Package org.dspace.importer.external.pubmed.service

Class PubmedImportMetadataSourceServiceImpl

java.lang.Object

org.dspace.importer.external.service.components.AbstractRemoteMetadataSource

org.dspace.importer.external.service.AbstractImportMetadataSourceService<org.apache.axiom.om.OMElement>

org.dspace.importer.external.pubmed.service.PubmedImportMetadataSourceServiceImpl

All Implemented Interfaces:

FileSource, MetadataSource, QuerySource

public class PubmedImportMetadataSourceServiceImpl
extends AbstractImportMetadataSourceService<org.apache.axiom.om.OMElement>
implements QuerySource, FileSource

Implements a data source for querying PubMed Central

Author:

Roeland Dillen (roeland at atmire dot com), Pasquale Cavallo (pasquale.cavallo at 4science dot it)

Field Summary

Fields

Modifier and Type	Field	Description
protected javax.ws.rs.client.WebTarget	pubmedWebTarget

Fields inherited from class org.dspace.importer.external.service.components.AbstractRemoteMetadataSource

error, exceptionHandlersMap, interRequestTime, lastRequest, lock, maxRetry, operationId, retry, warning

Constructor Summary

Constructors

Constructor	Description
PubmedImportMetadataSourceServiceImpl()

Method Summary

Modifier and Type	Method	Description
Collection<ImportRecord>	findMatchingRecords(Item item)	Finds records based on an item
Collection<ImportRecord>	findMatchingRecords(Query query)	Finds records based on query object.
String	getBaseAddress()	Return the baseAddress set to this object
String	getImportSource()	The string that identifies this import implementation.
ImportRecord	getRecord(InputStream inputStream)	Return an ImportRecord constructed from input file.
ImportRecord	getRecord(String id)	Get a single record from the source.
ImportRecord	getRecord(Query query)	Get a single record from the source.
List<ImportRecord>	getRecords(InputStream inputStream)	Return a list of ImportRecord constructed from input file.
Collection<ImportRecord>	getRecords(String query, int start, int count)	Find the number of records matching a string query.
Collection<ImportRecord>	getRecords(Query query)	Find records based on a object query.
int	getRecordsCount(String query)	Find the number of records matching a query;
int	getRecordsCount(Query query)	Find the number of records matching a query;
List<String>	getSupportedExtensions()	Get the file extensions (xml, csv, txt, ...) supported by the FileSource
void	init()	Initialize the class
void	setBaseAddress(String baseAddress)	Set the baseAddress to this object
void	setSupportedExtensions(List<String> supportedExtensions)	Set the file extensions supported by this metadata service

Methods inherited from class org.dspace.importer.external.service.AbstractImportMetadataSourceService

getGenerateQueryForItem, getMetadataFieldMapping, setGenerateQueryForItem, setMetadataFieldMapping, transformSourceRecords

Methods inherited from class org.dspace.importer.external.service.components.AbstractRemoteMetadataSource

getError, getExceptionHandler, getMaxRetry, getOperationId, getRetry, getWarning, handleException, initExceptionHandlers, retry, setError, setMaxRetry, setWarning, throwSourceException, throwSourceExceptionHook

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.dspace.importer.external.service.components.FileSource

isValidSourceForFile

Field Detail

pubmedWebTarget

protected javax.ws.rs.client.WebTarget pubmedWebTarget

Constructor Detail

PubmedImportMetadataSourceServiceImpl

public PubmedImportMetadataSourceServiceImpl()

Method Detail

setSupportedExtensions

public void setSupportedExtensions(List<String> supportedExtensions)

Set the file extensions supported by this metadata service

Parameters:

supportedExtensionsthe - file extensions (xml,txt,...) supported by this service

getSupportedExtensions

public List<String> getSupportedExtensions()

Description copied from interface: FileSource

Get the file extensions (xml, csv, txt, ...) supported by the FileSource

Specified by:

getSupportedExtensions in interface FileSource

getRecordsCount

public int getRecordsCount(String query)
                    throws MetadataSourceException

Find the number of records matching a query;

Specified by:

getRecordsCount in interface QuerySource

Parameters:

query - a query string to base the search on.

