16139: Add test

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index aa68933c6abc17f2d19860c2cd838a3026546257..62ceab2fa11c1895983cd518fb2d4370a49da986 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -60,7 +60,7 @@ setup(name='arvados-cwl-runner',
       ],
       test_suite='tests',
       tests_require=[
-          'mock>=1.0',
+          'mock>=1.0,<4',
           'subprocess32>=3.5.1',
       ],
       zip_safe=True

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 927e43ad76c1fe1e547fd91dc026282726c82a1c..397ae142253d26b41d11aee03586fbc3e352bb31 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -388,6 +388,19 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
+
+    @stubs
+    def test_submit_container_tool(self, stubs):
+        # test for issue #16139
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+                "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
     @stubs
     def test_submit_container_no_reuse(self, stubs):
         exited = arvados_cwl.main(

diff --git a/sdk/cwl/tests/tool/blub.txt.cat b/sdk/cwl/tests/tool/blub.txt.cat
new file mode 100644 (file)
index 0000000..d7c4221
--- /dev/null
+++ b/sdk/cwl/tests/tool/blub.txt.cat
@@ -0,0 +1 @@
+clipper clupper

diff --git a/sdk/cwl/tests/tool/tool_with_sf.cwl b/sdk/cwl/tests/tool/tool_with_sf.cwl
new file mode 100644 (file)
index 0000000..0beb7ad
--- /dev/null
+++ b/sdk/cwl/tests/tool/tool_with_sf.cwl
@@ -0,0 +1,24 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+# Test case for arvados-cwl-runner
+#
+# Used to test whether scanning a tool file for dependencies (e.g. default
+# value blub.txt) and uploading to Keep works as intended.
+
+class: CommandLineTool
+cwlVersion: v1.0
+requirements:
+  - class: DockerRequirement
+    dockerPull: debian:8
+inputs:
+  - id: x
+    type: File
+    secondaryFiles:
+      - .cat
+    inputBinding:
+      valueFrom: $(self.path).cat
+      position: 1
+outputs: []
+baseCommand: cat

diff --git a/sdk/cwl/tests/tool/tool_with_sf.yml b/sdk/cwl/tests/tool/tool_with_sf.yml
new file mode 100644 (file)
index 0000000..3f79d57
--- /dev/null
+++ b/sdk/cwl/tests/tool/tool_with_sf.yml
@@ -0,0 +1,3 @@
+x:
+  class: File
+  location: blub.txt

diff --git a/sdk/python/setup.py b/sdk/python/setup.py
index 87977c2187e014017a2d76c4314ee3b1eede6b9c..ff68e2a7fd8888d10d56b96e13a5a9bf2690a177 100644 (file)
--- a/sdk/python/setup.py
+++ b/sdk/python/setup.py
@@ -64,6 +64,6 @@ setup(name='arvados-python-client',
           'Programming Language :: Python :: 3',
       ],
       test_suite='tests',
-      tests_require=['pbr<1.7.0', 'mock>=1.0', 'PyYAML'],
+      tests_require=['pbr<1.7.0', 'mock>=1.0,<4', 'PyYAML'],
       zip_safe=False
       )