EVA-3669 New job for deprecating SVE variants by reading accessions of variants from file

eva-accession-deprecate/src/main/java/uk/ac/ebi/eva/accession/deprecate/batch/io/SubmittedVariantsFileReader.java

@@ -0,0 +1,149 @@
+/*
+ * Copyright 2022 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.accession.deprecate.batch.io;
+
+import com.mongodb.BasicDBObject;
+import com.mongodb.client.FindIterable;
+import com.mongodb.client.MongoCursor;
+import com.mongodb.client.model.Filters;
+import org.bson.Document;
+import org.bson.conversions.Bson;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.batch.item.ExecutionContext;
+import org.springframework.batch.item.ItemStreamException;
+import org.springframework.batch.item.ItemStreamReader;
+import org.springframework.data.mongodb.core.MongoTemplate;
+import org.springframework.data.mongodb.core.convert.MongoConverter;
+import uk.ac.ebi.eva.accession.core.model.eva.SubmittedVariantEntity;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Read all SubmittedVariants for a given study whose ids are given in the input file
+ */
+public class SubmittedVariantsFileReader implements ItemStreamReader<SubmittedVariantEntity> {
+
+    private static final Logger logger = LoggerFactory.getLogger(SubmittedVariantsFileReader.class);
+
+    private static final String ASSEMBLY_FIELD = "seq";
+    private static final String ACCESSION_FIELD = "accession";
+
+    private BufferedReader reader;
+    private boolean endOfFile = false;
+    private String assembly;
+    private String variantIdFile;
+    private MongoCursor<Document> evaCursor;
+    private MongoConverter converter;
+    private MongoTemplate mongoTemplate;
+    private int chunkSize;
+
+    public SubmittedVariantsFileReader(String assembly, String variantIdFile, MongoTemplate mongoTemplate, int chunkSize) {
+        this.assembly = assembly;
+        this.variantIdFile = variantIdFile;
+        this.mongoTemplate = mongoTemplate;
+        this.chunkSize = chunkSize;
+    }
+
+    @Override
+    public SubmittedVariantEntity read() {
+        if (evaCursor == null || !evaCursor.hasNext()) {
+            if (endOfFile) {
+                return null;
+            }
+
+            loadNextBatchAndQuery();
+
+            if (evaCursor == null || !evaCursor.hasNext()) {
+                return null;
+            }
+        }
+
+        Document nextElement = evaCursor.next();
+        return getSubmittedVariantEntity(nextElement);
+    }
+
+    private SubmittedVariantEntity getSubmittedVariantEntity(Document document) {
+        return converter.read(SubmittedVariantEntity.class, new BasicDBObject(document));
+    }
+
+    @Override
+    public void open(ExecutionContext executionContext) throws ItemStreamException {
+        try {
+            reader = new BufferedReader(new FileReader(variantIdFile));
+        } catch (IOException e) {
+            throw new ItemStreamException("Failed to open the file (" + variantIdFile + ") with variant IDs", e);
+        }
+        initializeReader();
+    }
+
+    public void initializeReader() {
+        converter = mongoTemplate.getConverter();
+        loadNextBatchAndQuery();
+    }
+
+    private void loadNextBatchAndQuery() {
+        List<Long> variantIds = new ArrayList<>();
+        String line;
+
+        try {
+            while (variantIds.size() < chunkSize && (line = reader.readLine()) != null) {
+                variantIds.add(Long.parseLong(line.trim()));
+            }
+            if (variantIds.isEmpty()) {
+                endOfFile = true;
+                return;
+            }
+        } catch (IOException e) {
+            throw new ItemStreamException("Error reading variant IDs from file", e);
+        }
+
+        Bson query = Filters.and(Filters.in(ACCESSION_FIELD, variantIds), Filters.eq(ASSEMBLY_FIELD, assembly));
+        logger.info("Issuing find in EVA collection for a batch of IDs: {}", query);
+        FindIterable<Document> submittedVariantsEVA = getSubmittedVariants(query, SubmittedVariantEntity.class);
+        evaCursor = submittedVariantsEVA.iterator();
+    }
+
+    private FindIterable<Document> getSubmittedVariants(Bson query, Class<?> entityClass) {
+        return mongoTemplate.getCollection(mongoTemplate.getCollectionName(entityClass))
+                .find(query)
+                .noCursorTimeout(true)
+                .batchSize(chunkSize);
+    }
+
+    @Override
+    public void update(ExecutionContext executionContext) throws ItemStreamException {
+
+    }
+
+    @Override
+    public void close() throws ItemStreamException {
+        try {
+            if (evaCursor != null) {
+                evaCursor.close();
+            }
+            if (reader != null) {
+                reader.close();
+            }
+        } catch (IOException e) {
+            throw new ItemStreamException("Exception while closing resources", e);
+        }
+    }
+}

eva-accession-deprecate/src/main/java/uk/ac/ebi/eva/accession/deprecate/configuration/BeanNames.java

