From 66ef73b96e38c87a84ae64bd19385d5d5e9e07ed Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Tue, 10 May 2022 15:34:07 -0400
Subject: [PATCH] 19109: Add test case for discovering & uploading secondary
 files

Correctly find secondary files in the optional "File?" case

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 .licenseignore                                |  1 +
 sdk/cwl/arvados_cwl/runner.py                 |  3 +++
 sdk/cwl/tests/19109-upload-secondary.cwl      | 22 +++++++++++++++++++
 sdk/cwl/tests/19109-upload-secondary.yml      |  7 ++++++
 .../tests/19109-upload-secondary/file1.txt    |  1 +
 .../19109-upload-secondary/file1.txt.tbi      |  1 +
 sdk/cwl/tests/arvados-tests.yml               | 13 +++++++++++
 sdk/cwl/tests/cat2.cwl                        | 17 ++++++++++++++
 8 files changed, 65 insertions(+)
 create mode 100644 sdk/cwl/tests/19109-upload-secondary.cwl
 create mode 100644 sdk/cwl/tests/19109-upload-secondary.yml
 create mode 100644 sdk/cwl/tests/19109-upload-secondary/file1.txt
 create mode 100644 sdk/cwl/tests/19109-upload-secondary/file1.txt.tbi
 create mode 100644 sdk/cwl/tests/cat2.cwl

diff --git a/.licenseignore b/.licenseignore
index 387aeda944..203c378bdc 100644
--- a/.licenseignore
+++ b/.licenseignore
@@ -50,6 +50,7 @@ docker/jobs/1078ECD7.key
 */script/rails
 sdk/cwl/tests/input/blorp.txt
 sdk/cwl/tests/tool/blub.txt
+sdk/cwl/tests/19109-upload-secondary/*
 sdk/cwl/tests/federation/data/*
 sdk/cwl/tests/fake-keep-mount/fake_collection_dir/.arvados#collection
 sdk/go/manifest/testdata/*_manifest
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 7d4310b0e0..f2517f9199 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -128,6 +128,9 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             set_secondary(fsaccess, builder, i, secondaryspec, primary, discovered)
         return
 
+    if inputschema == "File":
+        inputschema = {"type": "File"}
+
     if isinstance(inputschema, basestring):
         sd = search_schemadef(inputschema, reversed(builder.hints+builder.requirements))
         if sd:
diff --git a/sdk/cwl/tests/19109-upload-secondary.cwl b/sdk/cwl/tests/19109-upload-secondary.cwl
new file mode 100644
index 0000000000..cf5855ab19
--- /dev/null
+++ b/sdk/cwl/tests/19109-upload-secondary.cwl
@@ -0,0 +1,22 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.2
+class: Workflow
+inputs:
+  file1:
+    type: File?
+    secondaryFiles:
+      - pattern: .tbi
+        required: true
+outputs:
+  out:
+    type: File
+    outputSource: cat/out
+steps:
+  cat:
+    in:
+      inp: file1
+    run: cat2.cwl
+    out: [out]
diff --git a/sdk/cwl/tests/19109-upload-secondary.yml b/sdk/cwl/tests/19109-upload-secondary.yml
new file mode 100644
index 0000000000..c97850019b
--- /dev/null
+++ b/sdk/cwl/tests/19109-upload-secondary.yml
@@ -0,0 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+file1:
+  class: File
+  location: 19109-upload-secondary/file1.txt
diff --git a/sdk/cwl/tests/19109-upload-secondary/file1.txt b/sdk/cwl/tests/19109-upload-secondary/file1.txt
new file mode 100644
index 0000000000..41549dbf8c
--- /dev/null
+++ b/sdk/cwl/tests/19109-upload-secondary/file1.txt
@@ -0,0 +1 @@
+strawberry
diff --git a/sdk/cwl/tests/19109-upload-secondary/file1.txt.tbi b/sdk/cwl/tests/19109-upload-secondary/file1.txt.tbi
new file mode 100644
index 0000000000..c9438bd232
--- /dev/null
+++ b/sdk/cwl/tests/19109-upload-secondary/file1.txt.tbi
@@ -0,0 +1 @@
+blueberry
\ No newline at end of file
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 9e691bdba5..836e667008 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -449,3 +449,16 @@
   output: {}
   tool: 18994-basename/wf_ren.cwl
   doc: "Test issue 18994 - correctly stage file with modified basename"
+
+- job: 19109-upload-secondary.yml
+  output: {
+    "out": {
+        "basename": "catted",
+        "class": "File",
+        "location": "catted",
+        "size": 20,
+        "checksum": "sha1$c4cead17cebdd829f38c48e18a28f1da72339ef7"
+    }
+  }
+  tool: 19109-upload-secondary.cwl
+  doc: "Test issue 19109 - correctly discover & upload secondary files"
diff --git a/sdk/cwl/tests/cat2.cwl b/sdk/cwl/tests/cat2.cwl
new file mode 100644
index 0000000000..f8cd57822d
--- /dev/null
+++ b/sdk/cwl/tests/cat2.cwl
@@ -0,0 +1,17 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.2
+class: CommandLineTool
+inputs:
+  - id: inp
+    type: File
+    secondaryFiles:
+      - pattern: .tbi
+        required: true
+stdout: catted
+outputs:
+  out:
+    type: stdout
+arguments: [cat, '$(inputs.inp.path)', '$(inputs.inp.secondaryFiles[0].path)']
-- 
2.30.2