style: remove parameters that never change

Allows us to prune branches that are never executed
Add tests for docker mirroring singularity

Author: psafont

cwltool/docker.py

@@ -1,6 +1,7 @@
 """Enables Docker software containers via the {dx-,u,}docker runtimes."""
 from __future__ import absolute_import
 
+from distutils import spawn
 import datetime
 import os
 import re
@@ -182,32 +183,17 @@ def get_image(docker_requirement,     # type: Dict[Text, Text]
 
     def get_from_requirements(self,
                               r,                      # type: Dict[Text, Text]
-                              req,                    # type: bool
                               pull_image,             # type: bool
                               force_pull=False,       # type: bool
                               tmp_outdir_prefix=DEFAULT_TMP_PREFIX  # type: Text
                              ):  # type: (...) -> Optional[Text]
-        if r:
-            errmsg = None
-            try:
-                subprocess.check_output(["docker", "version"])
-            except subprocess.CalledProcessError as err:
-                errmsg = "Cannot communicate with docker daemon: " + Text(err)
-            except OSError as err:
-                errmsg = "'docker' executable not found: " + Text(err)
-
-            if errmsg is not None:
-                if req:
-                    raise WorkflowException(errmsg)
-                else:
-                    return None
+        if not spawn.find_executable('docker'):
+            raise WorkflowException("docker executable is not available")
 
-            if self.get_image(r, pull_image, force_pull, tmp_outdir_prefix):
-                return r["dockerImageId"]
-            if req:
-                raise WorkflowException(u"Docker image %s not found" % r["dockerImageId"])
 
-        return None
+        if self.get_image(r, pull_image, force_pull, tmp_outdir_prefix):
+            return r["dockerImageId"]
+        raise WorkflowException(u"Docker image %s not found" % r["dockerImageId"])
 
     @staticmethod
     def append_volume(runtime, source, target, writable=False):

cwltool/job.py

@@ -430,7 +430,6 @@ class ContainerCommandLineJob(with_metaclass(ABCMeta, JobBase)):
     @abstractmethod
     def get_from_requirements(self,
                               r,                      # type: Dict[Text, Text]
-                              req,                    # type: bool
                               pull_image,             # type: bool
                               force_pull=False,       # type: bool
                               tmp_outdir_prefix=DEFAULT_TMP_PREFIX  # type: Text
@@ -565,7 +564,7 @@ def run(self, runtimeContext):
                 if docker_req is not None and runtimeContext.use_container:
                     img_id = str(
                         self.get_from_requirements(
-                            docker_req, True, runtimeContext.pull_image,
+                            docker_req, runtimeContext.pull_image,
                             getdefault(runtimeContext.force_docker_pull, False),
                             getdefault(runtimeContext.tmp_outdir_prefix, DEFAULT_TMP_PREFIX)))
                 if img_id is None:

cwltool/singularity.py

@@ -124,8 +124,7 @@ def get_image(dockerRequirement,  # type: Dict[Text, Text]
         return found
 
     def get_from_requirements(self,
-                              r,                      # type: Optional[Dict[Text, Text]]
-                              req,                    # type: bool
+                              r,                      # type: Dict[Text, Text]
                               pull_image,             # type: bool
                               force_pull=False,       # type: bool
                               tmp_outdir_prefix=None  # type: Text
@@ -136,19 +135,12 @@ def get_from_requirements(self,
         hello-world-latest.img).
         """
 
-        if r is None:
-            return None
-
         if not bool(spawn.find_executable('singularity')):
-            if req:
-                raise WorkflowException('singularity executable is not available')
-            return None
+            raise WorkflowException('singularity executable is not available')
 
         if not self.get_image(r, pull_image, force_pull):
-            if req:
-                raise WorkflowException(u"Container image {} not "
-                                        "found".format(r["dockerImageId"]))
-            return None
+            raise WorkflowException(u"Container image {} not "
+                                    "found".format(r["dockerImageId"]))
 
         return os.path.abspath(r["dockerImageId"])
 

tests/test_docker.py

@@ -0,0 +1,33 @@
+import pytest
+
+from distutils import spawn
+
+from cwltool.docker import DockerCommandLineJob
+from cwltool.main import main
+
+from .util import get_data, get_main_output, needs_docker, needs_singularity
+
+@needs_docker
+def test_docker_workflow():
+    result_code, _, stderr = get_main_output(
+        ['--default-container', 'debian',
+         get_data("tests/wf/hello-workflow.cwl"), "--usermessage", "hello"])
+    assert "completed success" in stderr
+    assert result_code == 0
+
+def test_docker_iwdr():
+    result_code = main(
+        ['--default-container', 'debian',
+         get_data("tests/wf/iwdr-entry.cwl"), "--message", "hello"])
+    docker_installed = bool(spawn.find_executable('docker'))
+    if docker_installed:
+        assert result_code == 0
+    else:
+        assert result_code != 0
+
+@needs_docker
+def test_docker_incorrect_image_pull():
+    result_code = main(
+        ['--default-container', 'non-existant-weird-image',
+         get_data("tests/wf/hello-workflow.cwl"), "--usermessage", "hello"])
+    assert result_code != 0