Package psidev.psi.mi.jami.bridges.imex

Class DefaultImexCentralClient

java.lang.Object

psidev.psi.mi.jami.bridges.imex.DefaultImexCentralClient

All Implemented Interfaces:

PublicationFetcher, ImexCentralClient

public class DefaultImexCentralClient
extends Object
implements ImexCentralClient

Default IMEx Central Client.

Field Summary

Fields inherited from interface psidev.psi.mi.jami.bridges.imex.ImexCentralClient

IC_BETA, IC_PROD, IC_TEST, IDENTIFIER_MISSING, IDENTIFIER_UNKNOWN, INTERNAL_SERVER_ERROR, NO_IMEX_ID, NO_RECORD, NO_RECORD_CREATED, OPERATION_NOT_SUPPORTED, OPERATION_NOT_VALID, pubmed_regexp, STATUS_UNKNOWN, UNKNOWN_GROUP, UNKNOWN_USER, USER_NOT_AUTHORIZED

Constructor Summary

Constructors

Constructor	Description
DefaultImexCentralClient(String username, String password, String endPoint)	Constructor for DefaultImexCentralClient.

Method Summary

Modifier and Type	Method	Description
void	createPublication(Publication publication)	Create a new publication record in IMEx central (not implemented yet in production but can be used in test with the MockImexCentralClient)
Publication	createPublicationById(String identifier, String source)	Creates a publication given a valid pubmed id.
Publication	fetchByIdentifier(String identifier, String source)	Uses the identifier to search for a publication and return a completed record.
Collection<Publication>	fetchByIdentifiers(Map<String,Collection<String>> identifiers)	Uses the identifiers to search for publications and return completed records.
Publication	fetchPublicationImexAccession(String identifier, String source, boolean aBoolean)	Create a new IMEx id if requested for a given pubmed id
List<Publication>	fetchPublicationsByOwner(String owner, int first, int max)	Collect a list of publications associated with a specific owner.
List<Publication>	fetchPublicationsByStatus(String status, int first, int max)	Collect a list of publications having a specific status.
String	getEndpoint()	getEndpoint.
Publication	updatePublicationAdminGroup(String identifier, String source, Operation operation, String group)	Update the publication admin group given a valid pubmed identifier and a valid operator.
Publication	updatePublicationAdminUser(String identifier, String source, Operation operation, String user)	Update the publication admin user given a valid pubmed identifier and a valid operator.
Publication	updatePublicationIdentifier(String oldIdentifier, String oldSource, String newIdentifier, String source)	Update publication pubmed identifier, DOI number or internal identifier of an existing record in IMEx central.
Publication	updatePublicationStatus(String identifier, String source, PublicationStatus status)	Update the status of a publication associated with a valid pubmed identifier already registered in IMEx central

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultImexCentralClient

public DefaultImexCentralClient(String username,
                                String password,
                                String endPoint)
                         throws BridgeFailedException

Constructor for DefaultImexCentralClient.

Parameters:

username - a String object.

password - a String object.

endPoint - a String object.

Throws:

BridgeFailedException - if any.

Method Detail

getEndpoint

public String getEndpoint()

getEndpoint.

Specified by:

getEndpoint in interface ImexCentralClient

Returns:

a String object.

fetchPublicationsByOwner

public List<Publication> fetchPublicationsByOwner(String owner,
                                                  int first,
                                                  int max)
                                           throws BridgeFailedException

Collect a list of publications associated with a specific owner. Selects first and last results

Specified by:

fetchPublicationsByOwner in interface ImexCentralClient

Parameters:

owner - : login of owner

first - : first result

max - : last result

Returns:

list of publications associated with this owner, empty list if no results

Throws:

BridgeFailedException - if any.

fetchPublicationsByStatus

public List<Publication> fetchPublicationsByStatus(String status,
                                                   int first,
                                                   int max)
                                            throws BridgeFailedException

Collect a list of publications having a specific status. Selects first and last results

Specified by:

fetchPublicationsByStatus in interface ImexCentralClient

Parameters:

status - : the status of publication in IMEx central

first - : first result

max - : last result

Returns:

list of publications associated with this status, empty list if no results

Throws:

BridgeFailedException - if any.

updatePublicationStatus

public Publication updatePublicationStatus(String identifier,
                                           String source,
                                           PublicationStatus status)
                                    throws BridgeFailedException

Update the status of a publication associated with a valid pubmed identifier already registered in IMEx central

Specified by:

updatePublicationStatus in interface ImexCentralClient

Parameters:

identifier - : a valid pubmed identifier

source - : the source pubmed, doi or imex

status - : new status

Returns:

the updated record in IMEx central

Throws:

