Difference between revisions of "Template:Heidelberg/safetynet/JS"

Revision as of 12:06, 21 October 2017

console.log($("#hyperreference1"));

function pwncors(site) {

   var xmlSource = site

   var yqlURL = [
       "http://query.yahooapis.com/v1/public/yql",
       "?q=" + encodeURIComponent("select * from xml where url='" + xmlSource + "'"),
       "&format=xml&callback=?"
   ].join("");

 $.getJSON('http://www.whateverorigin.org/get?url=' + encodeURIComponent(site) + '&callback=?', function(data){

console.log(data.contents);

 });
 console.log("done!");

}

pwncors("http://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=put&DATABASE=swissprot&PROGRAM=blastp&QUERY=AAAAAAAAAA");

$("#hyperreference1").on('click', function() {

   var fastain = $('#push_sequence').val();
    var fastaout = "";
   var start = 0;
   //Fastain contains either a FASTA or a blank seqeunce
   if(fastain.startsWith('>')){
       start = 1;
   }
   fastain = fastain.split('\n');
   
   for(var i = start; i < fastain.length; i++){
       fastaout += fastain[i];
   }

   $("#first_input").append('<a target="_blank" href="http://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=put&DATABASE=swissprot&PROGRAM=blastp&QUERY=' + fastaout + '" id="link1" style="display: none">Link to NCBI</a>');
   $('#link1')[0].click();
   

});

$("#hyperreference0").click(function() {

   var fastain = $('#push_sequence').val();
   var fastaout = "";
   var start = 0;
   //Fastain contains either a FASTA or a blank seqeunce
   if(fastain.startsWith('>')){
       start = 1;
   }
   fastain = fastain.split('\n');
   
   for(var i = start; i < fastain.length; i++){
       fastaout += fastain[i];
   }

   pwncors("http://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=put&DATABASE=swissprot&PROGRAM=blastp&QUERY=" + fastaout);

});

$("#hyperreference2").one('click', function() {

   var ncbi_rid = $('#get_sequence').val();
    
   $("#second_input").append('<a target="_blank" href="http://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=get&FORMAT_TYPE=text&RID=' + ncbi_rid + '" id="link2" style="display: none">Link to NCBI Text</a>');
   $("#link2")[0].click();

});

$("#hyperreference3").one('click', function() {

   var ncbi_text_file = $('#get_safety').val();
    
   getShit(ncbi_text_file);

});

function getShit(msg) {

       var child_node = msg;
    

       var regexp = />|Gaps/g;

       var msd = [];
       while (regexp.exec(child_node) !== null) {
           msd.push(regexp.lastIndex);
       }

           
       var regexp_brackets = /\[(.+?)\]/g;
       var organism_match = [];
       var functionalities = [];
       var e_values = [];
       var identities_arr = [];
       var safety_arr = [];  
       var safety_onko = [];
       var ids = [];
       var mbd = [];
       var names = [];
       var GOs = [];
       var k=0;
   
   //Get results names & results_ID
   
   for(var i=0; i<=msd.length-1;i+=1) {
           var substring = child_node.substring(msd[i],msd[i+1]);
           var get_length = substring.search('Length');
           var header = substring.substring(0, get_length);
           var header_split = header.split(" ");
        
           var body = substring.substring(get_length);
           var body_split = body.split(" ");
            var expect = body_split.indexOf('Expect');
           var identities = body_split.indexOf('Identities');
       
       
       
       
       
       
       
       
           var search_recname = header_split.indexOf('RecName:');
           var search_altname = header_split.indexOf('AltName:');
    
       
           if(search_recname!=-1){

               var search_result_ID = header_split[0].substring(0,header_split[search_recname-1].length-2);
               var name = "";
               if(search_altname !=-1) {
                   for(var t=1; t<search_altname-search_recname; t++) {
                       name += header_split[search_recname+t] + " ";
                   }  
                   
