XspecT 0.1.2__py3-none-any.whl → 0.2.0__py3-none-any.whl

xspect/static/js.js

@@ -1,615 +0,0 @@
-// Sources:
-// https://stackoverflow.com/questions/39479090/read-n-lines-of-a-big-text-file
-// https://flask.palletsprojects.com/en/1.1.x/patterns/jquery/
-// https://stackoverflow.com/questions/6831918/node-js-read-a-text-file-into-an-array-each-line-an-item-in-the-array/12299566
-// https://stackoverflow.com/questions/6831918/node-js-read-a-text-file-into-an-array-each-line-an-item-in-the-array/12299566
-// https://www.freecodecamp.org/news/javascript-from-callbacks-to-async-await-1cc090ddad99/
-// https://developer.mozilla.org/de/docs/Web/JavaScript/Reference/Statements/async_function
-// https://simon-schraeder.de/posts/filereader-async/
-class TextReader {
-    // https://stackoverflow.com/a/55377748/9100798
-    CHUNK_SIZE = 8192000;
-    position = 0;
-    length = 0;
-
-    byteBuffer = new Uint8Array(0);
-
-    lines = [];
-    lineCount = 0;
-    lineIndexTracker = 0;
-
-    fileReader = new FileReader();
-    textDecoder = new TextDecoder(`utf-8`);
-
-    get allCachedLinesAreDispatched() {
-        return !(this.lineIndexTracker < this.lineCount);
-    }
-
-    get blobIsReadInFull() {
-        return !(this.position < this.length);
-    }
-
-    get bufferIsEmpty() {
-        return this.byteBuffer.length === 0;
-    }
-
-    get endOfStream() {
-        return this.blobIsReadInFull && this.allCachedLinesAreDispatched && this.bufferIsEmpty;
-    }
-
-    constructor(blob) {
-        this.blob = blob;
-        this.length = blob.size;
-    }
-
-    blob2arrayBuffer(blob) {
-        return new Promise((resolve, reject) => {
-            this.fileReader.onerror = reject;
-            this.fileReader.onload = () => {
-                resolve(this.fileReader.result);
-            };
-
-            this.fileReader.readAsArrayBuffer(blob);
-        });
-    }
-
-    read(offset, count) {
-        return new Promise(async (resolve, reject) => {
-            if (!Number.isInteger(offset) || !Number.isInteger(count) || count < 1 || offset < 0 || offset > this.length - 1) {
-                resolve(new ArrayBuffer(0));
-                return
-            }
-
-            let endIndex = offset + count;
-
-            if (endIndex > this.length) endIndex = this.length;
-
-            let blobSlice = this.blob.slice(offset, endIndex);
-
-            resolve(await this.blob2arrayBuffer(blobSlice));
-        });
-    }
-
-    readLine() {
-        return new Promise(async (resolve, reject) => {
-
-            if (!this.allCachedLinesAreDispatched) {
-                resolve(this.lines[this.lineIndexTracker++] + `\n`);
-                return;
-            }
-
-            while (!this.blobIsReadInFull) {
-                let arrayBuffer = await this.read(this.position, this.CHUNK_SIZE);
-                this.position += arrayBuffer.byteLength;
-
-                let tempByteBuffer = new Uint8Array(this.byteBuffer.length + arrayBuffer.byteLength);
-                tempByteBuffer.set(this.byteBuffer);
-                tempByteBuffer.set(new Uint8Array(arrayBuffer), this.byteBuffer.length);
-
-                this.byteBuffer = tempByteBuffer;
-
-                let lastIndexOfLineFeedCharacter = this.byteBuffer.lastIndexOf(10); // LINE FEED CHARACTER (\n) IS ONE BYTE LONG IN UTF-8 AND IS 10 IN ITS DECIMAL FORM
-
-                if (lastIndexOfLineFeedCharacter > -1) {
-                    let lines = this.textDecoder.decode(this.byteBuffer).split(`\n`);
-                    this.byteBuffer = this.byteBuffer.slice(lastIndexOfLineFeedCharacter + 1);
-
-                    let firstLine = lines[0];
-
-                    this.lines = lines.slice(1, lines.length - 1);
-                    this.lineCount = this.lines.length;
-                    this.lineIndexTracker = 0;
-
-                    resolve(firstLine + `\n`);
-                    return;
-                }
-            }
-
-            if (!this.bufferIsEmpty) {
-                let line = this.textDecoder.decode(this.byteBuffer);
-                this.byteBuffer = new Uint8Array(0);
-                resolve(line);
-                return;
-            }
-
-            resolve(null);
-        });
-    }
-}
-
-async function extract(Max_reads, checks, ext){
-    let file = document.getElementById("infile").files[0];
-    let textReader = new TextReader(file);
-    var name = document.getElementById('infile').files[0].name;
-    var reads = [];
-    var lineno = 1;
-    var max = Max_reads;
-    while (!textReader.endOfStream) {
-        let line = await textReader.readLine();
-        line = line.replace(/(\r\n|\n|\r)/gm, "");
-        // only using the sequence reads
