Update profile support

rocrate/model/metadata.py

@@ -44,7 +44,34 @@
 LEGACY_BASENAME = "ro-crate-metadata.jsonld"
 DETACHED_MD_NAME = re.compile(r".*-ro-crate-metadata.json$")
 
-WORKFLOW_PROFILE = "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
+# Mapping from RO-Crate version to Workflow RO-Crate version
+WROC_VERSION_MAP = {
+    "1.0": "1.0",
+    "1.0-DRAFT": "1.0",
+    "1.1": "1.0",
+    "1.1-DRAFT": "1.0",
+    "1.2": None,
+    "1.2-DRAFT": None,
+    "1.3": "1.1",
+    "1.3-DRAFT": "1.1",
+}
+DEFAULT_WROC_VERSION = "1.1"
+WROC_PROFILE_BASE = "https://w3id.org/workflowhub/workflow-ro-crate"
+
+# Mapping from RO-Crate version to Workflow Testing RO-Crate version
+WTROC_VERSION_MAP = {
+    "1.0": "0.1",
+    "1.0-DRAFT": "0.1",
+    "1.1": "0.1",
+    "1.1-DRAFT": "0.1",
+    "1.2": None,
+    "1.2-DRAFT": None,
+    "1.3": "0.2",
+    "1.3-DRAFT": "0.2",
+}
+DEFAULT_WTROC_VERSION = "0.2"
+WTROC_PROFILE_BASE = "https://w3id.org/ro/wftest"
+WTROC_CONTEXT = "https://w3id.org/ro/terms/test"
 
 
 class Metadata(File):
@@ -112,21 +139,3 @@ def write_detached(self, path):
     @property
     def root(self) -> Dataset:
         return self.crate.root_dataset
-
-
-# https://github.com/ResearchObject/ro-terms/tree/master/test
-TESTING_EXTRA_TERMS = {
-    "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
-    "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
-    "TestService": "https://w3id.org/ro/terms/test#TestService",
-    "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
-    "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
-    "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
-    "TravisService": "https://w3id.org/ro/terms/test#TravisService",
-    "GithubService": "https://w3id.org/ro/terms/test#GithubService",
-    "instance": "https://w3id.org/ro/terms/test#instance",
-    "runsOn": "https://w3id.org/ro/terms/test#runsOn",
-    "resource": "https://w3id.org/ro/terms/test#resource",
-    "definition": "https://w3id.org/ro/terms/test#definition",
-    "engineVersion": "https://w3id.org/ro/terms/test#engineVersion"
-}

rocrate/rocrate.py

@@ -57,7 +57,18 @@
     TestSuite,
     WorkflowDescription,
 )
-from .model.metadata import WORKFLOW_PROFILE, TESTING_EXTRA_TERMS, DEFAULT_VERSION, BASENAME, LEGACY_BASENAME
+from .model.metadata import (
+    WROC_VERSION_MAP,
+    DEFAULT_WROC_VERSION,
+    WROC_PROFILE_BASE,
+    WTROC_VERSION_MAP,
+    DEFAULT_WTROC_VERSION,
+    WTROC_PROFILE_BASE,
+    WTROC_CONTEXT,
+    DEFAULT_VERSION,
+    BASENAME,
+    LEGACY_BASENAME,
+)
 from .model.computationalworkflow import galaxy_to_abstract_cwl
 from .model.computerlanguage import get_lang
 from .model.testservice import get_service
@@ -682,6 +693,25 @@ def _all_streams(self, chunk_size=8192):
         for writeable_entity in self.data_entities + self.default_entities:
             yield from writeable_entity.stream(chunk_size=chunk_size)
 
