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

@Autowired
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:

ConverterException

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

highestImpactPerGraphId -

graphIds - List containing graphIds to color

colors - List of colors in the same order of the graphIds

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