a HashMap.
FieldConfigurationManager() - Constructor for class de.julielab.costosys.configuration.FieldConfigurationManager
fileStr - Variable in class de.julielab.costosys.cli.QueryOptions
findConfigurationFile() - Static method in class de.julielab.costosys.cli.CLI

G

get(Object) - Method in class de.julielab.costosys.configuration.FieldConfigurationManager
getActiveConfig(byte[], String) - Static method in class de.julielab.costosys.configuration.ConfigBase: Used to determine which of the elements in the configuration file is set as active.
getActiveDatabase() - Method in class de.julielab.costosys.configuration.DBConfig
getActiveDataPGSchema() - Method in class de.julielab.costosys.configuration.DBConfig
getActiveDataPGSchema() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getActiveDataSchema() - Method in class de.julielab.costosys.configuration.ConfigReader
getActiveDataTable() - Method in class de.julielab.costosys.configuration.ConfigReader
getActiveDataTable() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getActivePGSchema() - Method in class de.julielab.costosys.configuration.DBConfig
getActivePGSchema() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getActiveSchemaName() - Method in class de.julielab.costosys.configuration.ConfigReader
getActiveTableFieldConfiguration() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getActiveTableSchema() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getAutoCommit() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
getColumns() - Method in class de.julielab.costosys.configuration.FieldConfig
getColumnsToRetrieve() - Method in class de.julielab.costosys.configuration.FieldConfig
getConfig() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getConfigText() - Method in class de.julielab.costosys.configuration.FieldConfig
getConnection() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
getCount(Connection, String) - Static method in class de.julielab.costosys.dbconnection.QueryHelper: Returns the result of a query that returns a single count
getDatabaseConfig() - Method in class de.julielab.costosys.configuration.ConfigReader: Accessing the Database Configuration
getDbURL() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getEffectiveConfiguration() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Returns the effective XML configuration as a byte[].
getFeaturesToMapBinaryFromDb(DataBaseConnector, String) - Static method in class de.julielab.costosys.dbconnection.util.CoStoSysJedisTools
getField(String) - Method in class de.julielab.costosys.configuration.FieldConfig
getFieldConfigs() - Method in class de.julielab.costosys.configuration.ConfigReader: Accessing the Field Definitions.
getFieldConfiguration() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getFieldConfiguration(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getFields() - Method in class de.julielab.costosys.configuration.FieldConfig
getFieldsToRetrieve() - Method in class de.julielab.costosys.configuration.FieldConfig
getForEachXPath() - Method in class de.julielab.costosys.configuration.FieldConfig
getMaxConnections() - Method in class de.julielab.costosys.configuration.DBConfig
getMaxConnections() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getMedlineFiles(String) - Method in class de.julielab.costosys.medline.PubmedUpdater
getMergedConfigData() - Method in class de.julielab.costosys.configuration.ConfigReader
getMetaData() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
getMirrorSubsetNames(CoStoSysConnection, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getName() - Method in class de.julielab.costosys.configuration.FieldConfig
getName() - Method in class de.julielab.costosys.medline.ElasticSearchDocumentDeleter
getName() - Method in interface de.julielab.costosys.medline.IDocumentDeleter
getName() - Method in class de.julielab.costosys.medline.SimplePKDataTableDocumentDeleter
getNamespaceMap() - Method in class de.julielab.costosys.cli.BinaryDataHandler: Reads the UIMA XMI namespaces from the respective storage table in the database.
getNamespaceMap(DataBaseConnector, String) - Static method in class de.julielab.costosys.dbconnection.util.CoStoSysJedisTools
getNextDataTable(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Follows the foreign-key specifications of the given table to the referenced table.
getNextOrThisDataTable(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Determines the first data table on the reference path referencingTable -> table1 -> table2 -> ...
getNumColumnsAndFields(boolean, String[]) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Helper method to determine the columns that are returned in case of a joining operation.
getNumReservedConnections() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getNumReservedConnections(boolean) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getNumRows(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Returns the row count of the requested table.
getOptions() - Static method in class de.julielab.costosys.cli.CliOptionsProvider
getPassword(String) - Method in class de.julielab.costosys.configuration.HiddenConfig
getPMCFiles(String) - Method in class de.julielab.costosys.medline.PMCUpdater
getPrimaryKey() - Method in class de.julielab.costosys.configuration.FieldConfig
getPrimaryKeyFieldNumbers() - Method in class de.julielab.costosys.configuration.FieldConfig
getPrimaryKeyFields() - Method in class de.julielab.costosys.configuration.FieldConfig
getPrimaryKeyIndices() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Returns the indices of the primary keys, beginning with 0.
getPrimaryKeyString() - Method in class de.julielab.costosys.configuration.FieldConfig: Returns the names of the columns forming the primary key in a CSV format.
getProcessedPrimaryKeys(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Creates a query cursor to the given subset table and retrieves all those primary keys according to the active table schema that are marked as processed.
getProcessedPrimaryKeys(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Creates a query cursor to the given subset table and retrieves all those primary keys according to tableSchema that are marked as processed.
getQueryBatchSize() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getReferencedTable(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Returns the name of a table referenced by an SQL-foreign-key.
getReferencedTable(String, Integer) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Gets the - possibly indirectly - referenced table of startTable where posOfDataTable specifies the position of the desired table in the reference chain starting at startTable.
getReverseBinaryMappingFromDb() - Method in class de.julielab.costosys.cli.BinaryDataHandler
getReverseBinaryMappingFromDb(DataBaseConnector, String) - Static method in class de.julielab.costosys.dbconnection.util.CoStoSysJedisTools
getScheme() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getTableColumnInformation(String, String...) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Returns information about the columns in a table.
getTableColumnNames(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getTableDefinition(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector: Query the MetaData for the columns of a table
getTables() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
getTableSchemaNames() - Method in class de.julielab.costosys.configuration.ConfigReader
getTimestampFieldName() - Method in class de.julielab.costosys.configuration.FieldConfig
getTypeSystemFiles() - Method in class de.julielab.costosys.configuration.ConfigReader
getTypeSystemPaths(byte[]) - Method in class de.julielab.costosys.configuration.ConfigReader: Returns the type system files from the configuration.
getUrl() - Method in class de.julielab.costosys.configuration.DBConfig
getUsageNumber() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
getUsername(String) - Method in class de.julielab.costosys.configuration.HiddenConfig





