Pathmapper now has list of file objects and not just file names.

cwltool/builder.py

@@ -6,7 +6,7 @@
 from typing import Any, Union, AnyStr, Callable
 from .errors import WorkflowException
 from .stdfsaccess import StdFsAccess
-from .pathmapper import PathMapper
+from .pathmapper import PathMapper, adjustFileObjs, adjustDirObjs
 
 CONTENT_LIMIT = 64 * 1024
 
@@ -17,18 +17,6 @@ def substitute(value, replace):  # type: (str, str) -> str
     else:
         return value + replace
 
-def adjustFileObjs(rec, op):  # type: (Any, Callable[[Any], Any]) -> None
-    """Apply an update function to each File object in the object `rec`."""
-
-    if isinstance(rec, dict):
-        if rec.get("class") == "File":
-            op(rec)
-        for d in rec:
-            adjustFileObjs(rec[d], op)
-    if isinstance(rec, list):
-        for d in rec:
-            adjustFileObjs(d, op)
-
 class Builder(object):
 
     def __init__(self):  # type: () -> None
@@ -114,7 +102,7 @@ def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
             if schema["type"] == "File":
                 self.files.append(datum)
                 if binding and binding.get("loadContents"):
-                    with self.fs_access.open(datum["path"], "rb") as f:
+                    with self.fs_access.open(datum["location"], "rb") as f:
                         datum["contents"] = f.read(CONTENT_LIMIT)
 
                 if "secondaryFiles" in schema:
@@ -124,11 +112,11 @@ def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
                         if isinstance(sf, dict) or "$(" in sf or "${" in sf:
                             secondary_eval = self.do_eval(sf, context=datum)
                             if isinstance(secondary_eval, basestring):
-                                sfpath = {"path": secondary_eval, "class": "File"}
+                                sfpath = {"location": secondary_eval, "class": "File"}
                             else:
                                 sfpath = secondary_eval
                         else:
-                            sfpath = {"path": substitute(datum["path"], sf), "class": "File"}
+                            sfpath = {"location": substitute(datum["location"], sf), "class": "File"}
                         if isinstance(sfpath, list):
                             datum["secondaryFiles"].extend(sfpath)
                         else:
@@ -140,6 +128,10 @@ def _capture_files(f):
 
                 adjustFileObjs(datum.get("secondaryFiles", []), _capture_files)
 
+            if schema["type"] == "Directory":
+                self.files.append(datum)
+
+
         # Position to front of the sort key
         if binding:
             for bi in bindings:

cwltool/cwltest.py

@@ -37,10 +37,30 @@ def compare(a, b):  # type: (Any, Any) -> bool
                 # ignore empty collections
                 b = {k: v for k, v in b.iteritems()
                      if not isinstance(v, (list, dict)) or len(v) > 0}
+            elif a.get("class") == "Directory":
+                if len(a["listing"]) != len(b["listing"]):
+                    return False
+                for i in a["listing"]:
+                    found = False
+                    for j in b["listing"]:
+                        try:
+                            if compare(i, j):
+                                found = True
+                                break
+                        except:
+                            pass
+                    if not found:
+                        raise CompareFail(u"%s not in %s" % (json.dumps(i, indent=4, sort_keys=True), json.dumps(b, indent=4, sort_keys=True)))
+
+            a = {k: v for k, v in a.iteritems()
+                 if k not in ("path", "location", "listing")}
+            b = {k: v for k, v in b.iteritems()
+                 if k not in ("path", "location", "listing")}
+
             if len(a) != len(b):
                 raise CompareFail(u"expected %s\ngot %s" % (json.dumps(a, indent=4, sort_keys=True), json.dumps(b, indent=4, sort_keys=True)))
             for c in a:
-                if a.get("class") != "File" or c != "path":
+                if a.get("class") != "File" or c not in ("path", "location", "listing"):
                     if c not in b:
                         raise CompareFail(u"%s not in %s" % (c, b))
                     if not compare(a[c], b[c]):