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v1.24
+ Now add placeholders in Input Articles table when id was set (e.g. in custom list of IDs or via bookmarklet) but not found via API or an error occurred. + Now truely retrieve All References / All Citations also with Semantic Scholar (S2) by implementing API paging, not just the first 1000 per paper. * Optimized code to use recursive deepFreeze() instead of Object.freeze(), before actually adding article arrays/objects to Vue data tree, vastly increasing performance (especially noticable when All References & All Citations tables contain (tens of) thousands of rows). * Refactored code to improve readability (splitting up the createNewNetwork function in createNewNetwork, retrievedInputArticles, retrievedIncomingSuggestions, retrievedOutgoingSuggestions). * Added a few first end-to-end tests with cypress (more are needed for better maintainability). * Updated examples to also include placeholders.
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‎CHANGELOG

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08.06.2024 v1.24
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+ Now add placeholders in Input Articles table when id was set (e.g. in custom list of IDs or via bookmarklet) but not found via API or an error occurred.
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+ Now truely retrieve All References / All Citations also with Semantic Scholar (S2) by implementing API paging, not just the first 1000 per paper.
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* Optimized code to use recursive deepFreeze() instead of Object.freeze(), before actually adding article arrays/objects to Vue data tree, vastly increasing performance (especially noticable when All References & All Citations tables contain (tens of) thousands of rows).
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* Refactored code to improve readability (splitting up the createNewNetwork function in createNewNetwork, retrievedInputArticles, retrievedIncomingSuggestions, retrievedOutgoingSuggestions).
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* Added a few first end-to-end tests with cypress (more are needed for better maintainability).
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* Updated examples to also include placeholders.
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02.06.2024 v1.23
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+ Support Semantic Scholar API Keys (may occassionally speed up API, request one here: https://www.semanticscholar.org/product/api#api-key).
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* Refactored code to make use of Object.freeze() for large arrays containing articles, increasing performance.
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01.06.2024 v1.22
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+ For Input Articles: Added "Filter References" and "Filter Citations" in article details.
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+ For all articles: Added "Filter Input Articles cited by this" (corresponds to Out-Degree) and "Filter Input Articles citing this" (corresponds to In-Degree).
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+ Added "Too Long Didn't Read" (TLDR) summaries for Semantic Scholar (S2).
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+ Added "Too Long Didn't Read" (TLDR) summaries for Semantic Scholar (S2) (https://www.semanticscholar.org/faq#tldr).
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* Use batch API for Semantic Scholar (S2), which allows much faster retrievals and much fewer API-overloads (error 429). (Unfortunately seems to have a bug, compare below "Known bugs")
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* In case "All references" or "All citations" are retrieved (OA & S2 only): don't de-duplicate them anymore so that numbers in the respective tabs are correct, also when filtering them.
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* Let users choose number of articles per page.

‎README.md

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# Local-Citation-Network
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This web app aims to help scientists with their literature review using metadata from [OpenAlex](https://openalex.org/) (OA), [Semantic Scholar](https://semanticscholar.org/) (S2) and [Crossref](https://crossref.org/) (CR). Academic papers cite one another, thus creating a [citation network (= graph)](https://en.wikipedia.org/wiki/Citation_graph). Each node (= vertex) represents an article and each edge (= link / arrow) represents a reference / citation. Citation graphs are a topic of [bibliometrics, for which other great software exists as well](https://timwoelfle.github.io/Local-Citation-Network#bibliometrics).
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This web app aims to help scientists with their literature review using metadata from [OpenAlex](https://openalex.org/) (OA), [Semantic Scholar](https://semanticscholar.org/) (S2) and [Crossref](https://crossref.org/) (CR). Academic papers cite one another, thus creating a [citation network (= graph)](https://en.wikipedia.org/wiki/Citation_graph). Each node (= vertex) represents an article and each edge (= link / arrow) represents a reference / citation. Citation graphs are a topic of [bibliometrics, for which other great software exists as well](https://localcitationnetwork.github.io/#bibliometrics).
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This web app visualizes subsets of the global citation network that I call 'local citation networks', defined by the references (and citations) of a given set of input articles. In addition, the locally most relevant references (and citations) missing in the set of input articles are suggested for further review.
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‎cypress.config.js

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const { defineConfig } = require("cypress");
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module.exports = defineConfig({
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e2e: {
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setupNodeEvents(on, config) {
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// implement node event listeners here
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},
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},
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});

‎cypress/e2e/check-examples.cy.js

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‎cypress/e2e/load-bookmarklet-examples-from-scratch.cy.js

