Package ca.corefacility.bioinformatics.irida.ria.web.analysis

Class AnalysisAjaxController

java.lang.Object

ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

@RestController
@Scope("session")
@RequestMapping("/ajax/analysis")
public class AnalysisAjaxController
extends java.lang.Object

Controller for individual Analysis ajax requests (details page, analysis outputs, project analysis outputs)

Constructor Summary

Constructors

Constructor

Description

AnalysisAjaxController(AnalysisSubmissionService analysisSubmissionService, IridaWorkflowsService iridaWorkflowsService, UserService userService, SampleService sampleService, ProjectService projectService, UpdateAnalysisSubmissionPermission updateAnalysisPermission, MetadataTemplateService metadataTemplateService, SequencingObjectService sequencingObjectService, AnalysisSubmissionSampleProcessor analysisSubmissionSampleProcessor, org.springframework.context.MessageSource messageSource, ExecutionManagerConfig configFile, AnalysisAudit analysisAudit, AnalysisTypesService analysisTypesService, EmailController emailController, UpdateSamplePermission updateSamplePermission)

Method Summary

Modifier and Type	Method	Description
AnalysisInputFiles	ajaxGetAnalysisInputFiles(java.lang.Long submissionId, java.util.Locale locale)	Get analysis input files and their sizes
AnalysisDetails	ajaxGetDataForDetailsTab(java.lang.Long submissionId, java.util.Locale locale, javax.servlet.http.HttpServletResponse response)	Get analysis details
AnalysisJobError	ajaxGetJobErrors(java.lang.Long submissionId)	Get a dto with list of JobError for an AnalysisSubmission under key `galaxyJobErrors` and the `galaxyUrl` for the galaxy instance
ResponseDetails	ajaxUpdateEmailPipelineResult(AnalysisEmailPipelineResult parameters, java.util.Locale locale, javax.servlet.http.HttpServletResponse response)	Update an analysis email pipeline completion result
ResponseDetails	ajaxUpdateSubmission(AnalysisSubmissionInfo parameters, java.util.Locale locale, javax.servlet.http.HttpServletResponse response)	Update an analysis name and/or priority
java.util.Map<java.lang.String,java.lang.String>	deleteAjaxAnalysisSubmission(java.lang.Long analysisSubmissionId, java.util.Locale locale)	Delete an AnalysisSubmission by id.
void	getAjaxDownloadAnalysisSubmission(java.lang.Long analysisSubmissionId, javax.servlet.http.HttpServletResponse response)	Download all output files from an AnalysisSubmission
org.springframework.http.ResponseEntity<AnalysisInfo>	getAnalysisInfo(java.lang.Long submissionId, java.security.Principal principal, java.util.Locale locale)	Get the analysis details
org.springframework.http.ResponseEntity<java.lang.String>	getImageFile(java.lang.Long submissionId, java.lang.String filename)	Get an image file associated with a specific AnalysisSubmission by file name.
java.util.Map<java.lang.String,java.lang.Object>	getMetadataForAnalysisSamples(java.lang.Long submissionId)	Get the metadata associated with a template for an analysis.
java.util.Map<java.lang.String,java.lang.Object>	getMetadataTemplateFields(java.lang.Long templateId)	Generates a list of metadata fields for a five template.
java.util.Map<java.lang.String,java.lang.Object>	getMetadataTemplatesForAnalysis(java.lang.Long submissionId)	Get a list of all MetadataTemplates for the AnalysisSubmission
java.util.Map<java.lang.String,java.lang.Object>	getNewickForAnalysis(java.lang.Long submissionId)	Get a newick file associated with a specific AnalysisSubmission.
AnalysisTreeResponse	getNewickTree(java.lang.Long submissionId, java.util.Locale locale)	Construct the model parameters for results with a newick output Analysis
AnalysisOutputFileInfo	getOutputFile(java.lang.Long id, java.lang.Long fileId, java.lang.Long limit, java.lang.Long start, java.lang.Long end, java.lang.Long seek, java.lang.Long chunk, javax.servlet.http.HttpServletResponse response)	Read some lines or text from an AnalysisOutputFile.
java.util.List<AnalysisOutputFileInfo>	getOutputFilesInfo(java.lang.Long id)	For an AnalysisSubmission, get info about each AnalysisOutputFile
AnalysisProvenanceResponse	getProvenanceByFile(java.lang.Long submissionId, java.lang.String filename)	Get the full analysis provenance
java.util.List<ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController.SharedProjectResponse>	getSharedProjectsForAnalysis(java.lang.Long submissionId)	Get the status of projects that can be shared with the given analysis
AnalysisSistrResults	getSistrAnalysis(java.lang.Long id)	Get the sistr analysis information to display
org.springframework.http.ResponseEntity<UpdatedAnalysisProgress>	getUpdatedProgress(java.lang.Long submissionId, java.util.Locale locale)	Get the updated state and duration of an analysis
ExcelData	parseExcelFile(java.lang.Long submissionId, java.lang.String filename, java.lang.Integer sheetIndex)	Parse excel file and return an ExcelData dto which contains the row data as well as the headers.
ResponseDetails	saveResultsToSamples(java.lang.Long submissionId, java.util.Locale locale, javax.servlet.http.HttpServletResponse response)	Save the results of an analysis back to the samples
ResponseDetails	updateProjectShare(java.lang.Long submissionId, AnalysisProjectShare projectShare, java.util.Locale locale)	Update the share status of a given AnalysisSubmission for a given Project

