X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a4c37c079728f2013f5a299acc97f1b24c1e2884..91dc5f1d7f5ad9eb2640f6089e2d0476cbf87c8e:/sdk/cwl/arvados_cwl/pathmapper.py

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index e17264bcdd..73c81ceb0f 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -6,7 +6,7 @@ import os
 import arvados.commands.run
 import arvados.collection
 
-from cwltool.pathmapper import PathMapper, MapperEnt, abspath
+from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs
 from cwltool.workflow import WorkflowException
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -37,13 +37,16 @@ class ArvPathMapper(PathMapper):
                 # 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=self.file_pattern)
+                st = arvados.commands.run.statfile("", ab, fnPattern="keep:%s/%s")
                 if isinstance(st, arvados.commands.run.UploadFile):
                     uploadfiles.add((src, ab, st))
                 elif isinstance(st, arvados.commands.run.ArvFile):
-                    self._pathmap[src] = MapperEnt(ab, st.fn, "File")
-                elif src.startswith("_:") and "contents" in srcobj:
-                    pass
+                    self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File")
+                elif src.startswith("_:"):
+                    if "contents" in srcobj:
+                        pass
+                    else:
+                        raise WorkflowException("File literal '%s' is missing contents" % src)
                 else:
                     raise WorkflowException("Input file path '%s' is invalid" % st)
             if "secondaryFiles" in srcobj:
@@ -52,12 +55,14 @@ 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")
-            for l in srcobj["listing"]:
+            for l in srcobj.get("listing", []):
                 self.visit(l, uploadfiles)
 
     def addentry(self, obj, c, path, subdirs):
         if obj["location"] in self._pathmap:
             src, srcpath = self.arvrunner.fs_access.get_collection(self._pathmap[obj["location"]].resolved)
+            if srcpath == "":
+                srcpath = "."
             c.copy(srcpath, path + "/" + obj["basename"], source_collection=src, overwrite=True)
             for l in obj.get("secondaryFiles", []):
                 self.addentry(l, c, path, subdirs)
@@ -73,9 +78,11 @@ class ArvPathMapper(PathMapper):
 
     def setup(self, referenced_files, basedir):
         # type: (List[Any], unicode) -> None
-        self._pathmap = self.arvrunner.get_uploaded()
         uploadfiles = set()
 
+        for k,v in self.arvrunner.get_uploaded().iteritems():
+            self._pathmap[k] = MapperEnt(v.resolved, self.collection_pattern % v.resolved[5:], "File")
+
         for srcobj in referenced_files:
             self.visit(srcobj, uploadfiles)
 
@@ -84,18 +91,19 @@ class ArvPathMapper(PathMapper):
                                              self.arvrunner.api,
                                              dry_run=False,
                                              num_retries=self.arvrunner.num_retries,
-                                             fnPattern=self.file_pattern,
+                                             fnPattern="keep:%s/%s",
                                              name=self.name,
                                              project=self.arvrunner.project_uuid)
 
         for src, ab, st in uploadfiles:
-            self._pathmap[src] = MapperEnt("keep:" + st.keepref, st.fn, "File")
+            self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File")
             self.arvrunner.add_uploaded(src, self._pathmap[src])
 
         for srcobj in referenced_files:
             if srcobj["class"] == "Directory":
                 if srcobj["location"] not in self._pathmap:
                     c = arvados.collection.Collection(api_client=self.arvrunner.api,
+                                                      keep_client=self.arvrunner.keep_client,
                                                       num_retries=self.arvrunner.num_retries)
                     subdirs = []
                     for l in srcobj["listing"]:
@@ -114,6 +122,7 @@ class ArvPathMapper(PathMapper):
                 (srcobj["location"].startswith("_:") and "contents" in srcobj)):
 
                 c = arvados.collection.Collection(api_client=self.arvrunner.api,
+                                                  keep_client=self.arvrunner.keep_client,
                                                   num_retries=self.arvrunner.num_retries                                                  )
                 subdirs = []
                 self.addentry(srcobj, c, ".", subdirs)
@@ -145,11 +154,11 @@ class InitialWorkDirPathMapper(PathMapper):
 
     def visit(self, obj, stagedir, basedir, copy=False):
         # type: (Dict[unicode, Any], unicode, unicode, bool) -> None
+        loc = obj["location"]
         if obj["class"] == "Directory":
-            self._pathmap[obj["location"]] = MapperEnt(obj["location"], stagedir, "Directory")
+            self._pathmap[loc] = 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"])
@@ -167,10 +176,26 @@ class InitialWorkDirPathMapper(PathMapper):
 
         # 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)
+        self.visitlisting(referenced_files, self.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)
+
+
+class FinalOutputPathMapper(PathMapper):
+    def visit(self, obj, stagedir, basedir, copy=False):
+        # type: (Dict[unicode, Any], unicode, unicode, bool) -> None
+        loc = obj["location"]
+        if obj["class"] == "Directory":
+            self._pathmap[loc] = MapperEnt(loc, stagedir, "Directory")
+        elif obj["class"] == "File":
+            if loc in self._pathmap:
+                return
+            tgt = os.path.join(stagedir, obj["basename"])
+            self._pathmap[loc] = MapperEnt(loc, tgt, "File")
+            self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
+
+    def setup(self, referenced_files, basedir):
+        # type: (List[Any], unicode) -> None
+        self.visitlisting(referenced_files, self.stagedir, basedir)