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debugging callback
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@kermitt2
kermitt2 committed May 5, 2019
1 parent 3491b87 commit bfffebe
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6 changes: 6 additions & 0 deletions Readme.md
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Expand Up @@ -65,6 +65,12 @@ This will update the TEI header of the full text enrichment, generate the bibref

The ISTEX full text resources (all enrichment files and updated full text file) are available under `~/tmp/out`.

- match the extracted bibliographical references against CrossRef metadata using biblio-glutton and inject the DOI, ISTEX ID, PMID, PMC ID and ISTEX ark into the successfully matched bibliographical references:

> node inject-doi -in ~/tmp/selectedIstexIds.txt -out ~/tmp/out
This will update the TEI full text enrichment files and the bibref enrichment files. Be sure to use the same output (`~/tmp/out`) for having all the resources under the same hierarchy.


## Output

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135 changes: 91 additions & 44 deletions inject-doi.js
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Expand Up @@ -79,7 +79,9 @@ function matchDOI(options, istexId, callback) {
ind2 = refbibsSegment.indexOf("</biblStruct>", base2);
if ( (ind1 != -1) && (ind2 != -1) ) {
// here is the XML segment corresponding to an extracted citation
var citationSegment = refbibsSegment.substring(ind1, ind2+13);
var citationSegmentOriginal = refbibsSegment.substring(ind1, ind2+13);
var citationSegment = citationSegmentOriginal;
//console.log(citationSegment);

// if DOI is already there, we simply use it to get the ark

Expand Down Expand Up @@ -108,66 +110,111 @@ function matchDOI(options, istexId, callback) {
raw = raw.replace(/\n/g, " ");
raw = raw.replace(/\s\s+/g, ' ');
raw = raw.replace(/\s, /g, ', ');
raw = raw.trim();

console.log('raw: ' + raw);

console.log(citationSegment);
const doc = new dom().parseFromString(citationSegment);
const doc = new dom().parseFromString(citationSegmentOriginal);
//console.log(doc);
const select = xpath.useNamespaces({});

// try to get the title and first author last name
var title = select('//title[@level="a"]/text()', doc)[0];
if (!title)
title = select('//title[@level="m"]/text()', doc)[0];
console.log(title);
//console.log(title);

var firstAuthor = select('//surname[0]', doc);

// try to get journal, volume, first page
var jtitle = select('//title[@level="j"]', doc);
var volume = select('//biblScope[@unit="volume"]', doc);
var firstPage = select('//biblScope[@unit="page"][@from]', doc);
console.log(jtitle);
console.log(volume);
console.log(firstPage);

var service_host = options.glutton_host ;
var jtitle = select('//title[@level="j"]/text()', doc);
var volume = select('//biblScope[@unit="volume"]/text()', doc);
var firstPage = select('//biblScope[@unit="page"]/@from', doc);

var date = select('string(//date/@when)', doc);
if (date && date.length>3) {
date = date.substring(0,4);
raw += ", " + date;
}

//console.log('raw: ' + raw);

//console.log(jtitle);
//console.log(volume);
//console.log(firstPage);

var service_host = options.glutton_host;
if (options.glutton_port) {
service_host += options.glutton_port;
service_host += ":"+options.glutton_port;
}
var endpoints = [
{ host: service_host, path: "service/lookup?biblio="+encodeURIComponent(raw) },
{ host: service_host, path: "service/lookup?atitle="+encodeURIComponent(title)+
"&firstAuthor="+encodeURIComponent(firstAuthor) },
{ host: service_host, path: "service/lookup?jtitle="+encodeURIComponent(jtitle)+
"&volume="+encodeURIComponent(volume) + "&firstPage="+encodeURIComponent(firstPage) }
];

// parallel calls
async.parallel(endpoints, http.get, function(results) {
for (var response in results) {
if (response.status == 200) {
// get the DOI and ark
if (response.body) {
var resDOI = response.body.DOI;
var resArk = response.body.ark;
// inject in citationSegment
if (resDOI) {
var injection = '<idno type="DOI">'+resDOI+'</idno>';
if (resArk) {
injection += '\n<idno type="ark">'+resArk+'</idno>';
}

}
}
}
}
});

// create glutton query
var queryPath = "service/lookup?biblio="+encodeURIComponent(raw) ;
/*if (title && title.length > 0)
queryPath += "&atitle="+encodeURIComponent(title);
if (firstAuthor && firstAuthor.length >0)
queryPath += "&firstAuthor="+encodeURIComponent(firstAuthor);
if (jtitle && jtitle.length > 0)
queryPath += "&jtitle="+encodeURIComponent(jtitle);
if (volume && volume.length > 0)
queryPath += "&volume="+encodeURIComponent(volume);
if (firstPage && firstPage.length >0)
queryPath += "&firstPage="+encodeURIComponent(firstPage);
*/

var query_options = {
host: options.glutton_host,
port: options.glutton_port,
path: queryPath,
method: 'GET'
};

console.log('http://' + service_host + "/" + queryPath);

//var request = http.request(query_options, function(res) {
http.get('http://' + service_host + "/" + queryPath, (res) => {
//console.log('STATUS: ' + res.statusCode);
//console.log('HEADERS: ' + JSON.stringify(res.headers));
var gluttonBody = '';
res.on('data', function(chunk) {
gluttonBody += chunk;
});
res.on('end', function() {
//console.log(gluttonBody);
gluttonBody = JSON.parse(gluttonBody)
if (res.statusCode == 200) {
// get the DOI and ark
if (gluttonBody) {
var resDOI = gluttonBody.DOI;
var resArk = gluttonBody.ark;
var istexId = gluttonBody.istexId;
// inject in citationSegment
var injection = '';
if (resDOI) {
injection += '\t<idno type="DOI">'+resDOI+'</idno>';
}
if (resArk) {
injection += '\n\t\t<idno type="ark">'+resArk+'</idno>';
}
if (istexId) {
injection += '\n\t\t<idno type="istexId">'+istexId+'</idno>';
}
//console.log(injection);
// inject additional identifiers in the TEI document
citationSegmentOriginal =
citationSegmentOriginal.replace("</analytic>",
injection + "\n\t</analytic>");
console.log(citationSegmentOriginal);
}
}

});
}).on('error', function(e) {
console.log("Got error: " + e.message);
});

}
}
}
callback();

});
}

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