H

HAS_ERRORS - de.julielab.costosys.dbconnection.DataBaseConnector.StatusElement
 
HAS_ERRORS - Static variable in class de.julielab.costosys.Constants
 
hasErrors - Variable in class de.julielab.costosys.dbconnection.SubsetStatus
 
hasNext() - Method in class de.julielab.costosys.dbconnection.DBCThreadedIterator
 
hasUnfetchedRows(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
hasUnfetchedRows(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Utility **********************************

HIDDEN_CONFIG_PATH - Static variable in class de.julielab.costosys.Constants
 
HiddenConfig - Class in de.julielab.costosys.configuration

This class reads a hidden configuration file in the users home directory.

HiddenConfig() - Constructor for class de.julielab.costosys.configuration.HiddenConfig

Reads a hidden configuration file in the users home directory.

HOST_NAME - Static variable in class de.julielab.costosys.Constants
 




I

IDocumentDeleter - Interface in de.julielab.costosys.medline
 
importFromRowIterator(Iterator<Map<String, Object>>, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
importFromRowIterator(Iterator<Map<String, Object>>, String, boolean, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Internal method to import into an existing table

importFromRowIterator(Iterator<Map<String, Object>>, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
importFromXML(Iterable<byte[]>, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
importFromXML(Iterable<byte[]>, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Imports XMLs into a table.

importFromXMLFile(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Import new medline XMLs in a existing table from an XML file or a directory
 of XML files.

importFromXMLFile(String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Import new medline XMLs in a existing table from an XML file or a directory
 of XML files.

