Merge pull request #55 from sanctuuary/ape-update

Update RESTful APE: Version and Testing Enhancements

pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>nl.esciencecenter</groupId>
 	<artifactId>restape</artifactId>
-	<version>0.3.0</version>
+	<version>0.3.1</version>
 	<name>restape</name>
 	<description>RESTful API for the APE library</description>
 	<licenses>
@@ -42,7 +42,7 @@
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-web</artifactId>
-			<version>3.2.1</version>
+			<version>3.2.2</version>
 		</dependency>
 
 		<dependency>
@@ -61,28 +61,14 @@
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-actuator</artifactId>
-			<version>3.2.1</version>
+			<version>3.2.2</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>3.2.1</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>3.2.1</version>
-		</dependency>
-
-		<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-devtools -->
-		<dependency>
-			<groupId>org.springframework.boot</groupId>
-			<artifactId>spring-boot-devtools</artifactId>
-			<version>3.2.1</version>
+			<version>3.2.2</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/com.h2database/h2 -->
@@ -96,7 +82,7 @@
 		<dependency>
 			<groupId>io.github.sanctuuary</groupId>
 			<artifactId>APE</artifactId>
-			<version>2.2.6</version>
+			<version>2.3.0</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.springdoc/springdoc-openapi-starter-webmvc-ui -->

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

@@ -211,7 +211,7 @@ public ResponseEntity<String> runSynthesisAndBench(
                         @ApiResponse(responseCode = "400", description = "Invalid input"),
                         @ApiResponse(responseCode = "404", description = "Not found")
         })
-        public ResponseEntity<?> getImage(
+        public ResponseEntity<?> postImage(
                         @RequestBody(required = true) ImgFileInfo imgFileInfo) throws IOException {
 
                 Path path = imgFileInfo.calculatePath();
@@ -243,7 +243,7 @@ public ResponseEntity<?> getImage(
                         @ApiResponse(responseCode = "404", description = "Not found")
 
         })
-        public ResponseEntity<String> getCwl(
+        public ResponseEntity<String> postCwl(
                         @RequestBody(required = true) CWLFileInfo cwlInfoJson) throws IOException {
 
                 Path path = cwlInfoJson.calculatePath();
@@ -327,7 +327,7 @@ public ResponseEntity<String> getBenchmarks(
          * Retrieve the CWL solution files based on the provided run ID and CWL file
          * names.
          * TODO: Exeptions don't handle all cases or illegal arguments (e.g. invalid
-         * workflow name that ends with an open quotation`candidate_solution_1.cwl"`).
+         * workflow name that ends with an open quotation`candidate_workflow_1.cwl"`).
          * 
          * @param cwlFilesJson JSON object containing the run_id and the list of CWL
          *                     files.
@@ -343,17 +343,10 @@ public ResponseEntity<String> getBenchmarks(
                                                         @ApiResponse(responseCode = "500", description = "Internal server error"),
 
         })
-        public ResponseEntity<?> getZipCWLs(
+        public ResponseEntity<?> postZipCWLs(
                         @RequestBody(required = true) CWLZip cwlZipInfo) {
                 try {
-                        List<Path> cwlFilePaths = cwlZipInfo.getCWLPaths();
-
-                        // Add the CWL input file to the zip
-                        Path cwlInputPath = RestApeUtils.calculatePath(cwlZipInfo.getRunID(), "CWL", "input.yml");
-                        cwlFilePaths.add(cwlInputPath);
-
-                        // Zip the CWL files
-                        Path zipPath = IOUtils.zipFiles(cwlFilePaths, cwlInputPath.getParent());
+                        Path zipPath = IOUtils.zipFilesForLocalExecution(cwlZipInfo);
 
                         Resource zipResource = new UrlResource(zipPath.toUri());
                         String zipContentType = Files.probeContentType(zipPath);

src/main/java/nl/esciencecenter/controller/dto/CWLZip.java

@@ -11,6 +11,10 @@
 import lombok.Setter;
 import nl.esciencecenter.restape.RestApeUtils;
 
+/**
+ * The {@code CWLZip} class represents the structure of the request to zip CWL files. It contains the runID and the list of workflow file names.
+ 
+ */
 @Getter
 @Setter
 @NoArgsConstructor

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

@@ -1,7 +1,11 @@
 package nl.esciencecenter.restape;
 
+import java.io.BufferedInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -14,56 +18,101 @@
 
 import lombok.AccessLevel;
 import lombok.NoArgsConstructor;
+import nl.esciencecenter.controller.dto.CWLZip;
 
 /**
  * The {@code IOUtils} class provides static methods to read the input files.
  */
 @NoArgsConstructor(access = AccessLevel.PRIVATE)
 public class IOUtils {
 
-    /**
-     * 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, NoSuchFileException {
-        return FileUtils.readFileToString(filePath.toFile(), StandardCharsets.UTF_8);
-    }
+        /**
+         * 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";
 
-    /**
-     * Get the JSON content of the file at the given path.
-     * 
-     * @param filePath - path to the benchmarking JSON file
-     * @return CWL content of the file representing a workflow
-     * @throws IOException - if the file cannot be read
-     */
-    public static String getLocalBenchmarkFile(Path filePath) throws IOException {
-        return FileUtils.readFileToString(filePath.toFile(), StandardCharsets.UTF_8);
-    }
+        /**
+         * 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, NoSuchFileException {
+                return FileUtils.readFileToString(filePath.toFile(), StandardCharsets.UTF_8);
+        }
 
