From 883f63aa1e915db5f0a2e5ee912a1c00e49d8bca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20G=C3=B6ransson?= <github@mgor.se>
Date: Mon, 13 Apr 2015 19:14:38 +0200
Subject: [PATCH] Added parameter '--throw-exception', which can not be
 specified togheter with '--rna', that will remove the catch-exception code
 added the epilogue code if '--rna' isn't specified.

This feature, in combination with using Popen() instead of call(), will make it possible to catch errors in the RNA code,
when not specifying '--rna', which otherwise would go unnoticed.
---
 ribosome.py | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/ribosome.py b/ribosome.py
index bfd5ab8..c330e49 100755
--- a/ribosome.py
+++ b/ribosome.py
@@ -308,7 +308,9 @@ def rethrow(e, rnafile, linemap):
 parser = argparse.ArgumentParser(
     version = "ribosome code generator, version 1.14")
 parser.add_argument('dna', type=file)
-parser.add_argument('--rna', action='store_true')
+group = parser.add_mutually_exclusive_group()
+group.add_argument('--rna', action='store_true')
+group.add_argument('--throw-exception', action='store_true')
 
 # Pwd
 __dir__ = os.path.dirname(os.path.realpath(__file__))
@@ -353,7 +355,7 @@ def rnawrite(s):
 
 # Generate RNA Prologue code
 rnawrite(PROLOGUE)
-if not args.rna:
+if not args.rna and not args.throw_exception:
     rnawrite('try:\n')
 
 # Process the DNA file.
@@ -388,7 +390,7 @@ def rnawrite(s):
     # Lets save the left and right spaces, if any
     lspace = line.replace(line.lstrip(), '')
     # Add 4 spaces to accommodate our try except clause if not rna
-    if not args.rna:
+    if not args.rna and not args.throw_exception:
         lspace = lspace + ' ' * 4
     rspace = line.replace(line.rstrip(), '')
     # followed by stripping the line
@@ -477,7 +479,7 @@ def rnawrite(s):
 # Generate RNA epilogue code.
 dnastack = [[None, 'ribosome', __line__() + 1]]
 rna.write('\n')
-if not args.rna:
+if not args.rna and not args.throw_exception:
     rna.write('except Exception as e:\n')
     rna.write('    LINEMAP = [\n')
     last = None
@@ -501,7 +503,17 @@ def rnawrite(s):
 if not args.rna:
     import subprocess
     # Execute the RNA file. Pass it any arguments not used by ribosome.
-    subprocess.call(['python', rnafile] + sys.argv[2:])
+    pipes = subprocess.Popen(['python', rnafile] + sys.argv[2:], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    stdout, stderr = pipes.communicate()
+
+    # Print generated RNA file contents 
+    sys.stdout.write(stdout)
+
     # Delete the RNA file.
     os.remove(rnafile)
 
+    # If there was an error in the RNA file, print the error and exit with a non-zero status
+    if args.throw_exception and stderr is not None and len(stderr) > 0:
+	sys.stderr.write(stderr)
+        sys.exit(1)
+