org.molgenis.pathways

Class WikiPathwaysController

java.lang.Object

org.molgenis.ui.MolgenisPluginController

org.molgenis.pathways.WikiPathwaysController

@Controller
 @RequestMapping(value="/plugin/pathways")
public class WikiPathwaysController
extends MolgenisPluginController

Field Summary

Fields

Modifier and Type	Field and Description
static String	EFFECT_ATTRIBUTE_NAME
static String	URI

Fields inherited from class org.molgenis.ui.MolgenisPluginController

PLUGIN_URI_PREFIX

Constructor Summary

Constructors

Constructor and Description
WikiPathwaysController(WikiPathwaysService wikiPathwaysService)

Method Summary

Modifier and Type	Method and Description
Collection<Pathway>	getAllPathways() Retrieves all pathways.
String	getColoredPathway(String selectedVcf, String pathwayId) Retrieves a colored pathway.
Collection<Pathway>	getFilteredPathways(String searchTerm) Searches pathways.
Collection<Pathway>	getListOfPathwayNamesByGenes(String selectedVcf) Retrieves all pathways for the genes in a vcf.
String	getPathway(String pathwayId) Retrieves uncolored pathway image.
String	init(org.springframework.ui.Model model) Shows the start screen.

Methods inherited from class org.molgenis.ui.MolgenisPluginController

getId, getPluginSettings, getUri

Methods inherited from class java.lang.Object

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

Field Detail

URI

public static final String URI

See Also:

Constant Field Values

EFFECT_ATTRIBUTE_NAME

public static final String EFFECT_ATTRIBUTE_NAME

See Also:

Constant Field Values

Constructor Detail

WikiPathwaysController

@Autowired
public WikiPathwaysController(WikiPathwaysService wikiPathwaysService)

Method Detail

init

@RequestMapping(method=GET)
public String init(org.springframework.ui.Model model)

Shows the start screen.

Parameters:

model - the Model to fill

Returns:

the view name

getAllPathways

@RequestMapping(value="/allPathways",
                method=POST)
 @ResponseBody
public Collection<Pathway> getAllPathways()
                                                                                                                     throws ExecutionException

Retrieves all pathways.

Returns:

Collection of all Pathways.

Throws:

ExecutionException - if load from cache fails

getFilteredPathways

@RequestMapping(value="/filteredPathways",
                method=POST)
 @ResponseBody
public Collection<Pathway> getFilteredPathways(@RequestBody
                                                                                                                                      String searchTerm)
                                                                                                                               throws RemoteException,
                                                                                                                                      ExecutionException

Searches pathways.

Parameters:

searchTerm - string to search for

Returns:

Collection of all Pathways found for searchTerm

Throws:

RemoteException

ExecutionException

getPathway

@RequestMapping(value="/pathwayViewer/{pathwayId}",
                method=GET)
 @ResponseBody
public String getPathway(@PathVariable
                                                                                                                        String pathwayId)
                                                                                                                 throws ExecutionException

Retrieves uncolored pathway image.

Parameters:

pathwayId - the id of the pathway

Returns:

single-line svg string of the pathway image

Throws:

ExecutionException - if load from cache fails

getListOfPathwayNamesByGenes

@RequestMapping(value="/pathwaysByGenes",
                method=POST)
 @ResponseBody
public Collection<Pathway> getListOfPathwayNamesByGenes(@RequestBody
                                                                                                                                              String selectedVcf)
                                                                                                                                       throws ExecutionException

Retrieves all pathways for the genes in a vcf.

Parameters:

selectedVcf - the name of the vcf Repository

Returns:

Collection of Pathways found for genes in the VCF

Throws:

ExecutionException - if the loading from cache fails

getColoredPathway

@RequestMapping(value="/getColoredPathway/{selectedVcf}/{pathwayId}",
                method=GET)
 @ResponseBody
public String getColoredPathway(@PathVariable
                                                                                                                                                 String selectedVcf,
                                                                                                                                                 @PathVariable
                                                                                                                                                 String pathwayId)
                                                                                                                                          throws ParserConfigurationException,
                                                                                                                                                 SAXException,
                                                                                                                                                 IOException,
                                                                                                                                                 ExecutionException

Retrieves a colored pathway.

Parameters:

selectedVcf - name of the VCF Repository

pathwayId - ID of the pathway

Returns:

svg for the pathway, with the genes in the VCF colored according to their Impact

Throws:

ParserConfigurationException - if the creation of the DocumentBuilder fails

IOException - If any IO errors occur when parsing the GPML

SAXException - If any parse errors occur when parsing the GPML

ExecutionException - if the loading of the colored pathway from cache fails