Package ca.corefacility.bioinformatics.irida.service.export

Class ExportUploadService

java.lang.Object

ca.corefacility.bioinformatics.irida.service.export.ExportUploadService

@Service
public class ExportUploadService
extends java.lang.Object

Class which handles uploading a NcbiExportSubmission to NCBI

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	NCBI_ACCESSION_METADATA_LABEL

Constructor Summary

Constructors

Constructor	Description
ExportUploadService(NcbiExportSubmissionService exportSubmissionService, SampleService sampleService, MetadataTemplateService metadataTemplateService, org.thymeleaf.TemplateEngine templateEngine, EmailController emailController)

Method Summary

Modifier and Type	Method	Description
java.lang.String	createXml(NcbiExportSubmission submission)	Create the XML for an NcbiExportSubmission
void	launchUpload()	Check for new NcbiExportSubmissions to be uploaded and begin their upload
void	setConnectionDetails(java.lang.String ftpHost, int ftpPort, java.lang.String ftpUser, java.lang.String ftpPassword, java.lang.String baseDirectory)	Manually configure connection details for this service
void	updateRunningUploads()	Check local database for submissions which may have updates on the NCBI server and update them as necessary.
NcbiExportSubmission	uploadSubmission(NcbiExportSubmission submission, java.lang.String xml)	Upload an NcbiExportSubmission's files and submission xml to the configured ftp site

Methods inherited from class java.lang.Object

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

Field Detail

NCBI_ACCESSION_METADATA_LABEL

public static final java.lang.String NCBI_ACCESSION_METADATA_LABEL

See Also:

Constant Field Values

Constructor Detail

ExportUploadService

@Autowired
public ExportUploadService(NcbiExportSubmissionService exportSubmissionService,
                           SampleService sampleService,
                           MetadataTemplateService metadataTemplateService,
                           @Qualifier("exportUploadTemplateEngine")
                           org.thymeleaf.TemplateEngine templateEngine,
                           EmailController emailController)

Method Detail

setConnectionDetails

public void setConnectionDetails(java.lang.String ftpHost,
                                 int ftpPort,
                                 java.lang.String ftpUser,
                                 java.lang.String ftpPassword,
                                 java.lang.String baseDirectory)

Manually configure connection details for this service

Parameters:

ftpHost - The hostname to connect to

ftpPort - the ftp port to connect to

ftpUser - the username to authenticate with

ftpPassword - the password to authenticate with

baseDirectory - the base directory to upload new runs into

launchUpload

public void launchUpload()

Check for new NcbiExportSubmissions to be uploaded and begin their upload

updateRunningUploads

public void updateRunningUploads()

Check local database for submissions which may have updates on the NCBI server and update them as necessary.

createXml

public java.lang.String createXml(NcbiExportSubmission submission)

Create the XML for an NcbiExportSubmission

Parameters:

submission - the NcbiExportSubmission to create submission xml for

Returns:

String content of the xml

uploadSubmission

public NcbiExportSubmission uploadSubmission(NcbiExportSubmission submission,
                                             java.lang.String xml)
                                      throws UploadException

Upload an NcbiExportSubmission's files and submission xml to the configured ftp site

Parameters:

submission - The NcbiExportSubmission to upload

xml - The submission xml to upload

Returns:

true/false if upload was successful

Throws:

UploadException - if the upload failed