make fsaccess required

Author: mr-c

cwltool/main.py

@@ -600,6 +600,7 @@ def main(argsl=None,                   # type: Optional[List[str]]
                 _logger.error("--provenance incompatible with --no-compute-checksum")
                 return 1
             ro = ResearchObject(
+                getdefault(runtimeContext.make_fs_access, StdFsAccess),
                 temp_prefix_ro=args.tmpdir_prefix, orcid=args.orcid,
                 full_name=args.cwl_full_name)
             runtimeContext.research_obj = ro
@@ -679,7 +680,6 @@ def formatTime(self, record, datefmt=None):
 
             if args.provenance and runtimeContext.research_obj:
                 # Can't really be combined with args.pack at same time
-                runtimeContext.research_obj.fsaccess = getdefault(runtimeContext.make_fs_access, StdFsAccess)
                 runtimeContext.research_obj.packed_workflow(
                     print_pack(loadingContext.loader, processobj, uri, metadata))
 

cwltool/provenance.py

@@ -305,14 +305,11 @@ def __init__(self,
                  host_provenance,        # type: bool
                  user_provenance,        # type: bool
                  orcid,                  # type: str
-                 run_uuid=None,           # type: Optional[uuid.UUID],
-                 fsaccess=None           # type: Optional[StdFsAccess]
+                 fsaccess,               # type: StdFsAccess
+                 run_uuid=None           # type: Optional[uuid.UUID]
                 ):  # type: (...) -> None
         """Initialize the provenance profile."""
-        if not fsaccess:
-            fsaccess = StdFsAccess('')
         self.fsaccess = fsaccess
-
         self.orcid = orcid
         self.research_object = research_object
         self.folder = self.research_object.folder
@@ -948,9 +945,8 @@ def finalize_prov_profile(self, name):
 class ResearchObject():
     """CWLProv Research Object."""
 
-    def __init__(self, temp_prefix_ro="tmp", orcid='', full_name='', fsaccess=None):
-        # type: (str, Text, Text) -> None
-        # type: Optional[StdFsAccess]
+    def __init__(self, fsaccess, temp_prefix_ro="tmp", orcid='', full_name=''):
+        # type: (StdFsAccess, str, Text, Text) -> None
         """Initialize the ResearchObject."""
         self.temp_prefix = temp_prefix_ro
         self.orcid = '' if not orcid else _valid_orcid(orcid)

tests/test_provenance.py

@@ -24,6 +24,7 @@
 from cwltool.main import main
 from cwltool.resolver import Path
 from cwltool.context import RuntimeContext
+from cwltool.stdfsaccess import StdFsAccess
 
 from .util import get_data, needs_docker, temp_dir, working_directory
 
@@ -513,7 +514,7 @@ def check_prov(base_path, nested=False, single_tool=False, directory=False,
 
 @pytest.fixture
 def research_object():
-    re_ob = provenance.ResearchObject()
+    re_ob = provenance.ResearchObject(StdFsAccess(''))
     yield re_ob
     re_ob.close()