From 6f313a500efec4ddf0936460fccaee1c5b1f1215 Mon Sep 17 00:00:00 2001
From: Jake Fennick <jake.fennick@axleinfo.com>
Date: Wed, 12 Jun 2024 13:57:10 -1000
Subject: [PATCH] recursively insert output format

---
 cwltool/command_line_tool.py    | 15 +++++++++++++--
 tests/output_2D_file_format.cwl | 29 +++++++++++++++++++++++++++++
 tests/test_2D.py                | 17 +++++++++++++++++
 3 files changed, 59 insertions(+), 2 deletions(-)
 create mode 100644 tests/output_2D_file_format.cwl
 create mode 100644 tests/test_2D.py

diff --git a/cwltool/command_line_tool.py b/cwltool/command_line_tool.py
index b11bb4bc37..4afd84228c 100644
--- a/cwltool/command_line_tool.py
+++ b/cwltool/command_line_tool.py
@@ -1495,8 +1495,19 @@ def collect_output(
                             )
                         primary["format"] = format_eval
                 else:
-                    for primary in aslist(result):
-                        primary["format"] = format_field
+
+                    def recursively_insert(j_dict: Any, key: Any, val: Any) -> Any:
+                        """Recursively inserts a value into any dictionaries"""
+                        if isinstance(j_dict, List):
+                            return [recursively_insert(x, key, val) for x in j_dict]
+                        if isinstance(j_dict, Dict):
+                            if j_dict.get("class") == "File":
+                                j_dict[key] = val
+                            else:
+                                return {x: recursively_insert(y, key, val) for x, y in j_dict.items()}
+                        return j_dict
+
+                    result = recursively_insert(result, "format", format_field)
             # Ensure files point to local references outside of the run environment
             adjustFileObjs(result, revmap)
 
diff --git a/tests/output_2D_file_format.cwl b/tests/output_2D_file_format.cwl
new file mode 100644
index 0000000000..6211110615
--- /dev/null
+++ b/tests/output_2D_file_format.cwl
@@ -0,0 +1,29 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+baseCommand: 'true'
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs: {}
+
+outputs:
+  output_array:
+    type: {"type": "array", "items": {"type": "array", "items": "File"}}
+    outputBinding:
+      outputEval: |
+        ${
+          var out2d = [];
+          for (var i = 0; i < 2; i++) {
+            var out1d = [];
+            for (var j = 0; j < 2; j++) {
+              out1d.push({"class": "File", "location": "../../filename.txt"});
+            }
+            out2d.push(out1d);
+          }
+          return out2d;
+        }
+    format: some_format
diff --git a/tests/test_2D.py b/tests/test_2D.py
new file mode 100644
index 0000000000..305840bb91
--- /dev/null
+++ b/tests/test_2D.py
@@ -0,0 +1,17 @@
+import subprocess
+import sys
+
+from .util import get_data
+
+
+def test_output_2D_file_format() -> None:
+    """Test format tag for 2D output arrays."""
+
+    params = [
+        sys.executable,
+        "-m",
+        "cwltool",
+        get_data("tests/output_2D_file_format.cwl"),
+    ]
+
+    assert subprocess.check_call(params) == 0