Update utils & test to match renamed fields

Author: mr-c

create_cwl_from_objects.py

@@ -9,11 +9,11 @@
 
 def main() -> None:
     """Generate a CWL object to match "cat-tool.cwl"."""
-    inputs = [cwl.CommandInputParameter(id="file1", type="File")]
+    inputs = [cwl.CommandInputParameter(id="file1", type_="File")]
     outputs = [
         cwl.CommandOutputParameter(
             id="output",
-            type="File",
+            type_="File",
             outputBinding=cwl.CommandOutputBinding(glob="output"),
         )
     ]

cwl_utils/cwl_v1_0_expression_refactor.py

@@ -30,9 +30,9 @@ def _compare_records(
     This handles normalizing record names, which will be relative to workflow
     step, so that they can be compared.
     """
-    srcfields = {cwl.shortname(field.name): field.type for field in (src.fields or {})}
+    srcfields = {cwl.shortname(field.name): field.type_ for field in (src.fields or {})}
     sinkfields = {
-        cwl.shortname(field.name): field.type for field in (sink.fields or {})
+        cwl.shortname(field.name): field.type_ for field in (sink.fields or {})
     }
     for key in sinkfields.keys():
         if (
@@ -63,10 +63,10 @@ def _compare_type(type1: Any, type2: Any) -> bool:
         return _compare_type(type1.items, type2.items)
     elif isinstance(type1, cwl.RecordSchema) and isinstance(type2, cwl.RecordSchema):
         fields1 = {
-            cwl.shortname(field.name): field.type for field in (type1.fields or {})
+            cwl.shortname(field.name): field.type_ for field in (type1.fields or {})
         }
         fields2 = {
-            cwl.shortname(field.name): field.type for field in (type2.fields or {})
+            cwl.shortname(field.name): field.type_ for field in (type2.fields or {})
         }
         if fields1.keys() != fields2.keys():
             return False
@@ -184,7 +184,7 @@ def check_types(
         return "exception"
     if linkMerge == "merge_nested":
         return check_types(
-            cwl.ArraySchema(items=srctype, type="array"), sinktype, None, None
+            cwl.ArraySchema(items=srctype, type_="array"), sinktype, None, None
         )
     if linkMerge == "merge_flattened":
         return check_types(merge_flatten_type(srctype), sinktype, None, None)
@@ -212,7 +212,7 @@ def content_limit_respected_read(f: IO[bytes]) -> str:
 def convert_stdstreams_to_files(clt: cwl.CommandLineTool) -> None:
     """Convert stdout and stderr type shortcuts to files."""
     for out in clt.outputs:
-        if out.type == "stdout":
+        if out.type_ == "stdout":
             if out.outputBinding is not None:
                 raise ValidationException(
                     "Not allowed to specify outputBinding when using stdout shortcut."
@@ -223,9 +223,9 @@ def convert_stdstreams_to_files(clt: cwl.CommandLineTool) -> None:
                         json_dumps(clt.save(), sort_keys=True).encode("utf-8")
                     ).hexdigest()
                 )
-            out.type = "File"
+            out.type_ = "File"
             out.outputBinding = cwl.CommandOutputBinding(glob=clt.stdout)
-        elif out.type == "stderr":
+        elif out.type_ == "stderr":
             if out.outputBinding is not None:
                 raise ValidationException(
                     "Not allowed to specify outputBinding when using stderr shortcut."
@@ -236,7 +236,7 @@ def convert_stdstreams_to_files(clt: cwl.CommandLineTool) -> None:
                         json_dumps(clt.save(), sort_keys=True).encode("utf-8")
                     ).hexdigest()
                 )
-            out.type = "File"
+            out.type_ = "File"
             out.outputBinding = cwl.CommandOutputBinding(glob=clt.stderr)
 