IN_PROCESS - de.julielab.costosys.dbconnection.DataBaseConnector.StatusElement
 
IN_PROCESS - Static variable in class de.julielab.costosys.Constants
 
incrementUsageNumber() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
 
initMirrorSubset(String, String, boolean) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
initMirrorSubset(String, String, boolean, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Defines a mirror subset populating a subset table with primary keys from
 another table.

initRandomSubset(int, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
initRandomSubset(int, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Selects size rows of the given super set table randomly and
 inserts them into the subset table.

initSubset(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Initializes subsetTable by inserting one row for each entry in supersetTable.

initSubset(String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Defines a subset by populating a subset table with all primary keys from
 another table.

initSubset(List<String>, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Defines a subset by populating a subset table with primary keys from another
 table.

initSubset(List<String>, String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Defines a subset by populating a subset table with primary keys from another
 table.

initSubsetWithWhereClause(String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Defines a subset by populating a subset table with primary keys from another
 table.

initSubsetWithWhereClause(String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Defines a subset by populating a subset table with primary keys from another
 table.

inProcess - Variable in class de.julielab.costosys.dbconnection.SubsetStatus
 
INSERTION_INPUT - Static variable in class de.julielab.costosys.medline.ConfigurationConstants

Deprecated.

insertXmiColumnData(Path, String, String, DataBaseConnector) - Method in class de.julielab.costosys.cli.XmiColumnDataInserter
 
IS_PROCESSED - de.julielab.costosys.dbconnection.DataBaseConnector.StatusElement
 
IS_PROCESSED - Static variable in class de.julielab.costosys.Constants
 
isBinary() - Method in class de.julielab.costosys.configuration.FieldConfig
 
isBinary() - Method in class de.julielab.costosys.dbconnection.util.CoStoSysJedisTools.JedisDataFormat
 
isBinaryDataType(String) - Static method in class de.julielab.costosys.configuration.FieldConfig
 
isBooleanType(String) - Static method in class de.julielab.costosys.configuration.FieldConfig
 
isClosed() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
 
isDatabaseReachable() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
isDataTable(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
isEmpty(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Tests if a table contains entries.

isEmpty(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
isGzip() - Method in class de.julielab.costosys.dbconnection.util.CoStoSysJedisTools.JedisDataFormat
 
isIntegerType(String) - Static method in class de.julielab.costosys.configuration.FieldConfig
 
isKnownType(String) - Static method in class de.julielab.costosys.configuration.FieldConfig
 
isNsAware() - Method in class de.julielab.costosys.configuration.FieldConfig
 
isOfBinaryDataType(Map<String, String>) - Method in class de.julielab.costosys.configuration.FieldConfig
 
isOfIntegerType(Map<String, String>) - Method in class de.julielab.costosys.configuration.FieldConfig
 
isOfStringType(String) - Method in class de.julielab.costosys.configuration.FieldConfig
 
isOfStringType(Map<String, String>) - Method in class de.julielab.costosys.configuration.FieldConfig
 
isOfTimestampWithoutTZType(String) - Method in class de.julielab.costosys.configuration.FieldConfig
 
isOneOf(String...) - Method in interface de.julielab.costosys.medline.IDocumentDeleter
 
isProcessed - Variable in class de.julielab.costosys.dbconnection.SubsetStatus
 
isShared() - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection

Indicates if this connection can be shared between different code and threads.

isStringType(String) - Static method in class de.julielab.costosys.configuration.FieldConfig
 
isStringTypeArray(String) - Static method in class de.julielab.costosys.configuration.FieldConfig
 
isSubsetTable(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Checks if the given table is a subset table.

isTimestampWithoutTZType(String) - Static method in class de.julielab.costosys.configuration.FieldConfig

Returns true if the string type equals the SQL
 "timestamp without time zone" type.

isXmlType(String) - Static method in class de.julielab.costosys.configuration.FieldConfig
 




