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Merge pull request #231 from EyeSeeTea/feature/api-structural-hub
Replace covid19-data json for Django API endpoint
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79 changes: 79 additions & 0 deletions
79
app/assets/javascripts/3dbio_viewer/src/data/NMRScreening.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| import _ from "lodash"; | ||
| import { Codec, GetType, nullType, number, oneOf, string } from "purify-ts"; | ||
| import { NMRFragmentTarget } from "../domain/entities/Protein"; | ||
| import { commonLigand, pdbLigandC } from "./PdbLigands"; | ||
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| const featureTypeCodec = Codec.interface({ | ||
| dataSource: string, | ||
| name: string, // binding | not binding | ||
| description: string, | ||
| externalLink: string, | ||
| }); | ||
|
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| export const nmrFragmentCodec = Codec.interface({ | ||
| name: string, | ||
| description: string, | ||
| externalLink: string, | ||
| pdbentry: nullType, | ||
| uniprotentry: string, | ||
| ligandentity: oneOf([Codec.interface(commonLigand), pdbLigandC]), | ||
| details: Codec.interface({ | ||
| type: string, // binding | notbinding | ||
| entity: string, // NMR target | ||
| }), | ||
| start: number, | ||
| end: number, | ||
| featureType: featureTypeCodec, | ||
| }); | ||
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| export type NMRScreeningFragment = GetType<typeof nmrFragmentCodec>; | ||
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| export function getNMR(nmrScreenings: NMRScreeningFragment[]): NMRFragmentTarget[] { | ||
| const fragments = nmrScreenings.map(nmr => ({ | ||
| ...nmr, | ||
| binding: !nmr.details.type.toLowerCase().includes("not"), | ||
| })); | ||
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| const targets = _(fragments) | ||
| .groupBy(i => i.details.entity) | ||
| .toPairs() | ||
| .value(); | ||
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| return targets.flatMap(([name, targetFragments]) => { | ||
| const fragments = targetFragments.map( | ||
| ({ name, description, externalLink, binding, ligandentity, start, end }) => ({ | ||
| name, | ||
| description, | ||
| externalLink, | ||
| binding, | ||
| ligand: { | ||
| ...ligandentity, | ||
| inChI: ligandentity.IUPACInChIkey, | ||
| smiles: ligandentity.canonicalSMILES, | ||
| pubchemId: ligandentity.pubChemCompoundId, | ||
| formula: ligandentity.formula, | ||
| imageDataResource: undefined, | ||
| }, | ||
| start, | ||
| end, | ||
| }) | ||
| ); | ||
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| const start = _.first(fragments.map(({ start }) => start)); | ||
| const end = _.first(fragments.map(({ end }) => end)); | ||
| const uniprotId = _.first(targetFragments.map(({ uniprotentry }) => uniprotentry)); | ||
| if (!start || !end || !uniprotId) return []; | ||
|
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| return [ | ||
| { | ||
| name, | ||
| uniprotId, | ||
| fragments, | ||
| bindingCount: fragments.filter(({ binding }) => binding).length, | ||
| notBindingCount: fragments.filter(({ binding }) => !binding).length, | ||
| start, | ||
| end, | ||
| }, | ||
| ]; | ||
| }); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| import _ from "lodash"; | ||
| import { Codec, GetType, number, string } from "purify-ts"; | ||
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| export const nmrTargetCodec = Codec.interface({ | ||
| entity: string, | ||
| start: number, | ||
| end: number, | ||
| uniprot_acc: string, | ||
| }); | ||
|
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| export type NMRTarget = GetType<typeof nmrTargetCodec>; |
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21 changes: 21 additions & 0 deletions
21
app/assets/javascripts/3dbio_viewer/src/data/codec-utils.ts
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,21 @@ | ||
| import { Codec, array, nullable, number, optional, string } from "purify-ts"; | ||
|
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| export function paginationCodec<Data>(type: Codec<Data>): Codec<Pagination<Data>> { | ||
| return Codec.interface({ | ||
| count: number, | ||
| next: optional(nullable(string)), | ||
| previous: optional(nullable(string)), | ||
| results: array(type), | ||
| }); | ||
| } | ||
|
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| export function getResults<Data>(pagination?: Pagination<Data>) { | ||
| return pagination?.results ?? []; | ||
| } | ||
|
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| export type Pagination<K> = { | ||
| count: number; | ||
| next: string | null | undefined; | ||
| previous: string | null | undefined; | ||
| results: K[]; | ||
| }; |
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