Merge branch 'master' into httpinput

Author: kapilkd13

cwltool/pack.py

@@ -157,4 +157,9 @@ def rewrite_id(r, mainuri):
 
     import_embed(packed, set())
 
+    if len(packed["$graph"]) == 1:
+        # duplicate 'cwlVersion' inside $graph when there is a single item
+        # because we're printing contents inside '$graph' rather than whole dict
+        packed["$graph"][0]["cwlVersion"] = packed["cwlVersion"]
+
     return packed

jenkins.bash

@@ -14,29 +14,40 @@ cloneorpull() {
 }
 venv() {
         if ! test -d "$1" ; then
-                virtualenv "$1"
+                virtualenv -p python${PYTHON_VERSION} "$1"
         fi
 	# shellcheck source=/dev/null
         source "$1"/bin/activate
 }
-git clean --force -d -x || /bin/true
+
 cloneorpull common-workflow-language https://github.com/common-workflow-language/common-workflow-language.git
-venv cwltool-venv
 docker pull node:slim
-export PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/
-pip install -U setuptools wheel pip
-python setup.py install
-pip install "cwltest>=1.0.20160825151655"
-pushd common-workflow-language
+# clean both the repos before the loop
 git clean --force -d -x || /bin/true
-# shellcheck disable=SC2154
-if [[ "$version" = *dev* ]]
-then
-	EXTRA="EXTRA=--enable-dev"
-fi
-./run_test.sh --junit-xml=result.xml RUNNER=cwltool -j4 DRAFT="${version}" ${EXTRA}
-CODE=$?
-popd
+git -C common-workflow-language clean --force -d -x || /bin/true
+
+# Test for Python 2.7 and Python 3
+for PYTHON_VERSION in 2.7 3
+do
+	venv cwltool-venv${PYTHON_VERSION}
+	export PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/
+	# use pip2.7 and pip3 in separate loop runs
+	pip${PYTHON_VERSION} install -U setuptools wheel pip
+	pip${PYTHON_VERSION} install .
+	pip${PYTHON_VERSION} install "cwltest>=1.0.20160825151655"
+	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=${version}
+	CODE=$(($CODE+$?)) # capture return code of ./run_test.sh
+	deactivate
+	popd
+done
+
+# build new docker container
 if [ "$GIT_BRANCH" = "origin/master" ] && [[ "$version" = "v1.0" ]]
 then
   ./build-cwl-docker.sh && docker push commonworkflowlanguage/cwltool_module && docker push commonworkflowlanguage/cwltool

tests/test_pack.py

@@ -5,6 +5,7 @@
 from functools import partial
 
 import cwltool.pack
+from cwltool.main import print_pack as print_pack
 import cwltool.workflow
 from cwltool.load_tool import fetch_document, validate_document
 from cwltool.main import makeRelative
@@ -33,3 +34,29 @@ def test_pack(self):
         del expect_packed["$schemas"]
 
         self.assertEqual(expect_packed, packed)
+
+    def test_pack_missing_cwlVersion(self):
+        """Test to ensure the generated pack output is not missing
+        the `cwlVersion` in case of single tool workflow and single step workflow"""
+        # Since diff is longer than 3174 characters
+        self.maxDiff = None
+
+        # Testing single tool workflow
+        document_loader, workflowobj, uri = fetch_document(
+            get_data("tests/wf/hello_single_tool.cwl"))
+        document_loader, avsc_names, processobj, metadata, uri = validate_document(
+            document_loader, workflowobj, uri)
+        # generate pack output dict
+        packed = json.loads(print_pack(document_loader, processobj, uri, metadata))
+
+        self.assertEqual('v1.0', packed["cwlVersion"])
+
+        # Testing single step workflow
+        document_loader, workflowobj, uri = fetch_document(
+            get_data("tests/wf/hello-workflow.cwl"))
+        document_loader, avsc_names, processobj, metadata, uri = validate_document(
+            document_loader, workflowobj, uri)
+        # generate pack output dict
+        packed = json.loads(print_pack(document_loader, processobj, uri, metadata))
+
+        self.assertEqual('v1.0', packed["cwlVersion"])

tests/wf/hello-workflow.cwl

@@ -0,0 +1,38 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+
+label: "Hello World"
+doc: "Outputs a message using echo"
+
+inputs:
+  usermessage: string
+
+outputs:
+  response:
+    outputSource: step0/response
+    type: File
+
+steps:
+  step0:
+    run:
+      class: CommandLineTool
+      inputs:
+        message:
+          type: string
+          doc: "The message to print"
+          default: "Hello World"
+          inputBinding:
+            position: 1
+      baseCommand: echo
+      arguments:
+         - "-n"
+         - "-e"
+      stdout: response.txt
+      outputs:
+        response:
+          type: stdout
+    in:
+      message: usermessage
+    out: [response]

tests/wf/hello_single_tool.cwl

@@ -0,0 +1,9 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+inputs:
+  message:
+    type: string
+    inputBinding:
+      position: 1
+outputs: []