org.molgenis.wikipathways.client

Interface WikiPathwaysPortType

All Superinterfaces:

Remote

All Known Implementing Classes:

WikiPathwaysRESTBindingStub

public interface WikiPathwaysPortType
extends Remote

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)

Method Detail

updatePathway

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

Throws:

RemoteException

findPathwaysByXref

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

Throws:

RemoteException

getColoredPathway

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

Throws:

RemoteException

saveOntologyTag

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

Throws:

RemoteException

getPathwaysByParentOntologyTerm

WSPathwayInfo[] getPathwaysByParentOntologyTerm(String term)
                                         throws RemoteException

Throws:

RemoteException

getPathwayInfo

WSPathwayInfo getPathwayInfo(String pwId)
                      throws RemoteException

Throws:

RemoteException

listPathways

WSPathwayInfo[] listPathways(String organism)
                      throws RemoteException

Throws:

RemoteException

findPathwaysByLiterature

WSSearchResult[] findPathwaysByLiterature(String query)
                                   throws RemoteException

Throws:

RemoteException

removeCurationTag

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

Throws:

RemoteException

listOrganisms

String[] listOrganisms()
                throws RemoteException

Throws:

RemoteException

getCurationTagsByName

WSCurationTag[] getCurationTagsByName(String tagName)
                               throws RemoteException

Throws:

RemoteException

saveCurationTag

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

Throws:

RemoteException

getPathwayHistory

WSPathwayHistory getPathwayHistory(String pwId,
                                   String timestamp)
                            throws RemoteException

Throws:

RemoteException

getXrefList

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

Throws:

RemoteException

findPathwaysByText

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

Throws:

RemoteException

createPathway

WSPathwayInfo createPathway(String gpml,
                            WSAuth auth)
                     throws RemoteException

Throws:

RemoteException

getPathwayAs

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

Throws:

RemoteException

getCurationTagHistory

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

Throws:

RemoteException

getCurationTags

WSCurationTag[] getCurationTags(String pwId)
                         throws RemoteException

Throws:

RemoteException

findInteractions

WSSearchResult[] findInteractions(String query)
                           throws RemoteException

Throws:

RemoteException

login

String login(String name,
             String pass)
      throws RemoteException

Throws:

RemoteException

getRecentChanges

WSPathwayInfo[] getRecentChanges(String timestamp)
                          throws RemoteException

Throws:

RemoteException

getPathway

WSPathway getPathway(String pwId,
                     int revision)
              throws RemoteException

Throws:

RemoteException

getOntologyTermsByPathway

WSOntologyTerm[] getOntologyTermsByPathway(String pwId)
                                    throws RemoteException

Throws:

RemoteException

getPathwaysByOntologyTerm

WSPathwayInfo[] getPathwaysByOntologyTerm(String term)
                                   throws RemoteException

Throws:

RemoteException

getUserByOrcid

String getUserByOrcid(String orcid)
               throws RemoteException

Throws:

RemoteException

removeOntologyTag

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

Throws:

RemoteException