7824: Merge branch 'master' into 7824-arvls-arvput-collection-api-usage

[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 02e16567012c8644f49e974c4f49ef9b968bd30b..70aa69f669be6d6e8c0a7210ea3da0808af3e6bc 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -3,6 +3,7 @@ import os
 import errno
 import urlparse
 import re
+import logging
 
 import ruamel.yaml as yaml
 
@@ -13,9 +14,12 @@ import cwltool.resolver
 import arvados.util
 import arvados.collection
 import arvados.arvfile
+import arvados.errors
 
 from schema_salad.ref_resolver import DefaultFetcher
 
+logger = logging.getLogger('arvados.cwl-runner')
+
 class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
     """Implement the cwltool FsAccess interface for Arvados Collections."""
 
@@ -26,13 +30,14 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
         self.collections = {}
 
     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:]
+        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], "/".join(p[1:]))
+            return (self.collections[pdh], sp[1] if len(sp) == 2 else None)
         else:
             return (None, path)
 
@@ -146,11 +151,19 @@ class CollectionFetcher(DefaultFetcher):
         return super(CollectionFetcher, self).fetch_text(url)
 
     def check_exists(self, url):
-        if url.startswith("keep:"):
-            return self.fsaccess.exists(url)
-        if url.startswith("arvwf:"):
-            if self.fetch_text(url):
+        try:
+            if url.startswith("http://arvados.org/cwl"):
                 return True
+            if url.startswith("keep:"):
+                return self.fsaccess.exists(url)
+            if url.startswith("arvwf:"):
+                if self.fetch_text(url):
+                    return True
+        except arvados.errors.NotFoundError:
+            return False
+        except:
+            logger.exception("Got unexpected exception checking if file exists:")
+            return False
         return super(CollectionFetcher, self).check_exists(url)
 
     def urljoin(self, base_url, url):