shacl-shape

renku/command/graph.py

@@ -227,16 +227,17 @@ def _convert_entities_to_graph(
     for entity in entities:
         if entity.id in processed_plans:
             continue
-        if isinstance(entity, (Dataset, Activity, AbstractPlan)):
+        if isinstance(entity, (Dataset, Activity, AbstractPlan, WorkflowFileActivityCollection)):
             # NOTE: Since the database is read-only, it's OK to modify objects; they won't be written back
             entity.unfreeze()
             entity.project_id = project_id
 
-            if isinstance(entity, Activity):
+            if isinstance(entity, (Activity, WorkflowFileActivityCollection)):
                 entity.association.plan.unfreeze()
                 entity.association.plan.project_id = project_id
         schema = next(s for t, s in schemas.items() if isinstance(entity, t))
-        graph.extend(schema(flattened=True).dump(entity))
+        data = schema(flattened=True).dump(entity)
+        graph.extend(data)
 
         if not isinstance(entity, (Activity, WorkflowFileActivityCollection)):
             continue

renku/command/schema/activity.py

@@ -52,7 +52,7 @@ def __getattr__(self, name):
 def _fix_id(obj):
     """Fix ids under an activity that were wrong due to a bug."""
 
-    if not obj.id.startswith("/activities/"):
+    if not obj.id.startswith("/activities/") and not obj.id.startswith("/workflow-file-activity-collection/"):
         obj = _ObjectWrapper(obj, id=f"/activities/{obj.id}")
 
     return obj
@@ -179,7 +179,7 @@ class WorkflowFileActivityCollectionSchema(JsonLDSchema):
     class Meta:
         """Meta class."""
 
-        rdf_type = [prov.Activity, prov.Collection]
+        rdf_type = [renku.WorkflowFileActivityCollection, prov.Collection]
         model = WorkflowFileActivityCollection
         unknown = EXCLUDE
 

renku/data/shacl_shape.json

@@ -235,6 +235,13 @@
                },
                "sh:pattern": "http(s)?://[^/]+/activities/[0-9a-f]+"
             },
+            {
+               "path": "renku:hasActivityCollection",
+               "sh:class": {
+                  "@id": "renku:WorkflowFileActivityCollection"
+               },
+               "sh:pattern": "http(s)?://[^/]+/workflow-file-activity-collection/[0-9a-f]+"
+            },
             {
                "nodeKind": "sh:Literal",
                "path": "schema:keywords",
@@ -877,6 +884,74 @@
             }
          ]
       },
+      {
+         "@id": "_:workflowFileActivityCollectionShape",
+         "@type": "sh:NodeShape",
+         "ignoredProperties": [
+            {
+               "@id": "rdf:type"
+            }
+         ],
+         "closed": true,
+         "targetClass": "renku:WorkflowFileActivityCollection",
+         "property": [
+            {
+               "path": "prov:wasAssociatedWith",
+               "or": [
+                  {
+                     "sh:class": {
+                        "@id": "prov:SoftwareAgent"
+                     }
+                  },
+                  {
+                     "sh:class": {
+                        "@id": "schema:Person"
+                     }
+                  },
+                  {
+                     "nodeKind": "sh:IRI"
+                  }
+               ],
+               "minCount": 2,
+               "maxCount": 2
+            },
+            {
+               "path": "prov:qualifiedAssociation",
+               "sh:class": {
+                  "@id": "prov:Association"
+               },
+               "sh:pattern": "http(s)?://[^/]+/workflow-file-activity-collection/[0-9a-f]+/association"
+            },
+            {
+               "path": "schema:hasPart",
+               "sh:class": {
+                  "@id": "prov:Activity"
+               },
+               "sh:pattern": "http(s)?://[^/]+/activities/[0-9a-f]+"
+            },
+            {
+               "nodeKind": "sh:Literal",
+               "path": "prov:endedAtTime",
+               "datatype": {
+                  "@id": "xsd:dateTime"
+               },
+               "minCount": 1,
+               "maxCount": 1,
+               "sh:moreThanOrEquals": {
+                  "@id": "prov:startedAtTime"
+               }
+            },
+            {
+               "nodeKind": "sh:Literal",
+               "path": "prov:startedAtTime",
+               "datatype": {
+                  "@id": "xsd:dateTime"
+               },
+               "minCount": 1,
+               "maxCount": 1
+            }
+         ]
+      },
       {
          "@id": "_:associationShape",
          "@type": "sh:NodeShape",
@@ -998,7 +1073,7 @@
                   "@id": "renku:CommandParameter"
                },
                "path": "renku:hasArguments",
-               "sh:pattern": "http(s)?://[^/]+/plans/[0-9a-f-]+/parameters/[0-9a-z]+"
+               "sh:pattern": "http(s)?://[^/]+/plans/[0-9a-f-]+/parameters/[0-9a-zA-Z_-]+"
             },
             {
                "nodeKind": "sh:Literal",
@@ -1019,7 +1094,7 @@
                   "@id": "renku:CommandInput"
                },
                "path": "renku:hasInputs",
-               "sh:pattern": "http(s)?://[^/]+/plans/[0-9a-f-]+/inputs/(stdin|[0-9a-f]+)"
+               "sh:pattern": "http(s)?://[^/]+/plans/[0-9a-f-]+/inputs/([0-9a-zA-Z_-]+)"
             },
             {
                "nodeKind": "sh:Literal",
@@ -1034,7 +1109,7 @@
                   "@id": "renku:CommandOutput"
                },
                "path": "renku:hasOutputs",
-               "sh:pattern": "http(s)?://[^/]+/plans/[0-9a-f-]+/outputs/(stdout|stderr|[0-9a-f]+)"
+               "sh:pattern": "http(s)?://[^/]+/plans/[0-9a-f-]+/outputs/([0-9a-zA-Z_-]+)"
             },
             {
                "nodeKind": "sh:Literal",

