Merge pull request #48 from simleo/fix_check_runnable

Run module: fix check_runnable

src/runcrate/run.py

@@ -44,7 +44,7 @@ def check_runnable(crate):
     if "ComputationalWorkflow" not in as_list(wf.type):
         raise RuntimeError("mainEntity is not a ComputationalWorkflow")
     lang = wf.get("programmingLanguage")
-    if not lang or getattr(lang, "id", None) != CWL_ID:
+    if not lang or (getattr(lang, "id", None) != CWL_ID and lang != CWL_ID):
         raise RuntimeError(f"workflow language must be {CWL_ID}")
     actions = [_ for _ in crate.get_entities()
                if "CreateAction" in as_list(_.type) and _.get("instrument") is wf]

tests/test_run.py

@@ -0,0 +1,54 @@
+# Copyright 2023 CRS4.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import pytest
+from rocrate.model.contextentity import ContextEntity
+from rocrate.rocrate import ROCrate
+
+from runcrate.run import check_runnable
+
+
+CWL_ID = "https://w3id.org/workflowhub/workflow-ro-crate#cwl"
+
+
+def test_check_runnable(data_dir, tmpdir):
+    crate = ROCrate()
+    with pytest.raises(RuntimeError):
+        check_runnable(crate)  # no wf
+    crate.mainEntity = crate.add_file("http://example.org/example.pdf")
+    with pytest.raises(RuntimeError):
+        check_runnable(crate)  # not a ComputationalWorkflow
+    crate.mainEntity = crate.add_file("http://example.org/foo.a", properties={
+        "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"]
+    })
+    with pytest.raises(RuntimeError):
+        check_runnable(crate)  # no programmingLanguage in wf
+    crate.mainEntity = crate.add_file("http://example.org/foo.cwl", properties={
+        "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+        "programmingLanguage": CWL_ID
+    })
+    with pytest.raises(RuntimeError):
+        check_runnable(crate)  # no associated action
+    action = crate.add(ContextEntity(crate, properties={
+        "@type": "CreateAction",
+        "instrument": crate.mainEntity,
+    }))
+    assert check_runnable(crate) == (crate.mainEntity, action)
+    crate.add_workflow("http://example.org/bar.cwl", None, main=True, lang="cwl")
+    action = crate.add(ContextEntity(crate, properties={
+        "@type": "CreateAction",
+        "instrument": crate.mainEntity,
+    }))
+    assert crate.mainEntity.id == "http://example.org/bar.cwl"
+    assert check_runnable(crate) == (crate.mainEntity, action)