Merge pull request #4 from sanctuuary/cwl_input_yml

Cwl input yml

Dockerfile

@@ -1,4 +1,4 @@
 FROM eclipse-temurin:17-jdk-jammy
 WORKDIR /app
-COPY restape-0.2.2.jar /app
-ENTRYPOINT ["java", "-jar", "restape-0.2.2.jar"]
+COPY restape-0.2.4.jar /app
+ENTRYPOINT ["java", "-jar", "restape-0.2.4.jar"]

pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>nl.esciencecenter</groupId>
 	<artifactId>restape</artifactId>
-	<version>0.2.2</version>
+	<version>0.2.4</version>
 	<name>restape</name>
 	<description>RESTful API for the APE library</description>
 	<licenses>
@@ -41,6 +41,7 @@
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-web</artifactId>
+			<version>3.1.2</version>
 		</dependency>
 
 		<dependency>
@@ -58,25 +59,43 @@
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-actuator</artifactId>
+			<version>3.1.2</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-data-jpa -->
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-data-jpa</artifactId>
-			<version>3.1.0</version>
+			<version>3.1.2</version>
 		</dependency>
 
+		<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-validation -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-validation</artifactId>
+			<version>3.1.2</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-devtools -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-devtools</artifactId>
+			<version>3.1.2</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/com.h2database/h2 -->
 		<dependency>
 			<groupId>com.h2database</groupId>
 			<artifactId>h2</artifactId>
+			<version>2.2.220</version>
 			<scope>runtime</scope>
 		</dependency>
 
+
 		<dependency>
 			<groupId>io.github.sanctuuary</groupId>
 			<artifactId>APE</artifactId>
-			<version>2.1.5</version>
+			<version>2.1.8</version>
 		</dependency>
 
 		<dependency>
@@ -92,26 +111,13 @@
 			<version>22.3.2</version>
 		</dependency>
 
-
-		<dependency>
-			<groupId>org.springframework.boot</groupId>
-			<artifactId>spring-boot-starter-validation</artifactId>
-		</dependency>
-
-		<dependency>
-			<groupId>org.springframework.boot</groupId>
-			<artifactId>spring-boot-devtools</artifactId>
-		</dependency>
-
 		<!-- https://mvnrepository.com/artifact/org.projectlombok/lombok -->
 		<dependency>
 			<groupId>org.projectlombok</groupId>
 			<artifactId>lombok</artifactId>
 			<version>1.18.26</version>
 			<scope>provided</scope>
 		</dependency>
-
-
 	</dependencies>
 
 	<build>

src/main/java/nl/esciencecenter/RestapeApplication.java

@@ -1,19 +1,14 @@
 package nl.esciencecenter;
 
-import java.util.Arrays;
-
-import org.springframework.boot.CommandLineRunner;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.annotation.Bean;
 
 import io.swagger.v3.oas.annotations.OpenAPIDefinition;
 import io.swagger.v3.oas.annotations.info.Info;
 import io.swagger.v3.oas.annotations.servers.Server;
 
 @SpringBootApplication
-@OpenAPIDefinition(info = @Info(title = "RestApe API", version = "0.0.1", description = "RESTfull API for the APE (Automated Pipeline Explorer) library."), servers = @Server(url = "http://localhost:8080", description = "Local server"))
+@OpenAPIDefinition(info = @Info(title = "RestApe API", version = "0.0.1", description = "RESTfull API for the APE (Automated Pipeline Explorer) library."), servers = @Server(url = "http://localhost:4444", description = "Local server"))
 public class RestapeApplication {
 
 	public static void main(String[] args) {

src/main/java/nl/esciencecenter/models/documentation/ConstraintElem.java

@@ -1,20 +1,29 @@
 package nl.esciencecenter.models.documentation;
 
+import java.util.Map;
+
 import org.json.JSONArray;
 import org.json.JSONObject;
 
+import lombok.AllArgsConstructor;
+import lombok.NoArgsConstructor;
+
 /**
  * This class represents a single constraint template.
  * TODO: This class is not used at the moment, but it is a good idea to use it
  * in the future.
  * 
  */
+@NoArgsConstructor
+@AllArgsConstructor
 public class ConstraintElem {
     public String id;
     public String label;
-    public TaxonomyElem[] subsets;
+    public ConstraintParam[] parameters;
 
-    public ConstraintElem() {
-    }
+}
 
+class ConstraintParam {
+    public String dimension1Root;
+    public String dimension2Root;
 }

src/main/java/nl/esciencecenter/models/documentation/TaxonomyElem.java

@@ -1,21 +1,19 @@
 package nl.esciencecenter.models.documentation;
 
-import java.util.Map;
-
-import org.json.JSONArray;
-import org.json.JSONObject;
+import lombok.AllArgsConstructor;
+import lombok.NoArgsConstructor;
 
 /**
  * This class represents a single element of the taxonomy.
  * TODO: This class is not used at the moment, but it is a good idea to use it
  * in the future.
  * 
  */
+@NoArgsConstructor
+@AllArgsConstructor
 public class TaxonomyElem {
-    public String constraintID;
-    public String description;
-    public Map[] parameters;
-
-    public TaxonomyElem() {
-    }
+    public String id;
+    public String label;
+    public String root;
+    public TaxonomyElem[] subsets;
 }

