Fix failing tests. refs #9776

[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 0dc80fcaec1482d7348354df4b883f56ede19a04..e17264bcdd90d48f5972260bd49d6c76459e1cca 100644 (file)
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -1,6 +1,7 @@
 import re
 import logging
 import uuid
+import os
 
 import arvados.commands.run
 import arvados.collection
@@ -51,9 +52,8 @@ class ArvPathMapper(PathMapper):
         elif srcobj["class"] == "Directory":
             if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
                 self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "Directory")
-            else:
-                for l in srcobj["listing"]:
-                    self.visit(l, uploadfiles)
+            for l in srcobj["listing"]:
+                self.visit(l, uploadfiles)
 
     def addentry(self, obj, c, path, subdirs):
         if obj["location"] in self._pathmap:
@@ -140,3 +140,37 @@ class ArvPathMapper(PathMapper):
             return (target, "keep:" + target[len(self.keepdir)+1:])
         else:
             return super(ArvPathMapper, self).reversemap(target)
+
+class InitialWorkDirPathMapper(PathMapper):
+
+    def visit(self, obj, stagedir, basedir, copy=False):
+        # type: (Dict[unicode, Any], unicode, unicode, bool) -> None
+        if obj["class"] == "Directory":
+            self._pathmap[obj["location"]] = MapperEnt(obj["location"], stagedir, "Directory")
+            self.visitlisting(obj.get("listing", []), stagedir, basedir)
+        elif obj["class"] == "File":
+            loc = obj["location"]
+            if loc in self._pathmap:
+                return
+            tgt = os.path.join(stagedir, obj["basename"])
+            if "contents" in obj and obj["location"].startswith("_:"):
+                self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile")
+            else:
+                if copy:
+                    self._pathmap[loc] = MapperEnt(obj["path"], tgt, "WritableFile")
+                else:
+                    self._pathmap[loc] = MapperEnt(obj["path"], tgt, "File")
+                self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
+
+    def setup(self, referenced_files, basedir):
+        # type: (List[Any], unicode) -> None
+
+        # Go through each file and set the target to its own directory along
+        # with any secondary files.
+        stagedir = self.stagedir
+        for fob in referenced_files:
+            self.visit(fob, stagedir, basedir)
+
+        for path, (ab, tgt, type) in self._pathmap.items():
+            if type in ("File", "Directory") and ab.startswith("keep:"):
+                self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type)