               } else {
                   for(var s=1; s<header_split.length-search_recname; s++) {
                       name += header_split[search_recname+s] + " ";
                   }
               }
             
               name = name.replace( /\n/g, " " ).substring(5, name.length); 
               var recname = name.search('RecName:');
               var altname = name.search('AltName:');
              var result_name = "";
               if(recname !=-1) {
                   var next_split = name.split(" ");
            
                   for(var r=0; r<next_split.indexOf('RecName:')-1; r++) {
                       result_name += next_split[r] + " ";
                   }
               } else if(altname !=-1) {
                   result_name = name.substring(0, altname);
               } else {
                   result_name = name;
               }
               var comma = result_name.search(';');
               if(comma != -1) {
                   result_name = result_name.replace( /;/g, " " );
               }
    
              names.push(result_name);
            
               
               ids.push(search_result_ID);
               
               getProtein(search_result_ID);
               
               var expect_value = body_split[expect+2].substring(0,body_split[expect+2].length-1);
               
               e_values.push(expect_value);
               
               var identities_value = body_split[identities+3].substring(1, body_split[identities+3].length-2);
            
               identities_arr.push(identities_value);
               
              
       }
   }
   

setTimeout(function() {

       console.log(organism_match);
       console.log(safety_arr);
       console.log(names);
       var functionalities_safety = [];
       console.log(functionalities.length);
       for(var q=0; q<functionalities.length; q++) {
           var pusher = [1];
           
           functionalities_safety.push(pusher);
       }   
                   
              
       console.log(functionalities);
       console.log(functionalities_safety);
       console.log(ids);
       console.log(e_values);
       console.log(identities_arr);
   createTable(names, organism_match, safety_arr, functionalities, functionalities_safety, ids, identities_arr, e_values, safety_onko);
       
                   }, 1000);
               
 
           
           
           
           

function getProtein (id) { $.ajax({

   type: 'GET',
   url: 'http://www.uniprot.org/uniprot/'+id+'.txt',
   dataType: 'Text',
   async: 'false',
   success: function(result){
       console.log(result);
       var organism_safety = "";
       var _GOs = get_GOs(result);
       
       var GO_string = "";
       for(var x=0; x<2;x++) {
           GO_string = GO_string + Object.values(_GOs[x]) + ", ";
       }
       GO_string = GO_string.substring(0, GO_string.length-2);
      
       if(GO_string.charAt(GO_string.length-2) == ',') {
           GO_string = GO_string.substring(0, GO_string.length-2);
       }
      
       functionalities.push(GO_string);
        organism_match.push(_GOs[2][0]);
       organism_safety = _GOs[2][0].substring(0, _GOs[2][0].indexOf('(')-1);

       getSafety(organism_safety);
       getOnkogene(_GOs[3][0]);
 
       
   },error: function (request, status, error) {
   alert(request.responseText);
   }

});

}

function get_GOs(result) { uniprot_dict_F = {}; uniprot_dict_P = {}; curr_prot_id = ""; curr_GOs_F = []; curr_GOs_P = []; curr_GOs_functions = []; curr_GOs_pathways = []; organisms = []; onkogenes = [];

var lines = result.split("\n"); var organism = ""; var onkogene = ""; for(var a in lines) {

   var fields = lines[a].split(" ").filter(function(e) {return e.trim().length > 0;});
   flag = fields[0];
   if(flag == 'DR' && fields.length >=2){
       var target_line = fields.slice(1,fields.length);
       var target_line = fields.slice(1,fields.length);
       
           if(target_line[0] == 'GO;' && target_line[2].startsWith("F")) {
               curr_GOs_F.push(target_line[1].slice(3, -1));
               var function_name = "";
               for(var i=2; i<target_line.length-1; i++) {
                   function_name += target_line[i] + " ";
               }
               curr_GOs_functions.push(function_name.slice(2, function_name.length-2));
           }
           else if(target_line[0] == 'GO;' && target_line[2].startsWith("P")) {
                curr_GOs_P.push(target_line[1].slice(3, -1));
                var pathway_name = "";
               for(var i=2; i<target_line.length-1; i++) {
                   pathway_name += target_line[i] + " ";
               }
               curr_GOs_pathways.push(pathway_name.slice(2, pathway_name.length-2));
           }
   }
   else if(flag == 'OS') {
       
 
       for(var l=1; l<fields.length; l++) {
           organism += fields[l] + " ";
       }

