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

Class RESTSampleSequenceFilesController

java.lang.Object

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

@Controller
public class RESTSampleSequenceFilesController
extends java.lang.Object

Controller for managing relationships between Sample and SequenceFile.

Field Summary

Fields

Modifier and Type	Field	Description
static com.google.common.collect.BiMap<java.lang.Class<? extends SequencingObject>,java.lang.String>	objectLabels	Filetype labels for different SequencingObject subclasses.
static java.lang.String	REL_AUTOMATED_ASSEMBLY	rel for automated analyses associated with sequencing object
static java.lang.String	REL_PAIR	Rel to the SequenceFile pair
static java.lang.String	REL_PAIR_FORWARD	rel for forward and reverse files
static java.lang.String	REL_PAIR_REVERSE
static java.lang.String	REL_PAIR_SAMPLE
static java.lang.String	REL_QC_SEQFILE
static java.lang.String	REL_SAMPLE	Rel to get back to the Sample.
static java.lang.String	REL_SAMPLE_SEQUENCE_FILE_FAST5
static java.lang.String	REL_SAMPLE_SEQUENCE_FILE_PAIRS	Rel for paired sequence files for a given sample
static java.lang.String	REL_SAMPLE_SEQUENCE_FILE_UNPAIRED	rel for the unpaired sequence files for a given sample
static java.lang.String	REL_SAMPLE_SEQUENCE_FILES	Rel to get to the new location of the SequenceFile.
static java.lang.String	REL_SEQ_OBJECT	Rel to a sequencefile's sequencing object
static java.lang.String	REL_SEQ_QC	Rel for a sequencefile's fastqc info
static java.lang.String	REL_SEQUENCEFILE_SAMPLE
static java.lang.String	REL_SISTR_TYPING
static java.lang.String	SEQUENCE_FILE_ID_KEY	The key used in the request to add an existing SequenceFile to a Sample.

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	RESTSampleSequenceFilesController()
	RESTSampleSequenceFilesController(SampleService sampleService, SequencingRunService miseqRunService, SequencingObjectService sequencingObjectService, AnalysisService analysisService)

Method Summary

Modifier and Type	Method	Description
ResponseResource<SequenceFile>	addNewFast5FileToSample(java.lang.Long sampleId, org.springframework.web.multipart.MultipartFile file, SequenceFileResource fileResource, javax.servlet.http.HttpServletResponse response)	REST function to add new Fast5 object to a sample
ResponseResource<SequencingObject>	addNewSequenceFilePairToSample(java.lang.Long sampleId, org.springframework.web.multipart.MultipartFile file1, SequenceFileResource fileResource1, org.springframework.web.multipart.MultipartFile file2, SequenceFileResource fileResource2, javax.servlet.http.HttpServletResponse response)	Add a pair of SequenceFiles to a Sample
ResponseResource<SequenceFile>	addNewSequenceFileToSample(java.lang.Long sampleId, org.springframework.web.multipart.MultipartFile file, SequenceFileResource fileResource, javax.servlet.http.HttpServletResponse response)	Add a new SequenceFile to a Sample.
static <T extends SequencingObject> T	addSequencingObjectLinks(T sequencingObject, java.lang.Long sampleId)	Add the links for a SequencingObject to its sample, self, to each individual SequenceFile
ResponseResource<ResourceCollection<SequenceFile>>	getSampleSequenceFiles(java.lang.Long sampleId)	Get the SequenceFile entities associated with a specific Sample.
ResponseResource<ResourceCollection<SequencingObject>>	listSequencingObjectsOfTypeForSample(java.lang.Long sampleId, java.lang.String objectType)	List all SequencingObjects of a given type for a Sample
ResponseResource<AnalysisFastQC>	readQCForSequenceFile(java.lang.Long sampleId, java.lang.String objectType, java.lang.Long objectId, java.lang.Long fileId)	Get the fastqc metrics for a SequenceFile
ResponseResource<SequenceFile>	readSequenceFileForSequencingObject(java.lang.Long sampleId, java.lang.String objectType, java.lang.Long objectId, java.lang.Long fileId)	Read a single SequenceFile for a given Sample and SequencingObject
ResponseResource<SequencingObject>	readSequencingObject(java.lang.Long sampleId, java.lang.String objectType, java.lang.Long objectId)	Read a single SequencingObject of the given type from a Sample
ResponseResource<RootResource>	removeSequenceFileFromSample(java.lang.Long sampleId, java.lang.String objectType, java.lang.Long objectId)	Remove a SequencingObject from a 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

Rel to get back to the Sample.

