Merge pull request #285 from gijzelaerr/cleanup

cleanup

Author: mr-c

cwltool.py

@@ -6,6 +6,7 @@
 """
 
 import sys
+
 from cwltool import main
 
 if __name__ == "__main__":

cwltool/__main__.py

@@ -1,4 +1,5 @@
-from . import main
 import sys
 
+from . import main
+
 sys.exit(main.main())

cwltool/builder.py

@@ -1,13 +1,15 @@
 import copy
-from .utils import aslist
-from . import expression
+
 import avro
 import schema_salad.validate as validate
 from schema_salad.sourceline import SourceLine
 from typing import Any, Callable, Text, Type, Union
+
+from . import expression
 from .errors import WorkflowException
+from .pathmapper import PathMapper, adjustFileObjs, normalizeFilesDirs
 from .stdfsaccess import StdFsAccess
-from .pathmapper import PathMapper, adjustFileObjs, adjustDirObjs, normalizeFilesDirs
+from .utils import aslist
 
 CONTENT_LIMIT = 64 * 1024
 
@@ -18,8 +20,8 @@ def substitute(value, replace):  # type: (Text, Text) -> Text
     else:
         return value + replace
 
-class Builder(object):
 
+class Builder(object):
     def __init__(self):  # type: () -> None
         self.names = None  # type: avro.schema.Names
         self.schemaDefs = None  # type: Dict[Text, Dict[Text, Any]]
@@ -39,8 +41,12 @@ def __init__(self):  # type: () -> None
         self.build_job_script = None  # type: Callable[[List[str]], Text]
         self.debug = False  # type: bool
 
-    def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
+    def bind_input(self, schema, datum, lead_pos=None, tail_pos=None):
         # type: (Dict[Text, Any], Any, Union[int, List[int]], List[int]) -> List[Dict[Text, Any]]
+        if tail_pos is None:
+            tail_pos = []
+        if lead_pos is None:
+            lead_pos = []
         bindings = []  # type: List[Dict[Text,Text]]
         binding = None  # type: Dict[Text,Any]
         if "inputBinding" in schema and isinstance(schema["inputBinding"], dict):
@@ -137,7 +143,6 @@ def _capture_files(f):
             if schema["type"] == "Directory":
                 self.files.append(datum)
 
-
         # Position to front of the sort key
         if binding:
             for bi in bindings:
@@ -198,7 +203,7 @@ def do_eval(self, ex, context=None, pull_image=True, recursive=False):
         # type: (Union[Dict[Text, Text], Text], Any, bool, bool) -> Any
         if recursive:
             if isinstance(ex, dict):
-                return {k: self.do_eval(v, context, pull_image, recursive) for k,v in ex.iteritems()}
+                return {k: self.do_eval(v, context, pull_image, recursive) for k, v in ex.iteritems()}
             if isinstance(ex, list):
                 return [self.do_eval(v, context, pull_image, recursive) for v in ex]
 

cwltool/cwlrdf.py

@@ -1,11 +1,12 @@
-import json
 import urlparse
-from .process import Process
-from schema_salad.ref_resolver import Loader, ContextType
+
+from rdflib import Graph
 from schema_salad.jsonld_context import makerdf
-from rdflib import Graph, plugin, URIRef
-from rdflib.serializer import Serializer
-from typing import Any, Dict, IO, Text, Union
+from schema_salad.ref_resolver import ContextType
+from typing import Any, Dict, IO, Text
+
+from .process import Process
+
 
 def gather(tool, ctx):  # type: (Process, ContextType) -> Graph
     g = Graph()
@@ -16,14 +17,16 @@ def visitor(t):
     tool.visit(visitor)
     return g
 
+
 def printrdf(wf, ctx, sr, stdout):
     # type: (Process, ContextType, Text, IO[Any]) -> None
     stdout.write(gather(wf, ctx).serialize(format=sr))
 
+
 def lastpart(uri):  # type: (Any) -> Text
     uri = Text(uri)
     if "/" in uri:
-        return uri[uri.rindex("/")+1:]
+        return uri[uri.rindex("/") + 1:]
     else:
         return uri
 
@@ -84,6 +87,7 @@ def dot_with_parameters(g, stdout):  # type: (Graph, IO[Any]) -> None
     for (inp,) in qres:
         stdout.write(u'"%s" [shape=octagon]\n' % (lastpart(inp)))
 
+
 def dot_without_parameters(g, stdout):  # type: (Graph, IO[Any]) -> None
     dotname = {}  # type: Dict[Text,Text]
     clusternode = {}
@@ -163,7 +167,7 @@ def printdot(wf, ctx, stdout, include_parameters=False):
 
     stdout.write("digraph {")
 
-    #g.namespace_manager.qname(predicate)
+    # g.namespace_manager.qname(predicate)
 
     if include_parameters:
         dot_with_parameters(g, stdout)

cwltool/docker.py

@@ -1,15 +1,18 @@
-import subprocess
 import logging
-import sys
-import requests
 import os
-from .errors import WorkflowException
 import re
+import subprocess
+import sys
 import tempfile
-from typing import Any, Text, Union
+
+import requests
+from typing import Text
+
+from .errors import WorkflowException
 
 _logger = logging.getLogger("cwltool")
 
+
 def get_image(dockerRequirement, pull_image, dry_run=False):
     # type: (Dict[Text, Text], bool, bool) -> bool
     found = False
@@ -44,7 +47,7 @@ def get_image(dockerRequirement, pull_image, dry_run=False):
             with open(os.path.join(dockerfile_dir, "Dockerfile"), "w") as df:
                 df.write(dockerRequirement["dockerFile"])
             cmd = ["docker", "build", "--tag=%s" %
-                str(dockerRequirement["dockerImageId"]), dockerfile_dir]
+                   str(dockerRequirement["dockerImageId"]), dockerfile_dir]
             _logger.info(Text(cmd))
             if not dry_run:
                 subprocess.check_call(cmd, stdout=sys.stderr)
@@ -62,7 +65,7 @@ def get_image(dockerRequirement, pull_image, dry_run=False):
                     _logger.info(u"Sending GET request to %s", dockerRequirement["dockerLoad"])
                     req = requests.get(dockerRequirement["dockerLoad"], stream=True)
                     n = 0
-                    for chunk in req.iter_content(1024*1024):
+                    for chunk in req.iter_content(1024 * 1024):
                         n += len(chunk)
                         _logger.info("\r%i bytes" % (n))
                         loadproc.stdin.write(chunk)
@@ -73,7 +76,7 @@ def get_image(dockerRequirement, pull_image, dry_run=False):
                 found = True
         elif "dockerImport" in dockerRequirement:
             cmd = ["docker", "import", str(dockerRequirement["dockerImport"]),
-                str(dockerRequirement["dockerImageId"])]
+                   str(dockerRequirement["dockerImageId"])]
             _logger.info(Text(cmd))
             if not dry_run:
                 subprocess.check_call(cmd, stdout=sys.stderr)

cwltool/docker_uid.py

@@ -1,5 +1,6 @@
 import subprocess
-from typing import Text, Union
+
+from typing import Text
 
 
 def docker_vm_uid():  # type: () -> int