Merge branch 'main' into check_sourceline

Author: mr-c

cwltool/command_line_tool.py

@@ -1581,7 +1581,8 @@ def collect_output(
                     return None
 
         if (
-            not empty_and_optional
+            not result
+            and not empty_and_optional
             and isinstance(schema["type"], MutableMapping)
             and schema["type"]["type"] == "record"
         ):

tests/test_examples.py

@@ -1704,3 +1704,30 @@ def test_record_default_with_long() -> None:
     assert (
         result["sixth"]["checksum"] == "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"
     )
+
+
+def test_record_outputeval() -> None:
+    """Confirm that record types can be populated from outputEval."""
+    tool_path = get_data("tests/wf/record_outputeval.cwl")
+    err_code, stdout, stderr = get_main_output([tool_path])
+    assert err_code == 0
+    result = json.loads(stdout)["references"]
+    assert "genome_fa" in result
+    assert result["genome_fa"]["class"] == "File"
+    assert result["genome_fa"]["basename"] == "GRCm38.primary_assembly.genome.fa"
+    assert (
+        result["genome_fa"]["checksum"]
+        == "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"
+    )
+    assert result["genome_fa"]["size"] == 0
+    assert "annotation_gtf" in result
+    assert result["annotation_gtf"]["class"] == "File"
+    assert (
+        result["annotation_gtf"]["basename"]
+        == "gencode.vM21.primary_assembly.annotation.gtf"
+    )
+    assert (
+        result["annotation_gtf"]["checksum"]
+        == "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"
+    )
+    assert result["annotation_gtf"]["size"] == 0

tests/wf/record_outputeval.cwl

@@ -0,0 +1,36 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+   
+inputs:
+  gtf_version:
+    type: string
+    default: M21
+  organism:
+    type: string
+    default: mouse
+  organism_prefix:
+    type: string
+    default: m
+
+baseCommand:
+  - bash
+  - -c
+arguments:
+  - touch GRC$(inputs.organism_prefix)38.primary_assembly.genome.fa ; touch  gencode.v$(inputs.gtf_version).primary_assembly.annotation.gtf 
+outputs:
+  - id: references
+    type:
+        name: References
+        fields:
+          - name: genome_fa
+            type: File
+          - name: annotation_gtf
+            type: File
+        type: record
+    outputBinding:
+        outputEval: '$({ "genome_fa": { "class": "File", "path": runtime.outdir+"/"+"GRC"
+            + inputs.organism_prefix + "38.primary_assembly.genome.fa" }, "annotation_gtf":
+            { "class": "File", "path": runtime.outdir+"/"+"gencode.v" + inputs.gtf_version
+            + ".primary_assembly.annotation.gtf" } })'