From 51bdc3448e02502c235f59ed347c7987a6445d4c Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 14:27:55 +0200 Subject: [PATCH 01/14] add a create_node function --- atomrdf/graph.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/atomrdf/graph.py b/atomrdf/graph.py index cf025ea..e2b70b4 100644 --- a/atomrdf/graph.py +++ b/atomrdf/graph.py @@ -317,6 +317,11 @@ def remove(self, triple): return self.graph.remove(modified_triple) + def create_node(self, namestring, classtype): + item = URIRef(f'{self._name}_{namestring}') + self.add((item, RDF.type, classtype)) + return item + def _initialize_graph(self): """ Create the RDF Graph from the data stored @@ -349,9 +354,8 @@ 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: From 4f397627f04a6808d594dd6329c65066c18b331c Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 15:25:15 +0200 Subject: [PATCH 02/14] change triples --- atomrdf/graph.py | 11 +++++++++-- atomrdf/structure.py | 30 ++++++++++++++++-------------- 2 files changed, 25 insertions(+), 16 deletions(-) diff --git a/atomrdf/graph.py b/atomrdf/graph.py index e2b70b4..edf8b90 100644 --- a/atomrdf/graph.py +++ b/atomrdf/graph.py @@ -317,8 +317,15 @@ def remove(self, triple): return self.graph.remove(modified_triple) - def create_node(self, namestring, classtype): - item = URIRef(f'{self._name}_{namestring}') + def create_node(self, namestring, classtype, add_prefix=True): + + if add_prefix: + if namestring != "": + namestring = '_' + namestring + item = URIRef(f'{self._name}{namestring}') + else: + item = URIRef(namestring) + self.add((item, RDF.type, classtype)) return item diff --git a/atomrdf/structure.py b/atomrdf/structure.py index 0cef9e9..c7c3a9f 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -520,8 +520,7 @@ 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("", CMSO.AtomicScaleSample) self.sample = sample def _add_material(self): @@ -536,9 +535,8 @@ def _add_material(self): Returns ------- """ - material = URIRef(f'{self._name}_Material') + material = self.graph.create_node(f'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 +552,22 @@ 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'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, add_prefix=False) + 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): """ From a5fd8b02dab0e9627464df4c62e03679db4b06b0 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 15:29:20 +0200 Subject: [PATCH 03/14] change properties --- atomrdf/structure.py | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/atomrdf/structure.py b/atomrdf/structure.py index c7c3a9f..2420c11 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -582,9 +582,8 @@ def _add_simulation_cell(self): ------- """ - simulation_cell = URIRef(f'{self._name}_SimulationCell') + simulation_cell = self.graph.create_node(f'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))) @@ -607,40 +606,35 @@ def _add_simulation_cell_properties(self): Returns ------- """ - simulation_cell_length = URIRef(f'{self._name}_SimulationCellLength') + simulation_cell_length = self.graph.create_node(f'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'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'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'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'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))) From f3494cefb6ac9e5d611d348415b2b3f2ad98de35 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 15:37:17 +0200 Subject: [PATCH 04/14] fix names --- atomrdf/graph.py | 11 +- atomrdf/structure.py | 18 +- examples/01_getting_started.ipynb | 2955 +---------------------------- 3 files changed, 51 insertions(+), 2933 deletions(-) diff --git a/atomrdf/graph.py b/atomrdf/graph.py index edf8b90..4950fa4 100644 --- a/atomrdf/graph.py +++ b/atomrdf/graph.py @@ -317,15 +317,8 @@ def remove(self, triple): return self.graph.remove(modified_triple) - def create_node(self, namestring, classtype, add_prefix=True): - - if add_prefix: - if namestring != "": - namestring = '_' + namestring - item = URIRef(f'{self._name}{namestring}') - else: - item = URIRef(namestring) - + def create_node(self, namestring, classtype): + item = URIRef(namestring) self.add((item, RDF.type, classtype)) return item diff --git a/atomrdf/structure.py b/atomrdf/structure.py index 2420c11..28af4b4 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -520,7 +520,7 @@ def _generate_name(self, name_index=None): self._name = f'sample:{str(uuid.uuid4())}' def _add_sample(self): - sample = self.graph.create_node("", CMSO.AtomicScaleSample) + sample = self.graph.create_node(self._name, CMSO.AtomicScaleSample) self.sample = sample def _add_material(self): @@ -535,7 +535,7 @@ def _add_material(self): Returns ------- """ - material = self.graph.create_node(f'Material', CMSO.CrystallineMaterial) + material = self.graph.create_node(f'{self._name}_Material', CMSO.CrystallineMaterial) self.graph.add((self.sample, CMSO.hasMaterial, material)) self.material = material @@ -559,7 +559,7 @@ def _add_chemical_composition(self): break if valid: - chemical_species = self.graph.create_node(f'ChemicalSpecies', CMSO.ChemicalSpecies) + 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(): @@ -582,7 +582,7 @@ def _add_simulation_cell(self): ------- """ - simulation_cell = self.graph.create_node(f'SimulationCell', CMSO.