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

Class UIMetadataImportService

java.lang.Object

ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataImportService

@Component
public class UIMetadataImportService
extends java.lang.Object

UI service to handle importing metadata files, so they can be saved to the session.

Constructor Summary

Constructors

Constructor	Description
UIMetadataImportService(org.springframework.context.MessageSource messageSource, ProjectService projectService, SampleService sampleService, MetadataTemplateService metadataTemplateService, UIMetadataFileImportService metadataFileImportService)

Method Summary

Modifier and Type	Method	Description
void	clearProjectSampleMetadata(javax.servlet.http.HttpSession session, java.lang.Long projectId)	Clear any uploaded sample metadata stored into the session.
SampleMetadataStorage	createProjectSampleMetadata(javax.servlet.http.HttpSession session, java.lang.Long projectId, org.springframework.web.multipart.MultipartFile file)	Upload CSV or Excel file containing sample metadata and extract the headers.
SampleMetadataStorage	getProjectSampleMetadata(javax.servlet.http.HttpSession session, java.lang.Long projectId)	Get the currently stored metadata.
java.lang.String	saveProjectSampleMetadata(java.util.Locale locale, javax.servlet.http.HttpSession session, java.lang.Long projectId, java.util.List<java.lang.String> sampleNames)	Save uploaded metadata
java.lang.String	setProjectSampleMetadataSampleId(javax.servlet.http.HttpSession session, java.lang.Long projectId, java.lang.String sampleNameColumn)	Add the metadata to specific Sample based on the selected column to correspond to the Sample id.

Methods inherited from class java.lang.Object

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

Constructor Detail

UIMetadataImportService

@Autowired
public UIMetadataImportService(org.springframework.context.MessageSource messageSource,
                               ProjectService projectService,
                               SampleService sampleService,
                               MetadataTemplateService metadataTemplateService,
                               UIMetadataFileImportService metadataFileImportService)

Method Detail

createProjectSampleMetadata

public SampleMetadataStorage createProjectSampleMetadata(javax.servlet.http.HttpSession session,
                                                         java.lang.Long projectId,
                                                         org.springframework.web.multipart.MultipartFile file)
                                                  throws java.lang.Exception

Upload CSV or Excel file containing sample metadata and extract the headers. The file is stored in the session until the column that corresponds to a Sample identifier has been sent.

Parameters:

session - HttpSession

projectId - Long identifier for the current Project

file - MultipartFile The csv or excel file containing the metadata.

Returns:

Map of headers and rows from the csv or excel file for the user to select the header corresponding the Sample identifier.

Throws:

java.lang.Exception - if there is an error reading the file

setProjectSampleMetadataSampleId

public java.lang.String setProjectSampleMetadataSampleId(javax.servlet.http.HttpSession session,
                                                         java.lang.Long projectId,
                                                         java.lang.String sampleNameColumn)

Add the metadata to specific Sample based on the selected column to correspond to the Sample id.

Parameters:

session - HttpSession.

projectId - Long identifier for the current Project.

sampleNameColumn - String the header to used to represent the Sample identifier.

Returns:

String containing a complete message.

saveProjectSampleMetadata

public java.lang.String saveProjectSampleMetadata(java.util.Locale locale,
                                                  javax.servlet.http.HttpSession session,
                                                  java.lang.Long projectId,
                                                  java.util.List<java.lang.String> sampleNames)
                                           throws SavedMetadataException

Save uploaded metadata

Parameters:

locale - Locale of the current user.

session - HttpSession

projectId - Long identifier for the current project

sampleNames - List of String sample names

Returns:

String that returns a message and potential errors.

Throws:

SavedMetadataException - if there is an error saving the metadata

clearProjectSampleMetadata

public void clearProjectSampleMetadata(javax.servlet.http.HttpSession session,
                                       java.lang.Long projectId)

Clear any uploaded sample metadata stored into the session.

Parameters:

session - HttpSession

projectId - identifier for the Project currently uploaded metadata to.

getProjectSampleMetadata

public SampleMetadataStorage getProjectSampleMetadata(javax.servlet.http.HttpSession session,
                                                      java.lang.Long projectId)

Get the currently stored metadata.

Parameters:

session - HttpSession

projectId - Long identifier for the current Project

Returns:

the currently stored SampleMetadataStorage