parsers: don't sort entries when processing ID Maps (#343)

regenerated with common-workflow-language/schema_salad#899

Author: mr-c

cwl_utils/parser/cwl_v1_0.py

@@ -950,7 +950,7 @@ def load(
     ) -> Any:
         if isinstance(doc, MutableMapping):
             r: list[Any] = []
-            for k in sorted(doc.keys()):
+            for k in doc.keys():
                 val = doc[k]
                 if isinstance(val, CommentedMap):
                     v = copy.copy(val)

cwl_utils/parser/cwl_v1_0_utils.py

@@ -5,7 +5,7 @@
 from collections import namedtuple
 from collections.abc import MutableMapping, MutableSequence
 from io import StringIO
-from typing import Any, IO, Optional, Union, cast
+from typing import IO, Any, Optional, Union, cast
 from urllib.parse import urldefrag
 
 from schema_salad.exceptions import ValidationException

cwl_utils/parser/cwl_v1_1.py

@@ -950,7 +950,7 @@ def load(
     ) -> Any:
         if isinstance(doc, MutableMapping):
             r: list[Any] = []
-            for k in sorted(doc.keys()):
+            for k in doc.keys():
                 val = doc[k]
                 if isinstance(val, CommentedMap):
                     v = copy.copy(val)

cwl_utils/parser/cwl_v1_1_utils.py

@@ -5,7 +5,7 @@
 from collections import namedtuple
 from collections.abc import MutableMapping, MutableSequence
 from io import StringIO
-from typing import Any, IO, Optional, Union, cast
+from typing import IO, Any, Optional, Union, cast
 from urllib.parse import urldefrag
 
 from schema_salad.exceptions import ValidationException

cwl_utils/parser/cwl_v1_2.py

@@ -950,7 +950,7 @@ def load(
     ) -> Any:
         if isinstance(doc, MutableMapping):
             r: list[Any] = []
-            for k in sorted(doc.keys()):
+            for k in doc.keys():
                 val = doc[k]
                 if isinstance(val, CommentedMap):
                     v = copy.copy(val)

cwl_utils/parser/cwl_v1_2_utils.py

@@ -5,7 +5,7 @@
 from collections import namedtuple
 from collections.abc import MutableMapping, MutableSequence
 from io import StringIO
-from typing import Any, IO, Optional, Union, cast
+from typing import IO, Any, Optional, Union, cast
 from urllib.parse import urldefrag
 
 from schema_salad.exceptions import ValidationException

testdata/map-ordering-v1_0.cwl

@@ -0,0 +1,37 @@
+cwlVersion: v1.0
+class: Workflow
+inputs:
+ 09first_input: string
+ 05second_input: int
+ 01third_input: File
+steps:
+ zz_step_one:
+   run:
+     class: ExpressionTool
+     inputs: []
+     outputs: []
+     expression: ${return {}; }
+     requirements:
+       InlineJavascriptRequirement: {}
+   in: []
+   out: []
+ 00_step_two:
+   out: []
+   run:
+     inputs: []
+     requirements:
+       InlineJavascriptRequirement: {}
+     outputs: []
+     expression: ${return {}; }
+     class: ExpressionTool
+   in: []
+outputs:
+  zz_first_output:
+    type: File
+    outputSource: 01third_input
+  ll_second_output:
+    type: string
+    outputSource: 09first_input
+  aa_third_output:
+    type: int
+    outputSource: 05second_input

testdata/map-ordering-v1_1.cwl

@@ -0,0 +1,37 @@
+cwlVersion: v1.1
+class: Workflow
+inputs:
+ 09first_input: string
+ 05second_input: int
+ 01third_input: File
+steps:
+ zz_step_one:
+   run:
+     class: ExpressionTool
+     inputs: []
+     outputs: []
+     expression: ${return {}; }
+     requirements:
+       InlineJavascriptRequirement: {}
+   in: []
+   out: []
+ 00_step_two:
+   out: []
+   run:
+     inputs: []
+     requirements:
+       InlineJavascriptRequirement: {}
+     outputs: []
+     expression: ${return {}; }
+     class: ExpressionTool
+   in: []
+outputs:
+  zz_first_output:
+    type: File
+    outputSource: 01third_input
+  ll_second_output:
+    type: string
+    outputSource: 09first_input
+  aa_third_output:
+    type: int
+    outputSource: 05second_input

