Published
Edited
Nov 4, 2020
fetch_badge(altm.images.small)
function fetch_badge(url) {
return new Promise((resolve, reject) => {
const image = new Image();
image.crossOrigin = "anonymous";
image.src = url;
image.onload = () => resolve(image);
image.onerror = reject;
});
}
altm = d3.json("https://api.altmetric.com/v1/doi/" + dois[0])
d3.json(icite_term)
icite_term = {
let icite = "https://icite.od.nih.gov/api/pubs?pmids=";
return icite + pmid;
}
d3.text(
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&rettype=abstract&retmode=text&id=16239182"
)
{
let pubmed_abstract =
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&rettype=abstract&retmode=text&id=";
d3.json(pubmed_abstract + pmid);
}
pmids = pmid_result.flat()
pmid_result = {
let pmids = [];
uris.forEach(function(d) {
pmids.push(get_pmid(d));
});
return pmids;
}
uris = {
let uris = [];
search_terms.forEach(function(d) {
uris.push(construct_pubmed_uri(d));
});
return uris;
}
search_terms = {
let search_terms = [];
messages.forEach(function(d) {
search_terms.push(make_search_term(d));
});
return search_terms;
}
messages = {
let messages = [];
crossrefs.forEach(function(d) {
messages.push(get_crossref_message(d));
});
return messages;
}
crossrefs = {
let crossrefs = [];
dois.forEach(function(d) {
get_crossref(d).then(d => crossrefs.push(d));
});
return crossrefs;
}
dois = extract_dois_from_data(data)
function construct_pubmed_uri(pubmed_terms) {
let pub_med_base_url =
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmode=json&term=";
let and = "+AND+";
let uri =
pub_med_base_url +
pubmed_terms.title +
"[title]" +
and +
pubmed_terms.author +
"[author+-+first]" +
and +
pubmed_terms.journal +
"[journal]";
return uri;
}
function get_crossref_message(crossref_result) {
let message;
message = crossref_result.message;
return message;
}
typeof test
test = d3.json(uris[0]).then(d => d.esearchresult.idlist[0])
function get_pmid(uri) {
let pmid = [];
d3.json(uri).then(function(d) {
pmid.push(d.esearchresult.idlist[0]);
});
return pmid;
}
function make_search_term(crossref) {
let search_term = {};
search_term.title = encodeURI(crossref.title[0]);
search_term.author = encodeURI(crossref.author[0].family);
search_term.journal = encodeURI(crossref["container-title"][0]);
return search_term;
}
//Retrieve metadata from crossref
async function get_crossref(doi) {
let crossref_base = "https://api.crossref.org/works/";
let result = await d3.json(crossref_base.concat(doi));
return result;
}
function extract_dois_from_data(data) {
// Make array of DOIs from google sheet
let dois = [];
data.forEach(d => dois.push(d.doi));
return dois;
}
data = {
// URL for cors and google-docs spreadsheet, crossref and pubmed!
let cors = "https://cors-anywhere.herokuapp.com/";
let google_sheet_base = "https://docs.oogle.com/spreadsheets/d/e/";
let google_key =
"2PACX-1vT37fqbA5WV6eecRPONprlL_AMoEqAuywkvOhN2gZsBGHE65_1r_aUvml6ljmfOtPGGesOJCmd7zS8z";
let google_output = "/pub?output=csv";
let crossref_base = "https://api.crossref.org/works/";
// csv file as backup in case of corse failure! (Almost always)
let data = d3.csvParse(
await FileAttachment("reference_data - Sheet1.csv").text()
);
// Get csv from google docs!
//let data = d3.csv(cors + google_sheet_base + google_key + google_output);
return data;
}
d3 = require("d3@v5")
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