Merge pull request #68 from hicsail/generate_sbol

Generate SBOL 2.2

demos/server.js

@@ -2,6 +2,8 @@ let express = require('express');
 let app = express();
 let path = require('path');
 let bodyParser = require('body-parser');
+let FormData = require('form-data');
+const Readable = require('stream').Readable;
 let constellation = require('../lib/constellation');
 
 app.use(bodyParser.json());
@@ -50,3 +52,30 @@ app.post('/postSpecs', function(req,res) {
     res.status(405).send(String(error));
   }
 });
+
+app.post('/sendToKnox', function(req,res) {
+
+  let form = new FormData();
+  let sbolDocs = JSON.parse(req.body['sbolDocs[]']);
+
+  for(let sbol of sbolDocs){
+    let stream = new Readable();
+    stream.push(sbol);
+    stream.push(null);
+    form.append('inputSBOLFiles[]', stream, {
+      filename : 'test.xml',
+      contentType: 'application/xml',
+      knownLength: sbol.length
+    }); //extra fields necessary
+  }
+  form.append('outputSpaceID', req.body.designName);
+
+  form.submit('http://localhost:8080/sbol/importCombinatorial', function(error, result) {
+    if (error) {
+      console.log('Error!');
+      res.status(405).send(String(error));
+    } else{
+      res.status(200).send(String(result));
+    }
+  });
+});

demos/static/client.html

@@ -7,7 +7,8 @@
     <link rel="stylesheet" href="css/theme/solarized.css">
     <link rel="stylesheet" href="css/theme/ambiance.css">
 
-
+    <link rel="icon" href="favicon.png" type="image/x-icon" />
+
 
 
     <link href="https://fonts.googleapis.com/css?family=Montserrat:200,300" rel="stylesheet">
@@ -46,7 +47,7 @@ <h3>Constellation</h3>
       <br/>
       </div>
     </div>
-    
+
       <div class="row">
         <div class="col-sm">
           <col-sm-8>
@@ -94,6 +95,10 @@ <h3>Constellation</h3>
         <br/><br/><br/>
         <input id="submitBtn" class="btn" type="button" value="Submit">
       </div>
+      <div class="row">
+        <br/><br/><br/>
+        <input id="knoxBtn" class="btn" type="button" value="Store in Knox">
+      </div>
       <br/>
     </div>
   </body>

demos/static/css/style.css

@@ -31,6 +31,13 @@ textarea {
     font-size: 20px;
 }
 
+#knoxBtn {
+  margin: auto;
+  background-color: white;
+  display: block;
+  font-size: 20px;
+}
+
 h5 {
     color: rgb(120, 120, 120);
     font-family: 'Montserrat', 'monospace';
@@ -122,4 +129,4 @@ input[type="button"]{
 /* .dropdown:hover .dropdown-content {display: block;} */
 
 /* Change the background color of the dropdown button when the dropdown content is shown */
-/* .dropdown:hover .dropbtn {background-color: #30729f;} */
+/* .dropdown:hover .dropbtn {background-color: #30729f;} */

demos/static/js/client.js

@@ -5,7 +5,8 @@ const IMAGESIZE = 30;
 const RADIUS = 7;
 const INTERMEDIATE = 'intermediate';
 
-let nodePointer, linkPointer, simulationPointer, svgPointer, circlePointer, imagePointer, textPointer, width, height;
+let nodePointer, linkPointer, simulationPointer, svgPointer, circlePointer, imagePointer, textPointer, width, height, sbolDocs;
+let designName = 'Constellation';
 
 /* * * * * * */
 /*  DESIGNS  */
@@ -176,9 +177,10 @@ function drawNodes(nodes) {
     .append('svg:image')
     .attr('xlink:href', function(d) {
       switch (d.text) {
+        case 'ribosomeBindingSite':
         case 'promoter':
         case 'terminator':
-        case 'CDS':
+        case 'cds':
         case 'restriction_enzyme_assembly_scar':
         case 'restriction_enzyme_recognition_site':
         case 'protein_stability_element':
@@ -367,24 +369,34 @@ $(document).ready(function() {
 
   editors.specEditor.setOption("theme", THEME);
   editors.catEditor.setOption("theme", THEME);
-  editors.catEditor.setValue('{"promoter": ["BBa_R0040", "BBa_J23100"],\n "ribosomeBindingSite": ["BBa_B0032", "BBa_B0034"], \n"cds": ["BBa_E0040", "BBa_E1010"],\n"spacer": ["BBa_F0010"],\n"terminator": ["BBa_B0010"]}');
+  editors.catEditor.setValue('{"promoter": ["BBa_R0040", "BBa_J23100"],\n "ribosomeBindingSite": ["BBa_B0032", "BBa_B0034"], \n"cds": ["BBa_E0040", "BBa_E1010"],\n"nonCodingRna": ["BBa_F0010"],\n"terminator": ["BBa_B0010"]}');
   editors.designsEditor.setOption("theme", THEME);
 
   $('#demo-option').on('click', function() {
-    editors.specEditor.setValue('one-or-more(one-or-more(promoter then spacer)then cds then \n (zero-or-more \n (spacer or (one-or-more \n (spacer then promoter then spacer) then cds)) then \n (terminator or (terminator then spacer) or (spacer then terminator)))))')
+    editors.specEditor.setValue('one-or-more(one-or-more(promoter then nonCodingRna)then cds then \n (zero-or-more \n (nonCodingRna or (one-or-more \n (nonCodingRna then promoter then nonCodingRna) then cds)) then \n (terminator or (terminator then nonCodingRna) or (nonCodingRna then terminator)))))')
   });
-  
+
 
   $('#debug-option').on('click', function() {
     editors.specEditor.setValue('one-or-more (promoter or ribosomeBindingSite) then (zero-or-more cds) then terminator');
   });
 
-
+  $("#knoxBtn").prop("disabled",true);
+
+  $('#knoxBtn').on('click', function() {
+    $.post('http://localhost:8082/sendToKnox', {
+      'designName': designName,
+      'sbolDocs[]': JSON.stringify(sbolDocs)})
+      .fail((response) => {
+      alert(response.responseText);
+    });
+  });
+
+
   $("#submitBtn").click(function(){
     // Reset UI
     resetDiagram();
     displayDesigns(editors, '');
-    let designName = 'Constellation';
     let maxCycles = 0;
     let numDesigns = 10;
 
@@ -412,8 +424,14 @@ $(document).ready(function() {
       } else {
         displayDesigns(editors, JSON.stringify(data.designs, null, "\t"));
       }
+      sbolDocs = data.sbols;
+      $("#knoxBtn").prop("disabled",false);
     }).fail((response) => {
       alert(response.responseText);
     });
   });
+
+
 });
+
+