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, CMSO.hasVolume, Literal(np.round(self.schema.simulation_cell.volume(), decimals=2), @@ -606,33 +606,33 @@ def _add_simulation_cell_properties(self): Returns ------- """ - simulation_cell_length = self.graph.create_node(f'SimulationCellLength', CMSO.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, 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 = self.graph.create_node(f'SimulationCellVector_1', CMSO.SimulationCellVector) + 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, 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 = self.graph.create_node(f'SimulationCellVector_2', CMSO.SimulationCellVector) + 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, 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 = self.graph.create_node(f'SimulationCellVector_3', CMSO.SimulationCellVector) + 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, 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 = self.graph.create_node(f'SimulationCellAngle', CMSO.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, CMSO.hasAngle_alpha, Literal(data[0], datatype=XSD.float))) diff --git a/examples/01_getting_started.ipynb b/examples/01_getting_started.ipynb index 3079350..19394de 100644 --- a/examples/01_getting_started.ipynb +++ b/examples/01_getting_started.ipynb @@ -85,7 +85,23 @@ "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'KnowledgeGraph' object has no attribute '_name'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m struct_Fe \u001b[38;5;241m=\u001b[39m \u001b[43mSystem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mFe\u001b[49m\u001b[43m(\u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mkg\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:59\u001b[0m, in \u001b[0;36m_make_crystal\u001b[0;34m(structure, lattice_constant, repetitions, ca_ratio, noise, element, primitive, graph, names)\u001b[0m\n\u001b[1;32m 57\u001b[0m s\u001b[38;5;241m.\u001b[39matoms\u001b[38;5;241m.\u001b[39m_lattice_constant \u001b[38;5;241m=\u001b[39m lattice_constant\n\u001b[1;32m 58\u001b[0m s\u001b[38;5;241m.\u001b[39m_structure_dict \u001b[38;5;241m=\u001b[39m sdict\n\u001b[0;32m---> 59\u001b[0m \u001b[43ms\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_graph\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 60\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m s\n", + "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:501\u001b[0m, in \u001b[0;36mSystem.to_graph\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 498\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[1;32m 500\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_generate_name()\n\u001b[0;32m--> 501\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_add_sample\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 502\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_material()\n\u001b[1;32m 503\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_chemical_composition()\n", + "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:523\u001b[0m, in \u001b[0;36mSystem._add_sample\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_add_sample\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m--> 523\u001b[0m sample \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_node\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mCMSO\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mAtomicScaleSample\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 524\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample \u001b[38;5;241m=\u001b[39m sample\n", + "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/graph.py:325\u001b[0m, in \u001b[0;36mKnowledgeGraph.create_node\u001b[0;34m(self, namestring, classtype, add_prefix)\u001b[0m\n\u001b[1;32m 323\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m namestring \u001b[38;5;241m!=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m 324\u001b[0m namestring \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m_\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;241m+\u001b[39m namestring\n\u001b[0;32m--> 325\u001b[0m item \u001b[38;5;241m=\u001b[39m URIRef(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_name\u001b[49m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mnamestring\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 326\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 327\u001b[0m item \u001b[38;5;241m=\u001b[39m URIRef(namestring)\n", + "\u001b[0;31mAttributeError\u001b[0m: 'KnowledgeGraph' object has no attribute '_name'" + ] + } + ], "source": [ "struct_Fe = System.create.element.Fe(graph=kg)" ] @@ -100,706 +116,12 @@ }, { "cell_type": "code", - 