Relational data model

pom.xml

@@ -147,6 +147,13 @@
             <version>1.2.5.RELEASE</version>
         </dependency>
 
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <version>1.18.28</version>
+            <scope>provided</scope>
+        </dependency>
+
     </dependencies>
 
     <build>

src/main/java/uk/ac/ebi/eva/contigalias/entities/SeqColL1.java

@@ -0,0 +1,37 @@
+package uk.ac.ebi.eva.contigalias.entities;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.Id;
+
+@Entity
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+public class SeqColL1 {
+    @Id
+    private String digest;
+
+    @Column(nullable = false)
+    private String sequences;
+
+    @Column(nullable = false)
+    private String lengths;
+
+    @Column(nullable = false)
+    private String names;
+
+    @Column(nullable = false)
+    @Enumerated(EnumType.STRING)
+    private NamingConvention naming_convention;
+
+    public enum NamingConvention {
+        ENA, GENBANK, USCS
+    }
+}

src/main/java/uk/ac/ebi/eva/contigalias/entities/SeqColL2.java

@@ -0,0 +1,28 @@
+package uk.ac.ebi.eva.contigalias.entities;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.NoArgsConstructor;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.Id;
+import javax.persistence.IdClass;
+
+@Entity
+@IdClass(SeqColL2Id.class)
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+@EqualsAndHashCode
+public class SeqColL2 {
+    @Id
+    @Column(nullable = false)
+    private String digest;
+
+    @Id
+    @Column(nullable = false)
+    private String object; // The value of on of the seqCol's attribute
+
+}

src/main/java/uk/ac/ebi/eva/contigalias/entities/SeqColL2Id.java

@@ -0,0 +1,12 @@
+package uk.ac.ebi.eva.contigalias.entities;
+
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+import java.io.Serializable;
+@NoArgsConstructor
+@Data
+public class SeqColL2Id implements Serializable {
+    private String digest;
+    private String object;
+}

src/main/java/uk/ac/ebi/eva/contigalias/repo/SeqColL1Repository.java

@@ -0,0 +1,11 @@
+package uk.ac.ebi.eva.contigalias.repo;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+
+import uk.ac.ebi.eva.contigalias.entities.SeqColL1;
+
+@Repository
+public interface SeqColL1Repository extends JpaRepository<SeqColL1, String> {
+
+}

src/main/java/uk/ac/ebi/eva/contigalias/repo/SeqColL2Repository.java

@@ -0,0 +1,12 @@
+package uk.ac.ebi.eva.contigalias.repo;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+
+import uk.ac.ebi.eva.contigalias.entities.SeqColL2;
+import uk.ac.ebi.eva.contigalias.entities.SeqColL2Id;
+
+@Repository
+public interface SeqColL2Repository extends JpaRepository<SeqColL2, SeqColL2Id> {
+
+}

src/main/java/uk/ac/ebi/eva/contigalias/service/SeqColL1Service.java

@@ -0,0 +1,31 @@
+package uk.ac.ebi.eva.contigalias.service;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import uk.ac.ebi.eva.contigalias.entities.SeqColL1;
+import uk.ac.ebi.eva.contigalias.repo.SeqColL1Repository;
+
+import java.util.List;
+import java.util.Optional;
+
+@Service
+public class SeqColL1Service {
+    @Autowired
+    private SeqColL1Repository repository;
+
+
+    public Optional<SeqColL1> addSeqColL1(SeqColL1 seqColL1){
+        try {
+            SeqColL1 seqColL11 = repository.save(seqColL1);
+            return Optional.of(seqColL11);
+        } catch (Exception e){
+            System.out.println("SeqColL1 with digest: " + seqColL1.getDigest() + " already exists !");
+        }
+        return Optional.empty();
+    }
+
+    public List<SeqColL1> getAllSequenceCollections(){
+        return repository.findAll();
+    }
+}

src/main/java/uk/ac/ebi/eva/contigalias/service/SeqColL2Service.java

@@ -0,0 +1,34 @@
+package uk.ac.ebi.eva.contigalias.service;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import uk.ac.ebi.eva.contigalias.entities.SeqColL2;
+import uk.ac.ebi.eva.contigalias.repo.SeqColL2Repository;
+
+import java.util.List;
+import java.util.Optional;
+
+@Service
+public class SeqColL2Service {
+
+    @Autowired
+    private SeqColL2Repository repository;
+
+
+    public Optional<SeqColL2> addSeqColL2(SeqColL2 seqColL2){
+        try {
+            System.out.println("CHECK POINT: " + seqColL2.getDigest() + " | " + seqColL2.getObject());
+            SeqColL2 seqColL21 = repository.save(seqColL2);
+            return Optional.of(seqColL21);
+        } catch (Exception e){
+            System.out.println("Problem when inserting seqCol object: " + seqColL2.getDigest() + " already exists !");
+            e.printStackTrace();
+        }
+        return Optional.empty();
+    }
+
+    public List<SeqColL2> getAllSequenceCollections(){
+        return repository.findAll();
+    }
+}

src/main/resources/application.properties

@@ -14,8 +14,8 @@
 # limitations under the License.
 #
 
-controller.auth.admin.username=@contig-alias.admin-user@
-controller.auth.admin.password=@contig-alias.admin-password@
+controller.auth.admin.username=haroune
+controller.auth.admin.password=password
 
 management.endpoints.web.exposure.include=info,health
 management.endpoints.web.base-path=/
@@ -24,20 +24,21 @@ management.info.git.mode=full
 logging.level.uk.ac.ebi.eva.contigalias=DEBUG
 
