X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/4aa95be0abb99cdd2aa1317bf5ec350af412e595..55e73facf08cc8651eb71529a2ab4e0657d3c870:/sdk/cwl/arvados_cwl/fsaccess.py

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 16ec2b2f96..716cda335d 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -17,7 +17,7 @@ import logging
 import threading
 from collections import OrderedDict
 
-import ruamel.yaml as yaml
+import ruamel.yaml
 
 import cwltool.stdfsaccess
 from cwltool.pathmapper import abspath
@@ -100,7 +100,8 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
         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)
 
@@ -128,7 +129,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     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()))
@@ -234,7 +235,8 @@ class CollectionFetcher(DefaultFetcher):
                 return f.read()
         if url.startswith("arvwf:"):
             record = self.api_client.workflows().get(uuid=url[6:]).execute(num_retries=self.num_retries)
-            definition = yaml.round_trip_load(record["definition"])
+            yaml = ruamel.yaml.YAML(typ='rt', pure=True)
+            definition = yaml.load(record["definition"])
             definition["label"] = record["name"]
             return yaml.round_trip_dump(definition)
         return super(CollectionFetcher, self).fetch_text(url)
@@ -243,10 +245,11 @@ class CollectionFetcher(DefaultFetcher):
         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):
+            urld, _ = urllib.parse.urldefrag(url)
+            if urld.startswith("keep:"):
+                return self.fsaccess.exists(urld)
+            if urld.startswith("arvwf:"):
+                if self.fetch_text(urld):
                     return True
         except arvados.errors.NotFoundError:
             return False