Package ca.corefacility.bioinformatics.irida.web.controller.api.samples

Class RESTSampleAssemblyController

java.lang.Object

ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController

@Controller
public class RESTSampleAssemblyController
extends java.lang.Object

Controller for viewing and downloading assemblies for samples

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	REL_ASSEMBLY_ANALYSIS
static java.lang.String	REL_SAMPLE
static java.lang.String	REL_SAMPLE_ASSEMBLIES

Constructor Summary

Constructors

Constructor	Description
RESTSampleAssemblyController(SampleService sampleService, GenomeAssemblyService assemblyService)

Method Summary

Modifier and Type	Method	Description
ResponseResource<GenomeAssembly>	addNewAssemblyToSample(java.lang.Long sampleId, org.springframework.web.multipart.MultipartFile file, javax.servlet.http.HttpServletResponse response)	Upload a new GenomeAssembly and add it to a Sample
ResponseResource<ResourceCollection<GenomeAssembly>>	listAssembliesForSample(java.lang.Long sampleId)	List all the GenomeAssemblys for a given Sample
ResponseResource<GenomeAssembly>	readAssemblyForSample(java.lang.Long sampleId, java.lang.Long assemblyId)	Read an individual GenomeAssembly for a given Sample

Methods inherited from class java.lang.Object

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

Field Detail

REL_SAMPLE

public static final java.lang.String REL_SAMPLE

See Also:

Constant Field Values

REL_SAMPLE_ASSEMBLIES

public static final java.lang.String REL_SAMPLE_ASSEMBLIES

See Also:

Constant Field Values

REL_ASSEMBLY_ANALYSIS

public static final java.lang.String REL_ASSEMBLY_ANALYSIS

See Also:

Constant Field Values

Constructor Detail

RESTSampleAssemblyController

@Autowired
public RESTSampleAssemblyController(SampleService sampleService,
                                    GenomeAssemblyService assemblyService)

Method Detail

listAssembliesForSample

@RequestMapping(value="/api/samples/{sampleId}/assemblies",
                method=GET)
public ResponseResource<ResourceCollection<GenomeAssembly>> listAssembliesForSample(@PathVariable
                                                                                    java.lang.Long sampleId)

List all the GenomeAssemblys for a given Sample

Parameters:

sampleId - the id of the sample

Returns:

a list of details about the assemblies

readAssemblyForSample

@RequestMapping(value="/api/samples/{sampleId}/assemblies/{assemblyId}",
                method=GET)
public ResponseResource<GenomeAssembly> readAssemblyForSample(@PathVariable
                                                              java.lang.Long sampleId,
                                                              @PathVariable
                                                              java.lang.Long assemblyId)

Read an individual GenomeAssembly for a given Sample

Parameters:

sampleId - the id of the sample

assemblyId - the id of the assembly

Returns:

details about the requested assembly

addNewAssemblyToSample

@RequestMapping(value="/api/samples/{sampleId}/assemblies",
                method=POST,
                consumes="multipart/form-data")
public ResponseResource<GenomeAssembly> addNewAssemblyToSample(@PathVariable
                                                               java.lang.Long sampleId,
                                                               @RequestPart("file")
                                                               org.springframework.web.multipart.MultipartFile file,
                                                               javax.servlet.http.HttpServletResponse response)
                                                        throws java.io.IOException

Upload a new GenomeAssembly and add it to a Sample

Parameters:

sampleId - The ID of the sampleto add the assembly to

file - the file content

response - A response to send to the user

Returns:

a model with links to the created assembly

Throws:

java.io.IOException - if the upload fails