Pass flake8. (#23)

* flake8 ignore line length.

* Pass flake8.

* Newline in .flake8

Author: DailyDreaming

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 888

.gitignore

@@ -52,6 +52,9 @@ coverage.xml
 *.mo
 *.pot
 
+# PyCharm
+.idea/
+
 # Django stuff:
 *.log
 local_settings.py

cwl_flask.py

@@ -1,10 +1,8 @@
 from flask import Flask, Response, request, redirect
-import os
 import subprocess
 import tempfile
 import json
 import yaml
-import urlparse
 import signal
 import threading
 import time
@@ -15,6 +13,7 @@
 jobs_lock = threading.Lock()
 jobs = []
 
+
 class Job(threading.Thread):
     def __init__(self, jobid, path, inputobj):
         super(Job, self).__init__()
@@ -117,16 +116,19 @@ def logspooler(job):
                         break
                 time.sleep(1)
 
+
 @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'])
 def getjobs():
     with jobs_lock:
         jobscopy = copy.copy(jobs)
+
     def spool(jc):
         yield "["
         first = True
@@ -135,10 +137,11 @@ def spool(jc):
                 yield json.dumps(j.getstatus(), indent=4)
                 first = False
             else:
-                yield ", "  + json.dumps(j.getstatus(), indent=4)
+                yield ", " + json.dumps(j.getstatus(), indent=4)
         yield "]"
     return Response(spool(jobscopy))
 
+
 if __name__ == "__main__":
-    #app.debug = True
+    # app.debug = True
     app.run()

cwltool_stream.py

@@ -10,12 +10,13 @@
 _logger = logging.getLogger("cwltool")
 _logger.setLevel(logging.ERROR)
 
+
 def main(args=None):
     if args is None:
         args = sys.argv[1:]
 
     if len(args) == 0:
-        print "Workflow must be on command line"
+        print("Workflow must be on command line")
         return 1
 
     parser = cwltool.main.arg_parser()
@@ -38,5 +39,6 @@ def main(args=None):
         sys.stdout.write("\n\n")
         sys.stdout.flush()
 
+
 if __name__ == "__main__":
     sys.exit(main(sys.argv[1:]))

setup.py

@@ -1,11 +1,7 @@
 #!/usr/bin/env python
 
 import os
-import sys
-import setuptools.command.egg_info as egg_info_cmd
-import shutil
-
-from setuptools import setup, find_packages
+from setuptools import setup
 
 SETUP_DIR = os.path.dirname(__file__)
 
@@ -32,15 +28,13 @@
           'ruamel.yaml >= 0.12.4, < 0.15',
           'cwlref-runner',
           'schema-salad'
-        ],
+                        ],
       entry_points={
-          'console_scripts': [ "wes-server=wes_service:main",
-                               "wes-client=wes_client:main"]
-      },
+          'console_scripts': ["wes-server=wes_service:main",
+                              "wes-client=wes_client:main"]
+                    },
       extras_require={
-          "arvados": [
-              "arvados-cwl-runner"
-          ]
-      },
+          "arvados": ["arvados-cwl-runner"
+                      ]},
       zip_safe=False
-)
+      )

wes_client/__init__.py

@@ -1,28 +1,24 @@
 #!/usr/bin/env python
-
-from bravado.client import SwaggerClient
-from bravado.requests_client import RequestsClient
+import urlparse
+import pkg_resources  # part of setuptools
+import urllib
 import json
 import time
 import sys
 import os
 import argparse
 import logging
-import urlparse
-import pkg_resources  # part of setuptools
-from wes_service.util import visit
-import urllib
-import ruamel.yaml as yaml
 import schema_salad.ref_resolver
+from wes_service.util import visit
+from bravado.client import SwaggerClient
+from bravado.requests_client import RequestsClient
+
 