J

JedisDataFormat(boolean, boolean) - Constructor for class de.julielab.costosys.dbconnection.util.CoStoSysJedisTools.JedisDataFormat
 
join() - Method in class de.julielab.costosys.dbconnection.DBCThreadedIterator
 
join() - Method in class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
 
join() - Method in class de.julielab.costosys.dbconnection.ThreadedColumnsToRetrieveIterator
 




L

LAST_COMPONENT - de.julielab.costosys.dbconnection.DataBaseConnector.StatusElement
 
LAST_COMPONENT - Static variable in class de.julielab.costosys.Constants
 
LAST_DOCUMENT_TEXT_HASH - Static variable in class de.julielab.costosys.Constants
 
limitStr - Variable in class de.julielab.costosys.cli.QueryOptions
 
listExchanger - Variable in class de.julielab.costosys.dbconnection.DBCThreadedIterator
 
loadXmlConfiguration(File) - Static method in class de.julielab.costosys.cli.CLI
 
LOG - Static variable in class de.julielab.costosys.Constants
 




M

main(String[]) - Static method in class de.julielab.costosys.cli.CLI
 
main(String[]) - Static method in class de.julielab.costosys.cli.ExtractDeleteCitations
 
markAsProcessed(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Modifies a subset table, marking all its entries as processed.

markAsProcessed(String, List<Object[]>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Modifies a subset table, marking entries as processed.

MedlineUpdateException - Exception in de.julielab.costosys.medline
 
MedlineUpdateException() - Constructor for exception de.julielab.costosys.medline.MedlineUpdateException
 
MedlineUpdateException(String) - Constructor for exception de.julielab.costosys.medline.MedlineUpdateException
 
MedlineUpdateException(String, Throwable) - Constructor for exception de.julielab.costosys.medline.MedlineUpdateException
 
MedlineUpdateException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.costosys.medline.MedlineUpdateException
 
MedlineUpdateException(Throwable) - Constructor for exception de.julielab.costosys.medline.MedlineUpdateException
 
META_IN_ARRAY - Static variable in class de.julielab.costosys.dbconnection.DataBaseConnector

Deprecated.

MIRROR_COLLECTION_NAME - Static variable in class de.julielab.costosys.Constants
 
MIRROR_COLUMN_DATA_TABLE_NAME - Static variable in class de.julielab.costosys.Constants
 
MIRROR_COLUMN_DO_RESET - Static variable in class de.julielab.costosys.Constants
 
MIRROR_COLUMN_SUBSET_NAME - Static variable in class de.julielab.costosys.Constants
 
modifyTable(String, List<Object[]>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Executes a given SQL command (must end with "WHERE "!) an extends the
 WHERE-clause with the primary keys, set to the values in ids.

modifyTable(String, List<Object[]>, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Executes a given SQL command (must end with "WHERE "!) and extends the
 WHERE-clause with the primary keys, set to the values in ids.





N

next() - Method in class de.julielab.costosys.dbconnection.DBCThreadedIterator
 
NLM_ID_FIELD_NAME - Static variable in class de.julielab.costosys.Constants
 
NoReservedConnectionException - Exception in de.julielab.costosys.dbconnection.util
 
NoReservedConnectionException() - Constructor for exception de.julielab.costosys.dbconnection.util.NoReservedConnectionException
 
NoReservedConnectionException(String) - Constructor for exception de.julielab.costosys.dbconnection.util.NoReservedConnectionException
 
NoReservedConnectionException(String, Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.NoReservedConnectionException
 
NoReservedConnectionException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.costosys.dbconnection.util.NoReservedConnectionException
 
NoReservedConnectionException(Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.NoReservedConnectionException
 
numberRefHops - Variable in class de.julielab.costosys.cli.QueryOptions
 




O

obtainConnection() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Returns the connection associated with the current thread object if it exists.

obtainOrReserveConnection() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

This is just a convenience method for DataBaseConnector.obtainOrReserveConnection(boolean) with the parameter set to true.

obtainOrReserveConnection(boolean) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 This is the preferred way to obtain a database connection.





