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Merge pull request #76 from privrja/devel
Version 1.0.2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,103 @@ | ||
| import IFinder from "./IFinder"; | ||
| import SingleStructure from "./SingleStructure"; | ||
| import Sleep from "../helper/Sleep"; | ||
| import {ServerEnum} from "../enum/ServerEnum"; | ||
| import ComputeHelper from "../helper/ComputeHelper"; | ||
|
|
||
| const ENDPOINT_URI = "https://guarded-atoll-36331.herokuapp.com/https://coconut.naturalproducts.net/api/search/"; | ||
|
|
||
| interface Molecule { | ||
| coconut_id: string; | ||
| name: string; | ||
| unique_smiles: string; | ||
| molecular_formula: string; | ||
| } | ||
|
|
||
| class CoconutFinder implements IFinder { | ||
|
|
||
| async simpleFind(parameter: string, query: string = 'simple?query=') { | ||
| if (parameter === '') { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
| if (query.includes('simple?query')) { | ||
| query += parameter; | ||
| } | ||
| return fetch(ENDPOINT_URI + query).then(async response => { | ||
| if (response.status === 200) { | ||
| let json = await response.json().catch(() => []); | ||
| if (json.naturalProducts.length > 0) { | ||
| return json.naturalProducts.map((molecule: Molecule) => { | ||
| let mass = 0; | ||
| try { | ||
| mass = ComputeHelper.computeMass(ComputeHelper.removeUnnecessaryCharactersFromFormula(molecule.molecular_formula ?? '')); | ||
| } catch (e) { | ||
| } | ||
| return new SingleStructure( | ||
| molecule.coconut_id, | ||
| ServerEnum.COCONUT, | ||
| molecule.name, | ||
| molecule.unique_smiles, | ||
| molecule.molecular_formula, | ||
| mass | ||
| ) | ||
| }); | ||
| } | ||
| } | ||
| return []; | ||
| }).catch(() => []); | ||
| } | ||
|
|
||
| findByFormula(formula: string): Promise<SingleStructure[]> { | ||
| return this.simpleFind(formula); | ||
| } | ||
|
|
||
| async findByIdentifier(id: string): Promise<SingleStructure[]> { | ||
| if (id === '') { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
| return fetch(ENDPOINT_URI + 'simple?query=' + id).then(async response => { | ||
| if (response.status === 200) { | ||
| let json = await response.json().catch(() => []); | ||
| if (json.naturalProducts.length > 0) { | ||
| let mass = 0; | ||
| try { | ||
| mass = ComputeHelper.computeMass(ComputeHelper.removeUnnecessaryCharactersFromFormula(json.naturalProducts[0].molecular_formula ?? '')); | ||
| } catch (e) { | ||
| } | ||
| return [new SingleStructure( | ||
| json.naturalProducts[0].coconut_id, | ||
| ServerEnum.COCONUT, | ||
| json.naturalProducts[0].name, | ||
| json.naturalProducts[0].unique_smiles, | ||
| json.naturalProducts[0].molecular_formula, | ||
| mass | ||
| )]; | ||
| } else { | ||
| return []; | ||
| } | ||
| } else { | ||
| return []; | ||
| } | ||
| }).catch(() => []); | ||
| } | ||
|
|
||
| findByIdentifiers(ids: string[]): Promise<SingleStructure[]> { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
|
|
||
| findByMass(mass: number): Promise<SingleStructure[]> { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
|
|
||
| findByName(name: string): Promise<SingleStructure[]> { | ||
| return this.simpleFind(name); | ||
| } | ||
|
|
||
| findBySmiles(smiles: string): Promise<SingleStructure[]> { | ||
| return this.simpleFind(smiles, 'exact-structure?type=inchi&max-hits=100&smiles=' + smiles); | ||
| } | ||
|
|
||
|
|
||
| } | ||
|
|
||
| export default CoconutFinder; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,90 @@ | ||
| import IFinder from "./IFinder"; | ||
| import SingleStructure from "./SingleStructure"; | ||