 def main(argv=sys.argv[1:]):
     parser = argparse.ArgumentParser(description='Workflow Execution Service')
-    parser.add_argument(
-        "--host", type=str, default=os.environ.get("WES_API_HOST"))
-    parser.add_argument(
-        "--auth", type=str, default=os.environ.get("WES_API_AUTH"))
-    parser.add_argument(
-        "--proto", type=str, default=os.environ.get("WES_API_PROTO", "https"))
+    parser.add_argument("--host", type=str, default=os.environ.get("WES_API_HOST"))
+    parser.add_argument("--auth", type=str, default=os.environ.get("WES_API_AUTH"))
+    parser.add_argument("--proto", type=str, default=os.environ.get("WES_API_PROTO", "https"))
     parser.add_argument("--quiet", action="store_true", default=False)
     parser.add_argument("--outdir", type=str)
 
@@ -35,18 +31,16 @@ def main(argv=sys.argv[1:]):
     exgroup.add_argument("--version", action="store_true", default=False)
 
     exgroup = parser.add_mutually_exclusive_group()
-    exgroup.add_argument(
-        "--wait", action="store_true", default=True, dest="wait")
-    exgroup.add_argument(
-        "--no-wait", action="store_false", default=True, dest="wait")
+    exgroup.add_argument("--wait", action="store_true", default=True, dest="wait")
+    exgroup.add_argument("--no-wait", action="store_false", default=True, dest="wait")
 
     parser.add_argument("workflow_url", type=str, nargs="?", default=None)
     parser.add_argument("job_order", type=str, nargs="?", default=None)
     args = parser.parse_args(argv)
 
     if args.version:
         pkg = pkg_resources.require("wes_service")
-        print u"%s %s" % (sys.argv[0], pkg[0].version)
+        print(u"%s %s" % (sys.argv[0], pkg[0].version))
         exit(0)
 
     http_client = RequestsClient()

wes_service/__init__.py

@@ -1,15 +1,16 @@
+#!/usr/bin/env python
 import argparse
 import sys
 import ruamel.yaml
 import os
 import logging
-
-logging.basicConfig(level=logging.INFO)
-
 import connexion
 import connexion.utils as utils
 from connexion.resolver import Resolver
 
+logging.basicConfig(level=logging.INFO)
+
+
 def setup(args=None):
     if args is None:
         args = argparse.Namespace()
@@ -22,14 +23,12 @@ def setup(args=None):
         for c in config:
             setattr(args, c, config[c])
 
-
     logging.info("Using config:")
     for n in args.__dict__:
         logging.info("  %s: %s", n, getattr(args, n))
 
     app = connexion.App(__name__)
-    backend = utils.get_function_from_name(
-        args.backend + ".create_backend")(args.opt)
+    backend = utils.get_function_from_name(args.backend + ".create_backend")(args.opt)
 
     def rs(x):
         return getattr(backend, x)
@@ -43,8 +42,7 @@ def rs(x):
 
 def main(argv=sys.argv[1:]):
     parser = argparse.ArgumentParser(description='Workflow Execution Service')
-    parser.add_argument(
-        "--backend", type=str, default="wes_service.cwl_runner")
+    parser.add_argument("--backend", type=str, default="wes_service.cwl_runner")
     parser.add_argument("--port", type=int, default=8080)
     parser.add_argument("--opt", type=str, action="append")
     parser.add_argument("--debug", action="store_true", default=False)

wes_service/arvados_wes.py

@@ -13,9 +13,11 @@
 
 from wes_service.util import visit, WESBackend
 
+
 class MissingAuthorization(Exception):
     pass
 
+
 def get_api():
     if not connexion.request.headers.get('Authorization'):
         raise MissingAuthorization()
@@ -52,6 +54,7 @@ def catch_exceptions_wrapper(self, *args, **kwargs):
 
     return catch_exceptions_wrapper
 
+
 class ArvadosBackend(WESBackend):
     def GetServiceInfo(self):
         return {