EVA-3455 - Job specific to variantLoad

src/main/java/uk/ac/ebi/eva/pipeline/configuration/BeanNames.java

@@ -62,9 +62,11 @@ public class BeanNames {
     public static final String ACCESSION_IMPORT_STEP = "accession-import-step";
 
     public static final String AGGREGATED_VCF_JOB = "aggregated-vcf-job";
+    public static final String AGGREGATED_VARIANT_LOAD_VCF_JOB = "aggregated-variant-load-vcf-job";
     public static final String ANNOTATE_VARIANTS_JOB = "annotate-variants-job";
     public static final String INIT_DATABASE_JOB = "init-database-job";
     public static final String GENOTYPED_VCF_JOB = "genotyped-vcf-job";
+    public static final String GENOTYPED_VARIANT_LOAD_VCF_JOB = "genotyped-variant-load-vcf-job";
     public static final String CALCULATE_STATISTICS_JOB = "calculate-statistics-job";
     public static final String DROP_STUDY_JOB = "drop-study-job";
     public static final String ACCESSION_IMPORT_JOB = "accession-import-job";

src/main/java/uk/ac/ebi/eva/pipeline/configuration/jobs/AggregatedVariantLoadVcfJobConfiguration.java

@@ -0,0 +1,85 @@
+/*
+ * Copyright 2015-2017 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package uk.ac.ebi.eva.pipeline.configuration.jobs;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.batch.core.Job;
+import org.springframework.batch.core.Step;
+import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
+import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
+import org.springframework.batch.core.job.builder.FlowJobBuilder;
+import org.springframework.batch.core.job.builder.JobBuilder;
+import org.springframework.batch.core.job.flow.Flow;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.Scope;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.flows.AnnotationFlowOptionalConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.LoadFileStepConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.LoadVariantsStepConfiguration;
+import uk.ac.ebi.eva.pipeline.parameters.NewJobIncrementer;
+import uk.ac.ebi.eva.pipeline.parameters.validation.job.VariantLoadVcfJobParametersValidator;
+
+import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.*;
+
+/**
+ * Complete pipeline workflow for aggregated VCF. Aggregated statistics are provided in the VCF instead of the
+ * genotypes.
+ * <p>
+ * load --> (optionalAnnotationFlow: variantsAnnotGenerateInput --> (annotationCreate --> annotationLoad))
+ * <p>
+ * Steps in () are optional
+ */
+@Configuration
+@EnableBatchProcessing
+@Import({LoadVariantsStepConfiguration.class, LoadFileStepConfiguration.class, AnnotationFlowOptionalConfiguration.class})
+public class AggregatedVariantLoadVcfJobConfiguration {
+
+    private static final Logger logger = LoggerFactory.getLogger(AggregatedVariantLoadVcfJobConfiguration.class);
+
+    @Autowired
+    @Qualifier(VEP_ANNOTATION_OPTIONAL_FLOW)
+    private Flow annotationFlowOptional;
+
+    @Autowired
+    @Qualifier(LOAD_VARIANTS_STEP)
+    private Step variantLoaderStep;
+
+    @Autowired
+    @Qualifier(LOAD_FILE_STEP)
+    private Step loadFileStep;
+
+    @Bean(AGGREGATED_VARIANT_LOAD_VCF_JOB)
+    @Scope("prototype")
+    public Job aggregatedVcfJob(JobBuilderFactory jobBuilderFactory) {
+        logger.debug("Building '" + AGGREGATED_VARIANT_LOAD_VCF_JOB + "'");
+
+        JobBuilder jobBuilder = jobBuilderFactory
+                .get(AGGREGATED_VARIANT_LOAD_VCF_JOB)
+                .incrementer(new NewJobIncrementer())
+                .validator(new VariantLoadVcfJobParametersValidator());
+        FlowJobBuilder builder = jobBuilder
+                .flow(variantLoaderStep)
+                .next(loadFileStep)
+                .end();
+
+        return builder.build();
+    }
+}

src/main/java/uk/ac/ebi/eva/pipeline/configuration/jobs/GenotypedVariantLoadVcfJobConfiguration.java

