fix ui and add tsv export

index.html

@@ -124,7 +124,7 @@
  return "";
 }
 
- async function fetchENAXML(ENAall ,ENAURL){
+ async function fetchENAXML(ENAall, ENAURL){
  for (const [index, url] of ENAURL.entries()){ 
  try {
  //read xml and json from ENA server
@@ -163,7 +163,7 @@
  document.getElementById("samplesColumn").outerHTML= template(0, "samples");
  document.getElementById("sTemplate").disabled = false;
 
- document.getElementById("rawReadsColumn").outerHTML= templateJSON(1 ,"raw reads");
+ document.getElementById("rawReadsColumn").outerHTML= templateJSON(1, "raw reads");
  document.getElementById("rrTemplate").disabled = false;
 
  document.getElementById("dataAnalysesColumn").outerHTML= template(2, "data analyses");
@@ -172,6 +172,124 @@
  })
  .catch(err => {console.log("fetch of ena xml failed, error is ", err)})
 
+
+function ena2csv(id1){
+ var linkList = document.createElement('div');
+
+ const checklists1 = ENAall[id1].evaluate(
+ "//CHECKLIST",
+ ENAall[id1],
+ null,
+ XPathResult.ANY_TYPE,
+ null,
+ );
+
+ var list1 = checklists1.iterateNext();
+ var number = 0;
+ while (list1 != undefined){
+ var checklistNo = list1.getAttribute("accession");
+ number +=1;
+ console.log("number "+ number +"accession is "+ checklistNo);
+ const list2 = Array.prototype.slice.call(list1.querySelectorAll("FIELD"));
+ var text = "label\tmandatory2\tunits\tfieldType\tfieldValidate\n";
+ for (const [index, element] of Object.entries(list2) ){
+ const label = element.querySelector("LABEL").innerHTML;
+ const mandatory = element.querySelector("MANDATORY").innerHTML;
+ var units;
+ try{
+ units = element.querySelector("UNITS").querySelector("UNIT").innerHTML;
+ }catch(e){units = "no unit"; }
+ var fieldType
+ try{
+ fieldType = element.querySelector("FIELD_TYPE").childNodes[1].nodeName;
+ }catch(e){fieldType = " "; console.log("no field type", e)}
+ var fieldValidate;
+ try{
+ fieldValidate = element.querySelector("FIELD_TYPE").innerHTML.toString();
+ }catch(e){fieldValidate = " "}
+ //console.log("csv will be: "+ label+", "+ mandatory+", "+ units+", "+fieldType+", "+fieldValidate );
+ text += label+"\t"+ mandatory+"\t"+ units+"\t"+fieldType+"\t"+fieldValidate.replace(/(?:\r\n|\r|\n)/g, "").replace(/(?:\r\n|\r|\n)/g, "")+"\n"
+
+
+
+ }
+ var element2 = document.createElement('a');
+ element2.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(text));
+ element2.setAttribute('download', checklistNo+"_validation_info.tsv" );
+
+ element2.style.display = 'none';
+ document.body.appendChild(element2);
+
+ //element2.click();
+ linkList.appendChild(element2);
+ //console.log(linkList);
+ list1 = checklists1.iterateNext();
+ }
+
+ const listArray = Array.prototype.slice.call(linkList.querySelectorAll("a"));
+ //console.log(listArray);
+ //listArray[0].click();
+ for (const [ id, link] of Object.entries(listArray)){
+ //console.log("id "+id+ " "+link)
+ setTimeout(function() {
+ link.click();
+ }, 500+500* parseInt(id));
+
+ }
+
+
+}
+
+
+function enaJSON2csv(id1=1){
+ var linkList = document.createElement('div');
+
+ const checklists1 = ENAall[id1]
+
+ for (const lists of checklists1){
+ var text = "label\tmandatory\tvalueChoice\n";
+ var listName = lists.name;
+ console.log(listName);
+ for (const list1 of lists.fields) 
+ {
+ const label = list1.name;
+ const mandatory = list1.mandatory;
+ const valueChoice = list1.value_choice;
+
+ //console.log("csv will be: "+ label+", "+ mandatory+", "+ units+", "+fieldType+", "+fieldValidate );
+ text += label+"\t"+ mandatory+"\t"+valueChoice+"\n"
+ //console.log(text);
+ }
+ var element2 = document.createElement('a');
+ element2.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(text));
+ element2.setAttribute('download', listName+"_validation_info.tsv" );
+
+ element2.style.display = 'none';
+ document.body.appendChild(element2);
+
+ //element2.click();
+ linkList.appendChild(element2);
+ console.log(linkList);
+ }
+ const listArray = Array.prototype.slice.call(linkList.querySelectorAll("a"));
+ console.log(listArray);
+ //listArray[0].click();
+ for (const [ id, link] of Object.entries(listArray)){
+ console.log("id "+id+ " "+link);
+ setTimeout(function() {
+ link.click();
+ }, 500+500* parseInt(id));
+
+}
+
+ }
+
+
+
+
+
+
+
 // -------- 1. Create and manipulate object in datamodel ----------
 function template(id1, listName){
  //<label for="checkDataList" class="form-label">checklist </label> 
@@ -244,7 +362,6 @@
 
 
 
-
  function checkInput(checkName, id1){
  var selected = []; 
  document.querySelectorAll("input[name="+checkName+"]").forEach((ele)=> {if(ele.checked){ selected.push(ele.value) }} ); 
@@ -322,20 +439,13 @@
  </td>
  </tr>`;
 
-
-
  }
 
-
  }
 
  tableHTML1 += "</tbody> </table>";
  //console.log(tableHTML1);
  document.getElementById("modal"+id1+"body").innerHTML= tableHTML1;
-
-
-
-
  //callback(id1,selected);
  document.getElementById("modal"+id1+"button").click();
  }
@@ -412,8 +522,9 @@
  } 
  list1 = checklists.iterateNext();
  }
+ var link = document.createElement('a');
  window.location.href = "data:text/tab-separated-values," + encodeURIComponent(tsv);
- window.location.href = "data:text/tab-separated-values," + encodeURIComponent(tsvCompare);
+ //window.location.href = "data:text/tab-separated-values," + encodeURIComponent(tsvCompare);
  return tsv;
  }