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Merge pull request #738 from desci-labs/tay/external-pub
Tay/external pub
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17 changes: 17 additions & 0 deletions
17
desci-server/prisma/migrations/20241224113519_external_publications/migration.sql
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| -- CreateTable | ||
| CREATE TABLE "ExternalPublications" ( | ||
| "id" SERIAL NOT NULL, | ||
| "uuid" TEXT NOT NULL, | ||
| "score" DOUBLE PRECISION NOT NULL, | ||
| "doi" TEXT NOT NULL, | ||
| "publisher" TEXT NOT NULL, | ||
| "publishYear" TEXT NOT NULL, | ||
| "sourceUrl" TEXT NOT NULL, | ||
| "createdAt" TIMESTAMP(3) NOT NULL DEFAULT CURRENT_TIMESTAMP, | ||
| "updatedAt" TIMESTAMP(3) NOT NULL, | ||
|
|
||
| CONSTRAINT "ExternalPublications_pkey" PRIMARY KEY ("id") | ||
| ); | ||
|
|
||
| -- AddForeignKey | ||
| ALTER TABLE "ExternalPublications" ADD CONSTRAINT "ExternalPublications_uuid_fkey" FOREIGN KEY ("uuid") REFERENCES "Node"("uuid") ON DELETE RESTRICT ON UPDATE CASCADE; |
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193 changes: 193 additions & 0 deletions
193
desci-server/src/controllers/nodes/externalPublications.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,193 @@ | ||
| import { Response, NextFunction } from 'express'; | ||
| import { Searcher } from 'fast-fuzzy'; | ||
| import _ from 'lodash'; | ||
| import z from 'zod'; | ||
|
|
||
| import { prisma } from '../../client.js'; | ||
| import { NotFoundError } from '../../core/ApiError.js'; | ||
| import { SuccessMessageResponse, SuccessResponse } from '../../core/ApiResponse.js'; | ||
| import { logger as parentLogger } from '../../logger.js'; | ||
| import { RequestWithNode } from '../../middleware/authorisation.js'; | ||
| import { crossRefClient } from '../../services/index.js'; | ||
| import { NodeUuid } from '../../services/manifestRepo.js'; | ||
| import repoService from '../../services/repoService.js'; | ||
| import { ensureUuidEndsWithDot } from '../../utils.js'; | ||
|
|
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| const logger = parentLogger.child({ module: 'ExternalPublications' }); | ||
| export const externalPublicationsSchema = z.object({ | ||
| params: z.object({ | ||
| // quickly disqualify false uuid strings | ||
| uuid: z.string().min(10), | ||
| }), | ||
| }); | ||
|
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| export const addExternalPublicationsSchema = z.object({ | ||
| params: z.object({ | ||
| // quickly disqualify false uuid strings | ||
| uuid: z.string().min(10), | ||
| }), | ||
| body: z.object({ | ||
| // uuid: z.string(), | ||
| score: z.coerce.number(), | ||
| doi: z.string(), | ||
| publisher: z.string(), | ||
| publishYear: z.string(), | ||
| sourceUrl: z.string(), | ||
| }), | ||
| }); | ||
|
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| export const externalPublications = async (req: RequestWithNode, res: Response, _next: NextFunction) => { | ||
| const { uuid } = req.params as z.infer<typeof externalPublicationsSchema>['params']; | ||
| const node = await prisma.node.findFirst({ where: { uuid: ensureUuidEndsWithDot(uuid) } }); | ||
| if (!node) throw new NotFoundError(`Node ${uuid} not found`); | ||
|
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| const userIsNodeOwner = req.user?.id === node?.ownerId; | ||
|
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| logger.trace({ uuid, userIsNodeOwner }); | ||
|
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| const externalPublication = await prisma.externalPublications.findMany({ | ||
| where: { uuid: ensureUuidEndsWithDot(uuid) }, | ||
| }); | ||
|
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| if (externalPublication.length > 0) return new SuccessResponse(externalPublication).send(res); | ||
|
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| // return empty list if user is not node owner | ||
| if (!userIsNodeOwner) return new SuccessResponse([]).send(res); | ||
|
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| const manifest = await repoService.getDraftManifest({ uuid: uuid as NodeUuid, documentId: node.manifestDocumentId }); | ||
| const data = await crossRefClient.searchWorks({ queryTitle: manifest?.title }); | ||
|
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||
| if (data.length > 0) { | ||
| const titleSearcher = new Searcher(data, { keySelector: (entry) => entry.title }); | ||
| const titleResult = titleSearcher.search(manifest.title, { returnMatchData: true }); | ||
| logger.trace( | ||
| { | ||
| data: titleResult.map((data) => ({ | ||
| title: data.item.title, | ||
| publisher: data.item.publisher, | ||
| source_url: data.item?.resource?.primary?.URL || data.item.URL || '', | ||
