Merge branch 'master' into testing-windows

Author: mr-c

cwltool/update.py

@@ -5,6 +5,7 @@
 import traceback
 from typing import (Any, Callable, Dict, Text,  # pylint: disable=unused-import
                     Tuple, Union)
+from copy import deepcopy
 
 import six
 from six.moves import urllib
@@ -349,6 +350,7 @@ def _draft3toDraft4dev1(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Any
     if isinstance(doc, dict):
         if "class" in doc and doc["class"] == "Workflow":
+
             def fixup(f):  # type: (Text) -> Text
                 doc, frg = urllib.parse.urldefrag(f)
                 frg = '/'.join(frg.rsplit('.', 1))
@@ -371,6 +373,8 @@ def fixup(f):  # type: (Text) -> Text
             for out in doc["outputs"]:
                 out["source"] = fixup(out["source"])
         for key, value in doc.items():
+            if key == 'run':
+                value = deepcopy(value)
             doc[key] = _draft3toDraft4dev1(value, loader, baseuri)
     elif isinstance(doc, list):
         for i, a in enumerate(doc):
@@ -393,6 +397,8 @@ def _draft4Dev1toDev2(doc, loader, baseuri):
                 out["outputSource"] = out["source"]
                 del out["source"]
         for key, value in doc.items():
+            if key == 'run':
+                value = deepcopy(value)
             doc[key] = _draft4Dev1toDev2(value, loader, baseuri)
     elif isinstance(doc, list):
         for i, a in enumerate(doc):

jenkins.bash

@@ -1,24 +1,45 @@
-#!/usr/bin/bash
+#!/bin/bash
+if [ "$JENKINS_URL" == ""]
+then
+	echo "Looks like we're not being run by Jenkins, this is dangerous"
+	echo "due to use of git clean -fdx command."
+	exit 1
+fi
 cloneorpull() {
-        if test -d $1 ; then
-                (cd $1 && git pull)
+        if test -d "$1" ; then
+                (cd "$1" && git pull)
         else
-                git clone $2
+                git clone "$2"
         fi
 }
 venv() {
-        if ! test -d $1 ; then
-                virtualenv $1
+        if ! test -d "$1" ; then
+                virtualenv "$1"
         fi
-        . $1/bin/activate
+	# shellcheck source=/dev/null
+        source "$1"/bin/activate
 }
+git clean --force -d -x || /bin/true
 cloneorpull common-workflow-language https://github.com/common-workflow-language/common-workflow-language.git
 venv cwltool-venv
-(. cwltool-venv/bin/activate && PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/ pip install -U setuptools wheel pip)
-(. cwltool-venv/bin/activate && PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/ python setup.py install)
-(. cwltool-venv/bin/activate && PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/ pip install "cwltest>=1.0.20160825151655")
-# (. cwltool-venv/bin/activate && cd common-workflow-language && ./run_test.sh --junit-xml=result.xml RUNNER=cwltool DRAFT=draft-2)
-(. cwltool-venv/bin/activate && cd common-workflow-language && ./run_test.sh --junit-xml=result.xml RUNNER=cwltool DRAFT=draft-3)
-(. cwltool-venv/bin/activate && cd common-workflow-language && ./run_test.sh --junit-xml=result.xml RUNNER=cwltool)
-(. cwltool-venv/bin/activate && cd common-workflow-language && ./run_test.sh --junit-xml=result.xml RUNNER=cwltool DRAFT=v1.1.0-dev1 EXTRA=--enable-dev)
-(. cwltool-venv/bin/activate && ./build-cwl-docker.sh && docker push commonworkflowlanguage/cwltool_module && docker push commonworkflowlanguage/cwltool)
+docker pull node:slim
+export PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/
+pip install -U setuptools wheel pip
+python setup.py install
+pip install "cwltest>=1.0.20160825151655"
+pushd common-workflow-language
+git clean --force -d -x || /bin/true
+# shellcheck disable=SC2154
+if [[ "$version" = *dev* ]]
+then
+	EXTRA="EXTRA=--enable-dev"
+fi
+./run_test.sh --junit-xml=result.xml RUNNER=cwltool -j4 DRAFT="${version}" ${EXTRA}
+CODE=$?
+popd
+if [ "$GIT_BRANCH" = "origin/master" ] && [[ "$version" = "v1.0" ]]
+then
+  ./build-cwl-docker.sh && docker push commonworkflowlanguage/cwltool_module && docker push commonworkflowlanguage/cwltool
+fi
+#docker rm -v $(docker ps -a -f status=exited | sed 's/  */ /g' | cut -d' ' -f1)
+exit ${CODE}