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"\n", - "\n", - "cmso.hasElementRatio\n", - "\n", - "\n", - "\n", - "f2192f1b-6ec6-431b-93df-1737923af3d7\n", - "\n", - "Fe\n", - "\n", - "\n", - "\n", - "CHEBI.18248->f2192f1b-6ec6-431b-93df-1737923af3d7\n", - "\n", - "\n", - "cmso.hasChemicalSymbol\n", - "\n", - "\n", - "\n", - "sample_8dcdbda0-18be-4a2e-9ab0-9b899658a62b_Material->sample_8dcdbda0-18be-4a2e-9ab0-9b899658a62b_CrystalStructure\n", - "\n", - "\n", - "cmso.hasStructure\n", - "\n", - "\n", - "\n", - "sample_d56db4d7-c2b9-4d74-a691-594677aaf349_ChemicalSpecies->CHEBI.27573\n", - "\n", - "\n", - "cmso.hasElement\n", - "\n", - "\n", - "\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "kg.visualise(hide_types=True, size=(60,30))" ] @@ -2930,7 +187,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "id": "9a978f15-5101-4a76-b02e-5e2a36da36b3", "metadata": {}, "outputs": [], @@ -2940,7 +197,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "id": "4892d80f-1a68-486d-b127-4dd848a5e492", "metadata": {}, "outputs": [], @@ -2950,21 +207,10 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "id": "fdf78f08-2ca8-4fa1-b369-3792327f2bce", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "3" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "kg.n_samples" ] @@ -2995,7 +241,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "id": "8ffe7592-4349-4c46-bf40-7edea50c652c", "metadata": { "tags": [] @@ -3017,7 +263,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "id": "4a8eba1e-3ffb-4129-8818-5caf8ce0de4b", "metadata": { "tags": [] @@ -3037,55 +283,12 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "id": "f4b6f799-ff85-45c7-a318-f2598a32a48c", "metadata": { "tags": [] }, - "outputs": [ - { - "data": { - "text/html": [ - "
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symbol
0Pm-3m
\n", - "
" - ], - "text/plain": [ - " symbol\n", - "0 Pm-3m" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "res" ] @@ -3108,55 +311,10 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "id": "08f1d892-64a8-40ce-af52-657ef4f59baf", "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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hasAltNamevalueAtomicScaleSample
0bccsample:82616568-43bf-4dd4-a924-7bd374c1ea24
\n", - "
" - ], - "text/plain": [ - " hasAltNamevalue AtomicScaleSample\n", - "0 bcc sample:82616568-43bf-4dd4-a924-7bd374c1ea24" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "res = kg.query_sample(kg.ontology.terms.cmso.hasAltName, \n", " condition=(kg.ontology.terms.cmso.hasAltName=='bcc'))\n", @@ -3173,7 +331,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "id": "efde861c-b9dd-4b97-861b-a330bbd95de0", "metadata": {}, "outputs": [], @@ -3191,7 +349,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "id": "0cb6b043-abb3-41ca-bee7-fb3bf1e7e615", "metadata": { "tags": [] @@ -3203,34 +361,12 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "id": "ae884716-a31b-4170-b4d4-9cf8309a6d74", "metadata": { "tags": [] }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "bcc.data (written by ASE) \n", - "\n", - "2 \t atoms \n", - "1 atom types\n", - "0.0 2.8700000000000001 xlo xhi\n", - "0.0 2.8700000000000001 ylo yhi\n", - "0.0 2.8700000000000001 zlo zhi\n", - "\n", - "\n", - "Atoms \n", - "\n", - " 1 1 0 0 \n", - " 0\n", - " 2 1 1.4350000000000001 1.4350000000000001 1.43500000000000\n", - "01\n" - ] - } - ], + "outputs": [], "source": [ "! more bcc.data" ] @@ -3245,7 +381,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "id": "7ba5d551-f85b-4c33-be37-b997feffd7d7", "metadata": { "tags": [] @@ -3257,23 +393,12 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "id": "f4a90cbe-cf6a-4285-a0d2-b7525726c6dc", "metadata": { "tags": [] }, - "outputs": [ - { - "data": { - "text/plain": [ - "Atoms(symbols='Fe2', pbc=True, cell=[2.87, 2.87, 2.87])" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "aseobj" ] From f424c883956b273235049feea5229f176c5cb9e3 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 15:37:49 +0200 Subject: [PATCH 05/14] fix names --- atomrdf/structure.py | 2 +- examples/01_getting_started.ipynb | 13 ++++++------- 2 files changed, 7 insertions(+), 8 deletions(-) diff --git a/atomrdf/structure.py b/atomrdf/structure.py index 28af4b4..1e953a9 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -564,7 +564,7 @@ def _add_chemical_composition(self): for e, r in composition.items(): if e in element_indetifiers.keys(): - element = self.graph.create_node(element_indetifiers[e], CMSO.ChemicalElement, add_prefix=False) + 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))) diff --git a/examples/01_getting_started.ipynb b/examples/01_getting_started.ipynb index 19394de..819448e 100644 --- a/examples/01_getting_started.ipynb +++ b/examples/01_getting_started.ipynb @@ -87,18 +87,17 @@ }, "outputs": [ { - "ename": "AttributeError", - "evalue": "'KnowledgeGraph' object has no attribute '_name'", + "ename": "TypeError", + "evalue": "KnowledgeGraph.create_node() got an unexpected keyword argument 'add_prefix'", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", "Cell \u001b[0;32mIn[3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m struct_Fe \u001b[38;5;241m=\u001b[39m \u001b[43mSystem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mFe\u001b[49m\u001b[43m(\u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mkg\u001b[49m\u001b[43m)\u001b[49m\n", "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:59\u001b[0m, in \u001b[0;36m_make_crystal\u001b[0;34m(structure, lattice_constant, repetitions, ca_ratio, noise, element, primitive, graph, names)\u001b[0m\n\u001b[1;32m 57\u001b[0m s\u001b[38;5;241m.