Refactor codetool to use JSON input

janis_core/code/pythontool.py

@@ -179,7 +179,7 @@ def prepare_file_or_directory_type(file_or_directory, value):
 import argparse, json, sys
 from typing import Optional, List, Dict, Any
 cli = argparse.ArgumentParser("Argument parser for Janis PythonTool")
-{nl.join(self.generate_cli_binding_for_input(inp) for inp in ins)}
+cli.add_argument("--json", help="JSON file to parse")
 
 {type_annotation_declarations}
 {pt_decl}
@@ -189,8 +189,9 @@ def prepare_file_or_directory_type(file_or_directory, value):
 
 try:
     args = cli.parse_args()
-    result = code_block({argkwargs})
-{extra_param_parsing}
+    with open(args.json) as fp:
+        d = json.load(fp)
+    result = code_block(**d)
     print(json.dumps(result))
 except Exception as e:
     print(str(e), file=sys.stderr)

janis_core/tests/test_python_tool.py

@@ -75,6 +75,10 @@ def test_whole2(self):
         test = CwlTranslator.translate_code_tool_internal(PythonEchoTool())
         print(test)
 
+    def test_whole_cwl(self):
+        out = PythonEchoTool().translate("cwl", to_console=False)
+        print(out)
+
     # def test_build_code_block(self):
     #     script = PythonEchoTool().prepared_script()
     #     print(script)
@@ -112,10 +116,7 @@ def test_whole2(self):
 import argparse, json, sys
 from typing import Optional, List, Dict, Any
 cli = argparse.ArgumentParser("Argument parser for Janis PythonTool")
-cli.add_argument("--name", type=str, required=True)
-cli.add_argument("--infile", type=str, help='File to write to fout')
-cli.add_argument("--flag", action='store_true', help='Random boolean')
-cli.add_argument("--testvalue", type=str)
+cli.add_argument("--json", help="JSON file to parse")
 
 String = str
 Filename = str
@@ -152,18 +153,17 @@ def code_block(name: str, infile: Filename, flag: bool = True, testvalue="test")
 
 try:
     args = cli.parse_args()
-    result = code_block(name=args.name, infile=args.infile, flag=args.flag, testvalue=args.testvalue)
+    with open(args.json) as fp:
+        d = json.load(fp)
+    result = code_block(**d)
     print(json.dumps(result))
 except Exception as e:
     print(str(e), file=sys.stderr)
     raise
 
 EOT
     python echo_tool-script.py \\
-      --name '~{name}' \\
-      --infile '~{select_first([infile, "generated"])}' \\
-      ~{if defined(select_first([flag, true])) then "--flag" else ""} \\
-      ~{if defined(select_first([testvalue, "test"])) then ("--testvalue '" + select_first([testvalue, "test"]) + "'") else ""}
+      --json ~{write_json({"name": name, "infile": infile, "flag": flag, "testvalue": testvalue})}
   >>>
   runtime {
     disks: runtime_disks

janis_core/translations/cwl.py

@@ -682,21 +682,28 @@ def translate_code_tool_internal(
             inputs=[],
             outputs=[],
             requirements=[],
+            arguments=[],
+        )
+
+        tool_cwl.arguments.append(
+            cwlgen.CommandLineBinding(valueFrom="inputs.json", prefix="--json")
         )
 
+        tool_ins = tool.inputs()
+
         tool_cwl.inputs.extend(
             translate_tool_input(
                 ToolInput(
                     t.id(),
                     input_type=t.intype,
-                    prefix=f"--{t.id()}",
+                    # prefix=f"--{t.id()}",
                     default=t.default,
                     doc=t.doc.doc if t.doc else None,
                 ),
                 inputsdict=inputsdict,
                 tool=tool,
             )
-            for t in tool.inputs()
+            for t in tool_ins
         )
 
         for output in tool.tool_outputs():
@@ -724,13 +731,28 @@ def translate_code_tool_internal(
                 )
             )
 
+        ins = "[" + ", ".join(f'"{k.id()}"' for k in tool_ins) + "]"
+
         tool_cwl.requirements.append(
             cwlgen.InitialWorkDirRequirement(
                 listing=[
                     cwlgen.Dirent(
                         entryname=scriptname,
                         entry=tool.prepared_script(SupportedTranslation.CWL),
-                    )
+                    ),
+                    cwlgen.Dirent(
+                        entryname="inputs.json",
+                        entry=f"""${{
+var retval = {{}};
+{ins}.forEach(function(k) {{
+    if (inputs[k] != null && inputs[k].path) {{
+        retval[k] = inputs[k].path;
+    }} else {{
+        retval[k] = inputs[k];
+    }}
+}})
+return JSON.stringify(retval);\n}}""",
+                    ),
                 ]
             )
         )

janis_core/translations/wdl.py

@@ -436,7 +436,7 @@ def translate_code_tool_internal(
                 f"numbers or an underscore)"
             )
 
-        ins = cls.get_resource_override_inputs() + [
+        raw_ins = [
             ToolInput(
                 t.id(),
                 input_type=t.intype,
@@ -447,6 +447,8 @@ def translate_code_tool_internal(
             for t in tool.tool_inputs()
         ]
 
+        ins = cls.get_resource_override_inputs() + raw_ins
+
         tr_ins = cls.translate_tool_inputs(ins)
 
         outs = []
@@ -478,10 +480,18 @@ def translate_code_tool_internal(
             )
         )
 
-        command_ins = cls.build_command_from_inputs(ins)
-        bc = tool.base_command()
-        bcs = " ".join(bc) if isinstance(bc, list) else bc
-        commands.append(wdl.Task.Command(bcs, command_ins, []))
+        prepared_map = ", ".join(f'"{i.id()}": {i.id()}' for i in raw_ins)
+
+        tr_ins.append(
+            wdl.Input(
+                wdl.File,
+                "jsonFile__",
+                expression=f"write_json({{{prepared_map}}})",
+                requires_quotes=False,
+            )
+        )
+        command_ins = [wdl.Task.Command.CommandInput(f"--json '~{{jsonFile__}}'")]
+        commands.append(wdl.Task.Command(tool.base_command(), command_ins, []))
 
         r = wdl.Task.Runtime()
         if with_docker: