Added fix for detecting with singularity --userns is broken (#771)

Author: pvanheus

.travis.yml

@@ -1,6 +1,17 @@
+dist: trusty
 sudo: true
 services:
   - docker
+
+env:
+  - SINGVER=2.5.1
+
+before_install:
+- wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
+- sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
+- sudo apt-get update
+- sudo apt-get install -y singularity-container
+
 language: python
 cache: pip
 python:
@@ -15,7 +26,7 @@ install:
 jobs:
   include:
     - stage: release-test
-      script: RELEASE_SKIP=head ./release-test.sh
+      script: RELEASE_SKIP=head ${TRAVIS_BUILD_DIR}/release-test.sh
 script: tox
 branches:
   only:

cwltool/hello.simg

@@ -2,21 +2,23 @@
 from __future__ import absolute_import
 import logging
 import os
+import os.path
 import re
 import shutil
 import sys
 from io import open  # pylint: disable=redefined-builtin
-from typing import (Dict, List, Text, Optional, MutableMapping)
+from typing import (Dict, List, Text, Optional,  # pylint: disable=unused-import
+                    MutableMapping)
+from schema_salad.sourceline import SourceLine
 from .errors import WorkflowException
 from .job import ContainerCommandLineJob
-from .pathmapper import PathMapper, ensure_writable
+from .pathmapper import PathMapper, ensure_writable  # pylint: disable=unused-import
 from .process import (UnsupportedRequirement)
 from .utils import docker_windows_path_adjust
-from schema_salad.sourceline import SourceLine
 if os.name == 'posix':
-    from subprocess32 import (check_call, check_output,  # pylint: disable=import-error
-                              CalledProcessError, DEVNULL, PIPE, Popen,
-                              TimeoutExpired)
+    from subprocess32 import (  # pylint: disable=import-error,no-name-in-module
+        check_call, check_output, CalledProcessError, DEVNULL, PIPE, Popen,
+        TimeoutExpired)
 else:  # we're not on Unix, so none of this matters
     pass
 
@@ -27,8 +29,9 @@ def _singularity_supports_userns():  # type: ()->bool
     global _USERNS  # pylint: disable=global-statement
     if _USERNS is None:
         try:
+            hello_image = os.path.join(os.path.dirname(__file__), 'hello.simg')
             result = Popen(
-                [u"singularity", u"exec", u"--userns", u"/etc", u"true"],
+                [u"singularity", u"exec", u"--userns", hello_image, u"true"],
                 stderr=PIPE, stdout=DEVNULL,
                 universal_newlines=True).communicate(timeout=60)[1]
             _USERNS = "No valid /bin/sh" in result

cwltool/singularity.py

@@ -45,7 +45,8 @@
                                 'schemas/v1.1.0-dev1/salad/schema_salad/metaschema/*.md',
                                 'cwlNodeEngine.js',
                                 'cwlNodeEngineJSConsole.js',
-                                'extensions.yml']},
+                                'extensions.yml',
+                                'hello.simg']},
       include_package_data=True,
       install_requires=[
           'setuptools',

setup.py

@@ -27,7 +27,7 @@
 from cwltool.main import main
 from cwltool.utils import onWindows, subprocess
 
-from .util import (get_data, needs_docker, get_windows_safe_factory,
+from .util import (get_data, needs_docker, needs_singularity, get_windows_safe_factory,
         windows_needs_docker)
 
 
@@ -702,5 +702,21 @@ def test_no_compute_checksum(self):
         self.assertNotIn("checksum", stdout)
 
 
+@needs_singularity
+class TestChecksumSingularity(TestCmdLine):
+
+    def setUp(self):
+        self.cache_dir = tempfile.mkdtemp("cwltool_cache")
+
+    def tearDown(self):
+        shutil.rmtree(self.cache_dir)
+
+    def test_singularity_workflow(self):
+        error_code, stdout, stderr = self.get_main_output(
+            ['--singularity', '--default-container', 'debian',
+             get_data("tests/wf/hello-workflow.cwl"), "--usermessage", "hello"])
+        self.assertIn("completed success", stderr)
+        self.assertEquals(error_code, 0)
+
 if __name__ == '__main__':
     unittest.main()

tests/test_examples.py

@@ -44,6 +44,10 @@ def get_data(filename):
                                   reason="Requires the docker executable on the "
                                   "system path.")
 
+needs_singularity = pytest.mark.skipif(not bool(distutils.spawn.find_executable('singularity')),
+                                       reason="Requires the singularity executable on the "
+                                       "system path.")
+
 windows_needs_docker = pytest.mark.skipif(
         onWindows() and not bool(distutils.spawn.find_executable('docker')),
         reason="Running this test on MS Windows requires the docker executable "