From e985dd1f53ae8eee633acbbfc821bc3ef1ccec64 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 13 Mar 2020 15:00:35 +0000
Subject: [PATCH] TEST: fslsub tests
---
tests/test_fslsub.py | 102 ++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 101 insertions(+), 1 deletion(-)
diff --git a/tests/test_fslsub.py b/tests/test_fslsub.py
index 878e9b32c..07f5a39f0 100644
--- a/tests/test_fslsub.py
+++ b/tests/test_fslsub.py
@@ -3,9 +3,70 @@
# test_fslsub.py - Tests functions in the fsl.utils.fslsub module.
#
# Author: Michiel Cottaar <Michiel.Cottaar@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-from fsl.utils import fslsub
+
+import os
+import os.path as op
+import sys
+import textwrap as tw
+import contextlib
+
+from fsl.utils import fslsub
+from fsl.utils.tempdir import tempdir
+
+from . import mockFSLDIR
+
+
+mock_fsl_sub = f"""
+#!{sys.executable}
+
+import random
+import os
+import os.path as op
+import sys
+import subprocess as sp
+import fsl
+
+args = sys.argv[1:]
+
+for i in range(len(args)):
+ a = args[i]
+ if a[0] == '-':
+ if a[1] == 's':
+ i += 2
+ elif a[1] not in ('F', 'v'):
+ i += 1
+ continue
+ else:
+ break
+
+args = args[i:]
+
+env = dict(os.environ)
+env['PYTHONPATH'] = op.join(op.dirname(fsl.__file__), '..')
+
+cmd = op.basename(args[0])
+jobid = random.randint(1, 9999)
+
+with open(f'{{cmd}}.o{{jobid}}', 'w') as stdout, \
+ open(f'{{cmd}}.e{{jobid}}', 'w') as stderr:
+ result = sp.run(args, stdout=stdout, stderr=stderr, env=env)
+
+print(str(jobid))
+sys.exit(0)
+""".strip()
+
+
+@contextlib.contextmanager
+def fslsub_mockFSLDIR():
+ with mockFSLDIR() as fsldir:
+ fslsubbin = op.join(fsldir, 'bin', 'fsl_sub')
+ with open(fslsubbin, 'wt') as f:
+ f.write(mock_fsl_sub)
+ os.chmod(fslsubbin, 0o755)
+ yield fsldir
def test_flatten_jobids():
@@ -18,3 +79,42 @@ def test_flatten_jobids():
assert fslsub._flatten_job_ids([job_ids[:2], job_ids[2:]]) == res
assert fslsub._flatten_job_ids([set(job_ids[:2]), job_ids[2:]]) == res
assert fslsub._flatten_job_ids(((job_ids, ), job_ids + job_ids)) == res
+
+
+def test_submit():
+ script = tw.dedent("""#!/usr/bin/env bash
+ echo "standard output"
+ echo "standard error" >&2
+ exit 0
+ """).strip()
+
+ with fslsub_mockFSLDIR(), tempdir():
+ cmd = op.join('.', 'myscript')
+ with open(cmd, 'wt') as f:
+ f.write(script)
+ os.chmod(cmd, 0o755)
+
+ jid = fslsub.submit(cmd)
+ fslsub.wait(jid)
+ stdout, stderr = fslsub.output(jid)
+
+ assert stdout.strip() == 'standard output'
+ assert stderr.strip() == 'standard error'
+
+
+def myfunc():
+ print('standard output')
+ print('standard error', file=sys.stderr)
+
+
+def test_func_to_cmd():
+ with fslsub_mockFSLDIR(), tempdir():
+ cmd = fslsub.func_to_cmd(myfunc, (), {})
+ jid = fslsub.submit(cmd)
+
+ fslsub.wait(jid)
+
+ stdout, stderr = fslsub.output(jid)
+
+ assert stdout.strip() == 'standard output'
+ assert stderr.strip() == 'standard error'
--
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