+    def _add_wroc_profile(self):
+        wroc_version = WROC_VERSION_MAP.get(self.version)
+        if wroc_version is None:
+            warnings.warn(f"RO-Crate version '{self.version}' is not compatible with Workflow RO-Crate")
+            wroc_version = DEFAULT_WROC_VERSION
+        profile_id = f"{WROC_PROFILE_BASE}/{wroc_version}"
+        if wroc_version == "1.0":
+            profiles = set(_.rstrip("/") for _ in get_norm_value(self.metadata, "conformsTo"))
+            profiles.add(profile_id)
+            self.metadata["conformsTo"] = [{"@id": _} for _ in sorted(profiles)]
+        else:
+            if profile_id not in self:
+                profile_entity = self.add(ContextEntity(self, profile_id, properties={
+                    "@type": ["CreativeWork", "Profile"],
+                    "name": "Workflow RO-Crate",
+                    "version": wroc_version,
+                }))
+                self.root_dataset.append_to("conformsTo", profile_entity)
+
     def add_workflow(
             self, source=None, dest_path=None, fetch_remote=False, validate_url=False, properties=None,
             main=False, lang="cwl", lang_version=None, gen_cwl=False, cls=ComputationalWorkflow,
@@ -701,9 +731,7 @@ def add_workflow(
         workflow.lang = lang
         if main:
             self.mainEntity = workflow
-            profiles = set(_.rstrip("/") for _ in get_norm_value(self.metadata, "conformsTo"))
-            profiles.add(WORKFLOW_PROFILE)
-            self.metadata["conformsTo"] = [{"@id": _} for _ in sorted(profiles)]
+            self._add_wroc_profile()
         if gen_cwl and lang_str != "cwl":
             if lang_str != "galaxy":
                 raise ValueError(f"conversion from {lang.name} to abstract CWL not supported")
@@ -716,6 +744,25 @@ def add_workflow(
             workflow.subjectOf = cwl_workflow
         return workflow
 
+    def _add_wtroc_profile(self):
+        wtroc_version = WTROC_VERSION_MAP.get(self.version)
+        if wtroc_version is None:
+            warnings.warn(f"RO-Crate version '{self.version}' is not compatible with Workflow Testing RO-Crate")
+            wtroc_version = DEFAULT_WTROC_VERSION
+        profile_id = f"{WTROC_PROFILE_BASE}/{wtroc_version}"
+        if wtroc_version == "0.1":
+            pass
+        else:
+            if profile_id not in self:
+                profile_entity = self.add(ContextEntity(self, profile_id, properties={
+                    "@type": ["CreativeWork", "Profile"],
+                    "name": "Workflow Testing RO-Crate",
+                    "version": wtroc_version,
+                }))
+                self.root_dataset.append_to("conformsTo", profile_entity)
+        if WTROC_CONTEXT not in self.metadata.extra_contexts:
+            self.metadata.extra_contexts.append(WTROC_CONTEXT)
+
     def add_test_suite(self, identifier=None, name=None, main_entity=None, properties=None):
         test_ref_prop = "mentions"
         if not main_entity:
@@ -728,7 +775,7 @@ def add_test_suite(self, identifier=None, name=None, main_entity=None, propertie
         if main_entity:
             suite["mainEntity"] = main_entity
         self.root_dataset.append_to(test_ref_prop, suite)
-        self.metadata.extra_terms.update(TESTING_EXTRA_TERMS)
+        self._add_wtroc_profile()
         return suite
 
     def add_test_instance(self, suite, url, resource="", service="jenkins", identifier=None, name=None, properties=None):
@@ -745,7 +792,7 @@ def add_test_instance(self, suite, url, resource="", service="jenkins", identifi
         if not properties or "name" not in properties:
             instance.name = name or instance.id.lstrip("#")
         suite.append_to("instance", instance)
-        self.metadata.extra_terms.update(TESTING_EXTRA_TERMS)
+        self._add_wtroc_profile()
         return instance
 
     def add_test_definition(
@@ -766,7 +813,7 @@ def add_test_definition(
         if engine_version is not None:
             definition.engineVersion = engine_version
         suite.definition = definition
-        self.metadata.extra_terms.update(TESTING_EXTRA_TERMS)
+        self._add_wtroc_profile()
         return definition
 
