13306: Changes to arvados-cwl-runner code after running futurize --stage2

[arvados.git] / sdk / cwl / arvados_cwl / pathmapper.py

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 0b2a22788e6f98537b0f5a3437a2d540a57d47ee..7353d7239c2578622e7c409bd829d5e9e5fb1e80 100644 (file)
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -1,3 +1,7 @@
+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
+from past.builtins import basestring
 # Copyright (C) The Arvados Authors. All rights reserved.
 #
 # SPDX-License-Identifier: Apache-2.0
@@ -6,7 +10,7 @@ import re
 import logging
 import uuid
 import os
-import urllib
+import urllib.request, urllib.parse, urllib.error
 
 import arvados_cwl.util
 import arvados.commands.run
@@ -60,7 +64,7 @@ class ArvPathMapper(PathMapper):
             src = src[:src.index("#")]
 
         if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
-            self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.unquote(src[5:]), srcobj["class"], True)
+            self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.parse.unquote(src[5:]), srcobj["class"], True)
 
         debug = logger.isEnabledFor(logging.DEBUG)
 
@@ -77,7 +81,7 @@ class ArvPathMapper(PathMapper):
                     if isinstance(st, arvados.commands.run.UploadFile):
                         uploadfiles.add((src, ab, st))
                     elif isinstance(st, arvados.commands.run.ArvFile):
-                        self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % urllib.unquote(st.fn[5:]), "File", True)
+                        self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % urllib.parse.unquote(st.fn[5:]), "File", True)
                     else:
                         raise WorkflowException("Input file path '%s' is invalid" % st)
             elif src.startswith("_:"):
@@ -176,7 +180,7 @@ class ArvPathMapper(PathMapper):
                                          packed=False)
 
         for src, ab, st in uploadfiles:
-            self._pathmap[src] = MapperEnt(urllib.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:],
+            self._pathmap[src] = MapperEnt(urllib.parse.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:],
                                            "Directory" if os.path.isdir(ab) else "File", True)
 
         for srcobj in referenced_files:
@@ -228,7 +232,7 @@ class ArvPathMapper(PathMapper):
                                                               ab, "File", True)
                 if srcobj.get("secondaryFiles"):
                     ab = self.collection_pattern % c.portable_data_hash()
-                    self._pathmap["_:" + unicode(uuid.uuid4())] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
+                    self._pathmap["_:" + str(uuid.uuid4())] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
 
             if remap:
                 for loc, sub in remap:
@@ -301,7 +305,7 @@ class VwdPathMapper(StagingPathMapper):
         # with any secondary files.
         self.visitlisting(referenced_files, self.stagedir, basedir)
 
-        for path, (ab, tgt, type, staged) in self._pathmap.items():
+        for path, (ab, tgt, type, staged) in list(self._pathmap.items()):
             if type in ("File", "Directory") and ab.startswith("keep:"):
                 self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type, staged)