Methods inherited from class java.lang.Object

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

Constructor Detail

AnalysisAjaxController

@Autowired
public AnalysisAjaxController(AnalysisSubmissionService analysisSubmissionService,
                              IridaWorkflowsService iridaWorkflowsService,
                              UserService userService,
                              SampleService sampleService,
                              ProjectService projectService,
                              UpdateAnalysisSubmissionPermission updateAnalysisPermission,
                              MetadataTemplateService metadataTemplateService,
                              SequencingObjectService sequencingObjectService,
                              AnalysisSubmissionSampleProcessor analysisSubmissionSampleProcessor,
                              org.springframework.context.MessageSource messageSource,
                              ExecutionManagerConfig configFile,
                              AnalysisAudit analysisAudit,
                              AnalysisTypesService analysisTypesService,
                              EmailController emailController,
                              UpdateSamplePermission updateSamplePermission)

Method Detail

ajaxUpdateEmailPipelineResult

@RequestMapping(value="/update-email-pipeline-result",
                method=PATCH)
public ResponseDetails ajaxUpdateEmailPipelineResult(@RequestBody
                                                     AnalysisEmailPipelineResult parameters,
                                                     java.util.Locale locale,
                                                     javax.servlet.http.HttpServletResponse response)

Update an analysis email pipeline completion result

Parameters:

parameters - parameters which include the submission id and the new email pipeline result value

locale - User's locale

response - HTTP response object

Returns:

dto with message

ajaxGetDataForDetailsTab

@RequestMapping(value="/details/{submissionId}",
                method=GET)
public AnalysisDetails ajaxGetDataForDetailsTab(@PathVariable
                                                java.lang.Long submissionId,
                                                java.util.Locale locale,
                                                javax.servlet.http.HttpServletResponse response)

Get analysis details

Parameters:

submissionId - analysis submission id to get data for

locale - User's locale

response - HTTP response object

Returns:

dto of analysis details

ajaxGetAnalysisInputFiles

@RequestMapping(value="/inputs/{submissionId}",
                method=GET)
public AnalysisInputFiles ajaxGetAnalysisInputFiles(@PathVariable
                                                    java.lang.Long submissionId,
                                                    java.util.Locale locale)

Get analysis input files and their sizes

Parameters:

submissionId - analysis submission id to get data for

locale - User's locale

Returns:

dto of analysis input files data

ajaxUpdateSubmission

@RequestMapping(value="/update-analysis",
                method=PATCH)
public ResponseDetails ajaxUpdateSubmission(@RequestBody
                                            AnalysisSubmissionInfo parameters,
                                            java.util.Locale locale,
                                            javax.servlet.http.HttpServletResponse response)

Update an analysis name and/or priority

Parameters:

parameters - parameters which include the submission id and the new name and/or priority

locale - User's locale

response - HTTP response object

Returns:

dto with message

getOutputFilesInfo

@RequestMapping(value="/{id}/outputs",
                method=GET)
@ResponseBody
public java.util.List<AnalysisOutputFileInfo> getOutputFilesInfo(@PathVariable
                                                                 java.lang.Long id)

For an AnalysisSubmission, get info about each AnalysisOutputFile

Parameters:

id - AnalysisSubmission id

Returns:

map of info about each AnalysisOutputFile

getOutputFile

@RequestMapping(value="/{id}/outputs/{fileId}",
                method=GET)
@ResponseBody
public AnalysisOutputFileInfo getOutputFile(@PathVariable
                                            java.lang.Long id,
                                            @PathVariable
                                            java.lang.Long fileId,
                                            @RequestParam(defaultValue="100",required=false)
                                            java.lang.Long limit,
                                            @RequestParam(required=false)
                                            java.lang.Long start,
                                            @RequestParam(required=false)
                                            java.lang.Long end,
                                            @RequestParam(defaultValue="0",required=false)
                                            java.lang.Long seek,
                                            @RequestParam(required=false)
                                            java.lang.Long chunk,
                                            javax.servlet.http.HttpServletResponse response)

Read some lines or text from an AnalysisOutputFile.