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

@@ -112,6 +112,7 @@ private static JSONObject getPredicates(TaxonomyPredicate currType, AllPredicate
         }
         objType.put("id", currType.getPredicateID());
         objType.put("label", currType.getPredicateLabel());
+        objType.put("root", currType.getRootNodeID());
         if (arrayTypes.length() > 0) {
             objType.put("subsets", arrayTypes);
         }
@@ -144,56 +145,55 @@ public static JSONArray getConstraints(String configFileURL) throws OWLOntologyC
      * 
      * @param configJson - configuration of the synthesis run
      * @return - JSONArray with the results of the synthesis, each element describes
-     *         a workflow
+     *         a workflow solution (name,length, runID, etc.).
      * @throws IOException
      * @throws OWLOntologyCreationException
      */
     public static JSONArray runSynthesis(JSONObject configJson) throws OWLOntologyCreationException, IOException {
         JSONArray generatedSolutions = new JSONArray();
         APE apeFramework = null;
 
-        // set up the APE framework
-        apeFramework = new APE(configJson);
-
-
         String runID = RestApeUtils.generateUniqueString(configJson.toString());
         String solutionPath = RestApeUtils.createDirectory(runID);
 
-        SolutionsList solutions;
+        // configJson = IOUtils.extractConstraintsFromApeConfig(configJson);
+        // set up the APE framework
+        apeFramework = new APE(configJson);
 
         APERunConfig runConfig = new APERunConfig(configJson, apeFramework.getDomainSetup());
 
         runConfig.setSolutionPath(solutionPath);
         int maxSol = runConfig.getMaxNoSolutions();
         runConfig.setNoCWL(maxSol);
         runConfig.setNoGraphs(maxSol);
+        runConfig.setDebugMode(true);
         // run the synthesis and retrieve the solutions
-        solutions = apeFramework.runSynthesis(runConfig);
+        SolutionsList solutions = apeFramework.runSynthesis(runConfig);
 
         /*
          * Writing solutions to the specified file in human readable format
          */
         if (solutions.isEmpty()) {
-            return new JSONArray("The given problem is UNSAT");
+            return new JSONArray();
         } else {
-                // Write solutions to the file system.
-                APE.writeDataFlowGraphs(solutions, RankDir.TOP_TO_BOTTOM);
-                APE.writeCWLWorkflows(solutions);
-
-                // Generate objects that return the solutions in JSON format
-                int noSolutions = solutions.getNumberOfSolutions();
-                for (int i = 0; i < noSolutions; i++) {
-                    SolutionWorkflow sol = solutions.get(i);
-                    JSONObject solJson = new JSONObject();
-                    solJson.put("name", sol.getFileName());
-                    solJson.put("workflow_length", sol.getSolutionLength());
-                    solJson.put("cwl_name", sol.getFileName() + ".cwl");
-                    solJson.put("figure_name", sol.getFileName() + ".png");
-                    solJson.put("run_id", runID);
-
-                    generatedSolutions.put(solJson);
-                }
-                return generatedSolutions;
+            // Write solutions to the file system.
+            APE.writeDataFlowGraphs(solutions, RankDir.TOP_TO_BOTTOM);
+            APE.writeCWLWorkflows(solutions);
+
+            // Generate objects that return the solutions in JSON format
+            int noSolutions = solutions.getNumberOfSolutions();
+            for (int i = 0; i < noSolutions; i++) {
+                SolutionWorkflow sol = solutions.get(i);
+                JSONObject solJson = new JSONObject();
+                solJson.put("name", sol.getFileName());
+                solJson.put("workflow_length", sol.getSolutionLength());
+                solJson.put("cwl_name", sol.getFileName() + ".cwl");
+                solJson.put("figure_name", sol.getFileName() + ".png");
+                solJson.put("run_id", runID);
+
+                generatedSolutions.put(solJson);
+            }
+            return generatedSolutions;
         }
     }
 

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

@@ -5,20 +5,29 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.Optional;
+import java.nio.file.Paths;
+import java.nio.file.attribute.PosixFileAttributes;
+import java.nio.file.attribute.PosixFilePermission;
+import java.nio.file.attribute.PosixFilePermissions;
+import java.util.Set;
 
 import javax.imageio.ImageIO;
 
 import org.apache.commons.io.FileUtils;
+import org.json.JSONArray;
+import org.json.JSONException;
+import org.json.JSONObject;
 
 import nl.uu.cs.ape.io.APEFiles;
 
 public class IOUtils {
-
 
     /**
-     * Get byte array that represents the image from the file system at the given path.
+     * Get byte array that represents the image from the file system at the given
+     * path.
+     * 
      * @param filePath - path to the image
      * @return byte array that represents the image
      * @throws IOException - if the image cannot be read
@@ -36,11 +45,13 @@ public static byte[] getImageFromFileSystem(Path filePath) throws IOException {
 
     /**
      * Get the CWL content of the file at the given path.
+     * 
      * @param filePath - path to the CWL file
      * @return CWL content of the file representing a workflow
      * @throws IOException - if the file cannot be read
      */
     public static String getLocalCwlFile(Path filePath) throws IOException {
         return FileUtils.readFileToString(filePath.toFile(), StandardCharsets.UTF_8);
     }
+
 }