 
@@ -246,7 +246,7 @@ def merge_flatten_type(src: Any) -> Any:
         return [merge_flatten_type(t) for t in src]
     if isinstance(src, cwl.ArraySchema):
         return src
-    return cwl.ArraySchema(type="array", items=src)
+    return cwl.ArraySchema(type_="array", items=src)
 
 
 def type_for_step_input(
@@ -264,9 +264,9 @@ def type_for_step_input(
                 cast(str, step_input.id).split("#")[-1]
                 == cast(str, in_.id).split("#")[-1]
             ):
-                input_type = step_input.type
+                input_type = step_input.type_
                 if step.scatter is not None and in_.id in aslist(step.scatter):
-                    input_type = cwl.ArraySchema(items=input_type, type="array")
+                    input_type = cwl.ArraySchema(items=input_type, type_="array")
                 return input_type
     return "Any"
 
@@ -284,15 +284,15 @@ def type_for_step_output(
                 step_output.id.split("#")[-1].split("/")[-1]
                 == sourcename.split("#")[-1].split("/")[-1]
             ):
-                output_type = step_output.type
+                output_type = step_output.type_
                 if step.scatter is not None:
                     if step.scatterMethod == "nested_crossproduct":
                         for _ in range(len(aslist(step.scatter))):
                             output_type = cwl.ArraySchema(
-                                items=output_type, type="array"
+                                items=output_type, type_="array"
                             )
                     else:
-                        output_type = cwl.ArraySchema(items=output_type, type="array")
+                        output_type = cwl.ArraySchema(items=output_type, type_="array")
                 return output_type
     raise ValidationException(
         "param {} not found in {}.".format(
@@ -312,42 +312,44 @@ def type_for_source(
     scatter_context: List[Optional[Tuple[int, str]]] = []
     params = param_for_source_id(process, sourcenames, parent, scatter_context)
     if not isinstance(params, list):
-        new_type = params.type
+        new_type = params.type_
         if scatter_context[0] is not None:
             if scatter_context[0][1] == "nested_crossproduct":
                 for _ in range(scatter_context[0][0]):
-                    new_type = cwl.ArraySchema(items=new_type, type="array")
+                    new_type = cwl.ArraySchema(items=new_type, type_="array")
             else:
-                new_type = cwl.ArraySchema(items=new_type, type="array")
+                new_type = cwl.ArraySchema(items=new_type, type_="array")
         if linkMerge == "merge_nested":
-            new_type = cwl.ArraySchema(items=new_type, type="array")
+            new_type = cwl.ArraySchema(items=new_type, type_="array")
         elif linkMerge == "merge_flattened":
             new_type = merge_flatten_type(new_type)
         return new_type
     new_type = []
     for p, sc in zip(params, scatter_context):
         if isinstance(p, str) and not any(_compare_type(t, p) for t in new_type):
             cur_type = p
-        elif hasattr(p, "type") and not any(_compare_type(t, p.type) for t in new_type):
-            cur_type = p.type
+        elif hasattr(p, "type_") and not any(
+            _compare_type(t, p.type_) for t in new_type
+        ):
+            cur_type = p.type_
         else:
             cur_type = None
         if cur_type is not None:
             if sc is not None:
                 if sc[1] == "nested_crossproduct":
                     for _ in range(sc[0]):
-                        cur_type = cwl.ArraySchema(items=cur_type, type="array")
+                        cur_type = cwl.ArraySchema(items=cur_type, type_="array")
                 else:
-                    cur_type = cwl.ArraySchema(items=cur_type, type="array")
+                    cur_type = cwl.ArraySchema(items=cur_type, type_="array")
             new_type.append(cur_type)
     if len(new_type) == 1:
         new_type = new_type[0]
     if linkMerge == "merge_nested":
-        return cwl.ArraySchema(items=new_type, type="array")
+        return cwl.ArraySchema(items=new_type, type_="array")
     elif linkMerge == "merge_flattened":
         return merge_flatten_type(new_type)
     elif isinstance(sourcenames, List) and len(sourcenames) > 1:
-        return cwl.ArraySchema(items=new_type, type="array")
+        return cwl.ArraySchema(items=new_type, type_="array")
     else:
         return new_type
 

