First working version

.gitignore

@@ -9,3 +9,5 @@ buildNumber.properties
 .mvn/timing.properties
 # https://github.com/takari/maven-wrapper#usage-without-binary-jar
 .mvn/wrapper/maven-wrapper.jar
+.idea/
+.idea/misc.xml

Dockerfile

@@ -0,0 +1,6 @@
+FROM openjdk:17
+MAINTAINER protege.stanford.edu
+
+ARG JAR_FILE
+COPY target/${JAR_FILE} webprotege-file-submission-service.jar
+ENTRYPOINT ["java","-jar","/webprotege-file-submission-service.jar"]

pom.xml

@@ -5,14 +5,14 @@
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
-		<version>2.5.6</version>
+		<version>3.2.5</version>
 		<relativePath/> <!-- lookup parent from repository -->
 	</parent>
 	<groupId>edu.stanford.protege</groupId>
 	<artifactId>webprotege-file-submission-service</artifactId>
-	<version>0.1.0-SNAPSHOT</version>
+	<version>1.0.0</version>
 	<name>webprotege-file-submission-service</name>
-	<description>A service that accepts files uploaded to WebProtege</description>
+	<description>A service that stores files</description>
 	<properties>
 		<java.version>17</java.version>
 	</properties>
@@ -24,6 +24,7 @@
 		</snapshotRepository>
 	</distributionManagement>
 
+
 	<dependencies>
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
@@ -35,6 +36,57 @@
 			<artifactId>spring-boot-starter-test</artifactId>
 			<scope>test</scope>
 		</dependency>
+
+		<dependency>
+			<groupId>edu.stanford.protege</groupId>
+			<artifactId>webprotege-ipc</artifactId>
+			<version>1.0.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>edu.stanford.protege</groupId>
+			<artifactId>webprotege-jackson</artifactId>
+			<version>0.9.2</version>
+		</dependency>
+
+		<dependency>
+			<groupId>io.minio</groupId>
+			<artifactId>minio</artifactId>
+			<version>8.5.10</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.testcontainers</groupId>
+			<artifactId>minio</artifactId>
+			<version>1.19.7</version>
+			<scope>test</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>com.github.dasniko</groupId>
+			<artifactId>testcontainers-keycloak</artifactId>
+			<version>3.3.0</version>
+			<scope>test</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>org.testcontainers</groupId>
+			<artifactId>rabbitmq</artifactId>
+			<version>1.19.7</version>
+			<scope>test</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>org.testcontainers</groupId>
+			<artifactId>mongodb</artifactId>
+			<version>1.18.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-actuator</artifactId>
+		</dependency>
+
 	</dependencies>
 
 	<build>
@@ -43,6 +95,28 @@
 				<groupId>org.springframework.boot</groupId>
 				<artifactId>spring-boot-maven-plugin</artifactId>
 			</plugin>
+
+			<plugin>
+				<groupId>com.spotify</groupId>
+				<artifactId>dockerfile-maven-plugin</artifactId>
+				<version>1.4.13</version>
+				<executions>
+					<execution>
+						<id>default</id>
+						<goals>
+							<goal>build</goal>
+						</goals>
+					</execution>
+				</executions>
+				<configuration>
+					<repository>protegeproject/${project.artifactId}</repository>
+					<tag>${project.version}</tag>
+					<buildArgs>
+						<JAR_FILE>${project.build.finalName}.jar</JAR_FILE>
+					</buildArgs>
+				</configuration>
+			</plugin>
+
 		</plugins>
 	</build>
 

src/main/java/edu/stanford/protege/webprotege/filesub/FileContentsSizeCalculator.java

@@ -0,0 +1,49 @@
+package edu.stanford.protege.webprotege.filesub;
+
+import javax.annotation.Nonnull;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Enumeration;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import static com.google.common.base.Preconditions.checkNotNull;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2024-05-02
+ */
+public class FileContentsSizeCalculator {
+
+    @Nonnull
+    private final ZipInputStreamChecker checker;
+
+    public FileContentsSizeCalculator(@Nonnull ZipInputStreamChecker checker) {
+        this.checker = checkNotNull(checker);
+    }
+
+    /**
+     * Gets the size of the uploaded file.  If the file is a zip file then the size of the
+     * expanded contents is computed.
+     * @param file The file.
+     * @return The size of the contents
+     * @throws IOException If there was a problem reading the file or examining its contents.
+     */
+    public long getContentsSize(@Nonnull Path file) throws IOException {
+        if (!checker.isZipFile(file)) {
+            return Files.size(file);
+        }
+        try(ZipFile zipFile = new ZipFile(file.toFile())) {
+            Enumeration<? extends ZipEntry> entries = zipFile.entries();
+            long totalSize = 0;
+            while (entries.hasMoreElements()) {
+                ZipEntry entry = entries.nextElement();
+                long size = entry.getSize();
+                totalSize += size;
+            }
+            return totalSize;
+        }
+    }
+}

