Crunch script doesn't fail in file/directory literals that don't have a 'location...

[arvados.git] / sdk / cwl / arvados_cwl / fsaccess.py

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 3a3d16073833a6367876b5833b54cbb8f35584e7..534a675525ae60d90c08559e337dddc5b7d78934 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -4,6 +4,7 @@ import errno
 import urlparse
 import re
 import logging
+import threading
 
 import ruamel.yaml as yaml
 
@@ -20,24 +21,35 @@ from schema_salad.ref_resolver import DefaultFetcher
 
 logger = logging.getLogger('arvados.cwl-runner')
 
+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(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]
+
+
 class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
     """Implement the cwltool FsAccess interface for Arvados Collections."""
 
-    def __init__(self, basedir, api_client=None, keep_client=None):
+    def __init__(self, basedir, collection_cache=None):
         super(CollectionFsAccess, self).__init__(basedir)
-        self.api_client = api_client
-        self.keep_client = keep_client
-        self.collections = {}
+        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:]
-            if pdh not in self.collections:
-                self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client,
-                                                                            keep_client=self.keep_client)
-            return (self.collections[pdh], sp[1] if len(sp) == 2 else None)
+            return (self.collection_cache.get(pdh), sp[1] if len(sp) == 2 else None)
         else:
             return (None, path)
 
@@ -137,10 +149,10 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
             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):