propagate writable attribute to secondaryfiles

Fixes: #2131

Author: mr-c

cwltool/command_line_tool.py

@@ -611,10 +611,16 @@ def _initialworkdir(self, j: Optional[JobBase], builder: Builder) -> None:
                             continue
 
                     et: CWLObjectType = {}
+                    writable = t.get("writable", False)
+                    et["writable"] = writable
                     if isinstance(entry, Mapping) and entry.get("class") in (
                         "File",
                         "Directory",
                     ):
+                        if writable and "secondaryFiles" in entry:
+                            secFiles = cast(MutableSequence[CWLObjectType], entry["secondaryFiles"])
+                            for sf in secFiles:
+                                sf["writable"] = writable
                         et["entry"] = cast(CWLOutputType, entry)
                     else:
                         if isinstance(entry, str):
@@ -650,7 +656,6 @@ def _initialworkdir(self, j: Optional[JobBase], builder: Builder) -> None:
                             et["entryname"] = entryname_field
                     else:
                         et["entryname"] = None
-                    et["writable"] = t.get("writable", False)
                     ls.append(et)
                 else:
                     # Expression, must return a Dirent, File, Directory
@@ -700,13 +705,14 @@ def _initialworkdir(self, j: Optional[JobBase], builder: Builder) -> None:
                 )
 
             if t2.get("entryname") or t2.get("writable"):
-                t2 = copy.deepcopy(t2)
-                t2entry = cast(CWLObjectType, t2["entry"])
+                t2copy = copy.deepcopy(t2)
+                t2entry = cast(CWLObjectType, t2copy["entry"])
                 if t2.get("entryname"):
-                    t2entry["basename"] = t2["entryname"]
-                t2entry["writable"] = t2.get("writable")
+                    t2entry["basename"] = t2copy["entryname"]
+                t2entry["writable"] = t2copy.get("writable")
+                t2["entry"] = t2entry
 
-            ls[i] = cast(CWLObjectType, t2["entry"])
+            ls[i] = t2["entry"]
 
         for i, t3 in enumerate(ls):
             if t3.get("class") not in ("File", "Directory"):
@@ -753,14 +759,21 @@ def _initialworkdir(self, j: Optional[JobBase], builder: Builder) -> None:
             for entry in ls:
                 if "basename" in entry:
                     basename = cast(str, entry["basename"])
-                    entry["dirname"] = os.path.join(builder.outdir, os.path.dirname(basename))
+                    dirname = os.path.join(builder.outdir, os.path.dirname(basename))
+                    entry["dirname"] = dirname
                     entry["basename"] = os.path.basename(basename)
+                    if "secondaryFiles" in entry:
+                        for sec_file in cast(
+                            MutableSequence[CWLObjectType], entry["secondaryFiles"]
+                        ):
+                            sec_file["dirname"] = dirname
                 normalizeFilesDirs(entry)
                 self.updatePathmap(
                     cast(Optional[str], entry.get("dirname")) or builder.outdir,
                     cast(PathMapper, builder.pathmapper),
                     entry,
                 )
+
                 if "listing" in entry:
 
                     def remove_dirname(d: CWLObjectType) -> None:

cwltool/pathmapper.py

@@ -111,13 +111,13 @@ def visit(
         copy: bool = False,
         staged: bool = False,
     ) -> None:
+        if obj["location"] in self._pathmap:
+            return
         stagedir = cast(Optional[str], obj.get("dirname")) or stagedir
         tgt = os.path.join(
             stagedir,
             cast(str, obj["basename"]),
         )
-        if obj["location"] in self._pathmap:
-            return
         if obj["class"] == "Directory":
             location = cast(str, obj["location"])
             if location.startswith("file://"):

tests/iwdr_writable_secfile-inputs.json

@@ -0,0 +1,12 @@
+{
+    "example_file_with_secondary": {
+        "class": "File",
+        "location": "2.fasta",
+        "secondaryFiles": [
+            {
+                "class": "File",
+                "location": "2.fastq"
+            }
+        ]
+    }
+}

tests/iwdr_writable_secfile.cwl

@@ -0,0 +1,23 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement: 
+    listing:
+      - entry: $(inputs.example_file_with_secondary)
+        writable: true
+inputs:
+  example_file_with_secondary:
+    type: File
+    secondaryFiles:
+    - pattern: "^.fastq"
+      required: true
+outputs: 
+  same_file:
+    type: stdout
+
+baseCommand: cat
+arguments: 
+  - $(inputs.example_file_with_secondary.path)
+  - $(inputs.example_file_with_secondary.path.split('.')[0]+'.fastq')

tests/test_iwdr.py

@@ -376,3 +376,16 @@ def test_iwdr_permutations_singularity_inplace(
         )
         == 0
     )
+
+
+def test_iwdr_writable_secondaryfiles(tmp_path: Path) -> None:
+    """Confirm that a writable primary file and its secondary files are still co-located."""
+    err_code, _, _ = get_main_output(
+        [
+            "--outdir",
+            str(tmp_path),
+            get_data("tests/iwdr_writable_secfile.cwl"),
+            get_data("tests/iwdr_writable_secfile-inputs.json"),
+        ]
+    )
+    assert err_code == 0