   }
   else if(flag == 'GN') {
       onkogene = fields[1].substring(5, onkogene.length-1);
   }
   

} organisms.push(organism.substring(0, organism.length-2)); onkogenes.push(onkogene); for(var i=0; i< curr_GOs_F.length; i++) {

  uniprot_dict_F[curr_GOs_F[i]]=curr_GOs_functions[i];  

} for(var i=0; i< curr_GOs_P.length; i++) {

  uniprot_dict_P[curr_GOs_P[i]]=curr_GOs_pathways[i];  

} return [uniprot_dict_F, uniprot_dict_P, organisms, onkogenes]; }

function getSafety(blast_organism) {
     
     $.getJSON('Organisms.json', function(json_organisms) {
         
                  if(Object.keys(json_organisms).indexOf(blast_organism) >=0 ) {
                      var safety_values = Object.values(json_organisms[blast_organism]);
                      
                      safety_arr.push(safety_values);
                      
                  } else {
                      
                      safety_arr.push(['safe', 1]);
                  }
     });
     
               
  } 
   
   function getOnkogene(onkogene) {
       $.getJSON('Organisms.json', function(json_onkogenes) {
         
                  if(Object.keys(json_onkogenes).indexOf(onkogene) >=0 ) {
                      var safety_values = Object.values(json_onkogenes[onkogene]);
                      
                      safety_onko.push(safety_values);
                      
                  } else {
                      
                      safety_onko.push('No Onkogene');
                  }
     });
   }
  // Create Interactive HTML table
           
  
           
  

function createTable(name, organism, organism_safety, functionality, functionality_safety, id, identity, e_value, onkogenes) {

   var table_head = ['Name', 'Organism', 'Group', 'Functionality', 'ID', 'Identity', 'E-Value'];

   var div = document.getElementById('safety_table');
   var table = document.createElement('table');
   var thead = document.createElement('thead')
   var tbody = document.createElement('tbody');
       
   var tr_head = document.createElement('tr');
   for(var i=0; i<7; i++) {
       var td_head = document.createElement('td');
       td_head.append(document.createTextNode(table_head[i]));
       tr_head.appendChild(td_head);
   }
   thead.appendChild(tr_head);

   for(var j=0; j<organism.length; j++) {
       var table_body = [];
       
       table_body[0] = name[j];
       table_body[1] = organism[j];
       table_body[2] = organism_safety[j][0];
       table_body[3] = functionality[j];
  
       table_body[4] = id[j];
       table_body[5] = identity[j];
       table_body[6] = e_value[j];
       table_body[7] = onkogenes[j];
       
       var tr_body = document.createElement('tr');
       for(var k=0; k<8; k++) {
           var td_body = document.createElement('td');
           
           
           
           if(k==3) {
             
               var inner_func = table_body[k].split(',');
               for(var w=0; w<functionality[j].split(',').length; w++) {
                 var tr_inner = document.createElement('tr');
                 var td_inner = document.createElement('td');
                   td_inner.append(document.createTextNode(inner_func[w]));
                   tr_inner.appendChild(td_inner);
                   td_body.appendChild(tr_inner);
               }
               
           } else {
              td_body.append(document.createTextNode(table_body[k]));
           if(organism_safety[j][1]>1 && k==2 ) {
               td_body.style.backgroundColor = 'red';
           }
           else if(organism_safety[j][1]<=1 && k==2){
               td_body.style.backgroundColor = 'green';
           } else {
               // Nothing
               } 
           }
           
           
           
           
            if(functionality_safety[j][0]>1 && k==3 ) {
               td_body.style.backgroundColor = 'red';
           }
           else if(functionality_safety[j][0]<=1 && k==3){
               td_body.style.backgroundColor = 'green';
           } else {
               // Nothing
           }
           tr_body.appendChild(td_body);
       }
       tbody.appendChild(tr_body);
   }   
   
   table.appendChild(thead);
   table.appendChild(tbody);
   table.className = "table";
   div.appendChild(table);

} }