14198: Update version deps for schema-salad, cwltool, ruamel.yaml, requests

[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 0b577b06a2e324dbea743244da955f2661a52bea..b22b2ffd6f4574ea6a774064d782fbfd07c7a94d 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -22,6 +22,8 @@ import arvados.collection
 import arvados.arvfile
 import arvados.errors
 
+from googleapiclient.errors import HttpError
+
 from schema_salad.ref_resolver import DefaultFetcher
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -81,7 +83,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
         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)
+            return (self.collection_cache.get(pdh), urlparse.unquote(sp[1]) if len(sp) == 2 else None)
         else:
             return (None, path)
 
@@ -122,7 +124,13 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
             return super(CollectionFsAccess, self).open(self._abs(fn), mode)
 
     def exists(self, fn):
-        collection, rest = self.get_collection(fn)
+        try:
+            collection, rest = self.get_collection(fn)
+        except HttpError as err:
+            if err.resp.status == 404:
+                return False
+            else:
+                raise
         if collection is not None:
             if rest:
                 return collection.exists(rest)
@@ -131,6 +139,17 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
         else:
             return super(CollectionFsAccess, self).exists(fn)
 
+    def size(self, fn):  # type: (unicode) -> bool
+        collection, rest = self.get_collection(fn)
+        if collection is not None:
+            if rest:
+                arvfile = collection.find(rest)
+                if isinstance(arvfile, arvados.arvfile.ArvadosFile):
+                    return arvfile.size()
+            raise IOError(errno.EINVAL, "Not a path to a file %s" % (fn))
+        else:
+            return super(CollectionFsAccess, self).size(fn)
+
     def isfile(self, fn):  # type: (unicode) -> bool
         collection, rest = self.get_collection(fn)
         if collection is not None:
@@ -246,6 +265,12 @@ class CollectionFetcher(DefaultFetcher):
 
         return super(CollectionFetcher, self).urljoin(base_url, url)
 
+    schemes = [u"file", u"http", u"https", u"mailto", u"keep"]
+
+    def supported_schemes(self):  # type: () -> List[Text]
+        return self.schemes
+
+
 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}')