if m:
self.cap_cache(int(m.group(2)) * 128)
logger.debug("Creating collection reader for %s", locator)
- cr = arvados.collection.CollectionReader(locator, api_client=self.api_client,
- keep_client=self.keep_client,
- num_retries=self.num_retries)
+ try:
+ cr = arvados.collection.CollectionReader(locator, api_client=self.api_client,
+ keep_client=self.keep_client,
+ num_retries=self.num_retries)
+ except arvados.errors.ApiError as ap:
+ raise IOError(errno.ENOENT, "Could not access collection '%s': %s" % (locator, str(ap._get_reason())))
sz = len(cr.manifest_text()) * 128
self.collections[locator] = (cr, sz)
self.total += sz
if p.startswith("keep:") and (arvados.util.keep_locator_pattern.match(p[5:]) or
arvados.util.collection_uuid_pattern.match(p[5:])):
locator = p[5:]
- return (self.collection_cache.get(locator), urllib.parse.unquote(sp[1]) if len(sp) == 2 else None)
+ rest = os.path.normpath(urllib.parse.unquote(sp[1])) if len(sp) == 2 else None
+ return (self.collection_cache.get(locator), rest)
else:
return (None, path)
def glob(self, pattern):
collection, rest = self.get_collection(pattern)
- if collection is not None and not rest:
+ if collection is not None and rest in (None, "", "."):
return [pattern]
patternsegments = rest.split("/")
return sorted(self._match(collection, patternsegments, "keep:" + collection.manifest_locator()))
- def open(self, fn, mode):
+ def open(self, fn, mode, encoding=None):
collection, rest = self.get_collection(fn)
if collection is not None:
- return collection.open(rest, mode)
+ return collection.open(rest, mode, encoding=encoding)
else:
return super(CollectionFsAccess, self).open(self._abs(fn), mode)
return False
else:
raise
+ except IOError as err:
+ if err.errno == errno.ENOENT:
+ return False
+ else:
+ raise
if collection is not None:
if rest:
return collection.exists(rest)
self.fsaccess = fs_access
self.num_retries = num_retries
- def fetch_text(self, url):
+ def fetch_text(self, url, content_types=None):
if url.startswith("keep:"):
- with self.fsaccess.open(url, "r") as f:
+ with self.fsaccess.open(url, "r", encoding="utf-8") as f:
return f.read()
if url.startswith("arvwf:"):
record = self.api_client.workflows().get(uuid=url[6:]).execute(num_retries=self.num_retries)
- definition = record["definition"] + ('\nlabel: "%s"\n' % record["name"].replace('"', '\\"'))
- return definition
+ definition = yaml.round_trip_load(record["definition"])
+ definition["label"] = record["name"]
+ return yaml.round_trip_dump(definition)
return super(CollectionFetcher, self).fetch_text(url)
def check_exists(self, url):
locator = baseparts.pop(0)
if (basesp.scheme == "keep" and
- (not arvados.util.keep_locator_pattern.match(pdh)) and
- (not arvados.util.collection_uuid_pattern.match(pdh))):
+ (not arvados.util.keep_locator_pattern.match(locator)) and
+ (not arvados.util.collection_uuid_pattern.match(locator))):
raise IOError(errno.EINVAL, "Invalid Keep locator", base_url)
if urlsp.path.startswith("/"):