From ed55c1a7888b1b026851720dfccae4bd538a0b62 Mon Sep 17 00:00:00 2001
From: Dominic Fitzgerald <djf604@truman.edu>
Date: Fri, 23 Mar 2018 13:05:45 -0500
Subject: [PATCH] Better error if config is malformed

---
 operon/_cli/__init__.py              | 2 +-
 operon/_cli/_completer.py            | 2 +-
 operon/_cli/subcommands/configure.py | 4 ++--
 operon/_util/__init__.py             | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/operon/_cli/__init__.py b/operon/_cli/__init__.py
index c416104..7ddb39f 100644
--- a/operon/_cli/__init__.py
+++ b/operon/_cli/__init__.py
@@ -12,7 +12,7 @@ def get_operon_subcommands(classes=False):
         ]
     ]
     if not classes:
-        return operon_subcommands
+        return [o.replace('_', '-') for o in operon_subcommands]
 
     return {
         operon_subcommand: fetch_subcommand_class(operon_subcommand)
diff --git a/operon/_cli/_completer.py b/operon/_cli/_completer.py
index 288b3f7..6eadb89 100644
--- a/operon/_cli/_completer.py
+++ b/operon/_cli/_completer.py
@@ -46,7 +46,7 @@ def completer():
             stub=stub_token
         )
     elif num_completed_tokens == 2:
-        if phrase[-2] in {'run', 'configure', 'show', 'uninstall'}:
+        if phrase[-2] in {'run', 'batch-run', 'configure', 'show', 'uninstall'}:
             completion_options = get_completion_options(
                 options=get_pipeline_options(),
                 stub=stub_token
diff --git a/operon/_cli/subcommands/configure.py b/operon/_cli/subcommands/configure.py
index cb0bfcd..a4e0831 100644
--- a/operon/_cli/subcommands/configure.py
+++ b/operon/_cli/subcommands/configure.py
@@ -274,8 +274,8 @@ def run(self, subcommand_args):
             except (KeyboardInterrupt, EOFError):
                 sys.stderr.write('\nUser aborted configuration.\n')
                 sys.exit(EXIT_CMD_SUCCESS)
-            except AttributeError:
-                raise MalformedPipelineConfigError('Something about the configuration is malformed')
+            except AttributeError as e:
+                raise MalformedPipelineConfigError('Something about the configuration is malformed: {}'.format(e))
 
             # Write config out to file
             try:
diff --git a/operon/_util/__init__.py b/operon/_util/__init__.py
index cec5cc2..ad2db21 100644
--- a/operon/_util/__init__.py
+++ b/operon/_util/__init__.py
@@ -37,7 +37,7 @@ def execute_from_command_line(argv=None):
             parser.print_help()
             sys.exit(0)
         try:
-            operon_subcommand_classes[subcommand].run(argv[2:])
+            operon_subcommand_classes[subcommand.replace('-', '_')].run(argv[2:])
         except Exception as e:
             sys.stderr.write('Operon encountered an error when trying to execute {}:\n'.format(subcommand))
             sys.stderr.write(str(e) + '\n')