org.molgenis.ontology.controller

Class SortaServiceController

java.lang.Object

org.molgenis.ui.MolgenisPluginController

org.molgenis.ontology.controller.SortaServiceController

@Controller
 @RequestMapping(value="/plugin/sortaservice")
public class SortaServiceController
extends MolgenisPluginController

Field Summary

Fields

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

Fields inherited from class org.molgenis.ui.MolgenisPluginController

PLUGIN_URI_PREFIX

Constructor Summary

Constructors

Constructor and Description

SortaServiceController(org.molgenis.ontology.core.service.OntologyService ontologyService, SortaService sortaService, SortaJobFactory sortaMatchJobFactory, ExecutorService taskExecutor, org.molgenis.security.user.UserAccountService userAccountService, FileStore fileStore, org.molgenis.security.core.MolgenisPermissionService molgenisPermissionService, DataService dataService, LanguageService languageService, MenuReaderService menuReaderService, IdGenerator idGenerator, org.molgenis.security.permission.PermissionSystemService permissionSystemService, MatchingTaskContentMetaData matchingTaskContentMetaData, SortaJobExecutionMetaData sortaJobExecutionMetaData, org.molgenis.ontology.core.meta.OntologyTermMetaData ontologyTermMetaData, SortaJobExecutionFactory sortaJobExecutionFactory, EntityTypeFactory entityTypeFactory, AttributeFactory attrMetaFactory)

Method Summary

Modifier and Type	Method and 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, org.springframework.ui.Model model)
SortaServiceResponse	findMatchingOntologyTerms(Map<String,Object> request, javax.servlet.http.HttpServletRequest httpServletRequest)
List<Entity>	getJobs(org.springframework.ui.Model model)
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, javax.servlet.http.HttpServletRequest httpServletRequest)
SortaServiceResponse	search(Map<String,Object> request, javax.servlet.http.HttpServletRequest httpServletRequest)
String	updateThreshold(String threshold, String sortaJobExecutionId, org.springframework.ui.Model model)
String	upload(String jobName, String ontologyIri, javax.servlet.http.Part file, org.springframework.ui.Model model, javax.servlet.http.HttpServletRequest httpServletRequest)

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

MATCH_VIEW_NAME

public static final String MATCH_VIEW_NAME

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

URI

public static final String URI

See Also:

Constant Field Values

Constructor Detail

SortaServiceController

@Autowired
public SortaServiceController(org.molgenis.ontology.core.service.OntologyService ontologyService,
                                         SortaService sortaService,
                                         SortaJobFactory sortaMatchJobFactory,
                                         ExecutorService taskExecutor,
                                         org.molgenis.security.user.UserAccountService userAccountService,
                                         FileStore fileStore,
                                         org.molgenis.security.core.MolgenisPermissionService molgenisPermissionService,
                                         DataService dataService,
                                         LanguageService languageService,
                                         MenuReaderService menuReaderService,
                                         IdGenerator idGenerator,
                                         org.molgenis.security.permission.PermissionSystemService permissionSystemService,
                                         MatchingTaskContentMetaData matchingTaskContentMetaData,
                                         SortaJobExecutionMetaData sortaJobExecutionMetaData,
                                         org.molgenis.ontology.core.meta.OntologyTermMetaData ontologyTermMetaData,
                                         SortaJobExecutionFactory sortaJobExecutionFactory,
                                         EntityTypeFactory entityTypeFactory,
                                         AttributeFactory attrMetaFactory)

Method Detail

init

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

getJobs

@RequestMapping(method=GET,
                value="/jobs")
 @ResponseBody
public List<Entity> getJobs(org.springframework.ui.Model model)

matchTask

@RequestMapping(method=GET,
                value="/newtask")
public String matchTask(org.springframework.ui.Model model)

updateThreshold

@RequestMapping(method=POST,
                value="/threshold/{sortaJobExecutionId}")
public String updateThreshold(@RequestParam(value="threshold",required=true)
                                                                                                                     String threshold,
                                                                                                                     @PathVariable
                                                                                                                     String sortaJobExecutionId,
                                                                                                                     org.springframework.ui.Model model)

matchResult

@RequestMapping(method=GET,
                value="/result/{sortaJobExecutionId}")
public String matchResult(@PathVariable(value="sortaJobExecutionId")
                                                                                                             String sortaJobExecutionId,
                                                                                                             org.springframework.ui.Model model)

countMatchResult

@RequestMapping(method=GET,
                value="/count/{sortaJobExecutionId}")
 @ResponseBody
public Map<String,Object> countMatchResult(@PathVariable(value="sortaJobExecutionId")
                                                                                                                                            String sortaJobExecutionId)

deleteResult

@RequestMapping(method=POST,
                value="/delete/{sortaJobExecutionId}")
 @ResponseStatus(value=OK)
public String deleteResult(@PathVariable(value="sortaJobExecutionId")
                                                                                                                                          String sortaJobExecutionId,
                                                                                                                                          org.springframework.ui.Model model)

retrieveSortaJobResults

@RequestMapping(method=POST,
                value="/match/retrieve")
 @ResponseBody
public EntityCollectionResponse retrieveSortaJobResults(@RequestBody
                                                                                                                                             SortaServiceRequest sortaServiceRequest,
                                                                                                                                             javax.servlet.http.HttpServletRequest httpServletRequest)

match

@RequestMapping(method=POST,
                value="/match")
public String match(@RequestParam(value="taskName",required=true)
                                                                                 String jobName,
                                                                                 @RequestParam(value="selectOntologies",required=true)
                                                                                 String ontologyIri,
                                                                                 @RequestParam(value="inputTerms",required=true)
                                                                                 String inputTerms,
                                                                                 org.springframework.ui.Model model,
                                                                                 javax.servlet.http.HttpServletRequest httpServletRequest)
                                                                          throws Exception

Throws:

Exception

upload

@RequestMapping(method=POST,
                value="/match/upload",
                headers="Content-Type=multipart/form-data")
public String upload(@RequestParam(value="taskName",required=true)
                                                                                                                                                     String jobName,
                                                                                                                                                     @RequestParam(value="selectOntologies",required=true)
                                                                                                                                                     String ontologyIri,
                                                                                                                                                     @RequestParam(value="file",required=true)
                                                                                                                                                     javax.servlet.http.Part file,
                                                                                                                                                     org.springframework.ui.Model model,
                                                                                                                                                     javax.servlet.http.HttpServletRequest httpServletRequest)
                                                                                                                                              throws Exception

Throws:

Exception

findMatchingOntologyTerms

@RequestMapping(method=POST,
                value="/match/entity")
 @ResponseBody
public SortaServiceResponse findMatchingOntologyTerms(@RequestBody
                                                                                                                                         Map<String,Object> request,
                                                                                                                                         javax.servlet.http.HttpServletRequest httpServletRequest)

search

@RequestMapping(method=POST,
                value="/search")
 @ResponseBody
public SortaServiceResponse search(@RequestBody
                                                                                                                Map<String,Object> request,
                                                                                                                javax.servlet.http.HttpServletRequest httpServletRequest)

download

@RequestMapping(method=GET,
                value="/match/download/{sortaJobExecutionId}")
public void download(@PathVariable
                                                                                                                String sortaJobExecutionId,
                                                                                                                javax.servlet.http.HttpServletResponse response,
                                                                                                                org.springframework.ui.Model model)
                                                                                                         throws IOException

Throws:

IOException