| import Sleep from "../helper/Sleep"; | ||
| import {ServerEnum} from "../enum/ServerEnum"; | ||
| import ComputeHelper from "../helper/ComputeHelper"; | ||
|
|
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| const ENDPOINT_URI = "https://guarded-atoll-36331.herokuapp.com/https://www.npatlas.org/api/v1/"; | ||
|
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| interface Molecule { | ||
| npaid: string; | ||
| original_name: string; | ||
| smiles: string; | ||
| mol_formula: string; | ||
| } | ||
|
|
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| const BASIC_SEARCH = 'compounds/basicSearch?'; | ||
| const PARAMS = '&threshold=0&origin_type=all&rank=all&skip=0&limit=100'; | ||
|
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| class NPAtlasFinder implements IFinder { | ||
|
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| basicSearch(endpoint: string, method: string, oneResult: boolean = false): Promise<SingleStructure[]> { | ||
| return fetch(endpoint, {method: method}).then(async response => { | ||
| if (response.status === 200) { | ||
| let json = await response.json().catch(() => []); | ||
| if (oneResult) { | ||
| let mass = 0; | ||
| try { | ||
| mass = ComputeHelper.computeMass(ComputeHelper.removeUnnecessaryCharactersFromFormula(json.mol_formula ?? '')); | ||
| } catch (e) { | ||
| } | ||
| return [new SingleStructure(json.npaid, ServerEnum.NP_ATLAS, json.original_name, json.smiles, json.mol_formula, mass)]; | ||
| } else { | ||
| if (json.length > 0) { | ||
| return json.map((molecule: Molecule) => { | ||
| let mass = 0; | ||
| try { | ||
| mass = ComputeHelper.computeMass(ComputeHelper.removeUnnecessaryCharactersFromFormula(molecule.mol_formula ?? '')); | ||
| } catch (e) { | ||
| } | ||
| return new SingleStructure(molecule.npaid, ServerEnum.NP_ATLAS, molecule.original_name, molecule.smiles, molecule.mol_formula, mass); | ||
| }); | ||
| } | ||
| } | ||
| } | ||
| return []; | ||
| }).catch(() => []); | ||
| } | ||
|
|
||
| findByFormula(formula: string): Promise<SingleStructure[]> { | ||
| if (formula === '') { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
| return this.basicSearch(ENDPOINT_URI + BASIC_SEARCH + 'formula=' + formula + PARAMS, 'POST'); | ||
| } | ||
|
|
||
| async findByIdentifier(id: string): Promise<SingleStructure[]> { | ||
| if (id === '') { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
| return this.basicSearch(ENDPOINT_URI + 'compound/' + id, 'GET', true); | ||
| } | ||
|
|
||
| findByIdentifiers(ids: string[]): Promise<SingleStructure[]> { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
|
|
||
| findByMass(mass: number): Promise<SingleStructure[]> { | ||
| if (mass === 0) { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
| return this.basicSearch(ENDPOINT_URI + 'compounds/massSearch?mass=' + mass + '&type=exact_mass&range=100&skip=0&limit=100', 'POST'); | ||
| } | ||
|
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| findByName(name: string): Promise<SingleStructure[]> { | ||
| if (name === '') { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
| return this.basicSearch(ENDPOINT_URI + BASIC_SEARCH + 'name=' + name + PARAMS, 'POST'); | ||
| } | ||
|
|
||
| findBySmiles(smiles: string): Promise<SingleStructure[]> { | ||
| if (smiles === '') { | ||
| return Sleep.noSleepPromise(); | ||
| } | ||
| return this.basicSearch(ENDPOINT_URI + BASIC_SEARCH + 'smiles=' + smiles + '&method=sub' + PARAMS, 'POST'); | ||
| } | ||
|
|
||
| } | ||
|
|
||
| export default NPAtlasFinder; |
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