Merge branch 'master' into singularity-support

# Conflicts:
#	cwltool/job.py

Author: Anton Khodak

cwltool/builder.py

@@ -230,7 +230,7 @@ def generate_arg(self, binding):  # type: (Dict[Text,Any]) -> List[Text]
             return [prefix] if prefix else []
         elif value is True and prefix:
             return [prefix]
-        elif value is False or value is None:
+        elif value is False or value is None or (value is True and not prefix):
             return []
         else:
             l = [value]
@@ -251,7 +251,8 @@ def do_eval(self, ex, context=None, pull_image=True, recursive=False):
                 return {k: self.do_eval(v, context, pull_image, recursive) for k, v in iteritems(ex)}
             if isinstance(ex, list):
                 return [self.do_eval(v, context, pull_image, recursive) for v in ex]
-
+        if context is None and type(ex) is str and "self" in ex:
+            return None
         return expression.do_eval(ex, self.job, self.requirements,
                                   self.outdir, self.tmpdir,
                                   self.resources,

cwltool/job.py

@@ -324,6 +324,7 @@ def create_runtime(self, env, rm_container=True, **kwargs):
         # type: (MutableMapping[Text, Text], bool, **Any) -> List
         pass
 
+
     def run(self, pull_image=True, rm_container=True,
             rm_tmpdir=True, move_outputs="move", **kwargs):
         # type: (bool, bool, bool, Text, **Any) -> None

jenkins.bash

@@ -34,14 +34,15 @@ do
 	# use pip2.7 and pip3 in separate loop runs
 	pip${PYTHON_VERSION} install -U setuptools wheel pip
 	pip${PYTHON_VERSION} install .
-	pip${PYTHON_VERSION} install "cwltest>=1.0.20160825151655"
+	pip${PYTHON_VERSION} install "cwltest>=1.0.20180130081614"
 	pushd common-workflow-language
 	# shellcheck disable=SC2154
 	if [[ "$version" = *dev* ]]
 	then
 		EXTRA="EXTRA=--enable-dev"
 	fi
-	./run_test.sh --junit-xml=result${PYTHON_VERSION}.xml RUNNER=cwltool -j4 DRAFT=${version}
+	./run_test.sh --junit-xml=result${PYTHON_VERSION}.xml RUNNER=cwltool \
+		-j4 DRAFT=${version} --classname=py${PYTHON_VERSION}
 	CODE=$(($CODE+$?)) # capture return code of ./run_test.sh
 	deactivate
 	popd

tests/override/echo.cwl

@@ -15,5 +15,5 @@ outputs:
       glob: out.txt
       loadContents: true
       outputEval: $(self[0].contents)
-arguments: ["echo", "-n", $(inputs.m1), {shellQuote: false, valueFrom: "$MESSAGE"}]
+arguments: ["echo", $(inputs.m1), {shellQuote: false, valueFrom: "$MESSAGE"}]
 stdout: out.txt

tests/test_override.py

@@ -23,44 +23,44 @@ def test_overrides(self):
         self.assertEquals(main([get_data('tests/override/echo.cwl'),
                                 get_data('tests/override/echo-job.yml')],
                                stdout=sio), 0)
-        self.assertEquals({"out": "zing hello1"}, json.loads(sio.getvalue()))
+        self.assertEquals({"out": "zing hello1\n"}, json.loads(sio.getvalue()))
 
         sio = StringIO()
         self.assertEquals(main(["--overrides", get_data('tests/override/ov.yml'),
                                 get_data('tests/override/echo.cwl'),
                                 get_data('tests/override/echo-job.yml')],
                                stdout=sio), 0)
-        self.assertEquals({"out": "zing hello2"}, json.loads(sio.getvalue()))
+        self.assertEquals({"out": "zing hello2\n"}, json.loads(sio.getvalue()))
 
         sio = StringIO()
         self.assertEquals(main([get_data('tests/override/echo.cwl'),
                                 get_data('tests/override/echo-job-ov.yml')],
                                stdout=sio), 0)
-        self.assertEquals({"out": "zing hello3"}, json.loads(sio.getvalue()))
+        self.assertEquals({"out": "zing hello3\n"}, json.loads(sio.getvalue()))
 
         sio = StringIO()
         self.assertEquals(main([get_data('tests/override/echo-job-ov2.yml')],
                                stdout=sio), 0)
-        self.assertEquals({"out": "zing hello4"}, json.loads(sio.getvalue()))
+        self.assertEquals({"out": "zing hello4\n"}, json.loads(sio.getvalue()))
 
 
         sio = StringIO()
         self.assertEquals(main(["--overrides", get_data('tests/override/ov.yml'),
                                 get_data('tests/override/echo-wf.cwl'),
                                 get_data('tests/override/echo-job.yml')],
                                stdout=sio), 0)
-        self.assertEquals({"out": "zing hello2"}, json.loads(sio.getvalue()))
+        self.assertEquals({"out": "zing hello2\n"}, json.loads(sio.getvalue()))
 
         sio = StringIO()
         self.assertEquals(main(["--overrides", get_data('tests/override/ov2.yml'),
                                 get_data('tests/override/echo-wf.cwl'),
                                 get_data('tests/override/echo-job.yml')],
                                stdout=sio), 0)
-        self.assertEquals({"out": "zing hello5"}, json.loads(sio.getvalue()))
+        self.assertEquals({"out": "zing hello5\n"}, json.loads(sio.getvalue()))
 
         sio = StringIO()
         self.assertEquals(main(["--overrides", get_data('tests/override/ov3.yml'),
                                 get_data('tests/override/echo-wf.cwl'),
                                 get_data('tests/override/echo-job.yml')],
                                stdout=sio), 0)
-        self.assertEquals({"out": "zing hello6"}, json.loads(sio.getvalue()))
+        self.assertEquals({"out": "zing hello6\n"}, json.loads(sio.getvalue()))