Returns:

the sum of the matching records over this import source

Throws:

MetadataSourceException - if the underlying methods throw any exception.

getRecordsCount

public int getRecordsCount(Query query)
                    throws MetadataSourceException

Find the number of records matching a query;

Specified by:

getRecordsCount in interface QuerySource

Parameters:

query - a query object to base the search on.

Returns:

the sum of the matching records over this import source

Throws:

MetadataSourceException - if the underlying methods throw any exception.

getRecords

public Collection<ImportRecord> getRecords(String query,
                                           int start,
                                           int count)
                                    throws MetadataSourceException

Find the number of records matching a string query. Supports pagination

Specified by:

getRecords in interface QuerySource

Parameters:

query - a query string to base the search on.

start - offset to start at

count - number of records to retrieve.

Returns:

a set of records. Fully transformed.

Throws:

MetadataSourceException - if the underlying methods throw any exception.

getRecords

public Collection<ImportRecord> getRecords(Query query)
                                    throws MetadataSourceException

Find records based on a object query.

Specified by:

getRecords in interface QuerySource

Parameters:

query - a query object to base the search on.

Returns:

a set of records. Fully transformed.

Throws:

MetadataSourceException - if the underlying methods throw any exception.

getRecord

public ImportRecord getRecord(String id)
                       throws MetadataSourceException

Get a single record from the source.

Specified by:

getRecord in interface QuerySource

Parameters:

id - identifier for the record

Returns:

the first matching record

Throws:

MetadataSourceException - if the underlying methods throw any exception.

getRecord

public ImportRecord getRecord(Query query)
                       throws MetadataSourceException

Get a single record from the source.

Specified by:

getRecord in interface QuerySource

Parameters:

query - a query matching a single record

Returns:

the first matching record

Throws:

MetadataSourceException - if the underlying methods throw any exception.

getImportSource

public String getImportSource()

The string that identifies this import implementation. Preferable a URI

Specified by:

getImportSource in interface MetadataSource

Returns:

the identifying uri

findMatchingRecords

public Collection<ImportRecord> findMatchingRecords(Item item)
                                             throws MetadataSourceException

Finds records based on an item

Specified by:

findMatchingRecords in interface QuerySource

Parameters:

item - an item to base the search on

Returns:

a collection of import records. Only the identifier of the found records may be put in the record.

Throws:

MetadataSourceException - if the underlying methods throw any exception.

findMatchingRecords

public Collection<ImportRecord> findMatchingRecords(Query query)
                                             throws MetadataSourceException

Finds records based on query object. Delegates to one or more MetadataSource implementations based on the uri. Results will be aggregated.

Specified by:

findMatchingRecords in interface QuerySource

Parameters:

query - a query object to base the search on.

Returns:

a collection of import records. Only the identifier of the found records may be put in the record.

Throws:

MetadataSourceException - if the underlying methods throw any exception.

init

public void init()
          throws Exception

Initialize the class

Specified by:

init in class AbstractRemoteMetadataSource

Throws:

Exception - on generic exception

getBaseAddress

public String getBaseAddress()

Return the baseAddress set to this object

Returns:

The String object that represents the baseAddress of this object

setBaseAddress

public void setBaseAddress(String baseAddress)

Set the baseAddress to this object

Parameters:

baseAddress - The String object that represents the baseAddress of this object

getRecords

public List<ImportRecord> getRecords(InputStream inputStream)
                              throws FileSourceException

Description copied from interface: FileSource

Return a list of ImportRecord constructed from input file.

Specified by:

getRecords in interface FileSource

Returns:

A list of ImportRecord

Throws:

FileSourceException - if, for any reason, the file is not parsable

getRecord

public ImportRecord getRecord(InputStream inputStream)
                       throws FileSourceException,
                              FileMultipleOccurencesException

Description copied from interface: FileSource

Return an ImportRecord constructed from input file.

Specified by:

getRecord in interface FileSource

Returns:

An ImportRecord matching the file content

Throws:

FileSourceException - if, for any reason, the file is not parsable

FileMultipleOccurencesException - if the file contains more than one entry