terminate called after throwing an instance of 'YAML::BadSubscript'

[mr-c]

error message:

terminate called after throwing an instance of 'YAML::BadSubscript'
  what():  yaml-cpp: error at line 4, column 17: operator[] call on a scalar (key: "id")
Aborted

test program:

#include "cwl_v1_2.h"

#include <iostream>

/**
 * This test program creates loads and prints a CWL description.
 *
 * It assumes that printing to stdout works (see cwl_output_example).
 * It loads a CWL description from a file and populates C++ classes.
 */


// using shortened cwl:: namespace instead of https___w3id_org_cwl_cwl
namespace cwl = https___w3id_org_cwl_cwl;

int main(int argc, char** argv) {
    if (argc != 2) return 1;

    auto yaml = YAML::LoadFile(argv[1]);
    auto tool = cwl::Workflow{};
    fromYaml(yaml, tool);

    auto y = toYaml(tool);

    YAML::Emitter out;
    out << y;
    std::cout << out.c_str() << "\n";

    return 0;
}

CWL test file

cwlVersion: v1.2
class: Workflow
inputs:
 09first_input: string
 05second_input: int
 01third_input: File
steps:
 zz_step_one:
   run:
     class: ExpressionTool
     inputs: []
     outputs: []
     expression: ${return {}; }
     requirements:
       InlineJavascriptRequirement: {}
   in: []
   out: []
 00_step_two:
   out: []
   run:
     inputs: []
     requirements:
       InlineJavascriptRequirement: {}
     outputs: []
     expression: ${return {}; }
     class: ExpressionTool
   in: []
outputs:
  zz_first_output:
    type: File
    outputSource: 01third_input
  ll_second_output:
    type: string
    outputSource: 09first_input
  aa_third_output:
    type: int
    outputSource: 05second_input

[SGSSGene]

So, the parser is tripping over at least two things:

1. The inputs are not given in an expected way. We expect it to be:

inputs:
  - id: 09first_input
    type: string
  - id: 05second_input
    type: int

or in the more compact version:

inputs:
  09first_input:
    type: string
  05second_input
    type: int

This is according to https://www.commonwl.org/v1.2/SchemaSalad.html#Identifier_map_example

collapsing it down to, seems to be valid by

inputs:
  09first_input: string
  05second_input: int

This seems valid according to https://www.commonwl.org/v1.2/SchemaSalad.html#Domain_Specific_Language_for_types but is currently not supported by the schema_salad cpp generator.

2. There is some trouble with the expression field. It is defined in Workflow.yml as:

    - name: expression
      type: Expression
      doc: |
        The expression to execute.  The expression must return a plain
        Javascript object which matches the output parameters of the
        ExpressionTool.

As far as I can see, the type Expression is no where defined. It is neither a primitive type nor a record. I go for primitives by this list https://www.commonwl.org/v1.2/CommandLineTool.html#CWLType

[mr-c]

For Expression https://github.com/common-workflow-language/cwl-v1.2/blob/707ebcd2173889604459c5f4ffb55173c508abb3/Process.yml#L626-L634

It will need special handling, see

• https://github.com/common-workflow-language/schema_salad/blob/3dc90ded01bee5b6c8369c848c4a453b56b4df0d/schema_salad/dlang_codegen.py#L303-L304
• https://github.com/common-workflow-language/schema_salad/blob/3dc90ded01bee5b6c8369c848c4a453b56b4df0d/schema_salad/java_codegen.py#L571-L579 + https://github.com/common-workflow-language/schema_salad/blob/3dc90ded01bee5b6c8369c848c4a453b56b4df0d/schema_salad/java/main_utils/ExpressionLoader.java
• https://github.com/common-workflow-language/schema_salad/blob/3dc90ded01bee5b6c8369c848c4a453b56b4df0d/schema_salad/python_codegen.py#L483-L489 + https://github.com/common-workflow-language/schema_salad/blob/3dc90ded01bee5b6c8369c848c4a453b56b4df0d/schema_salad/python_codegen_support.py#L686-L703
• https://github.com/common-workflow-language/schema_salad/blob/3dc90ded01bee5b6c8369c848c4a453b56b4df0d/schema_salad/dotnet_codegen.py#L493-L501 + https://github.com/common-workflow-language/schema_salad/blob/3dc90ded01bee5b6c8369c848c4a453b56b4df0d/schema_salad/dotnet/util/Loaders/ExpressionLoader.cs
• https://github.com/common-workflow-language/schema_salad/blob/3dc90ded01bee5b6c8369c848c4a453b56b4df0d/schema_salad/typescript_codegen.py#L463-L470 + https://github.com/common-workflow-language/schema_salad/blob/3dc90ded01bee5b6c8369c848c4a453b56b4df0d/schema_salad/typescript/util/loaders/ExpressionLoader.ts

[SGSSGene]

Thank you! That was what I needed.

So there are two issues, that need separate fixing:

1. typeDSL is not handled in scheme_salad, but TDL can partially handle this. The code must move from TDL to schema_salad cpp-generator. (https://github.com/deNBI-cibi/tool_description_lib/blob/1f06b09ad61b3845495ce2acfa783af693c2c112/src/tdl/convertToCWL.cpp#L32-L58)

2. Handling of Expression needs a specialize std::string like type. and detect similar to how Any is detected.