Implement the interface + code cleaning

src/main/java/nl/esciencecenter/controller/NotYetAController.java

@@ -8,42 +8,42 @@
 import org.springframework.web.bind.annotation.PostMapping;
 import org.springframework.web.bind.annotation.RequestBody;
 
-import nl.esciencecenter.models.SynthesisRun;
-import nl.esciencecenter.service.SynthesisRunService;
+import nl.esciencecenter.models.Domain;
+import nl.esciencecenter.service.DomainService;
 
 /**
- * RestController to retch the SynthesisRun data from the database.
+ * RestController to handle the Domain data from the database.
  * Not yet implemented.
  */
 public class NotYetAController {
 
-    // autowired the SynthesisRunService class
+    // autowired the DomainService class
     @Autowired
-    SynthesisRunService synthesisRunService;
+    DomainService domainService;
 
     // creating a get mapping that retrieves all the synthesisRuns detail from the
     // database
-    @GetMapping("/synthesisRun")
-    private List<SynthesisRun> getAllSynthesisRun() {
-        return synthesisRunService.getAllSynthesisRun();
+    @GetMapping("/domain")
+    private List<Domain> getAllDomain() {
+        return domainService.getAllDomain();
     }
 
     // creating a get mapping that retrieves the detail of a specific synthesisRun
-    @GetMapping("/synthesisRun/{id}")
-    private SynthesisRun getSynthesisRun(@PathVariable("id") int id) {
-        return synthesisRunService.getSynthesisRunById(id);
+    @GetMapping("/domain/{id}")
+    private Domain getSynthesisRun(@PathVariable("id") int id) {
+        return domainService.getDomainById(id);
     }
 
     // creating a delete mapping that deletes a specific synthesisRun
-    @DeleteMapping("/synthesisRun/{id}")
-    private void deleteSynthesisRun(@PathVariable("id") int id) {
-        synthesisRunService.delete(id);
+    @DeleteMapping("/domain/{id}")
+    private void deleteDomain(@PathVariable("id") int id) {
+        domainService.delete(id);
     }
 
     // creating post mapping that post the synthesisRun detail in the database
-    @PostMapping("/synthesisRun")
-    private int saveSynthesisRun(@RequestBody SynthesisRun synthesisRun) {
-        synthesisRunService.saveOrUpdate(synthesisRun);
-        return synthesisRun.getId();
+    @PostMapping("/domain")
+    private int saveSynthesisRun(@RequestBody Domain domain) {
+        domainService.saveOrUpdate(domain);
+        return domain.getId();
     }
 }

src/main/java/nl/esciencecenter/controller/RestApeController.java

@@ -221,7 +221,7 @@ public ResponseEntity<?> getImage(
                 }
                 try {
                         return ResponseEntity.ok().contentType(mediaType)
-                                        .body(IOUtils.getImageFromFileSystem(path));
+                                        .body(IOUtils.getImageFromFileSystem(path, imgFormat.toLowerCase()));
                 } catch (IOException e) {
                         return ResponseEntity.badRequest().body("The image file could not be found.");
                 }

src/main/java/nl/esciencecenter/models/BenchmarkBase.java → src/main/java/nl/esciencecenter/models/benchmarks/BenchmarkBase.java

@@ -1,4 +1,4 @@
-package nl.esciencecenter.models;
+package nl.esciencecenter.models.benchmarks;
 
 import org.json.JSONObject;
 

src/main/java/nl/esciencecenter/models/BioToolsBenchmark.java → src/main/java/nl/esciencecenter/models/benchmarks/BioToolsBenchmark.java

@@ -1,4 +1,4 @@
-package nl.esciencecenter.models;
+package nl.esciencecenter.models.benchmarks;
 
 import java.util.ArrayList;
 import java.util.List;

src/main/java/nl/esciencecenter/models/OpenEBenchmark.java → src/main/java/nl/esciencecenter/models/benchmarks/OpenEBenchmark.java

@@ -1,4 +1,4 @@
-package nl.esciencecenter.models;
+package nl.esciencecenter.models.benchmarks;
 
 import java.util.ArrayList;
 import java.util.List;

src/main/java/nl/esciencecenter/models/WorkflowStepBench.java → src/main/java/nl/esciencecenter/models/benchmarks/WorkflowStepBench.java

