Merge pull request #100 from sundarvenkata-EBI/fix/eva2964_incorrect_…

…pagination

EVA-2964 - Fix incorrect pagination

src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminController.java

@@ -113,17 +113,6 @@ public void putChromosomeChecksumsByAccession(
         handler.putChromosomeChecksumsByAccession(accession, md5, trunc512);
     }
 
-    @ApiOperation(value = "Add MD5 and TRUNC512 checksums to all scaffolds by accession.",
-            notes = "Given an INSDC or RefSeq accession along with a MD5 or a TRUNC512 checksum, this endpoint will " +
-                    "add the given checksums to all scaffolds that match the given INSDC or RefSeq accession.")
-    @PutMapping(value = "scaffolds/{accession}/checksum")
-    public void putScaffoldChecksumsByAccession(
-            @PathVariable @ApiParam(value = "INSDC or Refseq scaffold accession. Eg: NC_000001.11") String accession,
-            @RequestParam(required = false) @ApiParam("The MD5 checksum associated with the scaffolds.") String md5,
-            @RequestParam(required = false) @ApiParam("The TRUNC512 checksum associated with the scaffolds.") String trunc512) {
-        handler.putScaffoldChecksumsByAccession(accession, md5, trunc512);
-    }
-
     @ApiOperation(value = "Delete an assembly from local database using its GenBank or RefSeq accession.",
             notes = "Given an assembly's accession this endpoint will delete the assembly that matches that " +
                     "accession from the local database. The accession can be either a INSDC or RefSeq accession and" +

src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminHandler.java

@@ -18,22 +18,15 @@
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.web.PagedResourcesAssembler;
-import org.springframework.hateoas.EntityModel;
-import org.springframework.hateoas.PagedModel;
 import org.springframework.stereotype.Service;
 
 import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
 import uk.ac.ebi.eva.contigalias.service.AssemblyService;
 import uk.ac.ebi.eva.contigalias.service.ChromosomeService;
-import uk.ac.ebi.eva.contigalias.service.ScaffoldService;
 
 import java.io.IOException;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
-
-import static uk.ac.ebi.eva.contigalias.controller.BaseHandler.convertToPage;
-import static uk.ac.ebi.eva.contigalias.controller.BaseHandler.generatePagedModelFromPage;
 
 @Service
 public class AdminHandler {
@@ -42,18 +35,14 @@ public class AdminHandler {
 
     private final ChromosomeService chromosomeService;
 
-    private final ScaffoldService scaffoldService;
-
     private final PagedResourcesAssembler<AssemblyEntity> assemblyAssembler;
 
     @Autowired
     public AdminHandler(AssemblyService assemblyService,
                         ChromosomeService chromosomeService,
-                        ScaffoldService scaffoldService,
                         PagedResourcesAssembler<AssemblyEntity> assemblyAssembler) {
         this.assemblyService = assemblyService;
         this.chromosomeService = chromosomeService;
-        this.scaffoldService = scaffoldService;
         this.assemblyAssembler = assemblyAssembler;
     }
 
@@ -76,8 +65,4 @@ public void putAssemblyChecksumsByAccession(String accession, String md5, String
     public void putChromosomeChecksumsByAccession(String accession, String md5, String trunc512) {
         chromosomeService.putChromosomeChecksumsByAccession(accession, md5, trunc512);
     }
-
-    public void putScaffoldChecksumsByAccession(String accession, String md5, String trunc512) {
-        scaffoldService.putScaffoldChecksumsByAccession(accession, md5, trunc512);
-    }
 }

src/main/java/uk/ac/ebi/eva/contigalias/datasource/ENAAssemblyDataSource.java

@@ -26,7 +26,6 @@
 import uk.ac.ebi.eva.contigalias.dus.ENABrowserFactory;
 import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
 import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
-import uk.ac.ebi.eva.contigalias.entities.ScaffoldEntity;
 import uk.ac.ebi.eva.contigalias.entities.SequenceEntity;
 
 import java.io.IOException;
@@ -37,7 +36,6 @@
 import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
-import java.util.stream.Stream;
 
