silence spurious warning when validating some documents with "cwltool" extensions

Author: mr-c

cwltool/extensions-v1.1.yml

@@ -1,6 +1,7 @@
 $base: http://commonwl.org/cwltool#
 $namespaces:
   cwl: "https://w3id.org/cwl/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
 $graph:
 - $import: https://w3id.org/cwl/CommonWorkflowLanguage.yml
 

cwltool/extensions-v1.2.yml

@@ -1,6 +1,7 @@
 $base: http://commonwl.org/cwltool#
 $namespaces:
   cwl: "https://w3id.org/cwl/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
 $graph:
 - $import: https://w3id.org/cwl/CommonWorkflowLanguage.yml
 

cwltool/loghandler.py

@@ -23,6 +23,8 @@ def configure_logging(
     rdflib_logger.setLevel(logging.ERROR)
     deps_logger = logging.getLogger("galaxy.tool_util.deps")
     deps_logger.addHandler(stderr_handler)
+    ss_logger = logging.getLogger("salad")
+    ss_logger.addHandler(stderr_handler)
     if quiet:
         # Silence STDERR, not an eventual provenance log file
         stderr_handler.setLevel(logging.WARN)

tests/test_ext.py

@@ -8,13 +8,16 @@
 import cwltool.process
 from cwltool.main import main
 
-from .util import get_data, needs_docker
+from .util import get_data, get_main_output, needs_docker
 
 
 @needs_docker
 def test_missing_enable_ext() -> None:
-    # Require that --enable-ext is provided.
-    assert main([get_data("tests/wf/listing_deep.cwl"), get_data("tests/listing-job.yml")]) != 0
+    """Require that --enable-ext is provided."""
+    error_code, _, _ = get_main_output(
+        [get_data("tests/wf/listing_deep.cwl"), get_data("tests/listing-job.yml")]
+    )
+    assert error_code != 0
 
 
 @needs_docker
@@ -67,13 +70,6 @@ def test_listing_v1_0() -> None:
     assert main([get_data("tests/wf/listing_v1_0.cwl"), get_data("tests/listing-job.yml")]) == 0
 
 
-@pytest.mark.skip(reason="This is not the default behaviour yet")
-@needs_docker
-def test_listing_v1_1() -> None:
-    # Default behavior in 1.1 will be no expansion
-    assert main([get_data("tests/wf/listing_v1_1.cwl"), get_data("tests/listing-job.yml")]) != 0
-
-
 @needs_docker
 def test_double_overwrite(tmp_path: Path) -> None:
     """Test that overwriting an input using cwltool:InplaceUpdateRequirement works."""
@@ -278,3 +274,14 @@ def test_warn_large_inputs() -> None:
         )
     finally:
         cwltool.process.FILE_COUNT_WARNING = was
+
+
+def test_ext_validation_no_namespace_warning() -> None:
+    error_code, stdout, stderr = get_main_output(
+        ["--validate", "--enable-ext", get_data("tests/wf/mpi_env.cwl")]
+    )
+    assert error_code == 0
+    assert (
+        "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you "
+        "missing a $namespaces section?"
+    ) not in stderr