Allow error messages to propagate through pipes

The Buddy modules will now detect a traceback and simply print it out and exit, instead of trying to otherwise process the input.
biologyguy · Feb 3, 2017 · f68ce05 · f68ce05
1 parent 0c3971f
commit f68ce05
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Showing 3 changed files with 15 additions and 3 deletions.
diff --git a/buddysuite/AlignBuddy.py b/buddysuite/AlignBuddy.py
@@ -90,7 +90,11 @@ def __init__(self, _input, in_format=None, out_format=None):
         # Handles
         if str(type(_input)) == "<class '_io.TextIOWrapper'>":
             if not _input.seekable():  # Deal with input streams (e.g., stdout pipes)
-                temp = StringIO(br.utf_encode(_input.read()))
+                input_txt = _input.read()
+                if re.search("Buddy::.* has crashed with the following traceback", input_txt):
+                    print(input_txt)
+                    sys.exit()
+                temp = StringIO(br.utf_encode(input_txt))
                 _input = temp
             _input.seek(0)
             in_handle = _input.read()

diff --git a/buddysuite/PhyloBuddy.py b/buddysuite/PhyloBuddy.py
@@ -167,7 +167,11 @@ def __init__(self, _input, _in_format=None, _out_format=None):
         # Handles
         if str(type(_input)) == "<class '_io.TextIOWrapper'>":
             if not _input.seekable():  # Deal with input streams (e.g., stdout pipes)
-                temp = StringIO(br.utf_encode(_input.read()))
+                input_txt = _input.read()
+                if re.search("Buddy::.* has crashed with the following traceback", input_txt):
+                    print(input_txt)
+                    sys.exit()
+                temp = StringIO(br.utf_encode(input_txt))
                 _input = temp
             _input.seek(0)
             in_from_handle = _input.read()

diff --git a/buddysuite/SeqBuddy.py b/buddysuite/SeqBuddy.py
@@ -185,7 +185,11 @@ def __init__(self, sb_input, in_format=None, out_format=None, alpha=None):
         # Handles
         if str(type(sb_input)) == "<class '_io.TextIOWrapper'>":
             if not sb_input.seekable():  # Deal with input streams (e.g., stdout pipes)
-                temp = StringIO(br.utf_encode(sb_input.read()))
+                input_txt = sb_input.read()
+                if re.search("Buddy::.* has crashed with the following traceback", input_txt):
+                    print(input_txt)
+                    sys.exit()
+                temp = StringIO(br.utf_encode(input_txt))
                 sb_input = temp
             sb_input.seek(0)
             in_handle = sb_input.read()