 @Repository("ENADataSource")
 public class ENAAssemblyDataSource implements AssemblyDataSource {
@@ -97,10 +95,6 @@ public void addENASequenceNamesToAssembly(Optional<AssemblyEntity> optional) thr
                                     sourceAssembly.getChromosomes() : Collections.emptyList(),
                             Objects.nonNull(targetAssembly.getChromosomes()) ?
                                     targetAssembly.getChromosomes() : Collections.emptyList());
-                    addENASequenceNames(Objects.nonNull(sourceAssembly.getScaffolds()) ?
-                                    sourceAssembly.getScaffolds() : Collections.emptyList(),
-                            Objects.nonNull(targetAssembly.getScaffolds()) ?
-                                    targetAssembly.getScaffolds() : Collections.emptyList());
                 }
             }
         }
@@ -109,10 +103,7 @@ public void addENASequenceNamesToAssembly(Optional<AssemblyEntity> optional) thr
     public boolean hasAllEnaSequenceNames(AssemblyEntity assembly) {
         List<ChromosomeEntity> chromosomes = Objects.nonNull(assembly.getChromosomes()) ?
                 assembly.getChromosomes() : Collections.emptyList();
-        List<ScaffoldEntity> scaffolds = Objects.nonNull(assembly.getScaffolds()) ?
-                assembly.getScaffolds() : Collections.emptyList();
-        return Stream.concat(chromosomes.stream(), scaffolds.stream())
-                .allMatch(sequence -> sequence.getEnaSequenceName() != null);
+        return chromosomes.stream().allMatch(sequence -> sequence.getEnaSequenceName() != null);
     }
 
     private void addENASequenceNames(

src/main/java/uk/ac/ebi/eva/contigalias/dus/AssemblyReportReader.java

@@ -18,7 +18,6 @@
 
 import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
 import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
-import uk.ac.ebi.eva.contigalias.entities.ScaffoldEntity;
 
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -80,7 +79,7 @@ public AssemblyEntity getAssemblyEntity() throws IOException {
 
     /**
      * Parses lines in assembly report containing Scaffold metadata. This array is used to set metadata to corresponding
-     * fields in {@link ScaffoldEntity}.
+     * fields in {@link ChromosomeEntity}.
      *
      * @param columns An array of fields in a line of the assembly report file not starting with "#".
      */

src/main/java/uk/ac/ebi/eva/contigalias/dus/ENAAssemblyReportReader.java

@@ -18,7 +18,7 @@
 
 import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
 import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
-import uk.ac.ebi.eva.contigalias.entities.ScaffoldEntity;
+import uk.ac.ebi.eva.contigalias.entities.SequenceEntity;
 
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -71,6 +71,7 @@ protected void parseChromosomeLine(String[] columns) {
             assemblyEntity = new AssemblyEntity();
         }
         chromosomeEntity.setAssembly(this.assemblyEntity);
+        chromosomeEntity.setContigType(SequenceEntity.ContigType.CHROMOSOME);
 
         List<ChromosomeEntity> chromosomes = this.assemblyEntity.getChromosomes();
         if (chromosomes == null) {
@@ -81,7 +82,7 @@ protected void parseChromosomeLine(String[] columns) {
     }
 
     protected void parseScaffoldLine(String[] columns) {
-        ScaffoldEntity scaffoldEntity = new ScaffoldEntity();
+        ChromosomeEntity scaffoldEntity = new ChromosomeEntity();
 
         scaffoldEntity.setGenbank(columns[0]);
         scaffoldEntity.setEnaSequenceName(columns[1]);
@@ -90,11 +91,12 @@ protected void parseScaffoldLine(String[] columns) {
             assemblyEntity = new AssemblyEntity();
         }
         scaffoldEntity.setAssembly(this.assemblyEntity);
+        scaffoldEntity.setContigType(SequenceEntity.ContigType.SCAFFOLD);
 
-        List<ScaffoldEntity> scaffolds = this.assemblyEntity.getScaffolds();
+        List<ChromosomeEntity> scaffolds = this.assemblyEntity.getChromosomes();
         if (scaffolds == null) {
             scaffolds = new LinkedList<>();
-            assemblyEntity.setScaffolds(scaffolds);
+            assemblyEntity.setChromosomes(scaffolds);
         }
         scaffolds.add(scaffoldEntity);
     }

src/main/java/uk/ac/ebi/eva/contigalias/dus/NCBIAssemblyReportReader.java

@@ -18,7 +18,7 @@
 
 import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
 import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
-import uk.ac.ebi.eva.contigalias.entities.ScaffoldEntity;
+import uk.ac.ebi.eva.contigalias.entities.SequenceEntity;
 
