Test for schedulers

Test files for each plugin and methods apart from the prepare method
Some minor fixes for problems that arose from testing

Longbow/corelibs/entrypoints.py

@@ -561,9 +561,9 @@ def main():
                  "Lightweight Remote Job Submission Tool. Journal of "
                  "Open Research Software, 4: e1, "
                  "DOI: http://dx.doi.org/10.5334/jors.95")
-        LOG.info("Python version: {0}".format(PYTHONVERSION))
-        LOG.info("Longbow version: {0}".format(LONGBOWVERSION))
-        LOG.info("Longbow Commandline: {0}".format(commandline))
+        LOG.info("Python version: %s", PYTHONVERSION)
+        LOG.info("Longbow version: %s", LONGBOWVERSION)
+        LOG.info("Longbow Commandline: %s", commandline)
 
         # Hosts - if a filename hasn't been provided default to hosts.conf
         if parameters["hosts"] is "":
@@ -640,7 +640,7 @@ def main():
                     .format(parameters["job"], os.getcwd(),
                             os.path.dirname(os.path.realpath(__file__))))
 
-        LOG.info("hosts file is: '{0}'".format(parameters["hosts"]))
+        LOG.info("hosts file is: '%s'", parameters["hosts"])
 
         # ---------------------------------------------------------------------
         # Call one of the main methods at the top level of the library.
@@ -795,7 +795,7 @@ def recovery(recoveryfile):
     # Load the jobs recovery file.
     if os.path.isfile(jobfile):
 
-        LOG.info("Recovery file found at '{0}'".format(jobfile))
+        LOG.info("Recovery file found at '%s'", jobfile)
 
         _, _, jobs = configuration.loadconfigs(jobfile)
 

Longbow/corelibs/exceptions.py

@@ -214,21 +214,6 @@ def __init__(self, message, path):
         self.path = path
 
 
-class ProtocolError(Exception):
-
-    """
-    Unknown protocol exception.
-    """
-
-    def __init__(self, message, protocol):
-
-        # Call the base class constructor.
-        super(ProtocolError, self).__init__(message)
-
-        # Bind the standard outputs.
-        self.path = protocol
-
-
 class RemotecopyError(Exception):
 
     """

Longbow/schedulers/lsf.py

@@ -75,18 +75,16 @@ def prepare(job):
     # Write the PBS script
     jobfile.write("#!/bin/bash --login\n")
 
-    if job["jobname"] is not "":
-
-        # Single job
-        if int(job["replicates"]) == 1:
+    # Single job
+    if int(job["replicates"]) == 1:
 
-            jobfile.write("#BSUB -J " + job["jobname"] + "\n")
+        jobfile.write("#BSUB -J " + job["jobname"] + "\n")
 
-        # Job array
-        elif int(job["replicates"]) > 1:
+    # Job array
+    elif int(job["replicates"]) > 1:
 
-            jobfile.write("#BSUB -J " + job["jobname"] + "[1-" +
-                          job["replicates"] + "]\n")
+        jobfile.write("#BSUB -J " + job["jobname"] + "[1-" +
+                      job["replicates"] + "]\n")
 
     if job["queue"] is not "":
 
@@ -205,9 +203,14 @@ def status(job):
 
         # Now match the jobid against the list of jobs, extract the line and
         # split it into a list
-        job = [line for line in stdout if job["jobid"] in line][0].split()
+        for line in stdout:
+
+            line = line.split()
+
+            if job["jobid"] in line[0]:
 
-        jobstate = states[job[2]]
+                jobstate = states[line[2]]
+                break
 
     except (IndexError, KeyError):
 

Longbow/schedulers/pbs.py

@@ -84,9 +84,7 @@ def prepare(job):
     jobfile.write("#!/bin/bash --login\n")
 
     # Job name (if supplied)
-    if job["jobname"] is not "":
-
-        jobfile.write("#PBS -N " + job["jobname"] + "\n")
+    jobfile.write("#PBS -N " + job["jobname"] + "\n")
 
     # Queue to submit to (if supplied)
     if job["queue"] is not "":
@@ -251,12 +249,14 @@ def status(job):
 
     try:
 
-        # Now match the jobid against the list of jobs, extract the line and
-        # split it into a list
-        job = [line for line in stdout if job["jobid"] in line][0].split()
+        for line in stdout:
+
+            line = line.split()
+
+            if job["jobid"] in line[0]:
 
-        # Look up the job state and convert it to Longbow terminology.
-        jobstate = states[job[9]]
+                jobstate = states[line[9]]
+                break
 
     except (IndexError, KeyError):
 
@@ -280,7 +280,7 @@ def submit(job):
 
     except exceptions.SSHError as inst:
 
-        if "would exceed" and "per-user limit" in inst.stderr:
+        if "would exceed" in inst.stderr and "per-user limit" in inst.stderr:
 
             raise exceptions.QueuemaxError
 

Longbow/schedulers/sge.py

@@ -76,9 +76,7 @@ def prepare(job):
     jobfile.write("#!/bin/bash --login\n"
                   "#$ -cwd -V\n")
 
