add parameters

src/main/java/es/bsc/inb/elixir/biotools/git/populous/Main.java

@@ -55,14 +55,15 @@ import org.eclipse.jgit.util.SystemReader;
 public class Main {
     
     private final static String HELP = 
-            "java -jar biotools-populouse.jar -g -u -p [-b] [--path]\n\n" +
+            "java -jar biotools-populouse.jar -g -u -p [-b] [--path] [--dirs]\n\n" +
             "parameters:\n\n" +
             "-h (--help)                - this help message\n" +
             "-g (--git)                 - git endpoint\n" +
             "-u (--user) 'username'     - github username\n" +
             "-p (--password) 'password' - github pasword\n" +
             "-b (--branch)              - git remote branch ['origin/master']\n" +
-            "--path                     - git path to put files ['/']\n\n" +
+            "--path                     - git path to put files ['/']\n" +
+            "--dirs                     - if present, put each tool into its own directory \n\n" +
             "example: >java -jar biotools-populous.jar -g https://github.com/xyz.git --path /biotools -u redmitry -p xyz\n";
 
     public final static String BRANCH = "origin/master";
@@ -83,6 +84,8 @@ public class Main {
         }
 
         final List<String> path = params.get("--path");
+        final List<String> suffix = params.get("--suffix");
+        final String sfx = suffix == null || suffix.isEmpty() ? ".opeb.json" : suffix.get(0);
         
         List<String> user = params.get("-u");
         if (user == null) {
@@ -108,12 +111,13 @@ public class Main {
             final String b = branch == null || branch.isEmpty() ? null : branch.get(0);
             
             process(g, b != null ? b : BRANCH, 
-                    path == null || path.isEmpty() ? "/" : path.get(0), u, p);
+                    path == null || path.isEmpty() ? "/" : path.get(0), 
+                    params.get("--dirs") != null, sfx, u, p);
         }
     }
     
     private static void process(final String endpoint, final String branch, final String path,
-            final String user, final String password) {
+            final boolean dirs, final String suffix, final String user, final String password) {
         
         final int idx = branch.lastIndexOf('/');
         final String local = idx < 0 ? branch : branch.substring(idx + 1);
@@ -126,7 +130,7 @@ public class Main {
                                     .build();
 
         final FileSystem fs = Jimfs.newFileSystem(config);
-        final Path root = fs.getPath(path);
+        final Path root = fs.getPath("/");
         
         try (Git git = Git.cloneRepository()
                          .setURI(endpoint)
@@ -144,10 +148,18 @@ public class Main {
 
                 final Tool tool = BiotoolsConverter.convert(jtool);
                 
-                final String _id = tool.getSummary().getToolID().trim();
+                final String _id = tool.getSummary().getToolID().trim().toLowerCase();
                 
-                final String file_name = _id + ".json";
-                final Path file_path = root.resolve(file_name);
+                final Path dir = dirs ? root.resolve(path).resolve(_id) : root.resolve(path);
+                if (!Files.exists(dir)) {
+                    try {
+                        Files.createDirectories(dir);
+                    } catch(IOException ex) {
+                         Logger.getLogger(Main.class.getName()).log(Level.SEVERE, "can't create dir: " + dir, ex.getMessage());
+                    }
+                }
+
+                final Path file_path = dir.resolve(_id + suffix);
 
                 try (Writer writer = Files.newBufferedWriter(file_path)) {
                     jsonb.toJson(tool, writer);
@@ -155,7 +167,7 @@ public class Main {
                     Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
                 }
             }
-            
+
             git.add().addFilepattern(".").call();
             git.commit().setMessage("biotools commit " + Instant.now()).call();
             git.push().setRemote(branch).setCredentialsProvider(
@@ -179,6 +191,8 @@ public class Main {
                 case "-b":
                 case "--branch":
                 case "--path":
+                case "--dirs":
+                case "--suffix":
                 case "-u":
                 case "--user":
                 case "-p":