Merge pull request #61 from pyscal/bug_fixes

Bug fixes
pyscal · Feb 13, 2024 · 4e0b0b6 · 4e0b0b6
2 parents 6e8b0f2 + bc93c34
commit 4e0b0b6
Show file tree

Hide file tree

Showing 11 changed files with 90 additions and 16 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.5
+current_version = 0.1.6
 commit = True
 tag = False
 

diff --git a/notebooks/create_onto.ipynb b/notebooks/create_onto.ipynb
@@ -112,7 +112,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/wrap_creation.ipynb b/notebooks/wrap_creation.ipynb
@@ -125,7 +125,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/pyscal_rdf/data/cmso.owl b/pyscal_rdf/data/cmso.owl
@@ -712,7 +712,6 @@
     <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroupSymbol">
         <rdfs:subPropertyOf rdf:resource="http://purls.helmholtz-metadaten.de/cmso/hasSymbol"/>
         <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/SpaceGroup"/>
-        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
         <rdfs:label>has space group symbol</rdfs:label>
         <skos:definition>A data property linking a crystal structure with its space group symbol.</skos:definition>
     </owl:DatatypeProperty>
@@ -723,6 +722,7 @@
 
     <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasSymbol">
         <rdfs:domain rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
         <rdfs:label>has symbol</rdfs:label>
         <skos:definition>A data property linking an entity with its symbol.</skos:definition>
     </owl:DatatypeProperty>
@@ -781,7 +781,7 @@
         <rdfs:label>Amorphous Material</rdfs:label>
         <skos:altLabel>Amorphous Solid</skos:altLabel>
         <skos:altLabel>Non-crystalline Solid</skos:altLabel>
-        <skos:definition>An amorphous material or solid is a material which has no defined long-range periodicity.</skos:definition>
+        <skos:definition>An amorphous material or solid is a material which has no defined long-range order.</skos:definition>
     </owl:Class>
 
 

diff --git a/pyscal_rdf/graph.py b/pyscal_rdf/graph.py
@@ -115,6 +115,7 @@ def __init__(self, graph_file=None,
         if ontology is None:
             ontology = read_ontology()
         self.ontology = ontology
+        self.terms = self.ontology.terms
         self._atom_ids = None
         self.store = store
 
@@ -291,7 +292,7 @@ def add_chemical_composition(self):
                 element = URIRef(element_indetifiers[e])
                 self.add((chemical_species, CMSO.hasElement, element))
                 self.add((element, RDF.type, CMSO.Element))
-                self.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string)))
+                self.add((element, CMSO.hasChemicalSymbol, Literal(e, datatype=XSD.string)))
                 self.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float)))
 
     def add_simulation_cell(self):
@@ -404,10 +405,12 @@ def add_space_group(self):
         Returns
         -------
         """
-        self.add((self.crystal_structure, CMSO.hasSpaceGroupSymbol, 
+        space_group = URIRef(f'{self._name}_SpaceGroup')
+        self.add((self.crystal_structure, CMSO.hasSpaceGroup, space_group))
+        self.add((space_group, CMSO.hasSpaceGroupSymbol, 
             Literal(self.system.schema.material.crystal_structure.spacegroup_symbol(), 
                 datatype=XSD.string)))
-        self.add((self.crystal_structure, CMSO.hasSpaceGroupNumber, 
+        self.add((space_group, CMSO.hasSpaceGroupNumber, 
             Literal(self.system.schema.material.crystal_structure.spacegroup_number(), 
                 datatype=XSD.integer)))
 
@@ -898,13 +901,27 @@ def query(self, inquery):
         raise ValueError("SPARQL query returned None")
 
     def auto_query(self, source, destination, 
-        condition=None, return_query=False, enforce_types=True):
-        query = self.ontology.create_query(source, destination, 
-            condition=condition, enforce_types=enforce_types)
-        if return_query:
-            return query
-        return self.query(query)
-
+        condition=None, 
+        return_query=False, 
+        enforce_types=None):
+
+        if enforce_types is None:
+            for val in [True, False]:
+                query = self.ontology.create_query(source, destination, 
+                    condition=condition, enforce_types=val)
+                if return_query:
+                    return query
+                res = self.query(query)
+                if len(res) != 0:
+                    return res
+        else:
+            query = self.ontology.create_query(source, destination, 
+                condition=condition, enforce_types=val)
+            if return_query:
+                return query
+            res = self.query(query)
+
+        return res    
 