See Also:

Constant Field Values

REL_PAIR

public static final java.lang.String REL_PAIR

Rel to the SequenceFile pair

See Also:

Constant Field Values

REL_SAMPLE_SEQUENCE_FILES

public static final java.lang.String REL_SAMPLE_SEQUENCE_FILES

Rel to get to the new location of the SequenceFile.

See Also:

Constant Field Values

REL_SAMPLE_SEQUENCE_FILE_PAIRS

public static final java.lang.String REL_SAMPLE_SEQUENCE_FILE_PAIRS

Rel for paired sequence files for a given sample

See Also:

Constant Field Values

REL_SAMPLE_SEQUENCE_FILE_UNPAIRED

public static final java.lang.String REL_SAMPLE_SEQUENCE_FILE_UNPAIRED

rel for the unpaired sequence files for a given sample

See Also:

Constant Field Values

REL_SAMPLE_SEQUENCE_FILE_FAST5

public static final java.lang.String REL_SAMPLE_SEQUENCE_FILE_FAST5

See Also:

Constant Field Values

REL_SEQUENCEFILE_SAMPLE

public static final java.lang.String REL_SEQUENCEFILE_SAMPLE

See Also:

Constant Field Values

REL_PAIR_SAMPLE

public static final java.lang.String REL_PAIR_SAMPLE

See Also:

Constant Field Values

REL_SEQ_OBJECT

public static final java.lang.String REL_SEQ_OBJECT

Rel to a sequencefile's sequencing object

See Also:

Constant Field Values

REL_SEQ_QC

public static final java.lang.String REL_SEQ_QC

Rel for a sequencefile's fastqc info

See Also:

Constant Field Values

REL_QC_SEQFILE

public static final java.lang.String REL_QC_SEQFILE

See Also:

Constant Field Values

REL_PAIR_FORWARD

public static final java.lang.String REL_PAIR_FORWARD

rel for forward and reverse files

See Also:

Constant Field Values

REL_PAIR_REVERSE

public static final java.lang.String REL_PAIR_REVERSE

See Also:

Constant Field Values

REL_AUTOMATED_ASSEMBLY

public static final java.lang.String REL_AUTOMATED_ASSEMBLY

rel for automated analyses associated with sequencing object

See Also:

Constant Field Values

REL_SISTR_TYPING

public static final java.lang.String REL_SISTR_TYPING

See Also:

Constant Field Values

SEQUENCE_FILE_ID_KEY

public static final java.lang.String SEQUENCE_FILE_ID_KEY

The key used in the request to add an existing SequenceFile to a Sample.

See Also:

Constant Field Values

objectLabels

public static com.google.common.collect.BiMap<java.lang.Class<? extends SequencingObject>,java.lang.String> objectLabels

Filetype labels for different SequencingObject subclasses. These will be used in the hrefs for reading SequencingObjects

Constructor Detail

RESTSampleSequenceFilesController

protected RESTSampleSequenceFilesController()

RESTSampleSequenceFilesController

@Autowired
public RESTSampleSequenceFilesController(SampleService sampleService,
                                         SequencingRunService miseqRunService,
                                         SequencingObjectService sequencingObjectService,
                                         AnalysisService analysisService)

Method Detail

getSampleSequenceFiles

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

Get the SequenceFile entities associated with a specific Sample.

Parameters:

sampleId - the identifier for the Sample.

Returns:

the SequenceFile entities associated with the Sample.

listSequencingObjectsOfTypeForSample

@RequestMapping(value="/api/samples/{sampleId}/{objectType}",
                method=GET)
public ResponseResource<ResourceCollection<SequencingObject>> listSequencingObjectsOfTypeForSample(@PathVariable
                                                                                                   java.lang.Long sampleId,
                                                                                                   @PathVariable
                                                                                                   java.lang.String objectType)

List all SequencingObjects of a given type for a Sample

Parameters:

sampleId - ID of the Sample to read from

objectType - SequencingObject type

Returns:

The SequencingObjects of the given type for the Sample

readSequencingObject

@RequestMapping(value="/api/samples/{sampleId}/{objectType}/{objectId}",
                method=GET)
public ResponseResource<SequencingObject> readSequencingObject(@PathVariable
                                                               java.lang.Long sampleId,
                                                               @PathVariable
                                                               java.lang.String objectType,
                                                               @PathVariable
                                                               java.lang.Long objectId)

Read a single SequencingObject of the given type from a Sample

Parameters:

sampleId - Sample identifier

objectType - type of SequencingObject

objectId - ID of the SequencingObject

Returns:

A single SequencingObject

readSequenceFileForSequencingObject

@RequestMapping(value="/api/samples/{sampleId}/{objectType}/{objectId}/files/{fileId}",
                method=GET)
public ResponseResource<SequenceFile> readSequenceFileForSequencingObject(@PathVariable
                                                                          java.lang.Long sampleId,
                                                                          @PathVariable
                                                                          java.lang.String objectType,
                                                                          @PathVariable
                                                                          java.lang.Long objectId,
                                                                          @PathVariable
                                                                          java.lang.Long fileId)

