remove version from ComputerLanguage

rocrate/model/computerlanguage.py

@@ -59,46 +59,24 @@ def url(self):
     def url(self, url):
         self["url"] = url
 
-    # Not listed as a property in "https://schema.org/ComputerLanguage"
-    @property
-    def version(self):
-        return self.get("version")
-
-    @version.setter
-    def version(self, version):
-        self["version"] = version
-
-
-# For workflow ro-crates. Note that
-# https://about.workflowhub.eu/Workflow-RO-Crate/ does not specify versions.
 
-CWL_DEFAULT_VERSION = "1.2"
-# https://github.com/galaxyproject/gxformat2 has some info on gxformat2 versions
-# version can probably be simply ignored for "native" *.ga workflows
-GALAXY_DEFAULT_VERSION = "21.09"
-KNIME_DEFAULT_VERSION = "4.5.0"
-NEXTFLOW_DEFAULT_VERSION = "21.10"
-SNAKEMAKE_DEFAULT_VERSION = "6.13"
-COMPSS_DEFAULT_VERSION = "2.10"
-AUTOSUBMIT_DEFAULT_VERSION = "3.14"
+# See https://w3id.org/workflowhub/workflow-ro-crate/1.0
 
-
-def cwl(crate, version=CWL_DEFAULT_VERSION):
+def cwl(crate):
     id_ = "https://w3id.org/workflowhub/workflow-ro-crate#cwl"
     return ComputerLanguage(crate, identifier=id_, properties={
         "name": "Common Workflow Language",
         "alternateName": "CWL",
         "identifier": {
-            "@id": f"https://w3id.org/cwl/{version}/"
+            "@id": "https://w3id.org/cwl/"
         },
         "url": {
             "@id": "https://www.commonwl.org/"
-        },
-        "version": version
+        }
     })
 
 
-def galaxy(crate, version=GALAXY_DEFAULT_VERSION):
+def galaxy(crate):
     id_ = "https://w3id.org/workflowhub/workflow-ro-crate#galaxy"
     return ComputerLanguage(crate, identifier=id_, properties={
         "name": "Galaxy",
@@ -107,12 +85,11 @@ def galaxy(crate, version=GALAXY_DEFAULT_VERSION):
         },
         "url": {
             "@id": "https://galaxyproject.org/"
-        },
-        "version": version
+        }
     })
 
 
-def knime(crate, version=KNIME_DEFAULT_VERSION):
+def knime(crate):
     id_ = "https://w3id.org/workflowhub/workflow-ro-crate#knime"
     return ComputerLanguage(crate, identifier=id_, properties={
         "name": "KNIME",
@@ -121,12 +98,11 @@ def knime(crate, version=KNIME_DEFAULT_VERSION):
         },
         "url": {
             "@id": "https://www.knime.com/"
-        },
-        "version": version
+        }
     })
 
 
-def nextflow(crate, version=NEXTFLOW_DEFAULT_VERSION):
+def nextflow(crate):
     id_ = "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
     return ComputerLanguage(crate, identifier=id_, properties={
         "name": "Nextflow",
@@ -135,12 +111,11 @@ def nextflow(crate, version=NEXTFLOW_DEFAULT_VERSION):
         },
         "url": {
             "@id": "https://www.nextflow.io/"
-        },
-        "version": version
+        }
     })
 
 
-def snakemake(crate, version=SNAKEMAKE_DEFAULT_VERSION):
+def snakemake(crate):
     id_ = "https://w3id.org/workflowhub/workflow-ro-crate#snakemake"
     return ComputerLanguage(crate, identifier=id_, properties={
         "name": "Snakemake",
@@ -149,28 +124,25 @@ def snakemake(crate, version=SNAKEMAKE_DEFAULT_VERSION):
         },
         "url": {
             "@id": "https://snakemake.readthedocs.io"
-        },
-        "version": version
+        }
     })
 
 
-def compss(crate, version=COMPSS_DEFAULT_VERSION):
+def compss(crate):
     return ComputerLanguage(crate, identifier="#compss", properties={
         "name": "COMPSs Programming Model",
         "alternateName": "COMPSs",
         "url": "http://compss.bsc.es/",
-        "citation": "https://doi.org/10.1007/s10723-013-9272-5",
-        "version": version
+        "citation": "https://doi.org/10.1007/s10723-013-9272-5"
     })
 
