de.julielab.jcore.reader.xml

Class XMLDBReader

java.lang.Object

org.apache.uima.resource.Resource_ImplBase

org.apache.uima.resource.ConfigurableResource_ImplBase

org.apache.uima.collection.CollectionReader_ImplBase

org.apache.uima.fit.component.JCasCollectionReader_ImplBase

de.julielab.jcore.reader.db.DBReaderBase

de.julielab.jcore.reader.db.DBSubsetReader

de.julielab.jcore.reader.db.DBReader

de.julielab.jcore.reader.xml.XMLDBReader

All Implemented Interfaces:

org.apache.uima.collection.base_cpm.BaseCollectionReader, org.apache.uima.collection.CollectionReader, org.apache.uima.resource.ConfigurableResource, org.apache.uima.resource.Resource

public class XMLDBReader
extends de.julielab.jcore.reader.db.DBReader

An UIMA CollectionReader that implements DBReader (a class that gets Documents by DB-based informations) using the XMLMapper

Author:

faessler

Nested Class Summary

Nested classes/interfaces inherited from class de.julielab.jcore.reader.db.DBReader

de.julielab.jcore.reader.db.DBReader.RetrievingThread

Field Summary

Fields

Modifier and Type	Field and Description
static String	DESC_MAPPING_FILE
static String	DESC_ROW_MAPPING
protected String	mappingFileStr
static String	PARAM_MAPPING_FILE
static String	PARAM_ROW_MAPPING
protected int	processedDocuments
protected String[]	rowMappingArray
protected int	totalDocumentCount
protected de.julielab.jcore.reader.xmlmapper.mapper.XMLMapper	xmlMapper Mapper which maps medline XML to a CAS with the specified UIMA type system via an XML configuration file.

Fields inherited from class de.julielab.jcore.reader.db.DBReader

dataTimestamp

Fields inherited from class de.julielab.jcore.reader.db.DBSubsetReader

additionalTableNames, additionalTableSchemas, dataTable, fetchIdsProactively, hostName, PARAM_ADDITIONAL_TABLES, PARAM_ADDITONAL_TABLES_STORAGE_PG_SCHEMA, PARAM_RESET_TABLE, pid, readDataTable, resetTable, schemas, tables

Fields inherited from class de.julielab.jcore.reader.db.DBReaderBase

batchSize, costosysConfig, dbc, driver, hasNext, joinTables, limitParameter, numberFetchedDocIDs, PARAM_BATCH_SIZE, PARAM_COSTOSYS_CONFIG_NAME, PARAM_TABLE, selectionOrder, tableName, whereCondition

Fields inherited from interface org.apache.uima.resource.Resource

PARAM_AGGREGATE_SOFA_MAPPINGS, PARAM_CONFIG_MANAGER, PARAM_CONFIG_PARAM_SETTINGS, PARAM_EXTERNAL_OVERRIDE_SETTINGS, PARAM_PERFORMANCE_TUNING_SETTINGS, PARAM_RESOURCE_MANAGER, PARAM_UIMA_CONTEXT

Constructor Summary

Constructors

Constructor and Description
XMLDBReader()

Method Summary

Modifier and Type	Method and Description
void	getNext(org.apache.uima.jcas.JCas jcas)
protected String	getReaderComponentName()
void	initialize(org.apache.uima.UimaContext context)

Methods inherited from class de.julielab.jcore.reader.db.DBReader

close, getNextArtifactData, getProgress, hasNext, setDBProcessingMetaData

Methods inherited from class de.julielab.jcore.reader.db.DBSubsetReader

checkAdditionalTableParameters, checkAndAdjustAdditionalTables, getAllRetrievedColumns

Methods inherited from class org.apache.uima.fit.component.JCasCollectionReader_ImplBase

getLogger, getNext, initialize

Methods inherited from class org.apache.uima.collection.CollectionReader_ImplBase

destroy, getCasInitializer, getProcessingResourceMetaData, initialize, isConsuming, reconfigure, setCasInitializer, typeSystemInit

Methods inherited from class org.apache.uima.resource.ConfigurableResource_ImplBase

getConfigParameterValue, getConfigParameterValue, setConfigParameterValue, setConfigParameterValue

Methods inherited from class org.apache.uima.resource.Resource_ImplBase

getCasManager, getMetaData, getRelativePathResolver, getResourceManager, getUimaContext, getUimaContextAdmin, setLogger, setMetaData

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.apache.uima.resource.ConfigurableResource

getConfigParameterValue, getConfigParameterValue, setConfigParameterValue, setConfigParameterValue

Methods inherited from interface org.apache.uima.resource.Resource

getMetaData, getResourceManager, getUimaContext, getUimaContextAdmin, setLogger

Field Detail

PARAM_ROW_MAPPING

public static final String PARAM_ROW_MAPPING

See Also:

Constant Field Values

PARAM_MAPPING_FILE

public static final String PARAM_MAPPING_FILE

See Also:

Constant Field Values

xmlMapper

protected de.julielab.jcore.reader.xmlmapper.mapper.XMLMapper xmlMapper

Mapper which maps medline XML to a CAS with the specified UIMA type system via an XML configuration file.

totalDocumentCount

protected int totalDocumentCount

processedDocuments

protected int processedDocuments

DESC_ROW_MAPPING

public static final String DESC_ROW_MAPPING

See Also:

Constant Field Values

rowMappingArray

protected String[] rowMappingArray

DESC_MAPPING_FILE

public static final String DESC_MAPPING_FILE

See Also:

Constant Field Values

mappingFileStr

protected String mappingFileStr

Constructor Detail

XMLDBReader

public XMLDBReader()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext context)
                throws org.apache.uima.resource.ResourceInitializationException

Overrides:

initialize in class de.julielab.jcore.reader.db.DBReader

Throws:

org.apache.uima.resource.ResourceInitializationException

getNext

public void getNext(org.apache.uima.jcas.JCas jcas)
             throws IOException,
                    org.apache.uima.collection.CollectionException

Specified by:

getNext in class org.apache.uima.fit.component.JCasCollectionReader_ImplBase

Throws:

IOException

org.apache.uima.collection.CollectionException

getReaderComponentName

protected String getReaderComponentName()

Specified by:

getReaderComponentName in class de.julielab.jcore.reader.db.DBReader