Merge pull request #24 from waterflow80/database-populator-test-suite

Test suite enhancements - SeqColWriter & AssemblyDataGenerator

src/main/java/uk/ac/ebi/eva/evaseqcol/repo/SeqColExtendedDataRepository.java

@@ -25,4 +25,8 @@ public interface SeqColExtendedDataRepository extends JpaRepository<SeqColExtend
     public Optional<List<String>> getSeqColExtendedDataByLevel0Digest(@Param("level0Digest") String seqColDigest);
 
     public Optional<SeqColExtendedDataEntity> getSeqColExtendedDataEntityByDigest(String digest);
+
+    void removeSeqColExtendedDataEntityByDigest(String digest);
+
+    void deleteAll();
 }

src/main/java/uk/ac/ebi/eva/evaseqcol/repo/SeqColLevelOneRepository.java

@@ -10,4 +10,8 @@ public interface SeqColLevelOneRepository extends JpaRepository<SeqColLevelOneEn
     SeqColLevelOneEntity findSeqColLevelOneEntityByDigest(String digest);
 
     long countSeqColLevelOneEntitiesByDigest(String digest);
+
+    void removeSeqColLevelOneEntityByDigest(String digest);
+
+    void deleteAll();
 }

src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColExtendedDataService.java

@@ -63,6 +63,27 @@ public List<SeqColExtendedDataEntity> addAll(List<SeqColExtendedDataEntity> seqC
         return repository.saveAll(seqColExtendedDataList);
     }
 
+    /**
+     * Remove all seqCol extended data entities that corresponds to the seqCol
+     * that has the given level0Digest*/
+    @Transactional
+    public void removeSeqColExtendedDataEntities(List<SeqColExtendedDataEntity> extendedDataEntities) {
+        for (SeqColExtendedDataEntity entity: extendedDataEntities) {
+            removeSeqColExtendedDataEntityByDigest(entity.getDigest());
+        }
+    }
+
+    /**
+     * Remove one extended data entity by its digest.
+     * NOTE!: The given digest is not the seqCol level 0 digest*/
+    public void removeSeqColExtendedDataEntityByDigest(String digest) {
+        repository.removeSeqColExtendedDataEntityByDigest(digest);
+    }
+
+    public void removeAllSeqColExtendedEntities() {
+        repository.deleteAll();
+    }
+
     /**
      * Return the extendedData object for the given digest*/
     public Optional<SeqColExtendedDataEntity> getExtendedAttributeByDigest(String digest) {

src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColLevelOneService.java

@@ -34,7 +34,6 @@ public Optional<SeqColLevelOneEntity> addSequenceCollectionL1(SeqColLevelOneEnti
         return Optional.of(seqCol);
     }
 
-
     public Optional<SeqColLevelOneEntity> getSeqColLevelOneByDigest(String digest){
         SeqColLevelOneEntity seqColL11 = repository.findSeqColLevelOneEntityByDigest(digest);
         if (seqColL11 != null) {
@@ -44,6 +43,14 @@ public Optional<SeqColLevelOneEntity> getSeqColLevelOneByDigest(String digest){
         }
     }
 
+    public void removeSeqColLevelOneByDigest(String digest) {
+        repository.removeSeqColLevelOneEntityByDigest(digest);
+    }
+
+    public void removeAllSeqCols() {
+        repository.deleteAll();
+    }
+
     public long countSeqColLevelOneEntitiesByDigest(String digest) {
         return repository.countSeqColLevelOneEntitiesByDigest(digest);
     }

src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java

@@ -94,6 +94,22 @@ public Optional<? extends SeqColEntity> getSeqColByDigestAndLevel(String digest,
        }
     }
 
+    /**
+     * Full remove of the seqCol object (level one and its extended data)*/
+    @Transactional
+    public void deleteFullSeqCol(String digest, List<SeqColExtendedDataEntity> extendedDataEntities) {
+        levelOneService.removeSeqColLevelOneByDigest(digest);
+        extendedDataService.removeSeqColExtendedDataEntities(extendedDataEntities);
+    }
+
+    /**
+     * Remove all seqCol entities (level 1 and the extended entities) from the database*/
+    @Transactional
+    public void removeAllSeqCol() {
+        levelOneService.removeAllSeqCols();
+        extendedDataService.removeAllSeqColExtendedEntities();
+    }
+
     /**
      * Fetch and insert all possible seqCol objects for the given assembly accession.
      * NOTE: All possible seqCol objects means with all possible/provided naming conventions that could be found in the