\u001b[39matoms\u001b[38;5;241m.\u001b[39m_lattice_constant \u001b[38;5;241m=\u001b[39m lattice_constant\n\u001b[1;32m 58\u001b[0m s\u001b[38;5;241m.\u001b[39m_structure_dict \u001b[38;5;241m=\u001b[39m sdict\n\u001b[0;32m---> 59\u001b[0m \u001b[43ms\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_graph\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 60\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m s\n", - "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:501\u001b[0m, in \u001b[0;36mSystem.to_graph\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 498\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[1;32m 500\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_generate_name()\n\u001b[0;32m--> 501\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_add_sample\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 502\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_material()\n\u001b[1;32m 503\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_chemical_composition()\n", - "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:523\u001b[0m, in \u001b[0;36mSystem._add_sample\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_add_sample\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m--> 523\u001b[0m sample \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_node\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mCMSO\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mAtomicScaleSample\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 524\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample \u001b[38;5;241m=\u001b[39m sample\n", - "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/graph.py:325\u001b[0m, in \u001b[0;36mKnowledgeGraph.create_node\u001b[0;34m(self, namestring, classtype, add_prefix)\u001b[0m\n\u001b[1;32m 323\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m namestring \u001b[38;5;241m!=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m 324\u001b[0m namestring \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m_\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;241m+\u001b[39m namestring\n\u001b[0;32m--> 325\u001b[0m item \u001b[38;5;241m=\u001b[39m URIRef(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_name\u001b[49m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mnamestring\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 326\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 327\u001b[0m item \u001b[38;5;241m=\u001b[39m URIRef(namestring)\n", - "\u001b[0;31mAttributeError\u001b[0m: 'KnowledgeGraph' object has no attribute '_name'" + "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:503\u001b[0m, in \u001b[0;36mSystem.to_graph\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 501\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_sample()\n\u001b[1;32m 502\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_material()\n\u001b[0;32m--> 503\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_add_chemical_composition\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 504\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_simulation_cell()\n\u001b[1;32m 505\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_simulation_cell_properties()\n", + "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:567\u001b[0m, in \u001b[0;36mSystem._add_chemical_composition\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 565\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m e, r \u001b[38;5;129;01min\u001b[39;00m composition\u001b[38;5;241m.\u001b[39mitems():\n\u001b[1;32m 566\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m e \u001b[38;5;129;01min\u001b[39;00m element_indetifiers\u001b[38;5;241m.\u001b[39mkeys():\n\u001b[0;32m--> 567\u001b[0m element \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_node\u001b[49m\u001b[43m(\u001b[49m\u001b[43melement_indetifiers\u001b[49m\u001b[43m[\u001b[49m\u001b[43me\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mCMSO\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mChemicalElement\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43madd_prefix\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 568\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgraph\u001b[38;5;241m.\u001b[39madd((chemical_species, CMSO\u001b[38;5;241m.\u001b[39mhasElement, element))\n\u001b[1;32m 569\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgraph\u001b[38;5;241m.