Merge pull request #19 from mbhall88/master

Add some catches for passed args

farmpy/lsf.py

@@ -52,10 +52,22 @@
 import subprocess
 import getpass
 import os
+from pathlib import Path
 
 
 class Error (Exception): pass
 
+
+class NoCommandGiven(Exception):
+    """Raised when no command is passed."""
+    pass
+
+
+class DirectoryDoesNotExist(Exception):
+    """Raised when log directory doesn't exist."""
+    pass
+
+
 class Job:
     def __init__(self, out, error, name, queue, mem, cmd,
                  array_start=0, array_end=0,
@@ -235,6 +247,21 @@ def _make_resources_string(self):
 
 
     def _make_output_files_string(self):
+        log_out_dir = Path(self.stdout_file).parent
+        log_err_dir = Path(self.stderr_file).parent
+
+        # make sure the log directories exist
+        if not log_out_dir.exists():
+            raise DirectoryDoesNotExist(
+                "Directory for stdout log does not exist: {}".format(
+                    str(log_out_dir.absolute()))
+            )
+        elif not log_err_dir.exists():
+            raise DirectoryDoesNotExist(
+                "Directory for stderr log does not exist: {}".format(
+                    str(log_err_dir.absolute()))
+            )
+
         if self.array_start > 0:
             return '-o ' + self.stdout_file + '.%I -e ' + self.stderr_file + '.%I'
         else:
@@ -259,6 +286,9 @@ def _make_dependencies_string(self):
 
 
     def _make_command_string(self):
+        if not self.command:
+            raise NoCommandGiven("No command given to run.")
+
         command = ''
 
         if self.checkpoint:

farmpy/tests/lsf_test.py

@@ -99,6 +99,12 @@ def test_make_output_files_string(self):
         self.assertEqual('-o out -e error', bsub._make_output_files_string())
         bsub = lsf.Job('out', 'error', 'name', 'queue', 1, 'cmd', array_start=1, array_end=42)
         self.assertEqual('-o out.%I -e error.%I', bsub._make_output_files_string())
+        bsub = lsf.Job('doesntexist/out', 'error', 'name', 'queue', 1, 'cmd')
+        with self.assertRaises(lsf.DirectoryDoesNotExist):
+            bsub._make_output_files_string()
+        bsub = lsf.Job('out', 'doesntexist/error', 'name', 'queue', 1, 'cmd')
+        with self.assertRaises(lsf.DirectoryDoesNotExist):
+            bsub._make_output_files_string()
 
     def test_make_job_name_string(self):
         '''Check that the name of the job is set correctly'''
@@ -128,6 +134,9 @@ def test_make_command_string(self):
         self.assertEqual('cmd.INDEX', bsub._make_command_string())
         bsub = lsf.Job('out', 'error', 'name', 'queue', 1, 'cmd.INDEX foo bar.INDEX', array_start=1, array_end=42)
         self.assertEqual('cmd.\$LSB_JOBINDEX foo bar.\$LSB_JOBINDEX', bsub._make_command_string())
+        bsub = lsf.Job('out', 'error', 'name', 'queue', 1, '')
+        with self.assertRaises(lsf.NoCommandGiven):
+            bsub._make_command_string()
 
     def test_add_dependency(self):
         bsub = lsf.Job('out', 'error', 'name', 'queue', 1, 'cmd')

setup.py

@@ -4,7 +4,7 @@
 
 setup(
     name='farmpy',
-    version='0.42.0',
+    version='0.42.1',
     description='Package to run farm jobs - currently LSF supported',
     author='Martin Hunt',
     author_email='[email protected]',