commit 85b0d182ffaae47be4e9c1c524d988a0896b4030 Author: argirok Date: Wed Nov 20 11:34:15 2024 +0200 first commit diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..7e087fe --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +.idea/ +node_modules diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..0ad25db --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published + by the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..97fc68a --- /dev/null +++ b/README.md @@ -0,0 +1,65 @@ +# README # + +### What is this repository for? ### + +PIDMR resolver parser service + +Gets a PID, makes a request to PIDMR service, and given the response parses it to a json object if there is a parser available for the given endpoint. + +* Version 1.0.0 + + +# Node.js Service + + +## Requirements + +- [Node.js](https://nodejs.org/) (v16+ recommended) +- [npm](https://www.npmjs.com/) + +--- + +## Installation + +Install dependencies: + + npm install + +Start the server: + + npm start + +#GET /:pid +Gets the PID, makes a request to PIDMR service, and given the response parses it to a json object if there is a parser available for the given endpoint. +pid Should be url encoded. + +Example Request: + +curl http://localhost:4001/10.5524%2F100005 + +Response: + + 200 OK: A json Object + + {"id":"10.5524/100005","type":"dataset","title":"Genomic data from the Emperor penguin (Aptenodytes forsteri)","result":{"accessRights":"OPEN","embargoEndDate":"","authors":["Li, J","Zhang, G","Lambert, D","Wang, J"],"editors":[],"source":"datacite","publisher":"GigaScience","journal":null,"DOI":"10.5524/100005","url":"https://doi.org/10.5524/100005","date":2011}} + + +#GET /supported-endpoints + +Retrieve a list of all available endpoints that can be parsed. + +Example Request: + +curl http://localhost:4001/supported-endpoints + +Response: + + 200 OK: An array of supported endpoints. + + ["api.crossref.org","api.datacite.org","zenodo.org"] + +### How to run locally? ### + +* "npm i" to install dependencies. +* "npm start" to start the service + diff --git a/model/Entity.js b/model/Entity.js new file mode 100644 index 0000000..721ea5b --- /dev/null +++ b/model/Entity.js @@ -0,0 +1,24 @@ +const Result = require("./Result"); + +/** + * @class Entity + * + * @property {string} id + * @property {string} type + * @property {string} title + * @property {Result} result + */ +class Entity { + + + constructor(id, type, title, description) { + this.id = id; + this.type = type; + this.title = title; + this.result = new Result(description); + } + +} + + +module.exports = Entity; diff --git a/model/Result.js b/model/Result.js new file mode 100644 index 0000000..7b351f6 --- /dev/null +++ b/model/Result.js @@ -0,0 +1,31 @@ + +/** + * @class Result + * + * @property {string} source + * @property {string} url + * @property {any} record + * @property {string} accessRights + * @property {string} embargoEndDate + * @property {string} date + * @property {string[]} authors + * @property {string} publisher + * @property {string} description + * @property {string} DOI + * @property {string[]} editors + * @property {string} journal + */ +class Result{ + + + constructor( description) { + this.description = description; + this.accessRights = "OPEN"; + this.embargoEndDate= ""; + this.authors = []; + this.editors = []; + } + +} + +module.exports = Result; diff --git a/package.json b/package.json new file mode 100644 index 0000000..b80425a --- /dev/null +++ b/package.json @@ -0,0 +1,21 @@ +{ + "name": "PIDMR-parser-service", + "version": "1.0.0", + "description": "PIDMR resolver parser service. Gets a PID, makes a request to PIDMR service, and given the response parses it to a json object if there is a parser available for the given endpoint.", + "main": "pidResolverService.js", + "scripts": { + "start": "node pidResolverService.js", + "prepare-dist": "rm -rf dist; mkdir dist; cp package.json ./dist; cp -r pidResolverService.js parsers model ./dist; cp properties.file ./dist;" + }, + "author": "Argiro Kokogiannaki ", + "dependencies": { + "axios": "^1.6.7", + "body-parser": "^1.20.2", + "express": "^4.18.2", + "properties-reader": "^2.2.0", + "xml2js": "^0.6.2" + }, + "engines": { + "node": ">=16.14.0" + } +} diff --git a/parsers/Arxiv.js b/parsers/Arxiv.js new file mode 100644 index 0000000..56aac92 --- /dev/null +++ b/parsers/Arxiv.js @@ -0,0 +1,62 @@ +const Entity = require("../model/Entity"); +const xml2js = require('xml2js'); + + +class Arxiv { + + async parse(pid, xml) { + try { + const entity = await this.parseXml(pid, xml); + console.log(entity) + return entity; + } catch (error) { + console.error('Parsing error:', error); + return null; + } + + } + + parseJson(pid, result) { + let entity = new Entity(pid); + entity.result.source = "arxiv"; + entity.id = pid; + let metadata = result['OAI-PMH']['GetRecord']['record']['metadata']['oai_dc:dc']; + entity.title = metadata['dc:title']; + entity.result.url = metadata['dc:identifier']; + entity.type = 'publication'; + entity.result.date = metadata['dc:date'].split("-")[0]; + + entity.result.accessRights = "OPEN"; + // entity.result.publisher = item.publisher; + entity.result.journal = null; + // entity.entityord = item; + entity.result.description = metadata['dc:description']; + + entity.result.authors = Array.isArray(metadata['dc:creator']) ? metadata['dc:creator'] : [metadata['dc:creator']]; + return entity; + } + + + async parseXml(pid, xml) { + return new Promise((resolve, reject) => { + const parser = new xml2js.Parser({ + trim: true, // Trims whitespace from text nodes + explicitArray: false, // Prevents wrapping single child nodes in an array + }); + + parser.parseString(xml, (err, result) => { + if (err) { + reject(err); // Reject the Promise if there's an error + } else { + console.log("parsed!") + console.log(result) + resolve(this.parseJson(pid, result)); // Resolve with the parsed result + } + }); + }); + } + + +} + +module.exports = Arxiv; diff --git a/parsers/Crossref.js b/parsers/Crossref.js new file mode 100644 index 0000000..375703f --- /dev/null +++ b/parsers/Crossref.js @@ -0,0 +1,60 @@ +const Entity = require("../model/Entity"); + +class Crossref { + + parse(pid, item) { + let entity = new Entity(pid); + entity.result.source = "crossref"; + entity.DOI = pid; + entity.title = item.title; + entity.result.url = item.URL; + entity.type = 'publication'; + if (item['indexed']) { + entity.result.date = item['created']['date-parts'][0][0]; + } + entity.result.accessRights = "OPEN"; + entity.result.publisher = item.publisher; + entity.result.journal = null; + entity.result.description = item.abstract; + if (item.author) { + entity.result.authors = []; + for (let j = 0; j < item.author.length; j++) { + let author = this.parseName(item.author[j]); + if (author) { + entity.result.authors.push(author); + } + } + } + if (item.editor) { + for (let j = 0; j < item.editor.length; j++) { + let editor = this.parseName(item.editor[j]); + if (editor) { + entity.result.authors.push(editor); + } + } + } + + return entity; + } + + parseName(authorObj) { + let author = ""; + if (authorObj.hasOwnProperty("family")) { + author += authorObj.family; + } + if (authorObj.hasOwnProperty("family") && authorObj.hasOwnProperty("given")) { + author += ", "; + } + if (authorObj.hasOwnProperty("given")) { + author += authorObj.given; + } + + if (!author && authorObj.hasOwnProperty("name")) { + author += authorObj.name; + } + + return author; + } +} + +module.exports = Crossref; diff --git a/parsers/Datacite.js b/parsers/Datacite.js new file mode 100644 index 0000000..d76f579 --- /dev/null +++ b/parsers/Datacite.js @@ -0,0 +1,30 @@ +const Entity = require("../model/Entity"); + +class Datacite { + parse(pid, item) { + let entity = new Entity(pid); + entity.result.source = "datacite"; + entity.result.publisher = null; + entity.result.journal = null; + entity.result.DOI = pid; + entity.id = pid; + entity.title = Array.isArray(item.attributes.titles) && item.attributes.titles[0].title ? item.attributes.titles[0].title : null; + entity.result.url = "https://doi.org/" + pid; + entity.type = 'dataset'; + entity.result.date = item.attributes.publicationYear; + entity.result.accessRights = "OPEN"; + entity.result.publisher = item.attributes['publisher']; + entity.result.journal = null; + if (item.attributes.creators) { + entity.result.authors = []; + for (let j = 0; j < item.attributes.creators.length; j++) { + const author = item.attributes.creators[j].name; + entity.result.authors.push(author); + } + } + return entity; + } + +} + +module.exports = Datacite; diff --git a/parsers/Googleapis.js b/parsers/Googleapis.js new file mode 100644 index 0000000..e03351d --- /dev/null +++ b/parsers/Googleapis.js @@ -0,0 +1,20 @@ +const Entity = require("../model/Entity"); +class Googleapis{ + parse(pid, item){ + let entity = new Entity(pid); + entity.result.source = "googleapis"; + entity.result.publisher = null; + entity.result.journal = null; + entity.id = pid; + entity.title = item['volumeInfo']['title'] + entity.result.url = item['volumeInfo']['infoLink']; + entity.type = 'publication'; + entity.result.date = item['volumeInfo']['publishedDate'].split('-')[0]; + entity.result.accessRights = "OPEN"; + + return entity; + } + +} + +module.exports = Googleapis; diff --git a/parsers/Handle.js b/parsers/Handle.js new file mode 100644 index 0000000..af927b2 --- /dev/null +++ b/parsers/Handle.js @@ -0,0 +1,32 @@ +const Entity = require("../model/Entity"); + +class Handle { + parse(pid, item) { + let entity = new Entity(pid); + entity.result.source = "handle"; + entity.DOI = pid; + entity.id = item.id; + + entity.title = item.title; + entity.result.url = item.doi_url; + entity.type = 'publication'; + entity.result.date = item.metadata.publication_date.split("-")[0]; + entity.result.accessRights = "OPEN"; + entity.result.journal = null; + entity.result.description = item.metadata.description; + if (item.metadata.creators) { + entity.result.authors = []; + for (let j = 0; j < item.metadata.creators.length; j++) { + let author = item.metadata.creators[j].name; + entity.result.authors.push(author); + + } + } + + + return entity; + } + +} + +module.exports = Zenodo; diff --git a/parsers/N2t.js b/parsers/N2t.js new file mode 100644 index 0000000..ac1cdee --- /dev/null +++ b/parsers/N2t.js @@ -0,0 +1,16 @@ +const Entity = require("../model/Entity"); +class N2t{ + + parse(pid, item){ + let entity = new Entity(pid); + entity.result.source = "n2t"; + entity.id = item.pid + entity.title = item.properties.name; + entity.result.url = item.target; + entity.type = 'dataset'; + return entity; + } + +} + +module.exports = N2t; diff --git a/parsers/ParserUtils.js b/parsers/ParserUtils.js new file mode 100644 index 0000000..42c95f5 --- /dev/null +++ b/parsers/ParserUtils.js @@ -0,0 +1,62 @@ +const Crossref = require("./Crossref"); +const CROSSREF_endpoint = "api.crossref.org"; +const CROSSREF = "crossref"; + +const Datacite = require("./Datacite"); +const DATACITE_endpoint = "api.datacite.org"; +const DATACITE = "datacite"; + +const N2t = require("./N2t"); +const N2T_endpoint = "n2t.net"; +const N2T = "n2t"; + +const Googleapis = require("./Googleapis"); +const GOOGLEAPIS_endpoint = "www.googleapis.com"; +const GOOGLEAPIS = "googleapis"; + +const Zenodo = require("./Zenodo"); +const Zenodo_endpoint = "zenodo.org"; +const ZENODOD = "zenodo"; + +const Arxiv = require("./Arxiv"); +const Arxiv_endpoint = "export.arxiv.org"; + +class ParserUtils { + getSupportedParsers() { + return [CROSSREF_endpoint, DATACITE_endpoint, Zenodo_endpoint/*, Arxiv_endpoint, N2T_endpoint, GOOGLEAPIS_endpoint*/]; + } + + getXMLParsers() { + return [Arxiv_endpoint]; + } + + parseJSON(pid, endpoint, data) { + console.log("parse JSON", pid, endpoint) + if (endpoint == CROSSREF_endpoint) { + const parser = new Crossref(); + return parser.parse(pid, data['message']); + } else if (endpoint == DATACITE_endpoint) { + const parser = new Datacite(); + return parser.parse(pid, data['data']); + } else if (endpoint == N2T_endpoint) { + const parser = new N2t(); + return parser.parse(pid, data); + } else if (endpoint == GOOGLEAPIS_endpoint) { + const parser = new Googleapis(); + return parser.parse(pid, data.items[0]); + } else if (endpoint == Zenodo_endpoint) { + const parser = new Zenodo(); + return parser.parse(pid, data); + } + } + + async parseXML(pid, endpoint, data) { + console.log("parse XML", pid, endpoint) + if (endpoint == Arxiv_endpoint) { + const parser = new Arxiv(); + return parser.parse(pid, data) + } + } +} + +module.exports = ParserUtils; diff --git a/parsers/Zenodo.js b/parsers/Zenodo.js new file mode 100644 index 0000000..0ecc86b --- /dev/null +++ b/parsers/Zenodo.js @@ -0,0 +1,29 @@ +const Entity = require("../model/Entity"); + +class Zenodo { + parse(pid, item) { + let entity = new Entity(pid); + entity.result.source = "datacite"; + entity.DOI = pid; + entity.id = item.id; + entity.title = item.title; + entity.result.url = item.doi_url; + entity.type = 'publication'; + entity.result.date = item.metadata.publication_date.split("-")[0]; + entity.result.accessRights = "OPEN"; + entity.result.journal = null; + entity.result.description = item.metadata.description; + if (item.metadata.creators) { + entity.result.authors = []; + for (let j = 0; j < item.metadata.creators.length; j++) { + let author = item.metadata.creators[j].name; + entity.result.authors.push(author); + + } + } + return entity; + } + +} + +module.exports = Zenodo; diff --git a/pidResolverService.js b/pidResolverService.js new file mode 100644 index 0000000..9d791d5 --- /dev/null +++ b/pidResolverService.js @@ -0,0 +1,115 @@ +const axios = require('axios'); +var express = require("express"); +var bodyParser = require("body-parser"); + +var PropertiesReader = require('properties-reader'); +var properties = PropertiesReader('./properties.file'); +var app = express(); +var http = null; + +const ParserUtils = require("./parsers/ParserUtils"); +let resolverAPI = properties.get('PIDMR_API_URL') +const url = require('url'); +const utils = new ParserUtils(); + +// Properties +if (properties.get('ssl')) { + http = require("https"); +} else { + http = require("http"); +} + +app.use(bodyParser.json()); +app.use(bodyParser.urlencoded({extended: true})); + + +app.use(function (req, res, next) { + res.header('Access-Control-Allow-Origin', req.headers.origin); + res.header('Access-Control-Allow-Headers', 'Origin, X-Requested-With, Content-Type, Accept, x-xsrf-token'); + res.header('Access-Control-Allow-Credentials', "true"); + res.header('Access-Control-Allow-Methods', 'GET, OPTIONS, POST, DELETE'); + res.header('Access-Control-Max-Age', "1800"); + next(); +}); + +app.get('/:pid', function (req, res) { + const pid = req.params.pid; + let requestUrl = resolverAPI + pid; + console.log("PIDMR url : " + requestUrl); + axios.get(requestUrl) + .then(function (response) { + // handle success + // console.log("status:", response.status, response.data.error); + if (response.status != 200 || response.data.error) { + res.status(response.data.error ? 500 : response.status).json({ + code: response.data.error ? 500 : response.status, + message: response.data.error ? response.data.error : ("An error occurred while resolving pid " + pid + ". ") + }); + return; + } + + const finalUrl = response.request.res.responseUrl; + // Parse the URL to extract the host + const parsedUrl = new url.URL(finalUrl); + const finalHost = parsedUrl.host; + /*if(finalHost.indexOf("pidmr.") != -1 ){ + res.status(500).json({ + + status: response.status, + message: "An error occurred while resolving pid " + pid + (response.data ? " - " + JSON.stringify(response.data) :"") + }); + return; + }*/ + + console.log('Final Redirected URL:', finalUrl); + console.log('Final Host:', finalHost); + if (utils.getSupportedParsers().indexOf(finalHost) == -1) { + console.log(finalHost + ": This endpoint is not supported for parsing"); + res.status(404).json({ + code: 404, + message: "This endpoint is not supported for parsing." + }); + return; + } + if (utils.getXMLParsers().indexOf(finalHost) != -1) { + utils.parseXML(pid, finalHost, response.data).then(entity => { + res.status(200).json(entity); + }) + } else { + let entity = utils.parseJSON(pid, finalHost, response.data) + if (entity) { + res.status(200).json(entity); + } else { + console.log("An error occurred while parsing from " + finalHost + " pid " + pid); + res.status(500).json({ + code: 500, + message: "An error occurred while parsing from " + finalHost + " pid " + pid + }); + } + } + + }) + .catch(function (error) { + console.log(error.response.status, error.response.data.errorCode) + res.status(error.response.data.errorCode ? error.response.data.errorCode : error.response.status).json( + (error.response.data ? error.response.data : { + code: error.response.code, + message: "An error occurred while resolving pid:" + pid + })); + return + }) + .finally(function () { + // always executed + }); + +}); +app.get('/supported-endpoints', function (req, res) { + res.status(200).json(utils.getSupportedParsers()); +}); + +const server = app.listen(properties.get('port'), function () { + console.log("Listening on port %s...", server.address().port); +}); + + + diff --git a/properties.file b/properties.file new file mode 100644 index 0000000..db241e6 --- /dev/null +++ b/properties.file @@ -0,0 +1,4 @@ +ssl = false +port = 4001 +PIDMR_API_URL = https://api.pidmr.devel.argo.grnet.gr/v1/metaresolvers/resolve?pidMode=metadata&redirect=true&pid= +