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describe('Load examples from scratch', () => {
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it('Load example from scratch: Amazon deforestation (S2)', () => {
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cy.visit('./index.html?API=Semantic%20Scholar&source=10.1038/S41558-022-01287-8&listOfIds=10.1073/PNAS.0705414105,10.1146/ANNUREV.ENERGY.28.050302.105532,10.1126/SCIENCE.1146961,10.1038/S41586-021-03629-6,10.1038/NATURE14283,10.1002/2015GB005133,10.1038/S41586-020-2035-0,10.1038/SREP41489,10.1038/35041539,10.1038/NATURE06960,10.1126/SCIADV.AAT2340,10.1126/SCIADV.ABA2949,10.1073/PNAS.1305499111,10.1111/J.1461-0248.2010.01497.X,10.1029/WR015I005P01250,10.1038/NGEO555,10.1111/GCB.13733,10.1038/NGEO1741,10.1016/S0304-3800(96)00034-8,10.1111/J.1365-2486.2009.02157.X,10.1111/J.1365-2486.2008.01626.X,10.1007/BF00384470,10.1038/NATURE08227,10.1038/307321A0,10.1073/PNAS.0802430105,10.1029/2004GL020972,10.1007/S12080-013-0191-7,10.1038/NCLIMATE1143,10.1073/PNAS.0811729106,10.1073/PNAS.2024192118,10.1038/S41558-021-01097-4,10.1038/NCLIMATE3108,10.5194/ESSD-12-177-2020,10.7289/V5ZG6QH9,10.1038/NCLIMATE2581,10.1038/386698A0,10.5067/MODIS/MCD12C1.006,10.1016/J.RSE.2016.02.056,10.1073/PNAS.1617988114,10.1038/SDATA.2015.66,10.1038/NCOMMS15519,10.1073/PNAS.1302584110,10.3389/FEART.2018.00228,10.1029/2018JD029537,10.1002/JOC.6335,10.1126/SCIENCE.1200807,10.1038/S41598-017-05373-2,10.1088/1748-9326/AB9CFF,10.1029/2002JD002670,10.1111/GCB.14413,585bf445ec84c1d9621b2726bdcce9f544b515c8,10.1175/JCLI-D-15-0828.1,10.1038/S41467-018-04881-7,10.1126/SCIENCE.1244693,10.1890/11-0889.1,10.3334/ORNLDAAC/1284,10.5281/ZENODO.5837469&bookmarkletURL=https://www.nature.com/articles/d41586-019-00857-9')
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cy.get('button').contains('Import').click()
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cy.window().its('app.__vue__').should(($vue) => {
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expect($vue.isLoading).to.be.true;
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})
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cy.waitUntil(() => cy.window().then(win => win.app.__vue__.isLoading === false), {
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timeout: 30000,
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interval: 5000
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})
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cy.get('#app').should(($app) => {
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expect($app[0].__vue__.currentGraph.input.length).to.equal(58);
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})
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cy.waitUntil(() => cy.window().then(win => win.app.__vue__.currentGraph.incomingSuggestions !== undefined), {
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timeout: 30000,
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interval: 5000
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})
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cy.get('#app').should(($app) => {
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expect($app[0].__vue__.currentGraph.incomingSuggestions.length).to.equal(10);
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})
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cy.waitUntil(() => cy.window().then(win => win.app.__vue__.currentGraph.outgoingSuggestions !== undefined), {
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timeout: 30000,
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interval: 5000
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})
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cy.get('#app').should(($app) => {
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expect($app[0].__vue__.currentGraph.outgoingSuggestions.length).to.equal(10);
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})
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})
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it('Load example from scratch: Medicine meta-research (OA)', () => {
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cy.visit('./index.html?API=OpenAlex&source=10.1371/JOURNAL.PMED.0020124&listOfIds=pmid:11302887,pmid:15158637,pmid:15158638,pmid:15705458,pmid:11600885,pmid:12642066,pmid:12727138,pmid:15705441,pmid:11159626,pmid:15026468,pmid:10866211,ISBN-13-978-0195083774,pmid:15470193,pmid:6528136,pmid:10694730,pmid:7618077,pmid:10521349,pmid:11323066,pmid:15545678,pmid:10532877,pmid:10584742,pmid:10789670,pmid:10755072,pmid:8015123,pmid:15161896,pmid:9693346,pmid:11405896,pmid:1535110,pmid:15878467,pmid:14602436,pmid:15057290,10.1093/BIOMET/44.1-2.187,10.1093/BIOMET/44.3-4.533,pmid:11434499,10.1056/NEJME048225,pmid:16014596,pmid:14584715&bookmarkletURL=https://pubmed.ncbi.nlm.nih.gov/16060722/')
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cy.get('button').contains('Import').click()
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cy.window().its('app.__vue__').should(($vue) => {
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expect($vue.isLoading).to.be.true;
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})
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cy.waitUntil(() => cy.window().then(win => win.app.__vue__.isLoading === false), {
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timeout: 30000,
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interval: 5000
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})
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cy.get('#app').should(($app) => {
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expect($app[0].__vue__.currentGraph.input.length).to.equal(38);
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})
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cy.waitUntil(() => cy.window().then(win => win.app.__vue__.currentGraph.incomingSuggestions !== undefined), {
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timeout: 30000,
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interval: 5000
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})
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cy.get('#app').should(($app) => {
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expect($app[0].__vue__.currentGraph.incomingSuggestions.length).to.equal(10);
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})
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cy.waitUntil(() => cy.window().then(win => win.app.__vue__.currentGraph.outgoingSuggestions !== undefined), {
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timeout: 30000,
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interval: 5000
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})
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cy.get('#app').should(($app) => {
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expect($app[0].__vue__.currentGraph.outgoingSuggestions.length).to.equal(10);
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})
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})
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it('Load example from scratch: Statistics (OC)', () => {
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cy.visit('./index.html?API=OpenCitations&source=10.1038/D41586-019-00857-9&listOfIds=10.1038/136474B0,10.1016/J.IJCARD.2014.09.205,10.1080/00031305.2019.1583913,10.1080/00031305.2018.1543616,10.1007/0-387-27605-X,10.1177/2515245918771329,10.1093/AJE/KWX259,10.1080/00031305.2018.1527253,10.1511/2014.111.460,10.1080/00031305.2018.1543137&bookmarkletURL=https://www.nature.com/articles/d41586-019-00857-9')
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cy.get('button').contains('Import').click()
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cy.window().its('app.__vue__').should(($vue) => {
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expect($vue.isLoading).to.be.true;
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})
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cy.waitUntil(() => cy.window().then(win => win.app.__vue__.isLoading === false), {
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timeout: 30000,
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interval: 5000
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})
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cy.get('#app').should(($app) => {
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expect($app[0].__vue__.currentGraph.input.length).to.equal(11);
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})
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cy.waitUntil(() => cy.window().then(win => win.app.__vue__.currentGraph.incomingSuggestions !== undefined), {
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timeout: 30000,
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interval: 5000
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})
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cy.get('#app').should(($app) => {
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expect($app[0].__vue__.currentGraph.incomingSuggestions.length).to.equal(10);
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})
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cy.waitUntil(() => cy.window().then(win => win.app.__vue__.currentGraph.outgoingSuggestions !== undefined), {
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timeout: 30000,
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interval: 5000
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})
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cy.get('#app').should(($app) => {
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expect($app[0].__vue__.currentGraph.outgoingSuggestions.length).to.equal(10);
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})
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})
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})

