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Reaction recommender #127

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Reaction recommender #127

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c9e1bd0
reaction recommender
Nov 17, 2022
8c79aa3
Update extension.ts
Nov 22, 2022
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10 changes: 4 additions & 6 deletions vscode-antimony/src/annotationRecommender.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -91,13 +91,11 @@ export async function singleStepInputRec(context: ExtensionContext, line: number
const prefix = annotation.split(':')[0].toLowerCase();
const id = annotation.split(':')[1]
var snippetText;
// if (prefix === 'rhea') {
// snippetText = `\n\${1:${initialQuery}} identity "https://www.rhea-db.org/rhea/${annotation}"`;
// } else if (prefix === 'ontology') {
// // snippetText = `\n\${1:${initialQuery}} identity "${entity['iri']}"`;
// } else {
if (prefix === 'rhea') {
snippetText = `\n\${1:${initialQuery}} identity "https://www.rhea-db.org/rhea/${id}"`;
} else {
snippetText = `\n\${1:${initialQuery}} identity "http://identifiers.org/${prefix}/${annotation}"`;
// }
}
const snippetStr = new vscode.SnippetString(snippetText);
const doc = vscode.window.activeTextEditor.document;
const pos = doc.lineAt(line).range.end;
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83 changes: 60 additions & 23 deletions vscode-antimony/src/server/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@
TextDocumentContentChangeEvent, TextDocumentPositionParams, Position)
import threading
import time
from AMAS import recommender, species_annotation
from AMAS import recommender, species_annotation, reaction_annotation
from bioservices import ChEBI

# TODO remove this for production
Expand Down Expand Up @@ -283,31 +283,68 @@ def recommend(ls: LanguageServer, args):
'error': "Did not select a symbol"
}
symbol = symbols[0]
if symbol.type != SymbolType.Species:
if symbol.type != SymbolType.Species and symbol.type != SymbolType.Reaction:
return {
'error': "Did not select species"
'error': "Please select species or reaction name"
}
if symbol.type == SymbolType.Species:
recom = recommender.Recommender()
display_name = symbol.display_name
if display_name is not None:
annotations = recom.getSpeciesAnnotation(pred_str=display_name.replace("\"", ""))
else:
annotations = recom.getSpeciesAnnotation(pred_str=symbol.name)
chebi = species_annotation.chebi_low_synonyms
ret = list()
limit = 0
for annotation in annotations.candidates:
sorted_chebi = sorted(chebi[annotation[0]], key=len)
ret.append({
'label': sorted_chebi[0],
'id': annotation[0]
})
limit += 1
if limit >= 10:
break
return {
'annotations': ret
}
recom = recommender.Recommender()
display_name = symbol.display_name
if display_name is not None:
annotations = recom.getSpeciesAnnotation(pred_str=display_name.replace("\"", ""))
else:
annotations = recom.getSpeciesAnnotation(pred_str=symbol.name)
chebi = species_annotation.chebi_low_synonyms
ret = list()
limit = 0
for annotation in annotations.candidates:
sorted_chebi = sorted(chebi[annotation[0]], key=len)
ret.append({
'label': sorted_chebi[0],
'id': annotation[0]
})
limit += 1
if limit >= 10:
break
return {
'annotations': ret
}
reaction = symbol.decl_node
species_list = []
for reactant in reaction.get_reactants():
species_list.append(reactant)
for product in reaction.get_products():
species_list.append(reaction.get_products())
species_dict = dict()
species_list = []
for species in species_list:
species_list.append(species.get_name_text())
species_dict[species.get_name_text()] = species.display_name
reaction_spec = dict()
reaction_spec[reaction.get_name_text()] = species_list

model_specs = []
model_specs.append((species_dict, dict()))
model_specs.append((reaction_spec, dict()))
recom = recommender.Recommender(model_specs=model_specs)
annotations = recom.getReactionAnnotation(reaction.get_name_text())
# rhea = reaction_annotation.ref_rhea_to_chebi
ret = list()
limit = 0
for annotation in annotations.candidates:
# sorted_rhea = sorted(rhea[annotation[0]], key=len)
ret.append({
'label': annotation[0],
'id': annotation[0]
})
limit += 1
if limit >= 10:
break
return {
'annotations': ret
}


#### Hover for displaying information ####
@server.feature(HOVER)
Expand Down