src/main/java/edu/stanford/protege/webprotege/filesub/FileSubmissionId.java

@@ -0,0 +1,18 @@
+package edu.stanford.protege.webprotege.filesub;
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonValue;
+
+public record FileSubmissionId(String id) {
+
+    @JsonCreator
+    public static FileSubmissionId valueOf(String id) {
+        return new FileSubmissionId(id);
+    }
+
+    @Override
+    @JsonValue
+    public String id() {
+        return id;
+    }
+}

src/main/java/edu/stanford/protege/webprotege/filesub/MinioProperties.java

@@ -0,0 +1,54 @@
+package edu.stanford.protege.webprotege.filesub;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2021-11-11
+ */
+@Configuration
+@ConfigurationProperties(prefix = "webprotege.minio")
+public class MinioProperties {
+
+    private String accessKey;
+
+    private String secretKey;
+
+    private String endPoint;
+
+    private String bucketName;
+
+    public void setAccessKey(String accessKey) {
+        this.accessKey = accessKey;
+    }
+
+    public void setSecretKey(String secretKey) {
+        this.secretKey = secretKey;
+    }
+
+    public void setEndPoint(String endPoint) {
+        this.endPoint = endPoint;
+    }
+
+    public String getAccessKey() {
+        return accessKey;
+    }
+
+    public String getSecretKey() {
+        return secretKey;
+    }
+
+    public String getEndPoint() {
+        return endPoint;
+    }
+
+    public void setBucketName(String bucketName) {
+        this.bucketName = bucketName;
+    }
+
+    public String getBucketName() {
+        return bucketName;
+    }
+}

src/main/java/edu/stanford/protege/webprotege/filesub/StorageException.java

@@ -0,0 +1,13 @@
+package edu.stanford.protege.webprotege.filesub;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2021-11-12
+ */
+public class StorageException extends RuntimeException {
+
+    public StorageException(Throwable cause) {
+        super(cause);
+    }
+}

src/main/java/edu/stanford/protege/webprotege/filesub/StorageService.java

@@ -0,0 +1,77 @@
+package edu.stanford.protege.webprotege.filesub;
+
+import io.minio.BucketExistsArgs;
+import io.minio.MakeBucketArgs;
+import io.minio.MinioClient;
+import io.minio.UploadObjectArgs;
+import io.minio.errors.MinioException;
+import org.apache.commons.io.FileUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.security.InvalidKeyException;
+import java.security.NoSuchAlgorithmException;
+import java.util.UUID;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2021-11-12
+ */
+public class StorageService {
+
+    private static final Logger logger = LoggerFactory.getLogger(StorageService.class);
+
+    private final MinioClient minioClient;
+
+    private final MinioProperties minioProperties;
+
+
+    public StorageService(MinioClient minioClient,
+                          MinioProperties minioProperties) {
+        this.minioClient = minioClient;
+        this.minioProperties = minioProperties;
+    }
+
+    public FileSubmissionId storeFile(Path tempFile) {
+        var fileIdentifier = UUID.randomUUID().toString();
+        logger.info("Storing file ({}) with an identifier of {}", getFileSizeInMB(tempFile), fileIdentifier);
+        createBucketIfNecessary();
+        uploadObject(tempFile, fileIdentifier);
+        return new FileSubmissionId(fileIdentifier);
+    }
+
+    private String getFileSizeInMB(Path tempFile) {
+        try {
+            return FileUtils.byteCountToDisplaySize(Files.size(tempFile));
+        } catch (IOException e) {
+            return "";
+        }
+    }
+
+    private void uploadObject(Path tempFile, String fileIdentifier) {
+        try {
+            minioClient.uploadObject(UploadObjectArgs.builder()
+                                                     .bucket(minioProperties.getBucketName())
+                                                     .object(fileIdentifier)
+                                                     .filename(tempFile.toString())
+                                                     .build());
+        } catch (MinioException | NoSuchAlgorithmException | InvalidKeyException | IOException e) {
+            throw new StorageException(e);
+        }
+    }
+
+    private void createBucketIfNecessary() {
+        try {
+            if (!minioClient.bucketExists(BucketExistsArgs.builder().bucket(minioProperties.getBucketName()).build())) {
+                minioClient.makeBucket(MakeBucketArgs.builder().bucket(minioProperties.getBucketName()).build());
+            }
+        } catch (MinioException | IOException | NoSuchAlgorithmException | IllegalArgumentException | InvalidKeyException e) {
+            throw new StorageException(e);
+        }
+    }
+
+}