BridgeFailedException - if no record found in IMEx central, no pubmed identifier or invalid status

updatePublicationAdminGroup

public Publication updatePublicationAdminGroup(String identifier,
                                               String source,
                                               Operation operation,
                                               String group)
                                        throws BridgeFailedException

Update the publication admin group given a valid pubmed identifier and a valid operator. The publication must be registered in IMEx central

Specified by:

updatePublicationAdminGroup in interface ImexCentralClient

Parameters:

identifier - : valid pubmed id

source - : the source pubmed, doi or imex

operation - : DROP or ADD

group - : the name of the admin group

Returns:

the updated record in IMEx central

Throws:

BridgeFailedException - if no record found in IMEX central, no pubmed identifiier or unknown group

updatePublicationAdminUser

public Publication updatePublicationAdminUser(String identifier,
                                              String source,
                                              Operation operation,
                                              String user)
                                       throws BridgeFailedException

Update the publication admin user given a valid pubmed identifier and a valid operator. The publication must be registered in IMEx central

Specified by:

updatePublicationAdminUser in interface ImexCentralClient

Parameters:

identifier - a String object.

source - pubmed, doi or imex

operation - a Operation object.

user - a String object.

Returns:

the updated record in IMEx central

Throws:

BridgeFailedException - if no record found in IMEX central, no pubmed identifiier or unknown user

updatePublicationIdentifier

public Publication updatePublicationIdentifier(String oldIdentifier,
                                               String oldSource,
                                               String newIdentifier,
                                               String source)
                                        throws BridgeFailedException

Update publication pubmed identifier, DOI number or internal identifier of an existing record in IMEx central. The new publication identifier should not be already registered in IMEx central

Specified by:

updatePublicationIdentifier in interface ImexCentralClient

Parameters:

oldIdentifier - : can be pubmed, imex, doi or internal identifier

oldSource - : the source of old identifier

newIdentifier - : can be pubmed, doi or internal identifier

source - : the source pubmed, doi or imex

Returns:

a Publication object.

Throws:

BridgeFailedException - if no record found in IMEX central, identifier not recognized or new identifier is associated with another publication in IMEx central

createPublication

public void createPublication(Publication publication)
                       throws BridgeFailedException

Create a new publication record in IMEx central (not implemented yet in production but can be used in test with the MockImexCentralClient)

Specified by:

createPublication in interface ImexCentralClient

Parameters:

publication - : the publication to create in IMEx central

Throws:

BridgeFailedException - if any.

createPublicationById

public Publication createPublicationById(String identifier,
                                         String source)
                                  throws BridgeFailedException

Creates a publication given a valid pubmed id.

Specified by:

createPublicationById in interface ImexCentralClient

Parameters:

identifier - : valid pubmed id

source - a String object.

Returns:

the newly created record

Throws:

BridgeFailedException - if identifier is not valid pubmed or if the pubmed id is already registered in IMEx central

fetchPublicationImexAccession

public Publication fetchPublicationImexAccession(String identifier,
                                                 String source,
                                                 boolean aBoolean)
                                          throws BridgeFailedException

Create a new IMEx id if requested for a given pubmed id

Specified by:

fetchPublicationImexAccession in interface ImexCentralClient

Parameters:

identifier - : a valid pubmed identifier

source - : a valid source (imex, pubmed or doi)

aBoolean - : true if we want to assign a new IMEx id, false otherwise

Returns:

the updated record in IMEx central

Throws:

BridgeFailedException - if not a valid pubmed id, not existing record and cannot generate a new IMEx id

fetchByIdentifier

public Publication fetchByIdentifier(String identifier,
                                     String source)
                              throws BridgeFailedException

Uses the identifier to search for a publication and return a completed record.

Specified by:

fetchByIdentifier in interface PublicationFetcher

Parameters:

identifier - The identifier of the publication to search for.

source - The database that the identifier is from (pubmed, doi, ...).

Returns:

A completed record for the publication or null if no publication could be found.

Throws:

BridgeFailedException - if any.

fetchByIdentifiers

public Collection<Publication> fetchByIdentifiers(Map<String,Collection<String>> identifiers)
                                           throws BridgeFailedException

Uses the identifiers to search for publications and return completed records.

Specified by:

fetchByIdentifiers in interface PublicationFetcher

Parameters:

identifiers - The identifiers of the publications to search for per publication identifier source (pubmed, doi, ...).

Returns:

Completed records for the publications.

Throws:

BridgeFailedException - if any.