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meteorgeo.js
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meteorgeo.js
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// Write your package code here!
// Variables exported by this module can be imported by other packages and
// applications. See meteorgeo-tests.js for an example of importing.
//import { HTTP } from 'meteor/http';
//export const name = 'meteorgeo';
export function sra (sra,callback){
var id = [];
var id2 = [];
var url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&retMode=JSON&term='+sra;
HTTP.call('GET',url,{timeout: 30000}, function(err,res){
if (err) console.log(err);
else
{
var json = JSON.parse(xmlToJson(res.content));
id.push(json.eSearchResult.IdList.Id)
var url1='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id='+id.join(',');
HTTP.call('GET',url1,{timeout: 30000}, function(err,result){
if (err) console.log(err);
else
{
var json2 = JSON.parse(xmlToJson(result.content))
id2.push(json2.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE)
callback({record:id2[0],id:id[0]});
}
});
//callback({result: json.eSearchResult.IdList.Id})
}
});
}
var xmlToJson = function(xml) {
//console.log($.parseXML(xml));
xml = $.parseXML(xml)
return xml2json(xml,"");
function xml2json(xml, tab) {
var X = {
toObj: function(xml) {
var o = {};
if (xml.nodeType==1) { // element node ..
if (xml.attributes.length) // element with attributes ..
for (var i=0; i<xml.attributes.length; i++)
o[xml.attributes[i].nodeName] = (xml.attributes[i].nodeValue||"").toString();
if (xml.firstChild) { // element has child nodes ..
var textChild=0, cdataChild=0, hasElementChild=false;
for (var n=xml.firstChild; n; n=n.nextSibling) {
if (n.nodeType==1) hasElementChild = true;
else if (n.nodeType==3 && n.nodeValue.match(/[^ \f\n\r\t\v]/)) textChild++; // non-whitespace text
else if (n.nodeType==4) cdataChild++; // cdata section node
}
if (hasElementChild) {
if (textChild < 2 && cdataChild < 2) { // structured element with evtl. a single text or/and cdata node ..
X.removeWhite(xml);
for (var n=xml.firstChild; n; n=n.nextSibling) {
if (n.nodeType == 3) // text node
o["#text"] = X.escape(n.nodeValue);
else if (n.nodeType == 4) // cdata node
o["#cdata"] = X.escape(n.nodeValue);
else if (o[n.nodeName]) { // multiple occurence of element ..
if (o[n.nodeName] instanceof Array)
o[n.nodeName][o[n.nodeName].length] = X.toObj(n);
else
o[n.nodeName] = [o[n.nodeName], X.toObj(n)];
}
else // first occurence of element..
o[n.nodeName] = X.toObj(n);
}
}
else { // mixed content
if (!xml.attributes.length)
o = X.escape(X.innerXml(xml));
else
o["#text"] = X.escape(X.innerXml(xml));
}
}
else if (textChild) { // pure text
if (!xml.attributes.length)
o = X.escape(X.innerXml(xml));
else
o["#text"] = X.escape(X.innerXml(xml));
}
else if (cdataChild) { // cdata
if (cdataChild > 1)
o = X.escape(X.innerXml(xml));
else
for (var n=xml.firstChild; n; n=n.nextSibling)
o["#cdata"] = X.escape(n.nodeValue);
}
}
if (!xml.attributes.length && !xml.firstChild) o = null;
}
else if (xml.nodeType==9) { // document.node
o = X.toObj(xml.documentElement);
}
else
alert("unhandled node type: " + xml.nodeType);
return o;
},
toJson: function(o, name, ind) {
var json = name ? ("\""+name+"\"") : "";
if (o instanceof Array) {
for (var i=0,n=o.length; i<n; i++)
o[i] = X.toJson(o[i], "", ind+"\t");
json += (name?":[":"[") + (o.length > 1 ? ("\n"+ind+"\t"+o.join(",\n"+ind+"\t")+"\n"+ind) : o.join("")) + "]";
}
else if (o == null)
json += (name&&":") + "null";
else if (typeof(o) == "object") {
var arr = [];
for (var m in o)
arr[arr.length] = X.toJson(o[m], m, ind+"\t");
json += (name?":{":"{") + (arr.length > 1 ? ("\n"+ind+"\t"+arr.join(",\n"+ind+"\t")+"\n"+ind) : arr.join("")) + "}";
}
else if (typeof(o) == "string")
json += (name&&":") + "\"" + o.toString() + "\"";
else
json += (name&&":") + o.toString();
return json;
},
innerXml: function(node) {
var s = ""
if ("innerHTML" in node)
s = node.innerHTML;
else {
var asXml = function(n) {
var s = "";
if (n.nodeType == 1) {
s += "<" + n.nodeName;
for (var i=0; i<n.attributes.length;i++)
s += " " + n.attributes[i].nodeName + "=\"" + (n.attributes[i].nodeValue||"").toString() + "\"";
if (n.firstChild) {
s += ">";
for (var c=n.firstChild; c; c=c.nextSibling)
s += asXml(c);
s += "</"+n.nodeName+">";
}
else
s += "/>";
}
else if (n.nodeType == 3)
s += n.nodeValue;
else if (n.nodeType == 4)
s += "<![CDATA[" + n.nodeValue + "]]>";
return s;
};
for (var c=node.firstChild; c; c=c.nextSibling)
s += asXml(c);
}
return s;
},
escape: function(txt) {
return txt.replace(/[\\]/g, "\\\\")
.replace(/[\"]/g, '\\"')
.replace(/[\n]/g, '\\n')
.replace(/[\r]/g, '\\r');
},
removeWhite: function(e) {
e.normalize();
for (var n = e.firstChild; n; ) {
if (n.nodeType == 3) { // text node
if (!n.nodeValue.match(/[^ \f\n\r\t\v]/)) { // pure whitespace text node
var nxt = n.nextSibling;
e.removeChild(n);
n = nxt;
}
else
n = n.nextSibling;
}
else if (n.nodeType == 1) { // element node
X.removeWhite(n);
n = n.nextSibling;
}
else // any other node
n = n.nextSibling;
}
return e;
}
};
if (xml.nodeType == 9) // document node
xml = xml.documentElement;
var json = X.toJson(X.toObj(X.removeWhite(xml)), xml.nodeName, "\t");
return "{\n" + tab + (tab ? json.replace(/\t/g, tab) : json.replace(/\t|\n/g, "")) + "\n}";
}
}