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -108,6 +108,7 @@ protected void parseChromosomeLine(String[] columns) {
             assemblyEntity = new AssemblyEntity();
         }
         chromosomeEntity.setAssembly(this.assemblyEntity);
+        chromosomeEntity.setContigType(SequenceEntity.ContigType.CHROMOSOME);
 
         List<ChromosomeEntity> chromosomes = this.assemblyEntity.getChromosomes();
         if (chromosomes == null) {
@@ -118,7 +119,7 @@ protected void parseChromosomeLine(String[] columns) {
     }
 
     protected void parseScaffoldLine(String[] columns) {
-        ScaffoldEntity scaffoldEntity = new ScaffoldEntity();
+        ChromosomeEntity scaffoldEntity = new ChromosomeEntity();
 
         scaffoldEntity.setGenbankSequenceName(columns[0]);
         scaffoldEntity.setGenbank(columns[4]);
@@ -135,11 +136,12 @@ protected void parseScaffoldLine(String[] columns) {
             assemblyEntity = new AssemblyEntity();
         }
         scaffoldEntity.setAssembly(this.assemblyEntity);
+        scaffoldEntity.setContigType(SequenceEntity.ContigType.SCAFFOLD);
 
-        List<ScaffoldEntity> scaffolds = this.assemblyEntity.getScaffolds();
+        List<ChromosomeEntity> scaffolds = this.assemblyEntity.getChromosomes();
         if (scaffolds == null) {
             scaffolds = new LinkedList<>();
-            assemblyEntity.setScaffolds(scaffolds);
+            assemblyEntity.setChromosomes(scaffolds);
         }
         scaffolds.add(scaffoldEntity);
     }

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

@@ -73,12 +73,6 @@ public class AssemblyEntity {
     @OneToMany(mappedBy = "assembly", cascade = CascadeType.ALL)
     private List<ChromosomeEntity> chromosomes;
 
-    @JsonIgnore
-    @ApiModelProperty(value = "List of all scaffolds of the assembly present in the database.")
-    @LazyCollection(LazyCollectionOption.FALSE)
-    @OneToMany(mappedBy = "assembly", cascade = CascadeType.ALL)
-    private List<ScaffoldEntity> scaffolds;
-
     public AssemblyEntity() {
     }
 
@@ -167,15 +161,6 @@ public AssemblyEntity setChromosomes(List<ChromosomeEntity> chromosomes) {
         return this;
     }
 
-    public List<ScaffoldEntity> getScaffolds() {
-        return scaffolds;
-    }
-
-    public AssemblyEntity setScaffolds(List<ScaffoldEntity> scaffolds) {
-        this.scaffolds = scaffolds;
-        return this;
-    }
-
     @Override
     public String toString() {
         StringBuilder builder = new StringBuilder();

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

@@ -22,6 +22,8 @@
 
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
@@ -59,6 +61,15 @@ public class SequenceEntity {
     @ApiModelProperty(value = "Sequence's TRUNC512 checksum value.")
     private String trunc512checksum;
 
+    public enum ContigType {
+        SCAFFOLD,
+        CHROMOSOME
+    }
+
+    @ApiModelProperty(value = "Type of contig: chromosome (or) scaffold")
+    @Enumerated(EnumType.STRING)
+    private ContigType contigType;
+
     @JsonInclude(JsonInclude.Include.NON_NULL)
     @ApiModelProperty(value = "Assembly that this sequence belongs to.")
     @ManyToOne(cascade = CascadeType.ALL)
@@ -132,6 +143,14 @@ public SequenceEntity setTrunc512checksum(String trunc512checksum) {
         return this;
     }
 
+    public ContigType getContigType() {
+        return contigType;
+    }
+
+    public void setContigType(ContigType contigType) {
+        this.contigType = contigType;
+    }
+
     public AssemblyEntity getAssembly() {
         return assembly;
     }