cwl_utils/cwl_v1_1_expression_refactor.py

@@ -30,9 +30,9 @@ def _compare_records(
     This handles normalizing record names, which will be relative to workflow
     step, so that they can be compared.
     """
-    srcfields = {cwl.shortname(field.name): field.type for field in (src.fields or {})}
+    srcfields = {cwl.shortname(field.name): field.type_ for field in (src.fields or {})}
     sinkfields = {
-        cwl.shortname(field.name): field.type for field in (sink.fields or {})
+        cwl.shortname(field.name): field.type_ for field in (sink.fields or {})
     }
     for key in sinkfields.keys():
         if (
@@ -63,10 +63,10 @@ def _compare_type(type1: Any, type2: Any) -> bool:
         return _compare_type(type1.items, type2.items)
     elif isinstance(type1, cwl.RecordSchema) and isinstance(type2, cwl.RecordSchema):
         fields1 = {
-            cwl.shortname(field.name): field.type for field in (type1.fields or {})
+            cwl.shortname(field.name): field.type_ for field in (type1.fields or {})
         }
         fields2 = {
-            cwl.shortname(field.name): field.type for field in (type2.fields or {})
+            cwl.shortname(field.name): field.type_ for field in (type2.fields or {})
         }
         if fields1.keys() != fields2.keys():
             return False
@@ -184,7 +184,7 @@ def check_types(
         return "exception"
     if linkMerge == "merge_nested":
         return check_types(
-            cwl.ArraySchema(items=srctype, type="array"), sinktype, None, None
+            cwl.ArraySchema(items=srctype, type_="array"), sinktype, None, None
         )
     if linkMerge == "merge_flattened":
         return check_types(merge_flatten_type(srctype), sinktype, None, None)
@@ -212,7 +212,7 @@ def content_limit_respected_read(f: IO[bytes]) -> str:
 def convert_stdstreams_to_files(clt: cwl.CommandLineTool) -> None:
     """Convert stdin, stdout and stderr type shortcuts to files."""
     for out in clt.outputs:
-        if out.type == "stdout":
+        if out.type_ == "stdout":
             if out.outputBinding is not None:
                 raise ValidationException(
                     "Not allowed to specify outputBinding when using stdout shortcut."
@@ -223,9 +223,9 @@ def convert_stdstreams_to_files(clt: cwl.CommandLineTool) -> None:
                         json_dumps(clt.save(), sort_keys=True).encode("utf-8")
                     ).hexdigest()
                 )
-            out.type = "File"
+            out.type_ = "File"
             out.outputBinding = cwl.CommandOutputBinding(glob=clt.stdout)
-        elif out.type == "stderr":
+        elif out.type_ == "stderr":
             if out.outputBinding is not None:
                 raise ValidationException(
                     "Not allowed to specify outputBinding when using stderr shortcut."
@@ -236,10 +236,10 @@ def convert_stdstreams_to_files(clt: cwl.CommandLineTool) -> None:
                         json_dumps(clt.save(), sort_keys=True).encode("utf-8")
                     ).hexdigest()
                 )
-            out.type = "File"
+            out.type_ = "File"
             out.outputBinding = cwl.CommandOutputBinding(glob=clt.stderr)
     for inp in clt.inputs:
-        if inp.type == "stdin":
+        if inp.type_ == "stdin":
             if inp.inputBinding is not None:
                 raise ValidationException(
                     "Not allowed to specify unputBinding when using stdin shortcut."
@@ -253,7 +253,7 @@ def convert_stdstreams_to_files(clt: cwl.CommandLineTool) -> None:
                     "$(inputs.%s.path)"
                     % cast(str, inp.id).rpartition("#")[2].split("/")[-1]
                 )
-                inp.type = "File"
+                inp.type_ = "File"
 
 
 def merge_flatten_type(src: Any) -> Any:
@@ -262,7 +262,7 @@ def merge_flatten_type(src: Any) -> Any:
         return [merge_flatten_type(t) for t in src]
     if isinstance(src, cwl.ArraySchema):
         return src
-    return cwl.ArraySchema(type="array", items=src)
+    return cwl.ArraySchema(type_="array", items=src)
 