     def add_action(self, instrument, identifier=None, object=None, result=None, properties=None):
@@ -967,8 +1014,9 @@ def stream(self, chunk_size=8192):
 
 
 def make_workflow_rocrate(workflow_path, wf_type, include_files=[],
-                          fetch_remote=False, cwl=None, diagram=None):
-    wf_crate = ROCrate()
+                          fetch_remote=False, cwl=None, diagram=None,
+                          version=DEFAULT_VERSION):
+    wf_crate = ROCrate(version=version)
     workflow_path = Path(workflow_path)
     wf_crate.add_workflow(
         workflow_path, workflow_path.name, fetch_remote=fetch_remote,

test/conftest.py

@@ -35,11 +35,12 @@
 BASE_URL = 'https://w3id.org/ro/crate'
 DEFAULT_VERSION = '1.3'
 LEGACY_VERSION = '1.0'
+DEFAULT_WROC_VERSION = "1.1"
 
 
 class Helpers:
 
-    WORKFLOW_PROFILE = "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
+    WROC_PROFILE_BASE = "https://w3id.org/workflowhub/workflow-ro-crate"
     METADATA_FILE_NAME = 'ro-crate-metadata.json'
     LEGACY_METADATA_FILE_NAME = 'ro-crate-metadata.jsonld'
     WORKFLOW_TYPES = {"File", "SoftwareSourceCode", "ComputationalWorkflow"}
@@ -74,16 +75,23 @@ def check_crate(cls, json_entities, root_id="./", data_entity_ids=None, version=
             assert data_entity_ids.issubset([_["@id"] for _ in root["hasPart"]])
 
     @classmethod
-    def check_wf_crate(cls, json_entities, wf_file_name, root_id="./"):
-        cls.check_crate(json_entities, root_id=root_id)
+    def check_wf_crate(cls, json_entities, wf_file_name, root_id="./", wroc_version=DEFAULT_WROC_VERSION):
+        if wroc_version == "1.0":
+            cls.check_crate(json_entities, root_id=root_id, version="1.1")
+        else:
+            cls.check_crate(json_entities, root_id=root_id)
         assert json_entities[root_id]["mainEntity"]["@id"] == wf_file_name
         assert wf_file_name in json_entities
         wf_entity = json_entities[wf_file_name]
         assert isinstance(wf_entity["@type"], list)
         assert cls.WORKFLOW_TYPES.issubset(wf_entity["@type"])
         assert "programmingLanguage" in wf_entity
         metadata = json_entities[cls.METADATA_FILE_NAME]
-        assert cls.WORKFLOW_PROFILE in get_norm_value(metadata, "conformsTo")
+        profile_id = f"{cls.WROC_PROFILE_BASE}/{wroc_version}"
+        if wroc_version == "1.0":
+            assert profile_id in get_norm_value(metadata, "conformsTo")
+        else:
+            assert profile_id in get_norm_value(json_entities[root_id], "conformsTo")
 
 
 @pytest.fixture

test/test-data/crate_with_subcrates/ro-crate-metadata.json

@@ -1,5 +1,5 @@
 {
-    "@context": "https://w3id.org/ro/crate/1.1/context",
+    "@context": "https://w3id.org/ro/crate/1.3/context",
     "@graph": [
         {
             "@id": "./",
@@ -27,7 +27,7 @@
                 "@id": "./"
             },
             "conformsTo": {
-                "@id": "https://w3id.org/ro/crate/1.1"
+                "@id": "https://w3id.org/ro/crate/1.3"
             }
         },
         {

test/test-data/crate_with_subcrates/subcrate/ro-crate-metadata.json

@@ -1,5 +1,5 @@
 {
-    "@context": "https://w3id.org/ro/crate/1.1/context",
+    "@context": "https://w3id.org/ro/crate/1.3/context",
     "@graph": [
         {
             "@id": "./",
@@ -21,7 +21,7 @@
                 "@id": "./"
             },
             "conformsTo": {
-                "@id": "https://w3id.org/ro/crate/1.1"
+                "@id": "https://w3id.org/ro/crate/1.3"
             }
         },
         {

