org.molgenis.wikipathways.client

Class WikiPathwaysRESTBindingStub

java.lang.Object

org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub

All Implemented Interfaces:

Remote, WikiPathwaysPortType

public class WikiPathwaysRESTBindingStub
extends Object
implements WikiPathwaysPortType

connects to the new WikiPathways REST webservice

Author:

msk

Constructor Summary

Constructors

Constructor and Description
WikiPathwaysRESTBindingStub(org.apache.http.client.HttpClient client, String baseUrl)

Method Summary

Modifier and Type	Method and Description
WSPathwayInfo	createPathway(String gpml, WSAuth auth)
WSSearchResult[]	findInteractions(String query)
WSSearchResult[]	findPathwaysByLiterature(String query)
WSSearchResult[]	findPathwaysByText(String query, String species)
WSSearchResult[]	findPathwaysByXref(String[] ids, String[] codes)
byte[]	getColoredPathway(String pwId, String revision, String[] graphId, String[] color, String fileType)
WSCurationTagHistory[]	getCurationTagHistory(String pwId, String timestamp)
WSCurationTag[]	getCurationTags(String pwId)
WSCurationTag[]	getCurationTagsByName(String tagName)
WSOntologyTerm[]	getOntologyTermsByPathway(String pwId)
WSPathway	getPathway(String pwId, int revision)
byte[]	getPathwayAs(String fileType, String pwId, int revision)
WSPathwayHistory	getPathwayHistory(String pwId, String timestamp)
WSPathwayInfo	getPathwayInfo(String pwId)
WSPathwayInfo[]	getPathwaysByOntologyTerm(String term)
WSPathwayInfo[]	getPathwaysByParentOntologyTerm(String term)
WSPathwayInfo[]	getRecentChanges(String timestamp)
String	getUserByOrcid(String orcid)
String[]	getXrefList(String pwId, String code)
String[]	listOrganisms()
WSPathwayInfo[]	listPathways(String organism)
String	login(String name, String pass)
boolean	removeCurationTag(String pwId, String tagName, WSAuth auth)
boolean	removeOntologyTag(String pwId, String termId, WSAuth auth)
boolean	saveCurationTag(String pwId, String tagName, String tagText, int revision, WSAuth auth)
boolean	saveOntologyTag(String pwId, String term, String termId, WSAuth auth)
boolean	updatePathway(String pwId, String description, String gpml, int revision, WSAuth auth)

Methods inherited from class java.lang.Object

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

Constructor Detail

WikiPathwaysRESTBindingStub

public WikiPathwaysRESTBindingStub(org.apache.http.client.HttpClient client,
                                   String baseUrl)

Method Detail

findInteractions

public WSSearchResult[] findInteractions(String query)
                                  throws RemoteException

Specified by:

findInteractions in interface WikiPathwaysPortType

Throws:

RemoteException

findPathwaysByLiterature

public WSSearchResult[] findPathwaysByLiterature(String query)
                                          throws RemoteException

Specified by:

findPathwaysByLiterature in interface WikiPathwaysPortType

Throws:

RemoteException

findPathwaysByText

public WSSearchResult[] findPathwaysByText(String query,
                                           String species)
                                    throws RemoteException

Specified by:

findPathwaysByText in interface WikiPathwaysPortType

Throws:

RemoteException

findPathwaysByXref

public WSSearchResult[] findPathwaysByXref(String[] ids,
                                           String[] codes)
                                    throws RemoteException

Specified by:

findPathwaysByXref in interface WikiPathwaysPortType

Throws:

RemoteException

getColoredPathway

public byte[] getColoredPathway(String pwId,
                                String revision,
                                String[] graphId,
                                String[] color,
                                String fileType)
                         throws RemoteException

Specified by:

getColoredPathway in interface WikiPathwaysPortType

Throws:

RemoteException

getCurationTagHistory

public WSCurationTagHistory[] getCurationTagHistory(String pwId,
                                                    String timestamp)
                                             throws RemoteException

Specified by:

getCurationTagHistory in interface WikiPathwaysPortType

Throws:

RemoteException

getCurationTags

public WSCurationTag[] getCurationTags(String pwId)
                                throws RemoteException

Specified by:

getCurationTags in interface WikiPathwaysPortType

Throws:

RemoteException

getCurationTagsByName

public WSCurationTag[] getCurationTagsByName(String tagName)
                                      throws RemoteException

