Created
May 3, 2019 01:22
-
-
Save slowkow/0bfb2a36da0af0d496eb0549f4e655b4 to your computer and use it in GitHub Desktop.
Get an HTML list of PubMed publications
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <!DOCTYPE html> | |
| <body> | |
| <!-- Copied directly from http://www.ephys.org/ by Damian J Williams --> | |
| <input placeholder="Kamil Slowikowski" name="name"/> | |
| <p id="demo"></p> | |
| <script> | |
| //From "http://www.alexhadik.com/blog/2014/6/12/create-pubmed-citations-automatically-using-pubmed-api" adapted from reply to blog post by Les Ansley | |
| var HTMLpublication = '%authors% (%date%) \'%title%\' <i>%journal%\</i>,<b>%volume%</b> %issue%%pages%PMID:<a href="%data%"target="_blank"> %PMID% </a></br></br>' //Formats output | |
| var publications, idStringList; | |
| var pubmedSearchAPI = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"; | |
| var pubmedSummaryAPI = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?"; | |
| var database = "db=pubmed"; | |
| var returnmode = "&retmode=json"; | |
| var returnmax = "&retmax=100"; | |
| var searchterm = "&term=Kamil Slowikowski[Author]"; | |
| var returntype = "&rettype=abstract"; | |
| var idURL = pubmedSearchAPI + database + returnmode + returnmax + searchterm | |
| console.log(idURL); | |
| var getPubmed = function(url) { //passed url | |
| return new Promise(function(resolve, reject) { | |
| var xhr = new XMLHttpRequest(); | |
| xhr.open('get', url, true); | |
| xhr.responseType = 'json'; | |
| xhr.onload = function() { | |
| var status = xhr.status; | |
| if (status == 200) { //status 200 signifies OK (http://www.w3schools.com/ajax/ajax_xmlhttprequest_onreadystatechange.asp) | |
| resolve(xhr.response); | |
| } else { | |
| reject(status); | |
| } | |
| }; | |
| xhr.send(); | |
| }); | |
| }; | |
| const input = document.querySelector('input'); | |
| const log = document.getElementById('demo'); | |
| // input.addEventListener('input', updateValue); | |
| input.onchange = updateValue; | |
| function updateValue(e) { | |
| searchterm = '&term=' + e.srcElement.value + '[Author]'; | |
| idURL = pubmedSearchAPI + database + returnmode + returnmax + searchterm | |
| console.log(idURL); | |
| getPubmed(idURL).then(function(data) { | |
| var idList = data.esearchresult.idlist; | |
| idStringList = idList.toString(); //converts the idlist to a string to be appended to the search url | |
| idStringList = '&id=' + idStringList; | |
| summaryURL = pubmedSummaryAPI + database + returnmode + returntype + idStringList; | |
| getPubmed(summaryURL).then(function(summary) { | |
| publications = formatReferences(summary); | |
| console.log(publications); | |
| document.getElementById("demo").innerHTML = publications; | |
| }, function(status) { | |
| publications = 'Something went wrong getting the ids.'; | |
| }); | |
| }, function(status) { | |
| publications = 'Something went wrong getting the ids.'; | |
| }); | |
| } | |
| function formatReferences(summary) { | |
| var publicationList = ''; | |
| for (refs in summary.result) { | |
| if (refs !== 'uids') { | |
| var authors = ''; | |
| var publication = ''; | |
| var authorCount = ((summary.result[refs].authors).length); | |
| var i = 0; | |
| while (i < authorCount - 1) { | |
| authors += summary.result[refs].authors[i].name + ', '; | |
| i++; | |
| } | |
| publication = HTMLpublication.replace('%data%', 'http://www.ncbi.nlm.nih.gov/pubmed/' + refs); | |
| authors += summary.result[refs].lastauthor; | |
| publication = publication.replace('%authors%', authors); | |
| publication = publication.replace('%title%', summary.result[refs].title); | |
| publication = publication.replace('%journal%', summary.result[refs].source); | |
| publication = publication.replace('%PMID%', summary.result[refs].uid); | |
| //Alter formatting if article is In Press | |
| if (summary.result[refs].volume !== '') { | |
| publication = publication.replace('%volume%', ' ' + summary.result[refs].volume); | |
| publication = publication.replace('%issue%', '(' + summary.result[refs].issue + ')'); | |
| publication = publication.replace('%pages%', ': ' + summary.result[refs].pages + '. '); | |
| var date = summary.result[refs].pubdate.slice(0, 4); | |
| publication = publication.replace('%date%', date + ''); | |
| } else { | |
| publication = publication.replace('%volume%', ' In Press'); | |
| publication = publication.replace('%issue%', '.'); | |
| publication = publication.replace('%pages%', ''); | |
| publication = publication.replace('%date%', ''); | |
| } | |
| publicationList = publication + publicationList; | |
| } | |
| } | |
| return (publicationList); | |
| } | |
| </script> | |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment