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

A

addData(Object...) - Method in class de.julielab.xmlData.dataBase.BatchInserter

Adds the given data to the batch.

addFieldConfiguration(FieldConfig) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

addPKAdaptedFieldConfiguration(List<Map<String, String>>, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

addXmiAnnotationFieldConfiguration(List<Map<String, String>>, boolean) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Adds an auto-generated field configuration that exhibits the given primary key and all the fields required to store XMI annotation data (not base documents) in database tables.

addXmiDocumentFieldConfiguration(List<Map<String, String>>, boolean) - Method in class de.julielab.xmlData.dataBase.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>>, boolean) - Method in class de.julielab.xmlData.dataBase.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.

AUTO_ID_FIELD_NAME - Static variable in class de.julielab.xmlData.Constants

B

backgroundThread - Variable in class de.julielab.xmlData.dataBase.DBCThreadedIterator

baseOutDirStr - Variable in class de.julielab.xmlData.cli.QueryOptions

BatchInserter - Class in de.julielab.xmlData.dataBase

A helper class to automate the common batch-insert process as far as possible.

BatchInserter(PreparedStatement, Class<?>[], int[]) - Constructor for class de.julielab.xmlData.dataBase.BatchInserter

Creates an instance of BatchInserter.

batchSizeStr - Variable in class de.julielab.xmlData.cli.QueryOptions

C

checkTableDefinition(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Checks whether the given table matches the active table schema.

checkTableDefinition(String, String) - Method in class de.julielab.xmlData.dataBase.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.

checkTableSchemaCompatibility(String, String[]) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

checkTableSchemaCompatibility(String...) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

CLI - Class in de.julielab.xmlData.cli

Command line interface for interaction with a databases holding e.g.

CLI() - Constructor for class de.julielab.xmlData.cli.CLI

close() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

close() - Method in class de.julielab.xmlData.dataBase.DBCIterator

Frees resources occupied by this iterator (e.g.

close() - Method in class de.julielab.xmlData.dataBase.DBCThreadedIterator

close() - Method in class de.julielab.xmlData.dataBase.ThreadedColumnsToRetrieveIterator

closeConnection() - Method in interface de.julielab.xmlData.dataBase.ConnectionClosable

closeConnection() - Method in class de.julielab.xmlData.dataBase.ThreadedColumnsIterator

commitTail() - Method in class de.julielab.xmlData.dataBase.BatchInserter

Commits to the database what has been added to the batch but not yet been committed.

ConfigBase - Class in de.julielab.xmlData.config

ConfigBase() - Constructor for class de.julielab.xmlData.config.ConfigBase

ConfigReader - Class in de.julielab.xmlData.config

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.xmlData.config.ConfigReader

ConnectionClosable - Interface in de.julielab.xmlData.dataBase

Constants - Class in de.julielab.xmlData

This class provides Constants useful for common tasks.

Constants() - Constructor for class de.julielab.xmlData.Constants

countRowsOfDataTable(String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

countRowsOfDataTable(String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

countUnprocessed(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

countUnprocessed(String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Counts the unprocessed rows in a subset table

createField(String...) - Static method in class de.julielab.xmlData.config.FieldConfig

createIndex(String, String...) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Creates an index for table table on the given columns.

createSchema(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Creates the PostgreSQL schema schemaName in the active database.

createSubsetTable(String, String, Integer, String) - Method in class de.julielab.xmlData.dataBase.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, String) - Method in class de.julielab.xmlData.dataBase.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.

createSubsetTable(String, String, Integer, String, String) - Method in class de.julielab.xmlData.dataBase.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.

createTable(String, String) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase.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.xmlData.dataBase.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.xmlData.dataBase

This class creates a connection with a database and allows for convenient queries and commands.

DataBaseConnector(String) - Constructor for class de.julielab.xmlData.dataBase.DataBaseConnector

Constructors ********************************

DataBaseConnector(InputStream) - Constructor for class de.julielab.xmlData.dataBase.DataBaseConnector

This class creates a connection with a database and allows for convenient queries and commands.

DataBaseConnector(InputStream, int) - Constructor for class de.julielab.xmlData.dataBase.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.xmlData.dataBase.DataBaseConnector

This class creates a connection with a database and allows for convenient queries and commands.

DataBaseConnector(String, String, String, String, String, InputStream) - Constructor for class de.julielab.xmlData.dataBase.DataBaseConnector

DataBaseConnector(String, String, String, String, int, InputStream) - Constructor for class de.julielab.xmlData.dataBase.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.xmlData.dataBase.DataBaseConnector

DataBaseConnector(String, String, String) - Constructor for class de.julielab.xmlData.dataBase.DataBaseConnector

This class creates a connection with a database and allows for convenient queries and commands.

DataBaseConnector.StatusElement - Enum in de.julielab.xmlData.dataBase

DATE_FIELD_NAME - Static variable in class de.julielab.xmlData.Constants

DBCIterator<E> - Class in de.julielab.xmlData.dataBase

Abstract class for iterators returned by the DataBaseConnector which hold JDBC Connection objects.

DBCIterator() - Constructor for class de.julielab.xmlData.dataBase.DBCIterator

DBCMedlineUtilities - Class in de.julielab.medline

DBCMedlineUtilities() - Constructor for class de.julielab.medline.DBCMedlineUtilities

DBConfig - Class in de.julielab.xmlData.config

DBConfig(byte[]) - Constructor for class de.julielab.xmlData.config.DBConfig

DBCThreadedIterator<E> - Class in de.julielab.xmlData.dataBase

This iterator class employs multiple Threads for database queries.

DBCThreadedIterator() - Constructor for class de.julielab.xmlData.dataBase.DBCThreadedIterator

de.julielab.hiddenConfig - package de.julielab.hiddenConfig

de.julielab.medline - package de.julielab.medline

de.julielab.xmlData - package de.julielab.xmlData

de.julielab.xmlData.cli - package de.julielab.xmlData.cli

de.julielab.xmlData.config - package de.julielab.xmlData.config

de.julielab.xmlData.dataBase - package de.julielab.xmlData.dataBase

de.julielab.xmlData.dataBase.util - package de.julielab.xmlData.dataBase.util

DEFAULT_DATA_SCHEMA - Static variable in class de.julielab.xmlData.Constants

The default PostgreSQL schema in which all data related tables are stored.

DEFAULT_DATA_TABLE_NAME - Static variable in class de.julielab.xmlData.Constants

Constant for the name of a database table holding at least document ID and document data (e.g.

DEFAULT_DEFINITION - Static variable in class de.julielab.xmlData.config.ConfigReader

DEFAULT_PIPELINE_STATE - Static variable in class de.julielab.xmlData.dataBase.DataBaseConnector

defineMirrorSubset(String, String, boolean, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

defineMirrorSubset(String, String, boolean, Integer, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

defineMirrorSubset(String, String, boolean, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

defineRandomSubset(int, String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

defineRandomSubset(int, String, String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

defineSubset(List<String>, String, String, String, String) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

defineSubset(String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

defineSubset(String, String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

defineSubsetWithWhereClause(String, String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

defineSubsetWithWhereClause(String, String, String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Convenience method for creating and initializing a subset in one step.

deleteFromTable(String, List<Object[]>) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Deletes entries from a table

deleteFromTableSimplePK(String, List<T>) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Deletes entries from a table where the primary key of this table must consist of exactly one column.

determineExistingSubsetRows(String, List<Object[]>, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

DOC_ID_FIELD_NAME - Static variable in class de.julielab.xmlData.Constants

Deprecated.

dropTable(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

E

expandPKNames(String[]) - Method in class de.julielab.xmlData.config.FieldConfig

Takes an array of format strings according to String.format(String, Object...) with a single %s symbol.

expandPKNames(String) - Method in class de.julielab.xmlData.config.FieldConfig

Applies each primary key element to the format string and returns the results as array.

extractConfigData(byte[], String) - Method in class de.julielab.xmlData.config.ConfigBase

Retrieves XML elements (determined by the used path) from the configuration.

extractConfigData(byte[]) - Static method in class de.julielab.xmlData.config.ConfigReader

Retrieves XML elements (determined by the used path) from the configuration.

ExtractDeleteCitations - Class in de.julielab.xmlData.cli

Extracts PMIDs of deleted Medline documents from Medline Update XML batches.

ExtractDeleteCitations() - Constructor for class de.julielab.xmlData.cli.ExtractDeleteCitations

F

FieldConfig - Class in de.julielab.xmlData.config

This class holds the definition of fields for the database table to work with.

FieldConfig(byte[], String) - Constructor for class de.julielab.xmlData.config.FieldConfig

FieldConfig(List<Map<String, String>>, String, String) - Constructor for class de.julielab.xmlData.config.FieldConfig

FieldConfigurationManager - Class in de.julielab.xmlData.config

This class is essentially a HashMap.

FieldConfigurationManager() - Constructor for class de.julielab.xmlData.config.FieldConfigurationManager

fileStr - Variable in class de.julielab.xmlData.cli.QueryOptions

findConfigurationFile() - Static method in class de.julielab.xmlData.cli.CLI

G

get(Object) - Method in class de.julielab.xmlData.config.FieldConfigurationManager

getActiveConfig(byte[], String) - Static method in class de.julielab.xmlData.config.ConfigBase

Used to determine which of the elements in the configuration file is set as active.

getActiveDatabase() - Method in class de.julielab.xmlData.config.DBConfig

getActiveDataPGSchema() - Method in class de.julielab.xmlData.config.DBConfig

getActiveDataPGSchema() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getActiveDataSchema() - Method in class de.julielab.xmlData.config.ConfigReader

getActiveDataTable() - Method in class de.julielab.xmlData.config.ConfigReader

getActiveDataTable() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getActivePGSchema() - Method in class de.julielab.xmlData.config.DBConfig

getActivePGSchema() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getActiveSchemaName() - Method in class de.julielab.xmlData.config.ConfigReader

getActiveTableFieldConfiguration() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getActiveTableSchema() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getColumns() - Method in class de.julielab.xmlData.config.FieldConfig

getColumnsToRetrieve() - Method in class de.julielab.xmlData.config.FieldConfig

getConfig() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getConfigText() - Method in class de.julielab.xmlData.config.FieldConfig

getConn() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getCount(Connection, String) - Static method in class de.julielab.xmlData.dataBase.QueryHelper

Returns the result of a query that returns a single count

getDatabaseConfig() - Method in class de.julielab.xmlData.config.ConfigReader

Accessing the Database Configuration

getDbURL() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getEffectiveConfiguration() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Returns the effective XML configuration as a byte[].

getField(String) - Method in class de.julielab.xmlData.config.FieldConfig

getFieldConfigs() - Method in class de.julielab.xmlData.config.ConfigReader

Accessing the Field Definitions.

getFieldConfiguration() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getFieldConfiguration(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getFields() - Method in class de.julielab.xmlData.config.FieldConfig

getFieldsToRetrieve() - Method in class de.julielab.xmlData.config.FieldConfig

getForEachXPath() - Method in class de.julielab.xmlData.config.FieldConfig

getMaxConnections() - Method in class de.julielab.xmlData.config.DBConfig

getMergedConfigData() - Method in class de.julielab.xmlData.config.ConfigReader

getName() - Method in class de.julielab.xmlData.config.FieldConfig

getNextDataTable(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Follows the foreign-key specifications of the given table to the referenced table.

getNextOrThisDataTable(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Determines the first data table on the reference path referencingTable -> table1 -> table2 -> ...

getNumColumnsAndFields(boolean, String[]) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Helper method to determine the columns that are returned in case of a joining operation.

getNumRows(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Returns the row count of the requested table.

getPassword(String) - Method in class de.julielab.hiddenConfig.HiddenConfig

getPrimaryKey() - Method in class de.julielab.xmlData.config.FieldConfig

getPrimaryKeyFieldNumbers() - Method in class de.julielab.xmlData.config.FieldConfig

getPrimaryKeyFields() - Method in class de.julielab.xmlData.config.FieldConfig

getPrimaryKeyIndices() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Returns the indices of the primary keys, beginning with 0.

getPrimaryKeyString() - Method in class de.julielab.xmlData.config.FieldConfig

Returns the names of the columns forming the primary key in a CSV format.

getQueryBatchSize() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getReferencedTable(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Returns the name of a table referenced by an SQL-foreign-key.

getReferencedTable(String, Integer) - Method in class de.julielab.xmlData.dataBase.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.

getScheme() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getTableDefinition(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Query the MetaData for the columns of a table

getTables() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

getTableSchemaNames() - Method in class de.julielab.xmlData.config.ConfigReader

getTimestampFieldName() - Method in class de.julielab.xmlData.config.FieldConfig

getUrl() - Method in class de.julielab.xmlData.config.DBConfig

getUsername(String) - Method in class de.julielab.hiddenConfig.HiddenConfig

H

HAS_ERRORS - Static variable in class de.julielab.xmlData.Constants

hasErrors - Variable in class de.julielab.xmlData.dataBase.SubsetStatus

hasNext() - Method in class de.julielab.xmlData.dataBase.DBCThreadedIterator

hasUnfetchedRows(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

hasUnfetchedRows(String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

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

HIDDEN_CONFIG_PATH - Static variable in class de.julielab.xmlData.Constants

HiddenConfig - Class in de.julielab.hiddenConfig

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

HiddenConfig() - Constructor for class de.julielab.hiddenConfig.HiddenConfig

Reads a hidden config file in the users home directory.

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

I

importFromRowIterator(Iterator<Map<String, Object>>, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

importFromRowIterator(Iterator<Map<String, Object>>, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

importFromRowIterator(Iterator<Map<String, Object>>, String, Connection, boolean, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Internal method to import into an existing table

importFromXML(Iterable<byte[]>, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

importFromXML(Iterable<byte[]>, String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Imports XMLs into a table.

importFromXMLFile(String, String) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase.DataBaseConnector

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

IN_PROCESS - Static variable in class de.julielab.xmlData.Constants

initMirrorSubset(String, String, boolean) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

initMirrorSubset(String, String, boolean, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

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

initRandomSubset(int, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

initRandomSubset(int, String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

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

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

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

initSubset(String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

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

initSubset(String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

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

initSubsetWithWhereClause(String, String, String) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase.DataBaseConnector

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

inProcess - Variable in class de.julielab.xmlData.dataBase.SubsetStatus

IS_PROCESSED - Static variable in class de.julielab.xmlData.Constants

isBinaryDataType(String) - Static method in class de.julielab.xmlData.config.FieldConfig

isBooleanType(String) - Static method in class de.julielab.xmlData.config.FieldConfig

isDatabaseReachable() - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

isDataTable(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

isEmpty(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Tests if a table contains entries.

isIntegerType(String) - Static method in class de.julielab.xmlData.config.FieldConfig

isKnownType(String) - Static method in class de.julielab.xmlData.config.FieldConfig

isOfBinaryDataType(Map<String, String>) - Method in class de.julielab.xmlData.config.FieldConfig

isOfIntegerType(Map<String, String>) - Method in class de.julielab.xmlData.config.FieldConfig

isOfStringType(String) - Method in class de.julielab.xmlData.config.FieldConfig

isOfStringType(Map<String, String>) - Method in class de.julielab.xmlData.config.FieldConfig

isOfTimestampWithoutTZType(String) - Method in class de.julielab.xmlData.config.FieldConfig

isProcessed - Variable in class de.julielab.xmlData.dataBase.SubsetStatus

isStringType(String) - Static method in class de.julielab.xmlData.config.FieldConfig

isStringTypeArray(String) - Static method in class de.julielab.xmlData.config.FieldConfig

isSubsetTable(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Checks if the given table is a subset table.

isTimestampWithoutTZType(String) - Static method in class de.julielab.xmlData.config.FieldConfig

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

isXmlType(String) - Static method in class de.julielab.xmlData.config.FieldConfig

L

LAST_COMPONENT - Static variable in class de.julielab.xmlData.Constants

limitStr - Variable in class de.julielab.xmlData.cli.QueryOptions

listExchanger - Variable in class de.julielab.xmlData.dataBase.DBCThreadedIterator

LOG - Static variable in class de.julielab.xmlData.config.ConfigBase

LOG - Static variable in class de.julielab.xmlData.Constants

M

main(String[]) - Static method in class de.julielab.xmlData.cli.CLI

main(String[]) - Static method in class de.julielab.xmlData.cli.ExtractDeleteCitations

main(String[]) - Static method in class de.julielab.xmlData.cli.Test

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

Modifies a subset table, marking entries as processed.

mergeConfigData(byte[], byte[]) - Static method in class de.julielab.xmlData.config.ConfigReader

Inserts the user schemes into the default configuration.

META_IN_ARRAY - Static variable in class de.julielab.xmlData.dataBase.DataBaseConnector

Deprecated.

MIRROR_COLLECTION_NAME - Static variable in class de.julielab.xmlData.Constants

MIRROR_COLUMN_DATA_TABLE_NAME - Static variable in class de.julielab.xmlData.Constants

MIRROR_COLUMN_DO_RESET - Static variable in class de.julielab.xmlData.Constants

MIRROR_COLUMN_SUBSET_NAME - Static variable in class de.julielab.xmlData.Constants

modifyTable(String, List<Object[]>) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase.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.

N

next() - Method in class de.julielab.xmlData.dataBase.DBCThreadedIterator

NLM_ID_FIELD_NAME - Static variable in class de.julielab.xmlData.Constants

numberRefHops - Variable in class de.julielab.xmlData.cli.QueryOptions

P

performBatchUpdate(List<Object[]>, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

PID - Static variable in class de.julielab.xmlData.Constants

pipelineStates - Variable in class de.julielab.xmlData.dataBase.SubsetStatus

PMID_FIELD_NAME - Static variable in class de.julielab.xmlData.Constants

PROCESSED - Static variable in class de.julielab.xmlData.Constants

PROCESSING_TIMESTAMP - Static variable in class de.julielab.xmlData.Constants

pubmedArticleSet - Variable in class de.julielab.xmlData.cli.QueryOptions

Q

query(String) - Static method in class de.julielab.xmlData.cli.QueryPubMed

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

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

Returns the requested fields from the requested table.

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

Returns the requested fields from the requested table.

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

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

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

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

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

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

queryDataTable(String, String) - Method in class de.julielab.xmlData.dataBase.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) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase

QueryHelper() - Constructor for class de.julielab.xmlData.dataBase.QueryHelper

QueryOptions - Class in de.julielab.xmlData.cli

QueryOptions() - Constructor for class de.julielab.xmlData.cli.QueryOptions

QueryPubMed - Class in de.julielab.xmlData.cli

QueryPubMed() - Constructor for class de.julielab.xmlData.cli.QueryPubMed

queryStr - Variable in class de.julielab.xmlData.cli.QueryOptions

querySubset(String, long) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

querySubset(String, String, long, Integer, String) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase.DataBaseConnector

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

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

R

remove() - Method in class de.julielab.xmlData.dataBase.DBCThreadedIterator

unsupported

resetSubset(String) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase.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.xmlData.dataBase.DataBaseConnector

resetSubset(String, List<Object[]>, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

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

retrieveAndMark(String, String, String, String) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase.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.xmlData.dataBase.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.xmlData.dataBase.DataBaseConnector

Retrieves row values of table from the database.

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

Retrieves row values of table from the database.

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

Retrieves data from the database over multiple tables.

S

schemaExists(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Tests if a schema exists.

setActivePGSchema(String) - Method in class de.julielab.xmlData.config.DBConfig

setActivePGSchema(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

setActiveTableSchema(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

setDbURL(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

setException(String, ArrayList<byte[][]>, HashMap<byte[][], String>) - Method in class de.julielab.xmlData.dataBase.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.xmlData.config.FieldConfig

setHost(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

setPassword(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

setPort(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

setPort(Integer) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

setProcessed(String, ArrayList<byte[][]>) - Method in class de.julielab.xmlData.dataBase.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.xmlData.dataBase.DataBaseConnector

setUser(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

status(String, Set<DataBaseConnector.StatusElement>) - Method in class de.julielab.xmlData.dataBase.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.xmlData.config.ConfigBase

Used to get an element by its relative xpath.

subsetColumns - Static variable in class de.julielab.xmlData.dataBase.DataBaseConnector

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

SubsetStatus - Class in de.julielab.xmlData.dataBase

SubsetStatus() - Constructor for class de.julielab.xmlData.dataBase.SubsetStatus

T

tableExists(Connection, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Tests if a table exists.

tableExists(String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Tests if a table exists.

tableName - Variable in class de.julielab.xmlData.cli.QueryOptions

TableNotFoundException - Exception in de.julielab.xmlData.cli

TableNotFoundException() - Constructor for exception de.julielab.xmlData.cli.TableNotFoundException

TableNotFoundException(String) - Constructor for exception de.julielab.xmlData.cli.TableNotFoundException

tableSchema - Variable in class de.julielab.xmlData.cli.QueryOptions

TableSchemaDoesNotExistException - Exception in de.julielab.xmlData.config

TableSchemaMismatchException - Exception in de.julielab.xmlData.dataBase.util

TableSchemaMismatchException() - Constructor for exception de.julielab.xmlData.dataBase.util.TableSchemaMismatchException

TableSchemaMismatchException(String) - Constructor for exception de.julielab.xmlData.dataBase.util.TableSchemaMismatchException

TableSchemaMismatchException(String, Throwable) - Constructor for exception de.julielab.xmlData.dataBase.util.TableSchemaMismatchException

TableSchemaMismatchException(Throwable) - Constructor for exception de.julielab.xmlData.dataBase.util.TableSchemaMismatchException

TableSchemaMismatchException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.xmlData.dataBase.util.TableSchemaMismatchException

Test - Class in de.julielab.xmlData.cli

Test() - Constructor for class de.julielab.xmlData.cli.Test

ThreadedColumnsIterator - Class in de.julielab.xmlData.dataBase

Retrieves a list of fields from the requested table.

ThreadedColumnsIterator(DataBaseConnector, List<String[]>, List<String>, String, String) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsIterator

ThreadedColumnsIterator(DataBaseConnector, Connection, List<String[]>, List<String>, String, String) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsIterator

ThreadedColumnsIterator(DataBaseConnector, Connection, List<String[]>, List<String>, String, long, String) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsIterator

ThreadedColumnsIterator(DataBaseConnector, List<String>, String) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsIterator

ThreadedColumnsIterator(DataBaseConnector, Connection, List<String>, String) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsIterator

ThreadedColumnsIterator(DataBaseConnector, List<String>, String, long) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsIterator

ThreadedColumnsIterator(DataBaseConnector, Connection, List<String>, String, long) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsIterator

ThreadedColumnsToRetrieveIterator - Class in de.julielab.xmlData.dataBase

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, Connection, List<Object[]>, String, String) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsToRetrieveIterator

ThreadedColumnsToRetrieveIterator(DataBaseConnector, List<Object[]>, String, String) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsToRetrieveIterator

ThreadedColumnsToRetrieveIterator(DataBaseConnector, List<Object[]>, String, String, String) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsToRetrieveIterator

ThreadedColumnsToRetrieveIterator(DataBaseConnector, Connection, List<Object[]>, String, String, String) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsToRetrieveIterator

ThreadedColumnsToRetrieveIterator(DataBaseConnector, Connection, List<Object[]>, String[], String[]) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsToRetrieveIterator

Retrieves data from the database over multiple tables.

ThreadedColumnsToRetrieveIterator(DataBaseConnector, List<Object[]>, String[], String[]) - Constructor for class de.julielab.xmlData.dataBase.ThreadedColumnsToRetrieveIterator

TIMESTAMP_FIELD_NAME - Static variable in class de.julielab.xmlData.Constants

toString() - Method in class de.julielab.xmlData.cli.QueryOptions

toString() - Method in class de.julielab.xmlData.config.DBConfig

toString() - Method in class de.julielab.xmlData.config.FieldConfig

toString() - Method in class de.julielab.xmlData.dataBase.SubsetStatus

TOTAL - Static variable in class de.julielab.xmlData.Constants

total - Variable in class de.julielab.xmlData.dataBase.SubsetStatus

TYPE_BINARY_DATA - Static variable in class de.julielab.xmlData.Constants

TYPE_BOOLEAN - Static variable in class de.julielab.xmlData.Constants

TYPE_INTEGER - Static variable in class de.julielab.xmlData.Constants

TYPE_TEXT - Static variable in class de.julielab.xmlData.Constants

TYPE_TEXT_ARRAY - Static variable in class de.julielab.xmlData.Constants

TYPE_TIMESTAMP_WITHOUT_TIMEZONE - Static variable in class de.julielab.xmlData.Constants

Constant for a possible value of type.

TYPE_VARCHAR_ARRAY - Static variable in class de.julielab.xmlData.Constants

TYPE_XML - Static variable in class de.julielab.xmlData.Constants

U

UnobtainableConnectionException - Exception in de.julielab.xmlData.dataBase.util

UnobtainableConnectionException() - Constructor for exception de.julielab.xmlData.dataBase.util.UnobtainableConnectionException

UnobtainableConnectionException(String) - Constructor for exception de.julielab.xmlData.dataBase.util.UnobtainableConnectionException

UnobtainableConnectionException(String, Throwable) - Constructor for exception de.julielab.xmlData.dataBase.util.UnobtainableConnectionException

UnobtainableConnectionException(Throwable) - Constructor for exception de.julielab.xmlData.dataBase.util.UnobtainableConnectionException

UnobtainableConnectionException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.xmlData.dataBase.util.UnobtainableConnectionException

update() - Method in class de.julielab.xmlData.dataBase.DBCThreadedIterator

updateFromRowIterator(Iterator<Map<String, Object>>, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Updates a table with the entries yielded by the iterator.

updateFromRowIterator(Iterator<Map<String, Object>>, String, Connection, boolean, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Updates a table with the entries yielded by the iterator.

updateFromXML(String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

updateFromXML(String, String, String) - Method in class de.julielab.xmlData.dataBase.DataBaseConnector

Updates an existing database.

useDelimiter - Variable in class de.julielab.xmlData.cli.QueryOptions

USER_SCHEME_DEFINITION - Static variable in class de.julielab.xmlData.cli.CLI

V

VALUE - Static variable in class de.julielab.xmlData.Constants

valueOf(String) - Static method in enum de.julielab.xmlData.dataBase.DataBaseConnector.StatusElement

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

values() - Static method in enum de.julielab.xmlData.dataBase.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.xmlData.cli.QueryOptions

writeDocumentsIntoMedlineCitationSet(Iterator<byte[][]>, int) - Method in class de.julielab.medline.DBCMedlineUtilities

X

XML_FIELD_NAME - Static variable in class de.julielab.xmlData.Constants

xpath - Variable in class de.julielab.xmlData.cli.QueryOptions

XPATH_ACTIVE_DB - Static variable in class de.julielab.xmlData.config.ConfigReader

XPATH_ACTIVE_PG_SCHEMA - Static variable in class de.julielab.xmlData.config.ConfigReader

XPATH_ACTIVE_TABLE_SCHEMA - Static variable in class de.julielab.xmlData.config.ConfigReader

XPATH_CONF_DB - Static variable in class de.julielab.xmlData.config.ConfigReader

XPATH_CONF_DBS - Static variable in class de.julielab.xmlData.config.ConfigReader

XPATH_CONF_SCHEMA - Static variable in class de.julielab.xmlData.config.ConfigReader

XPATH_CONF_SCHEMAS - Static variable in class de.julielab.xmlData.config.ConfigReader

XPATH_MAX_CONNS - Static variable in class de.julielab.xmlData.config.ConfigReader

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