Package org.molgenis.ontology.sorta.controller

Class 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 java.lang.String ID  
      static java.lang.String MATCH_VIEW_NAME  
      static java.lang.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

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

    • 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 java.lang.String init​(org.springframework.ui.Model model)

      • getJobs

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

      • matchTask

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

      • updateThreshold

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

      • matchResult

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

      • countMatchResult

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

      • deleteResult

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

      • match

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

      • upload

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

      • findMatchingOntologyTerms

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

      • download

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