@@ -19,12 +19,18 @@ public class BeanNames {
 
     public static final String STUDY_SUMITTED_VARIANTS_READER = "STUDY_SUMITTED_VARIANTS_READER";
 
+    public static final String SUBMITTED_VARIANTS_FILE_READER = "SUBMITTED_VARIANTS_FILE_READER";
+
     public static final String STUDY_DEPRECATION_WRITER = "STUDY_DEPRECATION_WRITER";
 
     public static final String DEPRECATE_STUDY_SUBMITTED_VARIANTS_STEP = "DEPRECATE_STUDY_SUBMITTED_VARIANTS_STEP";
 
     public static final String DEPRECATE_STUDY_SUBMITTED_VARIANTS_JOB = "DEPRECATE_STUDY_SUBMITTED_VARIANTS_JOB";
 
+    public static final String DEPRECATE_SUBMITTED_VARIANTS_FROM_FILE_STEP = "DEPRECATE_SUBMITTED_VARIANTS_FROM_FILE_STEP";
+
+    public static final String DEPRECATE_SUBMITTED_VARIANTS_FROM_FILE_JOB = "DEPRECATE_SUBMITTED_VARIANTS_FROM_FILE_JOB";
+
     public static final String DEPRECATION_PROGRESS_LISTENER = "DEPRECATION_PROGRESS_LISTENER";
 
 }

eva-accession-deprecate/src/main/java/uk/ac/ebi/eva/accession/deprecate/configuration/batch/io/StudySubmittedVariantsFileReaderConfiguration.java

@@ -0,0 +1,38 @@
+/*
+ * Copyright 2024 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.accession.deprecate.configuration.batch.io;
+
+import org.springframework.batch.core.configuration.annotation.StepScope;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+import org.springframework.data.mongodb.core.MongoTemplate;
+import uk.ac.ebi.eva.accession.core.configuration.nonhuman.MongoConfiguration;
+import uk.ac.ebi.eva.accession.deprecate.batch.io.SubmittedVariantsFileReader;
+import uk.ac.ebi.eva.accession.deprecate.configuration.BeanNames;
+import uk.ac.ebi.eva.accession.deprecate.parameters.InputParameters;
+
+@Configuration
+@Import({MongoConfiguration.class})
+public class StudySubmittedVariantsFileReaderConfiguration {
+
+    @Bean(BeanNames.SUBMITTED_VARIANTS_FILE_READER)
+    @StepScope
+    SubmittedVariantsFileReader submittedVariantsFileReader(MongoTemplate mongoTemplate, InputParameters parameters) {
+        return new SubmittedVariantsFileReader(parameters.getAssemblyAccession(), parameters.getVariantIdFile(),
+                mongoTemplate, parameters.getChunkSize());
+    }
+}

eva-accession-deprecate/src/main/java/uk/ac/ebi/eva/accession/deprecate/configuration/batch/jobs/DeprecateSubmittedVariantsFromFileJobConfiguration.java

@@ -0,0 +1,56 @@
+/*
+ * Copyright 2024 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.accession.deprecate.configuration.batch.jobs;
+
+import org.springframework.batch.core.Job;
+import org.springframework.batch.core.Step;
+import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
+import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
+import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
+import org.springframework.batch.core.launch.support.RunIdIncrementer;
+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 uk.ac.ebi.eva.accession.deprecate.configuration.BeanNames;
+import uk.ac.ebi.eva.commons.batch.configuration.SpringBoot1CompatibilityConfiguration;
+
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+
+@Configuration
+@EnableBatchProcessing
+public class DeprecateSubmittedVariantsFromFileJobConfiguration {
+
+    @Autowired
+    @Qualifier(BeanNames.DEPRECATE_SUBMITTED_VARIANTS_FROM_FILE_STEP)
+    private Step deprecateSubmittedVariantsFromFileStep;
+
+    @Bean(BeanNames.DEPRECATE_SUBMITTED_VARIANTS_FROM_FILE_JOB)
+    public Job deprecateStudySubmittedVariantsFromFileJob(JobBuilderFactory jobBuilderFactory) {
+        return jobBuilderFactory.get(BeanNames.DEPRECATE_SUBMITTED_VARIANTS_FROM_FILE_JOB)
+                .incrementer(new RunIdIncrementer())
+                .start(deprecateSubmittedVariantsFromFileStep)
+                .build();
+    }
+
+    @Bean
+    public BatchConfigurer configurer(DataSource dataSource, EntityManagerFactory entityManagerFactory)
+            throws Exception {
+        return SpringBoot1CompatibilityConfiguration.getSpringBoot1CompatibleBatchConfigurer(dataSource,
+                entityManagerFactory);
+    }
+}

eva-accession-deprecate/src/main/java/uk/ac/ebi/eva/accession/deprecate/configuration/batch/steps/DeprecateSubmittedVariantsFromFileStepConfiguration.java

