2020 refresh

.travis.yml

@@ -1,12 +1,10 @@
 language: python
 python:
-- '2.7'
-- '3.5'
 - '3.6'
+- '3.7'
+- '3.8'
 before_install:
-- sudo apt-get update -qq
-- pip install toil[all]==3.20.0
-- pip install . --process-dependency-links
+- pip install .[toil]
 - pip install -r dev-requirements.txt
 script:
 - flake8 wes_service wes_client

Dockerfile

@@ -12,8 +12,8 @@ RUN apt-get update && \
     sh -c 'echo deb https://oss-binaries.phusionpassenger.com/apt/passenger stretch main > /etc/apt/sources.list.d/passenger.list'
 
 RUN apt-get update && \
-    apt-get install -y --no-install-recommends passenger python-setuptools build-essential python-dev python-pip git && \
-    pip install pip==9.0.3
+    apt-get install -y --no-install-recommends passenger python3-setuptools build-essential python3-dev python3-pip git && \
+    pip3 install pip==9.0.3
 
 RUN apt-get install -y --no-install-recommends libcurl4-openssl-dev libssl1.0-dev
 

cwl_flask.py

@@ -27,24 +27,27 @@ def begin(self):
         loghandle, self.logname = tempfile.mkstemp()
         with self.updatelock:
             self.outdir = tempfile.mkdtemp()
-            self.proc = subprocess.Popen(["cwl-runner", self.path, "-"],
-                                         stdin=subprocess.PIPE,
-                                         stdout=subprocess.PIPE,
-                                         stderr=loghandle,
-                                         close_fds=True,
-                                         cwd=self.outdir)
+            self.proc = subprocess.Popen(
+                ["cwl-runner", self.path, "-"],
+                stdin=subprocess.PIPE,
+                stdout=subprocess.PIPE,
+                stderr=loghandle,
+                close_fds=True,
+                cwd=self.outdir,
+            )
             self.status = {
                 "id": "%sjobs/%i" % (request.url_root, self.jobid),
                 "log": "%sjobs/%i/log" % (request.url_root, self.jobid),
                 "run": self.path,
                 "state": "Running",
                 "input": json.loads(self.inputobj),
-                "output": None}
+                "output": None,
+            }
 
     def run(self):
         self.stdoutdata, self.stderrdata = self.proc.communicate(self.inputobj)
         if self.proc.returncode == 0:
-            outobj = yaml.load(self.stdoutdata)
+            outobj = yaml.load(self.stdoutdata, Loader=yaml.FullLoader)
             with self.updatelock:
                 self.status["state"] = "Success"
                 self.status["output"] = outobj
@@ -75,7 +78,7 @@ def resume(self):
                 self.status["state"] = "Running"
 
 
-@app.route("/run", methods=['POST'])
+@app.route("/run", methods=["POST"])
 def runworkflow():
     path = request.args["wf"]
     with jobs_lock:
@@ -86,11 +89,11 @@ def runworkflow():
     return redirect("/jobs/%i" % jobid, code=303)
 
 
-@app.route("/jobs/<int:jobid>", methods=['GET', 'POST'])
+@app.route("/jobs/<int:jobid>", methods=["GET", "POST"])
 def jobcontrol(jobid):
     with jobs_lock:
         job = jobs[jobid]
-    if request.method == 'POST':
+    if request.method == "POST":
         action = request.args.get("action")
         if action:
             if action == "cancel":
@@ -117,14 +120,14 @@ def logspooler(job):
                 time.sleep(1)
 
 
-@app.route("/jobs/<int:jobid>/log", methods=['GET'])
+@app.route("/jobs/<int:jobid>/log", methods=["GET"])
 def getlog(jobid):
     with jobs_lock:
         job = jobs[jobid]
     return Response(logspooler(job))
 
 
-@app.route("/jobs", methods=['GET'])
+@app.route("/jobs", methods=["GET"])
 def getjobs():
     with jobs_lock:
         jobscopy = copy.copy(jobs)
@@ -139,6 +142,7 @@ def spool(jc):
             else:
                 yield ", " + json.dumps(j.getstatus(), indent=4)
         yield "]"
+
     return Response(spool(jobscopy))
 
