def visit(self, srcobj, uploadfiles):
src = srcobj["location"]
- if srcobj["class"] == "File":
- if "#" in src:
- src = src[:src.index("#")]
- if isinstance(src, basestring) and ArvPathMapper.pdh_path.match(src):
- self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.unquote(src[5:]), "File")
- if src not in self._pathmap:
+ if "#" in src:
+ src = src[:src.index("#")]
+
+ if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
+ self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.unquote(src[5:]), srcobj["class"], True)
+
+ if src not in self._pathmap:
+ 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")
+ 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")
- elif src.startswith("_:"):
- if "contents" in srcobj:
- pass
- else:
- raise WorkflowException("File literal '%s' is missing contents" % src)
- elif src.startswith("arvwf:"):
- self._pathmap[src] = MapperEnt(src, src, "File")
+ self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % urllib.unquote(st.fn[5:]), "File", True)
else:
raise WorkflowException("Input file path '%s' is invalid" % st)
- if "secondaryFiles" in srcobj:
- for l in srcobj["secondaryFiles"]:
- self.visit(l, uploadfiles)
- elif srcobj["class"] == "Directory":
- if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
- self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.unquote(src[5:]), "Directory")
+ 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", []):
+ self.visit(l, uploadfiles)
+ with SourceLine(srcobj, "listing", WorkflowException):
for l in srcobj.get("listing", []):
self.visit(l, uploadfiles)
for l in obj.get("secondaryFiles", []):
self.addentry(l, c, path, subdirs)
elif obj["class"] == "Directory":
- for l in obj["listing"]:
+ for l in obj.get("listing", []):
self.addentry(l, c, path + "/" + obj["basename"], subdirs)
subdirs.append((obj["location"], path + "/" + obj["basename"]))
elif obj["location"].startswith("_:") and "contents" in obj:
loc = k["location"]
if loc in already_uploaded:
v = already_uploaded[loc]
- self._pathmap[loc] = MapperEnt(v.resolved, self.collection_pattern % urllib.unquote(v.resolved[5:]), "File")
+ 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)
project=self.arvrunner.project_uuid)
for src, ab, st in uploadfiles:
- self._pathmap[src] = MapperEnt(urllib.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:], "File")
+ 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])
for srcobj in referenced_files:
+ 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"]:
+ for l in srcobj.get("listing", []):
self.addentry(l, c, ".", subdirs)
check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
c.save_new(owner_uuid=self.arvrunner.project_uuid)
ab = self.collection_pattern % c.portable_data_hash()
- self._pathmap[srcobj["location"]] = MapperEnt(ab, ab, "Directory")
- for loc, sub in subdirs:
- ab = self.file_pattern % (c.portable_data_hash(), sub[2:])
- self._pathmap[loc] = MapperEnt(ab, ab, "Directory")
+ self._pathmap[srcobj["location"]] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
elif srcobj["class"] == "File" and (srcobj.get("secondaryFiles") or
(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)
check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
c.save_new(owner_uuid=self.arvrunner.project_uuid)
ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
- self._pathmap[srcobj["location"]] = MapperEnt(ab, ab, "File")
+ self._pathmap[srcobj["location"]] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), srcobj["basename"]),
+ ab, "File", True)
if srcobj.get("secondaryFiles"):
ab = self.collection_pattern % c.portable_data_hash()
- self._pathmap["_:" + unicode(uuid.uuid4())] = MapperEnt(ab, ab, "Directory")
+ self._pathmap["_:" + unicode(uuid.uuid4())] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
+
+ if subdirs:
for loc, sub in subdirs:
+ # subdirs will all start with "./", strip it off
ab = self.file_pattern % (c.portable_data_hash(), sub[2:])
- self._pathmap[loc] = MapperEnt(ab, ab, "Directory")
+ self._pathmap[loc] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), sub[2:]),
+ ab, "Directory", True)
self.keepdir = None
class StagingPathMapper(PathMapper):
_follow_dirs = True
- def visit(self, obj, stagedir, basedir, copy=False):
+ def visit(self, obj, stagedir, basedir, copy=False, staged=False):
# type: (Dict[unicode, Any], unicode, unicode, bool) -> None
loc = obj["location"]
tgt = os.path.join(stagedir, obj["basename"])
if obj["class"] == "Directory":
- self._pathmap[loc] = MapperEnt(loc, tgt, "Directory")
+ self._pathmap[loc] = MapperEnt(loc, tgt, "Directory", staged)
if loc.startswith("_:") or self._follow_dirs:
self.visitlisting(obj.get("listing", []), tgt, basedir)
elif obj["class"] == "File":
if loc in self._pathmap:
return
if "contents" in obj and loc.startswith("_:"):
- self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile")
+ self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile", staged)
else:
if copy:
- self._pathmap[loc] = MapperEnt(loc, tgt, "WritableFile")
+ self._pathmap[loc] = MapperEnt(loc, tgt, "WritableFile", staged)
else:
- self._pathmap[loc] = MapperEnt(loc, tgt, "File")
+ self._pathmap[loc] = MapperEnt(loc, tgt, "File", staged)
self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
# with any secondary files.
self.visitlisting(referenced_files, self.stagedir, basedir)
- for path, (ab, tgt, type) in self._pathmap.items():
+ for path, (ab, tgt, type, staged) in self._pathmap.items():
if type in ("File", "Directory") and ab.startswith("keep:"):
- self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type)
+ self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type, staged)
class NoFollowPathMapper(StagingPathMapper):
projects / arvados.git / blobdiff