Merge pull request #48 from common-workflow-language/main_is_default

 defaulting to #main for CWL $graphs

Author: mr-c

CommandLineTool.yml

@@ -57,8 +57,8 @@ $graph:
         * When defining record types with `CommandInputRecordSchema`, fields of
           type `File` may now include `format`, `loadContents`,
           `secondaryFiles` and `streamable`.
-        * `CommandInputRecordSchema`, `CommandOutputRecordSchema`,
-          `CommandInputEnumSchema and `CommandInputArraySchema` now have an optional
+        * `CommandInputRecordSchema`, `CommandOutputRecordSchema`, 
+          `CommandInputEnumSchema and `CommandInputArraySchema` now have an optional 
           `doc` field.
         * `inputBinding` has been added as an optional field for
           `CommandInputRecordSchema` (was previously in CWL `draft-3` but
@@ -108,6 +108,8 @@ $graph:
         * [Better explain](#map) the `map<…>` notation that has existed since v1.0.
         * Fixed schema error where the `type` field inside the `inputs` and
           `outputs` field was incorrectly listed as optional.
+        * For multi-Process CWL documents, if no particular process is named then
+          the process with the `id` of `#main` is chosen.
 
       See also the [CWL Workflow Description, v1.1.0-dev1 changelog](Workflow.html#Changelog).
 

Workflow.yml

@@ -92,6 +92,8 @@ $graph:
         * Fixed schema error where the `type` field inside the `inputs` and
           `outputs` fields for both `Workflow` and `ExpressionTool` was
            incorrectly listed as optional.
+        * For multi-Process CWL documents, if no particular process is named then
+          the process with the `id` of `#main` is chosen.
 
       See also the [CWL Command Line Tool Description, v1.1.0-dev1 changelog](CommandLineTool.html#Changelog).
 

concepts.md

@@ -366,15 +366,19 @@ of [process requirements](#Requirements_and_hints).
 The generic execution sequence of a CWL process (including workflows and
 command line line tools) is as follows.
 
-1. Load, process and validate a CWL document, yielding a process object.
-2. Load input object.
-3. Validate the input object against the `inputs` schema for the process.
-4. Validate process requirements are met.
-5. Perform any further setup required by the specific process type.
-6. Execute the process.
-7. Capture results of process execution into the output object.
-8. Validate the output object against the `outputs` schema for the process.
-9. Report the output object to the process caller.
+1. Load input object.
+1. Load, process and validate a CWL document, yielding one or more process objects.
+1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph))
+and which process object to start with is not specified in the input object (via
+a [`cwl:tool`](#Executing_CWL_documents_as_scripts) entry) or by any other means
+(like a URL fragment) then choose the process with the `id` of "#main" or "main".
+1. Validate the input object against the `inputs` schema for the process.
+1. Validate process requirements are met.
+1. Perform any further setup required by the specific process type.
+1. Execute the process.
+1. Capture results of process execution into the output object.
+1. Validate the output object against the `outputs` schema for the process.
+1. Report the output object to the process caller.
 
 ## Requirements and hints
 

conformance_tests.yaml

@@ -3200,3 +3200,22 @@
     code: 7
   doc: Can access exit code in outputEval
   tags: [ command_line_tool, required ]
+
+- tool: tests/echo-tool-packed.cwl
+  job: tests/env-job.json
+  output:
+    {"out": "hello test env\n"}
+  label: any_input_param_graph_no_default
+  doc: Test use of $graph without specifying which process to run
+  tags: [ required, command_line_tool ]
+
+- tool: tests/echo-tool-packed2.cwl
+  job: tests/env-job.json
+  output:
+    {"out": "hello test env\n"}
+  label: any_input_param_graph_no_default_hashmain
+  doc: |
+    Test use of $graph without specifying which process to run,
+    hash-prefixed "main"
+  tags: [ required, command_line_tool ]
+

tests/echo-tool-packed.cwl

@@ -0,0 +1,31 @@
+cwlVersion: v1.1.0-dev1
+$graph:
+  - class: CommandLineTool
+    id: first
+    inputs:
+      in:
+        type: Any
+    outputs:
+      out:
+        type: string
+        outputBinding:
+          glob: out.txt
+          loadContents: true
+          outputEval: $(self[0].contents)
+    baseCommand: [ echo, first ]
+    stdout: out.txt
+  - class: CommandLineTool
+    id: main
+    inputs:
+      in:
+        type: Any
+        inputBinding: {}
+    outputs:
+      out:
+        type: string
+        outputBinding:
+          glob: out.txt
+          loadContents: true
+          outputEval: $(self[0].contents)
+    baseCommand: echo
+    stdout: out.txt

tests/echo-tool-packed2.cwl

@@ -0,0 +1,31 @@
+cwlVersion: v1.1.0-dev1
+$graph:
+  - class: CommandLineTool
+    id: first
+    inputs:
+      in:
+        type: Any
+    outputs:
+      out:
+        type: string
+        outputBinding:
+          glob: out.txt
+          loadContents: true
+          outputEval: $(self[0].contents)
+    baseCommand: [ echo, first ]
+    stdout: out.txt
+  - class: CommandLineTool
+    id: '#main'
+    inputs:
+      in:
+        type: Any
+        inputBinding: {}
+    outputs:
+      out:
+        type: string
+        outputBinding:
+          glob: out.txt
+          loadContents: true
+          outputEval: $(self[0].contents)
+    baseCommand: echo
+    stdout: out.txt