Parameters:

id - AnalysisSubmission id

fileId - AnalysisOutputFile id

limit - Optional limit to number of lines to read from file

start - Optional line to start reading from

end - Optional line to stop reading at

seek - Optional file byte position to seek to and begin reading

chunk - Optional number of bytes to read from file

response - HTTP response object

Returns:

JSON with file text or lines as well as information about the file.

ajaxGetJobErrors

@RequestMapping(value="/{submissionId}/job-errors",
                method=GET)
@ResponseBody
public AnalysisJobError ajaxGetJobErrors(@PathVariable
                                         java.lang.Long submissionId)

Get a dto with list of JobError for an AnalysisSubmission under key `galaxyJobErrors` and the `galaxyUrl` for the galaxy instance

Parameters:

submissionId - AnalysisSubmission id

Returns:

dto with galaxyJobErrors and galaxyUrl

getSharedProjectsForAnalysis

@RequestMapping(value="/{submissionId}/share",
                method=GET)
@ResponseBody
public java.util.List<ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController.SharedProjectResponse> getSharedProjectsForAnalysis(@PathVariable
                                                                                                                                                       java.lang.Long submissionId)

Get the status of projects that can be shared with the given analysis

Parameters:

submissionId - the AnalysisSubmission id

Returns:

a list of AnalysisAjaxController.SharedProjectResponse

updateProjectShare

@RequestMapping(value="/{submissionId}/share",
                method=POST)
public ResponseDetails updateProjectShare(@PathVariable
                                          java.lang.Long submissionId,
                                          @RequestBody
                                          AnalysisProjectShare projectShare,
                                          java.util.Locale locale)

Update the share status of a given AnalysisSubmission for a given Project

Parameters:

submissionId - the AnalysisSubmission id to share/unshare

projectShare - AnalysisProjectShare describes of the project and the share status.

locale - Locale of the logged in user

Returns:

Success message if successful

saveResultsToSamples

@RequestMapping(value="/{submissionId}/save-results",
                method=POST)
@ResponseBody
public ResponseDetails saveResultsToSamples(@PathVariable
                                            java.lang.Long submissionId,
                                            java.util.Locale locale,
                                            javax.servlet.http.HttpServletResponse response)

Save the results of an analysis back to the samples

Parameters:

submissionId - ID of the AnalysisSubmission

locale - locale of the logged in user

response - HTTP response object

Returns:

success message

getSistrAnalysis

@RequestMapping("/sistr/{id}")
@ResponseBody
public AnalysisSistrResults getSistrAnalysis(@PathVariable
                                             java.lang.Long id)

Get the sistr analysis information to display

Parameters:

id - ID of the analysis submission

Returns:

dto with SISTR analysis results

deleteAjaxAnalysisSubmission

@RequestMapping("/delete/{analysisSubmissionId}")
@ResponseBody
public java.util.Map<java.lang.String,java.lang.String> deleteAjaxAnalysisSubmission(@PathVariable
                                                                                           java.lang.Long analysisSubmissionId,
                                                                                           java.util.Locale locale)

Delete an AnalysisSubmission by id.

Parameters:

analysisSubmissionId - the submission ID to delete.

locale - Locale of the logged in user

Returns:

A message stating the submission was deleted

getAjaxDownloadAnalysisSubmission

@RequestMapping(value="/download/{analysisSubmissionId}",
                produces="application/json")
public void getAjaxDownloadAnalysisSubmission(@PathVariable
                                              java.lang.Long analysisSubmissionId,
                                              javax.servlet.http.HttpServletResponse response)

Download all output files from an AnalysisSubmission

Parameters:

analysisSubmissionId - Id for a AnalysisSubmission

response - HttpServletResponse

getNewickForAnalysis

@RequestMapping("/{submissionId}/newick")
@ResponseBody
public java.util.Map<java.lang.String,java.lang.Object> getNewickForAnalysis(@PathVariable
                                                                                   java.lang.Long submissionId)
                                                                            throws java.io.IOException

Get a newick file associated with a specific AnalysisSubmission.

