if obj.get("location", "").startswith("keep:") and "listing" in obj:
del obj["listing"]
+collection_pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+$')
+collection_pdh_pattern = re.compile(r'^keep:([0-9a-f]{32}\+\d+)(/.*)?')
+collection_uuid_pattern = re.compile(r'^keep:([a-z0-9]{5}-4zz18-[a-z0-9]{15})(/.*)?$')
class ArvPathMapper(PathMapper):
"""Convert container-local paths to and from Keep collection ids."""
- pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+$')
- pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.*)?$')
-
def __init__(self, arvrunner, referenced_files, input_basedir,
collection_pattern, file_pattern, name=None, single_collection=False):
self.arvrunner = arvrunner
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.parse.unquote(src[5:]), srcobj["class"], True)
- if arvados_cwl.util.collectionUUID in srcobj:
- self.pdh_to_uuid[src.split("/", 1)[0][5:]] = srcobj[arvados_cwl.util.collectionUUID]
-
debug = logger.isEnabledFor(logging.DEBUG)
+ if isinstance(src, basestring) and src.startswith("keep:"):
+ if collection_pdh_pattern.match(src):
+ self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.parse.unquote(src[5:]), srcobj["class"], True)
+ if arvados_cwl.util.collectionUUID in srcobj:
+ self.pdh_to_uuid[src.split("/", 1)[0][5:]] = srcobj[arvados_cwl.util.collectionUUID]
+ elif not collection_uuid_pattern.match(src):
+ with SourceLine(srcobj, "location", WorkflowException, debug):
+ raise WorkflowException("Invalid keep reference '%s'" % src)
+
if src not in self._pathmap:
if src.startswith("file:"):
# Local FS ref, may need to be uploaded or may be on keep
class StagingPathMapper(PathMapper):
+ # Note that StagingPathMapper internally maps files from target to source.
+ # Specifically, the 'self._pathmap' dict keys are the target location and the
+ # values are 'MapperEnt' named tuples from which we use the 'resolved' attribute
+ # as the file identifier. This makes it possible to map an input file to multiple
+ # target directories. The exception is for file literals, which store the contents of
+ # the file in 'MapperEnt.resolved' and are therefore still mapped from source to target.
+
_follow_dirs = True
def __init__(self, referenced_files, basedir, stagedir, separateDirs=True):
loc = obj["location"]
tgt = os.path.join(stagedir, obj["basename"])
basetgt, baseext = os.path.splitext(tgt)
+
+ def targetExists():
+ return tgt in self.targets and ("contents" not in obj) and (self._pathmap[tgt].resolved != loc)
+ def literalTargetExists():
+ return tgt in self.targets and "contents" in obj
+
n = 1
- if tgt in self.targets and (self.reversemap(tgt)[0] != loc):
+ if targetExists() or literalTargetExists():
while tgt in self.targets:
n += 1
tgt = "%s_%i%s" % (basetgt, n, baseext)
if tgt in self._pathmap:
return
if "contents" in obj and loc.startswith("_:"):
- self._pathmap[tgt] = MapperEnt(obj["contents"], tgt, "CreateFile", staged)
+ self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile", staged)
else:
if copy or obj.get("writable"):
self._pathmap[tgt] = MapperEnt(loc, tgt, "WritableFile", staged)
self._pathmap[tgt] = MapperEnt(loc, tgt, "File", staged)
self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
- def mapper(self, src): # type: (Text) -> MapperEnt
+ def mapper(self, src): # type: (Text) -> MapperEnt.
+ # Overridden to maintain the use case of mapping by source (identifier) to
+ # target regardless of how the map is structured interally.
+ def getMapperEnt(src):
+ for k,v in viewitems(self._pathmap):
+ if (v.type != "CreateFile" and v.resolved == src) or (v.type == "CreateFile" and k == src):
+ return v
+
if u"#" in src:
- i = src.index(u"#")
- for k,v in self._pathmap.items():
- if v.resolved == src[:i]:
- return MapperEnt(v.resolved, v.target + src[i:], v.type, v.staged)
-
- for k,v in self._pathmap.items():
- if v.resolved == src:
- return self._pathmap[k]
+ i = src.index(u"#")
+ v = getMapperEnt(src[i:])
+ return MapperEnt(v.resolved, v.target + src[i:], v.type, v.staged)
+ return getMapperEnt(src)
class VwdPathMapper(StagingPathMapper):