Merge branch 'bf/fslsub' into 'master'

Bf/fslsub

See merge request fsl/fslpy!207

CHANGELOG.rst

@@ -55,6 +55,7 @@ Fixed
 * Updated the :func:`.prepareArgs` function to use ``shlex.split`` when
   preparing shell command arguments, instead of performing a naive whitespace
   split.
+* Fixed some bugs in the :func:`.fslsub.info` function.
 
 
 2.8.4 (Monday 2nd March 2020)

fsl/utils/fslsub.py

@@ -40,8 +40,7 @@ Example usage, building a short pipeline::
 """
 
 
-from six import string_types, BytesIO
-import subprocess as sp
+from six import BytesIO
 import os.path as op
 import glob
 import time
@@ -149,8 +148,9 @@ def info(job_id):
     :return:     dictionary with information on the submitted job (empty
                  if job does not exist)
     """
+    from fsl.utils.run import run
     try:
-        result = sp.call(['qstat', '-j', job_id]).decode('utf-8')
+        result = run(['qstat', '-j', job_id])
     except FileNotFoundError:
         log.debug("qstat not found; assuming not on cluster")
         return {}
@@ -158,7 +158,7 @@ def info(job_id):
         return {}
     res = {}
     for line in result.splitlines()[1:]:
-        key, value = line.split(':', nsplit=1)
+        key, value = line.split(':', 1)
         res[key.strip()] = value.strip()
     return res
 

tests/test_fslsub.py

@@ -102,6 +102,29 @@ def test_submit():
         assert stderr.strip() == 'standard error'
 
 
+def test_info():
+    mock_qstat = tw.dedent("""
+    #!/usr/bin/env bash
+    echo "#####################"
+    echo "job_number:        1 "
+    echo "exec_file:         2 "
+    echo "submission_time:   3 "
+    echo "owner:             4 "
+    """).strip()
+
+    with mockFSLDIR() as fsldir:
+        qstatbin = op.join(fsldir, 'bin', 'qstat')
+        with open(qstatbin, 'wt') as f:
+            f.write(mock_qstat)
+        os.chmod(qstatbin, 0o755)
+
+        exp = {'job_number'      : '1',
+               'exec_file'       : '2',
+               'submission_time' : '3',
+               'owner'           : '4'}
+        assert fslsub.info('12345') == exp
+
+
 def myfunc():
     print('standard output')
     print('standard error', file=sys.stderr)