job loading: allow inputs named "id"

Co-authored-by: Simon Gene Gottlieb <[email protected]>

Author: mr-c

cwltool/load_tool.py

@@ -43,14 +43,23 @@
 from .update import ALLUPDATES
 from .utils import CWLObjectType, ResolverType, visit_class
 
-jobloaderctx: ContextType = {
+docloaderctx: ContextType = {
     "cwl": "https://w3id.org/cwl/cwl#",
     "cwltool": "http://commonwl.org/cwltool#",
     "path": {"@type": "@id"},
     "location": {"@type": "@id"},
     "id": "@id",
 }
 
+jobloader_id_name = "__id"
+jobloaderctx: ContextType = {
+    "cwl": "https://w3id.org/cwl/cwl#",
+    "cwltool": "http://commonwl.org/cwltool#",
+    "path": {"@type": "@id"},
+    "location": {"@type": "@id"},
+    jobloader_id_name: "@id",
+}
+
 
 overrides_ctx: ContextType = {
     "overrideTarget": {"@type": "@id"},
@@ -72,7 +81,7 @@ def default_loader(
     doc_cache: bool = True,
 ) -> Loader:
     return Loader(
-        jobloaderctx,
+        docloaderctx,
         fetcher_constructor=fetcher_constructor,
         allow_attachments=lambda r: enable_dev,
         doc_cache=doc_cache,

cwltool/main.py

@@ -70,6 +70,7 @@
 from .load_tool import (
     default_loader,
     fetch_document,
+    jobloader_id_name,
     jobloaderctx,
     load_overrides,
     make_tool,
@@ -446,7 +447,7 @@ def init_job_order(
                 _logger.exception("Failed to resolv job_order: %s", cmd_line["job_order"])
                 exit(1)
         else:
-            job_order_object = {"id": args.workflow}
+            job_order_object = {jobloader_id_name: args.workflow}
 
         del cmd_line["job_order"]
 
@@ -506,7 +507,7 @@ def expand_formats(p: CWLObjectType) -> None:
             process.inputs_record_schema, job_order_object, discover_secondaryFiles=True
         )
         basedir: Optional[str] = None
-        uri = cast(str, job_order_object["id"])
+        uri = cast(str, job_order_object[jobloader_id_name])
         if uri == args.workflow:
             basedir = os.path.dirname(uri)
             uri = ""
@@ -529,8 +530,8 @@ def expand_formats(p: CWLObjectType) -> None:
 
     if "cwl:tool" in job_order_object:
         del job_order_object["cwl:tool"]
-    if "id" in job_order_object:
-        del job_order_object["id"]
+    if jobloader_id_name in job_order_object:
+        del job_order_object[jobloader_id_name]
     return job_order_object
 
 

tests/test_examples.py

@@ -1859,3 +1859,16 @@ def test_invalid_nested_array() -> None:
     assert (
         "tests/nested-array.cwl:6:5: Field 'type' references unknown identifier 'string[][]'"
     ) in stderr
+
+
+def test_input_named_id() -> None:
+    """Confirm that it is valid to have an input named "id"."""
+    exit_code, stdout, stderr = get_main_output(
+        [
+            "--validate",
+            "--debug",
+            get_data("tests/wf/input_named_id.cwl"),
+            get_data("tests/wf/input_named_id.yaml"),
+        ]
+    )
+    assert exit_code == 0, stderr

tests/wf/input_named_id.cwl

@@ -0,0 +1,13 @@
+label: FeatureFinderIdentification
+doc: ""
+inputs:
+  id:
+    doc: featureXML or consensusXML file
+    type: File
+outputs:
+  []
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+  - FeatureFinderIdentification
+

tests/wf/input_named_id.yaml

@@ -0,0 +1,3 @@
+id:
+  class: File
+  path: ../2.fastq