genevalidatorapp in genevalidatorapp-1.5.4

- old
+ new

@@ -32,10 +32,14 @@
 
     on 'c', 'config_file=',
        'Use the given configuration file',
        argument: true
 
+    on 'g', 'gv_public_dir=',
+       'The public directory that is served to the web application.',
+       argument: true
+
     on 'b', 'bin=',
        'Load BLAST+ and/or MAFFT binaries from this directory',
        argument: true,
        as: Array
 
@@ -109,63 +113,62 @@
       # The aim of following error recovery scenarios is to guide user to a
       # working GeneValidatorApp installation. We expect to land following
       # error scenarios either when creating a new GeneValidatorApp (first
       # time or later), or updating config values using -s CLI option.
 
-      rescue GeneValidatorApp::CONFIG_FILE_ERROR,
-             GeneValidatorApp::BLAST_DATABASE_ERROR => e
+      rescue GeneValidatorApp::CONFIG_FILE_ERROR => e
 
         puts e
         exit!
 
-      rescue GeneValidatorApp::BIN_DIR_NOT_FOUND => e
+      rescue GeneValidatorApp::NUM_THREADS_INCORRECT => e
 
         puts e
 
-        unless bin?
+        unless num_threads?
           puts 'You can set the correct value by running:'
           puts
-          puts '  genevalidatorapp -s -b <value>'
+          puts '  genevalidatorapp -s -n <value>'
           puts
         end
 
         exit!
 
-      rescue GeneValidatorApp::DATABASE_DIR_NOT_FOUND => e
+      rescue GeneValidatorApp::BIN_DIR_NOT_FOUND => e
 
         puts e
 
-        unless database_dir?
+        unless bin?
           puts 'You can set the correct value by running:'
           puts
-          puts '  genevalidatorapp -s -d <value>'
+          puts '  genevalidatorapp -s -b <value>'
           puts
         end
 
         exit!
 
-      rescue GeneValidatorApp::NUM_THREADS_INCORRECT => e
+      rescue GeneValidatorApp::EXTENSION_FILE_NOT_FOUND => e
 
         puts e
 
-        unless num_threads?
+        unless require?
           puts 'You can set the correct value by running:'
           puts
-          puts '  genevalidatorapp -s -n <value>'
+          puts '  genevalidatorapp -s -r <value>'
           puts
         end
 
         exit!
 
-      rescue GeneValidatorApp::EXTENSION_FILE_NOT_FOUND => e
+      rescue GeneValidatorApp::DATABASE_DIR_NOT_FOUND => e
 
         puts e
 
-        unless require?
+        unless database_dir?
           puts 'You can set the correct value by running:'
           puts
-          puts '  genevalidatorapp -s -r <value>'
+          puts '  genevalidatorapp -s -d <value>'
           puts
         end
 
         exit!
 
@@ -198,10 +201,11 @@
           fetch_option(:bin).value = File.join(response)
           puts
           redo
         end
 
+
       rescue GeneValidatorApp::DATABASE_DIR_NOT_SET => e
 
         # Show original error message.
         puts
         puts e
@@ -223,19 +227,24 @@
         puts
         response = Readline.readline('>> ').to_s.strip
         fetch_option(:database_dir).value = response
         redo
 
-      rescue GeneValidatorApp::NO_BLAST_DATABASE_FOUND => e
+      rescue GeneValidatorApp::NO_BLAST_DATABASE_FOUND,
+             GeneValidatorApp::NO_PROTEIN_BLAST_DATABASE_FOUND => e
         unless list_databases?
-
           # Print error raised.
           puts
           puts e
-
+          exit!
         end
 
+      rescue GeneValidatorApp::BLAST_DATABASE_ERROR => e
+
+        puts e
+        exit!
+
       rescue => e
         # This will catch any unhandled error and some very special errors.
         # Ideally we will never hit this block. If we do, there's a bug in
         # GeneValidatorApp or something really weird going on. If we hit this
         # error block we show the stacktrace to the user requesting them to
@@ -248,10 +257,10 @@
 https://github.com/wurmlab/genevalidatorapp/issues
 
 Error:
 #{e.backtrace.unshift(e.message).join("\n")}
 MSG
-        exit
+        exit!
       end
 
       if list_databases?
         puts GeneValidatorApp::Database.all
         exit