-        if ((ext === 'fq')||(ext === 'fastq')){
-            if (((lineno)%2==0)&&((lineno)%4!=0)){
-                reads.push(line);
-            }
-        }else{
-            //fasta file: taking all lines
-            if (line.charAt(0) !== '>'){
-                reads.push(line);
-            }
-            else{
-                reads.push('>');
-            }
-        }
-
-        // stopping after n lines
-        if (reads.length == max){
-            break;
-        }
-
-        lineno++;
-    }
-    reads.push(name);
-    result = reads.concat(checks)
-    return result
-}
-
-async function asyncCall(ext) {
-  document.getElementById("extracter").style.display = "block";
-  var max_reads = document.getElementById("reads_max").value;
-  var checks = [];
-
-  // saving checkbox info so the Form can be hidden
-  checks.push(document.getElementById("quick").checked);
-  checks.push(document.getElementById("IC1").checked);
-  checks.push(document.getElementById("IC2").checked);
-  checks.push(document.getElementById("IC3").checked);
-  checks.push(document.getElementById("IC4").checked);
-  checks.push(document.getElementById("IC5").checked);
-  checks.push(document.getElementById("IC6").checked);
-  checks.push(document.getElementById("IC7").checked);
-  checks.push(document.getElementById("IC8").checked);
-  checks.push(document.getElementById("added").checked);
-  checks.push(document.getElementById("OXA").checked);
-  // Deactivating Checkboxes etc while extracting reads
-  document.getElementById("opt").style.display = "none";
-
-  // Complete fileupload (Max 100.000 lines) if fasta file
-  if ((ext == 'fasta') || (ext == 'fna')){
-    max_reads = 100000;
-  }
-  if (((ext == 'fq') || (ext == 'fastq')) && (document.getElementById("OXA").checked)){
-    max_reads = 250000;
-  }
-  // Assigning
-  const result = await extract(max_reads, checks, ext);
-
-  return result;
-}
-
-async function asyncCallspec(ext) {
-  var max_reads = document.getElementById("reads_max").value;
-  var checks = [];
-
-  // saving checkbox info so the Form can be hidden
-  checks.push(document.getElementById("quick").checked);
-  checks.push(document.getElementById("OXA").checked);
-  checks.push(document.getElementById("metagenome").checked);
-  //checks.push(document.getElementById("added").checked);
-  // Deactivating Checkboxes etc while extracting reads
-  //document.getElementById("opt").style.display = "none";
-
-  // Complete fileupload (Max 100.000 lines) if fasta file
-  if ((ext == 'fasta') || (ext == 'fna')){
-    max_reads = 5000000;
-  }
-  //if (((ext == 'fq') || (ext == 'fastq')) && (document.getElementById("OXA").checked)){
-  //  max_reads = 250000;
-  //}
-
-  // Assigning
-  const result = await extract(max_reads, checks, ext);
-
-  return result;
-}
-
-// Source:
-// https://stackoverflow.com/questions/53694709/passing-javascript-array-in-python-flask
-$(document).ready(function () {
-    $("#submit").on("click", async function() {
-        // prevent default send
-        event.preventDefault();
-
-        let file = document.getElementById("infile").files[0];
-        if (!file) {
-            alert('No file selected, please select a .fq file that contains sequence reads');
-            return;
-        }
-        name = document.getElementById('infile').files[0].name;
-        ext = name.split('.').pop();
-
-        if ((ext !== 'fq') && (ext !== 'fasta') && (ext !== 'fna') && (ext !== 'fastq')){
-            alert('Wrong file-type, please select a FASTQ or FASTA/FNA file');
-            return;
-        }
-
-        var number = document.getElementById("reads_max").value;
-
-        // Converting Number field to String, then checking if
-        // only numbers are in string (to prevent entering '.' or '+'
-        var not_int = !(/^\d+$/.test(number.toString()));
-
-        if ((not_int) || (number < 500) || (number > 1000000)){
-            alert('Error: Number of reads must be between 500 and 100.000 and also be a Integer!');
-            return;
-        }
-
-        // Getting Reads
-        var js_data = JSON.stringify(await asyncCall(ext));
-
-        if (js_data == null){
-            alert('Error: This Tool does not support your Browser, please use a modern Browser.');
-            return;
-        }
-
-        $.ajax({
-            url: '/ic',
-            type : 'post',
-            contentType: 'application/json',
-            dataType : 'json',
-            data : js_data,
-            success: function(){
-          //  document.getElementById("content").style.display = "none";
-        //    document.getElementById("loading-display").style.display = "block";
-            window.location.href = '/assign'
