Package de.julielab.jcore.reader.xml

Class 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 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 Description
      XMLDBReader()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method 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 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

      • 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

      • rowMappingArray

        protected String[] rowMappingArray

      • 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