org.molgenis.pathways.service

Class WikiPathwaysService

java.lang.Object

org.molgenis.pathways.service.WikiPathwaysService

@Component
public class WikiPathwaysService
extends Object

Interacts with WikiPathways. Caches results.

Constructor Summary

Constructors

Constructor and Description
WikiPathwaysService(WikiPathwaysPortType wikiPathwaysProxy) Creates a new WikiPathwaysService.

Method Summary

Modifier and Type	Method and Description
Collection<Pathway>	getAllPathways(String species) Retrieves all pathways for a species.
String	getColoredPathwayImage(String pathwayId, Map<String,Impact> impactPerGraphId) Retrieves a colored pathway image
Collection<Pathway>	getFilteredPathways(String searchTerm, String species) Searches pathways.
String	getPathwayGPML(String pathwayId) Retrieves the GPML of the current version of a pathway
Collection<Pathway>	getPathwaysForGene(String gene, String species) Retrieves pathways according to gene, filtered for a certain species.
String	getUncoloredPathwayImage(String pathwayId) Retrieves an uncolored pathway image

Methods inherited from class java.lang.Object

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

Constructor Detail

WikiPathwaysService

public WikiPathwaysService(WikiPathwaysPortType wikiPathwaysProxy)

Creates a new WikiPathwaysService. creates all the caches with their proper loaders.

Parameters:

wikiPathwaysProxy - WikiPathwaysPortType proxy for the REST api that the caches use to load their data from

Method Detail

getFilteredPathways

public Collection<Pathway> getFilteredPathways(String searchTerm,
                                               String species)
                                        throws RemoteException

Searches pathways.

Parameters:

searchTerm - string to search for

Returns:

Map with all matching pathway ids mapped to pathway name

Throws:

RemoteException

getPathwayGPML

public String getPathwayGPML(String pathwayId)
                      throws RemoteException

Retrieves the GPML of the current version of a pathway

Parameters:

pathwayId - ID of the pathway in WikiPathways

Returns:

String containing the pathway GPML

Throws:

RemoteException

getColoredPathwayImage

public String getColoredPathwayImage(String pathwayId,
                                     Map<String,Impact> impactPerGraphId)
                              throws ExecutionException

Retrieves a colored pathway image

Parameters:

pathwayId - ID of the pathway from WikiPathways

Returns:

String containing the pathway svg

Throws:

ExecutionException - if loading of the cache fails

getUncoloredPathwayImage

public String getUncoloredPathwayImage(String pathwayId)
                                throws ExecutionException

Retrieves an uncolored pathway image

Parameters:

pathwayId - Id of the pathway from WikiPathways

Returns:

String containing pathway svg

Throws:

ExecutionException - if loading of the cache fails

getPathwaysForGene

public Collection<Pathway> getPathwaysForGene(String gene,
                                              String species)
                                       throws ExecutionException

Retrieves pathways according to gene, filtered for a certain species.

Parameters:

gene - HGNC gene name

species - String with species name, e.g. Homo sapiens

Returns:

Collection of Pathways

Throws:

ExecutionException - if loading of the cache fails

getAllPathways

public Collection<Pathway> getAllPathways(String species)
                                   throws ExecutionException

Retrieves all pathways for a species.

Parameters:

species - String with species name, e.g. Homo sapiens

Returns:

Map mapping id to pathway name

Throws:

ExecutionException - if loading of the cache fails