From 4bb5329997cb84562a40733b5c2f55600b1a741a Mon Sep 17 00:00:00 2001
From: Francis Charette-Migneault <francis.charette.migneault@gmail.com>
Date: Mon, 9 Sep 2024 12:49:51 -0400
Subject: [PATCH] fix `loadContents` for `File[]` (#2036)

---
 .gitignore                    |  3 ++-
 cwltool/builder.py            |  4 ++--
 tests/load_contents-1.txt     |  1 +
 tests/load_contents-2.txt     |  1 +
 tests/load_contents-array.cwl | 24 ++++++++++++++++++++++++
 tests/load_contents-array.yml |  5 +++++
 tests/test_load_contents.py   | 22 ++++++++++++++++++++++
 7 files changed, 57 insertions(+), 3 deletions(-)
 create mode 100644 tests/load_contents-1.txt
 create mode 100644 tests/load_contents-2.txt
 create mode 100644 tests/load_contents-array.cwl
 create mode 100644 tests/load_contents-array.yml
 create mode 100644 tests/test_load_contents.py

diff --git a/.gitignore b/.gitignore
index 5941627f8..fbe4b24fc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,8 @@
 # Generated during tests
 pytestdebug.log
 tmp/
+*.sif
+involucro
 
 # Python temps
 __pycache__/
@@ -59,4 +61,3 @@ cwltool/_version.py
 cwltool_deps
 docs/_build/
 docs/autoapi/
-
diff --git a/cwltool/builder.py b/cwltool/builder.py
index ff1c099e5..2ba1e6543 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -282,7 +282,7 @@ def bind_input(
                 and "itemSeparator" not in binding
             ):
                 st["inputBinding"] = {}
-            for k in ("secondaryFiles", "format", "streamable"):
+            for k in ("secondaryFiles", "format", "streamable", "loadContents"):
                 if k in schema:
                     st[k] = schema[k]
             if value_from_expression:
@@ -349,7 +349,7 @@ def bind_input(
                         "type": schema["items"],
                         "inputBinding": b2,
                     }
-                    for k in ("secondaryFiles", "format", "streamable"):
+                    for k in ("secondaryFiles", "format", "streamable", "loadContents"):
                         if k in schema:
                             itemschema[k] = schema[k]
                     bindings.extend(
diff --git a/tests/load_contents-1.txt b/tests/load_contents-1.txt
new file mode 100644
index 000000000..d00491fd7
--- /dev/null
+++ b/tests/load_contents-1.txt
@@ -0,0 +1 @@
+1
diff --git a/tests/load_contents-2.txt b/tests/load_contents-2.txt
new file mode 100644
index 000000000..0cfbf0888
--- /dev/null
+++ b/tests/load_contents-2.txt
@@ -0,0 +1 @@
+2
diff --git a/tests/load_contents-array.cwl b/tests/load_contents-array.cwl
new file mode 100644
index 000000000..f6b786ec6
--- /dev/null
+++ b/tests/load_contents-array.cwl
@@ -0,0 +1,24 @@
+cwlVersion: "v1.2"
+class: CommandLineTool
+baseCommand: echo
+requirements:
+  InlineJavascriptRequirement: {}
+inputs:
+  files:
+    type:
+      type: array
+      items: File
+    loadContents: true
+    inputBinding:
+      valueFrom: |
+        ${
+          return JSON.stringify({
+            "data": inputs.files.map(item => parseInt(item.contents))
+          });
+        }
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: "data.json"
+stdout: "data.json"
diff --git a/tests/load_contents-array.yml b/tests/load_contents-array.yml
new file mode 100644
index 000000000..b7a919340
--- /dev/null
+++ b/tests/load_contents-array.yml
@@ -0,0 +1,5 @@
+files:
+  - class: File
+    path: load_contents-1.txt
+  - class: File
+    path: load_contents-2.txt
diff --git a/tests/test_load_contents.py b/tests/test_load_contents.py
new file mode 100644
index 000000000..36e9da2ab
--- /dev/null
+++ b/tests/test_load_contents.py
@@ -0,0 +1,22 @@
+"""Test the loadContents feature."""
+
+import json
+from pathlib import Path
+
+from cwltool.main import main
+
+from .util import get_data
+
+
+def test_load_contents_file_array(tmp_path: Path) -> None:
+    """Ensures that a File[] input with loadContents loads each file."""
+    params = [
+        "--outdir",
+        str(tmp_path),
+        get_data("tests/load_contents-array.cwl"),
+        str(Path(__file__) / "../load_contents-array.yml"),
+    ]
+    assert main(params) == 0
+    with open(tmp_path / "data.json") as out_fd:
+        data = json.load(out_fd)
+    assert data == {"data": [1, 2]}