Add travis yml

Flake fixes

Author: david4096

.travis.yml

@@ -0,0 +1,16 @@
+language: python
+python:
+- '2.7'
+before_install:
+- sudo apt-get update -qq
+- pip install . --process-dependency-links
+- pip install -r python/dev-requirements.txt
+script:
+- flake8 wes_service wes_client
+deploy:
+  provider: pypi
+  on:
+    tags: true
+  user: david4096
+  password:
+    secure: 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

wes_service/__init__.py

@@ -1,18 +1,10 @@
-import connexion
-from connexion.resolver import Resolver
-import connexion.utils as utils
-
-import threading
-import tempfile
-import subprocess
-import uuid
-import os
-import json
-import urllib
 import argparse
 import sys
 
-from pkg_resources import resource_stream
+import connexion
+import connexion.utils as utils
+from connexion.resolver import Resolver
+
 
 def main(argv=sys.argv[1:]):
     parser = argparse.ArgumentParser(description='Workflow Execution Service')
@@ -24,12 +16,14 @@ def main(argv=sys.argv[1:]):
 
     app = connexion.App(__name__)
     backend = utils.get_function_from_name(args.backend + ".create_backend")(args.opt)
+
     def rs(x):
         return getattr(backend, x)
 
     app.add_api('openapi/workflow_execution_service.swagger.yaml', resolver=Resolver(rs))
 
     app.run(port=args.port, debug=args.debug)
 
+
 if __name__ == "__main__":
     main(sys.argv[1:])

wes_service/arvados_wes.py

@@ -7,6 +7,7 @@
 import tempfile
 from wes_service.util import visit, WESBackend
 
+
 def get_api():
     return arvados.api_from_config(version="v1", apiconfig={
         "ARVADOS_API_HOST": os.environ["ARVADOS_API_HOST"],
@@ -23,6 +24,7 @@ def get_api():
     "Cancelled": "Canceled"
 }
 
+
 class ArvadosBackend(WESBackend):
     def GetServiceInfo(self):
         return {
@@ -36,11 +38,7 @@ def GetServiceInfo(self):
             "key_values": {}
         }
 
-    def ListWorkflows(self, body=None):
-        # body["page_size"]
-        # body["page_token"]
-        # body["key_value_search"]
-
+    def ListWorkflows(self):
         api = get_api()
 
         requests = api.container_requests().list(filters=[["requesting_container_uuid", "=", None]],
@@ -75,7 +73,6 @@ def RunWorkflow(self, body):
                                                    body.get("workflow_url"), inputtemp.name], env=env).strip()
         return {"workflow_id": workflow_id}
 
-
     def GetWorkflowLog(self, workflow_id):
         api = get_api()
 
@@ -87,9 +84,11 @@ def GetWorkflowLog(self, workflow_id):
             c = arvados.collection.CollectionReader(request["output_uuid"])
             with c.open("cwl.output.json") as f:
                 outputobj = json.load(f)
+
                 def keepref(d):
                     if isinstance(d, dict) and "location" in d:
                         d["location"] = "keep:%s/%s" % (c.portable_data_hash(), d["location"])
+
                 visit(outputobj, keepref)
 
         stderr = ""
@@ -117,8 +116,7 @@ def keepref(d):
             r["workflow_log"]["exitCode"] = container["exit_code"]
         return r
 
-
-    def CancelJob(self, workflow_id):
+    def CancelJob(self, workflow_id):  #  NOQA
         api = get_api()
         request = api.container_requests().update(body={"priority": 0}).execute()
         return {"workflow_id": request["uuid"]}
@@ -130,5 +128,6 @@ def GetWorkflowStatus(self, workflow_id):
         return {"workflow_id": request["uuid"],
                 "state": statemap[container["state"]]}
 
+
 def create_backend(opts):
-    return ArvadosBackend(optdict)
+    return ArvadosBackend(opts)

wes_service/cwl_runner.py

@@ -1,12 +1,11 @@
-import threading
-import tempfile
-import subprocess
-import uuid
-import os
 import json
+import os
+import subprocess
 import urllib
-import sys
-from wes_service.util import visit, WESBackend
+import uuid
+
+from wes_service.util import WESBackend
+
 
 class Workflow(object):
     def __init__(self, workflow_id):
@@ -22,13 +21,17 @@ def run(self, request, opts):
         with open(os.path.join(self.workdir, "request.json"), "w") as f:
             json.dump(request, f)
 
-        with open(os.path.join(self.workdir, "cwl.input.json"), "w") as inputtemp:
+        with open(os.path.join(
+                self.workdir, "cwl.input.json"), "w") as inputtemp:
             json.dump(request["workflow_params"], inputtemp)
 
         if request.get("workflow_descriptor"):
-            with open(os.path.join(self.workdir, "workflow.cwl"), "w") as f:
+            with open(os.path.join(
+                    self.workdir, "workflow.cwl"), "w") as f:
+                # FIXME #14 workflow_descriptor isn't defined
                 f.write(workflow_descriptor)
-                workflow_url = urllib.pathname2url(os.path.join(self.workdir, "workflow.cwl"))
+                workflow_url = urllib.pathname2url(
+                    os.path.join(self.workdir, "workflow.cwl"))
         else:
             workflow_url = request.get("workflow_url")
 
@@ -38,7 +41,7 @@ def run(self, request, opts):
         runner = opts.getopt("runner", "cwl-runner")
         extra = opts.getoptlist("extra")
 
-        proc = subprocess.Popen([runner]+extra+[workflow_url, inputtemp.name],
+        proc = subprocess.Popen([runner] + extra + [workflow_url, inputtemp.name],
                                 stdout=output,
                                 stderr=stderr,
                                 close_fds=True,
@@ -68,7 +71,7 @@ def getstate(self):
                     with open(exc, "w") as f:
                         f.write(str(exit_code))
                     os.unlink(os.path.join(self.workdir, "pid"))
-            except OSError as e:
+            except OSError:
                 os.unlink(os.path.join(self.workdir, "pid"))
                 exit_code = 255
 
@@ -77,7 +80,7 @@ def getstate(self):
         elif exit_code != -1:
             state = "EXECUTOR_ERROR"
 
-        return (state, exit_code)
+        return state, exit_code
 
     def getstatus(self):
         state, exit_code = self.getstate()
@@ -134,11 +137,8 @@ def GetServiceInfo(self):
             "key_values": {}
         }
 
-    def ListWorkflows(self ,body=None):
-        # body["page_size"]
-        # body["page_token"]
-        # body["key_value_search"]
-
+    def ListWorkflows(self):
+        # FIXME #15 results don't page
         wf = []
         for l in os.listdir(os.path.join(os.getcwd(), "workflows")):
             if os.path.isdir(os.path.join(os.getcwd(), "workflows", l)):
@@ -169,5 +169,6 @@ def GetWorkflowStatus(self, workflow_id):
         job = Workflow(workflow_id)
         return job.getstatus()
 
+
 def create_backend(opts):
     return CWLRunnerBackend(opts)

wes_service/util.py

@@ -7,6 +7,7 @@ def visit(d, op):
         for i in d.itervalues():
             visit(i, op)
 
+
 class WESBackend(object):
     def __init__(self, opts):
         self.pairs = []
@@ -15,7 +16,7 @@ def __init__(self, opts):
             self.pairs.append((k, v))
 
     def getopt(self, p, default=None):
-        for k,v in self.pairs:
+        for k, v in self.pairs:
             if k == p:
                 return v
         return default