P

performBatchUpdate(CoStoSysConnection, List<Object[]>, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
PID - Static variable in class de.julielab.costosys.Constants
 
pipelineStates - Variable in class de.julielab.costosys.dbconnection.SubsetStatus
 
PMCUpdater - Class in de.julielab.costosys.medline
 
PMCUpdater(HierarchicalConfiguration<ImmutableNode>) - Constructor for class de.julielab.costosys.medline.PMCUpdater
 
PMID_FIELD_NAME - Static variable in class de.julielab.costosys.Constants
 
POSTGRES_VERSION - Static variable in class de.julielab.costosys.dbconnection.DataBaseConnector

The PostgreSQL version against which this version of CoStoSys is developed and tested.

prepareStatement(String) - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
 
printConnectionPoolStatus() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
process(DataBaseConnector, boolean) - Method in class de.julielab.costosys.medline.PMCUpdater
 
process(DataBaseConnector, boolean) - Method in class de.julielab.costosys.medline.PubmedUpdater
 
PROCESSED - Static variable in class de.julielab.costosys.Constants
 
PROCESSING_TIMESTAMP - Static variable in class de.julielab.costosys.Constants
 
pubmedArticleSet - Variable in class de.julielab.costosys.cli.QueryOptions
 
PubmedUpdater - Class in de.julielab.costosys.medline
 
PubmedUpdater(HierarchicalConfiguration<ImmutableNode>) - Constructor for class de.julielab.costosys.medline.PubmedUpdater
 




Q

query(DataBaseConnector) - Method in interface de.julielab.costosys.dbconnection.DbcQuery
 
query(String) - Static method in class de.julielab.costosys.cli.QueryPubMed

Query PubMed via REST-API, returning up to 10e8 matched PMIDs.

query(String, List<String>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Returns the requested fields from the requested table.

query(String, List<String>, long) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Returns the requested fields from the requested table.

query(List<String[]>, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Returns the values the the column DataBaseConnector.DEFAULT_FIELD in the given table.

query(List<String[]>, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Returns the values the the column DataBaseConnector.DEFAULT_FIELD in the given table.

queryAll(List<String>, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Returns an iterator over the column field in the table
 table.

queryDataTable(String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Returns all column data from the data table tableName which is
 marked as 'to be retrieved' in the table scheme specified by the active table
 scheme.

queryDataTable(String, String, String[], String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
queryDataTable(String, String, String[], String[]) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Returns all column data from the data table tableName which is
 marked as 'to be retrieved' in the table scheme specified by
 schemaName.

QueryHelper - Class in de.julielab.costosys.dbconnection
 
QueryHelper() - Constructor for class de.julielab.costosys.dbconnection.QueryHelper
 
QueryOptions - Class in de.julielab.costosys.cli
 
QueryOptions() - Constructor for class de.julielab.costosys.cli.QueryOptions
 
QueryPubMed - Class in de.julielab.costosys.cli
 
QueryPubMed() - Constructor for class de.julielab.costosys.cli.QueryPubMed
 
queryStr - Variable in class de.julielab.costosys.cli.QueryOptions
 
querySubset(String, long) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
querySubset(String, String, long, Integer, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Retrieves XML field values in the data table referenced by the subset table
 tableName or tableName itself if it is a data
 table.

queryWithTime(List<Object[]>, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
queryWithTime(List<Object[]>, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Returns an iterator over all rows in the table with matching id and a
 timestamp newer (>) than timestamp.





