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Ubiquity command more-like-this
CmdUtils.CreateCommand({
//to subscribe to the command, go to http://gist.github.com/15544
//code maintained at http://code.google.com/p/tl-ubiquity-commands/
author: {name: "thomas lemberger", email: "thomas.lemberger@embo.org"},
license: "GPL",
name: "more-like-this",
takes: {"selected text": noun_arb_text},
help: "The command is based on Jane (http://www.biosemantics.org/jane/, Schuemie & Kors (2008) Bioinformatics.24:727). It lists PubMed records related to the selected text (typically an abstract).",
execute: function(directObj) {
var selectedText=directObj.text;
params={//as used on the form submitted from the webpage
text: selectedText,
findauthors: "Find authors"
};
jQuery.ajax(
{type: "POST",
data: params,
url: "http://www.biosemantics.org/jane/suggestions.php",
dataType: "text",
success: function(html){
var newTab = Application.activeWindow.open(Utils.url("http://www.biosemantics.org/jane/suggestions.php"));
newTab.events.addListener("load", function() { newTab.document.body.innerHTML = html });
newTab.focus()
}
}
)
},
preview: function(pblock, directObj) {
var selectedText=directObj.text;
pblock.innerHTML="Querying Jane...";
params={
text: selectedText
};
jQuery.ajax(
{type: "POST",
data: params,
url: "http://biosemantics.org:8080/jane/authors",
dataType: "xml",
success: function(response){
var names=[];
var articles={};
var pmids=[]; pmids[0]=[];//array of arrays
jQuery("results>author",response).each(function(i){
var section=this;
var name=jQuery("author:first",section).text();//author's name is there
if (name){
names.push(name);
pmids[name]=[];
jQuery("evidence>article",section).each(function(j){//goes through articles assoc with author
var article=jQuery(this);
var score=parseInt(article.attr("score"));
var title=jQuery("title",article).text();
var journal=jQuery("journalname",article).text();
var year=jQuery("year",article).text();
var pmid=jQuery("pmid",article).text();
var authors=[];
jQuery("authors>author",article).each(function(){authors.push(jQuery(this).text())});
if (pmid){
pmids[name].push(pmid);
articles[pmid]={au: authors, ti: title, jo: journal, yr: year, score: score};
};
//pblock.innerHTML="Parsing results:<br>"+title;
});
};
});
//after http://news.hping.org/comp.lang.javascript.archive/0867.html
function sortAssoc(aInput){
var aTemp = [];
for (var sKey in aInput) aTemp.push([sKey, aInput[sKey]]);
aTemp.sort(function () {return arguments[0][1].score > arguments[1][1].score});
var aOutput = [];
for (var nIndex = aTemp.length-1; nIndex >=0; nIndex--)
aOutput[aTemp[nIndex][0]] = aTemp[nIndex][1];
return aOutput;
};
var orderedScores=sortAssoc(articles);
const MAX_DISPLAYED_TITLES=12;
var html="";
var style="<style type='text/css'>"+
"span.header {position: relative; bottom:1px;font: small-caps bold 10px arial; padding:2px 2px 0px 2px; background-color:white; color: black} "+
"#headerTitles{cursor:pointer} "+
"#headerTitles, #details {color:black;border: solid 1px white} "+
".displayTitles, .dyn {font: 10px arial; padding:10px 5px; background-color:white;color: #666666} "+
"a {text-decoration: none}"+
"a:hover {text-decoration: underline; color: red} "+
".dyn {font: 12px arial} "+
"dyn li {padding: 3px 0px} "+
"displayTitles li {padding: 2px 0px}"+
"span.stars {color:red;font-style:bold}"+
"</style>";
html+="<p>Similar PubMed abstracts (via <b><a style='color:yellow' href='http://www.biosemantics.org/jane/'>Jane</a></b>):</p>";
html+="<span id='headerTitles' class='header'>Titles</span>";
html+="<div class='displayTitles' id='titles'>";
var count=0;
html+="<ul>";
for (pmid in orderedScores){
var article=articles[pmid];
var s=Math.round(article.score/10);
var stars="";
for (var j=1;j<=s;j++){stars+="*"};
var names=article.au;
var linkedNames="";
for (i in names){
var name=names[i];
linkedNames+="<a href='http://www.ncbi.nlm.nih.gov/pubmed/"+pmids[name].join(",")+"'>"+name.replace(/ /,"&nbsp;")+"</a>, ";
};
linkedNames=linkedNames.replace(/, $/,"");//remove last comma at the end
//var source="<span class='journal'>"+article.jo+" ("+article.yr+")</span>";
html+="<li><a href='http://www.ncbi.nlm.nih.gov/pubmed/"+pmid+"' onmouseover='document.getElementById(\"rel\").innerHTML=unescape(\""+escape(linkedNames)+"\")'>"+article.ti+"</a>&nbsp;<span class='stars'>"+stars+"</span></li>";
count++;
if (count>MAX_DISPLAYED_TITLES) break;
};
html+="</ul>";
html+="</div>";
html+="<br/><br/>";
html+="<span id='details' class='header'>Authors:</span>";
html+="<div id='rel' class='dyn'></div>";
pblock.innerHTML=style+html;
}
}
)
}
})
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