@@ -1,4 +1,4 @@
-package nl.esciencecenter.models;
+package nl.esciencecenter.models.benchmarks;
 
 import java.util.Collection;
 

src/main/java/nl/esciencecenter/restape/ApeAPI.java

@@ -8,8 +8,8 @@
 import java.util.Collection;
 import java.util.List;
 
-import nl.esciencecenter.models.BenchmarkBase;
-import nl.esciencecenter.models.BioToolsBenchmark;
+import nl.esciencecenter.models.benchmarks.BenchmarkBase;
+import nl.esciencecenter.models.benchmarks.BioToolsBenchmark;
 import nl.uu.cs.ape.APE;
 import nl.uu.cs.ape.configuration.APECoreConfig;
 import nl.uu.cs.ape.configuration.APERunConfig;
@@ -163,8 +163,8 @@ public static JSONArray runSynthesis(JSONObject configJson, boolean benchmark)
 
         // Write solutions (as CWL files and figures) to the file system.
         APE.writeCWLWorkflows(candidateSolutions);
-        APE.writeTavernaDesignGraphs(candidateSolutions, Format.PNG);
         APE.writeTavernaDesignGraphs(candidateSolutions, Format.SVG);
+        APE.writeTavernaDesignGraphs(candidateSolutions, Format.PNG);
 
         // benchmark workflows if required
         if (benchmark) {

src/main/java/nl/esciencecenter/restape/IOUtils.java

@@ -20,16 +20,18 @@ public class IOUtils {
      * Get byte array that represents the image from the file system at the given
      * path.
      * 
-     * @param filePath - path to the image
+     * @param filePath   - path to the image
+     * @param formatName - a {@code String} containing the informal name of the
+     *                   format.
      * @return byte array that represents the image
      * @throws IOException - if the image cannot be read
      */
-    public static byte[] getImageFromFileSystem(Path filePath) throws IOException {
+    public static byte[] getImageFromFileSystem(Path filePath, String formatName) throws IOException {
         File currFile = filePath.toFile();
         BufferedImage image = ImageIO.read(currFile);
 
         ByteArrayOutputStream byteArray = new ByteArrayOutputStream();
-        ImageIO.write(image, "png", byteArray);
+        ImageIO.write(image, formatName, byteArray);
 
         return byteArray.toByteArray();
 

src/main/java/nl/esciencecenter/restape/ToolBenchmarkingAPIs.java

@@ -22,8 +22,8 @@
 
 import lombok.AccessLevel;
 import lombok.NoArgsConstructor;
-import nl.esciencecenter.models.BenchmarkBase;
-import nl.esciencecenter.models.BioToolsBenchmark;
+import nl.esciencecenter.models.benchmarks.BenchmarkBase;
+import nl.esciencecenter.models.benchmarks.BioToolsBenchmark;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionsList;
 import nl.uu.cs.ape.utils.APEFiles;

src/main/java/nl/esciencecenter/service/DomainService.java

@@ -2,6 +2,9 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.NoSuchElementException;
+import java.util.Optional;
+
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
@@ -16,14 +19,21 @@ public class DomainService {
 
     // getting all domain records
     public List<Domain> getAllDomain() {
-        List<Domain> domains = new ArrayList<Domain>();
-        domainRepository.findAll().forEach(domain -> domains.add(domain));
+        List<Domain> domains = new ArrayList<>();
+        domainRepository.findAll().forEach(domains::add);
         return domains;
     }
 
-    // getting a specific record
+    /**
+     * Get the domain object with the given id.
+     * 
+     * @param id - id of the domain
+     * @return - Domain object with the given id
+     * @throws NoSuchElementException - if no domain with the given id exists
+     */
     public Domain getDomainById(int id) {
-        return domainRepository.findById(id).get();
+        Optional<Domain> optionalDomain = domainRepository.findById(id);
+        return optionalDomain.orElseThrow(() -> new NoSuchElementException("No domain found with id: " + id));
     }
 
     public void saveOrUpdate(Domain domain) {