Merge pull request #86 from pyscal/reorder_triples

Reorder triples

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.1
+current_version = 0.5.2
 commit = True
 tag = False
 

CITATION.cff

@@ -20,4 +20,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.5.1
+version: 0.5.2

atomrdf/graph.py

@@ -134,6 +134,14 @@ def add_structure(self, structure):
         structure.graph = self
         structure.to_graph()
 
+    def _is_valid(self, input_list):
+        valid = False
+        for x in input_list:
+            if x is not None:
+                valid = True
+                break
+        return valid
+
     def _is_ontoterm(self, term):
         return type(term).__name__ == 'OntoTerm'
 
@@ -317,6 +325,11 @@ def remove(self, triple):
         return self.graph.remove(modified_triple)
 
 
+    def create_node(self, namestring, classtype):
+        item = URIRef(namestring)
+        self.add((item, RDF.type, classtype))
+        return item
+
     def _initialize_graph(self):
         """
         Create the RDF Graph from the data stored
@@ -349,9 +362,8 @@ def _initialize_graph(self):
 
 
     def add_calculated_quantity(self, sample, propertyname, value, unit=None):
-        prop = URIRef(f'{self._name}_{propertyname}')
+        prop = self.create_node(propertyname, CMSO.CalculatedProperty)
         self.add((sample, CMSO.hasCalculatedProperty, prop))
-        self.add((prop, RDF.type, CMSO.CalculatedProperty))
         self.add((prop, RDFS.label, Literal(propertyname)))
         self.add((prop, CMSO.hasValue, Literal(value)))
         if unit is not None:

atomrdf/workflow/workflow.py

@@ -71,10 +71,44 @@ def _prepare_job(self, workflow_object):
             parent_structure.to_graph()
             parent_sample = parent_structure.sample
 
+        self.structure = structure
         self.sample = sample
         self.mdict = method_dict
         self.parent_sample = parent_sample
 
+    def _get_lattice_properties(self, ):
+        if self.parent_sample is None:
+            return
+
+        material = list([k[2] for k in self.kg.triples((self.parent_sample, CMSO.hasMaterial, None))])[0]
+        crystal_structure = self.kg.value(material, CMSO.hasStructure)
+
+        altname = self.kg.value(crystal_structure, CMSO.hasAltName)
+
+        space_group = self.kg.value(crystal_structure, CMSO.hasSpaceGroup)
+        space_group_symbol = self.kg.value(space_group, CMSO.hasSpaceGroupSymbol)
+        space_group_number = self.kg.value(space_group, CMSO.hasSpaceGroupNumber)
+
+        unit_cell = self.kg.value(crystal_structure, CMSO.hasUnitCell)
+        blattice = self.kg.value(unit_cell, Namespace("http://purls.helmholtz-metadaten.de/cmso/").hasBravaisLattice)
+
+        lattice_parameter = self.kg.value(unit_cell, CMSO.hasLatticeParameter)
+        lattice_parameter_x = self.kg.value(lattice_parameter, CMSO.hasLength_x)
+        lattice_parameter_y = self.kg.value(lattice_parameter, CMSO.hasLength_y)
+        lattice_parameter_z = self.kg.value(lattice_parameter, CMSO.hasLength_z)
+
+        lattice_angle = self.kg.value(unit_cell, CMSO.hasAngle)
+        lattice_angle_x = self.kg.value(lattice_angle, CMSO.hasAngle_alpha)
+        lattice_angle_y = self.kg.value(lattice_angle, CMSO.hasAngle_beta)
+        lattice_angle_z = self.kg.value(lattice_angle, CMSO.hasAngle_gamma)
+
+        targets = [altname, space_group_symbol, space_group_number, blattice,
+        [lattice_parameter_x, lattice_parameter_y, lattice_parameter_z],
+        [lattice_angle_x, lattice_angle_y, lattice_angle_z]]
+
+        self.structure._add_crystal_structure(targets=targets)
+
+
     def _add_inherited_properties(self, ):
         #Here we need to add inherited info: CalculatedProperties will be lost
         #Defects will be inherited
@@ -102,52 +136,15 @@ def _add_inherited_properties(self, ):
         for triple in self.kg.triples((parent_simcell, PODO.hasNumberOfVacancies, None)):
             self.kg.graph.add((simcell, triple[1], triple[2]))
 
-    def _get_lattice_properties(self, ):
-        if self.parent_sample is None:
-            return
-
-        parent_material = list([k[2] for k in self.kg.triples((self.parent_sample, CMSO.hasMaterial, None))])[0]
-        parent_crystal_structure = self.kg.value(parent_material, CMSO.hasStructure)
-        parent_altname = self.kg.value(parent_crystal_structure, CMSO.hasAltName)
-
-        #add this to new structure
-        material = list([k[2] for k in self.kg.triples((self.sample, CMSO.hasMaterial, None))])[0]
-        crystal_structure = self.kg.value(material, CMSO.hasStructure)
-        self.kg.add((crystal_structure, CMSO.hasAltName, parent_altname))
-
-        #space group
-        parent_space_group = self.kg.value(parent_crystal_structure, CMSO.hasSpaceGroup)
-        space_group = self.kg.value(crystal_structure, CMSO.hasSpaceGroup)
-        for triple in self.kg.triples((parent_space_group, None, None)):
-            self.kg.graph.add((space_group, triple[1], triple[2]))
-
-        #unit cell
-        parent_unit_cell = self.kg.value(parent_crystal_structure, CMSO.hasUnitCell)
-        parent_bv = self.kg.value(parent_unit_cell, Namespace("http://purls.helmholtz-metadaten.de/cmso/").hasBravaisLattice)
-
-        unit_cell = self.kg.value(crystal_structure, CMSO.hasUnitCell)
-        self.kg.graph.add((unit_cell, Namespace("http://purls.helmholtz-metadaten.de/cmso/").hasBravaisLattice, parent_bv))
-
-        #lattice parameter
-        parent_lattice_parameter = self.kg.value(parent_unit_cell, CMSO.hasLatticeParameter)
-        lattice_parameter = self.kg.value(unit_cell, CMSO.hasLatticeParameter)
-        for triple in self.kg.triples((parent_lattice_parameter, None, None)):
-            self.kg.graph.add((lattice_parameter, triple[1], triple[2]))
-
-        #lattice angle
-        parent_lattice_angle = self.kg.value(parent_unit_cell, CMSO.hasAngle)
-        lattice_angle = self.kg.value(unit_cell, CMSO.hasAngle)
-        for triple in self.kg.triples((parent_lattice_angle, None, None)):
-            self.kg.graph.add((lattice_angle, triple[1], triple[2]))
 
 
     def add_structural_relation(self, ):
         self.kg.add((self.sample, RDF.type, PROV.Entity))
         if self.parent_sample is not None:
             self.kg.add((self.parent_sample, RDF.type, PROV.Entity))
             self.kg.add((self.sample, PROV.wasDerivedFrom, self.parent_sample))
-            self._add_inherited_properties()
             self._get_lattice_properties()
+            self._add_inherited_properties()
 
 
     def add_method(self, ):