TASK-7610 - Extend Workflows data model

commons-lib/src/main/java/org/opencb/commons/exec/Command.java

@@ -59,6 +59,29 @@ public class Command extends RunnableProcess {
     private final String[] cmdArray;
     private boolean printOutput = true;
 
+    private String stdinInput;
+
+    // Add a constructor that takes stdin input
+    public Command(String commandLine, String stdinInput) {
+        this(commandLine);
+        this.stdinInput = stdinInput;
+    }
+
+    public Command(String commandLine, List<String> environment, String stdinInput) {
+        this(commandLine, environment);
+        this.stdinInput = stdinInput;
+    }
+
+    public Command(String[] cmdArray, List<String> environment, String stdinInput) {
+        this(cmdArray, environment);
+        this.stdinInput = stdinInput;
+    }
+
+    public Command(String[] cmdArray, Map<String, String> environment, String stdinInput) {
+        this(cmdArray, environment);
+        this.stdinInput = stdinInput;
+    }
+
     public Command(String commandLine) {
         this.commandLine = commandLine;
         cmdArray = Commandline.translateCommandline(getCommandLine());
@@ -109,6 +132,14 @@ public Future<Status> run(boolean background) {
             }
             setStatus(Status.RUNNING);
 
+            // Write to stdin if input is provided
+            if (stdinInput != null) {
+                try (OutputStream stdin = proc.getOutputStream()) {
+                    stdin.write(stdinInput.getBytes());
+                    stdin.flush();
+                }
+            }
+
             InputStream stdout = proc.getInputStream();
             Future<?> readOutputStreamThread = readOutputStream(stdout);
             InputStream stderr = proc.getErrorStream();
@@ -310,6 +341,15 @@ public Command setPrintOutput(boolean printOutput) {
         return this;
     }
 
+    public String getStdinInput() {
+        return stdinInput;
+    }
+
+    public Command setStdinInput(String stdinInput) {
+        this.stdinInput = stdinInput;
+        return this;
+    }
+
     public Process getProc() {
         return proc;
     }

commons-lib/src/main/java/org/opencb/commons/utils/DockerUtils.java

@@ -159,6 +159,58 @@ private static List<String> getPaths(String entryPoint) {
         return new ArrayList<>(res);
     }
 
+    /**
+     * Login into dockerhub with the given credentials.
+     *
+     * @param registry  Docker registry URL
+     * @param username  Docker registry username
+     * @param password  Docker registry password
+     * @return True if login was successful, false otherwise
+     * @throws IOException IO exception
+     */
+    public static boolean login(String registry, String username, String password) throws IOException {
+        if (StringUtils.isEmpty(username) || StringUtils.isEmpty(password)) {
+            throw new IllegalArgumentException("Username and password are required");
+        }
+        if (registry == null) {
+            // Leave it empty (defaults to dockerhub)
+            registry = "";
+        }
+
+        String commandLine = "docker login " + registry + " --username " + username + " --password-stdin";
+
+        LOGGER.info("Running docker login command");
+        Command cmd = new Command(commandLine, password);
+        cmd.run();
+
+        if (cmd.getExitValue() != 0) {
+            LOGGER.error("Docker login failed: {}", cmd.getError());
+            return false;
+        }
+
+        return true;
+    }
+
+    /**
+     * Create and run the command line to execute the docker image with optional registry authentication.
+     *
+     * @param image         Docker image name
+     * @param inputBindings Array of bind mounts for docker input volumes (source-target)
+     * @param outputBinding Bind mount for docker output volume (source-target)
+     * @param cmdParams     Image command parameters
+     * @param dockerParams  Docker parameters
+     * @param registry      Docker registry URL
+     * @param username      Optional Docker registry username
+     * @param password      Optional Docker registry password
+     * @return The command line
+     * @throws IOException IO exception
+     */
+    public static String run(String image, List<AbstractMap.SimpleEntry<String, String>> inputBindings,
+                             AbstractMap.SimpleEntry<String, String> outputBinding, String cmdParams,
+                             Map<String, String> dockerParams, String registry, String username, String password) throws IOException {
+        return run(image, inputBindings, outputBinding != null ? Collections.singletonList(outputBinding) : null,
+                cmdParams, dockerParams, registry, username, password);
+    }
 
