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

Class RESTAnalysisSubmissionController

java.lang.Object

ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController<AnalysisSubmission>

ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

@Controller
@RequestMapping("/api/analysisSubmissions")
public class RESTAnalysisSubmissionController
extends RESTGenericController<AnalysisSubmission>

REST controller to manage sharing of AnalysisSubmission, Analysis, and AnalysisOutputFile classes.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	ANALYSIS_REL
static java.util.Map<java.lang.String,AnalysisType>	ANALYSIS_TYPES
static java.lang.String	FILE_REL
static java.lang.String	INPUT_FILES_PAIRED_REL
static java.lang.String	INPUT_FILES_UNPAIRED_REL
static java.lang.String	SUBMISSIONS_REL

Fields inherited from class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

crudService, REL_COLLECTION, REL_RELATIONSHIP, RELATED_RESOURCES_NAME, RESOURCE_NAME

Constructor Summary

Constructors

Constructor	Description
RESTAnalysisSubmissionController(AnalysisSubmissionService analysisSubmissionService, SampleService sampleService, SequencingObjectService sequencingObjectService, IridaWorkflowsService iridaWorkflowsService)

Method Summary

Modifier and Type	Method	Description
protected java.util.Collection<org.springframework.hateoas.Link>	constructCollectionResourceLinks(ResourceCollection<AnalysisSubmission> list)	Get custom links to the ResourceCollection being called by RESTGenericController.listAllResources().
protected java.util.Collection<org.springframework.hateoas.Link>	constructCustomResourceLinks(AnalysisSubmission resource)	Construct a collection of Links for a specific resource.
ResponseResource<AnalysisSubmission>	create(AnalysisSubmission resource, javax.servlet.http.HttpServletResponse response)	Create a new instance of Type in the database, then respond to the client with the location of the resource.
ResponseResource<RootResource>	delete(java.lang.Long identifier)	Delete the instance of the resource identified by a specific identifier.
ResponseResource<Analysis>	getAnalysisForSubmission(java.lang.Long identifier)	Get the Analysis for an AnalysisSubmission.
ResponseResource<ResourceCollection<SequenceFilePair>>	getAnalysisInputFilePairs(java.lang.Long identifier)	Get the SequenceFilePairs used for the AnalysisSubmission
ResponseResource<ResourceCollection<SequencingObject>>	getAnalysisInputUnpairedFiles(java.lang.Long identifier)	get the SequenceFiles not in SequenceFilePairs used for the AnalysisSubmission
ResponseResource<AnalysisOutputFile>	getAnalysisOutputFile(java.lang.Long submissionId, java.lang.Long fileId)	Get an analysis output file for a given submission
org.springframework.core.io.FileSystemResource	getAnalysisOutputFileContents(java.lang.Long submissionId, java.lang.Long fileId)	Get the actual file contents for an analysis output file.
ResponseResource<AnalysisSubmission>	getResource(java.lang.Long identifier)	Retrieve and serialize an individual instance of a resource by identifier.
ResponseResource<ResourceCollection<AnalysisSubmission>>	listAllResources()	Get all resources in the application.
ResponseResource<ResourceCollection<AnalysisSubmission>>	listOfType(java.lang.String type)	Get all analyses of a given type
ResponseResource<RootResource>	update(java.lang.Long identifier, java.util.Map<java.lang.String,java.lang.Object> representation)	Update some of the fields of an individual resource in the database.

Methods inherited from class java.lang.Object

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

Field Detail

ANALYSIS_REL

public static final java.lang.String ANALYSIS_REL

See Also:

Constant Field Values

FILE_REL

public static final java.lang.String FILE_REL

See Also:

Constant Field Values

SUBMISSIONS_REL

public static final java.lang.String SUBMISSIONS_REL

See Also:

Constant Field Values

INPUT_FILES_UNPAIRED_REL

public static final java.lang.String INPUT_FILES_UNPAIRED_REL

See Also:

Constant Field Values

INPUT_FILES_PAIRED_REL

public static final java.lang.String INPUT_FILES_PAIRED_REL

See Also:

Constant Field Values

ANALYSIS_TYPES

public static java.util.Map<java.lang.String,AnalysisType> ANALYSIS_TYPES

Constructor Detail

RESTAnalysisSubmissionController

@Autowired
public RESTAnalysisSubmissionController(AnalysisSubmissionService analysisSubmissionService,
                                        SampleService sampleService,
                                        SequencingObjectService sequencingObjectService,
                                        IridaWorkflowsService iridaWorkflowsService)

Method Detail

listAllResources

public ResponseResource<ResourceCollection<AnalysisSubmission>> listAllResources()

Get all resources in the application.

Overrides:

listAllResources in class RESTGenericController<AnalysisSubmission>

Returns:

a model containing all resources of the specified type in the application.

getResource

public ResponseResource<AnalysisSubmission> getResource(@PathVariable
                                                        java.lang.Long identifier)

Retrieve and serialize an individual instance of a resource by identifier.

Overrides:

getResource in class RESTGenericController<AnalysisSubmission>

Parameters:

identifier - the identifier of the resource to retrieve from the database.

