Fix writable flag. Was not correctly propagated from 'entry' to path mapper,

and job.py was overwriting the modified output file by accident.

Author: Peter Amstutz

cwltool/draft2tool.py

@@ -295,6 +295,7 @@ def rm_pending_output_callback(output_callback, jobcachepending,
                             et["entryname"] = builder.do_eval(t["entryname"])
                         else:
                             et["entryname"] = None
+                        et["writable"] = t.get("writable", False)
                         ls.append(et)
                     else:
                         ls.append(builder.do_eval(t))
@@ -304,12 +305,14 @@ def rm_pending_output_callback(output_callback, jobcachepending,
                         ls[i] = {
                             "class": "File",
                             "basename": t["entryname"],
-                            "contents": t["entry"]
+                            "contents": t["entry"],
+                            "writable": t.get("writable")
                         }
                     else:
                         if t["entryname"]:
                             t = copy.deepcopy(t)
                             t["entry"]["basename"] = t["entryname"]
+                            t["entry"]["writable"] = t.get("writable")
                         ls[i] = t["entry"]
             j.generatefiles[u"listing"] = ls
 

cwltool/job.py

@@ -58,7 +58,7 @@ def __init__(self):  # type: () -> None
         self.outdir = None  # type: str
         self.tmpdir = None  # type: str
         self.environment = None  # type: Dict[str,str]
-        self.generatefiles = None  # type: Dict[unicode, Union[List[Dict[str, str]], Dict[str,str], str]] 
+        self.generatefiles = None  # type: Dict[unicode, Union[List[Dict[str, str]], Dict[str,str], str]]
         self.stagedir = None  # type: unicode
 
     def run(self, dry_run=False, pull_image=True, rm_container=True,
@@ -251,7 +251,7 @@ def linkoutdir(src, tgt):
                     if os.path.exists(tgt) and os.path.islink(tgt):
                         os.remove(tgt)
                         os.symlink(src, tgt)
-                stageFiles(generatemapper, linkoutdir)
+                stageFiles(generatemapper, linkoutdir, ignoreWritable=True)
 
             outputs = self.collect_outputs(self.outdir)
 

cwltool/process.py

@@ -169,16 +169,16 @@ def getListing(fs_access, rec):
                 listing.append({"class": "File", "location": ld})
         rec["listing"] = listing
 
-def stageFiles(pm, stageFunc):
+def stageFiles(pm, stageFunc, ignoreWritable=False):
     # type: (PathMapper, Callable[..., Any]) -> None
     for f, p in pm.items():
         if not os.path.exists(os.path.dirname(p.target)):
             os.makedirs(os.path.dirname(p.target), 0755)
         if p.type == "File":
             stageFunc(p.resolved, p.target)
-        elif p.type == "WritableFile":
+        elif p.type == "WritableFile" and not ignoreWritable:
             shutil.copy(p.resolved, p.target)
-        elif p.type == "CreateFile":
+        elif p.type == "CreateFile" and not ignoreWritable:
             with open(p.target, "w") as n:
                 n.write(p.resolved.encode("utf-8"))