 
 def type_for_step_input(
@@ -280,9 +280,9 @@ def type_for_step_input(
                 cast(str, step_input.id).split("#")[-1]
                 == cast(str, in_.id).split("#")[-1]
             ):
-                input_type = step_input.type
+                input_type = step_input.type_
                 if step.scatter is not None and in_.id in aslist(step.scatter):
-                    input_type = cwl.ArraySchema(items=input_type, type="array")
+                    input_type = cwl.ArraySchema(items=input_type, type_="array")
                 return input_type
     return "Any"
 
@@ -300,15 +300,15 @@ def type_for_step_output(
                 output.id.split("#")[-1].split("/")[-1]
                 == sourcename.split("#")[-1].split("/")[-1]
             ):
-                output_type = output.type
+                output_type = output.type_
                 if step.scatter is not None:
                     if step.scatterMethod == "nested_crossproduct":
                         for _ in range(len(aslist(step.scatter))):
                             output_type = cwl.ArraySchema(
-                                items=output_type, type="array"
+                                items=output_type, type_="array"
                             )
                     else:
-                        output_type = cwl.ArraySchema(items=output_type, type="array")
+                        output_type = cwl.ArraySchema(items=output_type, type_="array")
                 return output_type
     raise ValidationException(
         "param {} not found in {}.".format(
@@ -328,42 +328,44 @@ def type_for_source(
     scatter_context: List[Optional[Tuple[int, str]]] = []
     params = param_for_source_id(process, sourcenames, parent, scatter_context)
     if not isinstance(params, list):
-        new_type = params.type
+        new_type = params.type_
         if scatter_context[0] is not None:
             if scatter_context[0][1] == "nested_crossproduct":
                 for _ in range(scatter_context[0][0]):
-                    new_type = cwl.ArraySchema(items=new_type, type="array")
+                    new_type = cwl.ArraySchema(items=new_type, type_="array")
             else:
-                new_type = cwl.ArraySchema(items=new_type, type="array")
+                new_type = cwl.ArraySchema(items=new_type, type_="array")
         if linkMerge == "merge_nested":
-            new_type = cwl.ArraySchema(items=new_type, type="array")
+            new_type = cwl.ArraySchema(items=new_type, type_="array")
         elif linkMerge == "merge_flattened":
             new_type = merge_flatten_type(new_type)
         return new_type
     new_type = []
     for p, sc in zip(params, scatter_context):
         if isinstance(p, str) and not any(_compare_type(t, p) for t in new_type):
             cur_type = p
-        elif hasattr(p, "type") and not any(_compare_type(t, p.type) for t in new_type):
-            cur_type = p.type
+        elif hasattr(p, "type_") and not any(
+            _compare_type(t, p.type_) for t in new_type
+        ):
+            cur_type = p.type_
         else:
             cur_type = None
         if cur_type is not None:
             if sc is not None:
                 if sc[1] == "nested_crossproduct":
                     for _ in range(sc[0]):
-                        cur_type = cwl.ArraySchema(items=cur_type, type="array")
+                        cur_type = cwl.ArraySchema(items=cur_type, type_="array")
                 else:
-                    cur_type = cwl.ArraySchema(items=cur_type, type="array")
+                    cur_type = cwl.ArraySchema(items=cur_type, type_="array")
             new_type.append(cur_type)
     if len(new_type) == 1:
         new_type = new_type[0]
     if linkMerge == "merge_nested":
-        return cwl.ArraySchema(items=new_type, type="array")
+        return cwl.ArraySchema(items=new_type, type_="array")
     elif linkMerge == "merge_flattened":
         return merge_flatten_type(new_type)
     elif isinstance(sourcenames, List) and len(sourcenames) > 1:
-        return cwl.ArraySchema(items=new_type, type="array")
+        return cwl.ArraySchema(items=new_type, type_="array")
     else:
         return new_type