diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 34a4fc7..f9b37e4 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.5.1 +current_version = 0.5.2 commit = True tag = False diff --git a/CITATION.cff b/CITATION.cff index 7c24658..63dba64 100644 --- a/CITATION.cff +++ b/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 diff --git a/atomrdf/graph.py b/atomrdf/graph.py index cf025ea..f69a47e 100644 --- a/atomrdf/graph.py +++ b/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: diff --git a/atomrdf/structure.py b/atomrdf/structure.py index 0cef9e9..e0015d3 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -258,6 +258,7 @@ def delete(self, ids=None, indices=None, condition=None, selection=False): self.graph.add((self.sample, CMSO.hasNumberOfAtoms, Literal(actual_natoms-val, datatype=XSD.integer))) #revamp composition #remove existing chem composution + chemical_species = self.graph.value(self.sample, CMSO.hasSpecies) #start by cleanly removing elements for s in self.graph.triples((chemical_species, CMSO.hasElement, None)): @@ -268,18 +269,22 @@ def delete(self, ids=None, indices=None, condition=None, selection=False): #now recalculate and add it again composition = self.schema.material.element_ratio() - - chemical_species = URIRef(f'{self._name}_ChemicalSpecies') - self.graph.add((self.sample, CMSO.hasSpecies, chemical_species)) - self.graph.add((chemical_species, RDF.type, CMSO.ChemicalSpecies)) - + valid = False for e, r in composition.items(): if e in element_indetifiers.keys(): - element = URIRef(element_indetifiers[e]) - self.graph.add((chemical_species, CMSO.hasElement, element)) - self.graph.add((element, RDF.type, CMSO.ChemicalElement)) - self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string))) - self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float))) + valid = True + break + + if valid: + chemical_species = self.graph.create_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies) + self.graph.add((self.sample, CMSO.hasSpecies, chemical_species)) + + for e, r in composition.items(): + if e in element_indetifiers.keys(): + element = self.graph.create_node(element_indetifiers[e], CMSO.ChemicalElement) + self.graph.add((chemical_species, CMSO.hasElement, element)) + self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string))) + self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float))) #we also have to read in file and clean it up filepath = self.graph.value(URIRef(f'{self.sample}_Position'), CMSO.hasPath).toPython() @@ -326,20 +331,23 @@ def substitute_atoms(self, substitution_element, ids=None, indices=None, conditi self.graph.remove((chemical_species, None, None)) self.graph.remove((self.sample, CMSO.hasSpecies, None)) - #now recalculate and add it again composition = self.schema.material.element_ratio() - - chemical_species = URIRef(f'{self._name}_ChemicalSpecies') - self.graph.add((self.sample, CMSO.hasSpecies, chemical_species)) - self.graph.add((chemical_species, RDF.type, CMSO.ChemicalSpecies)) - + valid = False for e, r in composition.items(): if e in element_indetifiers.keys(): - element = URIRef(element_indetifiers[e]) - self.graph.add((chemical_species, CMSO.hasElement, element)) - self.graph.add((element, RDF.type, CMSO.ChemicalElement)) - self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string))) - self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float))) + valid = True + break + + if valid: + chemical_species = self.graph.create_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies) + self.graph.add((self.sample, CMSO.hasSpecies, chemical_species)) + + for e, r in composition.items(): + if