src/test/java/uk/ac/ebi/eva/evaseqcol/io/AssemblyDataGenerator.java

@@ -0,0 +1,62 @@
+package uk.ac.ebi.eva.evaseqcol.io;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import uk.ac.ebi.eva.evaseqcol.dus.NCBIAssemblyReportReader;
+import uk.ac.ebi.eva.evaseqcol.dus.NCBIAssemblyReportReaderFactory;
+import uk.ac.ebi.eva.evaseqcol.dus.NCBIAssemblySequenceReader;
+import uk.ac.ebi.eva.evaseqcol.dus.NCBIAssemblySequenceReaderFactory;
+import uk.ac.ebi.eva.evaseqcol.entities.AssemblyEntity;
+import uk.ac.ebi.eva.evaseqcol.entities.AssemblySequenceEntity;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+
+@Component
+public class AssemblyDataGenerator {
+
+    private final String REPORT_FILE_PATH = "src/test/resources/GCA_000146045.2_R64_assembly_report.txt";
+    private final String SEQUENCES_FILE_PATH = "src/test/resources/GCA_000146045.2_genome_sequence.fna";
+
+    private static final String GCA_ACCESSION = "GCA_000146045.2";
+
+    private static InputStreamReader sequencesStreamReader;
+    private static InputStream sequencesStream;
+
+    private static InputStreamReader reportStreamReader;
+    private static InputStream reportStream;
+
+    @Autowired
+    private NCBIAssemblyReportReaderFactory reportReaderFactory;
+    private NCBIAssemblyReportReader reportReader;
+
+    @Autowired
+    private NCBIAssemblySequenceReaderFactory sequenceReaderFactory;
+    private NCBIAssemblySequenceReader sequenceReader;
+
+    /**
+     * Return the Assembly entity that corresponds to the assembly report located
+     * under REPORT_FILE_PATH (see variable content above) having as assembly accession: "GCA_000146045.2"*/
+    public AssemblyEntity generateAssemblyEntity() throws IOException {
+        reportStream = new FileInputStream(
+                new File(REPORT_FILE_PATH));
+        reportStreamReader = new InputStreamReader(reportStream);
+        reportReader = reportReaderFactory.build(reportStreamReader);
+        return reportReader.getAssemblyEntity();
+    }
+
+    /**
+     * Return the AssemblySequenceEntity that corresponds to the sequences FASTA file
+     * located under SEQUENCES_FILE_PATH (see variable content above) having as assembly accession: "GCA_000146045.2"*/
+    public AssemblySequenceEntity generateAssemblySequenceEntity() throws IOException {
+        sequencesStream = new FileInputStream(
+                new File(SEQUENCES_FILE_PATH));
+        sequencesStreamReader = new InputStreamReader(sequencesStream);
+        sequenceReader = sequenceReaderFactory.build(sequencesStreamReader, GCA_ACCESSION);
+        return sequenceReader.getAssemblySequencesEntity();
+    }
+}

