fix problem in scheduler plugins

Longbow/schedulers/lsf.py

@@ -241,7 +241,7 @@ def submit(job):
             raise exceptions.JobsubmitError(
                 "Something went wrong when submitting. The following output "
                 "came back from the SSH call:\nstdout: {0}\nstderr {1}"
-                .format(shellout[0], shellout[1]))
+                .format(inst.stdout, inst.stderr))
 
     try:
 

Longbow/schedulers/pbs.py

@@ -337,7 +337,7 @@ def submit(job):
             raise exceptions.JobsubmitError(
                 "Something went wrong when submitting. The following output "
                 "came back from the SSH call:\nstdout: {0}\nstderr {1}"
-                .format(shellout[0], shellout[1]))
+                .format(inst.stdout, inst.stderr))
 
     try:
 

Longbow/schedulers/sge.py

@@ -232,7 +232,7 @@ def submit(job):
             raise exceptions.JobsubmitError(
                 "Something went wrong when submitting. The following output "
                 "came back from the SSH call:\nstdout: {0}\nstderr {1}"
-                .format(shellout[0], shellout[1]))
+                .format(inst.stdout, inst.stderr))
 
     try:
 

Longbow/schedulers/slurm.py

@@ -248,7 +248,7 @@ def submit(job):
             raise exceptions.JobsubmitError(
                 "Something went wrong when submitting. The following output "
                 "came back from the SSH call:\nstdout: {0}\nstderr {1}"
-                .format(shellout[0], shellout[1]))
+                .format(inst.stdout, inst.stderr))
 
     try:
 

Longbow/schedulers/soge.py

@@ -250,7 +250,7 @@ def submit(job):
             raise exceptions.JobsubmitError(
                 "Something went wrong when submitting. The following output "
                 "came back from the SSH call:\nstdout: {0}\nstderr {1}"
-                .format(shellout[0], shellout[1]))
+                .format(inst.stdout, inst.stderr))
 
     try:
 

Tests/unit/schedulers_pbs/test_submit1.py

@@ -0,0 +1,56 @@
+
+# Longbow is Copyright (C) of James T Gebbie-Rayet and Gareth B Shannon 2015.
+#
+# This file is part of the Longbow software which was developed as part of the
+# HECBioSim project (http://www.hecbiosim.ac.uk/).
+#
+# HECBioSim facilitates and supports high-end computing within the UK
+# biomolecular simulation community on resources such as ARCHER.
+#
+# Longbow is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 2 of the License, or (at your option) any later
+# version.
+#
+# Longbow is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# Longbow.  If not, see <http://www.gnu.org/licenses/>.
+
+"""
+This test module contains tests for the PBS scheduler plugin.
+"""
+
+try:
+
+    from unittest import mock
+
+except ImportError:
+
+    import mock
+
+import pytest
+
+import Longbow.corelibs.exceptions as exceptions
+import Longbow.schedulers.pbs as pbs
+
+
+@mock.patch('Longbow.corelibs.shellwrappers.sendtossh')
+def test_submit_except1(mock_ssh):
+
+    """
+    """
+
+    job = {
+        "destdir": "/path/to/destdir",
+        "subfile": "submit.file"
+    }
+
+    mock_ssh.side_effect = exceptions.SSHError("Error", ("out", "err", 0))
+    mock_ssh.return_value = ("success", "error", 0)
+
+    with pytest.raises(exceptions.JobsubmitError):
+
+        pbs.submit(job)