Repository: RDFLib/pySHACL

Issue:
sh:or with or without --shape
First off, thanks for creating this awesome SHACL validator! 

I’m trying to define a predicate whose value can be either xsd:string or xsd:int. While I can validate the data as expected without the --shape flag, I encounter an error when using it alongside `sh:or`.

Below are the details.

SHACL file: test.shacl
-----------------------
```
@prefix ex: <http://example.org/> .
@prefix sh: <http://www.w3.org/ns/shacl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

ex:DescriptorShape
  a sh:NodeShape ;

  sh:targetClass ex:Descriptor ;

  sh:property [
    sh:path ex:hasValue ;
    sh:or (
        [ sh:datatype xsd:string ]
        [ sh:datatype xsd:int ]
    ) ;
    sh:minCount 1 ;
    sh:maxCount 1 ;
  ] .
```

Data file: test.ttl
------------
```
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix ex: <http://example.org/> .

ex:Example
    a ex:Descriptor ;
    ex:hasValue "1"^^xsd:decimal.
```

without `--shape`, validation worked as expected, and the data did not conform because the value 1 was of type xsd:decimal, which does not satisfy the sh:or constraint.
```
$ pyshacl -s test.shacl test.ttl 
Validation Report
Conforms: False
Results (1):
Constraint Violation in OrConstraintComponent (http://www.w3.org/ns/shacl#OrConstraintComponent):
        Severity: sh:Violation
        Source Shape: [ sh:maxCount Literal("1", datatype=xsd:integer) ; sh:minCount Literal("1", datatype=xsd:integer) ; sh:or ( [ sh:datatype xsd:string ] [ sh:datatype xsd:int ] ) ; sh:path ex:hasValue ]
        Focus Node: ex:Example
        Value Node: Literal("1", datatype=xsd:decimal)
        Result Path: ex:hasValue
        Message: Node Literal("1", datatype=xsd:decimal) must conform to one or more shapes in [ sh:datatype xsd:string ] , [ sh:datatype xsd:int ]
```

When specifying the shape explicitly using the `--shape` flag, I received the following runtime error:
```
$ pyshacl -s test.shacl test.ttl --shape ex:DescriptorShape
Validator encountered a Runtime Error:
Shape pointed to by sh:or does not exist or is not a well-formed SHACL Shape.
If you believe this is a bug in pyshacl, open an Issue on the pyshacl github page.
```

The error indicates that the source shape referenced in `sh:or` is not found (or harvested):
```
Source Shape [ sh:maxCount Literal("1", datatype=xsd:integer) ; sh:minCount Literal("1", datatype=xsd:integer) ; sh:or ( [ sh:datatype xsd:string ] [ sh:datatype xsd:int ] ) ; sh:path ex:hasValue ]
```

By digging into the code, I noticed differences in how shapes are processed with and without the `--shape` flag:

without `--shape`, all shapes are harvested as follows:
```
shapes = self.shacl_graph.shapes        # validator.py
self._build_node_shape_cache()        # shapes_graph.py
```

with `--shape`, only the specified shapes are loaded:
```
shapes = self.shacl_graph.shapes_from_uris(expanded_use_shapes)        # validator.py
self._build_node_shape_cache_from_list(shapes_uris)        # shapes_graph.py
```

It seems this might be a design choice, but it would make sense to:

1. Always harvest all shapes in the SHACL graph first.
2. Apply a filter for the shape specified with `--shape`.

This approach would ensure the dependencies (like shapes referenced in sh:or) are available for validation.

Discussion:

Patch:
diff --git a/pyshacl/shapes_graph.py b/pyshacl/shapes_graph.py
index 1be67e3..d3ed90a 100644
--- a/pyshacl/shapes_graph.py
+++ b/pyshacl/shapes_graph.py
@@ -416,7 +416,12 @@ class ShapesGraph(object):
                     for _p in has_shape_expecting_p.keys():
                         property_entries = list(g.objects(s, _p))
                         for p_e in property_entries:
-                            if isinstance(p_e, rdflib.BNode):
+                            if _p in (SH_or, SH_xone, SH_and):
+                                # These are list-expecting variants of shape-expecting constraints.
+                                for item in g.items(p_e):
+                                    if isinstance(item, rdflib.BNode):
+                                        _found_child_bnodes.append(item)
+                            elif isinstance(p_e, rdflib.BNode):
                                 _found_child_bnodes.append(p_e)
                 if len(_found_child_bnodes) > 0:
                     _gather_shapes(_found_child_bnodes, recurse_depth=recurse_depth + 1)


Test patch:
diff --git a/test/test_manual_targeting.py b/test/test_manual_targeting.py
index 9b5ff32..31ffb32 100644
--- a/test/test_manual_targeting.py
+++ b/test/test_manual_targeting.py
@@ -84,10 +84,11 @@ exShape:HumanShape a sh:NodeShape ;
 
 exShape:AnimalShape a sh:NodeShape ;
     sh:property [
-        sh:datatype xsd:integer ;
         sh:path exOnt:nLegs ;
-        sh:maxInclusive 4 ;
-        sh:minInclusive 1 ;
+        sh:or (
+            [ sh:datatype xsd:integer ; sh:minInclusive 0 ; sh:maxInclusive 0 ]
+            [ sh:datatype xsd:integer ; sh:minInclusive 1 ; sh:maxInclusive 8 ]
+        ) ;
     ] ;
     sh:targetClass exOnt:Animal .
 """
@@ -195,6 +196,21 @@ def test_validate_fail_manual_targeting_shape():
     assert "Results (2)" in string
     assert not conforms
 
+def test_validate_fail_manual_targeting_shape_or():
+    res = validate(
+        data_file_text_bad,
+        shacl_graph=shacl_file_text,
+        data_graph_format='turtle',
+        shacl_graph_format='turtle',
+        ont_graph=ontology_file_text,
+        ont_graph_format="turtle",
+        inference='rdfs',
+        use_shapes=["exShape:AnimalShape"],
+        debug=True,
+    )
+    conforms, graph, string = res
+    assert "Results (2)" in string
+    assert not conforms
 
 def test_validate_fail_manual_targeting_focus_with_shape():
     res = validate(