Add categories to Design-time benchmarks

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

@@ -15,6 +15,8 @@ public class BenchmarkBase {
     @NonNull
     private String benchmarkTitle;
     @NonNull
+    private String benchmarkCategory;
+    @NonNull
     private String benchmarkDescription;
     @NonNull
     private String unit;
@@ -24,6 +26,7 @@ public class BenchmarkBase {
     public JSONObject getTitleJson() {
         JSONObject benchmarkJson = new JSONObject();
         benchmarkJson.put("title", benchmarkTitle);
+        benchmarkJson.put("category", benchmarkCategory);
         benchmarkJson.put("description", benchmarkDescription);
         benchmarkJson.put("unit", unit);
         return benchmarkJson;

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

@@ -96,63 +96,63 @@ static boolean computeBenchmarks(SolutionsList candidateSolutions, String runID)
    }
 
    /**
-    * Get the Pubmetric benchmarks for the workflow.
-    * @param workflow
-    * @return
-    */
-   public static JSONObject getPubmetricBenchmarks(SolutionWorkflow workflow) {
-      // Generate the CWL file content
+     * Get the Pubmetric benchmarks for the workflow.
+     * @param workflow the SolutionWorkflow instance
+     * @return JSON response from Pubmetric API
+     */
+    public static JSONObject getPubmetricBenchmarks(SolutionWorkflow workflow) {
       DefaultCWLCreator cwlCreator = new DefaultCWLCreator(workflow);
       String cwlFileContent = cwlCreator.generate();
-
-      // Convert the CWL content to a byte array
       byte[] cwlFileBytes = cwlFileContent.getBytes();
 
       return sendPostToPubmetric(cwlFileBytes);
-   }
-
-
-   /**
-    * Send a POST request to the Pubmetric API to get the benchmarks for the CWL file.
-    * @param cwlFileBytes
-    * @return
-    */
-   public static JSONObject sendPostToPubmetric(byte[] cwlFileBytes) {
-      // Create the HTTP client
-      CloseableHttpClient httpClient = HttpClients.createDefault();
-      HttpPost uploadFile = new HttpPost("http://pubmetric:8000/score_workflow/");
-
-      // Create a multipart entity with the CWL file
+  }
+
+  /**
+   * Send a POST request to the Pubmetric API to get benchmarks.
+   * @param cwlFileBytes byte array of CWL file content
+   * @return JSON response from Pubmetric API
+   */
+  public static JSONObject sendPostToPubmetric(byte[] cwlFileBytes) {
+      try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
+          HttpPost uploadFile = createHttpPost(cwlFileBytes);
+          return executeRequest(httpClient, uploadFile);
+      } catch (IOException | JSONException e) {
+          log.error("Error while processing Pubmetric benchmarks", e);
+          return new JSONObject(); // return empty JSON if an error occurs
+      }
+  }
+
+  /**
+   * Creates an HttpPost request with the provided CWL content.
+   * @param cwlFileBytes byte array of CWL file content
+   * @return configured HttpPost request
+   */
+  private static HttpPost createHttpPost(byte[] cwlFileBytes) {
+      HttpPost uploadFile = new HttpPost("http://localhost:8000/score_workflow/");
       MultipartEntityBuilder builder = MultipartEntityBuilder.create();
-      builder.addBinaryBody("cwl_file", cwlFileBytes, org.apache.http.entity.ContentType.DEFAULT_BINARY,
-            "workflow.cwl");
-
-      HttpEntity multipart = builder.build();
-      uploadFile.setEntity(multipart);
-
-      // Execute the request
-      CloseableHttpResponse response;
-      try {
-         response = httpClient.execute(uploadFile);
-         HttpEntity responseEntity = response.getEntity();
-
-         // Print the response
-         if (responseEntity != null) {
-            String responseString = EntityUtils.toString(responseEntity);
-            return new JSONObject(responseString);
-         }
-
-         // Close resources
-         response.close();
-         httpClient.close();
-      } catch (IOException e) {
-         log.error("Error while fetching the Pubmetric benchmarks");
-      } catch (JSONException e) {
-         log.error("Error while parsing the Pubmetric benchmarks");
+      builder.addBinaryBody("cwl_file", cwlFileBytes, org.apache.http.entity.ContentType.DEFAULT_BINARY, "workflow.cwl");
+      uploadFile.setEntity(builder.build());
+      return uploadFile;
+  }
+
+  /**
+   * Executes the HTTP request and returns the response as a JSONObject.
+   * @param httpClient the HTTP client
+   * @param uploadFile the configured HttpPost request
+   * @return JSON response from Pubmetric API
+   * @throws IOException if an error occurs during the HTTP call
+   */
+  private static JSONObject executeRequest(CloseableHttpClient httpClient, HttpPost uploadFile) throws IOException {
+      try (CloseableHttpResponse response = httpClient.execute(uploadFile)) {
+          HttpEntity responseEntity = response.getEntity();
+          if (responseEntity != null) {
+              String responseString = EntityUtils.toString(responseEntity);
+              return new JSONObject(responseString);
+          }
+          return new JSONObject(); // return empty JSON if no response entity
       }
-
-      return new JSONObject();
-   }
+  }
 
    /**
     * Compute the benchmarks (based on bio.tools and OpenEBench APIs) for the
@@ -210,15 +210,15 @@ private static List<Benchmark> computeBiotoolsBenchmark(SolutionWorkflow workflo
       List<Benchmark> benchmarks = new ArrayList<>();
 
