Package org.dspace.importer.external.pubmedeurope

Class PubmedEuropeMetadataSourceServiceImpl

java.lang.Object

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

org.dspace.importer.external.service.AbstractImportMetadataSourceService<org.jdom2.Element>

org.dspace.importer.external.pubmedeurope.PubmedEuropeMetadataSourceServiceImpl

All Implemented Interfaces:

MetadataSource, QuerySource

public class PubmedEuropeMetadataSourceServiceImpl
extends AbstractImportMetadataSourceService<org.jdom2.Element>
implements QuerySource

Implements a data source for querying PubMed Europe

Author:

Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	PubmedEuropeMetadataSourceServiceImpl.FindMatchingRecordCallable	This class is a Callable implementation to search PubMed Europe entries using author, title and year.

Field Summary

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
PubmedEuropeMetadataSourceServiceImpl()

Method Summary

Modifier and Type	Method	Description
Integer	count(String query)	Returns the total number of PubMed Europe publications returned by a specific query
Collection<ImportRecord>	findMatchingRecords(Item item)	Finds records based on an item Delegates to one or more MetadataSource implementations based on the uri.
Collection<ImportRecord>	findMatchingRecords(Query query)	Finds records based on query object.
List<ImportRecord>	getByPubmedEuropeID(String pubmedID, Integer start, Integer size)
String	getImportSource()	The string that identifies this import implementation.
ImportRecord	getRecord(String id)	Get a single record from the PubMed Europe.
ImportRecord	getRecord(Query query)	Get a single record from the PubMed Europe.
Collection<ImportRecord>	getRecords(String query, int start, int count)	Find 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;
String	getUrl()
void	init()	Attempts to init a session
List<ImportRecord>	search(String query, Integer size, Integer start)	Returns a list of PubMed Europe publication records
List<ImportRecord>	search(String title, String author, int year, int count, int start)
void	setUrl(String url)

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, setInterRequestTime, setMaxRetry, setWarning, throwSourceException, throwSourceExceptionHook

Methods inherited from class java.lang.Object

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

Constructor Detail

PubmedEuropeMetadataSourceServiceImpl

public PubmedEuropeMetadataSourceServiceImpl()

Method Detail

getImportSource

public String getImportSource()

Description copied from interface: MetadataSource

The string that identifies this import implementation. Preferable a URI

Specified by:

getImportSource in interface MetadataSource

Returns:

the identifying uri

getRecord

public ImportRecord getRecord(String id)
                       throws MetadataSourceException

Get a single record from the PubMed Europe.

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.

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 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.

getRecords

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

Find records matching a string query.

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(Query query)
                       throws MetadataSourceException

Get a single record from the PubMed Europe.

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.

findMatchingRecords

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

Finds records based on query object.

Specified by:

findMatchingRecords in interface QuerySource

Parameters:

query - A query object to base the search on.

Returns:

A collection of import records.

Throws:

MetadataSourceException - If the underlying methods throw any exception.

findMatchingRecords

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

Description copied from interface: QuerySource

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

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.

init

public void init()
          throws Exception

Description copied from class: AbstractRemoteMetadataSource

Attempts to init a session

Specified by:

init in class AbstractRemoteMetadataSource

Throws:

Exception - on generic exception

getByPubmedEuropeID

public List<ImportRecord> getByPubmedEuropeID(String pubmedID,
                                              Integer start,
                                              Integer size)
                                       throws IOException,
                                              org.apache.http.HttpException

Throws:

IOException

org.apache.http.HttpException

count

public Integer count(String query)
              throws URISyntaxException,
                     org.apache.http.client.ClientProtocolException,
                     IOException,
                     org.jaxen.JaxenException

Returns the total number of PubMed Europe publications returned by a specific query

Parameters:

query - A keyword or combination of keywords to be searched

Throws:

URISyntaxException - If URI syntax error

org.apache.http.client.ClientProtocolException - The client protocol exception

IOException - If IO error

org.jaxen.JaxenException - If Xpath evaluation failed

search

public List<ImportRecord> search(String title,
                                 String author,
                                 int year,
                                 int count,
                                 int start)
                          throws IOException

Throws:

IOException

search

public List<ImportRecord> search(String query,
                                 Integer size,
                                 Integer start)
                          throws IOException

Returns a list of PubMed Europe publication records

Parameters:

query - A keyword or combination of keywords to be searched

size - The number of search results per page

start - Start number for the acquired search result list

Throws:

IOException - If IO error

getUrl

public String getUrl()

setUrl

public void setUrl(String url)