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add new creation routines #19

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Jun 13, 2023
Merged

add new creation routines #19

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2 changes: 1 addition & 1 deletion pyscal_rdf/graph.py
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Original file line number Diff line number Diff line change
Expand Up @@ -310,7 +310,7 @@ def add_gb(self, gb_dict, name=None):

def add_vacancy(self, concentration, number=None, name=None):
vacancy_01 = BNode(name)
self.add((self.sample, CMSO.hasDefect, vacancy_01))
self.add((self.material, CMSO.hasDefect, vacancy_01))
self.add((vacancy_01, RDF.type, PODO.Vacancy))
self.add((vacancy_01, PODO.hasVacancyConcentration, Literal(concentration, datatype=XSD.float)))
if number is not None:
Expand Down
37 changes: 32 additions & 5 deletions pyscal_rdf/network.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@ class Network:
def __init__(self):
self.g = nx.DiGraph()

def add(self, sub, pred, obj, dtype=None):
def add(self, sub, pred, obj, dtype=None, pred_prefix="cmso"):
pred = f'{pred_prefix}:{pred}'
self.g.add_node(sub, node_type="object")
self.g.add_node(pred, node_type="property")
if dtype is not None:
Expand Down Expand Up @@ -78,7 +79,30 @@ def __init__(self):
self.add("LatticeAngle", "hasAngle_alpha", "LatticeAngle_alpha", dtype="float")
self.add("LatticeAngle", "hasAngle_beta", "LatticeAngle_beta", dtype="float")
self.add("LatticeAngle", "hasAngle_gamma", "LatticeAngle_gamma", dtype="float")


#add GB properties
self.add("Material", "hasDefect", "Defect", pred_prefix="pldo")
self.add("Defect", "type", "GrainBoundary", pred_prefix="rdf")
self.add("Defect", "type", "TwistBoundary", pred_prefix="rdf")
self.add("Defect", "type", "TiltBoundary", pred_prefix="rdf")
self.add("Defect", "type", "SymmetricTiltBoundary", pred_prefix="rdf")
self.add("Defect", "type", "MixedBoundary", pred_prefix="rdf")
self.add("Defect", "hasSigmaValue", "Sigma", dtype="integer", pred_prefix="pldo")
self.add("Defect", "hasGBPlane", "GBPlane", pred_prefix="pldo")
self.add("GBPlane", "hasMillerIndices", "MillerIndices", dtype="string", pred_prefix="pldo")
self.add("Defect", "hasRotationAxis", "RotationAxis", pred_prefix="pldo")
self.add("RotationAxis", "hasComponentX", "RotationAxis_x", dtype="float", pred_prefix="pldo")
self.add("RotationAxis", "hasComponentY", "RotationAxis_y", dtype="float", pred_prefix="pldo")
self.add("RotationAxis", "hasComponentZ", "RotationAxis_z", dtype="float", pred_prefix="pldo")
self.add("Defect", "hasMisorientationAngle", "MisorientationAngle", pred_prefix="pldo")
self.add("MisorientationAngle", "hasAngle", "Angle", pred_prefix="pldo")

#add vacancy
self.add("Defect", "type", "Vacancy", pred_prefix="rdf")
self.add("Vacancy", "hasVacancyConcentration", "VacancyConcentration", pred_prefix="podo", dtype="float")
self.add("Vacancy", "hasNumberOfVacancy", "NumberOfVacancy", pred_prefix="podo", dtype="integer")


def get_path_from_sample(self, target):
path = self.get_shortest_path(source="Sample", target=target)
triplets = []
Expand All @@ -100,16 +124,19 @@ def formulate_query(self, target, value):
def _formulate_query_path(self, triplets):
query = []
query.append("PREFIX cmso: <https://purls.helmholtz-metadaten.de/cmso/>")
query.append("PREFIX pldo: <https://purls.helmholtz-metadaten.de/pldo/>")
query.append("PREFIX podo: <https://purls.helmholtz-metadaten.de/podo/>")
query.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
query.append("SELECT DISTINCT ?sample")
query.append("WHERE {")
for triple in triplets:
query.append(" ?%s cmso:%s ?%s ."%(triple[0].lower(),
query.append(" ?%s %s ?%s ."%(triple[0].lower(),
triple[1],
triple[2].lower()))
return query

def _formulate_filter_expression(self, triplets, value):
value, datatype = self._check_value(value)
def _formulate_filter_expression(self, triplets, value):
value, datatype = self._check_value(value)
last_val = self.g.nodes[triplets[-1][-1]]
last_val_name = triplets[-1][-1].lower()

