From d1c29f988f4958a080d774fea7fd2b2614009d63 Mon Sep 17 00:00:00 2001
From: Vedran Kasalica <v.kasalica@esciencecenter.nl>
Date: Mon, 29 Apr 2024 16:21:23 +0200
Subject: [PATCH] Fix serialisation issue when returning object by the API

---
 .../OpenEBenchBenchmarkProcessor.java         |  7 +++++-
 .../restape/APEWorkflowMetadata.java          | 24 +++++++++----------
 .../restape/ToolBenchmarkingAPIs.java         |  7 +-----
 3 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchBenchmarkProcessor.java b/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchBenchmarkProcessor.java
index cf9375c..518dda1 100644
--- a/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchBenchmarkProcessor.java
+++ b/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchBenchmarkProcessor.java
@@ -7,6 +7,8 @@
 import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import lombok.AccessLevel;
 import lombok.NoArgsConstructor;
@@ -15,6 +17,7 @@
 import nl.esciencecenter.models.benchmarks.BenchmarkBase;
 import nl.esciencecenter.models.benchmarks.WorkflowStepBenchmark;
 import nl.esciencecenter.restape.LicenseType;
+import nl.esciencecenter.restape.ToolBenchmarkingAPIs;
 
 /**
  * Class {@link OpenEBenchBenchmarkProcessor} used to compute the design-time benchmarks for a workflow using the
@@ -27,6 +30,8 @@
 @NoArgsConstructor(access = AccessLevel.PRIVATE)
 public class OpenEBenchBenchmarkProcessor {
 
+    private static final Logger log = LoggerFactory.getLogger(OpenEBenchBenchmarkProcessor.class);
+
     /**
      * Benchmark for each tool in the workflow the license type according to the openness of the license. The licensed are characterized according to {@link LicenseType}.
      * 
@@ -151,7 +156,7 @@ private static List<WorkflowStepBenchmark> countCitationPerTool(List<JSONObject>
                 biotoolsEntryBenchmark.setDescription(String.valueOf(count));
                 biotoolsEntries.add(biotoolsEntryBenchmark);
             } catch (JSONException e) {
-                e.printStackTrace();
+                log.warn("No publication data found for tool: {}", toolAnnot.getString(ToolBenchmarkingAPIs.restAPEtoolID));
                 // set case for each license type
                 biotoolsEntryBenchmark.setDesirabilityValue(0);
                 biotoolsEntryBenchmark.setValue("0");
diff --git a/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java b/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java
index 0e32af4..7304bce 100644
--- a/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java
+++ b/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java
@@ -1,6 +1,9 @@
 package nl.esciencecenter.restape;
 
 import org.json.JSONObject;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
 import lombok.Getter;
 import lombok.NoArgsConstructor;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow;
@@ -15,13 +18,21 @@
 @NoArgsConstructor
 public class APEWorkflowMetadata {
     
+    @JsonProperty("workflow_name")
     private String workflowName;
+    @JsonProperty("descriptive_name")
     private String descriptiveName;
+    @JsonProperty("description")
     private String description;
+    @JsonProperty("workflow_length")
     private int workflowLength;
+    @JsonProperty("run_id")
     private String runId;
+    @JsonProperty("cwl_name")
     private String cwlName;
+    @JsonProperty("figure_name")
     private String figureName;
+    @JsonProperty("benchmark_file")
     private String benchmarkFile; // Optional, indicates if benchmark data should be included.
 
     /**
@@ -72,17 +83,6 @@ public JSONObject toJSONObject() {
      * @return A JSON string representation of the APEWorkflowMetadata instance.
      */
     public String toString() {
-        JSONObject json = new JSONObject();
-        json.put("workflow_name", this.workflowName);
-        json.put("descriptive_name", this.descriptiveName);
-        json.put("description", this.description);
-        json.put("workflow_length", this.workflowLength);
-        json.put("run_id", this.runId);
-        json.put("cwl_name", this.cwlName);
-        json.put("figure_name", this.figureName);
-        if (this.benchmarkFile != null && !this.benchmarkFile.isEmpty()) {
-            json.put("benchmark_file", this.benchmarkFile);
-        }
-        return json.toString();
+        return toJSONObject().toString();
     }
 }
diff --git a/src/main/java/nl/esciencecenter/restape/ToolBenchmarkingAPIs.java b/src/main/java/nl/esciencecenter/restape/ToolBenchmarkingAPIs.java
index f953cf8..855d099 100644
--- a/src/main/java/nl/esciencecenter/restape/ToolBenchmarkingAPIs.java
+++ b/src/main/java/nl/esciencecenter/restape/ToolBenchmarkingAPIs.java
@@ -2,16 +2,11 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 
 import okhttp3.OkHttpClient;
-import okhttp3.Request;
-import okhttp3.Response;
-
-import org.apache.commons.io.FileUtils;
 import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
@@ -130,7 +125,7 @@ private static List<Benchmark> computeBiotoolsBenchmark(SolutionWorkflow workflo
          try {
             biotoolsEntry = BioToolsRestClient.fetchToolFromBioTools(toolID);
          } catch (JSONException | IOException e) {
-            e.printStackTrace();
+           log.warn(e.getMessage());
          } finally {
             biotoolsEntry.put(ToolBenchmarkingAPIs.restAPEtoolID, toolNode.getUsedModule().getPredicateLabel());
             biotoolsAnnotations.add(biotoolsEntry);