Update for subscope and __eq__ support

cwl_utils/expression_refactor.py

@@ -11,7 +11,6 @@
     TYPE_CHECKING,
     Any,
     Callable,
-    Dict,
     List,
     MutableMapping,
     MutableSequence,

cwl_utils/parser/cwl_v1_0.py

@@ -11069,7 +11069,7 @@ def fromDoc(
             try:
                 default = load_field(
                     _doc.get("default"),
-                    union_of_None_type_or_Any_type,
+                    union_of_None_type_or_FileLoader_or_DirectoryLoader_or_Any_type,
                     baseuri,
                     loadingOptions,
                 )
@@ -13448,12 +13448,6 @@ def save(
 uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_2 = _URILoader(
     union_of_None_type_or_strtype_or_array_of_strtype, False, False, 2
 )
-union_of_None_type_or_Any_type = _UnionLoader(
-    (
-        None_type,
-        Any_type,
-    )
-)
 array_of_WorkflowStepInputLoader = _ArrayLoader(WorkflowStepInputLoader)
 idmap_in__array_of_WorkflowStepInputLoader = _IdMapLoader(
     array_of_WorkflowStepInputLoader, "id", "source"

cwl_utils/parser/cwl_v1_1.py

@@ -12982,7 +12982,7 @@ def fromDoc(
             try:
                 default = load_field(
                     _doc.get("default"),
-                    union_of_None_type_or_Any_type,
+                    union_of_None_type_or_FileLoader_or_DirectoryLoader_or_Any_type,
                     baseuri,
                     loadingOptions,
                 )
@@ -13520,11 +13520,13 @@ def fromDoc(
                 )
         else:
             hints = None
+
+        subscope_baseuri = expand_url('run', baseuri, loadingOptions, True)
         try:
             run = load_field(
                 _doc.get("run"),
                 uri_union_of_strtype_or_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_False_False_None,
-                baseuri,
+                subscope_baseuri,
                 loadingOptions,
             )
         except ValidationException as e:
@@ -15515,12 +15517,6 @@ def save(
 uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_2 = _URILoader(
     union_of_None_type_or_strtype_or_array_of_strtype, False, False, 2
 )
-union_of_None_type_or_Any_type = _UnionLoader(
-    (
-        None_type,
-        Any_type,
-    )
-)
 array_of_WorkflowStepInputLoader = _ArrayLoader(WorkflowStepInputLoader)
 idmap_in__array_of_WorkflowStepInputLoader = _IdMapLoader(
     array_of_WorkflowStepInputLoader, "id", "source"

cwl_utils/parser/cwl_v1_2.py

@@ -13191,7 +13191,7 @@ def fromDoc(
             try:
                 default = load_field(
                     _doc.get("default"),
-                    union_of_None_type_or_Any_type,
+                    union_of_None_type_or_FileLoader_or_DirectoryLoader_or_Any_type,
                     baseuri,
                     loadingOptions,
                 )
@@ -13763,11 +13763,13 @@ def fromDoc(
                 )
         else:
             hints = None
+
+        subscope_baseuri = expand_url('run', baseuri, loadingOptions, True)
         try:
             run = load_field(
                 _doc.get("run"),
                 uri_union_of_strtype_or_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_OperationLoader_False_False_None,
-                baseuri,
+                subscope_baseuri,
                 loadingOptions,
             )
         except ValidationException as e:
@@ -16995,12 +16997,6 @@ def save(
 uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_2 = _URILoader(
     union_of_None_type_or_strtype_or_array_of_strtype, False, False, 2
 )
-union_of_None_type_or_Any_type = _UnionLoader(
-    (
-        None_type,
-        Any_type,
-    )
-)
 array_of_WorkflowStepInputLoader = _ArrayLoader(WorkflowStepInputLoader)
 idmap_in__array_of_WorkflowStepInputLoader = _IdMapLoader(
     array_of_WorkflowStepInputLoader, "id", "source"

tests/test_subscope.py

@@ -0,0 +1,37 @@
+# SPDX-License-Identifier: Apache-2.0
+"""Test that scoping of identifiers in Workflow.steps[].run is correct."""
+
+from pathlib import Path
+
+from cwl_utils.parser import Workflow, load_document_by_uri
+
+HERE = Path(__file__).resolve().parent
+
+
+def test_workflow_step_process_scope_v1_0() -> None:
+    """CWL v1.0 IDs under Workflow.steps[].run should not be scoped in the "run" scope."""
+    uri = Path(HERE / "../testdata/workflow_input_format_expr.cwl").resolve().as_uri()
+    cwl_obj: Workflow = load_document_by_uri(uri)
+    assert cwl_obj.steps[0].run.inputs[0].id.endswith("#format_extract/target")
+
+
+def test_workflow_step_process_scope_v1_1() -> None:
+    """CWL v1.1 IDs under Workflow.steps[].run should be scoped in the "run" scope."""
+    uri = (
+        Path(HERE / "../testdata/workflow_input_format_expr_v1_1.cwl")
+        .resolve()
+        .as_uri()
+    )
+    cwl_obj: Workflow = load_document_by_uri(uri)
+    assert cwl_obj.steps[0].run.inputs[0].id.endswith("#format_extract/run/target")
+
+
+def test_workflow_step_process_scope_v1_2() -> None:
+    """CWL v1.2 IDs under Workflow.steps[].run should be scoped in the "run" scope."""
+    uri = (
+        Path(HERE / "../testdata/workflow_input_format_expr_v1_2.cwl")
+        .resolve()
+        .as_uri()
+    )
+    cwl_obj: Workflow = load_document_by_uri(uri)
+    assert cwl_obj.steps[0].run.inputs[0].id.endswith("#format_extract/run/target")