| doi: data.item.DOI, | ||
| key: data.key, | ||
| match: data.match, | ||
| score: data.score, | ||
| })), | ||
| }, | ||
| 'Title search result', | ||
| ); | ||
|
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| const descSearcher = new Searcher(data, { keySelector: (entry) => entry?.abstract ?? '' }); | ||
| const descResult = descSearcher.search(manifest.description ?? '', { returnMatchData: true }); | ||
| logger.trace( | ||
| { | ||
| data: descResult.map((data) => ({ | ||
| title: data.item.title, | ||
| key: data.key, | ||
| match: data.match, | ||
| score: data.score, | ||
| })), | ||
| }, | ||
| 'Abstract search result', | ||
| ); | ||
|
|
||
| const authorsSearchScores = data.map((work) => { | ||
| const authorSearcher = new Searcher(work.author, { keySelector: (entry) => `${entry.given} ${entry.family}` }); | ||
|
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||
| const nodeAuthorsMatch = manifest.authors.map((author) => | ||
| authorSearcher.search(author.name, { returnMatchData: true }), | ||
| ); | ||
| return { | ||
| publisher: work.publisher, | ||
| score: nodeAuthorsMatch.flat().reduce((total, match) => (total += match.score), 0) / manifest.authors.length, | ||
| match: nodeAuthorsMatch.flat().map((data) => ({ | ||
| key: data.key, | ||
| match: data.match, | ||
| score: data.score, | ||
| author: data.item, | ||
| publisher: work.publisher, | ||
| doi: work.DOI, | ||
| })), | ||
| }; | ||
| }); | ||
|
|
||
| logger.trace( | ||
| { | ||
| data: descResult.map((data) => ({ | ||
| title: data.item.title, | ||
| key: data.key, | ||
| match: data.match, | ||
| score: data.score, | ||
| })), | ||
| }, | ||
| 'Authors search result', | ||
| ); | ||
|
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| const publications = data | ||
| .map((data) => ({ | ||
| publisher: data.publisher, | ||
| sourceUrl: data?.resource?.primary?.URL || data.URL || '', | ||
| doi: data.DOI, | ||
| 'is-referenced-by-count': data['is-referenced-by-count'] ?? 0, | ||
| publishYear: | ||
| data.published['date-parts']?.[0]?.[0].toString() ?? | ||
| data.license | ||
| .map((licence) => licence.start['date-parts']?.[0]?.[0]) | ||
| .filter(Boolean)?.[0] | ||
| .toString(), | ||
| title: titleResult | ||
| .filter((res) => res.item.publisher === data.publisher) | ||
| .map((data) => ({ | ||
| title: data.item.title, | ||
| key: data.key, | ||
| match: data.match, | ||
| score: data.score, | ||
| }))?.[0], | ||
| abstract: descResult | ||
| .filter((res) => res.item.publisher === data.publisher) | ||
| .map((data) => ({ | ||
| key: data.key, | ||
| match: data.match, | ||
| score: data.score, | ||
| abstract: data.item?.abstract ?? '', | ||
| }))?.[0], | ||
| authors: authorsSearchScores | ||
| .filter((res) => res.publisher === data.publisher) | ||
| .map((data) => ({ | ||
| score: data.score, | ||
| authors: data.match, | ||
| }))?.[0], | ||
| })) | ||
| .map((publication) => ({ | ||
| ...publication, | ||
| score: | ||
| ((publication.title?.score ?? 0) + (publication.abstract?.score ?? 0) + (publication.authors?.score ?? 0)) / | ||
| 3, | ||
| })) | ||
| .filter((entry) => entry.score >= 0.8); | ||
|
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| logger.trace({ publications, uuid }, 'externalPublications'); | ||
|
|
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| if (publications.length > 0) return new SuccessResponse(publications).send(res); | ||
| } | ||
|
|
||
| return new SuccessResponse([]).send(res); | ||
| }; | ||
|
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| export const addExternalPublication = async (req: RequestWithNode, res: Response, _next: NextFunction) => { | ||
| const { uuid } = req.params as z.infer<typeof addExternalPublicationsSchema>['params']; | ||
|
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| const node = await prisma.node.findFirst({ where: { uuid: ensureUuidEndsWithDot(uuid) } }); | ||
| if (!node) throw new NotFoundError(`Node ${uuid} not found`); | ||
|
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| const { doi, sourceUrl, publishYear, publisher, score } = req.body as z.infer< | ||
| typeof addExternalPublicationsSchema | ||
| >['body']; | ||
|
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| const exists = await prisma.externalPublications.findFirst({ where: { AND: [{ uuid }, { publisher }] } }); | ||
| if (exists) return new SuccessMessageResponse().send(res); | ||
|
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| const entry = await prisma.externalPublications.create({ | ||
| data: { doi, score, sourceUrl, publisher, publishYear, uuid: ensureUuidEndsWithDot(uuid) }, | ||
| }); | ||
|
|
||
| return new SuccessResponse(entry).send(res); | ||
| }; |
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