Merge pull request #8 from qbicsoftware/feature/transfer-to-seek

Feature/transfer to seek
qbicsoftware · Oct 7, 2024 · bd16a56 · bd16a56
2 parents 7b20a9c + a87fed8
commit bd16a56
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Showing 24 changed files with 2,608 additions and 54 deletions.
diff --git a/src/main/java/life/qbic/io/commandline/AuthenticationOptions.java b/src/main/java/life/qbic/io/commandline/AuthenticationOptions.java
@@ -8,6 +8,8 @@
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.StringJoiner;
 import java.util.TreeMap;
 import org.apache.logging.log4j.LogManager;
@@ -23,26 +25,32 @@ 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"},
-      description = "ApplicationServer URL",
+      description = "OpenBIS ApplicationServer URL",
       scope = CommandLine.ScopeType.INHERIT)
   private String as_url;
 
   @Option(
-      names = {"-dss", "-dss_url"},
-      description = "DatastoreServer URL",
+      names = {"-dss", "--dss_url"},
+      description = "OpenBIS 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",
@@ -52,45 +60,76 @@ 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;
   }
 
-  public String getDSS() {
+  public String getOpenbisDSS() {
     if(dss_url == null & configPath!=null && !configPath.isBlank()) {
       dss_url = ReadProperties.getProperties(configPath).get("dss");
     }
     return dss_url;
   }
 
-  public String getAS() {
+  public String getOpenbisAS() {
     if(as_url == null & configPath!=null && !configPath.isBlank()) {
       as_url = ReadProperties.getProperties(configPath).get("as");
     }
     return as_url;
   }
 
+  public char[] getSeekPassword() {
+    return seekPasswordOptions.getPassword();
+  }
+
   public char[] getOpenbisPassword() {
     return openbisPasswordOptions.getPassword();
   }
 
+  public String getOpenbisBaseURL() throws MalformedURLException {
+    URL asURL = new URL(as_url);
+    String res = asURL.getProtocol()+ "://" +asURL.getHost();
+    if(asURL.getPort()!=-1) {
+      res+=":"+asURL.getPort();
+    }
+    System.err.println(res);
+    return res;
+  }
+
   /**
    * <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 +155,43 @@ 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() + "[", "]")

diff --git a/src/main/java/life/qbic/io/commandline/CommandLineOptions.java b/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, TransferSampleTypesToSeekCommand.class,
+        DownloadPetabCommand.class, UploadPetabResultCommand.class, UploadDatasetCommand.class,
+        SpaceStatisticsCommand.class, TransferDataToSeekCommand.class, FindDatasetsCommand.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"},

diff --git a/src/main/java/life/qbic/io/commandline/DownloadPetabCommand.java b/src/main/java/life/qbic/io/commandline/DownloadPetabCommand.java
@@ -27,7 +27,7 @@ public class DownloadPetabCommand implements Runnable {
 
     @Override
     public void run() {
-      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS(), auth.getDSS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getOpenbisAS(), auth.getOpenbisDSS());
       OpenbisConnector openbis = new OpenbisConnector(authentication);
 
       List<DataSet> datasets = openbis.findDataSets(Collections.singletonList(datasetCode));

diff --git a/src/main/java/life/qbic/io/commandline/FindDatasetsCommand.java b/src/main/java/life/qbic/io/commandline/FindDatasetsCommand.java
@@ -39,7 +39,7 @@ public void run() {
       } else {
         System.out.println("Querying experiment in all available spaces...");
       }
-      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getOpenbisAS());
       OpenbisConnector openbis = new OpenbisConnector(authentication);
       List<DataSet> datasets = openbis.listDatasetsOfExperiment(spaces, experimentCode).stream()
           .sorted(Comparator.comparing(

diff --git a/src/main/java/life/qbic/io/commandline/SampleHierarchyCommand.java b/src/main/java/life/qbic/io/commandline/SampleHierarchyCommand.java
@@ -43,7 +43,7 @@ public void run() {
         } else {
           summary.add("Querying samples in all available spaces...");
         }
-        OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS());
+        OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getOpenbisAS());
         OpenbisConnector openbis = new OpenbisConnector(authentication);
         Map<SampleTypeConnection, Integer> hierarchy = openbis.queryFullSampleHierarchy(spaces);
 

diff --git a/src/main/java/life/qbic/io/commandline/SpaceStatisticsCommand.java b/src/main/java/life/qbic/io/commandline/SpaceStatisticsCommand.java
@@ -50,7 +50,7 @@ public void run() {
       } else {
         summary.add("Querying samples in all available spaces...");
       }
-      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getOpenbisAS());
       OpenbisConnector openbis = new OpenbisConnector(authentication);
 
       if (spaces.isEmpty()) {