e in element_indetifiers.keys(): + element = self.graph.create_node(element_indetifiers[e], CMSO.ChemicalElement) + self.graph.add((chemical_species, CMSO.hasElement, element)) + self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string))) + self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float))) #we also have to read in file and clean it up filepath = self.graph.value(URIRef(f'{self.sample}_Position'), CMSO.hasPath).toPython() @@ -450,20 +458,23 @@ def add_interstitial_impurities(self, element, void_type='tetrahedral', lattice_ self.graph.remove((chemical_species, None, None)) self.graph.remove((self.sample, CMSO.hasSpecies, None)) - #now recalculate and add it again - composition = sysn.schema.material.element_ratio() - - chemical_species = URIRef(f'{self._name}_ChemicalSpecies') - self.graph.add((self.sample, CMSO.hasSpecies, chemical_species)) - self.graph.add((chemical_species, RDF.type, CMSO.ChemicalSpecies)) - + composition = self.schema.material.element_ratio() + valid = False for e, r in composition.items(): if e in element_indetifiers.keys(): - element = URIRef(element_indetifiers[e]) - self.graph.add((chemical_species, CMSO.hasElement, element)) - self.graph.add((element, RDF.type, CMSO.ChemicalElement)) - self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string))) - self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float))) + valid = True + break + + if valid: + chemical_species = self.graph.create_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies) + self.graph.add((self.sample, CMSO.hasSpecies, chemical_species)) + + for e, r in composition.items(): + if e in element_indetifiers.keys(): + element = self.graph.create_node(element_indetifiers[e], CMSO.ChemicalElement) + self.graph.add((chemical_species, CMSO.hasElement, element)) + self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string))) + self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float))) #we also have to read in file and clean it up filepath = self.graph.value(URIRef(f'{self.sample}_Position'), CMSO.hasPath).toPython() @@ -504,13 +515,9 @@ def to_graph(self): self._add_simulation_cell() self._add_simulation_cell_properties() self._add_crystal_structure() - self._add_space_group() - self._add_unit_cell() - self._add_lattice_properties() self._add_atoms() - def _generate_name(self, name_index=None): if self.names: if name_index is None: @@ -520,8 +527,7 @@ def _generate_name(self, name_index=None): self._name = f'sample:{str(uuid.uuid4())}' def _add_sample(self): - sample = URIRef(f'{self._name}') - self.graph.add((sample, RDF.type, CMSO.AtomicScaleSample)) + sample = self.graph.create_node(self._name, CMSO.AtomicScaleSample) self.sample = sample def _add_material(self): @@ -536,9 +542,8 @@ def _add_material(self): Returns ------- """ - material = URIRef(f'{self._name}_Material') + material = self.graph.create_node(f'{self._name}_Material', CMSO.CrystallineMaterial) self.graph.add((self.sample, CMSO.hasMaterial, material)) - self.graph.add((material, RDF.type, CMSO.CrystallineMaterial)) self.material = material def _add_chemical_composition(self): @@ -554,18 +559,22 @@ def _add_chemical_composition(self): ------- """ composition = self.schema.material.element_ratio() - - chemical_species = URIRef(f'{self._name}_ChemicalSpecies') - self.graph.add((self.sample, CMSO.hasSpecies, chemical_species)) - self.graph.add((chemical_species, RDF.type, CMSO.ChemicalSpecies)) - + valid = False for e, r in composition.items(): if e in element_indetifiers.keys(): - element = URIRef(element_indetifiers[e]) - self.graph.add((chemical_species, CMSO.hasElement, element)) - self.graph.add((element, RDF.type, CMSO.ChemicalElement)) - self.graph.add((element, CMSO.hasChemicalSymbol, Literal(e, datatype=XSD.string))) - self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float))) + valid = True + break + + if valid: + chemical_species = self.graph.create_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies) + self.graph.add((self.sample, CMSO.hasSpecies, chemical_species)) + + for e, r in composition.items(): + if e in element_indetifiers.keys(): + element = self.graph.create_node(element_indetifiers[e], CMSO.ChemicalElement) + self.graph.add((chemical_species, CMSO.hasElement, element)) + self.graph.add((element, CMSO.hasChemicalSymbol, Literal(e, datatype=XSD.string))) + self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float))) def _add_simulation_cell(self): """ @@ -580,9 +589,8 @@ def _add_simulation_cell(self): ------- """ - simulation_cell = URIRef(f'{self._name}_SimulationCell') + simulation_cell = self.graph.create_node(f'{self._name}_SimulationCell', CMSO.SimulationCell) self.graph.add((self.sample, CMSO.hasSimulationCell, simulation_cell)) - self.graph.add((simulation_cell, RDF.type, CMSO.SimulationCell)) self.graph.add((simulation_cell, CMSO.hasVolume, Literal(np.round(self.schema.simulation_cell.volume(), decimals=2), datatype=XSD.float))) @@ -605,46 +613,41 @@ def _add_simulation_cell_properties(self): Returns ------- """ - simulation_cell_length = URIRef(f'{self._name}_SimulationCellLength') + simulation_cell_length = self.graph.create_node(f'{self._name}_SimulationCellLength', CMSO.SimulationCellLength) self.graph.add((self.simulation_cell, CMSO.hasLength, simulation_cell_length)) data = self.schema.simulation_cell.length() - self.graph.add((simulation_cell_length, RDF.type, CMSO.SimulationCellLength)) self.graph.add((simulation_cell_length, CMSO.hasLength_x, Literal(data[0], datatype=XSD.float))) self.graph.add((simulation_cell_length, CMSO.hasLength_y, Literal(data[1], datatype=XSD.float))) self.graph.add((simulation_cell_length, CMSO.hasLength_z, Literal(data[2], datatype=XSD.float))) - simulation_cell_vector_01 = URIRef(f'{self._name}_SimulationCellVector_1') + simulation_cell_vector_01 = self.graph.create_node(f'{self._name}_SimulationCellVector_1', CMSO.SimulationCellVector) data = self.schema.simulation_cell.vector() self.graph.add((self.simulation_cell, CMSO.hasVector, simulation_cell_vector_01)) - self.graph.add((simulation_cell_vector_01, RDF.type, CMSO.SimulationCellVector)) self.graph.add((simulation_cell_vector_01, CMSO.hasComponent_x, Literal(data[0][0], datatype=XSD.float))) self.graph.add((simulation_cell_vector_01, CMSO.hasComponent_y, Literal(data[0][1], datatype=XSD.float))) self.graph.add((simulation_cell_vector_01, CMSO.hasComponent_z, Literal(data[0][2], datatype=XSD.float))) - simulation_cell_vector_02 = URIRef(f'{self._name}_SimulationCellVector_2') + simulation_cell_vector_02 = self.graph.create_node(f'{self._name}_SimulationCellVector_2', CMSO.SimulationCellVector) self.graph.add((self.simulation_cell, CMSO.hasVector, simulation_cell_vector_02)) - self.graph.add((simulation_cell_vector_02, RDF.type, CMSO.SimulationCellVector)) self.graph.add((simulation_cell_vector_02, CMSO.hasComponent_x, Literal(data[1][0], datatype=XSD.float))) self.graph.add((simulation_cell_vector_02, CMSO.hasComponent_y, Literal(data[1][1], datatype=XSD.float))) self.graph.add((simulation_cell_vector_02, CMSO.hasComponent_z, Literal(data[1][2], datatype=XSD.float))) - simulation_cell_vector_03 = URIRef(f'{self._name}_SimulationCellVector_3') + simulation_cell_vector_03 = self.graph.create_node(f'{self._name}_SimulationCellVector_3', CMSO.SimulationCellVector) self.graph.add((self.simulation_cell, CMSO.hasVector, simulation_cell_vector_03)) - self.graph.add((simulation_cell_vector_03, RDF.type, CMSO.SimulationCellVector)) self.graph.add((simulation_cell_vector_03, CMSO.hasComponent_x, Literal(data[2][0], datatype=XSD.float))) self.graph.add((simulation_cell_vector_03, CMSO.hasComponent_y, Literal(data[2][1], datatype=XSD.float))) self.graph.add((simulation_cell_vector_03, CMSO.hasComponent_z, Literal(data[2][2], datatype=XSD.float))) - simulation_cell_angle = URIRef(f'{self._name}_SimulationCellAngle') + simulation_cell_angle = self.graph.create_node(f'{self._name}_SimulationCellAngle', CMSO.SimulationCellAngle) data = self.schema.simulation_cell.angle() self.graph.add((self.simulation_cell, CMSO.hasAngle, simulation_cell_angle)) - self.graph.add((simulation_cell_angle, RDF.type, CMSO.SimulationCellAngle)) self.graph.add((simulation_cell_angle, CMSO.hasAngle_alpha, Literal(data[0], datatype=XSD.float))) self.graph.add((simulation_cell_angle, CMSO.hasAngle_beta, Literal(data[1], datatype=XSD.float))) self.graph.add((simulation_cell_angle, CMSO.hasAngle_gamma, Literal(data[2], datatype=XSD.float))) - def _add_crystal_structure(self): + def _add_crystal_structure(self, targets=None): """ Add a CMSO Crystal Structure @@ -656,16 +659,40 @@ def _add_crystal_structure(self): Returns ------- """ + if targets is None: + targets = [self.schema.material.crystal_structure.name(), + self.schema.material.crystal_structure.spacegroup_symbol(), + self.schema.material.crystal_structure.spacegroup_number(), + self.schema.material.crystal_structure.unit_cell.bravais_lattice(), + self.schema.material.crystal_structure.unit_cell.lattice_parameter(), + self.schema.material.crystal_structure.unit_cell.angle() + ] + + valid = self.graph._is_valid(targets) + + if valid: + crystal_structure = self.graph.create_node(f'{self._name}_CrystalStructure', CMSO.CrystalStructure) + self.graph.add((self.material, CMSO.hasStructure, crystal_structure)) + self.graph.add((crystal_structure, CMSO.hasAltName, + Literal(targets[0], + datatype=XSD.string))) + self.crystal_structure = crystal_structure + + if targets[1] is not None: + self._add_space_group(targets[1], targets[2]) + + #now see if unit cell needs to be added + valid = self.graph._is_valid(targets[3:]) + if valid: + self._add_unit_cell() + if targets[3] is not None: + self._add_bravais_lattice(targets[3]) + if targets[4] is not None: + self._add_lattice_properties(targets[4], targets[5]) + - crystal_structure = URIRef(f'{self._name}_CrystalStructure') - self.graph.add((self.material, CMSO.hasStructure, crystal_structure)) - self.graph.add((crystal_structure, RDF.type, CMSO.CrystalStructure)) - self.graph.add((crystal_structure, CMSO.hasAltName, - Literal(self.schema.material.crystal_structure.name(), - datatype=XSD.string))) - self.crystal_structure = crystal_structure - def _add_space_group(self): + def _add_space_group(self, spacegroup_symbol, spacegroup_number): """ Add a CMSO Space Group @@ -680,11 +707,9 @@ def _add_space_group(self): space_group = URIRef(f'{self._name}_SpaceGroup') self.graph.add((self.crystal_structure, CMSO.hasSpaceGroup, space_group)) self.graph.add((space_group, CMSO.hasSpaceGroupSymbol, - Literal(self.schema.material.crystal_structure.spacegroup_symbol(), - datatype=XSD.string))) + Literal(spacegroup_symbol, datatype=XSD.string))) self.graph.add((space_group, CMSO.hasSpaceGroupNumber, - Literal(self.schema.material.crystal_structure.spacegroup_number(), - datatype=XSD.integer))) + Literal(spacegroup_number, datatype=XSD.integer))) def _add_unit_cell(self): @@ -700,18 +725,17 @@ def _add_unit_cell(self): ------- """ - unit_cell = URIRef(f'{self._name}_UnitCell') + unit_cell = self.graph.create_node(f'{self._name}_UnitCell', CMSO.UnitCell) self.graph.add((self.crystal_structure, CMSO.hasUnitCell, unit_cell)) - self.graph.add((unit_cell, RDF.type, CMSO.UnitCell)) self.unit_cell = unit_cell + + def _add_bravais_lattice(self, bv): #add bravais lattice - bv = self.schema.material.crystal_structure.unit_cell.bravais_lattice() - if bv is not None: - bv = URIRef(bv) - self.graph.add((self.unit_cell, Namespace("http://purls.helmholtz-metadaten.de/cmso/").hasBravaisLattice, bv)) + bv = URIRef(bv) + self.graph.add((self.unit_cell, Namespace("http://purls.helmholtz-metadaten.de/cmso/").hasBravaisLattice, bv)) - def _add_lattice_properties(self): + def _add_lattice_properties(self, lattice_parameter_value, lattice_angle_value): """ Add CMSO lattice properties such as Lattice Parameter, and its lengths and angles. @@ -724,21 +748,17 @@ def _add_lattice_properties(self): Returns ------- """ - data = self.schema.material.crystal_structure.unit_cell.lattice_parameter() - lattice_parameter = URIRef(f'{self._name}_LatticeParameter') + lattice_parameter = self.graph.create_node(f'{self._name}_LatticeParameter', CMSO.LatticeParameter) self.graph.add((self.unit_cell, CMSO.hasLatticeParameter, lattice_parameter)) - self.graph.add((lattice_parameter, RDF.type, CMSO.LatticeParameter)) - self.graph.add((lattice_parameter, CMSO.hasLength_x, Literal(data[0], datatype=XSD.float))) - self.graph.add((lattice_parameter, CMSO.hasLength_y, Literal(data[1], datatype=XSD.float))) - self.graph.add((lattice_parameter, CMSO.hasLength_z, Literal(data[2], datatype=XSD.float))) + self.graph.add((lattice_parameter, CMSO.hasLength_x, Literal(lattice_parameter_value[0], datatype=XSD.float))) + self.graph.add((lattice_parameter, CMSO.hasLength_y, Literal(lattice_parameter_value[1], datatype=XSD.float))) + self.graph.add((lattice_parameter, CMSO.hasLength_z, Literal(lattice_parameter_value[2], datatype=XSD.float))) - lattice_angle = URIRef(f'{self._name}_LatticeAngle') - data = self.schema.material.crystal_structure.unit_cell.angle() + lattice_angle = self.graph.create_node(f'{self._name}_LatticeAngle', CMSO.LatticeAngle) self.graph.add((self.unit_cell, CMSO.hasAngle, lattice_angle)) - self.graph.add((lattice_angle, RDF.type, CMSO.LatticeAngle)) - self.graph.add((lattice_angle, CMSO.hasAngle_alpha, Literal(data[0], datatype=XSD.float))) - self.graph.add((lattice_angle, CMSO.hasAngle_beta, Literal(data[1], datatype=XSD.float))) - self.graph.add((lattice_angle, CMSO.hasAngle_gamma, Literal(data[2], datatype=XSD.float))) + self.graph.add((lattice_angle, CMSO.hasAngle_alpha, Literal(lattice_angle_value[0], datatype=XSD.float))) + self.graph.add((lattice_angle, CMSO.hasAngle_beta, Literal(lattice_angle_value[1], datatype=XSD.float))) + self.graph.add((lattice_angle, CMSO.hasAngle_gamma, Literal(lattice_angle_value[2], datatype=XSD.float))) def _save_atom_attributes(self, position_identifier, species_identifier): @@ -784,17 +804,15 @@ def _add_atoms(self): outfile = self._save_atom_attributes(position_identifier, species_identifier) if "positions" in self.atoms.keys(): - position = URIRef(f'{self._name}_Position') + position = self.graph.create_node(f'{self._name}_Position', CMSO.AtomAttribute) self.graph.add((self.sample, Namespace("http://purls.helmholtz-metadaten.de/cmso/").hasAttribute, position)) - self.graph.add((position, RDF.type, CMSO.AtomAttribute)) self.graph.add((position, CMSO.hasName, Literal('Position', datatype=XSD.string))) self.graph.add((position, CMSO.hasIdentifier, Literal(position_identifier, datatype=XSD.string))) self.graph.add((position, CMSO.hasPath, Literal(outfile, datatype=XSD.string))) if "species" in self.atoms.keys(): - species = URIRef(f'{self._name}_Species') + species = self.graph.create_node(f'{self._name}_Species', CMSO.AtomAttribute) self.graph.add((self.sample, Namespace("http://purls.helmholtz-metadaten.de/cmso/").hasAttribute, species)) - self.graph.add((species, RDF.type, CMSO.AtomAttribute)) self.graph.add((species, CMSO.hasName, Literal('Species', datatype=XSD.string))) self.graph.add((species, CMSO.hasIdentifier, Literal(species_identifier, datatype=XSD.string))) self.graph.add((species, CMSO.hasPath, Literal(outfile, datatype=XSD.string))) @@ -840,9 +858,8 @@ def add_vacancy(self, concentration, number=None): if self.graph is None: return - vacancy = URIRef(f'{self._name}_Vacancy') + vacancy = self.graph.create_node(f'{self._name}_Vacancy', PODO.Vacancy) self.graph.add((self.material, CMSO.hasDefect, vacancy)) - self.graph.add((vacancy, RDF.type, PODO.Vacancy)) self.graph.add((self.simulation_cell, PODO.hasVacancyConcentration, Literal(concentration, datatype=XSD.float))) if number is not None: self.graph.add((self.simulation_cell, PODO.hasNumberOfVacancies, Literal(number, datatype=XSD.integer))) @@ -868,24 +885,19 @@ def add_gb(self, gb_dict): return if gb_dict["GBType"] is None: - plane_defect = URIRef(f'{self._name}_GrainBoundary') - self.graph.add((plane_defect, RDF.type, PLDO.GrainBoundary)) + plane_defect = self.graph.create_node(f'{self._name}_GrainBoundary') elif gb_dict["GBType"] == "Twist": - plane_defect = URIRef(f'{self._name}_TwistGrainBoundary') - self.graph.add((plane_defect, RDF.type, PLDO.TwistGrainBoundary)) + plane_defect = self.graph.create_node(f'{self._name}_TwistGrainBoundary', PLDO.TwistGrainBoundary) elif gb_dict["GBType"] == "Tilt": - plane_defect = URIRef(f'{self._name}_TiltGrainBoundary') - self.graph.add((plane_defect, RDF.type, PLDO.TiltGrainBoundary)) + plane_defect = self.graph.create_node(f'{self._name}_TiltGrainBoundary', PLDO.TiltGrainBoundary) elif gb_dict["GBType"] == "Symmetric Tilt": - plane_defect = URIRef(f'{self._name}_SymmetricalTiltGrainBoundary') - self.graph.add((plane_defect, RDF.type, PLDO.SymmetricalTiltGrainBoundary)) + plane_defect = self.graph.create_node(f'{self._name}_SymmetricalTiltGrainBoundary', PLDO.SymmetricalTiltGrainBoundary) elif gb_dict["GBType"] == "Mixed": - plane_defect = URIRef(f'{self._name}_MixedGrainBoundary') - self.graph.add((plane_defect, RDF.type, PLDO.MixedGrainBoundary)) + plane_defect = self.graph.create_node(f'{self._name}_MixedGrainBoundary', PLDO.MixedGrainBoundary) self.graph.add((self.material, CMSO.hasDefect, plane_defect)) self.graph.add((plane_defect, PLDO.hasSigmaValue, Literal(gb_dict["sigma"], datatype=XSD.integer))) diff --git a/atomrdf/workflow/workflow.py b/atomrdf/workflow/workflow.py index 2c37d6e..ff0b3cc 100644 --- a/atomrdf/workflow/workflow.py +++ b/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 @@ -102,43 +136,6 @@ 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, ): @@ -146,8 +143,8 @@ def add_structural_relation(self, ): 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)) - 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\n", " 0\n", " bcc\n", - " sample:82616568-43bf-4dd4-a924-7bd374c1ea24\n", + " sample:836942a9-9109-43e9-bcae-aadbc311e866\n", "
