Doc/improved example

Makefile

@@ -35,8 +35,8 @@ regen_parser: cwl_v1_*.h
 
 ## tests        : compile and run the tests
 tests: FORCE cwl_output_example
-	@result="$(shell ./cwl_output_example | md5sum)" ; \
-	expected="917791e054e1703bd42b181154b885d7  -" ;\
+	@result="$(shell ./cwl_output_example | md5sum -b)" ; \
+	expected="$(shell cat expected_cwl.cwl | md5sum -b)" ; \
 	if [ "$$result" = "$$expected" ] ; \
 		then echo test passed ; \
 	else echo test failed $$result != $$expected; exit 1; \

README.md

@@ -0,0 +1,14 @@
+# cwl-cpp-auto
+
+Autogenerated classes for reading CWL files using the C++ language.
+
+It Provides following features:
+    - Support CWL v1.2 documents
+    - Store CWL to YAML nodes
+
+
+## How to use
+The [cwl_v1.2.h](cwl_v1.2.h) header was generated using schema salad code generator applied to the CWL specification.
+It is a single header and can be copied into your own project for any usage.
+
+The usage can be seen in the [cwl_output_example.cpp](cwl_output_example.cpp) file, which show cases on how to describe your tools.

cwl_output_example.cpp

@@ -1,44 +1,107 @@
 #include "cwl_v1_2.h"
+
 #include <iostream>
 
-using namespace https___w3id_org_cwl_cwl;
+// using shortened cwl:: namespace instead of https___w3id_org_cwl_cwl
+namespace cwl = https___w3id_org_cwl_cwl;
 
 int main() {
-   auto tool = CommandLineTool{};
-   *tool.cwlVersion = CWLVersion::v1_2;
-   *tool.id         = "Some id";
-   *tool.label      = "some label";
-   *tool.doc        = "documentation that is brief";
-   *tool.stdout_    = "log.txt";
+    // declaring information about this tool in general
+    auto tool = cwl::CommandLineTool{};
+    tool.cwlVersion = cwl::CWLVersion::v1_2;
+    tool.id         = "Some id";
+    tool.label      = "some label";
+    tool.doc        = "documentation that is brief";
+    tool.stdout_    = "log.txt";
+
+    {
+        // Demonstrates a binding to `--first-option <SOMENUMBER>`.
+        // It will be exposed as `--firstOption <SOMENUMBER>`.
+        auto input = cwl::CommandInputParameter{};
+        input.id   = "firstOption";
+        input.type = cwl::CWLType::long_;
+
+        auto binding       = cwl::CommandLineBinding{};
+        binding.prefix     = "--first-option";
+        input.inputBinding = binding;
+
+        tool.inputs->push_back(input);
+    }
+    {
+        // Demonstrates a binding to `--input-file <FILE>`.
+        // It will be exposed as `--inputFile <FILE>`
+        auto input = cwl::CommandInputParameter{};
+        input.id   = "inputFile";
+        input.type = cwl::CWLType::File;
+
+        auto binding       = cwl::CommandLineBinding{};
+        binding.prefix     = "--input-file";
+        input.inputBinding = binding;
+
+        tool.inputs->push_back(input);
+    }
+    {
+        // Demonstrates output binding to `--output-file <FILE>`
+        // The exposed parameter is `--outputFile <FILE>`.
+        //
+        // This works in two steps:
+        // 1. We register a option that can be set by the user
+        auto input = cwl::CommandInputParameter{};
+        input.id   = "outputFile";
+        input.type = cwl::CWLType::string;
+
+        auto binding       = cwl::CommandLineBinding{};
+        binding.prefix     = "--output-file";
+        input.inputBinding = binding;
+
+        tool.inputs->push_back(input);
+
+        // 2. We use the input value to declare that we will
+        // write a file there
+        auto output = cwl::CommandOutputParameter{};
+        output.id   = "outputFile";
+        output.type = cwl::CWLType::File;
+
+        auto outputBinding = cwl::CommandOutputBinding{};
+        // the 'outupt-file' referes to the id of our CommandInputParameter
+        outputBinding.glob = "$(inputs.outputFile)";
+
+        output.outputBinding = outputBinding;
 
-   {
-       auto input = CommandInputParameter{};
-       *input.id = "first";
-       auto record = CommandInputRecordSchema{};
+        tool.outputs->push_back(output);
+    }
+    {
+        // Demonstrates a record with a single field `species`
+        // the `species` field can have the values `homo_sapiens`,
+        // `mus_musculus` or just be null.
+        // It will be exposed as `--speciesSelection.species [homo_sapiens|mus_musculus]`
+        auto input  = cwl::CommandInputParameter{};
+        input.id    = "speciesSelection";
+        auto record = cwl::CommandInputRecordSchema{};
 
-       auto fieldEntry = CommandInputRecordField{};
-       *fieldEntry.name = "species";
+        auto fieldEntry  = cwl::CommandInputRecordField{};
+        *fieldEntry.name = "species";
 
-       auto species = CommandInputEnumSchema{};
-       species.symbols->push_back("homo_sapiens");
-       species.symbols->push_back("mus_musculus");
+        auto species = cwl::CommandInputEnumSchema{};
+        species.symbols->push_back("homo_sapiens");
+        species.symbols->push_back("mus_musculus");
 
-       using ListType = std::vector<std::variant<CWLType, CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema, std::string>>;
-       *fieldEntry.type = ListType{species, "null"};
+        using ListType = std::vector<std::variant<cwl::CWLType, cwl::CommandInputRecordSchema, cwl::CommandInputEnumSchema, cwl::CommandInputArraySchema, std::string>>;
+        fieldEntry.type = ListType{species, "null"};
 
-       using ListType2 = std::vector<CommandInputRecordField>;
-       *record.fields = ListType2{fieldEntry};
+        using ListType2 = std::vector<cwl::CommandInputRecordField>;
+        record.fields = ListType2{fieldEntry};
 
-       using ListType3 = std::vector<std::variant<CWLType, CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema, std::string>>;
-       *input.type = ListType3{record};
+        using ListType3 = std::vector<std::variant<cwl::CWLType, cwl::CommandInputRecordSchema, cwl::CommandInputEnumSchema, cwl::CommandInputArraySchema, std::string>>;
+        input.type = ListType3{record};
 
-       tool.inputs->push_back(input);
-   }
+        tool.inputs->push_back(input);
+    }
 
 
-   auto y = toYaml(tool);
+    auto y = toYaml(tool);
 
-   YAML::Emitter out;
-   out << y;
-   std::cout << out.c_str() << "\n";
+    YAML::Emitter out;
+    out << y;
+    std::cout << out.c_str() << "\n";
 }

expected_cwl.cwl

@@ -0,0 +1,35 @@
+id: Some id
+label: some label
+doc: documentation that is brief
+inputs:
+  firstOption:
+    type: long
+    inputBinding:
+      prefix: --first-option
+  inputFile:
+    type: File
+    inputBinding:
+      prefix: --input-file
+  outputFile:
+    type: string
+    inputBinding:
+      prefix: --output-file
+  speciesSelection:
+    type:
+      - fields:
+          species:
+            type:
+              - symbols:
+                  - homo_sapiens
+                  - mus_musculus
+                type: enum
+              - "null"
+        type: record
+outputs:
+  outputFile:
+    type: File
+    outputBinding:
+      glob: $(inputs.outputFile)
+cwlVersion: v1.2
+class: CommandLineTool
+stdout: log.txt