Add tests for relative reference in cwl.output.json (#199)

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: tetron

conformance_tests.yaml

@@ -963,6 +963,36 @@
     and just 'location' is provided.
   tags: [ shell_command, command_line_tool ]
 
+- job: tests/empty.json
+  output: {
+    "foo": {
+        "location": "foo",
+        "class": "File",
+        "checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
+        "size": 4
+    }
+  }
+  tool: tests/test-cwl-out3.cwl
+  id: json_output_path_relative
+  doc: >-
+    Test support for reading cwl.output.json where 'path' is relative path in output dir.
+  tags: [ shell_command, command_line_tool ]
+
+- job: tests/empty.json
+  output: {
+    "foo": {
+        "location": "foo",
+        "class": "File",
+        "checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
+        "size": 4
+    }
+  }
+  tool: tests/test-cwl-out4.cwl
+  id: json_output_location_relative
+  doc: >-
+    Test support for reading cwl.output.json where 'location' is relative reference to output dir.
+  tags: [ shell_command, command_line_tool ]
+
 - job: tests/abc.json
   output:
     files: [{
@@ -3314,7 +3344,7 @@
     `echo a && echo b > out.txt`, but instead will produce the correct `echo a && echo b`,
     and capture the output correctly.
   tags: [ shell_command, command_line_tool ]
-  
+
 - label: multiple-input-feature-requirement
   output: {
     "hello_world_in_two_lines": [

invocation.md

@@ -156,9 +156,29 @@ The exit code of the process is available to expressions in
 
 ## Output binding
 
-If the output directory contains a file named "cwl.output.json", that file
-must be loaded and used as the output object.  Otherwise, the output object
-must be generated by walking the parameters listed in `outputs` and
-applying output bindings to the tool output.  Output bindings are
-associated with output parameters using the `outputBinding` field.  See
+If the output directory contains a file named "cwl.output.json", that
+file must be loaded and used as the output object.  In this case, the
+output object should still be type-checked against the `outputs`
+section, but `outputBinding` is ignored.
+
+For Files and Directories, if the value of `path` is a relative path
+pattern (does not begin with a slash '/') then it is resolved relative
+to the output directory.  If the value of the "path" is an absolute
+path pattern (it does begin with a slash '/') then it must refer to a
+path within the output directory.  It is an error for "path" to refer
+outside the output directory.
+
+Similarly, if a File or Directory "cwl.output.json" contains
+`location`, it is resolved as relative reference URI with a base URI
+representing the output directory.  If `location` contains some other
+absolute URI with a scheme supported by the implementation, the
+implementation may choose to accept it.
+
+If both `path` and `location` are provided on a File or Directory in
+"cwl.output.json", `path` takes precedence.
+
+If there is no "cwl.output.json", the output object must be generated
+by walking the parameters listed in `outputs` and applying output
+bindings to the tool output.  Output bindings are associated with
+output parameters using the `outputBinding` field.  See
 [`CommandOutputBinding`](#CommandOutputBinding) for details.

tests/test-cwl-out3.cwl

@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: v1.2
+requirements:
+  - class: ShellCommandRequirement
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+
+inputs: []
+
+outputs:
+  - id: foo
+    type: File
+
+arguments:
+   - valueFrom: >
+       echo foo > foo && echo '{"foo": {"path": "foo", "class": "File"} }' > cwl.output.json
+     shellQuote: false

tests/test-cwl-out4.cwl

@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: v1.2
+requirements:
+  - class: ShellCommandRequirement
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+
+inputs: []
+
+outputs:
+  - id: foo
+    type: File
+
+arguments:
+   - valueFrom: >
+       echo foo > foo && echo '{"foo": {"location": "foo", "class": "File"} }' > cwl.output.json
+     shellQuote: false