[ARVADOS] created: 2.1.0-1034-g0f4385a7c

[Git user]

        at  0f4385a7cdfc6dbf8f640046ac819c24bda1725d (commit)


commit 0f4385a7cdfc6dbf8f640046ac819c24bda1725d
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Wed Jul 7 10:02:05 2021 -0400

    17858: Add ExpressionTool to classes checked for ids when visiting
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 7664abef7..9dc73f52f 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -471,7 +471,7 @@ def packed_workflow(arvrunner, tool, merged_map):
 
     def visit(v, cur_id):
         if isinstance(v, dict):
-            if v.get("class") in ("CommandLineTool", "Workflow"):
+            if v.get("class") in ("CommandLineTool", "Workflow", "ExpressionTool"):
                 if tool.metadata["cwlVersion"] == "v1.0" and "id" not in v:
                     raise SourceLine(v, None, Exception).makeError("Embedded process object is missing required 'id' field, add an 'id' or use to cwlVersion: v1.1")
                 if "id" in v:

commit 7940cb2365ed072f82704fbfd53fbbdc5afb16bd
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Wed Jul 7 13:42:13 2021 -0400

    17858: Integration test passes
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/tests/17858-pack-visit-crash.cwl b/sdk/cwl/tests/17858-pack-visit-crash.cwl
index ceb54546b..0c34d7dc5 100644
--- a/sdk/cwl/tests/17858-pack-visit-crash.cwl
+++ b/sdk/cwl/tests/17858-pack-visit-crash.cwl
@@ -12,4 +12,6 @@ inputs:
       location: keep:f225e6259bdd63bc7240599648dde9f1+97/hg19.fa
 outputs:
   val: string
-expression: "$({val: inputs.file1.path})"
+requirements:
+  InlineJavascriptRequirement: {}
+expression: "$({val: inputs.file1.location})"
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index f00a7c6c3..717636cd3 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -430,6 +430,6 @@
 
 - job: null
   output:
-    "file1": ""
+    "val": "keep:f225e6259bdd63bc7240599648dde9f1+97/hg19.fa"
   tool: 17858-pack-visit-crash.cwl
   doc: "Test issue 17858 - keep ref default inputs on ExpressionTool"

commit 0b2f7e6bd1fb1aeca2edd113398bb2972f89a11b
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Wed Jul 7 09:51:09 2021 -0400

    17858: Add test to reproduce bug
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/tests/17858-pack-visit-crash.cwl b/sdk/cwl/tests/17858-pack-visit-crash.cwl
new file mode 100644
index 000000000..ceb54546b
--- /dev/null
+++ b/sdk/cwl/tests/17858-pack-visit-crash.cwl
@@ -0,0 +1,15 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.1
+class: ExpressionTool
+inputs:
+  file1:
+    type: File
+    default:
+      class: File
+      location: keep:f225e6259bdd63bc7240599648dde9f1+97/hg19.fa
+outputs:
+  val: string
+expression: "$({val: inputs.file1.path})"
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index b22c9aaa2..f00a7c6c3 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -427,3 +427,9 @@
   }
   tool: 17801-runtime-outdir.cwl
   doc: "Test issue 17801 - bug using $(runtime.outdir) to capture the output directory"
+
+- job: null
+  output:
+    "file1": ""
+  tool: 17858-pack-visit-crash.cwl
+  doc: "Test issue 17858 - keep ref default inputs on ExpressionTool"

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