Parameters:

submissionId - Long id for an AnalysisSubmission

Returns:

Map containing the newick file contents.

Throws:

java.io.IOException - IOException if the newick file is not found

getImageFile

@RequestMapping("{submissionId}/image")
@ResponseBody
public org.springframework.http.ResponseEntity<java.lang.String> getImageFile(@PathVariable
                                                                              java.lang.Long submissionId,
                                                                              java.lang.String filename)

Get an image file associated with a specific AnalysisSubmission by file name.

Parameters:

submissionId - Long id for an AnalysisSubmission

filename - String filename for an AnalysisOutputFile

Returns:

String containing the image file contents as a base64 encoded string.

getMetadataForAnalysisSamples

@RequestMapping("/{submissionId}/metadata")
@ResponseBody
public java.util.Map<java.lang.String,java.lang.Object> getMetadataForAnalysisSamples(@PathVariable
                                                                                            java.lang.Long submissionId)

Get the metadata associated with a template for an analysis.

Parameters:

submissionId - Long identifier for the AnalysisSubmission

Returns:

Map

getMetadataTemplatesForAnalysis

@RequestMapping("/{submissionId}/metadata-templates")
@ResponseBody
public java.util.Map<java.lang.String,java.lang.Object> getMetadataTemplatesForAnalysis(@PathVariable
                                                                                              java.lang.Long submissionId)

Get a list of all MetadataTemplates for the AnalysisSubmission

Parameters:

submissionId - id of the AnalysisSubmission

Returns:

a map of MetadataTemplates

getMetadataTemplateFields

@RequestMapping("/{submissionId}/metadata-template-fields")
@ResponseBody
public java.util.Map<java.lang.String,java.lang.Object> getMetadataTemplateFields(@RequestParam
                                                                                        java.lang.Long templateId)

Generates a list of metadata fields for a five template.

Parameters:

templateId - Long id for the MetadataTemplate that the fields are required.

Returns:

Map

getNewickTree

@RequestMapping("/{submissionId}/tree")
public AnalysisTreeResponse getNewickTree(@PathVariable
                                          java.lang.Long submissionId,
                                          java.util.Locale locale)
                                   throws java.io.IOException

Construct the model parameters for results with a newick output Analysis

Parameters:

submissionId - The analysis submission id

locale - The users current Locale

Returns:

dto which contains the newick string and an optional message

Throws:

java.io.IOException - If the tree file couldn't be read

parseExcelFile

@RequestMapping("/{submissionId}/parseExcel")
@ResponseBody
public ExcelData parseExcelFile(@PathVariable
                                java.lang.Long submissionId,
                                java.lang.String filename,
                                java.lang.Integer sheetIndex)

Parse excel file and return an ExcelData dto which contains the row data as well as the headers.

Parameters:

submissionId - The analysis submission id

filename - The name of the excel file to parse

sheetIndex - The index of the sheet in the excel workbook to parse

Returns:

dto which contains the headers and rows of the excel file

getProvenanceByFile

@RequestMapping("/{submissionId}/provenance")
@ResponseBody
public AnalysisProvenanceResponse getProvenanceByFile(@PathVariable
                                                      java.lang.Long submissionId,
                                                      java.lang.String filename)

Get the full analysis provenance

Parameters:

submissionId - The analysis submission id

filename - The name of the file for which to get the provenance

Returns:

dto which contains the file provenance

getUpdatedProgress

@RequestMapping("/{submissionId}/updated-progress")
public org.springframework.http.ResponseEntity<UpdatedAnalysisProgress> getUpdatedProgress(@PathVariable
                                                                                           java.lang.Long submissionId,
                                                                                           java.util.Locale locale)

Get the updated state and duration of an analysis

Parameters:

submissionId - The analysis submission id

locale - The user's locale

Returns:

dto which contains the updated analysis state and duration

getAnalysisInfo

@RequestMapping("/{submissionId}/analysis-details")
public org.springframework.http.ResponseEntity<AnalysisInfo> getAnalysisInfo(@PathVariable
                                                                             java.lang.Long submissionId,
                                                                             java.security.Principal principal,
                                                                             java.util.Locale locale)

Get the analysis details

Parameters:

submissionId - The analysis submission id

principal - Principal User

locale - The users current Locale

Returns:

dto which contains the analysis details