Upgraded to rdflib>=6.0.0 and pyshacl==v0.17.2: (BlueBrain#201)

* Upgraded to rdflib>=6.0.0 and pyshacl==v0.17.2:
* removed rdflib-jsonld dependancy which is now part of rdflib from rdflib>=6.0.0
* Added a ShapeWrapper class extending pyshacl.shape to workaround added __slots__ preventing from dynamically adding methods

* Removed python==3.6 support

.travis.yml

@@ -1,7 +1,6 @@
 language: python
 
 python:
-  - "3.6"
   - "3.7"
   - "3.8"
 

kgforge/core/commons/context.py

@@ -13,12 +13,10 @@
 # along with Blue Brain Nexus Forge. If not, see <https://choosealicense.com/licenses/lgpl-3.0/>.
 
 from typing import Optional, Union, Dict, List
+from rdflib.plugins.shared.jsonld.context import source_to_json, Context as JSONLD_Context
 
-from rdflib_jsonld.context import Context as RdflibContext
-from rdflib_jsonld.util import source_to_json
 
-
-class Context(RdflibContext):
+class Context(JSONLD_Context):
     """Context class will hold a JSON-LD context in two forms: iri and document.
 
     See also: https://w3c.github.io/json-ld-syntax/#the-context

kgforge/core/conversions/rdf.py

@@ -13,6 +13,8 @@
 # along with Blue Brain Nexus Forge. If not, see <https://choosealicense.com/licenses/lgpl-3.0/>.
 
 from copy import deepcopy
+
+from rdflib.plugins.shared.jsonld.keys import CONTEXT, TYPE, GRAPH
 from typing import Union, Dict, List, Tuple, Optional, Callable, Any
 from urllib.error import URLError, HTTPError
 
@@ -21,9 +23,7 @@
 from rdflib import Graph, Literal
 import json
 from collections import OrderedDict
-
 from rdflib.namespace import RDF
-from rdflib_jsonld.keys import CONTEXT, GRAPH, TYPE, ID
 
 from kgforge.core.commons.actions import LazyAction
 from kgforge.core.commons.context import Context
@@ -214,7 +214,7 @@ def _as_jsonld_one(resource: Resource, form: Form, store_metadata: bool,
             context.expand(resource_type) for resource_type in resource_types]
     resource.type = resource_types
     if store_metadata is True and len(metadata_graph) > 0:
-        metadata_expanded = json.loads(metadata_graph.serialize(format="json-ld").decode("utf-8"))
+        metadata_expanded = json.loads(metadata_graph.serialize(format="json-ld"))
         metadata_framed = jsonld.frame(metadata_expanded, {"@id": resource.id})
         if form is Form.COMPACTED:
             data_compacted = jsonld.compact(data_framed, resolved_context)

kgforge/specializations/models/rdf/service.py

@@ -13,6 +13,7 @@
 # along with Blue Brain Nexus Forge. If not, see <https://choosealicense.com/licenses/lgpl-3.0/>.
 import types
 from abc import abstractmethod
+from pyshacl.constraints import ALL_CONSTRAINT_PARAMETERS
 from typing import List, Dict, Tuple, Set, Optional
 from pyshacl.shape import Shape
 from pyshacl.shapes_graph import ShapesGraph
@@ -89,6 +90,17 @@ def traverse(self, predecessors: Set[URIRef]) -> Tuple[List, Dict]:
     return properties, attributes
 
 
+class ShapeWrapper(Shape):
+    __slots__ = ('__dict__',)
+
+    def __init__(self, shape: Shape) -> None:
+        super().__init__(shape.sg, shape.node, shape._p, shape._path, shape.logger)
+
+    def parameters(self):
+        return (p for p, v in self.sg.predicate_objects(self.node)
+                if p in ALL_CONSTRAINT_PARAMETERS)
+
+
 class ShapesGraphWrapper(ShapesGraph):
 
     def __init__(self, graph: Graph) -> None:
@@ -105,10 +117,12 @@ def lookup_shape_from_node(self, node: URIRef) -> Shape:
         Returns:
             Shape: The Shacl shape of the requested node.
         """
-
         shape = self._node_shape_cache[node]
-        if not hasattr(shape, "traverse"):
-            shape.traverse = types.MethodType(traverse, shape)
+        if shape:
+            shape_wrapper = ShapeWrapper(self._node_shape_cache[node])
+            if not hasattr(shape_wrapper, "traverse"):
+                shape_wrapper.traverse = types.MethodType(traverse, shape_wrapper)
+            return shape_wrapper
         return shape
 
 

setup.py

@@ -35,7 +35,7 @@
     keywords="framework knowledge graph data science",
     url="https://github.com/BlueBrain/nexus-forge",
     packages=find_packages(),
-    python_requires=">=3.6",
+    python_requires=">=3.7",
     setup_requires=[
         "setuptools_scm",
     ],
@@ -46,13 +46,12 @@
         "nexus-sdk",
         "aiohttp",
         "nest_asyncio",
-        "rdflib<6.0.0",
+        "rdflib>=6.0.0",
         "pyLD",
-        "pyshacl==0.11.6.post1",
-        "rdflib-jsonld<0.6.1",
+        "pyshacl==v0.17.2",
         "nest-asyncio>=1.5.1",
-        "pyparsing==2.*",
-        "owlrl>=5.2.1, < 6.0.2"
+        "pyparsing>=2.0.2",
+        "owlrl>=5.2.3"
     ],
     extras_require={
         "dev": ["tox", "pytest", "pytest-bdd==3.4.0", "pytest-cov", "pytest-mock", "codecov"],