R

releaseConnections() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Releases all connections associated with the current thread back to the connection pool.

remove() - Method in class de.julielab.costosys.dbconnection.DBCThreadedIterator

unsupported

removeTableFromMirrorSubsetList(CoStoSysConnection, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Removes an entry from the table listing mirror subsets, located at MIRROR_COLLECTION_NAME.

reserveConnection() - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Just delegates to reserveConnection(true).

reserveConnection(boolean) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Only use when you are sure you need this method.

resetSubset(CoStoSysConnection, String, List<Object[]>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
resetSubset(CoStoSysConnection, String, List<Object[]>, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Sets the values in the is_processed and
 is_in_process rows of a subset to FALSE.

resetSubset(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Sets the values in the is_processed, is_in_process,
 has_errors and log columns of a subset to
 FALSE.

resetSubset(String, boolean, boolean, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Sets the values in the is_processed, is_in_process,
 has_errors and log columns of a subset to
 FALSE where the corresponding rows are
 is_in_process or is_processed.

resetSubset(String, List<Object[]>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
retrieveAndMark(String, String, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Retrieves from a subset-table limit primary keys whose rows are
 not marked to be in process or finished being processed and sets the rows of
 the retrieved primary keys as being "in process".

retrieveAndMark(String, String, String, String, int, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Retrieves primary keys from a subset table and marks them as being "in
 process".

retrieveAndMark(String, String, String, String, String, int, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Retrieves from a subset-table limit primary keys whose rows are
 not marked to be in process or finished being processed and sets the rows of
 the retrieved primary keys as being "in process".

retrieveColumnsByTableSchema(List<Object[]>, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Retrieves row values of table from the database.

retrieveColumnsByTableSchema(List<Object[]>, String[], String[]) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Retrieves data from the database over multiple tables.

retrieveColumnsByTableSchema(List<Object[]>, String, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Retrieves row values of table from the database.





S

schemaExists(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

crea
 Tests if a schema exists.

setActivePGSchema(String) - Method in class de.julielab.costosys.configuration.DBConfig
 
setActivePGSchema(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
setActiveTableSchema(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
setAutoCommit(boolean) - Method in class de.julielab.costosys.dbconnection.CoStoSysConnection
 
setDbc(DataBaseConnector) - Method in class de.julielab.costosys.medline.SimplePKDataTableDocumentDeleter
 
setDbURL(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
setException(String, ArrayList<byte[][]>, HashMap<byte[][], String>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Sets the value of has_errors to TRUE and adds a
 description in log for exceptions which occured during the
 processing of a collection of documents according to the given primary keys.

setForEachXPath(String) - Method in class de.julielab.costosys.configuration.FieldConfig
 
setHost(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
setMaxConnections(int) - Method in class de.julielab.costosys.configuration.DBConfig
 
setMaxConnections(int) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
setPassword(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
setPort(Integer) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
setPort(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
setProcessed(String, List<byte[][]>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Sets the values of is_processed to TRUE and of
 is_in_process to FALSE for a collection of
 documents according to the given primary keys.

setQueryBatchSize(int) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
setUser(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
SimplePKDataTableDocumentDeleter - Class in de.julielab.costosys.medline
 
SimplePKDataTableDocumentDeleter() - Constructor for class de.julielab.costosys.medline.SimplePKDataTableDocumentDeleter
 
status(String, Set<DataBaseConnector.StatusElement>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Returns a map with information about how many rows are marked as
 is_in_process, is_processed and how many rows there are in
 total.

 The respective values are stored under with the keys
 IN_PROCESS, PROCESSED and
 TOTAL.

stringFromXpath(AutoPilot, String) - Method in class de.julielab.costosys.configuration.ConfigBase

Used to get an element by its relative xpath.

subsetColumns - Static variable in class de.julielab.costosys.dbconnection.DataBaseConnector

This is the definition of subset tables except the primary key.

SubsetStatus - Class in de.julielab.costosys.dbconnection
 
SubsetStatus() - Constructor for class de.julielab.costosys.dbconnection.SubsetStatus
 




T

TABLE - Static variable in class de.julielab.costosys.medline.ConfigurationConstants
 
tableExists(CoStoSysConnection, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Tests if a table exists.

tableExists(String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Tests if a table exists.

tableName - Variable in class de.julielab.costosys.cli.QueryOptions
 
TableNotFoundException - Exception in de.julielab.costosys.cli
 
TableNotFoundException() - Constructor for exception de.julielab.costosys.cli.TableNotFoundException
 
