Package ca.corefacility.bioinformatics.irida.config.services

Class IridaApiServicesConfig

java.lang.Object

ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

@Configuration
@Import({IridaApiSecurityConfig.class,IridaApiAspectsConfig.class,IridaApiRepositoriesConfig.class,ExecutionManagerConfig.class,AnalysisExecutionServiceConfig.class,WebEmailConfig.class,IridaScheduledTasksConfig.class,IridaPluginConfig.class,IridaWorkflowsConfig.class})
@ComponentScan(basePackages={"ca.corefacility.bioinformatics.irida.service","ca.corefacility.bioinformatics.irida.processing","ca.corefacility.bioinformatics.irida.pipeline.results.updater"})
public class IridaApiServicesConfig
extends java.lang.Object

Configuration for the IRIDA platform.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IridaApiServicesConfig.IridaLocaleList	Inner class storing the enabled locales for IRIDA

Constructor Summary

Constructors

Constructor	Description
IridaApiServicesConfig()

Method Summary

Modifier and Type	Method	Description
AnalysisSubmissionCleanupService	analysisSubmissionCleanupService(AnalysisSubmissionRepository analysisSubmissionRepository, UserService userService)
java.util.concurrent.Executor	analysisTaskExecutor(UserService userService)	Builds a new Executor for analysis tasks.
org.thymeleaf.spring5.SpringTemplateEngine	exportUploadTemplateEngine()
org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor	fileProcessingChainExecutor()
FileProcessingChain	fileProcessorChain(SequencingObjectRepository sequencingObjectRepository, QCEntryRepository qcRepository, GzipFileProcessor gzipFileProcessor, FastqcFileProcessor fastQcFileProcessor, ChecksumFileProcessor checksumProcessor, CoverageFileProcessor coverageProcessor, AutomatedAnalysisFileProcessor automatedAnalysisFileProcessor)
org.springframework.beans.factory.config.BeanPostProcessor	forbidJpqlUpdateDeletePostProcessor()
IridaApiServicesConfig.IridaLocaleList	installedLocales()
org.springframework.context.MessageSource	messageSource()
TaxonomyService	taxonomyService()
java.util.concurrent.Executor	uploadExecutor()
javax.validation.Validator	validator()

Methods inherited from class java.lang.Object

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

Constructor Detail

IridaApiServicesConfig

public IridaApiServicesConfig()

Method Detail

forbidJpqlUpdateDeletePostProcessor

@Bean
public org.springframework.beans.factory.config.BeanPostProcessor forbidJpqlUpdateDeletePostProcessor()

installedLocales

@Bean
public IridaApiServicesConfig.IridaLocaleList installedLocales()

messageSource

@Bean
public org.springframework.context.MessageSource messageSource()

fileProcessorChain

@Bean(name="uploadFileProcessingChain")
public FileProcessingChain fileProcessorChain(SequencingObjectRepository sequencingObjectRepository,
                                              QCEntryRepository qcRepository,
                                              GzipFileProcessor gzipFileProcessor,
                                              FastqcFileProcessor fastQcFileProcessor,
                                              ChecksumFileProcessor checksumProcessor,
                                              CoverageFileProcessor coverageProcessor,
                                              AutomatedAnalysisFileProcessor automatedAnalysisFileProcessor)

fileProcessingChainExecutor

@Bean(name="fileProcessingChainExecutor")
public org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor fileProcessingChainExecutor()

validator

@Bean
public javax.validation.Validator validator()

taxonomyService

@Bean
public TaxonomyService taxonomyService()
                                throws java.net.URISyntaxException

Throws:

java.net.URISyntaxException

analysisTaskExecutor

@Bean
@DependsOn("springLiquibase")
public java.util.concurrent.Executor analysisTaskExecutor(UserService userService)

Builds a new Executor for analysis tasks.

Parameters:

userService - a reference to the user service.

Returns:

A new Executor for analysis tasks.

analysisSubmissionCleanupService

@Bean
@DependsOn("springLiquibase")
@Profile({"prod","analysis"})
public AnalysisSubmissionCleanupService analysisSubmissionCleanupService(AnalysisSubmissionRepository analysisSubmissionRepository,
                                                                         UserService userService)

uploadExecutor

@Bean
public java.util.concurrent.Executor uploadExecutor()

Returns:

An Executor for handling uploads to Galaxy.

exportUploadTemplateEngine

@Bean(name="exportUploadTemplateEngine")
public org.thymeleaf.spring5.SpringTemplateEngine exportUploadTemplateEngine()