CommandLineAnnotatorConfig.java

package org.molgenis.annotation.cmd;

import org.molgenis.CommandLineOnlyConfiguration;
import org.molgenis.annotation.cmd.conversion.EffectStructureConverter;
import org.molgenis.annotation.cmd.data.CmdLineDataService;
import org.molgenis.annotation.cmd.data.CmdLineSettingsEntity;
import org.molgenis.annotation.cmd.utils.VcfValidator;
import org.molgenis.data.*;
import org.molgenis.data.annotation.core.utils.JarRunnerImpl;
import org.molgenis.data.convert.DateToStringConverter;
import org.molgenis.data.convert.StringToDateConverter;
import org.molgenis.data.meta.model.*;
import org.molgenis.data.meta.EntityTypeDependencyResolver;
import org.molgenis.data.meta.model.AttributeMetadata;
import org.molgenis.data.meta.model.EntityTypeMetadata;
import org.molgenis.data.meta.model.PackageMetadata;
import org.molgenis.data.meta.model.TagMetadata;
import org.molgenis.data.populate.AutoValuePopulator;
import org.molgenis.data.populate.DefaultValuePopulator;
import org.molgenis.data.populate.EntityPopulator;
import org.molgenis.data.populate.UuidGenerator;
import org.molgenis.data.vcf.utils.VcfUtils;
import org.molgenis.util.GenericDependencyResolver;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.ApplicationContext;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
import org.springframework.core.convert.ConversionService;
import org.springframework.core.convert.support.DefaultConversionService;

import javax.annotation.PostConstruct;

import static com.google.common.collect.Lists.newArrayList;

/**
 * Commandline-specific annotator configuration.
 */
@Configuration
@CommandLineOnlyConfiguration
@ComponentScan({ "org.molgenis.data.meta.model", "org.molgenis.data.system.model", "org.molgenis.data.vcf.model",
		"org.molgenis.data.annotation.core.effects" })
public class CommandLineAnnotatorConfig
{
	@Autowired
	ApplicationContext applicationContext;

	@Autowired
	EntityTypeFactory entityTypeFactory;

	@Autowired
	AttributeFactory attributeFactory;

	@PostConstruct
	public void bootstrap()
	{
		EntityTypeMetadata entityTypeMeta = applicationContext.getBean(EntityTypeMetadata.class);
		entityTypeMeta.setBackendEnumOptions(newArrayList("test"));
		applicationContext.getBean(AttributeMetadata.class).bootstrap(entityTypeMeta);
		applicationContext.getBean(EntityTypeMetadata.class).bootstrap(entityTypeMeta);
		applicationContext.getBean(PackageMetadata.class).bootstrap(entityTypeMeta);
		applicationContext.getBean(TagMetadata.class).bootstrap(entityTypeMeta);
	}

	@Value("${vcf-validator-location:@null}")
	private String vcfValidatorLocation;

	/**
	 * Needed to make @Value annotations with property placeholders work!
	 * <p>
	 * https://stackoverflow.com/questions/17097521/spring-3-2-value-annotation-with-pure-java-configuration-does-not
	 * -work-but-env
	 */
	@Bean
	public static PropertySourcesPlaceholderConfigurer propertyPlaceholderConfigurer()
	{
		PropertySourcesPlaceholderConfigurer result = new PropertySourcesPlaceholderConfigurer();
		result.setNullValue("@null");
		return result;
	}

	@Bean
	VcfUtils vcfUtils()
	{
		return new VcfUtils();
	}


	@Bean
	EffectStructureConverter effectStructureConverter()
	{
		return new EffectStructureConverter(entityTypeFactory, attributeFactory);
	}

	@Bean
	public DataService dataService()
	{
		return new CmdLineDataService();
	}

	@Bean
	public VcfValidator vcfValidator()
	{
		return new VcfValidator(vcfValidatorLocation);
	}

	@Bean
	ConversionService conversionService()
	{
		DefaultConversionService registry = new DefaultConversionService();
		registry.addConverter(new DateToStringConverter());
		registry.addConverter(new StringToDateConverter());
		return registry;
	}

	@Bean
	EntityFactoryRegistry entityFactoryRegistry()
	{
		return new EntityFactoryRegistry();
	}

	@Bean
	EntityReferenceCreator entityReferenceCreator()
	{
		return new EntityReferenceCreatorImpl(dataService(), entityFactoryRegistry());
	}

	@Bean
	EntityManager entityManager()
	{
		return new EntityManagerImpl(dataService(), entityFactoryRegistry(), entityPopulator(),
				entityReferenceCreator());
	}

	@Bean
	public CmdLineAnnotator cmdLineAnnotator()
	{
		return new CmdLineAnnotator();
	}

	@Bean
	public AutoValuePopulator autoValuePopulator()
	{
		return new AutoValuePopulator(uuidGenerator());
	}

	@Bean
	public DefaultValuePopulator defaultValuePopulator()
	{
		return new DefaultValuePopulator(entityReferenceCreator());
	}

	@Bean
	public EntityPopulator entityPopulator()
	{
		return new EntityPopulator(autoValuePopulator(), defaultValuePopulator());
	}

	@Bean
	public EntityTypeDependencyResolver entityTypeDependencyResolver()
	{
		return new EntityTypeDependencyResolver(genericDependencyResolver());
	}

	@Bean
	public GenericDependencyResolver genericDependencyResolver()
	{
		return new GenericDependencyResolver();
	}

	@Bean
	public UuidGenerator uuidGenerator()
	{
		return new UuidGenerator();
	}

	@Bean
	public JarRunnerImpl jarRunner()
	{
		return new JarRunnerImpl();
	}

	@Bean
	public Entity snpEffAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity goNLAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity thousendGenomesAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity CGDAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity clinvarAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity dannAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity exacAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity caddAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity fitConAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity HPOAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity gavinAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}

	@Bean
	public Entity omimAnnotatorSettings()
	{
		return new CmdLineSettingsEntity();
	}
}