     /**
      * Create and run the command line to execute the docker image.
@@ -191,8 +243,37 @@ public static String run(String image, List<AbstractMap.SimpleEntry<String, Stri
     public static String run(String image, List<AbstractMap.SimpleEntry<String, String>> inputBindings,
                              List<AbstractMap.SimpleEntry<String, String>> outputBindings, String cmdParams,
                              Map<String, String> dockerParams) throws IOException {
+        return run(image, inputBindings, outputBindings, cmdParams, dockerParams, null, null, null);
+    }
+
+    /**
+     * Create and run the command line to execute the docker image with optional registry authentication.
+     *
+     * @param image         Docker image name
+     * @param inputBindings Array of bind mounts for docker input volumes (source-target)
+     * @param outputBindings Array of bind mount for docker output volume (source-target)
+     * @param cmdParams     Image command parameters
+     * @param dockerParams  Docker parameters
+     * @param registry      Optional Docker registry URL (null if not using private registry)
+     * @param username      Optional Docker registry username
+     * @param password      Optional Docker registry password
+     * @return The command line
+     * @throws IOException IO exception
+     */
+    public static String run(String image, List<AbstractMap.SimpleEntry<String, String>> inputBindings,
+                             List<AbstractMap.SimpleEntry<String, String>> outputBindings, String cmdParams,
+                             Map<String, String> dockerParams, String registry, String username, String password) throws IOException {
+
         checkDockerDaemonAlive();
 
+        // Login to registry if credentials provided
+        if (StringUtils.isNotEmpty(username) && StringUtils.isNotEmpty(password)) {
+            boolean loginSuccess = login(registry, username, password);
+            if (!loginSuccess) {
+                throw new IOException("Failed to authenticate to Dockerhub");
+            }
+        }
+
         String commandLine = buildCommandLine(image, inputBindings, outputBindings, cmdParams, dockerParams);
 
         LOGGER.info("Run docker command line");
@@ -222,7 +303,6 @@ public static String run(String image, List<AbstractMap.SimpleEntry<String, Stri
         return commandLine;
     }
 
-
     public static void checkDockerDaemonAlive() throws IOException {
         int maxAttempts = 12;
         for (int i = 0; i < maxAttempts; i++) {

commons-lib/src/test/java/org/opencb/commons/utils/DockerUtilsTest.java

@@ -3,10 +3,13 @@
 import org.junit.Test;
 
 import java.io.IOException;
+import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
+import static org.junit.Assert.assertTrue;
+
 public class DockerUtilsTest {
 
     @Test
@@ -24,4 +27,31 @@ public void buildMountPathsCommandLine() throws IOException {
 
     }
 
+    @Test
+    public void testDockerLogin() throws IOException {
+        // Skip test if environment variables are not set
+        String registry = System.getenv("DOCKER_REGISTRY_URL");
+        String username = System.getenv("DOCKER_USERNAME");
+        String password = System.getenv("DOCKER_PASSWORD");
+
+        // Skip test if credentials are not provided
+        org.junit.Assume.assumeTrue("Skipping test: Docker credentials not provided in environment variables",
+                org.apache.commons.lang3.StringUtils.isNotEmpty(username) && org.apache.commons.lang3.StringUtils.isNotEmpty(password));
+
+        try {
+            // First, check if docker is available
+            DockerUtils.checkDockerDaemonAlive();
+
+            // Execute private docker image with authentication
+            assertTrue(DockerUtils.login(registry, username, password));
+
+            System.out.println("Successfully logged in");
+
+        } catch (IOException e) {
+            System.err.println("Test failed: " + e.getMessage());
+            throw e;
+        }
+    }
+
+
 }