-
-         },
-            error: function() {
-              //  document.getElementById("opt").style.display = "block";
-              //  document.getElementById("extracter").style.display = "none";
-              //  document.getElementById("loading-display").style.display = "none";
-                alert("Your Browser does not support this Tool. Please use a valid Browser");
-            }
-        });
-    });
-});
-
-
-
-function myFunc(literature){
-    for (let i = 0; i < literature[0].length; i++) {
-        const test1 = document.createElement("li");
-        const test2 = document.createElement("p");
-        test2.style.lineHeight = "75%";
-        const test3 = document.createElement("a");
-        test3.setAttribute('href',literature[0][i]);
-        test3.innerText = literature[1][i];
-        const test4 = document.createElement("a");
-        test4.className = "btn";
-        test4.setAttribute("data-bs-toggle", "collapse");
-        test4.setAttribute("data-bs-target", "#" + literature[5][i]);
-        const test5 = document.createElement("small");
-        test5.innerText = "[View Details]";
-        const test6_1 = document.createElement("br");
-        const test6_2 = document.createElement("br");
-        const test6_3 = document.createElement("br");
-        //const test6_4 = document.createElement("br");
-        //const test6_5 = document.createElement("br");
-        const test7 = document.createElement("small");
-        const test8 = document.createElement("small");
-        const test9 = document.createElement("font");
-        test9.setAttribute('color',"4d8055");
-        const test6 = document.createElement("br");
-        const test10 = document.createElement("p");
-        test10.className = "collapse";
-        test10.setAttribute('id', literature[5][i]);
-        const test11 = document.createElement("b");
-        test11.innerText = "Abstract:"
-
-        test10.appendChild(test11);
-        test10.appendChild(test6);
-        var newContent = document.createTextNode(literature[2][i]);
-        test10.appendChild(newContent);
-
-        var newContent = document.createTextNode(literature[4][i]);
-        test9.appendChild(newContent);
-        test8.appendChild(test9);
-        var newContent = document.createTextNode(literature[3][i]);
-        test7.appendChild(newContent);
-        test4.appendChild(test5);
-
-        test2.appendChild(test3);
-        test2.appendChild(test4);
-        test2.append(test6_1);
-        test2.appendChild(test7);
-        test2.append(test6_2);
-        test2.append(test6_3);
-      //  test2.append(test6_4);
-        //test2.append(test6_5);
-        test2.appendChild(test8);
-
-        test1.appendChild(test2);
-        test1.appendChild(test10);
-
-        document.getElementById("literature").appendChild(test1);
-      }
-      return literature
-    }
-
-
-$(document).ready(function(){
-  $("#close_popup").on("click", async function() {
-    event.preventDefault();
-    document.getElementById("popup-1").classList.toggle("active");
-  });
-});
-
-
-$(document).ready(function(){
-  $("#tab-3").on("click", async function() {
-    event.preventDefault();
-    if (document.getElementById("popup-2").classList == "popup-2 active") {
-    document.getElementById("popup-2").classList.remove("active");
-}
-  });
-});
-
-
-$(document).ready(function(){
-  $("#Display_options").on("click", async function() {
-    event.preventDefault();
-    document.getElementById("popup-2").classList.toggle("active");
-  });
-});
-
-
-
-$(document).ready(function(){
-        $("#infile").change(function(){
-          name = document.getElementById('infile').files[0].name;
-          if (document.getElementById("popup-1").classList == "popup") {
-          document.getElementById("popup-1").classList.add("active");
-    }
-          ext = name.split('.').pop();
-          if ((ext == 'fq') || (ext == 'fastq')){
-              y = document.getElementById("AspecTinput");
-              y.style.display = "block";
-              }
-          else {
-              y = document.getElementById("AspecTinput");
-              y.style.display = "none";
-          }
-          if ((ext == 'fasta') || (ext == 'fna')){
-              y = document.getElementById("AspecTinput-2");
-              y.style.display = "block";
-              }
-          else {
-              y = document.getElementById("AspecTinput-2");
-              y.style.display = "none";
-          }
-        });
-    });
-
-
-$(document).ready(function(literature) {
-    $("#apply").on("click", async function() {
-      // prevent default send
-      event.preventDefault();