       String unitOS = "supported / not supported";
-      BenchmarkBase linuxBenchmark = new BenchmarkBase("Linux", "Linux (OS) supported tools",
+      BenchmarkBase linuxBenchmark = new BenchmarkBase("Linux", "OS", "Linux (OS) supported tools",
             unitOS, "operatingSystem", "Linux");
       benchmarks.add(BioToolsBenchmarkProcessor.benchmarkOSSupport(biotoolsAnnotations, linuxBenchmark));
 
-      BenchmarkBase macOSBenchmark = new BenchmarkBase("Mac OS", "Mac OS supported tools",
+      BenchmarkBase macOSBenchmark = new BenchmarkBase("Mac OS", "OS", "Mac OS supported tools",
             unitOS, "operatingSystem", "Mac");
       benchmarks.add(BioToolsBenchmarkProcessor.benchmarkOSSupport(biotoolsAnnotations, macOSBenchmark));
 
-      BenchmarkBase windowsBenchmark = new BenchmarkBase("Windows", "Windows (OS) supported tools",
+      BenchmarkBase windowsBenchmark = new BenchmarkBase("Windows", "OS", "Windows (OS) supported tools",
             unitOS, "operatingSystem", "Windows");
       benchmarks.add(BioToolsBenchmarkProcessor.benchmarkOSSupport(biotoolsAnnotations, windowsBenchmark));
 
@@ -259,11 +259,11 @@ private static List<Benchmark> computeOpenEBenchmarks(SolutionWorkflow workflow)
 
       List<Benchmark> benchmarks = new ArrayList<>();
 
-      BenchmarkBase licenseBenchmark = new BenchmarkBase("License", "License information available",
+      BenchmarkBase licenseBenchmark = new BenchmarkBase("License", "License", "License information available",
             "license type", "license", null);
       benchmarks.add(OpenEBenchBenchmarkProcessor.benchmarkLicenses(openEBenchBiotoolsMetrics, licenseBenchmark));
 
-      BenchmarkBase citationsBenchmark = new BenchmarkBase("Citations", "Citations annotated per tool",
+      BenchmarkBase citationsBenchmark = new BenchmarkBase("Citations", "Bibliometrics", "Citations annotated per tool",
             "citation count", "citation", null);
       benchmarks.add(OpenEBenchBenchmarkProcessor.countCitationsBenchmark(openEBenchBiotoolsMetrics, citationsBenchmark));
 

src/test/java/nl/esciencecenter/PubmetricBenchmarksTest.java

@@ -0,0 +1,81 @@
+package nl.esciencecenter;
+
+import org.json.JSONObject;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertFalse;
+
+import java.io.IOException;
+
+import nl.esciencecenter.restape.ToolBenchmarkingAPIs;
+
+public class PubmetricBenchmarksTest {
+
+    // @Test
+    // public void testSendPostToPubmetricWithFile() throws IOException {
+    //     // Read CWL file content from the file system
+    //     File cwlFile = new File("/Users/vedran/Downloads/candidate_workflow_4.cwl"); // Replace with the actual path
+    //     byte[] fileContent = Files.readAllBytes(cwlFile.toPath());
+
+    //     // Call the method to test
+    //     JSONObject response = ToolBenchmarkingAPIs.sendPostToPubmetric(fileContent);
+
+    //     // Verify that the response is not null
+    //     assertFalse(response.isEmpty());
+    // }
+
+    @Test
+    public void testSendPostToPubmetricWithString() throws IOException {
+        // Hardcoded CWL content string
+        String cwlFileContent = """
+                # WorkflowNo_3
+# This workflow is generated by APE (https://github.com/sanctuuary/APE).
+cwlVersion: v1.2
+class: Workflow
+
+label: WorkflowNo_3
+doc: A workflow including the tool(s) Comet, idconvert, ProteinProphet.
+
+inputs:
+  input_1:
+    type: File
+    format: "http://edamontology.org/format_3244" # mzML
+  input_2:
+    type: File
+    format: "http://edamontology.org/format_1929" # FASTA
+steps:
+  Comet_01:
+    run: https://raw.githubusercontent.com/Workflomics/containers/main/cwl/tools/Comet/Comet.cwl
+    in:
+      Comet_in_1: input_1
+      Comet_in_2: input_2
+    out: [Comet_out_1, Comet_out_2, Comet_out_3]
+  idconvert_02:
+    run: https://raw.githubusercontent.com/Workflomics/containers/main/cwl/tools/idconvert/idconvert_to_pepXML.cwl
+    in:
+      idconvert_in_1: Comet_01/Comet_out_2
+    out: [idconvert_out_1]
+  ProteinProphet_03:
+    run: https://raw.githubusercontent.com/Workflomics/containers/main/cwl/tools/ProteinProphet/ProteinProphet.cwl
+    in:
+      ProteinProphet_in_1: idconvert_02/idconvert_out_1
+      ProteinProphet_in_2: input_2
+    out: [ProteinProphet_out_1, ProteinProphet_out_2]
+outputs:
+  output_1:
+    type: File
+    format: "http://edamontology.org/format_3747" # protXML
+    outputSource: ProteinProphet_03/ProteinProphet_out_1
+
+                """;
+
+        // Convert the string to a byte array
+        byte[] cwlFileBytes = cwlFileContent.getBytes();
+
+        // Call the method to test
+        JSONObject response = ToolBenchmarkingAPIs.sendPostToPubmetric(cwlFileBytes);
+
+        // Verify that the response is not null
+        assertFalse(response.isEmpty());
+    }
+}