org.molgenis.gavin.controller

Class GavinController

java.lang.Object

org.molgenis.ui.MolgenisPluginController

org.molgenis.ui.controller.AbstractStaticContentController

org.molgenis.gavin.controller.GavinController

@Controller
 @RequestMapping(value="/plugin/gavin-app")
 @EnableScheduling
public class GavinController
extends AbstractStaticContentController

Field Summary

Fields

Modifier and Type	Field and Description
static String	GAVIN_APP
static String	GZ
static String	TSV
static String	TSV_GZ

Fields inherited from class org.molgenis.ui.MolgenisPluginController

PLUGIN_URI_PREFIX

Constructor Summary

Constructors

Constructor and Description
GavinController(ExecutorService executorService, GavinJobFactory gavinJobFactory, GavinJobExecutionFactory gavinJobExecutionFactory, FileStore fileStore, UserAccountService userAccountService, MenuReaderService menuReaderService, IdGenerator idGenerator)

Method Summary

Modifier and Type	Method and Description
org.springframework.http.ResponseEntity<String>	annotateFile(org.springframework.web.multipart.MultipartFile inputFile, String entityName) Starts a job to annotate a VCF file
void	cleanUp() Removes old files in the gavin working directory from the file store.
org.springframework.core.io.FileSystemResource	download(javax.servlet.http.HttpServletResponse response, String jobIdentifier) Downloads the result of a gavin annotation job.
org.springframework.core.io.Resource	downloadErrorReport(javax.servlet.http.HttpServletResponse response, String jobIdentifier) Downloads the error report of a gavin annotation job.
GavinJobExecution	getGavinJobExecution(String jobIdentifier) Retrieves GavinJobExecution job.
void	handleFileNotFound(FileNotFoundException ex, javax.servlet.http.HttpServletResponse res)
void	handleJobNotFound(JobNotFoundException ex, javax.servlet.http.HttpServletResponse res)
ErrorMessageResponse	handleRuntimeException(RuntimeException e)
String	init(org.springframework.ui.Model model) Shows the gavin page.
String	result(String jobIdentifier, org.springframework.ui.Model model, javax.servlet.http.HttpServletRequest request) Shows result page for a job.

Methods inherited from class org.molgenis.ui.controller.AbstractStaticContentController

initEditView, submitContent

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

GAVIN_APP

public static final String GAVIN_APP

See Also:

Constant Field Values

TSV_GZ

public static final String TSV_GZ

See Also:

Constant Field Values

TSV

public static final String TSV

See Also:

Constant Field Values

GZ

public static final String GZ

See Also:

Constant Field Values

Constructor Detail

GavinController

@Autowired
public GavinController(@Qualifier(value="gavinExecutors")
                                  ExecutorService executorService,
                                  GavinJobFactory gavinJobFactory,
                                  GavinJobExecutionFactory gavinJobExecutionFactory,
                                  FileStore fileStore,
                                  UserAccountService userAccountService,
                                  MenuReaderService menuReaderService,
                                  IdGenerator idGenerator)

Method Detail

init

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

Shows the gavin page. This page shows the configuration wheels if the annotation resources are not yet properly configured. If the annotation resources are fine, it shows the upload control.

Overrides:

init in class AbstractStaticContentController

Returns:

the view name

annotateFile

@RequestMapping(value="/annotate-file",
                method=POST)
public org.springframework.http.ResponseEntity<String> annotateFile(@RequestParam(value="file")
                                                                                                                                         org.springframework.web.multipart.MultipartFile inputFile,
                                                                                                                                         @RequestParam
                                                                                                                                         String entityName)
                                                                                                                                  throws IOException

Starts a job to annotate a VCF file

Parameters:

inputFile - the uploaded input file

entityName - the name of the file

Returns:

the ID of the created GavinJobExecution

Throws:

IOException - if interaction with the file store fails

getGavinJobExecution

@RequestMapping(value="/job/{jobIdentifier}",
                method=GET,
                produces="application/json")
 @ResponseBody
public GavinJobExecution getGavinJobExecution(@PathVariable(value="jobIdentifier")
                                                                                                                                                                                    String jobIdentifier)
                                                                                                                                                                             throws JobNotFoundException

Retrieves GavinJobExecution job. May be called by anyone who has the identifier.

Parameters:

jobIdentifier - identifier of the annotation job

Returns:

GavinJobExecution, or null if no GavinJobExecution exists with this ID.

Throws:

JobNotFoundException

result

@RequestMapping(value="/result/{jobIdentifier}",
                method=GET)
public String result(@PathVariable(value="jobIdentifier")
                                                                                                  String jobIdentifier,
                                                                                                  org.springframework.ui.Model model,
                                                                                                  javax.servlet.http.HttpServletRequest request)
                                                                                           throws JobNotFoundException

Shows result page for a job. The job may still be running.

Parameters:

jobIdentifier - identifier of the annotation job

Returns:

FileSystemResource with the annotated file

Throws:

JobNotFoundException

download

@RequestMapping(value="/download/{jobIdentifier}",
                method=GET,
                produces="application/octet-stream")
 @ResponseBody
public org.springframework.core.io.FileSystemResource download(javax.servlet.http.HttpServletResponse response,
                                                                                                                                                                                                                  @PathVariable(value="jobIdentifier")
                                                                                                                                                                                                                  String jobIdentifier)
                                                                                                                                                                                                           throws FileNotFoundException,
                                                                                                                                                                                                                  JobNotFoundException

Downloads the result of a gavin annotation job.

Parameters:

response - HttpServletResponse to write the Content-Disposition header to with the filename

jobIdentifier - GAVIN_APP of the annotation job

Returns:

FileSystemResource with the annotated file

Throws:

FileNotFoundException

JobNotFoundException

downloadErrorReport

@RequestMapping(value="/error/{jobIdentifier}",
                method=GET,
                produces="application/octet-stream")
 @ResponseBody
public org.springframework.core.io.Resource downloadErrorReport(javax.servlet.http.HttpServletResponse response,
                                                                                                                                                                                                                @PathVariable(value="jobIdentifier")
                                                                                                                                                                                                                String jobIdentifier)
                                                                                                                                                                                                         throws FileNotFoundException,
                                                                                                                                                                                                                JobNotFoundException

Downloads the error report of a gavin annotation job.

Parameters:

response - HttpServletResponse to write the Content-Disposition header to with the filename

jobIdentifier - GAVIN_APP of the annotation job

Returns:

FileSystemResource with the annotated file

Throws:

FileNotFoundException

JobNotFoundException

handleFileNotFound

@ExceptionHandler(value=java.io.FileNotFoundException.class)
public void handleFileNotFound(FileNotFoundException ex,
                                                                                            javax.servlet.http.HttpServletResponse res)
                                                                                     throws IOException

Throws:

IOException

handleJobNotFound

@ExceptionHandler(value=JobNotFoundException.class)
public void handleJobNotFound(JobNotFoundException ex,
                                                                                  javax.servlet.http.HttpServletResponse res)
                                                                           throws IOException

Throws:

IOException

handleRuntimeException

@ExceptionHandler(value=java.lang.RuntimeException.class)
 @ResponseBody
 @ResponseStatus(value=BAD_REQUEST)
public ErrorMessageResponse handleRuntimeException(RuntimeException e)

cleanUp

@Scheduled(cron="0 0 * * * *")
public void cleanUp()

Removes old files in the gavin working directory from the file store.