@@ -0,0 +1,88 @@
+/*
+ * Copyright 2015-2017 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package uk.ac.ebi.eva.pipeline.configuration.jobs;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.batch.core.Job;
+import org.springframework.batch.core.Step;
+import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
+import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
+import org.springframework.batch.core.job.builder.FlowJobBuilder;
+import org.springframework.batch.core.job.builder.JobBuilder;
+import org.springframework.batch.core.job.flow.Flow;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.Scope;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.flows.ParallelStatisticsAndAnnotationFlowConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.LoadFileStepConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.LoadVariantsStepConfiguration;
+import uk.ac.ebi.eva.pipeline.parameters.NewJobIncrementer;
+import uk.ac.ebi.eva.pipeline.parameters.validation.job.GenotypedVcfJobParametersValidator;
+import uk.ac.ebi.eva.pipeline.parameters.validation.job.VariantLoadVcfJobParametersValidator;
+
+import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.*;
+
+/**
+ * Variant load pipeline workflow:
+ * <p>
+ * |--> (optionalStatisticsFlow: statsCreate --> statsLoad)
+ * transform ---> load -+
+ * |--> (optionalAnnotationFlow: variantsAnnotGenerateInput --> (annotationCreate --> annotationLoad))
+ * <p>
+ * Steps in () are optional
+ */
+@Configuration
+@EnableBatchProcessing
+@Import({LoadVariantsStepConfiguration.class, LoadFileStepConfiguration.class, ParallelStatisticsAndAnnotationFlowConfiguration.class})
+public class GenotypedVariantLoadVcfJobConfiguration {
+
+    private static final Logger logger = LoggerFactory.getLogger(GenotypedVariantLoadVcfJobConfiguration.class);
+
+    @Autowired
+    @Qualifier(PARALLEL_STATISTICS_AND_ANNOTATION)
+    private Flow parallelStatisticsAndAnnotation;
+
+    @Autowired
+    @Qualifier(LOAD_VARIANTS_STEP)
+    private Step variantLoaderStep;
+
+    @Autowired
+    @Qualifier(LOAD_FILE_STEP)
+    private Step loadFileStep;
+
+    @Bean(GENOTYPED_VARIANT_LOAD_VCF_JOB)
+    @Scope("prototype")
+    public Job genotypedVcfJob(JobBuilderFactory jobBuilderFactory) {
+        logger.debug("Building '" + GENOTYPED_VARIANT_LOAD_VCF_JOB + "'");
+
+        JobBuilder jobBuilder = jobBuilderFactory
+                .get(GENOTYPED_VARIANT_LOAD_VCF_JOB)
+                .incrementer(new NewJobIncrementer())
+                .validator(new VariantLoadVcfJobParametersValidator());
+        FlowJobBuilder builder = jobBuilder
+                .flow(variantLoaderStep)
+                .next(loadFileStep)
+                .end();
+
+        return builder.build();
+    }
+
+}

src/main/java/uk/ac/ebi/eva/pipeline/parameters/validation/job/VariantLoadVcfJobParametersValidator.java

@@ -0,0 +1,52 @@
+/*
+ * Copyright 2017 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package uk.ac.ebi.eva.pipeline.parameters.validation.job;
+
+import org.springframework.batch.core.JobParameters;
+import org.springframework.batch.core.JobParametersInvalidException;
+import org.springframework.batch.core.JobParametersValidator;
+import org.springframework.batch.core.job.CompositeJobParametersValidator;
+import org.springframework.batch.core.job.DefaultJobParametersValidator;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.GenotypedVariantLoadVcfJobConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.AggregatedVcfJobConfiguration;
+import uk.ac.ebi.eva.pipeline.parameters.validation.step.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Validates the job parameters necessary to execute an {@link GenotypedVariantLoadVcfJobConfiguration}
+ * or an {@link AggregatedVcfJobConfiguration}
+ */
+public class VariantLoadVcfJobParametersValidator extends DefaultJobParametersValidator {
+
+    @Override
+    public void validate(JobParameters parameters) throws JobParametersInvalidException {
+        compositeJobParametersValidator(parameters).validate(parameters);
+    }
+
+    private CompositeJobParametersValidator compositeJobParametersValidator(JobParameters jobParameters) {
+        List<JobParametersValidator> jobParametersValidators = new ArrayList<>();
+
+        jobParametersValidators.add(new LoadVariantsStepParametersValidator());
+        jobParametersValidators.add(new LoadFileStepParametersValidator());
+
+        CompositeJobParametersValidator compositeJobParametersValidator = new CompositeJobParametersValidator();
+        compositeJobParametersValidator.setValidators(jobParametersValidators);
+        return compositeJobParametersValidator;
+    }
+
+}