testdata/map-ordering-v1_2.cwl

@@ -0,0 +1,37 @@
+cwlVersion: v1.2
+class: Workflow
+inputs:
+ 09first_input: string
+ 05second_input: int
+ 01third_input: File
+steps:
+ zz_step_one:
+   run:
+     class: ExpressionTool
+     inputs: []
+     outputs: []
+     expression: ${return {}; }
+     requirements:
+       InlineJavascriptRequirement: {}
+   in: []
+   out: []
+ 00_step_two:
+   out: []
+   run:
+     inputs: []
+     requirements:
+       InlineJavascriptRequirement: {}
+     outputs: []
+     expression: ${return {}; }
+     class: ExpressionTool
+   in: []
+outputs:
+  zz_first_output:
+    type: File
+    outputSource: 01third_input
+  ll_second_output:
+    type: string
+    outputSource: 09first_input
+  aa_third_output:
+    type: int
+    outputSource: 05second_input

tests/test_parser.py

@@ -121,3 +121,45 @@ def test_graph_load_all() -> None:
     uri = Path(get_data("testdata/js-expr-req-wf.cwl")).resolve().as_uri()
     cwl_objs = load_document_by_uri(uri, load_all=True)
     assert len(cwl_objs) == 2
+
+
+def test_map_ordering_v1_0() -> None:
+    """Confirm that ID map entries are not sorted during parsing, CWL v1.0."""
+    uri = Path(get_data("testdata/map-ordering-v1_0.cwl")).resolve().as_uri()
+    cwl_obj = load_document_by_uri(uri)
+    assert cwl_obj.inputs[0].id == f"{uri}#09first_input"
+    assert cwl_obj.inputs[1].id == f"{uri}#05second_input"
+    assert cwl_obj.inputs[2].id == f"{uri}#01third_input"
+    assert cwl_obj.steps[0].id == f"{uri}#zz_step_one"
+    assert cwl_obj.steps[1].id == f"{uri}#00_step_two"
+    assert cwl_obj.outputs[0].id == f"{uri}#zz_first_output"
+    assert cwl_obj.outputs[1].id == f"{uri}#ll_second_output"
+    assert cwl_obj.outputs[2].id == f"{uri}#aa_third_output"
+
+
+def test_map_ordering_v1_1() -> None:
+    """Confirm that ID map entries are not sorted during parsing, CWL v1.1."""
+    uri = Path(get_data("testdata/map-ordering-v1_1.cwl")).resolve().as_uri()
+    cwl_obj = load_document_by_uri(uri)
+    assert cwl_obj.inputs[0].id == f"{uri}#09first_input"
+    assert cwl_obj.inputs[1].id == f"{uri}#05second_input"
+    assert cwl_obj.inputs[2].id == f"{uri}#01third_input"
+    assert cwl_obj.steps[0].id == f"{uri}#zz_step_one"
+    assert cwl_obj.steps[1].id == f"{uri}#00_step_two"
+    assert cwl_obj.outputs[0].id == f"{uri}#zz_first_output"
+    assert cwl_obj.outputs[1].id == f"{uri}#ll_second_output"
+    assert cwl_obj.outputs[2].id == f"{uri}#aa_third_output"
+
+
+def test_map_ordering_v1_2() -> None:
+    """Confirm that ID map entries are not sorted during parsing, CWL v1.2."""
+    uri = Path(get_data("testdata/map-ordering-v1_2.cwl")).resolve().as_uri()
+    cwl_obj = load_document_by_uri(uri)
+    assert cwl_obj.inputs[0].id == f"{uri}#09first_input"
+    assert cwl_obj.inputs[1].id == f"{uri}#05second_input"
+    assert cwl_obj.inputs[2].id == f"{uri}#01third_input"
+    assert cwl_obj.steps[0].id == f"{uri}#zz_step_one"
+    assert cwl_obj.steps[1].id == f"{uri}#00_step_two"
+    assert cwl_obj.outputs[0].id == f"{uri}#zz_first_output"
+    assert cwl_obj.outputs[1].id == f"{uri}#ll_second_output"
+    assert cwl_obj.outputs[2].id == f"{uri}#aa_third_output"