Package org.molgenis.ontology.sorta.controller

Class SortaController

java.lang.Object

org.molgenis.web.PluginController

org.molgenis.ontology.sorta.controller.SortaController

@Controller
@RequestMapping("/plugin/sorta")
public class SortaController
extends org.molgenis.web.PluginController

Field Summary

Fields

Modifier and Type	Field	Description
static double	DEFAULT_THRESHOLD
static String	ID
static String	MATCH_VIEW_NAME
static String	URI

Fields inherited from class org.molgenis.web.PluginController

PLUGIN_URI_PREFIX

Constructor Summary

Constructors

Constructor

Description

SortaController(org.molgenis.ontology.core.service.OntologyService ontologyService, SortaService sortaService, org.molgenis.security.user.UserAccountService userAccountService, org.molgenis.data.file.FileStore fileStore, org.molgenis.security.core.UserPermissionEvaluator permissionService, org.molgenis.data.DataService dataService, org.molgenis.web.menu.MenuReaderService menuReaderService, org.molgenis.data.populate.IdGenerator idGenerator, org.molgenis.data.security.permission.PermissionSystemService permissionSystemService, MatchingTaskContentMetaData matchingTaskContentMetaData, SortaJobExecutionMetadata sortaJobExecutionMetaData, org.molgenis.ontology.core.meta.OntologyTermMetadata ontologyTermMetadata, SortaJobExecutionFactory sortaJobExecutionFactory, org.molgenis.data.meta.model.EntityTypeFactory entityTypeFactory, org.molgenis.data.meta.model.AttributeFactory attrMetaFactory, org.molgenis.jobs.JobExecutor jobExecutor)

Method Summary

Modifier and Type	Method	Description
Map<String,Object>	countMatchResult(String sortaJobExecutionId)
String	deleteResult(String sortaJobExecutionId, org.springframework.ui.Model model)
void	download(String sortaJobExecutionId, javax.servlet.http.HttpServletResponse response)
SortaServiceResponse	findMatchingOntologyTerms(Map<String,Object> request)
List<SortaJobExecution>	getJobs()
String	init(org.springframework.ui.Model model)
String	match(String jobName, String ontologyIri, String inputTerms, org.springframework.ui.Model model, javax.servlet.http.HttpServletRequest httpServletRequest)
String	matchResult(String sortaJobExecutionId, org.springframework.ui.Model model)
String	matchTask(org.springframework.ui.Model model)
EntityCollectionResponse	retrieveSortaJobResults(SortaServiceRequest sortaServiceRequest)
String	updateThreshold(String threshold, String sortaJobExecutionId, org.springframework.ui.Model model)
String	upload(String jobName, String ontologyIri, org.springframework.web.multipart.MultipartFile file, org.springframework.ui.Model model, javax.servlet.http.HttpServletRequest httpServletRequest)

Methods inherited from class org.molgenis.web.PluginController

getId, getPluginSettings, getUri

Methods inherited from class java.lang.Object

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

Field Detail

ID

public static final String ID

See Also:

Constant Field Values

URI

public static final String URI

See Also:

Constant Field Values

MATCH_VIEW_NAME

public static final String MATCH_VIEW_NAME

See Also:

Constant Field Values

DEFAULT_THRESHOLD

public static final double DEFAULT_THRESHOLD

See Also:

Constant Field Values

Constructor Detail

SortaController

public SortaController(org.molgenis.ontology.core.service.OntologyService ontologyService,
                       SortaService sortaService,
                       org.molgenis.security.user.UserAccountService userAccountService,
                       org.molgenis.data.file.FileStore fileStore,
                       org.molgenis.security.core.UserPermissionEvaluator permissionService,
                       org.molgenis.data.DataService dataService,
                       org.molgenis.web.menu.MenuReaderService menuReaderService,
                       org.molgenis.data.populate.IdGenerator idGenerator,
                       org.molgenis.data.security.permission.PermissionSystemService permissionSystemService,
                       MatchingTaskContentMetaData matchingTaskContentMetaData,
                       SortaJobExecutionMetadata sortaJobExecutionMetaData,
                       org.molgenis.ontology.core.meta.OntologyTermMetadata ontologyTermMetadata,
                       SortaJobExecutionFactory sortaJobExecutionFactory,
                       org.molgenis.data.meta.model.EntityTypeFactory entityTypeFactory,
                       org.molgenis.data.meta.model.AttributeFactory attrMetaFactory,
                       org.molgenis.jobs.JobExecutor jobExecutor)

Method Detail

init

@GetMapping
public String init(org.springframework.ui.Model model)

getJobs

@GetMapping("/jobs")
@ResponseBody
public List<SortaJobExecution> getJobs()

matchTask

@GetMapping("/newtask")
public String matchTask(org.springframework.ui.Model model)

updateThreshold

@PostMapping("/threshold/{sortaJobExecutionId}")
public String updateThreshold(@RequestParam("threshold")
                              String threshold,
                              @PathVariable
                              String sortaJobExecutionId,
                              org.springframework.ui.Model model)

matchResult

@GetMapping("/result/{sortaJobExecutionId}")
public String matchResult(@PathVariable("sortaJobExecutionId")
                          String sortaJobExecutionId,
                          org.springframework.ui.Model model)

countMatchResult

@GetMapping("/count/{sortaJobExecutionId}")
@ResponseBody
public Map<String,Object> countMatchResult(@PathVariable("sortaJobExecutionId")
                                                 String sortaJobExecutionId)

deleteResult

@PostMapping("/delete/{sortaJobExecutionId}")
@ResponseStatus(OK)
public String deleteResult(@PathVariable("sortaJobExecutionId")
                           String sortaJobExecutionId,
                           org.springframework.ui.Model model)

retrieveSortaJobResults

@PostMapping("/match/retrieve")
@ResponseBody
public EntityCollectionResponse retrieveSortaJobResults(@RequestBody
                                                        SortaServiceRequest sortaServiceRequest)

match

@PostMapping("/match")
public String match(@RequestParam("taskName")
                    String jobName,
                    @RequestParam("selectOntologies")
                    String ontologyIri,
                    @RequestParam("inputTerms")
                    String inputTerms,
                    org.springframework.ui.Model model,
                    javax.servlet.http.HttpServletRequest httpServletRequest)
             throws IOException

Throws:

IOException

upload

@PostMapping(value="/match/upload",
             headers="Content-Type=multipart/form-data")
public String upload(@RequestParam("taskName")
                     String jobName,
                     @RequestParam("selectOntologies")
                     String ontologyIri,
                     @RequestParam("file")
                     org.springframework.web.multipart.MultipartFile file,
                     org.springframework.ui.Model model,
                     javax.servlet.http.HttpServletRequest httpServletRequest)
              throws IOException

Throws:

IOException

findMatchingOntologyTerms

@PostMapping("/match/entity")
@ResponseBody
public SortaServiceResponse findMatchingOntologyTerms(@RequestBody
                                                      Map<String,Object> request)

download

@GetMapping("/match/download/{sortaJobExecutionId}")
public void download(@PathVariable
                     String sortaJobExecutionId,
                     javax.servlet.http.HttpServletResponse response)
              throws IOException

Throws:

IOException