TableNotFoundException(String) - Constructor for exception de.julielab.costosys.cli.TableNotFoundException
 
tableSchema - Variable in class de.julielab.costosys.cli.QueryOptions
 
TableSchemaDoesNotExistException - Exception in de.julielab.costosys.configuration
 
TableSchemaMismatchException - Exception in de.julielab.costosys.dbconnection.util
 
TableSchemaMismatchException() - Constructor for exception de.julielab.costosys.dbconnection.util.TableSchemaMismatchException
 
TableSchemaMismatchException(String) - Constructor for exception de.julielab.costosys.dbconnection.util.TableSchemaMismatchException
 
TableSchemaMismatchException(String, Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.TableSchemaMismatchException
 
TableSchemaMismatchException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.costosys.dbconnection.util.TableSchemaMismatchException
 
TableSchemaMismatchException(Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.TableSchemaMismatchException
 
ThreadedColumnsIterator - Class in de.julielab.costosys.dbconnection

Retrieves a list of fields from the requested table.

ThreadedColumnsIterator(DataBaseConnector, CoStoSysConnection, List<String[]>, List<String>, String, long, String) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
 
ThreadedColumnsIterator(DataBaseConnector, CoStoSysConnection, List<String[]>, List<String>, String, String) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
 
ThreadedColumnsIterator(DataBaseConnector, CoStoSysConnection, List<String>, String) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
 
ThreadedColumnsIterator(DataBaseConnector, CoStoSysConnection, List<String>, String, long) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
 
ThreadedColumnsIterator(DataBaseConnector, List<String[]>, List<String>, String, String) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
 
ThreadedColumnsIterator(DataBaseConnector, List<String>, String) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
 
ThreadedColumnsIterator(DataBaseConnector, List<String>, String, long) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsIterator
 
ThreadedColumnsToRetrieveIterator - Class in de.julielab.costosys.dbconnection

An iterator that returns documents stored in the database identified by the
 primary keys delivered in a list upon creation of the iterator.

ThreadedColumnsToRetrieveIterator(DataBaseConnector, CoStoSysConnection, List<Object[]>, String[], String[]) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsToRetrieveIterator

Retrieves data from the database over multiple tables.

ThreadedColumnsToRetrieveIterator(DataBaseConnector, CoStoSysConnection, List<Object[]>, String, String) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsToRetrieveIterator
 
ThreadedColumnsToRetrieveIterator(DataBaseConnector, CoStoSysConnection, List<Object[]>, String, String, String) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsToRetrieveIterator
 
ThreadedColumnsToRetrieveIterator(DataBaseConnector, List<Object[]>, String[], String[]) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsToRetrieveIterator
 
ThreadedColumnsToRetrieveIterator(DataBaseConnector, List<Object[]>, String, String) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsToRetrieveIterator
 
ThreadedColumnsToRetrieveIterator(DataBaseConnector, List<Object[]>, String, String, String) - Constructor for class de.julielab.costosys.dbconnection.ThreadedColumnsToRetrieveIterator
 
TIMESTAMP_FIELD_NAME - Static variable in class de.julielab.costosys.Constants
 
TO_DELETE_QUEUE - Static variable in class de.julielab.costosys.medline.ElasticSearchDocumentDeleter
 
toString() - Method in class de.julielab.costosys.cli.QueryOptions
 
toString() - Method in class de.julielab.costosys.configuration.DBConfig
 
toString() - Method in class de.julielab.costosys.configuration.FieldConfig
 
toString() - Method in class de.julielab.costosys.dbconnection.SubsetStatus
 
total - Variable in class de.julielab.costosys.dbconnection.SubsetStatus
 
TOTAL - de.julielab.costosys.dbconnection.DataBaseConnector.StatusElement
 
TOTAL - Static variable in class de.julielab.costosys.Constants
 
TYPE_BINARY_DATA - Static variable in class de.julielab.costosys.Constants
 
TYPE_BOOLEAN - Static variable in class de.julielab.costosys.Constants
 
TYPE_INTEGER - Static variable in class de.julielab.costosys.Constants
 
TYPE_TEXT - Static variable in class de.julielab.costosys.Constants
 
TYPE_TEXT_ARRAY - Static variable in class de.julielab.costosys.Constants
 
TYPE_TIMESTAMP_WITHOUT_TIMEZONE - Static variable in class de.julielab.costosys.Constants

Constant for a possible value of type.