renku/domain_model/provenance/activity.py

@@ -342,3 +342,6 @@ def from_activities(
     def generate_id() -> str:
         """Generate an identifier."""
         return f"/workflow-file-activity-collection/{uuid4().hex}"
+
+    def __repr__(self):
+        return f"<WorkflowFileActivityCollection '{self.id}': {self.association.plan.name} @ {self.ended_at_time}>"

tests/cli/test_workflow_file.py

@@ -161,13 +161,14 @@ def test_export_graph_with_workflow_file(runner, workflow_file_project):
     result = runner.invoke(cli, ["run", workflow_file_project.workflow_file])
     assert 0 == result.exit_code, format_result_exception(result)
 
-    result = runner.invoke(cli, ["graph", "export", "--full"])
+    result = runner.invoke(cli, ["graph", "export", "--full", "--strict"])
     assert 0 == result.exit_code, format_result_exception(result)
 
     assert "workflow-file" in result.output
     assert "workflow-file.head" in result.output
     assert "workflow-file.tail" in result.output
     assert "workflow-file.line-count" in result.output
+    assert "renku-ontology#WorkflowFileActivityCollection" in result.output
     assert "renku-ontology#WorkflowFileCompositePlan" in result.output
     assert "renku-ontology#WorkflowFilePlan" in result.output
 
@@ -467,3 +468,12 @@ def test_workflow_file_status(runner, workflow_file_project):
 
     assert "Outdated workflow files and their outputs(1):" in result.output
     assert "workflow-file.yml: intermediate, results/output.csv, results/output.csv.wc" in result.output
+
+    result = runner.invoke(cli, ["run", workflow_file_project.workflow_file])
+    assert 0 == result.exit_code, format_result_exception(result)
+
+    result = runner.invoke(cli, ["status"])
+    assert 0 == result.exit_code, format_result_exception(result)
+
+    assert "Outdated workflow files and their outputs(1):" not in result.output
+    assert "Everything is up-to-date" in result.output