‎cypress/fixtures/example.json

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{
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"name": "Using fixtures to represent data",
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"email": "[email protected]",
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"body": "Fixtures are a great way to mock data for responses to routes"
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}

‎cypress/support/commands.js

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// ***********************************************
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// This example commands.js shows you how to
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// create various custom commands and overwrite
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// existing commands.
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//
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// For more comprehensive examples of custom
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// commands please read more here:
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// https://on.cypress.io/custom-commands
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// ***********************************************
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//
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//
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// -- This is a parent command --
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// Cypress.Commands.add('login', (email, password) => { ... })
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//
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//
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// -- This is a child command --
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// Cypress.Commands.add('drag', { prevSubject: 'element'}, (subject, options) => { ... })
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//
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//
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// -- This is a dual command --
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// Cypress.Commands.add('dismiss', { prevSubject: 'optional'}, (subject, options) => { ... })
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//
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//
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// -- This will overwrite an existing command --
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// Cypress.Commands.overwrite('visit', (originalFn, url, options) => { ... })
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import 'cypress-wait-until';

‎cypress/support/e2e.js

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// ***********************************************************
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// This example support/e2e.js is processed and
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// loaded automatically before your test files.
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//
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// This is a great place to put global configuration and
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// behavior that modifies Cypress.
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//
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// You can change the location of this file or turn off
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// automatically serving support files with the
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// 'supportFile' configuration option.
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//
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// You can read more here:
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// https://on.cypress.io/configuration
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// ***********************************************************
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// Import commands.js using ES2015 syntax:
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import './commands'
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// Alternatively you can use CommonJS syntax:
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// require('./commands')

‎examples.json

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