TYPE_VARCHAR_ARRAY - Static variable in class de.julielab.costosys.Constants
 
TYPE_XML - Static variable in class de.julielab.costosys.Constants
 




U

UnobtainableConnectionException - Exception in de.julielab.costosys.dbconnection.util
 
UnobtainableConnectionException() - Constructor for exception de.julielab.costosys.dbconnection.util.UnobtainableConnectionException
 
UnobtainableConnectionException(String) - Constructor for exception de.julielab.costosys.dbconnection.util.UnobtainableConnectionException
 
UnobtainableConnectionException(String, Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.UnobtainableConnectionException
 
UnobtainableConnectionException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.costosys.dbconnection.util.UnobtainableConnectionException
 
UnobtainableConnectionException(Throwable) - Constructor for exception de.julielab.costosys.dbconnection.util.UnobtainableConnectionException
 
update() - Method in class de.julielab.costosys.dbconnection.DBCThreadedIterator
 
UPDATE_INPUT - Static variable in class de.julielab.costosys.medline.ConfigurationConstants

Deprecated.

UPDATE_TABLE - Static variable in class de.julielab.costosys.medline.PMCUpdater

Name of the table that keeps track of already imported and finished Medline
 update files.

UPDATE_TABLE - Static variable in class de.julielab.costosys.medline.PubmedUpdater

Name of the table that keeps track of already imported and finished Medline
 update files.

updateFromRowIterator(Iterator<Map<String, Object>>, String, boolean) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Updates a table with the entries yielded by the iterator.

updateFromRowIterator(Iterator<Map<String, Object>>, String, boolean, boolean, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector


 Updates a table with the entries yielded by the iterator.

updateFromXML(String, String, boolean) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
updateFromXML(String, String, boolean, String) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector

Updates an existing database.

useDelimiter - Variable in class de.julielab.costosys.cli.QueryOptions
 
USER_SCHEME_DEFINITION - Static variable in class de.julielab.costosys.cli.CLI
 




V

VALUE - Static variable in class de.julielab.costosys.Constants
 
valueOf(String) - Static method in enum de.julielab.costosys.dbconnection.DataBaseConnector.StatusElement

Returns the enum constant of this type with the specified name.

values() - Static method in enum de.julielab.costosys.dbconnection.DataBaseConnector.StatusElement

Returns an array containing the constants of this enum type, in
the order they are declared.





W

whereClause - Variable in class de.julielab.costosys.cli.QueryOptions
 
withConnectionExecute(DbcExecution) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
withConnectionQuery(DbcQuery<?>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
withConnectionQueryBoolean(DbcQuery<Boolean>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
withConnectionQueryDouble(DbcQuery<Double>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
withConnectionQueryInteger(DbcQuery<Integer>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
withConnectionQueryString(DbcQuery<String>) - Method in class de.julielab.costosys.dbconnection.DataBaseConnector
 
writeDocumentsIntoMedlineCitationSet(Iterator<byte[][]>, int) - Method in class de.julielab.costosys.medline.DBCMedlineUtilities
 




X

XmiColumnDataInserter - Class in de.julielab.costosys.cli
 
XmiColumnDataInserter() - Constructor for class de.julielab.costosys.cli.XmiColumnDataInserter
 
XML_FIELD_NAME - Static variable in class de.julielab.costosys.Constants
 
xpath - Variable in class de.julielab.costosys.cli.QueryOptions
 
XPATH_TYPE_SYSTEM - Static variable in class de.julielab.costosys.configuration.ConfigReader
 
XPATH_TYPE_SYSTEM_FILE - Static variable in class de.julielab.costosys.configuration.ConfigReader
 

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