Package de.julielab.jcore.reader.db

Class DBReader

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

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 abstract class DBReader
extends DBSubsetReader

Base for UIMA collection readers using a (PostgreSQL) database to retrieve their documents from.

The reader interacts with two tables: One 'subset' table listing the document collection with one document per row. Additionally, each row contains fields for information about current processing status of a document as well as error status and processing host. This table will be locked while getting a batch of documents to process, thus it furthermore serves as a synchronization medium.

The second table holds the actual data, thus we say 'data table'. The subset table has to define foreign keys to the data table. In this way, the reader is able to determine from which table to retrieve the document data.

This data management is done by the julie-medline-manager package.

Please note that this class does not implement JCasCollectionReader_ImplBase.getNext(org.apache.uima.cas.CAS). Instead, getNextArtifactData() is offered to expose the documents read from the database. Until this point, no assumption about the document's structure has been made. That is, we don't care in this class whether we deal with Medline abstracts, plain texts, some HTML documents or whatever. Translating these documents into a CAS with respect to a particular type system is delegated to the extending class.

Author:

landefeld/hellrich/faessler

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected class	DBReader.RetrievingThread	This class is charged with retrieving batches of document IDs and documents while previously fetched documents are in process.

Field Summary

Fields

Modifier and Type	Field	Description
protected String	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, processedDocuments, selectionOrder, tableName, totalDocumentCount, 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
DBReader()

Method Summary

Modifier and Type	Method	Description
void	close()
byte[][]	getNextArtifactData()	Returns the next byte[][] containing a byte[] for the pmid at [0] and a byte[] for the XML at [1] or null if there are no unprocessed documents left.
org.apache.uima.util.Progress[]	getProgress()
protected abstract String	getReaderComponentName()
boolean	hasNext()
void	initialize(org.apache.uima.UimaContext context)
static String	setDBProcessingMetaData(de.julielab.costosys.dbconnection.DataBaseConnector dbc, boolean readDataTable, String tableName, byte[][] data, org.apache.uima.jcas.JCas cas)

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, 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

dataTimestamp

protected String dataTimestamp

Constructor Detail

DBReader

public DBReader()

Method Detail

setDBProcessingMetaData

public static String setDBProcessingMetaData(de.julielab.costosys.dbconnection.DataBaseConnector dbc,
                                             boolean readDataTable,
                                             String tableName,
                                             byte[][] data,
                                             org.apache.uima.jcas.JCas cas)

initialize

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

Overrides:

initialize in class DBSubsetReader

Throws:

org.apache.uima.resource.ResourceInitializationException

hasNext

public boolean hasNext()
                throws IOException,
                       org.apache.uima.collection.CollectionException

Throws:

IOException

org.apache.uima.collection.CollectionException

getNextArtifactData

public byte[][] getNextArtifactData()
                             throws org.apache.uima.collection.CollectionException

Returns the next byte[][] containing a byte[] for the pmid at [0] and a byte[] for the XML at [1] or null if there are no unprocessed documents left.

Returns:

Document document - the document

Throws:

org.apache.uima.collection.CollectionException

getProgress

public org.apache.uima.util.Progress[] getProgress()

close

public void close()

Specified by:

close in interface org.apache.uima.collection.base_cpm.BaseCollectionReader

Overrides:

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

getReaderComponentName

protected abstract String getReaderComponentName()

Returns:

The component name of the reader to fill in the subset table's pipeline status field