Expand Down
74 changes: 52 additions & 22 deletions wrap_creation.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -9,65 +9,95 @@
},
"outputs": [],
"source": [
"from pyscal_rdf import StructureGraph"
"from pyscal_rdf.network import OntologyNetwork"
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 2,
"id": "9a21e979-8497-4d0e-88f3-4452bab8b85d",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"sg = StructureGraph()"
"n = OntologyNetwork()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "4f8d7425-24ed-4d62-a562-22cb7be78130",
"metadata": {},
"execution_count": 10,
"id": "1ce29502-3322-41fd-960b-e7d3d792cd74",
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Fe\n"
"I3m\n",
"[['Sample', 'cmso:hasMaterial', 'Material'], ['Material', 'cmso:hasStructure', 'CrystalStructure'], ['CrystalStructure', 'cmso:hasSpaceGroup', 'SpaceGroup'], ['SpaceGroup', 'cmso:hasSpaceGroupSymbol', 'SpaceGroupSymbol']]\n",
"['I3m'] single_string\n"
]
},
{
"data": {
"text/plain": [
"'PREFIX cmso: <https://purls.helmholtz-metadaten.de/cmso/> PREFIX pldo: <https://purls.helmholtz-metadaten.de/pldo/> PREFIX podo: <https://purls.helmholtz-metadaten.de/podo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> SELECT DISTINCT ?sample WHERE { ?sample cmso:hasMaterial ?material . ?material cmso:hasStructure ?crystalstructure . ?crystalstructure cmso:hasSpaceGroup ?spacegroup . ?spacegroup cmso:hasSpaceGroupSymbol ?spacegroupsymbol . FILTER (?spacegroupsymbol=\"I3m\"^^xsd:string) }'"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sys = sg.create_element(\"Fe\")"
"triplets = n.formulate_query(\"SpaceGroupSymbol\", \"I3m\")\n",
"triplets"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "a8915d92-1e95-4612-ac71-fab71e662c86",
"metadata": {
"tags": []
},
"execution_count": 9,
"id": "4f8d7425-24ed-4d62-a562-22cb7be78130",
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "b82e539b32664ccfbf6a2963d562b1b9",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"CytoscapeWidget(cytoscape_layout={'name': 'cola', 'avoidOverlap': True, 'animate': True}, cytoscape_style=[{'s…"
"['PREFIX cmso: <https://purls.helmholtz-metadaten.de/cmso/>',\n",
" 'PREFIX pldo: <https://purls.helmholtz-metadaten.de/pldo/>',\n",
" 'PREFIX podo: <https://purls.helmholtz-metadaten.de/podo/>',\n",
" 'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>',\n",
" 'SELECT DISTINCT ?sample',\n",
" 'WHERE {',\n",
" ' ?sample cmso:hasMaterial ?material .',\n",
" ' ?material cmso:hasStructure ?crystalstructure .',\n",
" ' ?crystalstructure cmso:hasSpaceGroup ?spacegroup .',\n",
" ' ?spacegroup cmso:hasSpaceGroupSymbol ?spacegroupsymbol .']"
]
},
"execution_count": 5,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sg.visualise()"
"query = n._formulate_query_path(triplets)\n",
"query"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a8915d92-1e95-4612-ac71-fab71e662c86",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"xx"
]
},
{
Expand Down Expand Up @@ -95,7 +125,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.16"
"version": "3.11.3"
}
},
"nbformat": 4,
Expand Down