Merge pull request #9 from qbicsoftware/feature/update-seek-node

update existing seek nodes and fix stuff

src/main/java/life/qbic/App.java

@@ -1,6 +1,9 @@
 package life.qbic;
 
 import ch.ethz.sis.openbis.generic.OpenBIS;
+import java.util.HashMap;
+import java.util.Map;
+import life.qbic.io.PropertyReader;
 import life.qbic.io.commandline.CommandLineOptions;
 import life.qbic.model.Configuration;
 import life.qbic.model.download.AuthenticationException;
@@ -18,6 +21,7 @@
 public class App {
 
   private static final Logger LOG = LogManager.getLogger(App.class);
+  public static Map<String, String> configProperties = new HashMap<>();
 
   public static void main(String[] args) {
     LOG.debug("command line arguments: " + Arrays.deepToString(args));
@@ -26,6 +30,14 @@ public static void main(String[] args) {
     System.exit(exitCode);
   }
 
+  public static void readConfig() {
+    System.err.println("reading config");
+    String configPath = CommandLineOptions.getConfigPath();
+    if(configPath != null && !configPath.isEmpty()) {
+      configProperties = PropertyReader.getProperties(configPath);
+    }
+  }
+
   /**
    * checks if the commandline parameter for reading out the password from the environment variable
    * is correctly provided
@@ -57,7 +69,9 @@ public static OpenBIS loginToOpenBIS(
       char[] password, String user, String url, String dssUrl) {
     setupLog();
 
-    OpenBIS authentication = new OpenBIS(url, dssUrl);
+    int generousTimeOut = 30*60*1000; //30 mins
+
+    OpenBIS authentication = new OpenBIS(url, dssUrl, generousTimeOut);
 
     return tryLogin(authentication, user, password);
   }

src/main/java/life/qbic/io/PropertyReader.java

@@ -0,0 +1,44 @@
+package life.qbic.io;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.TreeMap;
+
+public class PropertyReader {
+
+    public static TreeMap<String, String> getProperties(String infile) {
+
+      TreeMap<String, String> properties = new TreeMap<>();
+      BufferedReader bfr = null;
+      try {
+        bfr = new BufferedReader(new FileReader(new File(infile)));
+      } catch (FileNotFoundException e) {
+        throw new RuntimeException(e);
+      }
+
+      String line;
+      while (true) {
+        try {
+          if ((line = bfr.readLine()) == null)
+            break;
+        } catch (IOException e) {
+          throw new RuntimeException(e);
+        }
+        if (!line.startsWith("#") && !line.isEmpty()) {
+          String[] property = line.trim().split("=");
+          properties.put(property[0].trim(), property[1].trim());
+        }
+      }
+
+      try {
+        bfr.close();
+      } catch (IOException e) {
+        throw new RuntimeException(e);
+      }
+
+      return(properties);
+    }
+}

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

@@ -17,17 +17,24 @@ public class CommandLineOptions {
 
   private static final Logger LOG = LogManager.getLogger(CommandLineOptions.class);
 
+  @Option(names = {"-config", "--config_file"},
+      description = "Config file path to provide server and user information.",
+      scope = CommandLine.ScopeType.INHERIT)
+  static String configPath;
+
   @Option(names = {"-V", "--version"},
-          versionHelp = true,
-          description = "print version information",
-          scope = CommandLine.ScopeType.INHERIT)
+      versionHelp = true,
+      description = "print version information",
+      scope = CommandLine.ScopeType.INHERIT)
   boolean versionRequested = false;
 
-  @Option(
-          names = {"-h", "--help"},
-          usageHelp = true,
-          description = "display a help message and exit",
-          scope = CommandLine.ScopeType.INHERIT)
+  @Option(names = {"-h", "--help"},
+      usageHelp = true,
+      description = "display a help message and exit",
+      scope = CommandLine.ScopeType.INHERIT)
   public boolean helpRequested = false;
 
+  public static String getConfigPath() {
+    return configPath;
+  }
 }