Read a single SequenceFile for a given Sample and SequencingObject

Parameters:

sampleId - ID of the Sample

objectType - type of SequencingObject

objectId - id of the SequencingObject

fileId - ID of the SequenceFile to read

Returns:

a SequenceFile

readQCForSequenceFile

@RequestMapping(value="/api/samples/{sampleId}/{objectType}/{objectId}/files/{fileId}/qc",
                method=GET)
public ResponseResource<AnalysisFastQC> readQCForSequenceFile(@PathVariable
                                                              java.lang.Long sampleId,
                                                              @PathVariable
                                                              java.lang.String objectType,
                                                              @PathVariable
                                                              java.lang.Long objectId,
                                                              @PathVariable
                                                              java.lang.Long fileId)

Get the fastqc metrics for a SequenceFile

Parameters:

sampleId - Sample id of the file

objectType - type of SequencingObject

objectId - id of the SequencingObject

fileId - id of the SequenceFile

Returns:

an AnalysisFastQC for the file

addNewSequenceFileToSample

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

Add a new SequenceFile to a Sample.

Parameters:

sampleId - the identifier for the Sample.

file - the content of the SequenceFile.

fileResource - the parameters for the file

response - the servlet response.

Returns:

a response indicating the success of the submission.

Throws:

java.io.IOException - if we can't write the file to disk.

addNewFast5FileToSample

@RequestMapping(value="/api/samples/{sampleId}/fast5",
                method=POST,
                consumes="multipart/form-data")
public ResponseResource<SequenceFile> addNewFast5FileToSample(@PathVariable
                                                              java.lang.Long sampleId,
                                                              @RequestPart("file")
                                                              org.springframework.web.multipart.MultipartFile file,
                                                              @RequestPart(value="parameters",required=false)
                                                              SequenceFileResource fileResource,
                                                              javax.servlet.http.HttpServletResponse response)
                                                       throws java.io.IOException

REST function to add new Fast5 object to a sample

Parameters:

sampleId - the ID of the sample to add

file - The multipart file uploa to create

fileResource - the parameters for the file

response - the servlet response.

Returns:

a response indicating the success of the submission.

Throws:

java.io.IOException - if we can't write the file to disk.

addNewSequenceFilePairToSample

@RequestMapping(value="/api/samples/{sampleId}/pairs",
                method=POST,
                consumes="multipart/form-data")
public ResponseResource<SequencingObject> addNewSequenceFilePairToSample(@PathVariable
                                                                         java.lang.Long sampleId,
                                                                         @RequestPart("file1")
                                                                         org.springframework.web.multipart.MultipartFile file1,
                                                                         @RequestPart("parameters1")
                                                                         SequenceFileResource fileResource1,
                                                                         @RequestPart("file2")
                                                                         org.springframework.web.multipart.MultipartFile file2,
                                                                         @RequestPart("parameters2")
                                                                         SequenceFileResource fileResource2,
                                                                         javax.servlet.http.HttpServletResponse response)
                                                                  throws java.io.IOException

Add a pair of SequenceFiles to a Sample

Parameters:

sampleId - The Sample id to add to

file1 - The first multipart file

fileResource1 - The metadata for the first file

file2 - The second multipart file

fileResource2 - the metadata for the second file

response - a reference to the servlet response.

Returns:

Response containing the locations for the created files

Throws:

java.io.IOException - if we can't write the files to disk

removeSequenceFileFromSample

@RequestMapping(value="/api/samples/{sampleId}/{objectType}/{objectId}",
                method=DELETE)
public ResponseResource<RootResource> removeSequenceFileFromSample(@PathVariable
                                                                   java.lang.Long sampleId,
                                                                   @PathVariable
                                                                   java.lang.String objectType,
                                                                   @PathVariable
                                                                   java.lang.Long objectId)

Remove a SequencingObject from a Sample.

Parameters:

sampleId - the source Sample identifier.

objectType - The type of sequencing object being removed

objectId - the identifier of the SequencingObject to move.

Returns:

a status indicating the success of the move.

addSequencingObjectLinks

public static <T extends SequencingObject> T addSequencingObjectLinks(T sequencingObject,
                                                                      java.lang.Long sampleId)

Add the links for a SequencingObject to its sample, self, to each individual SequenceFile

Type Parameters:

T - The subclass of SequencingObject being enhanced by this method

Parameters:

sequencingObject - SequencingObject to enhance

sampleId - ID of the Sample for the object

Returns:

the enhanced SequencingObject