Returns:

the model and view for the individual resource.

create

public ResponseResource<AnalysisSubmission> create(@RequestBody
                                                   AnalysisSubmission resource,
                                                   javax.servlet.http.HttpServletResponse response)

Create a new instance of Type in the database, then respond to the client with the location of the resource.

Overrides:

create in class RESTGenericController<AnalysisSubmission>

Parameters:

resource - the Type that we should de-serialize to get an instance of Type to persist.

response - a reference to the servlet response.

Returns:

a response containing the location of the newly persisted resource.

delete

public ResponseResource<RootResource> delete(@PathVariable
                                             java.lang.Long identifier)

Delete the instance of the resource identified by a specific identifier.

Overrides:

delete in class RESTGenericController<AnalysisSubmission>

Parameters:

identifier - the identifier that should be deleted from the database.

Returns:

a response indicating that the resource was deleted.

update

public ResponseResource<RootResource> update(@PathVariable
                                             java.lang.Long identifier,
                                             @RequestBody
                                             java.util.Map<java.lang.String,java.lang.Object> representation)

Update some of the fields of an individual resource in the database. The client should only send the key-value pairs for the properties that are to be updated in the database.

Overrides:

update in class RESTGenericController<AnalysisSubmission>

Parameters:

identifier - the identifier of the resource to be updated.

representation - the properties to be updated and their new values.

Returns:

a response indicating that the resource was updated.

listOfType

@RequestMapping(value="/analysisType/{type}",
                method=GET)
public ResponseResource<ResourceCollection<AnalysisSubmission>> listOfType(@PathVariable
                                                                           java.lang.String type)

Get all analyses of a given type

Parameters:

type - The type to request

Returns:

A list of AnalysisSubmissions

constructCollectionResourceLinks

protected java.util.Collection<org.springframework.hateoas.Link> constructCollectionResourceLinks(ResourceCollection<AnalysisSubmission> list)

Get custom links to the ResourceCollection being called by RESTGenericController.listAllResources(). This method can be overridden by extending classes to add links to the returned list.

Overrides:

constructCollectionResourceLinks in class RESTGenericController<AnalysisSubmission>

Parameters:

list - ResourceCollection to add links to

Returns:

Collection of links to add to the ResourceCollection

getAnalysisInputFilePairs

@RequestMapping(value="/{identifier}/sequenceFiles/pairs",
                method=GET)
public ResponseResource<ResourceCollection<SequenceFilePair>> getAnalysisInputFilePairs(@PathVariable
                                                                                        java.lang.Long identifier)

Get the SequenceFilePairs used for the AnalysisSubmission

Parameters:

identifier - AnalysisSubmission id

Returns:

list of SequenceFilePairs

getAnalysisInputUnpairedFiles

@RequestMapping(value="/{identifier}/sequenceFiles/unpaired",
                method=GET)
public ResponseResource<ResourceCollection<SequencingObject>> getAnalysisInputUnpairedFiles(@PathVariable
                                                                                            java.lang.Long identifier)

get the SequenceFiles not in SequenceFilePairs used for the AnalysisSubmission

Parameters:

identifier - the AnalysisSubmission id

Returns:

list of SequenceFiles

getAnalysisForSubmission

@RequestMapping(value="/{identifier}/analysis",
                method=GET)
public ResponseResource<Analysis> getAnalysisForSubmission(@PathVariable
                                                           java.lang.Long identifier)

Get the Analysis for an AnalysisSubmission.

Parameters:

identifier - AnalysisSubmission identifier to read

Returns:

An Analysis

getAnalysisOutputFile

@RequestMapping(value="/{submissionId}/analysis/file/{fileId}",
                method=GET)
public ResponseResource<AnalysisOutputFile> getAnalysisOutputFile(@PathVariable
                                                                  java.lang.Long submissionId,
                                                                  @PathVariable
                                                                  java.lang.Long fileId)

Get an analysis output file for a given submission

Parameters:

submissionId - The AnalysisSubmission id

fileId - The AnalysisOutputFile id

Returns:

An AnalysisOutputFile

getAnalysisOutputFileContents

@RequestMapping(value="/{submissionId}/analysis/file/{fileId}",
                produces="text/plain")
@ResponseBody
public org.springframework.core.io.FileSystemResource getAnalysisOutputFileContents(@PathVariable
                                                                                    java.lang.Long submissionId,
                                                                                    @PathVariable
                                                                                    java.lang.Long fileId)

Get the actual file contents for an analysis output file.

Parameters:

submissionId - The AnalysisSubmission id

fileId - The AnalysisOutputFile id

Returns:

a FileSystemResource containing the contents of the AnalysisOutputFile.

constructCustomResourceLinks

protected java.util.Collection<org.springframework.hateoas.Link> constructCustomResourceLinks(AnalysisSubmission resource)

Construct a collection of Links for a specific resource. Each resource may have custom links that refer to other controllers, but not all will. This method is called by the getResource method. add analysis rel if available

Overrides:

constructCustomResourceLinks in class RESTGenericController<AnalysisSubmission>

Parameters:

resource - the resource to generate the links for.

Returns:

a collection of links.