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')
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
+ 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:
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 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"]:
(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)
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"])
# 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)