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update delete method to modify files #71

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Apr 4, 2024
Merged

update delete method to modify files #71

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30 changes: 29 additions & 1 deletion pyscal_rdf/structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -281,7 +281,35 @@ def delete(self, ids=None, indices=None, condition=None, selection=False):
self.graph.add((chemical_species, CMSO.hasElement, element))
self.graph.add((element, RDF.type, CMSO.Element))
self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string)))
self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float)))
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.graph.value(URIRef(f'{self.sample}_Position'), CMSO.hasPath).toPython()
position_identifier = self.graph.graph.value(URIRef(f'{self.sample}_Position'), CMSO.hasIdentifier).toPython()
species_identifier = self.graph.graph.value(URIRef(f'{self.sample}_Species'), CMSO.hasIdentifier).toPython()

#open the file for reading
with open(filepath, 'r') as fin:
data = json.load(fin)
positions = data[position_identifier]['value']
species = data[species_identifier]['value']

#clean up items
positions = [pos for count, pos in enumerate(positions) if count not in delete_ids]
species = [pos for count, pos in enumerate(species) if count not in delete_ids]

datadict = {
position_identifier:{
"value": positions,
"label": "position",
},
species_identifier:{
"value": species,
"label": "species",
},
}
outfile = os.path.join(self.graph.structure_store, str(self._name).split(':')[-1])
json_io.write_file(outfile, datadict)


def __delitem__(self, val):
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