\u001b[39madd((element, CMSO\u001b[38;5;241m.\u001b[39mhasChemicalSymbol, Literal(e, datatype\u001b[38;5;241m=\u001b[39mXSD\u001b[38;5;241m.\u001b[39mstring)))\n", + "\u001b[0;31mTypeError\u001b[0m: KnowledgeGraph.create_node() got an unexpected keyword argument 'add_prefix'" ] } ], From 1beaa39e30f7d6b566030f94223b5a742f053d2f Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 16:28:00 +0200 Subject: [PATCH 06/14] add more triples --- atomrdf/graph.py | 8 + atomrdf/structure.py | 89 +- examples/01_getting_started.ipynb | 2956 ++++++++++++++++++++++++++++- 3 files changed, 2974 insertions(+), 79 deletions(-) diff --git a/atomrdf/graph.py b/atomrdf/graph.py index 4950fa4..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' diff --git a/atomrdf/structure.py b/atomrdf/structure.py index 1e953a9..a03bffd 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -504,13 +504,9 @@ 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: @@ -653,15 +649,39 @@ def _add_crystal_structure(self): ------- """ - 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 + 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.add_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]) + + - def _add_space_group(self): + def _add_space_group(self, spacegroup_symbol, spacegroup_number): """ Add a CMSO Space Group @@ -676,11 +696,9 @@ 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): @@ -696,18 +714,17 @@ def _add_unit_cell(self): ------- """ - unit_cell = URIRef(f'{self._name}_UnitCell') + unit_cell = self.graph.add_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. @@ -720,21 +737,17 @@ 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.add_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.add_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): @@ -780,17 +793,15 @@ 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.add_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.add_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))) diff --git a/examples/01_getting_started.ipynb b/examples/01_getting_started.ipynb index 819448e..4ce2f0f 100644 --- a/examples/01_getting_started.ipynb +++ b/examples/01_getting_started.ipynb @@ -51,7 +51,7 @@ "metadata": {}, "outputs": [], "source": [ - "kg = KnowledgeGraph()" + "kg = KnowledgeGraph(enable_log=True)" ] }, { @@ -85,22 +85,7 @@ "metadata": { "tags": [] }, - "outputs": [ - { - "ename": "TypeError", - "evalue": "KnowledgeGraph.create_node() got an unexpected keyword argument 'add_prefix'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m struct_Fe \u001b[38;5;241m=\u001b[39m \u001b[43mSystem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mFe\u001b[49m\u001b[43m(\u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mkg\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:59\u001b[0m, in \u001b[0;36m_make_crystal\u001b[0;34m(structure, lattice_constant, repetitions, ca_ratio, noise, element, primitive, graph, names)\u001b[0m\n\u001b[1;32m 57\u001b[0m s\u001b[38;5;241m.\u001b[39matoms\u001b[38;5;241m.\u001b[39m_lattice_constant \u001b[38;5;241m=\u001b[39m lattice_constant\n\u001b[1;32m 58\u001b[0m s\u001b[38;5;241m.\u001b[39m_structure_dict \u001b[38;5;241m=\u001b[39m sdict\n\u001b[0;32m---> 59\u001b[0m \u001b[43ms\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_graph\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 60\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m s\n", - "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:503\u001b[0m, in \u001b[0;36mSystem.to_graph\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 501\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_sample()\n\u001b[1;32m 502\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_material()\n\u001b[0;32m--> 503\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_add_chemical_composition\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 504\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_simulation_cell()\n\u001b[1;32m 505\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_simulation_cell_properties()\n", - "File \u001b[0;32m~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py:567\u001b[0m, in \u001b[0;36mSystem._add_chemical_composition\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 565\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m e, r \u001b[38;5;129;01min\u001b[39;00m composition\u001b[38;5;241m.\u001b[39mitems():\n\u001b[1;32m 566\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m e \u001b[38;5;129;01min\u001b[39;00m element_indetifiers\u001b[38;5;241m.\u001b[39mkeys():\n\u001b[0;32m--> 567\u001b[0m element \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_node\u001b[49m\u001b[43m(\u001b[49m\u001b[43melement_indetifiers\u001b[49m\u001b[43m[\u001b[49m\u001b[43me\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mCMSO\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mChemicalElement\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43madd_prefix\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 568\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgraph\u001b[38;5;241m.