     #################################
     # Methods to interact with sample

diff --git a/pyscal_rdf/network/network.py b/pyscal_rdf/network/network.py
@@ -235,6 +235,7 @@ def create_query(self, source, destinations, condition=None, enforce_types=True)
         #now add corresponding triples
         for destination in destination_names:
             for triple in all_triplets[destination]:
+                print(triple)
                 query.append("    ?%s %s ?%s ."%(self.strip_name(triple[0]), 
                                                  triple[1], 
                                                  self.strip_name(triple[2])))

diff --git a/pyscal_rdf/network/ontology.py b/pyscal_rdf/network/ontology.py
@@ -32,7 +32,12 @@ def read_ontology():
 	combo.add_term('http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'object_property', delimiter='#', namespace='rdf')
 
 	#add paths
+
+	#General fixes
 	combo.add_path(('cmso:CrystalStructure', 'cmso:hasAltName', 'string'))
+	combo.add_path(('cmso:ChemicalElement', 'cmso:hasSymbol', 'string'))
+
+	#interontology paths
 	combo.add_path(('cmso:Material', 'cmso:hasDefect', 'pldo:PlanarDefect'))
 	combo.add_path(('cmso:Material', 'cmso:hasDefect', 'podo:Vacancy'))
 	combo.add_path(('cmso:SimulationCell', 'podo:hasVacancyConcentration', 'float'))

diff --git a/pyscal_rdf/network/parser.py b/pyscal_rdf/network/parser.py
@@ -1,4 +1,6 @@
 from pyscal_rdf.network.term import OntoTerm, strip_name 
+from pyscal_rdf.network.patch import patch_terms
+
 from owlready2 import get_ontology
 import owlready2
 
@@ -98,6 +100,22 @@ def _parse_data_property(self):
                 rn = [r.__name__ for r in rn[0].Classes if r is not None]
             except:
                 rn = [r.__name__ for r in rn if r is not None]
+
+
+            #Subproperties
+            #Commented out for now
+            #subprops = self.tree.search(subproperty_of=getattr(self.tree, c.name))
+            #for subprop in subprops:
+            #    if subprop.iri != iri:
+            #        #print(subprop.iri)
+            #        pass
+
+            #PATCH
+            #Here: we patch specific items specifically for pyscal rdf
+            rn  = patch_terms(iri, rn)
+
+            #print(iri, rn)
+            #print(iri, dm)
             term = OntoTerm(iri, delimiter=self.delimiter)
             term.domain = dm
             term.range = rn
@@ -107,6 +125,10 @@ def _parse_data_property(self):
             for d in dm:
                 if d!='07:owl#Thing':
                     self.attributes['class'][d].is_range_of.append(term.name)
+
+
+            #subproperties should be treated the same
+
 
     def _parse_object_property(self):
         for c in self.tree.object_properties():

diff --git a/pyscal_rdf/network/patch.py b/pyscal_rdf/network/patch.py
@@ -0,0 +1,28 @@
+"""
+These are patches specifically designed for pyscal-rdf.
+
+These may or may not be implemented in the ontology. As it is implemented; it can be removed
+from the patches
+"""
+
+import os
+
+def patch_terms(iri, rn):
+    """
+    Remove functions as patching is done
+    """
+    #Term: hasSymbol
+    #Ontology: CMSO
+    #Reason: Range is not specified in the owl file. 
+    #This prevents owlready2 from reading in this property correctly. 
+    if iri == 'http://purls.helmholtz-metadaten.de/cmso/hasSymbol':
+        rn = ['str']
+    #Term: hasValue
+    #Ontology: CMSO
+    #Reason: Range is Literal(); however here we use this for number values, hence we can fix this.
+    #See fn: `add_calculated_property`
+    elif iri == 'http://purls.helmholtz-metadaten.de/cmso/hasValue':
+        rn = ['float']
+
+    return rn
+
diff --git a/pyscal_rdf/network/term.py b/pyscal_rdf/network/term.py
@@ -70,6 +70,7 @@ def __init__(self, uri,
         #identifier
         self.node_id = node_id
         self.subclasses = []
+        self.subproperties = []
         self.delimiter = delimiter
         self.is_domain_of = []
         self.is_range_of = []

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name='pyscal_rdf',
-    version='0.1.5',
+    version='0.1.6',
     author='Abril Azocar Guzman, Sarath Menon',
     author_email='[email protected]',
     description='Ontology based structural manipulation and quering',