Merge branch '10111-cr-provenance-graph'

[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 3a0c69b08a84ce0f1cc882a39b3a589c3dd31009..cddb4088b7bfcbbdb211d6785ba650e8ea36901e 100644 (file)
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -2,6 +2,7 @@ import re
 import logging
 import uuid
 import os
+import urllib
 
 import arvados.commands.run
 import arvados.collection
@@ -17,7 +18,7 @@ class ArvPathMapper(PathMapper):
     """Convert container-local paths to and from Keep collection ids."""
 
     pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+$')
-    pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.+)?$')
+    pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.*)?$')
 
     def __init__(self, arvrunner, referenced_files, input_basedir,
                  collection_pattern, file_pattern, name=None, **kwargs):
@@ -34,29 +35,30 @@ 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 % src[5:], srcobj["class"], True)
+            self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.unquote(src[5:]), srcobj["class"], True)
 
         if src not in self._pathmap:
-            # Local FS ref, may need to be uploaded or may be on keep
-            # mount.
-            ab = abspath(src, self.input_basedir)
-            st = arvados.commands.run.statfile("", ab,
-                                               fnPattern="keep:%s/%s",
-                                               dirPattern="keep:%s/%s")
-            with SourceLine(srcobj, "location", WorkflowException):
-                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 % st.fn[5:], "File", True)
-                elif src.startswith("_:"):
-                    if "contents" in srcobj:
-                        pass
+            if src.startswith("file:"):
+                # Local FS ref, may need to be uploaded or may be on keep
+                # mount.
+                ab = abspath(src, self.input_basedir)
+                st = arvados.commands.run.statfile("", ab,
+                                                   fnPattern="keep:%s/%s",
+                                                   dirPattern="keep:%s/%s")
+                with SourceLine(srcobj, "location", WorkflowException):
+                    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)
                     else:
-                        raise WorkflowException("File literal '%s' is missing contents" % src)
-                elif src.startswith("arvwf:"):
-                    self._pathmap[src] = MapperEnt(src, src, "File", True)
-                else:
-                    raise WorkflowException("Input file path '%s' is invalid" % st)
+                        raise WorkflowException("Input file path '%s' is invalid" % st)
+            elif src.startswith("_:"):
+                if srcobj["class"] == "File" and "contents" not in srcobj:
+                    raise WorkflowException("File literal '%s' is missing `contents`" % src)
+                if srcobj["class"] == "Directory" and "listing" not in srcobj:
+                    raise WorkflowException("Directory literal '%s' is missing `listing`" % src)
+            else:
+                self._pathmap[src] = MapperEnt(src, src, srcobj["class"], True)
 
         with SourceLine(srcobj, "secondaryFiles", WorkflowException):
             for l in srcobj.get("secondaryFiles", []):
@@ -92,7 +94,7 @@ class ArvPathMapper(PathMapper):
             loc = k["location"]
             if loc in already_uploaded:
                 v = already_uploaded[loc]
-                self._pathmap[loc] = MapperEnt(v.resolved, self.collection_pattern % v.resolved[5:], "File", True)
+                self._pathmap[loc] = MapperEnt(v.resolved, self.collection_pattern % urllib.unquote(v.resolved[5:]), "File", True)
 
         for srcobj in referenced_files:
             self.visit(srcobj, uploadfiles)
@@ -107,7 +109,7 @@ class ArvPathMapper(PathMapper):
                                              project=self.arvrunner.project_uuid)
 
         for src, ab, st in uploadfiles:
-            self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.keepref,
+            self._pathmap[src] = MapperEnt(urllib.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:],
                                            "Directory" if os.path.isdir(ab) else "File", True)
             self.arvrunner.add_uploaded(src, self._pathmap[src])