Add Directory type

This breaks the project for the v1 spec, and makes you use:
- cromwell >= 37
- "version development"

Author: illusional

wdlgen/task.py

@@ -65,54 +65,82 @@ def get_string(self):
 
         class CommandInput(CommandArgument):
             def __init__(self, name: str, optional: bool=False, prefix: str=None, position: int=None,
-                         separate_value_from_prefix: bool=True, default=None):
+                         separate_value_from_prefix: bool=True, default=None, separator=None, true=None, false=None, separate_arrays=None):
                 super().__init__(prefix=prefix, value=None, position=position,
                                  separate_value_from_prefix=separate_value_from_prefix)
                 self.name = name
                 self.optional = optional
                 self.default = default
+                self.separator = separator
+                self.true = true
+                self.false = false
+                self.separate_arrays = separate_arrays
 
             @staticmethod
             def from_input(inp: Input, prefix: str=None, position: int=None):
                 return Task.Command.CommandInput(inp.name, inp.type.optional, prefix, position)
 
             def get_string(self):
-                pr = self.prefix if self.prefix else ""
-                sp = " " if self.separate else ""
-                bc = pr + sp
-                default = f'default="{self.default}" ' if self.default else ''
+                name, array_sep, default, true, false = self.name, self.separator, self.default, self.true, self.false
 
-                if self.optional and not default:
-                    return '${{"{pre}" + {val}}}'.format(pre=bc, val=self.name, default=default)
+                pr = self.prefix if self.prefix else ""
+                bc = pr + (" " if self.separate else "")
+
+                if self.separate_arrays:
+                    if array_sep or default or true or false:
+                        print("separate_array take preferences over: separator, default, true, false")
+                    if self.optional:
+                        # Ugly optional workaround: https://github.com/openwdl/wdl/issues/25#issuecomment-315424063
+                        internal_pref = f'if defined({name}) then "--pre " else ""'
+                        return f'${{{internal_pref}}}${{sep="{bc}" {name}}}'
+                    return f'${{sep=" " prefix("{bc}", {name})}}'
+
+                options = []
+                if default:
+                    options.append(f'default="{default}"')
+                if array_sep:
+                    options.append(f'sep="{array_sep}"')
+                if true or false:
+                    options.append(f'true="{true if true else ""}"')
+                    options.append(f'false="{false if false else ""}"')
+
+                stroptions = "".join(o + " " for o in options)
+
+                if self.optional:
+                    prewithquotes = f'"{bc}" + ' if bc.strip() else ''
+                    return f'${{{stroptions}{prewithquotes}{name}}}'
                 else:
-                    return bc + "${{{default}{val}}}".format(val=self.name, default=default)
+                    return bc + f"${{{stroptions}{name}}}"
 
         def __init__(self, command, inputs: Optional[List[CommandInput]]=None, arguments: Optional[List[CommandArgument]]=None):
             self.command = command
             self.inputs = inputs if inputs else []
             self.arguments = arguments if arguments else []
 
         def get_string(self, indent: int=0):
+            tb = "  "
             base_command = self.command if self.command else ""
             if not (self.inputs or self.arguments):
-                return base_command
+                return indent * tb + base_command
 
             # build up command
             args = sorted([*self.inputs, *self.arguments], key=lambda a: a.position if a.position else 0)
             command: str = base_command if isinstance(base_command, str) else " ".join(base_command)
-            tb = "  "
             tbed_arg_indent = tb * (indent + 1)
 
             return indent * tb + command + "".join([" \\\n" + tbed_arg_indent + a.get_string() for a in args])
 
-    def __init__(self, name: str, inputs: List[Input]=None, outputs: List[Output]=None, command: Command=None, runtime: Runtime=None):
+    def __init__(self, name: str, inputs: List[Input]=None, outputs: List[Output]=None, command: Command=None, runtime: Runtime=None, version="draft-2"):
         self.name = name
         self.inputs = inputs if inputs else []
         self.outputs = outputs if outputs else []
         self.command = command
         self.runtime = runtime
+        self.version = version
 
         self.format = """
+version {version}
+
 task {name} {{
 {inputs_block}
 {command_block}
@@ -128,7 +156,7 @@ def get_string(self):
         inputs_block, command_block, runtime_block, output_block = "", "", "", ""
 
         if self.inputs:
-            inputs_block = "\n".join(tb + i.get_string() for i in self.inputs)
+            inputs_block = f"{tb}input {{\n" + "\n".join(2*tb + i.get_string() for i in self.inputs) + f"\n{tb}}}"
 
         if self.outputs:
             output_block = "{tb}output {{\n{outs}\n{tb}}}".format(
@@ -137,9 +165,14 @@ def get_string(self):
             )
 
         if self.command:
+
+            if isinstance(self.command, list):
+                com = "\n".join(c.get_string(indent=2) for c in self.command)
+            else:
+                com = self.command.get_string(indent=2)
             command_block = "{tb}command {{\n{args}\n{tb}}}".format(
                 tb=tb,
-                args=self.command.get_string(indent=2)
+                args=com
             )
 
         if self.runtime:
@@ -153,5 +186,6 @@ def get_string(self):
             inputs_block=inputs_block,
             command_block=command_block,
             runtime_block=runtime_block,
-            output_block=output_block
+            output_block=output_block,
+            version=self.version
         )

wdlgen/types.py

@@ -14,9 +14,11 @@ class PrimitiveType:
     kString = "String"
     kFile = "File"
 
+    kDirectory = "Directory"    # development branch
+
     DEF_TYPE = kString
 
-    types = [kBoolean, kInt, kFloat, kFile, kString]
+    types = [kBoolean, kInt, kFloat, kFile, kString, kDirectory]
 
     def __init__(self, prim_type):
         if prim_type not in self.types:
@@ -166,3 +168,4 @@ def check_quantifiers(t: str):
 Float = WdlType(PrimitiveType(PrimitiveType.kFloat))
 File = WdlType(PrimitiveType(PrimitiveType.kFile))
 String = WdlType(PrimitiveType(PrimitiveType.kString))
+Directory = WdlType(PrimitiveType(PrimitiveType.kDirectory))

wdlgen/workflow.py

@@ -9,7 +9,7 @@
 class Workflow(WdlBase):
 
     def __init__(self, name, inputs: List[Input]=None, outputs: List[str]=None, calls: List[WorkflowCallBase]=None,
-                 imports: List[Any]=None):
+                 imports: List[Any]=None, version="draft-2"):
         """
 
         :param name:
@@ -27,8 +27,11 @@ def __init__(self, name, inputs: List[Input]=None, outputs: List[str]=None, call
         self.outputs = outputs if outputs else []
         self.calls = calls if calls else []
         self.imports = imports if imports else []
+        self.version = version
 
         self.format = """
+version {version}
+
 {imports_block}
 
 workflow {name} {{
@@ -51,7 +54,7 @@ def get_string(self):
                     ins.extend(tb + ii for ii in wd)
                 else:
                     ins.append(tb + wd)
-            inputs_block = "\n".join(ins)
+            inputs_block = f"{tb}input {{\n" + "\n".join(ins) + f"\n{tb}}}"
 
         if self.outputs:
             outs = []
@@ -84,7 +87,8 @@ def get_string(self):
             inputs_block=inputs_block,
             output_block=output_block,
             call_block=call_block,
-            imports_block=imports_block
+            imports_block=imports_block,
+            version=self.version
         )
 
     class WorkflowImport(WdlBase):