Merge branch '9307-cwl-use-tmp-output' closes #9307 closes #9308

[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 06edac91758d16234410884d2c622be493ea15f6..89a4308bf14ef2d5f9f3275ddcc4201e749205d8 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -1,18 +1,21 @@
 import fnmatch
 import os
+import errno
 
-import cwltool.process
+import cwltool.stdfsaccess
 from cwltool.pathmapper import abspath
 
 import arvados.util
 import arvados.collection
 import arvados.arvfile
 
-class CollectionFsAccess(cwltool.process.StdFsAccess):
+class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
     """Implement the cwltool FsAccess interface for Arvados Collections."""
 
-    def __init__(self, basedir):
+    def __init__(self, basedir, api_client=None, keep_client=None):
         super(CollectionFsAccess, self).__init__(basedir)
+        self.api_client = api_client
+        self.keep_client = keep_client
         self.collections = {}
 
     def get_collection(self, path):
@@ -20,7 +23,8 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
         if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]):
             pdh = p[0][5:]
             if pdh not in self.collections:
-                self.collections[pdh] = arvados.collection.CollectionReader(pdh)
+                self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client,
+                                                                            keep_client=self.keep_client)
             return (self.collections[pdh], "/".join(p[1:]))
         else:
             return (None, path)
@@ -49,6 +53,8 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
 
     def glob(self, pattern):
         collection, rest = self.get_collection(pattern)
+        if collection and not rest:
+            return [pattern]
         patternsegments = rest.split("/")
         return self._match(collection, patternsegments, "keep:" + collection.manifest_locator())
 
@@ -69,21 +75,48 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
     def isfile(self, fn):  # type: (unicode) -> bool
         collection, rest = self.get_collection(fn)
         if collection:
-            return isinstance(collection.find(rest), arvados.arvfile.ArvadosFile)
+            if rest:
+                return isinstance(collection.find(rest), arvados.arvfile.ArvadosFile)
+            else:
+                return False
         else:
             return super(CollectionFsAccess, self).isfile(fn)
 
     def isdir(self, fn):  # type: (unicode) -> bool
         collection, rest = self.get_collection(fn)
         if collection:
-            return isinstance(collection.find(rest), arvados.arvfile.Collection)
+            if rest:
+                return isinstance(collection.find(rest), arvados.collection.RichCollectionBase)
+            else:
+                return True
         else:
             return super(CollectionFsAccess, self).isdir(fn)
 
     def listdir(self, fn):  # type: (unicode) -> List[unicode]
         collection, rest = self.get_collection(fn)
-        dir = collection.find(rest)
         if collection:
+            if rest:
+                dir = collection.find(rest)
+            else:
+                dir = collection
+            if dir is None:
+                raise IOError(errno.ENOENT, "Directory '%s' in '%s' not found" % (rest, collection.portable_data_hash()))
+            if not isinstance(dir, arvados.collection.RichCollectionBase):
+                raise IOError(errno.ENOENT, "Path '%s' in '%s' is not a Directory" % (rest, collection.portable_data_hash()))
             return [abspath(l, fn) for l in dir.keys()]
         else:
             return super(CollectionFsAccess, self).listdir(fn)
+
+    def join(self, path, *paths): # type: (unicode, *unicode) -> unicode
+        if paths and paths[-1].startswith("keep:") and arvados.util.keep_locator_pattern.match(paths[-1][5:]):
+            return paths[-1]
+        return os.path.join(path, *paths)
+
+    def realpath(self, path):
+        if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"):
+            return path
+        collection, rest = self.get_collection(path)
+        if collection:
+            return path
+        else:
+            return os.path.realpath(path)