X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a734789218122d8ab0d8f766bac4d69c04db91bf..0bb435a47e427b12fa2351141a22a1ba1e28a49d:/sdk/cwl/arvados_cwl/fsaccess.py

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 3a3d160738..5bdd8dd085 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -1,9 +1,14 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 import fnmatch
 import os
 import errno
 import urlparse
 import re
 import logging
+import threading
 
 import ruamel.yaml as yaml
 
@@ -20,24 +25,35 @@ 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)
 
@@ -65,21 +81,21 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def glob(self, pattern):
         collection, rest = self.get_collection(pattern)
-        if collection and not rest:
+        if collection is not None and not rest:
             return [pattern]
         patternsegments = rest.split("/")
         return self._match(collection, patternsegments, "keep:" + collection.manifest_locator())
 
     def open(self, fn, mode):
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             return collection.open(rest, mode)
         else:
             return super(CollectionFsAccess, self).open(self._abs(fn), mode)
 
     def exists(self, fn):
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             if rest:
                 return collection.exists(rest)
             else:
@@ -89,7 +105,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def isfile(self, fn):  # type: (unicode) -> bool
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             if rest:
                 return isinstance(collection.find(rest), arvados.arvfile.ArvadosFile)
             else:
@@ -99,7 +115,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def isdir(self, fn):  # type: (unicode) -> bool
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             if rest:
                 return isinstance(collection.find(rest), arvados.collection.RichCollectionBase)
             else:
@@ -109,7 +125,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def listdir(self, fn):  # type: (unicode) -> List[unicode]
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             if rest:
                 dir = collection.find(rest)
             else:
@@ -131,19 +147,22 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
         if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"):
             return path
         collection, rest = self.get_collection(path)
-        if collection:
+        if collection is not None:
             return path
         else:
             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, overrides=None):
         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
+        self.overrides = overrides if overrides else {}
 
     def fetch_text(self, url):
+        if url in self.overrides:
+            return self.overrides[url]
         if url.startswith("keep:"):
             with self.fsaccess.open(url, "r") as f:
                 return f.read()
@@ -154,6 +173,8 @@ class CollectionFetcher(DefaultFetcher):
         return super(CollectionFetcher, self).fetch_text(url)
 
     def check_exists(self, url):
+        if url in self.overrides:
+            return True
         try:
             if url.startswith("http://arvados.org/cwl"):
                 return True
@@ -206,6 +227,9 @@ workflow_uuid_pattern = re.compile(r'[a-z0-9]{5}-7fd4e-[a-z0-9]{15}')
 pipeline_template_uuid_pattern = re.compile(r'[a-z0-9]{5}-p5p6p-[a-z0-9]{15}')
 
 def collectionResolver(api_client, document_loader, uri, num_retries=4):
+    if uri.startswith("keep:") or uri.startswith("arvwf:"):
+        return uri
+
     if workflow_uuid_pattern.match(uri):
         return "arvwf:%s#main" % (uri)