Specified by:

getCurationTagsByName in interface WikiPathwaysPortType

Throws:

RemoteException

getOntologyTermsByPathway

public WSOntologyTerm[] getOntologyTermsByPathway(String pwId)
                                           throws RemoteException

Specified by:

getOntologyTermsByPathway in interface WikiPathwaysPortType

Throws:

RemoteException

getPathway

public WSPathway getPathway(String pwId,
                            int revision)
                     throws RemoteException

Specified by:

getPathway in interface WikiPathwaysPortType

Throws:

RemoteException

getPathwayAs

public byte[] getPathwayAs(String fileType,
                           String pwId,
                           int revision)
                    throws RemoteException

Specified by:

getPathwayAs in interface WikiPathwaysPortType

Throws:

RemoteException

getPathwaysByOntologyTerm

public WSPathwayInfo[] getPathwaysByOntologyTerm(String term)
                                          throws RemoteException

Specified by:

getPathwaysByOntologyTerm in interface WikiPathwaysPortType

Throws:

RemoteException

getPathwaysByParentOntologyTerm

public WSPathwayInfo[] getPathwaysByParentOntologyTerm(String term)
                                                throws RemoteException

Specified by:

getPathwaysByParentOntologyTerm in interface WikiPathwaysPortType

Throws:

RemoteException

getPathwayHistory

public WSPathwayHistory getPathwayHistory(String pwId,
                                          String timestamp)
                                   throws RemoteException

Specified by:

getPathwayHistory in interface WikiPathwaysPortType

Throws:

RemoteException

getPathwayInfo

public WSPathwayInfo getPathwayInfo(String pwId)
                             throws RemoteException

Specified by:

getPathwayInfo in interface WikiPathwaysPortType

Throws:

RemoteException

getRecentChanges

public WSPathwayInfo[] getRecentChanges(String timestamp)
                                 throws RemoteException

Specified by:

getRecentChanges in interface WikiPathwaysPortType

Throws:

RemoteException

getUserByOrcid

public String getUserByOrcid(String orcid)
                      throws RemoteException

Specified by:

getUserByOrcid in interface WikiPathwaysPortType

Throws:

RemoteException

getXrefList

public String[] getXrefList(String pwId,
                            String code)
                     throws RemoteException

Specified by:

getXrefList in interface WikiPathwaysPortType

Throws:

RemoteException

listOrganisms

public String[] listOrganisms()
                       throws RemoteException

Specified by:

listOrganisms in interface WikiPathwaysPortType

Throws:

RemoteException

listPathways

public WSPathwayInfo[] listPathways(String organism)
                             throws RemoteException

Specified by:

listPathways in interface WikiPathwaysPortType

Throws:

RemoteException

login

public String login(String name,
                    String pass)
             throws RemoteException

Specified by:

login in interface WikiPathwaysPortType

Throws:

RemoteException

removeCurationTag

public boolean removeCurationTag(String pwId,
                                 String tagName,
                                 WSAuth auth)
                          throws RemoteException

Specified by:

removeCurationTag in interface WikiPathwaysPortType

Throws:

RemoteException

saveCurationTag

public boolean saveCurationTag(String pwId,
                               String tagName,
                               String tagText,
                               int revision,
                               WSAuth auth)
                        throws RemoteException

Specified by:

saveCurationTag in interface WikiPathwaysPortType

Throws:

RemoteException

saveOntologyTag

public boolean saveOntologyTag(String pwId,
                               String term,
                               String termId,
                               WSAuth auth)
                        throws RemoteException

Specified by:

saveOntologyTag in interface WikiPathwaysPortType

Throws:

RemoteException

removeOntologyTag

public boolean removeOntologyTag(String pwId,
                                 String termId,
                                 WSAuth auth)
                          throws RemoteException

Specified by:

removeOntologyTag in interface WikiPathwaysPortType

Throws:

RemoteException

updatePathway

public boolean updatePathway(String pwId,
                             String description,
                             String gpml,
                             int revision,
                             WSAuth auth)
                      throws RemoteException

Specified by:

updatePathway in interface WikiPathwaysPortType

Throws:

RemoteException

createPathway

public WSPathwayInfo createPathway(String gpml,
                                   WSAuth auth)
                            throws RemoteException

Specified by:

createPathway in interface WikiPathwaysPortType

Throws:

RemoteException