Merge pull request #1233 from illusional/secondary-rename

Allow specification of file object in sec expression

Author: mr-c

cwltool/builder.py

@@ -390,31 +390,56 @@ def _capture_files(f):  # type: (Dict[str, str]) -> Dict[str, str]
                             if not sfname:
                                 continue
                             found = False
+
+                            if isinstance(sfname, str):
+                                sf_location = (
+                                    datum["location"][
+                                        0 : datum["location"].rindex("/") + 1
+                                    ]
+                                    + sfname
+                                )
+                                sfbasename = sfname
+                            elif isinstance(sfname, MutableMapping):
+                                sf_location = sfname["location"]
+                                sfbasename = sfname["basename"]
+                            else:
+                                raise WorkflowException(
+                                    "Expected secondaryFile expression to return type 'str' or 'MutableMapping', received '%s'"
+                                    % (type(sfname))
+                                )
+
                             for d in datum["secondaryFiles"]:
                                 if not d.get("basename"):
                                     d["basename"] = d["location"][
                                         d["location"].rindex("/") + 1 :
                                     ]
-                                if d["basename"] == sfname:
+                                if d["basename"] == sfbasename:
                                     found = True
+
                             if not found:
-                                sf_location = (
-                                    datum["location"][
-                                        0 : datum["location"].rindex("/") + 1
-                                    ]
-                                    + sfname
-                                )
+
+                                def addsf(
+                                    files: MutableSequence[MutableMapping[str, Any]],
+                                    newsf: MutableMapping[str, Any],
+                                ) -> None:
+                                    for f in files:
+                                        if f["location"] == newsf["location"]:
+                                            f["basename"] = newsf["basename"]
+                                            return
+                                    files.append(newsf)
+
                                 if isinstance(sfname, MutableMapping):
-                                    datum["secondaryFiles"].append(sfname)
+                                    addsf(datum["secondaryFiles"], sfname)
                                 elif discover_secondaryFiles and self.fs_access.exists(
                                     sf_location
                                 ):
-                                    datum["secondaryFiles"].append(
+                                    addsf(
+                                        datum["secondaryFiles"],
                                         {
                                             "location": sf_location,
                                             "basename": sfname,
                                             "class": "File",
-                                        }
+                                        },
                                     )
                                 elif sf_required:
                                     raise WorkflowException(