PEP-8 style fixes.

.gitignore

@@ -0,0 +1,3 @@
+*pyc
+.tox
+cwltool.egg-info/

cwltool/builder.py

@@ -3,15 +3,18 @@
 import expression
 import avro
 import schema_salad.validate as validate
+from .errors import WorkflowException
 
 CONTENT_LIMIT = 64 * 1024
 
+
 def substitute(value, replace):
     if replace[0] == "^":
         return substitute(value[0:value.rindex('.')], replace[1:])
     else:
         return value + replace
 
+
 class Builder(object):
 
     def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):

cwltool/cwlrdf.py

@@ -1,24 +1,25 @@
 import json
-from rdflib import Graph, plugin
-from rdflib.serializer import Serializer
+from rdflib import Graph
+
 
 def printrdf(workflow, wf, ctx, sr):
     wf["@context"] = ctx
     g = Graph().parse(data=json.dumps(wf), format='json-ld', location=workflow)
     print(g.serialize(format=sr))
 
+
 def printdot(workflow, wf, ctx, sr):
     wf["@context"] = ctx
     g = Graph().parse(data=json.dumps(wf), format='json-ld', location=workflow)
 
     print "digraph {"
 
-    #g.namespace_manager.qname(predicate)
+    # g.namespace_manager.qname(predicate)
 
     def lastpart(uri):
         uri = str(uri)
         if "/" in uri:
-            return uri[uri.rindex("/")+1:]
+            return uri[uri.rindex("/") + 1:]
         else:
             return uri
 
@@ -76,5 +77,4 @@ def lastpart(uri):
     for (inp,) in qres:
         print '"%s" [shape=octagon]' % (lastpart(inp))
 
-
     print "}"

cwltool/cwltest.py

@@ -17,6 +17,7 @@
 
 UNSUPPORTED_FEATURE = 33
 
+
 def compare(a, b):
     try:
         if isinstance(a, dict):
@@ -47,6 +48,7 @@ def compare(a, b):
     except:
         return False
 
+
 def run_test(args, i, t):
     out = {}
     outdir = None
@@ -92,7 +94,7 @@ def run_test(args, i, t):
         _logger.error(outstr)
         _logger.error("Parse error %s", str(e))
 
-    pwd = os.path.abspath(os.path.dirname(t["job"]))
+    os.path.abspath(os.path.dirname(t["job"]))
     # t["args"] = map(lambda x: x.replace("$PWD", pwd), t["args"])
     # if "stdin" in t:
     #     t["stdin"] = t["stdin"].replace("$PWD", pwd)
@@ -110,9 +112,9 @@ def run_test(args, i, t):
                 _logger.warn(t.get("doc"))
                 failed = True
             _logger.warn("%s expected %s\n%s      got %s", key,
-                                                            t.get(key),
-                                                            " " * len(key),
-                                                            out.get(key))
+                         t.get(key),
+                         " " * len(key),
+                         out.get(key))
 
     if outdir:
         shutil.rmtree(outdir)
@@ -144,14 +146,14 @@ def main():
 
     if args.n is not None:
         sys.stderr.write("\rTest [%i/%i] " % (args.n, len(tests)))
-        rt = run_test(args, args.n-1, tests[args.n-1])
+        rt = run_test(args, args.n - 1, tests[args.n - 1])
         if rt == 1:
             failures += 1
         elif rt == UNSUPPORTED_FEATURE:
             unsupported += 1
     else:
         for i, t in enumerate(tests):
-            sys.stderr.write("\rTest [%i/%i] " % (i+1, len(tests)))
+            sys.stderr.write("\rTest [%i/%i] " % (i + 1, len(tests)))
             sys.stderr.flush()
             rt = run_test(args, i, t)
             if rt == 1:
@@ -160,8 +162,8 @@ def main():
                 unsupported += 1
 
     if failures == 0 and unsupported == 0:
-         _logger.info("All tests passed")
-         return 0
+        _logger.info("All tests passed")
+        return 0
     else:
         _logger.warn("%i failures, %i unsupported features", failures, unsupported)
         return 1

cwltool/docker.py

@@ -9,6 +9,7 @@
 
 _logger = logging.getLogger("cwltool")
 
+
 def get_image(dockerRequirement, pull_image, dry_run=False):
     found = False
 

cwltool/draft2tool.py

@@ -1,4 +1,3 @@
-import avro.schema
 import json
 import copy
 from flatten import flatten
@@ -7,23 +6,19 @@
 from pathmapper import PathMapper, DockerPathMapper
 from job import CommandLineJob
 import yaml
-import glob
 import logging
 import hashlib
-import random
 from process import Process, shortname
 from errors import WorkflowException
 import schema_salad.validate as validate
 from aslist import aslist
-import expression
-import re
-import urlparse
 import tempfile
 from builder import CONTENT_LIMIT, substitute
 import shellescape
 
