fix typeshed error

Author: mr-c

cwltool/provenance.py

@@ -1018,13 +1018,13 @@ def _initialize_bagit(self):  # type: () -> None
     def open_log_file_for_activity(self, uuid_uri): # type: (Text) -> IO
         self.self_check()
         # Ensure valid UUID for safe filenames
-        activity_uuid = uuid.UUID(uuid_uri.replace("urn:uuid:", ""))
+        activity_uuid = uuid.UUID(uuid_uri)
         if activity_uuid.urn == self.engine_uuid:
             # It's the engine aka cwltool!
             name = "engine"
         else:
             name = "activity"
-        p = os.path.join(LOGS, "%s.%s.txt" % (name, activity_uuid))
+        p = os.path.join(LOGS, "{}.{}.txt".format(name, activity_uuid))
         _logger.debug("[provenance] Opening log file for %s: %s" % (name, p))
         self.add_annotation(activity_uuid.urn, [p], CWLPROV["log"].uri)
         return self.write_bag_file(p)
@@ -1363,8 +1363,8 @@ def _write_bag_info(self):
 
     def generate_snapshot(self, prov_dep):
         # type: (MutableMapping[Text, Any]) -> None
-        self.self_check()
         """Copy all of the CWL files to the snapshot/ directory."""
+        self.self_check()
         for key, value in prov_dep.items():
             if key == "location" and value.split("/")[-1]:
                 filename = value.split("/")[-1]

typeshed/2and3/uuid.pyi

@@ -0,0 +1,94 @@
+# Stubs for uuid
+
+import sys
+from typing import Tuple, Optional, Any, Union
+
+# Because UUID has properties called int and bytes we need to rename these temporarily.
+_Int = int
+_Bytes = bytes
+_FieldsType = Tuple[int, int, int, int, int, int]
+if sys.version_info >= (3,):
+    _Text = str
+else:
+    _Text = Union[str, unicode]
+
+class UUID:
+    def __init__(self, hex: Optional[_Text] = ...,
+                 bytes: Optional[_Bytes] = ...,
+                 bytes_le: Optional[_Bytes] = ...,
+                 fields: Optional[_FieldsType] = ...,
+                 int: Optional[_Int] = ...,
+                 version: Optional[_Int] = ...) -> None: ...
+    @property
+    def bytes(self) -> _Bytes: ...
+    @property
+    def bytes_le(self) -> _Bytes: ...
+    @property
+    def clock_seq(self) -> _Int: ...
+    @property
+    def clock_seq_hi_variant(self) -> _Int: ...
+    @property
+    def clock_seq_low(self) -> _Int: ...
+    @property
+    def fields(self) -> _FieldsType: ...
+    @property
+    def hex(self) -> str: ...
+    @property
+    def int(self) -> _Int: ...
+    @property
+    def node(self) -> _Int: ...
+    @property
+    def time(self) -> _Int: ...
+    @property
+    def time_hi_version(self) -> _Int: ...
+    @property
+    def time_low(self) -> _Int: ...
+    @property
+    def time_mid(self) -> _Int: ...
+    @property
+    def urn(self) -> str: ...
+    @property
+    def variant(self) -> str: ...
+    @property
+    def version(self) -> Optional[_Int]: ...
+
+    def __int__(self) -> _Int: ...
+
+    if sys.version_info >= (3,):
+        def __eq__(self, other: Any) -> bool: ...
+        def __lt__(self, other: Any) -> bool: ...
+        def __le__(self, other: Any) -> bool: ...
+        def __gt__(self, other: Any) -> bool: ...
+        def __ge__(self, other: Any) -> bool: ...
+    else:
+        def get_bytes(self) -> _Bytes: ...
+        def get_bytes_le(self) -> _Bytes: ...
+        def get_clock_seq(self) -> _Int: ...
+        def get_clock_seq_hi_variant(self) -> _Int: ...
+        def get_clock_seq_low(self) -> _Int: ...
+        def get_fields(self) -> _FieldsType: ...
+        def get_hex(self) -> str: ...
+        def get_node(self) -> _Int: ...
+        def get_time(self) -> _Int: ...
+        def get_time_hi_version(self) -> _Int: ...
+        def get_time_low(self) -> _Int: ...
+        def get_time_mid(self) -> _Int: ...
+        def get_urn(self) -> str: ...
+        def get_variant(self) -> str: ...
+        def get_version(self) -> Optional[_Int]: ...
+        def __cmp__(self, other: Any) -> _Int: ...
+
+def getnode() -> int: ...
+def uuid1(node: Optional[_Int] = ..., clock_seq: Optional[_Int] = ...) -> UUID: ...
+def uuid3(namespace: UUID, name: str) -> UUID: ...
+def uuid4() -> UUID: ...
+def uuid5(namespace: UUID, name: str) -> UUID: ...
+
+NAMESPACE_DNS = ...  # type: UUID
+NAMESPACE_URL = ...  # type: UUID
+NAMESPACE_OID = ...  # type: UUID
+NAMESPACE_X500 = ...  # type: UUID
+RESERVED_NCS = ...  # type: str
+RFC_4122 = ...  # type: str
+RESERVED_MICROSOFT = ...  # type: str
+RESERVED_FUTURE = ...  # type: str