Add code that calls pubmetric

pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>nl.esciencecenter</groupId>
 	<artifactId>restape</artifactId>
-	<version>0.3.3</version>
+	<version>0.4.0</version>
 	<name>restape</name>
 	<description>RESTful API for the APE library</description>
 	<licenses>

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

@@ -75,7 +75,7 @@ public String index() {
                 parameters = {
                         @Parameter(name = "config_path", 
                                 description = "URL to the APE configuration file.",
-                                example = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json")
+                                example = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json")
                 },
                 externalDocs = @ExternalDocumentation(description = "More information about the APE configuration file can be found here.",
                                                         url = "https://ape-framework.readthedocs.io/en/latest/docs/specifications/setup.html#configuration-file"),
@@ -110,7 +110,7 @@ public ResponseEntity<String> getData(
                 parameters = {
                         @Parameter(name = "config_path", 
                                 description = "URL to the APE configuration file.",
-                                example = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json")
+                                example = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json")
                 },
                 externalDocs = @ExternalDocumentation(description = "More information about the APE configuration file can be found here.",
                                                         url = "https://ape-framework.readthedocs.io/en/latest/docs/specifications/setup.html#configuration-file"),
@@ -144,7 +144,7 @@ public ResponseEntity<String> getTools(
                 parameters = {
                         @Parameter(name = "config_path", 
                                 description = "URL to the APE configuration file.",
-                                example = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json")
+                                example = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json")
                 },
                 externalDocs = @ExternalDocumentation(description = "More information about the APE configuration file can be found here.",
                                                         url = "https://ape-framework.readthedocs.io/en/latest/docs/specifications/setup.html#configuration-file"),

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

@@ -130,7 +130,19 @@ public static JSONArray getConstraints(String configFileURL) throws OWLOntologyC
         APE apeFramework = setupApe(configFileURL);
         Collection<ConstraintTemplate> constraints = apeFramework.getConstraintTemplates();
         JSONArray arrayConstraints = new JSONArray();
-        constraints.forEach(constraint -> arrayConstraints.put(constraint.toJSON()));
+        constraints.forEach(constraint -> {
+            JSONObject constraintJson = constraint.toJSON();
+            if (constraint.getConstraintID().equals("connected_op")) {
+                constraintJson.remove("label");
+                constraintJson.put("label", "Use operations sequentially.");
+            } else if (constraint.getConstraintID().equals("not_connected_op")) {
+                constraintJson.remove("label");
+                constraintJson.put("label", "Do not use operations sequentially.");
+            }
+
+            arrayConstraints.put(constraintJson);
+
+        });
 
         return arrayConstraints;
     }

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

@@ -29,7 +29,7 @@ public class IOUtils {
         /**
          * URL to the README file containing instructions on how to run the workflows.
          */
-        private static final String README_URL = "https://raw.githubusercontent.com/Workflomics/containers/add_instructions/instructions.txt";
+        private static final String README_URL = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/add_instructions/instructions.txt";
 
         /**
          * Get the CWL content of the file at the given path.

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

@@ -7,6 +7,14 @@
 import java.util.List;
 
 import okhttp3.OkHttpClient;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.mime.MultipartEntityBuilder;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.util.EntityUtils;
 import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
@@ -23,6 +31,7 @@
 import nl.esciencecenter.models.benchmarks.BenchmarkBase;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionsList;
+import nl.uu.cs.ape.solver.solutionStructure.cwl.DefaultCWLCreator;
 import nl.uu.cs.ape.utils.APEFiles;
 
 /**
@@ -63,7 +72,14 @@ static boolean computeBenchmarks(SolutionsList candidateSolutions, String runID)
           * Compute the benchmarks for the workflow and save them in a JSON file.
           */
          JSONObject workflowBenchmarks = computeWorkflowSpecificFields(workflow, runID);
-         workflowBenchmarks.put("benchmarks", computeWorkflowBenchmarks(workflow));
+         JSONArray benchmarks = computeWorkflowBenchmarks(workflow);
+         JSONObject additionalBenchmarks = getPubmetricBenchmarks(workflow);
+
+         if (!additionalBenchmarks.isEmpty() && additionalBenchmarks.has("benchmarks")) {
+            additionalBenchmarks.getJSONArray("benchmarks").forEach(benchmark -> benchmarks.put(benchmark));
+         }
+
+         workflowBenchmarks.put("benchmarks", benchmarks);
 
          String titleBenchmark = workflow.getFileName() + ".json";
          Path solFolder = candidateSolutions.getRunConfiguration().getSolutionDirPath2CWL();
@@ -79,6 +95,65 @@ static boolean computeBenchmarks(SolutionsList candidateSolutions, String runID)
       return true;
    }
 
+   /**
+    * Get the Pubmetric benchmarks for the workflow.
+    * @param workflow
+    * @return
+    */
+   public static JSONObject getPubmetricBenchmarks(SolutionWorkflow workflow) {
+      // Generate the CWL file content
+      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
+      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");
+      }
+
+      return new JSONObject();
+   }
+
    /**
     * Compute the benchmarks (based on bio.tools and OpenEBench APIs) for the
     * workflows and return it in JSON format.

