From 6fd9a1cffc50d6751c4e9e7b52fab1a81cc08aa3 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Sat, 19 Feb 2022 13:43:56 +0100
Subject: [PATCH] Test for outputEval on a record type itself, not its fields

---
 conformance_tests.yaml           | 30 ++++++++++++++++++++++++++
 tests/record_outputeval.cwl      | 36 ++++++++++++++++++++++++++++++++
 tests/record_outputeval_nojs.cwl | 26 +++++++++++++++++++++++
 3 files changed, 92 insertions(+)
 create mode 100644 tests/record_outputeval.cwl
 create mode 100644 tests/record_outputeval_nojs.cwl

diff --git a/conformance_tests.yaml b/conformance_tests.yaml
index 151cac5d..86f4ee38 100644
--- a/conformance_tests.yaml
+++ b/conformance_tests.yaml
@@ -3484,3 +3484,33 @@
   tool: tests/paramref_arguments_roundtrip.cwl
   doc: Confirm that records with defaults are accepted
   tags: [ required, command_line_tool ]
+
+- label: record_outputeval
+  output:
+    references:
+      genome_fa:
+        class: File
+        basename: GRCm38.primary_assembly.genome.fa
+        checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+        size: 0
+      annotation_gtf:
+        class: File
+        basename: gencode.vM21.primary_assembly.annotation.gtf
+        checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+        size: 0
+  tool: tests/record_outputeval.cwl
+  doc: Use of outputEval on a record itself, not the fields of the record
+  tags: [ inline_javascript, command_line_tool ]
+
+- label: record_outputeval_nojs
+  output:
+    references:
+      annotation_gtf: gencode.vM21.primary_assembly.annotation.gtf
+      genome_fa: GRCm38.primary_assembly.genome.fa
+    summary:
+      class: File
+      checksum: sha1$c0bf6c4db73d4fc08ee24c7288825c09f9cb3cea
+      size: 79
+  tool: tests/record_outputeval_nojs.cwl
+  doc: Use of outputEval on a record itself, not the fields of the record (without javascript)
+  tags: [ required, command_line_tool ]
diff --git a/tests/record_outputeval.cwl b/tests/record_outputeval.cwl
new file mode 100644
index 00000000..6540c1e1
--- /dev/null
+++ b/tests/record_outputeval.cwl
@@ -0,0 +1,36 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  gtf_version:
+    type: string
+    default: M21
+  organism:
+    type: string
+    default: mouse
+  organism_prefix:
+    type: string
+    default: m
+
+baseCommand:
+  - bash
+  - -c
+arguments:
+  - touch GRC$(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" } })'
diff --git a/tests/record_outputeval_nojs.cwl b/tests/record_outputeval_nojs.cwl
new file mode 100644
index 00000000..b29c6622
--- /dev/null
+++ b/tests/record_outputeval_nojs.cwl
@@ -0,0 +1,26 @@
+cwlVersion: v1.2
+class: CommandLineTool
+inputs:
+  ref:
+    type:
+      type: record
+      fields:
+        genome_fa: string
+        annotation_gtf: string
+    default: { genome_fa: GRCm38.primary_assembly.genome.fa,
+               annotation_gtf: gencode.vM21.primary_assembly.annotation.gtf }
+
+baseCommand: echo
+arguments:
+ - $(inputs.ref.genome_fa) $(inputs.ref.annotation_gtf)
+outputs:
+  references:
+    type:
+      type: record
+      fields:
+        genome_fa: string
+        annotation_gtf: string
+    outputBinding:
+        outputEval: $(inputs.ref)
+  summary:
+    type: stdout