import urlparse
import re
import logging
+import threading
import ruamel.yaml as yaml
logger = logging.getLogger('arvados.cwl-runner')
-class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
- """Implement the cwltool FsAccess interface for Arvados Collections."""
-
- def __init__(self, basedir, api_client=None, keep_client=None):
- super(CollectionFsAccess, self).__init__(basedir)
+class CollectionCache(object):
+ def __init__(self, api_client, keep_client, num_retries):
self.api_client = api_client
self.keep_client = keep_client
self.collections = {}
+ self.lock = threading.Lock()
- def get_collection(self, path):
- p = path.split("/")
- if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]):
- pdh = p[0][5:]
+ def get(self, pdh):
+ with self.lock:
if pdh not in self.collections:
+ logger.debug("Creating collection reader for %s", pdh)
self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client,
keep_client=self.keep_client)
- return (self.collections[pdh], "/".join(p[1:]))
+ return self.collections[pdh]
+
+
+class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
+ """Implement the cwltool FsAccess interface for Arvados Collections."""
+
+ def __init__(self, basedir, collection_cache=None):
+ super(CollectionFsAccess, self).__init__(basedir)
+ self.collection_cache = collection_cache
+
+ def get_collection(self, path):
+ sp = path.split("/", 1)
+ p = sp[0]
+ if p.startswith("keep:") and arvados.util.keep_locator_pattern.match(p[5:]):
+ pdh = p[5:]
+ return (self.collection_cache.get(pdh), sp[1] if len(sp) == 2 else None)
else:
return (None, path)
def exists(self, fn):
collection, rest = self.get_collection(fn)
if collection:
- return collection.exists(rest)
+ if rest:
+ return collection.exists(rest)
+ else:
+ return True
else:
return super(CollectionFsAccess, self).exists(fn)
return os.path.realpath(path)
class CollectionFetcher(DefaultFetcher):
- def __init__(self, cache, session, api_client=None, keep_client=None, num_retries=4):
+ def __init__(self, cache, session, api_client=None, fs_access=None, num_retries=4):
super(CollectionFetcher, self).__init__(cache, session)
self.api_client = api_client
- self.fsaccess = CollectionFsAccess("", api_client=api_client, keep_client=keep_client)
+ self.fsaccess = fs_access
self.num_retries = num_retries
def fetch_text(self, url):
def check_exists(self, url):
try:
+ if url.startswith("http://arvados.org/cwl"):
+ return True
if url.startswith("keep:"):
return self.fsaccess.exists(url)
if url.startswith("arvwf:"):