 

cwltool_stream.py

@@ -34,7 +34,12 @@ def main(args=None):
 
         t = StringIO.StringIO(msg)
         err = StringIO.StringIO()
-        if cwltool.main.main(["--outdir="+outdir] + args + ["-"], stdin=t, stderr=err) != 0:
+        if (
+            cwltool.main.main(
+                ["--outdir=" + outdir] + args + ["-"], stdin=t, stderr=err
+            )
+            != 0
+        ):
             sys.stdout.write(json.dumps({"cwl:error": err.getvalue()}))
         sys.stdout.write("\n\n")
         sys.stdout.flush()

dev-requirements.txt

@@ -1,2 +1,3 @@
 flake8
 pytest
+black

setup.py

@@ -10,47 +10,50 @@
 with open("README.pypi.rst") as readmeFile:
     long_description = readmeFile.read()
 
-setup(name='wes-service',
-      version='3.3',
-      description='GA4GH Workflow Execution Service reference implementation',
-      long_description=long_description,
-      author='GA4GH Containers and Workflows task team',
-      author_email='[email protected]',
-      url="https://github.com/common-workflow-language/cwltool-service",
-      download_url="https://github.com/common-workflow-language/cwltool-service",
-      license='Apache 2.0',
-      packages=["wes_service", "wes_client"],
-      package_data={'wes_service': ['openapi/workflow_execution_service.swagger.yaml']},
-      include_package_data=True,
-      install_requires=[
-          'future',
-          'connexion >= 2.0.2, < 3',
-          'ruamel.yaml >= 0.12.4, <= 0.15.77',
-          'schema-salad',
-          'subprocess32==3.5.2'
-                        ],
-      entry_points={
-          'console_scripts': ["wes-server=wes_service.wes_service_main:main",
-                              "wes-client=wes_client.wes_client_main:main"]
-                    },
-      extras_require={
-          "cwltool": ['cwlref-runner'],
-          "arvados": ["arvados-cwl-runner"
-                      ],
-          "toil": ["toil[all]==3.20.0"
-                   ]},
-      zip_safe=False,
-      platforms=['MacOS X', 'Posix'],
-      classifiers=[
-          'Intended Audience :: Developers',
-          'License :: OSI Approved :: Apache Software License',
-          'Operating System :: MacOS :: MacOS X',
-          'Operating System :: POSIX',
-          'Programming Language :: Python',
-          'Programming Language :: Python :: 2.7',
-          'Programming Language :: Python :: 3.5',
-          'Programming Language :: Python :: 3.6',
-          'Programming Language :: Python :: 3.7',
-          'Topic :: Software Development :: Libraries :: Python Modules'
+setup(
+    name="wes-service",
+    version="4.0",
+    description="GA4GH Workflow Execution Service reference implementation",
+    long_description=long_description,
+    author="GA4GH Containers and Workflows task team",
+    author_email="[email protected]",
+    url="https://github.com/common-workflow-language/cwltool-service",
+    download_url="https://github.com/common-workflow-language/cwltool-service",
+    license="Apache 2.0",
+    python_requires="~=3.5",
+    setup_requires=['pytest-runner'],
+    tests_require=['pytest'],
+    packages=["wes_service", "wes_client"],
+    package_data={"wes_service": ["openapi/workflow_execution_service.swagger.yaml"]},
+    include_package_data=True,
+    install_requires=[
+        "connexion >= 2.0.2, < 3",
+        "ruamel.yaml >= 0.15.78, < 0.16",
+        "schema-salad",
+        "subprocess32==3.5.2",
+    ],
+    entry_points={
+        "console_scripts": [
+            "wes-server=wes_service.wes_service_main:main",
+            "wes-client=wes_client.wes_client_main:main",
         ]
-      )
+    },
+    extras_require={
+        "cwltool": ["cwlref-runner"],
+        "arvados": ["arvados-cwl-runner"],
+        "toil": ["toil[cwl]==4.1.0"],
+    },
+    zip_safe=False,
+    platforms=["MacOS X", "Posix"],
+    classifiers=[
+        "Intended Audience :: Developers",
+        "License :: OSI Approved :: Apache Software License",
+        "Operating System :: MacOS :: MacOS X",
+        "Operating System :: POSIX",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+    ],
+)

test/test_client_util.py

@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 import unittest
 import os
 import logging

test/test_integration.py

@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 import unittest
 import time
 import os