TEST: fslsub tests

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'