-    /**
-         * Zip the provided CWL files as well as the CWL input file (`inputs.yml`).
+        /**
+         * Get the JSON content of the file at the given path.
+         * 
+         * @param filePath - path to the benchmarking JSON file
+         * @return CWL content of the file representing a workflow
+         * @throws IOException - if the file cannot be read
+         */
+        public static String getLocalBenchmarkFile(Path filePath) throws IOException {
+                return FileUtils.readFileToString(filePath.toFile(), StandardCharsets.UTF_8);
+        }
+
+        /**
+         * Zip the provided CWL files as well as the CWL input file (`inputs.yml`) into
+         * a single zip file. In addition, a `readme.txt` file with instructions on how
+         * to run the workflows is added to the zip.
+         * 
+         * @param cwlZipInfo - the CWL zip information, containing the runID and the list of workflow file names.
          * 
-         * @param cwlFilePaths    List of CWL file names (with extensions).
-         * @param locationDirPath Path to the directory where the zip file will be
-         *                        created.
          * @return Path to the created zip file.
          * @throws IOException Error is thrown if the zip file cannot be created or
          *                     written to.
          */
-        public static Path zipFiles(List<Path> cwlFilePaths, Path locationDirPath) throws IOException {
-                Path zipPath = locationDirPath.resolve("workflows.zip");
+        public static Path zipFilesForLocalExecution(CWLZip cwlZipInfo) throws IOException {
+
+                List<Path> cwlFilePaths = cwlZipInfo.getCWLPaths();
+
+                // Add the CWL input file to the zip
+                Path cwlInputPath = RestApeUtils.calculatePath(cwlZipInfo.getRunID(), "CWL", "input.yml");
+                cwlFilePaths.add(cwlInputPath);
+
+                Path zipPath = cwlInputPath.getParent().resolve("workflows.zip");
                 try (FileOutputStream fos = new FileOutputStream(zipPath.toFile());
                                 ZipOutputStream zipOut = new ZipOutputStream(fos)) {
                         for (Path file : cwlFilePaths) {
                                 zipOut.putNextEntry(new ZipEntry(file.getFileName().toString()));
                                 Files.copy(file, zipOut);
                                 zipOut.closeEntry();
                         }
+                        addReadmeToZip(zipOut);
                 }
                 return zipPath;
         }
 
+        /**
+         * Add the `readme.txt` file to the zip from the given URL. The file contains
+         * instructions on how to run the workflows.
+         * 
+         * @param zipOut - the zip output stream
+         * @throws IOException - if the README file cannot be read
+         */
+        private static void addReadmeToZip(ZipOutputStream zipOut) throws IOException {
+                // Download readme.txt and add to the zip
+                URL readmeUrl = new URL(README_URL);
+                HttpURLConnection httpURLConnection = (HttpURLConnection) readmeUrl.openConnection();
+                httpURLConnection.setRequestMethod("GET");
+                // Ensure the connection timeout is set to a reasonable value
+                httpURLConnection.setConnectTimeout(5000); // 5 seconds
+                httpURLConnection.setReadTimeout(5000); // 5 seconds
+
+                try (InputStream in = new BufferedInputStream(httpURLConnection.getInputStream())) {
+                        zipOut.putNextEntry(new ZipEntry("readme.txt"));
+
+                        byte[] buffer = new byte[1024];
+                        int count;
+                        while ((count = in.read(buffer)) != -1) {
+                                zipOut.write(buffer, 0, count);
+                        }
+
+                        zipOut.closeEntry();
+                } finally {
+                        httpURLConnection.disconnect();
+                }
+        }
 }

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

@@ -94,19 +94,19 @@ public static boolean isValidRunID(String runID) {
 
     /**
      * Checks whether the file name is valid, by checking its format. The name
-     * should start with `candidate_solution_` followed by a number and without an
+     * should start with `candidate_workflow_` followed by a number and without an
      * extension.
      * 
      * @param fileName - file name to be verified
      * @return true if the file name is valid, false otherwise.
      */
     public static boolean isValidAPEFileNameNoExtension(String fileName) {
-        return fileName != null && fileName.matches("candidate_solution_\\d+");
+        return fileName != null && fileName.matches("candidate_workflow_\\d+");
     }
 
     /**
      * Checks whether the file name is valid, by checking its format. The name
-     * should start with `candidate_solution_` followed by a number and with an
+     * should start with `candidate_workflow_` followed by a number and with an
      * extension.
      * 
      * @param fileName - file name to be verified
@@ -118,15 +118,15 @@ public static boolean isValidFileNameWithExtension(String fileName) {
 
     /**
      * Checks whether the file name is valid, by checking its extension and format.
-     * The name should start with `candidate_solution_` followed by a number and end
+     * The name should start with `candidate_workflow_` followed by a number and end
      * with the specified extension.
      * 
      * @param fileName  - file name to be verified
      * @param extension - extension of the file
      * @return true if the file name is valid, false otherwise.
      */
     public static boolean isValidAPEFileName(String fileName, String extension) {
-        return fileName != null && fileName.matches("candidate_solution_\\d+\\." + extension);
+        return fileName != null && fileName.matches("candidate_workflow_\\d+\\." + extension);
     }
 
     /**

src/test/java/nl/esciencecenter/RestApeApplicationTest.java

@@ -1,13 +1,21 @@
 package nl.esciencecenter;
 
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
 import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.context.ApplicationContext;
 
 @SpringBootTest
 class RestApeApplicationTest {
 
-	@Test
-	void contextLoads() {
+	@Autowired
+    private ApplicationContext context;
+
+    @Test
+    void contextLoads() {
+        assertNotNull(context, "Application context should not be null");
 
 	}