 _logger = logging.getLogger("cwltool")
 
+
 class ExpressionTool(Process):
     def __init__(self, toolpath_object, **kwargs):
         super(ExpressionTool, self).__init__(toolpath_object, **kwargs)
@@ -106,12 +101,11 @@ def job(self, joborder, input_basedir, output_callback, **kwargs):
         j.hints = self.hints
 
         _logger.debug("[job %s] initializing from %s%s",
-                     id(j),
-                     self.tool.get("id", ""),
-                     " as part of %s" % kwargs["part_of"] if "part_of" in kwargs else "")
+                      id(j),
+                      self.tool.get("id", ""),
+                      " as part of %s" % kwargs["part_of"] if "part_of" in kwargs else "")
         _logger.debug("[job %s] %s", id(j), json.dumps(joborder, indent=4))
 
-
         builder.pathmapper = None
 
         if self.tool.get("stdin"):
@@ -246,7 +240,6 @@ def collect_output(self, schema, builder, outdir):
                     if not builder.fs_access.exists(sf["path"]):
                         raise WorkflowException("Missing secondary file of '%s' of primary file '%s'" % (sf["path"], r["path"]))
 
-
         if not r and schema["type"] == "record":
             r = {}
             for f in schema["fields"]:

cwltool/expression.py

@@ -3,22 +3,20 @@
 import json
 from aslist import aslist
 import logging
-import os
 from errors import WorkflowException
 import process
-import yaml
-import schema_salad.validate as validate
 import schema_salad.ref_resolver
 
 _logger = logging.getLogger("cwltool")
 
+
 def exeval(ex, jobinput, requirements, outdir, tmpdir, context, pull_image):
     if ex["engine"] == "https://w3id.org/cwl/cwl#JsonPointer":
         try:
             obj = {"job": jobinput, "context": context, "outdir": outdir, "tmpdir": tmpdir}
             return schema_salad.ref_resolver.resolve_json_pointer(obj, ex["script"])
         except ValueError as v:
-            raise WorkflowException("%s in %s" % (v,  obj))
+            raise WorkflowException("%s in %s" % (v, obj))
 
     for r in reversed(requirements):
         if r["class"] == "ExpressionEngineRequirement" and r["id"] == ex["engine"]:
@@ -56,13 +54,13 @@ class DR(object):
 
             _logger.debug("Invoking expression engine %s with %s",
                           runtime + aslist(r["engineCommand"]),
-                                           json.dumps(inp, indent=4))
+                          json.dumps(inp, indent=4))
 
             sp = subprocess.Popen(runtime + aslist(r["engineCommand"]),
-                             shell=False,
-                             close_fds=True,
-                             stdin=subprocess.PIPE,
-                             stdout=subprocess.PIPE)
+                                  shell=False,
+                                  close_fds=True,
+                                  stdin=subprocess.PIPE,
+                                  stdout=subprocess.PIPE)
 
             (stdoutdata, stderrdata) = sp.communicate(json.dumps(inp) + "\n\n")
             if sp.returncode != 0:
@@ -72,6 +70,7 @@ class DR(object):
 
     raise WorkflowException("Unknown expression engine '%s'" % ex["engine"])
 
+
 def do_eval(ex, jobinput, requirements, outdir, tmpdir, context=None, pull_image=True):
     if isinstance(ex, dict) and "engine" in ex and "script" in ex:
         return exeval(ex, jobinput, requirements, outdir, tmpdir, context, pull_image)

cwltool/job.py

@@ -1,12 +1,8 @@
 import subprocess
 import os
-import tempfile
-import glob
 import json
-import yaml
 import logging
 import sys
-import requests
 import docker
 from process import get_feature, empty_subtree
 from errors import WorkflowException
@@ -20,6 +16,7 @@
 
 needs_shell_quoting = re.compile(r"""(^$|[\s|&;()<>\'"$@])""").search
 
+
 def deref_links(outputs):
     if isinstance(outputs, dict):
         if outputs.get("class") == "File":
@@ -33,12 +30,13 @@ def deref_links(outputs):
         for v in outputs:
             deref_links(v)
 
+
 class CommandLineJob(object):
     def run(self, dry_run=False, pull_image=True, rm_container=True, rm_tmpdir=True, move_outputs=True, **kwargs):
         if not os.path.exists(self.outdir):
             os.makedirs(self.outdir)
 
-        #with open(os.path.join(outdir, "cwl.input.json"), "w") as fp:
+        # with open(os.path.join(outdir, "cwl.input.json"), "w") as fp:
         #    json.dump(self.joborder, fp)
 
         runtime = []
@@ -74,7 +72,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True, rm_tmpdir=True,
 
             runtime.append("--env=TMPDIR=/tmp/job_tmp")
 
-            for t,v in self.environment.items():
+            for t, v in self.environment.items():
                 runtime.append("--env=%s=%s" % (t, v))
 
             runtime.append(img_id)