 # Database configuration
-spring.datasource.url=@contig-alias.db-url@
-spring.datasource.username=@contig-alias.db-username@
-spring.datasource.password=@contig-alias.db-password@
-spring.jpa.hibernate.ddl-auto=@contig-alias.ddl-behaviour@
+spring.datasource.url=jdbc:postgresql://localhost:5432/contig_db55
+spring.datasource.username=haroune
+spring.datasource.password=123
+spring.jpa.hibernate.ddl-auto=update
 spring.datasource.driver-class-name=org.postgresql.Driver
 spring.jpa.database-platform=org.hibernate.dialect.PostgreSQLDialect
 spring.jpa.generate-ddl=true
 
 server.servlet.context-path=/eva/webservices/contig-alias
+server.port=8081
 
-ftp.proxy.host=@ftp.proxy.host@
-ftp.proxy.port=@ftp.proxy.port@
+ftp.proxy.host=null
+ftp.proxy.port=0
 
-config.scaffolds.enabled = @contig-alias.scaffolds-enabled@
+config.scaffolds.enabled = true
 
 asm.file.download.dir=/tmp
 

src/test/java/uk/ac/ebi/eva/contigalias/service/SeqColL1ServiceTest.java

@@ -0,0 +1,124 @@
+package uk.ac.ebi.eva.contigalias.service;
+
+import net.minidev.json.JSONObject;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+
+import uk.ac.ebi.eva.contigalias.entities.SeqColL1;
+import uk.ac.ebi.eva.contigalias.entities.SeqColL2;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+@SpringBootTest
+class SeqColL1ServiceTest {
+
+    @Autowired
+    private SeqColL1Service seqColL1Service;
+
+    @Autowired
+    private SeqColL2Service seqColL2Service;
+
+    private final String BASE_DIGEST = "a6748aa0__";
+
+    private final String BASE_NAMES = "ce04be12__";
+
+    private final String BASE_LENGTHS = "4925cdbd";
+
+    private final String BASE_SEQUENCES = "3b379221";
+
+    private final List<String> NAMES_ARRAY = Arrays.asList("AB__", "CD__", "EF__", "GH__");
+    private final List<String> LENGTHS_ARRAY = Arrays.asList("12", "34", "56", "78");
+    private final List<String> SEQUENCES_ARRAY = Arrays.asList("AA__", "TT__", "GG__", "CC__");
+
+    /**
+     * Generate a unique sample of a sequence collection object
+     * */
+    SeqColL1 generateSeqColL1(String id, int random){
+        SeqColL1 seqColL1 = new SeqColL1();
+        seqColL1.setDigest(BASE_DIGEST + id);
+        seqColL1.setLengths(BASE_LENGTHS);
+        seqColL1.setNames(BASE_NAMES + id);
+        seqColL1.setSequences(BASE_SEQUENCES);
+        seqColL1.setNaming_convention((random % 2 == 0) ? SeqColL1.NamingConvention.ENA : SeqColL1.NamingConvention.GENBANK);
+        return seqColL1;
+    }
+
+    /**
+     * Generate unique names samples
+     * The only difference will be in the names array*/
+    List<String> generateNamesValues(String id){
+        List<String> names = new ArrayList<>();
+        for (String name: NAMES_ARRAY){
+            names.add(name + id);
+        }
+        return names;
+    }
+
+    List<String> generateLengthsValues(String id){
+        List<String> lengths = new ArrayList<>();
+        for (String length: LENGTHS_ARRAY) {
+            lengths.add(length + id);
+        }
+        return lengths;
+    }
+
+    List<String> generateSequencesValues(String id) {
+        List<String> sequences = new ArrayList<>();
+        for (String seq: SEQUENCES_ARRAY) {
+            sequences.add(seq);
+        }
+        return sequences;
+    }
+
+    @BeforeEach
+    void setUp() {
+    }
+
+    @AfterEach
+    void tearDown() {
+    }
+
+    @Test
+    /**
+     * Insert 3 Sequence collection objects in different levels*/
+    void addSeqColL() {
+        List<String> sharedSequencesList = generateSequencesValues("XXXX");
+        List<String> sharedLengthsList = generateLengthsValues("5555");
+
+        for (int i=1000; i<1003; i++) {
+            SeqColL1 seqColL1 = generateSeqColL1(Integer.toString(i), i);
+            seqColL1Service.addSeqColL1(seqColL1);
+
+            // Adding the attributes of the sequence collection object
+            // Adding names values
+            for (String name: generateNamesValues(Integer.toString(i))){
+                SeqColL2 seqColL2 = new SeqColL2(seqColL1.getNames(), name);
+                seqColL2Service.addSeqColL2(seqColL2);
+            }
+
+            // Adding sequences values
+            for (String seq: sharedSequencesList){
+                SeqColL2 seqColL2 = new SeqColL2(seqColL1.getSequences(), seq);
+                seqColL2Service.addSeqColL2(seqColL2);
+            }
+
+            // Adding lengths values
+            for (String len: sharedLengthsList) {
+                SeqColL2 seqColL2 = new SeqColL2(seqColL1.getLengths(), len);
+                seqColL2Service.addSeqColL2(seqColL2);
+            }
+        }
+        List<SeqColL1> seqColL1List = seqColL1Service.getAllSequenceCollections();
+        List<SeqColL2> seqColL2List = seqColL2Service.getAllSequenceCollections();
+
+        assertNotNull(seqColL1List);
+        assertNotNull(seqColL2List);
+    }
+}