src/main/resources/static/data.sql

@@ -1,3 +1,3 @@
 INSERT INTO DOMAIN VALUES (1, 'Proteomics', "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/MassSpectometry/config.json");    
-INSERT INTO DOMAIN VALUES (2, 'Wombat-P', "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json");    
+INSERT INTO DOMAIN VALUES (2, 'Wombat-P', "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json");    
 

src/test/java/nl/esciencecenter/controller/RestApeControllerTest.java

@@ -58,7 +58,7 @@ void testGetDataFail() throws Exception {
      */
     @Test
     void testGetData() throws Exception {
-        String path = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+        String path = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
 
         mvc.perform(MockMvcRequestBuilders.get("/data_taxonomy?config_path=" + path).accept(MediaType.APPLICATION_JSON))
                 .andExpect(status().isOk())
@@ -83,7 +83,7 @@ void testGetToolsFail() throws Exception {
      */
     @Test
     void testGetTools() throws Exception {
-        String path = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+        String path = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
 
         mvc.perform(
                 MockMvcRequestBuilders.get("/tools_taxonomy?config_path=" + path).accept(MediaType.APPLICATION_JSON))
@@ -121,7 +121,7 @@ void testRunSynthesisFail() throws Exception {
     @Test
     void testRunSynthesisPass() throws Exception {
 
-        String configPath = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+        String configPath = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
         String jsonContent = FileUtils.readFileToString(APEFiles.readPathToFile(configPath),
                 StandardCharsets.UTF_8);
 
@@ -134,7 +134,7 @@ void testRunSynthesisPass() throws Exception {
     @Test
     void testPostZipCWLs() throws Exception {
 
-            String path = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+            String path = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
             String content = FileUtils.readFileToString(APEFiles.readPathToFile(path),
                             StandardCharsets.UTF_8);
             JSONObject jsonObject = new JSONObject(content);

src/test/java/nl/esciencecenter/restape/ApeAPITest.java

@@ -27,7 +27,7 @@ class ApeAPITest {
      */
     @Test
     void runSynthesisFail() throws IOException, OWLOntologyCreationException {
-        String configPath = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+        String configPath = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
         String content = FileUtils.readFileToString(APEFiles.readPathToFile(configPath),
                 StandardCharsets.UTF_8);
         JSONObject jsonObject = new JSONObject(content);
@@ -45,7 +45,7 @@ void runSynthesisFail() throws IOException, OWLOntologyCreationException {
      */
     @Test
     void runSynthesisPass() throws IOException, OWLOntologyCreationException {
-        String configPath = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+        String configPath = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
         String content = FileUtils.readFileToString(APEFiles.readPathToFile(configPath),
                 StandardCharsets.UTF_8);
         JSONObject jsonObject = new JSONObject(content);
@@ -63,7 +63,7 @@ void runSynthesisPass() throws IOException, OWLOntologyCreationException {
      */
     @Test
     void runSynthesisAndBenchmarkPass() throws IOException, OWLOntologyCreationException {
-        String configPath = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+        String configPath = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
         String content = FileUtils.readFileToString(APEFiles.readPathToFile(configPath),
                 StandardCharsets.UTF_8);
         JSONObject jsonObject = new JSONObject(content);

src/test/java/nl/esciencecenter/restape/IOUtilsTest.java

@@ -19,7 +19,7 @@ class IOUtilsTest {
     @Test
     void testZipFilesForLocalExecution() throws Exception {
 
-            String path = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+            String path = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
             String content = FileUtils.readFileToString(APEFiles.readPathToFile(path),
                             StandardCharsets.UTF_8);
             JSONObject jsonObject = new JSONObject(content);

src/test/java/nl/esciencecenter/restape/RestApeUtilsTest.java

@@ -17,7 +17,7 @@ class RestApeUtilsTest {
      */
     @Test
     void loadURLPath() {
-        String urlPath = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+        String urlPath = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
 
         assertDoesNotThrow(() -> ApeAPI.setupApe(urlPath));
 
@@ -31,7 +31,7 @@ void loadLocalPath() {
 
         assertDoesNotThrow(() -> {
             File config = APEFiles.readPathToFile(
-                    "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json");
+                    "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json");
             ApeAPI.setupApe(config.getAbsolutePath());
         });
 
@@ -43,7 +43,7 @@ void loadLocalPath() {
      */
     @Test
     void getTypesFromURLPath() {
-        String urlPath = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+        String urlPath = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
 
         assertDoesNotThrow(() -> ApeAPI.getData(urlPath));
 
@@ -55,7 +55,7 @@ void getTypesFromURLPath() {
      */
     @Test
     void getToolsFromURLPath() {
-        String urlPath = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/WombatP_tools/config.json";
+        String urlPath = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/config.json";
 
         assertDoesNotThrow(() -> ApeAPI.getTools(urlPath));