wip

src/main/java/life/qbic/io/commandline/AuthenticationOptions.java

@@ -23,7 +23,9 @@ public class AuthenticationOptions {
       description = "openBIS user name")
   private String openbisUser;
   @ArgGroup(multiplicity = "1") // ensures the password is provided once with at least one of the possible options.
-  PasswordOptions openbisPasswordOptions;
+  OpenbisPasswordOptions openbisPasswordOptions;
+  @ArgGroup(multiplicity = "1")
+  SeekPasswordOptions seekPasswordOptions;
 
   @Option(
       names = {"-as", "-as_url"},
@@ -32,17 +34,21 @@ public class AuthenticationOptions {
   private String as_url;
 
   @Option(
-      names = {"-dss", "-dss_url"},
+      names = {"-dss", "--dss_url"},
       description = "DatastoreServer URL",
       scope = CommandLine.ScopeType.INHERIT)
   private String dss_url;
 
   @Option(
-      names = {"-config", "-config_file"},
-      description = "Config file path to provide openbis server information.",
+      names = {"-config", "--config_file"},
+      description = "Config file path to provide server and user information.",
       scope = CommandLine.ScopeType.INHERIT)
   public String configPath;
-
+  @Option(
+      names = {"-su", "--seek-user"},
+      description = "Seek user name (email)",
+      scope = CommandLine.ScopeType.INHERIT)
+  private String seekUser;
   @Option(
       names = {"-seek-server", "-seek_url"},
       description = "SEEK API URL",
@@ -52,13 +58,30 @@ public class AuthenticationOptions {
   public String getOpenbisUser() {
     if(openbisUser == null & configPath!=null && !configPath.isBlank()) {
       openbisUser = ReadProperties.getProperties(configPath).get("user");
+    } else {
+      log.error("No openBIS user provided.");
+      System.exit(2);
     }
     return openbisUser;
   }
 
+  public String getSeekUser() {
+    if(seekUser == null & configPath!=null && !configPath.isBlank()) {
+      seekUser = ReadProperties.getProperties(configPath).get("seek_user");
+    } else {
+      log.error("No SEEK user/email provided.");
+      System.exit(2);
+    }
+    return seekUser;
+  }
+
   public String getSeekURL() {
-    log.error("No URL to the SEEK address provided.");
-    System.exit(2);
+    if(seek_url == null & configPath!=null && !configPath.isBlank()) {
+      seek_url = ReadProperties.getProperties(configPath).get("seek_url");
+    } else {
+      log.error("No URL to the SEEK address provided.");
+      System.exit(2);
+    }
     return seek_url;
   }
 
@@ -76,21 +99,25 @@ public String getAS() {
     return as_url;
   }
 
+  public char[] getSeekPassword() {
+    return seekPasswordOptions.getPassword();
+  }
+
   public char[] getOpenbisPassword() {
     return openbisPasswordOptions.getPassword();
   }
 
   /**
    * <a href="https://picocli.info/#_optionally_interactive">official picocli documentation example</a>
    */
-  static class PasswordOptions {
-    @Option(names = "--password:env", arity = "1", paramLabel = "<environment-variable>", description = "provide the name of an environment variable to read in your password from")
+  static class OpenbisPasswordOptions {
+    @Option(names = "--openbis-pw:env", arity = "1", paramLabel = "<environment-variable>", description = "provide the name of an environment variable to read in your password from")
     protected String passwordEnvironmentVariable = "";
 
-    @Option(names = "--password:prop", arity = "1", paramLabel = "<system-property>", description = "provide the name of a system property to read in your password from")
+    @Option(names = "--openbis-pw:prop", arity = "1", paramLabel = "<system-property>", description = "provide the name of a system property to read in your password from")
     protected String passwordProperty = "";
 
-    @Option(names = "--password", arity = "0", description = "please provide your password", interactive = true)
+    @Option(names = "--openbis-pw", arity = "0", description = "please provide your openBIS password", interactive = true)
     protected char[] password = null;
 
     /**
@@ -116,9 +143,43 @@ char[] getPassword() {
       System.exit(2);
       return null; // not reachable due to System.exit in previous line
     }
-
   }
 
+  static class SeekPasswordOptions {
+    @Option(names = "--seek-pw:env", arity = "1", paramLabel = "<environment-variable>", description = "provide the name of an environment variable to read in your password from")
+    protected String passwordEnvironmentVariable = "";
+
+    @Option(names = "--seek-pw:prop", arity = "1", paramLabel = "<system-property>", description = "provide the name of a system property to read in your password from")
+    protected String passwordProperty = "";
+
+    @Option(names = "--seek-pw", arity = "0", description = "please provide your SEEK password", interactive = true)
+    protected char[] password = null;
+
+    /**
+     * Gets the password. If no password is provided, the program exits.
+     * @return the password provided by the user.
+     */
+    char[] getPassword() {
+      if (nonNull(password)) {
+        return password;
+      }
+      // System.getProperty(String key) does not work for empty or blank keys.
+      if (!passwordProperty.isBlank()) {
+        String systemProperty = System.getProperty(passwordProperty);
+        if (nonNull(systemProperty)) {
+          return systemProperty.toCharArray();
+        }
+      }
+      String environmentVariable = System.getenv(passwordEnvironmentVariable);
+      if (nonNull(environmentVariable) && !environmentVariable.isBlank()) {
+        return environmentVariable.toCharArray();
+      }
+      log.error("No password provided. Please provide your password.");
+      System.exit(2);
+      return null; // not reachable due to System.exit in previous line
+    }
+
+  }
   @Override
   public String toString() {
     return new StringJoiner(", ", AuthenticationOptions.class.getSimpleName() + "[", "]")

src/main/java/life/qbic/io/commandline/CommandLineOptions.java

@@ -8,11 +8,13 @@
 
 // main command with format specifiers for the usage help message
 @Command(name = "openbis-scripts",
-        subcommands = { SampleHierarchyCommand.class, FindDatasetsCommand.class, DownloadPetabCommand.class,
-            UploadPetabResultCommand.class, UploadDatasetCommand.class, SpaceStatisticsCommand.class },
-        description = "A client software for querying openBIS.",
-        mixinStandardHelpOptions = true, versionProvider = ManifestVersionProvider.class)
+    subcommands = {SampleHierarchyCommand.class, FindDatasetsCommand.class,
+        DownloadPetabCommand.class, UploadPetabResultCommand.class, UploadDatasetCommand.class,
+        SpaceStatisticsCommand.class, TransferDataToSeekCommand.class},
+    description = "A client software for querying openBIS.",
+    mixinStandardHelpOptions = true, versionProvider = ManifestVersionProvider.class)
 public class CommandLineOptions {
+
   private static final Logger LOG = LogManager.getLogger(CommandLineOptions.class);
 
   @Option(names = {"-V", "--version"},