-    if job["jobname"] is not "":
-
-        jobfile.write("#$ -N " + job["jobname"] + "\n")
+    jobfile.write("#$ -N " + job["jobname"] + "\n")
 
     if job["queue"] is not "":
 
@@ -196,9 +194,14 @@ def status(job):
 
         # Now match the jobid against the list of jobs, extract the line and
         # split it into a list
-        job = [line for line in stdout if job["jobid"] in line][0].split()
+        for line in stdout:
+
+            line = line.split()
+
+            if job["jobid"] in line[0]:
 
-        jobstate = states[job[4]]
+                jobstate = states[line[4]]
+                break
 
     except (IndexError, KeyError):
 
@@ -223,7 +226,7 @@ def submit(job):
 
     except exceptions.SSHError as inst:
 
-        if "per user" or "per-user" in inst.stderr:
+        if "per user" in inst.stderr or "per-user" in inst.stderr:
 
             raise exceptions.QueuemaxError
 

Longbow/schedulers/slurm.py

@@ -76,10 +76,7 @@ def prepare(job):
     # Write the SLURM script
     jobfile.write("#!/bin/bash --login\n")
 
-    # Job name (if supplied)
-    if job["jobname"] is not "":
-
-        jobfile.write("#SBATCH -J " + job["jobname"] + "\n")
+    jobfile.write("#SBATCH -J " + job["jobname"] + "\n")
 
     # Queue to submit to (if supplied)
     if job["queue"] is not "":
@@ -212,9 +209,14 @@ def status(job):
 
         # Now match the jobid against the list of jobs, extract the line and
         # split it into a list
-        job = [line for line in stdout if job["jobid"] in line][0].split()
+        for line in stdout:
+
+            line = line.split()
+
+            if job["jobid"] in line[0]:
 
-        jobstate = states[job[4]]
+                jobstate = states[line[4]]
+                break
 
     except (IndexError, KeyError):
 
@@ -239,7 +241,7 @@ def submit(job):
 
     except exceptions.SSHError as inst:
 
-        if "violates" and "job submit limit" in inst.stderr:
+        if "violates" in inst.stderr and "job submit limit" in inst.stderr:
 
             raise exceptions.QueuemaxError
 

Longbow/schedulers/soge.py

@@ -78,9 +78,7 @@ def prepare(job):
     jobfile.write("#!/bin/bash --login\n"
                   "#$ -cwd -V\n")
 
-    if job["jobname"] is not "":
-
-        jobfile.write("#$ -N " + job["jobname"] + "\n")
+    jobfile.write("#$ -N " + job["jobname"] + "\n")
 
     if job["queue"] is not "":
 
@@ -214,9 +212,14 @@ def status(job):
 
         # Now match the jobid against the list of jobs, extract the line and
         # split it into a list
-        job = [line for line in stdout if job["jobid"] in line][0].split()
+        for line in stdout:
+
+            line = line.split()
+
+            if job["jobid"] in line[0]:
 
-        jobstate = states[job[4]]
+                jobstate = states[line[4]]
+                break
 
     except (IndexError, KeyError):
 
@@ -241,7 +244,7 @@ def submit(job):
 
     except exceptions.SSHError as inst:
 
-        if "per user" or "per-user" in inst.stderr:
+        if "per user" in inst.stderr or "per-user" in inst.stderr:
 
             raise exceptions.QueuemaxError
 

Tests/unit/schedulers_pbs/test_lsf_delete.py

@@ -0,0 +1,78 @@
+# 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 LSF scheduler plugin.
+"""
+
+try:
+
+    from unittest import mock
+
+except ImportError:
+
+    import mock
+
+import pytest
+
+import Longbow.corelibs.exceptions as exceptions
+import Longbow.schedulers.lsf as lsf
+
+
+@mock.patch('Longbow.corelibs.shellwrappers.sendtossh')
+def test_delete_test1(mock_ssh):
+
+    """
+    Test if job id is grabbed.
+    """
+
+    job = {
+        "jobid": "12345",
+        "replicates": "1"
+    }
+
+    mock_ssh.return_value = ("Success", "", 0)
+
+    output = lsf.delete(job)
+
+    args = mock_ssh.call_args[0][1]
+
+    assert output == "Success"
+    assert " ".join(args) == "bkill 12345"
+
+
+@mock.patch('Longbow.corelibs.shellwrappers.sendtossh')
+def test_delete_except1(mock_ssh):
+
+    """
+    Test if Queuemax exception is triggered based on output from scheduler.
+    """
+
+    job = {
+        "jobid": "12345",
+        "replicates": "1"
+    }
+
+    mock_ssh.side_effect = exceptions.SSHError(
+        "Error", ("out", "", 0))
+
+    with pytest.raises(exceptions.JobdeleteError):
+
+        lsf.delete(job)