 
-def autosubmit(crate, version=AUTOSUBMIT_DEFAULT_VERSION):
+def autosubmit(crate):
     return ComputerLanguage(crate, identifier="#autosubmit", properties={
         "name": "Autosubmit",
         "alternateName": "AS",
         "url": "https://autosubmit.readthedocs.io/",
-        "citation": "https://doi.org/10.1109/HPCSim.2016.7568429",
-        "version": version
+        "citation": "https://doi.org/10.1109/HPCSim.2016.7568429"
     })
 
 
@@ -185,9 +157,9 @@ def autosubmit(crate, version=AUTOSUBMIT_DEFAULT_VERSION):
 }
 
 
-def get_lang(crate, name, version=None):
+def get_lang(crate, name):
     try:
         func = LANG_MAP[name.lower()]
     except KeyError:
         raise ValueError(f"Unknown language: {name}")
-    return func(crate, version=version) if version else func(crate)
+    return func(crate)

rocrate/rocrate.py

@@ -438,8 +438,11 @@ def add_workflow(
         if isinstance(lang, ComputerLanguage):
             assert lang.crate is self
         else:
-            kwargs = {"version": lang_version} if lang_version else {}
+            kwargs = {}
+            lang_str = lang
             lang = get_lang(self, lang, **kwargs)
+            if lang_str.lower() == "cwl" and lang_version:
+                lang["identifier"] = f"https://w3id.org/cwl/{lang_version}/"
             self.add(lang)
         lang_str = lang.id.rsplit("#", 1)[1]
         workflow.lang = lang

test/test_workflow_ro_crate.py

@@ -16,8 +16,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import pytest
+
 from rocrate.rocrate import ROCrate, make_workflow_rocrate
-from rocrate.model.computerlanguage import CWL_DEFAULT_VERSION, GALAXY_DEFAULT_VERSION
 
 WF_CRATE = "https://w3id.org/workflowhub/workflow-ro-crate"
 
@@ -33,7 +34,6 @@ def test_galaxy_wf_crate(test_data_dir, tmpdir, helpers):
     assert wf_crate.mainEntity is wf
     lang = wf_crate.dereference(f"{WF_CRATE}#galaxy")
     assert hasattr(lang, "name")
-    assert lang.version == GALAXY_DEFAULT_VERSION
     assert wf.get("programmingLanguage") is lang
     assert wf.get("subjectOf") is not None
     assert helpers.WORKFLOW_DESC_TYPES.issubset(wf["subjectOf"].type)
@@ -68,7 +68,6 @@ def test_cwl_wf_crate(test_data_dir, tmpdir, helpers):
     assert wf_crate.mainEntity is wf
     lang = wf_crate.dereference(f"{WF_CRATE}#cwl")
     assert hasattr(lang, "name")
-    assert lang.version == CWL_DEFAULT_VERSION
     assert wf.get("programmingLanguage") is lang
     assert "subjectOf" not in wf
 
@@ -99,7 +98,6 @@ def test_create_wf_include(test_data_dir, tmpdir, helpers):
     assert wf_crate.mainEntity is wf
     lang = wf_crate.dereference(f"{WF_CRATE}#galaxy")
     assert hasattr(lang, "name")
-    assert lang.version == GALAXY_DEFAULT_VERSION
     assert wf.get("programmingLanguage") is lang
     assert wf.get("subjectOf") is not None
     assert helpers.WORKFLOW_DESC_TYPES.issubset(wf["subjectOf"].type)
@@ -124,3 +122,16 @@ def test_create_wf_include(test_data_dir, tmpdir, helpers):
     assert file2.exists()
     with open(extra_file2) as f1, open(file2) as f2:
         assert f1.read() == f2.read()
+
+
+@pytest.mark.parametrize("lang_version", [None, "1.2"])
+def test_cwl_lang_version(test_data_dir, lang_version):
+    wf_id = 'sample_cwl_wf.cwl'
+    wf_path = test_data_dir / wf_id
+    crate = ROCrate()
+    workflow = crate.add_workflow(wf_path, wf_id, lang_version=lang_version)
+    lang_id = workflow["programmingLanguage"]["identifier"]
+    if lang_version is None:
+        assert lang_id == "https://w3id.org/cwl/"
+    else:
+        assert lang_id == "https://w3id.org/cwl/1.2/"