test/test-data/crate_with_subcrates/subcrate/subsubcrate/ro-crate-metadata.json

@@ -1,5 +1,5 @@
 {
-    "@context": "https://w3id.org/ro/crate/1.1/context",
+    "@context": "https://w3id.org/ro/crate/1.3/context",
     "@graph": [
         {
             "@id": "./",
@@ -18,7 +18,7 @@
                 "@id": "./"
             },
             "conformsTo": {
-                "@id": "https://w3id.org/ro/crate/1.1"
+                "@id": "https://w3id.org/ro/crate/1.3"
             }
         },
         {

test/test-data/crate_with_subcrates/subcrate2/ro-crate-metadata.json

@@ -1,5 +1,5 @@
 {
-    "@context": "https://w3id.org/ro/crate/1.1/context",
+    "@context": "https://w3id.org/ro/crate/1.3/context",
     "@graph": [
         {
             "@id": "./",
@@ -18,7 +18,7 @@
                 "@id": "./"
             },
             "conformsTo": {
-                "@id": "https://w3id.org/ro/crate/1.1"
+                "@id": "https://w3id.org/ro/crate/1.3"
             }
         },
         {

test/test-data/detached-ro-crate-metadata.json

@@ -1,5 +1,5 @@
 {
-    "@context": "https://w3id.org/ro/crate/1.2/context",
+    "@context": "https://w3id.org/ro/crate/1.3/context",
     "@graph": [
         {
             "@id": "ro-crate-metadata.json",
@@ -8,7 +8,7 @@
                 "@id": "https://raw.githubusercontent.com/ResearchObject/ro-crate-py/master/test/test-data/"
             },
             "conformsTo": {
-                "@id": "https://w3id.org/ro/crate/1.2"
+                "@id": "https://w3id.org/ro/crate/1.3"
             }
         },
         {

test/test-data/detached_crate_with_subcrates/subcrates-ro-crate-metadata.json

@@ -1,5 +1,5 @@
 {
-    "@context": "https://w3id.org/ro/crate/1.2/context",
+    "@context": "https://w3id.org/ro/crate/1.3/context",
     "@graph": [
         {
             "@id": "https://raw.githubusercontent.com/ResearchObject/ro-crate-py/master/test/test-data/detached_crate_with_subcrates/",
@@ -24,7 +24,7 @@
                 "@id": "https://raw.githubusercontent.com/ResearchObject/ro-crate-py/master/test/test-data/detached_crate_with_subcrates/"
             },
             "conformsTo": {
-                "@id": "https://w3id.org/ro/crate/1.2"
+                "@id": "https://w3id.org/ro/crate/1.3"
             }
         },
         {

test/test-data/read_crate/ro-crate-metadata.json

@@ -14,6 +14,9 @@
         {
             "@id": "./",
             "@type": "Dataset",
+            "conformsTo": {
+                "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.1"
+            },
             "datePublished": "2020-06-25 17:03:04.098286",
             "hasPart": [
                 {
@@ -45,6 +48,15 @@
                 "@id": "test_galaxy_wf.ga"
             }
         },
+        {
+            "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.1",
+            "@type": [
+                "CreativeWork",
+                "Profile"
+            ],
+            "name": "Workflow RO-Crate",
+            "version": "1.1"
+        },
         {
             "@id": "ro-crate-preview.html",
             "@type": "CreativeWork",

test/test-data/read_extra/ro-crate-metadata.json

@@ -1,5 +1,5 @@
 {
-    "@context": "https://w3id.org/ro/crate/1.2/context",
+    "@context": "https://w3id.org/ro/crate/1.3/context",
     "@graph": [
         {
             "@id": "./",
@@ -24,7 +24,7 @@
                 "@id": "./"
             },
             "conformsTo": {
-                "@id": "https://w3id.org/ro/crate/1.2"
+                "@id": "https://w3id.org/ro/crate/1.3"
             }
         },
         {