\n", " \n", "\n", @@ -3149,7 +3149,7 @@ ], "text/plain": [ " hasAltNamevalue AtomicScaleSample\n", - "0 bcc sample:82616568-43bf-4dd4-a924-7bd374c1ea24" + "0 bcc sample:836942a9-9109-43e9-bcae-aadbc311e866" ] }, "execution_count": 14, diff --git a/examples/06_workflow_pyiron.ipynb b/examples/06_workflow_pyiron.ipynb new file mode 100644 index 0000000..4c9e529 --- /dev/null +++ b/examples/06_workflow_pyiron.ipynb @@ -0,0 +1,770 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "05f9d6ba-0d79-4f5b-b1ac-b185491ee9e3", + "metadata": {}, + "source": [ + "# Annotating workflows" + ] + }, + { + "cell_type": "markdown", + "id": "9a4831f2-6ce8-431b-8a21-67e8d442fb50", + "metadata": {}, + "source": [ + "Annotating workflows with pyiron as example. Note that `pyiron_atomistics` needs to be installed for this notebook." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "7af3b5ba-493c-4689-aee5-99c9de36601d", + "metadata": {}, + "outputs": [], + "source": [ + "%config IPCompleter.evaluation='unsafe'" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "136f88af-af89-44d6-a9f6-7ad1d458e625", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/menon/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\\x00\\xd0\\xcc\\xcc\\xcc\\xcc\\xcc\\xcc\\xfb\\xbf\\x00\\x00\\x00\\x00\\x00\\x00' for does not match any known type: falling back to type probe function.\n", + "This warnings indicates broken support for the dtype!\n", + " machar = _get_machar(dtype)\n", + "2024-04-16 18:35:17,228 - pyiron_log - WARNING - pyiron found a 'templates' folder in the /home/menon/pyiron/resources resource directory. These are no longer supported in pyiron_base >=0.7.0. They are replaced by Project.create_job_class() and Project.wrap_python_function().\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "569131161c9642049116b50ce92ca869", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "from pyiron_atomistics import Project\n", + "from atomrdf import KnowledgeGraph, System, Workflow\n", + "import numpy as np" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "c274b896-e491-401b-a1a4-5610544537f3", + "metadata": {}, + "outputs": [], + "source": [ + "pr = Project('wf9')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "66c3020b-9515-4f41-872a-4ca799a16fcb", + "metadata": {}, + "outputs": [], + "source": [ + "kg = KnowledgeGraph(store=pr)" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "68afbc43-b458-4cce-9055-2c6710f839bb", + "metadata": {}, + "outputs": [], + "source": [ + "wf = Workflow(kg, environment='pyiron')" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "db033de3-b2e6-4c56-800e-b2fa0383a88c", + "metadata": {}, + "outputs": [], + "source": [ + "structure = pr.create.structure.annotated_structure.bulk('Cu', cubic=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "f647313a-6522-473f-a8ea-b5ec89057516", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "sample_0394fcda-2d6a-470a-a72a-1b98ac5ce1a3\n", + "\n", + "sample_0394fcda-2d6a-470a-a72a-1b98ac5ce1a3\n", + "\n", + "\n", + "\n", + "Entity\n", + "\n", + "Entity\n", + "\n", + "\n", + "\n", + "sample_0394fcda-2d6a-470a-a72a-1b98ac5ce1a3->Entity\n", + "\n", + "\n", + "type\n", + "\n", + "\n", + "\n", + "sample_cc0c55d8-fa4c-43ff-8a18-2e1d9e077ca7\n", + "\n", + "sample_cc0c55d8-fa4c-43ff-8a18-2e1d9e077ca7\n", + "\n", + "\n", + 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"display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.8" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/setup.py b/setup.py index 9c7bb12..612ef77 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ setup( name='atomrdf', - version='0.5.1', + version='0.5.2', author='Abril Azocar Guzman, Sarath Menon', author_email='sarath.menon@pyscal.org', description='Ontology based structural manipulation and quering',