\u001b[39madd((chemical_species, CMSO\u001b[38;5;241m.\u001b[39mhasElement, element))\n\u001b[1;32m 569\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgraph\u001b[38;5;241m.\u001b[39madd((element, CMSO\u001b[38;5;241m.\u001b[39mhasChemicalSymbol, Literal(e, datatype\u001b[38;5;241m=\u001b[39mXSD\u001b[38;5;241m.\u001b[39mstring)))\n", - "\u001b[0;31mTypeError\u001b[0m: KnowledgeGraph.create_node() got an unexpected keyword argument 'add_prefix'" - ] - } - ], + "outputs": [], "source": [ "struct_Fe = System.create.element.Fe(graph=kg)" ] @@ -115,12 +100,706 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "id": "79772707-5981-4ae5-8131-a7ef8455858c", "metadata": { "tags": [] }, - "outputs": [], + 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"execution_count": 9, "id": "4892d80f-1a68-486d-b127-4dd848a5e492", "metadata": {}, "outputs": [], @@ -206,10 +2950,21 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "id": "fdf78f08-2ca8-4fa1-b369-3792327f2bce", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "3" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kg.n_samples" ] @@ -240,7 +2995,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "id": "8ffe7592-4349-4c46-bf40-7edea50c652c", "metadata": { "tags": [] @@ -262,7 +3017,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "id": "4a8eba1e-3ffb-4129-8818-5caf8ce0de4b", "metadata": { "tags": [] @@ -282,12 +3037,55 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 13, "id": "f4b6f799-ff85-45c7-a318-f2598a32a48c", "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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symbol
0Pm-3m
\n", + "
" + ], + "text/plain": [ + " symbol\n", + "0 Pm-3m" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "res" ] @@ -310,10 +3108,55 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 14, "id": "08f1d892-64a8-40ce-af52-657ef4f59baf", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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hasAltNamevalueAtomicScaleSample
0bccsample:dd8dab55-8100-4fef-bd16-166637058ca1
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" + ], + "text/plain": [ + " hasAltNamevalue AtomicScaleSample\n", + "0 bcc sample:dd8dab55-8100-4fef-bd16-166637058ca1" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "res = kg.query_sample(kg.ontology.terms.cmso.hasAltName, \n", " condition=(kg.ontology.terms.cmso.hasAltName=='bcc'))\n", @@ -330,7 +3173,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 15, "id": "efde861c-b9dd-4b97-861b-a330bbd95de0", "metadata": {}, "outputs": [], @@ -348,7 +3191,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 16, "id": "0cb6b043-abb3-41ca-bee7-fb3bf1e7e615", "metadata": { "tags": [] @@ -360,12 +3203,34 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "id": "ae884716-a31b-4170-b4d4-9cf8309a6d74", "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "bcc.data (written by ASE) \n", + "\n", + "2 \t atoms \n", + "1 atom types\n", + "0.0 2.8700000000000001 xlo xhi\n", + "0.0 2.8700000000000001 ylo yhi\n", + "0.0 2.8700000000000001 zlo zhi\n", + "\n", + "\n", + "Atoms \n", + "\n", + " 1 1 0 0 \n", + " 0\n", + " 2 1 1.4350000000000001 1.4350000000000001 1.43500000000000\n", + "01\n" + ] + } + ], "source": [ "! more bcc.data" ] @@ -380,7 +3245,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "id": "7ba5d551-f85b-4c33-be37-b997feffd7d7", "metadata": { "tags": [] @@ -392,12 +3257,23 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 19, "id": "f4a90cbe-cf6a-4285-a0d2-b7525726c6dc", "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "Atoms(symbols='Fe2', pbc=True, cell=[2.87, 2.87, 2.87])" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "aseobj" ] From c80b4b3f526340276dd85acae68ec27406ecbe31 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 16:34:35 +0200 Subject: [PATCH 07/14] add defect triples --- atomrdf/structure.py | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/atomrdf/structure.py b/atomrdf/structure.py index a03bffd..01637f8 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -847,9 +847,8 @@ def add_vacancy(self, concentration, number=None): if self.graph is None: return - vacancy = URIRef(f'{self._name}_Vacancy') + vacancy = self.graph.add_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))) @@ -875,24 +874,19 @@ 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.add_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.add_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.add_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.add_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.add_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))) From 6034195fd45af74c54027007abd41c43bd77bb69 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 16:40:32 +0200 Subject: [PATCH 08/14] fix system modification triples --- atomrdf/structure.py | 77 +++++++++++++++++++++++++------------------- 1 file changed, 44 insertions(+), 33 