src/test/java/uk/ac/ebi/eva/evaseqcol/io/SeqColWriter.java

@@ -0,0 +1,176 @@
+package uk.ac.ebi.eva.evaseqcol.io;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+
+import uk.ac.ebi.eva.evaseqcol.dus.NCBIAssemblyReportReader;
+import uk.ac.ebi.eva.evaseqcol.dus.NCBIAssemblyReportReaderFactory;
+import uk.ac.ebi.eva.evaseqcol.dus.NCBIAssemblySequenceReader;
+import uk.ac.ebi.eva.evaseqcol.dus.NCBIAssemblySequenceReaderFactory;
+import uk.ac.ebi.eva.evaseqcol.entities.AssemblyEntity;
+import uk.ac.ebi.eva.evaseqcol.entities.AssemblySequenceEntity;
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColEntity;
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColExtendedDataEntity;
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelOneEntity;
+import uk.ac.ebi.eva.evaseqcol.service.SeqColExtendedDataService;
+import uk.ac.ebi.eva.evaseqcol.service.SeqColLevelOneService;
+import uk.ac.ebi.eva.evaseqcol.service.SeqColService;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+
+/**
+ * This class is responsible for saving and deleting seqCol
+ * objects to and from the database.*/
+@Component
+public class SeqColWriter {
+
+    private static final Logger logger = LoggerFactory.getLogger(SeqColWriter.class);
+
+    private List<SeqColExtendedDataEntity> extendedDataEntitiesUcsc;
+
+    private List<SeqColExtendedDataEntity> extendedDataEntitiesGenbank;
+
+    private SeqColLevelOneEntity levelOneEntityUcsc;
+
+    private SeqColLevelOneEntity levelOneEntityGenbank;
+
+    private final String REPORT_FILE_PATH_1 = "src/test/resources/GCA_000146045.2_R64_assembly_report.txt";
+
+    private final String SEQUENCES_FILE_PATH_1 = "src/test/resources/GCA_000146045.2_genome_sequence.fna";
+
+    private static final String GCA_ACCESSION = "GCA_000146045.2";
+
+    private List<String> insertedSeqColDigests; // Holds the digests of the seqCol objects inserted by this class
+
+    private static InputStreamReader sequencesStreamReader;
+
+    private static InputStream sequencesStream;
+
+    private static InputStreamReader reportStreamReader;
+
+    private static InputStream reportStream;
+
+
+    private NCBIAssemblyReportReaderFactory reportReaderFactory;
+
+    private NCBIAssemblyReportReader reportReader;
+
+
+    private NCBIAssemblySequenceReaderFactory sequenceReaderFactory;
+
+    private NCBIAssemblySequenceReader sequenceReader;
+
+
+    private SeqColLevelOneService levelOneService;
+
+
+    private SeqColExtendedDataService extendedDataService;
+
+
+    private SeqColService seqColService;
+
+    @Autowired
+    public SeqColWriter(NCBIAssemblyReportReaderFactory reportReaderFactory, NCBIAssemblySequenceReaderFactory sequenceReaderFactory,
+                        SeqColLevelOneService levelOneService, SeqColExtendedDataService extendedDataService, SeqColService seqColService) {
+        this.reportReaderFactory = reportReaderFactory;
+        this.sequenceReaderFactory = sequenceReaderFactory;
+        this.levelOneService = levelOneService;
+        this.extendedDataService = extendedDataService;
+        this.seqColService = seqColService;
+    }
+
+    /**
+     * Setup the report reader (assembly report reader),
+     * the sequences' reader (assembly FASTA file reader)
+     * and other necessary objects.
+     * */
+    private void setUp() throws FileNotFoundException {
+        reportStream = new FileInputStream(
+                new File(REPORT_FILE_PATH_1));
+        reportStreamReader = new InputStreamReader(reportStream);
+        reportReader = reportReaderFactory.build(reportStreamReader);
+
+        sequencesStream = new FileInputStream(
+                new File(SEQUENCES_FILE_PATH_1));
+        sequencesStreamReader = new InputStreamReader(sequencesStream);
+        sequenceReader = sequenceReaderFactory.build(sequencesStreamReader, GCA_ACCESSION);
+
+        insertedSeqColDigests = new ArrayList<>();
+    }
+
+    /**
+     * Close streams and streams readers*/
+    private void tearDown() throws IOException {
+        reportStream.close();
+        reportStreamReader.close();
+        sequencesStream.close();
+        sequencesStreamReader.close();
+    }
+
+    /**
+     * Save seqCol objects of assembly GCA_ACCESSION (see variable content above) for naming conventions UCSC and GENBANK
+     * NOTE: The assembly report and the sequences FASTA file for this assembly are already downloaded
+     * and put into "src/test/resources/"
+     * */
+    public void write() throws IOException {
+        setUp();
+        AssemblyEntity assemblyEntity = reportReader.getAssemblyEntity();
+        AssemblySequenceEntity assemblySequenceEntity = sequenceReader.getAssemblySequencesEntity();
+
+        // Insert seqCol for UCSC naming convention
+        extendedDataEntitiesUcsc = extendedDataService.constructExtendedSeqColDataList(
+                assemblyEntity, assemblySequenceEntity, SeqColEntity.NamingConvention.UCSC
+        );
+        levelOneEntityUcsc = levelOneService.constructSeqColLevelOne(
+                extendedDataEntitiesUcsc, SeqColEntity.NamingConvention.UCSC);
+        Optional<String> resultDigestUcsc = seqColService.addFullSequenceCollection(levelOneEntityUcsc, extendedDataEntitiesUcsc);
+        if (resultDigestUcsc.isPresent()) {
+            logger.info("Successfully inserted seqCol object with the assembly accession " + GCA_ACCESSION + " for " +
+                                "naming convention " + SeqColEntity.NamingConvention.UCSC);
+        } else {
+            logger.error("Could not insert seqCol object with the assembly accession " + GCA_ACCESSION + " for " +
+                                 "naming convention " + SeqColEntity.NamingConvention.UCSC);
+        }
+        insertedSeqColDigests.add(resultDigestUcsc.get());
+
+        // Insert seqCol for GENBANK naming convention
+        extendedDataEntitiesGenbank = extendedDataService.constructExtendedSeqColDataList(
+                assemblyEntity, assemblySequenceEntity, SeqColEntity.NamingConvention.GENBANK
+        );
+        levelOneEntityGenbank = levelOneService.constructSeqColLevelOne(
+                extendedDataEntitiesGenbank, SeqColEntity.NamingConvention.GENBANK);
+        Optional<String> resultDigestGenbank = seqColService.addFullSequenceCollection(levelOneEntityGenbank, extendedDataEntitiesGenbank);
+        if (resultDigestGenbank.isPresent()) {
+            logger.info("Successfully inserted seqCol object with the assembly accession " + GCA_ACCESSION + " for " +
+                                "naming convention " + SeqColEntity.NamingConvention.GENBANK);
+        } else {
+            logger.error("Could not insert seqCol object with the assembly accession " + GCA_ACCESSION + " for " +
+                                 "naming convention " + SeqColEntity.NamingConvention.GENBANK);
+        }
+        insertedSeqColDigests.add(resultDigestGenbank.get());
+
+        // Clear streams
+        tearDown();
+    }
+
+    /**
+     * Remove all inserted seqCol objects from the database.
+     * */
+    public void clearData() {
+        seqColService.removeAllSeqCol();
+    }
+
+}