@@ -0,0 +1,60 @@
+/*
+ * Copyright 2024 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.accession.deprecate.configuration.batch.steps;
+
+import org.springframework.batch.core.Step;
+import org.springframework.batch.core.StepExecutionListener;
+import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
+import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
+import org.springframework.batch.core.step.tasklet.TaskletStep;
+import org.springframework.batch.item.ItemStreamReader;
+import org.springframework.batch.item.ItemWriter;
+import org.springframework.batch.repeat.policy.SimpleCompletionPolicy;
+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 uk.ac.ebi.eva.accession.core.model.eva.SubmittedVariantEntity;
+import uk.ac.ebi.eva.accession.deprecate.configuration.BeanNames;
+
+@Configuration
+@EnableBatchProcessing
+public class DeprecateSubmittedVariantsFromFileStepConfiguration {
+
+    @Autowired
+    @Qualifier(BeanNames.SUBMITTED_VARIANTS_FILE_READER)
+    private ItemStreamReader<SubmittedVariantEntity> submittedVariantsFileReader;
+
+    @Autowired
+    @Qualifier(BeanNames.STUDY_DEPRECATION_WRITER)
+    private ItemWriter<SubmittedVariantEntity> submittedVariantDeprecationWriter;
+
+    @Autowired
+    @Qualifier(BeanNames.DEPRECATION_PROGRESS_LISTENER)
+    private StepExecutionListener progressListener;
+
+    @Bean(BeanNames.DEPRECATE_SUBMITTED_VARIANTS_FROM_FILE_STEP)
+    public Step deprecateSubmittedVariantsFromFileStep(StepBuilderFactory stepBuilderFactory,
+                                               SimpleCompletionPolicy chunkSizeCompletionPolicy) {
+        TaskletStep step = stepBuilderFactory.get(BeanNames.DEPRECATE_SUBMITTED_VARIANTS_FROM_FILE_STEP)
+                .<SubmittedVariantEntity, SubmittedVariantEntity>chunk(chunkSizeCompletionPolicy)
+                .reader(submittedVariantsFileReader)
+                .writer(submittedVariantDeprecationWriter)
+                .listener(progressListener)
+                .build();
+        return step;
+    }
+}

eva-accession-deprecate/src/main/java/uk/ac/ebi/eva/accession/deprecate/parameters/InputParameters.java

@@ -27,6 +27,8 @@ public class InputParameters {
 
     private String deprecationReason;
 
+    private String variantIdFile;
+
     public int getChunkSize() {
         return chunkSize;
     }
@@ -66,4 +68,12 @@ public String getDeprecationReason() {
     public void setDeprecationReason(String deprecationReason) {
         this.deprecationReason = deprecationReason;
     }
+
+    public String getVariantIdFile() {
+        return variantIdFile;
+    }
+
+    public void setVariantIdFile(String variantIdFile) {
+        this.variantIdFile = variantIdFile;
+    }
 }

eva-accession-deprecate/src/test/java/uk/ac/ebi/eva/accession/deprecate/MongoTestDatabaseSetup.java

@@ -83,6 +83,22 @@ public static void populateTestDB(MongoTemplate mongoTemplate) {
         mongoTemplate.save(rs2, mongoTemplate.getCollectionName(ClusteredVariantEntity.class));
     }
 
+    public static void populateTestDBForFile(MongoTemplate mongoTemplate) {
+        // rs1 -> ss1,ss2
+        // rs2 -> ss3,ss4
+        ss1 = createSS(STUDY1, 5L, 1L, 100L, "C", "T");
+        ss2 = createSS(STUDY1, 6L, 1L, 100L, "C", "A");
+        ss3 = createSS(STUDY2, 7L, 5L, 102L, "T", "G");
+        ss4 = createSS(STUDY2, 8L, 5L, 102L, "T", "A");
+
+        rs1 = createRS(ss1);
+        mongoTemplate.save(rs1, mongoTemplate.getCollectionName(DbsnpClusteredVariantEntity.class));
+
+        mongoTemplate.insert(Arrays.asList(ss1, ss2, ss3, ss4), SubmittedVariantEntity.class);
+        rs2 = createRS(ss3);
+        mongoTemplate.save(rs2, mongoTemplate.getCollectionName(ClusteredVariantEntity.class));
+    }
+
     public static void assertPostDeprecationDatabaseState(MongoTemplate mongoTemplate) {
         // ss4 was not deprecated and still remains
         assertEquals(1, mongoTemplate.findAll(SubmittedVariantEntity.class).size());