deletions(-) diff --git a/atomrdf/structure.py b/atomrdf/structure.py index 01637f8..02e40c8 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.add_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.add_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.add_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.add_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.add_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.add_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() From 2b53e038dc6c088290b78041e61f9106452db28f Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 18:30:56 +0200 Subject: [PATCH 09/14] add workflow triples --- atomrdf/structure.py | 18 ++++----- atomrdf/workflow/workflow.py | 73 +++++++++++++++++------------------- 2 files changed, 44 insertions(+), 47 deletions(-) diff --git a/atomrdf/structure.py b/atomrdf/structure.py index 02e40c8..1ade7a5 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -647,7 +647,7 @@ def _add_simulation_cell_properties(self): 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 @@ -659,14 +659,14 @@ def _add_crystal_structure(self): Returns ------- """ - - 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() - ] + 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) diff --git a/atomrdf/workflow/workflow.py b/atomrdf/workflow/workflow.py index 2c37d6e..be74a93 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, spacegroup_symbol, spacegroup_number, blattice, + [lattice_parameter_x, lattice_parameter_y, lattice_parameter_z], + [lattice_angle_x, lattice_angle_y, lattice_angle_z]] + + 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)) - self._add_inherited_properties() self._get_lattice_properties() + self._add_inherited_properties() def add_method(self, ): From 7ac4dddab0c61bea54ae9fb29d5570b29cff25b6 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 18:33:24 +0200 Subject: [PATCH 10/14] fix nodes --- atomrdf/structure.py | 36 +- examples/01_getting_started.ipynb | 4566 ++++++++++++++--------------- 2 files changed, 2301 insertions(+), 2301 deletions(-) diff --git a/atomrdf/structure.py b/atomrdf/structure.py index 1ade7a5..e0015d3 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -276,12 +276,12 @@ def delete(self, ids=None, indices=None, condition=None, selection=False): break if valid: - chemical_species = self.graph.add_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies) + 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.add_node(element_indetifiers[e], CMSO.ChemicalElement) + 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))) @@ -339,12 +339,12 @@ def substitute_atoms(self, substitution_element, ids=None, indices=None, conditi break if valid: - chemical_species = self.graph.add_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies) + 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.add_node(element_indetifiers[e], CMSO.ChemicalElement) + 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))) @@ -466,12 +466,12 @@ def add_interstitial_impurities(self, element, void_type='tetrahedral', lattice_ break if valid: - chemical_species = self.graph.add_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies) + 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.add_node(element_indetifiers[e], CMSO.ChemicalElement) + 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))) @@ -671,7 +671,7 @@ def _add_crystal_structure(self, targets=None): valid = self.graph._is_valid(targets) if valid: - crystal_structure = self.graph.add_node(f'{self._name}_CrystalStructure', CMSO.CrystalStructure) + 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], @@ -725,7 +725,7 @@ def _add_unit_cell(self): ------- """ - unit_cell = self.graph.add_node(f'{self._name}_UnitCell', CMSO.UnitCell) + unit_cell = self.graph.create_node(f'{self._name}_UnitCell', CMSO.UnitCell) self.graph.add((self.crystal_structure, CMSO.hasUnitCell, unit_cell)) self.unit_cell = unit_cell @@ -748,13 +748,13 @@ def _add_lattice_properties(self, lattice_parameter_value, lattice_angle_value): Returns ------- """ - lattice_parameter = self.graph.add_node(f'{self._name}_LatticeParameter', CMSO.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, 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 = self.graph.add_node(f'{self._name}_LatticeAngle', CMSO.LatticeAngle) + 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, 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))) @@ -804,14 +804,14 @@ def _add_atoms(self): outfile = self._save_atom_attributes(position_identifier, species_identifier) if "positions" in self.atoms.keys(): - position = self.graph.add_node(f'{self._name}_Position', CMSO.AtomAttribute) + 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, 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 = self.graph.add_node(f'{self._name}_Species', CMSO.AtomAttribute) + 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, CMSO.hasName, Literal('Species', datatype=XSD.string))) self.graph.add((species, CMSO.hasIdentifier, Literal(species_identifier, datatype=XSD.string))) @@ -858,7 +858,7 @@ def add_vacancy(self, concentration, number=None): if self.graph is None: return - vacancy = self.graph.add_node(f'{self._name}_Vacancy', PODO.Vacancy) + vacancy = self.graph.create_node(f'{self._name}_Vacancy', PODO.Vacancy) self.graph.add((self.material, CMSO.hasDefect, vacancy)) self.graph.add((self.simulation_cell, PODO.hasVacancyConcentration, Literal(concentration, datatype=XSD.float))) if number is not None: @@ -885,19 +885,19 @@ def add_gb(self, gb_dict): return if gb_dict["GBType"] is None: - plane_defect = self.graph.add_node(f'{self._name}_GrainBoundary') + plane_defect = self.graph.create_node(f'{self._name}_GrainBoundary') elif gb_dict["GBType"] == "Twist": - plane_defect = self.graph.add_node(f'{self._name}_TwistGrainBoundary', PLDO.TwistGrainBoundary) + plane_defect = self.graph.create_node(f'{self._name}_TwistGrainBoundary', PLDO.TwistGrainBoundary) elif gb_dict["GBType"] == "Tilt": - plane_defect = self.graph.add_node(f'{self._name}_TiltGrainBoundary', PLDO.TiltGrainBoundary) + plane_defect = self.graph.create_node(f'{self._name}_TiltGrainBoundary', PLDO.TiltGrainBoundary) elif gb_dict["GBType"] == "Symmetric Tilt": - plane_defect = self.graph.add_node(f'{self._name}_SymmetricalTiltGrainBoundary', PLDO.SymmetricalTiltGrainBoundary) + plane_defect = self.graph.create_node(f'{self._name}_SymmetricalTiltGrainBoundary', PLDO.SymmetricalTiltGrainBoundary) elif gb_dict["GBType"] == "Mixed": - plane_defect = self.graph.add_node(f'{self._name}_MixedGrainBoundary', 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/examples/01_getting_started.ipynb b/examples/01_getting_started.ipynb index 4ce2f0f..1165104 100644 --- a/examples/01_getting_started.ipynb +++ b/examples/01_getting_started.ipynb @@ -115,684 +115,684 @@ "\n", "\n", - "\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", + "\n", "\n", - "sample_dd8dab55-8100-4fef-bd16-166637058ca1\n", - "\n", - "sample_dd8dab55-8100-4fef-bd16-166637058ca1\n", + "sample_836942a9-9109-43e9-bcae-aadbc311e866_SimulationCellAngle\n", + "\n", + "sample_836942a9-9109-43e9-bcae-aadbc311e866_SimulationCellAngle\n", "\n", - 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"" + "" ] }, "execution_count": 7, @@ -3141,7 +3141,7 @@ "
\n", " 0\n", " bcc\n", - " sample:dd8dab55-8100-4fef-bd16-166637058ca1\n", + " sample:836942a9-9109-43e9-bcae-aadbc311e866\n", "
\n", " \n", "\n", @@ -3149,7 +3149,7 @@ ], "text/plain": [ " hasAltNamevalue AtomicScaleSample\n", - "0 bcc sample:dd8dab55-8100-4fef-bd16-166637058ca1" + "0 bcc sample:836942a9-9109-43e9-bcae-aadbc311e866" ] }, "execution_count": 14, From a0e04499373d30fe6e65631ac89aeea6684164dd Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 18:34:45 +0200 Subject: [PATCH 11/14] fix workflow --- atomrdf/workflow/workflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/atomrdf/workflow/workflow.py b/atomrdf/workflow/workflow.py index be74a93..71acba1 100644 --- a/atomrdf/workflow/workflow.py +++ b/atomrdf/workflow/workflow.py @@ -102,7 +102,7 @@ def _get_lattice_properties(self, ): lattice_angle_y = self.kg.value(lattice_angle, CMSO.hasAngle_beta) lattice_angle_z = self.kg.value(lattice_angle, CMSO.hasAngle_gamma) - targets = [altname, spacegroup_symbol, spacegroup_number, blattice, + 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]] From c9a19220df972e537bf4bbbfe601a3a192847828 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Tue, 16 Apr 2024 18:35:00 +0200 Subject: [PATCH 12/14] fix workflow --- atomrdf/workflow/workflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/atomrdf/workflow/workflow.py b/atomrdf/workflow/workflow.py index 71acba1..ff0b3cc 100644 --- a/atomrdf/workflow/workflow.py +++ b/atomrdf/workflow/workflow.py @@ -106,7 +106,7 @@ def _get_lattice_properties(self, ): [lattice_parameter_x, lattice_parameter_y, lattice_parameter_z], [lattice_angle_x, lattice_angle_y, lattice_angle_z]] - structure._add_crystal_structure(targets=targets) + self.structure._add_crystal_structure(targets=targets) def _add_inherited_properties(self, ): From c3e04bcab6f15b80e3976fcda9b7d045004c8798 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Wed, 17 Apr 2024 09:09:14 +0200 Subject: [PATCH 13/14] add workflow example --- examples/06_workflow_pyiron.ipynb | 770 ++++++++++++++++++++++++++++++ 1 file changed, 770 insertions(+) create mode 100644 examples/06_workflow_pyiron.ipynb 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": [], + 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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 +} From dd95a927cf2ae5ef6270f63d6b2183e2b481aafa Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Wed, 17 Apr 2024 09:09:38 +0200 Subject: [PATCH 14/14] =?UTF-8?q?Bump=20version:=200.5.1=20=E2=86=92=200.5?= =?UTF-8?q?.2?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- CITATION.cff | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) 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/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',