-      document.getElementById("popup-2").classList.toggle("active");
-    //  const clear_literature = document.getElementById("literature");
-    //  clear_literature.innerHTML = '';
-
-      var js_data1 = document.getElementById("literature_max").value;
-      var js_data2 = document.getElementById("id_sort").value;
-      const js_data = JSON.stringify([js_data1, js_data2]);
-
-      $.ajax({
-          url: '/resultsspec',
-          type : 'post',
-          contentType: 'application/json; charset=utf-8',
-          dataType : 'json',
-          data : js_data,
-          success: function(data){
-            const clear_literature = document.getElementById("literature");
-            clear_literature.innerHTML = '';
-            myFunc(data);
-
-         },
-          error: function() {
-            const clear_literature = document.getElementById("literature");
-            clear_literature.innerHTML = '';
-            myFunc(data);
-            }
-      });
-      });
-    });
-
-
-$(document).ready(function () {
-    $("#submitspec").on("click", async function() {
-        // prevent default send
-        event.preventDefault();
-
-        // Zeige den "assigning..."-Text und den Loader an, verstecke den "submit"-Text
-        $("#assignment_text, #assignment_loader").show();
-        $("#submit_text").hide();
-
-        let file = document.getElementById("infile").files[0];
-        if (!file) {
-            alert('No file selected, please select a .fq file that contains sequence reads');
-            return;
-        }
-
-        name = document.getElementById('infile').files[0].name;
-        ext = name.split('.').pop();
-
-        if ((ext !== 'fq') && (ext !== 'fasta') && (ext !== 'fna') && (ext !== 'fastq')){
-            alert('Wrong file-type, please select a FASTQ or FASTA/FNA file');
-            return;
-        }
-
-        test = document.getElementById("genusSelect").value;
-        if (test == "0"){
-            // Keine Option ausgewählt, zeige Popup an
-            alert("No genus selected, please select a genus");
-            return;
-            } 
-
-        var number = document.getElementById("reads_max").value;
-
-        // Converting Number field to String, then checking if
-        // only numbers are in string (to prevent entering '.' or '+'
-        var not_int = !(/^\d+$/.test(number.toString()));
-
-        if ((not_int) || (number < 5000) || (number > 10000000)){
-            alert('Error: Number of reads must be between 5000 and 10.000.000 and also be a Integer!');
-            return;
-        }
-
-        // Getting Reads
-      //  var data = await asyncCallspec(ext)
-      //  var js_data="[";
-      //    for(var indx=0;indx<data.length-1;indx++){
-      //      js_data+=JSON.stringify(data[indx],null,4)+",";
-      //    }
-      //    js_data+=JSON.stringify(data[data.length-1],null,4)+"]";
-        var js_data = JSON.stringify(await asyncCallspec(ext));
-
-        if (js_data == null){
-            alert('Error: This Tool does not support your Browser, please use a modern Browser.');
-            return;
-        }
-
-
-        $.ajax({
-            url: '/species',
-            type : 'post',
-            contentType: 'application/json',
-            dataType : 'json',
-            data : js_data,
-            success: function(){
-            // Zeige den "submit"-Text an, verstecke den Loader und den "assigning..."-Text
-            //$("#submit_text").show();
-            //$("#assignment_loader, #assignment_text").hide();
-            window.location.href = '/assignspec';
-
-         },
-            error: function() {
-                // Zeige den "submit"-Text an, verstecke den Loader und den "assigning..."-Text
-                //$("#submit_text").show();
-                //$("#assignment_loader, #assignment_text").hide();
-                //document.getElementById("opt").style.display = "block";
-                alert("Your Browser does not support this Tool. Please use a valid Browser");
-            }
-        });
-
-    });
-});
-
-
-$(document).ready(function () {
-    // Überwache Änderungen am Select-Element
-    $(".form-select").change(function () {
-        // show loader
-        $("#load_BF").show();
-
-        // Holen Sie sich den ausgewählten Wert
-        var selectedGenus = $(this).val();
-        console.log(selectedGenus);
-        
-
-        // Sende die Informationen an das Python-Backend (AJAX-POST-Anfrage)
-        $.ajax({
-            type: "POST",
-            url: "/change_genus", // Ersetze dies durch den tatsächlichen Endpunkt deines Backends
-            data: { genus: selectedGenus },
-            success: function (response) {
-                $("#load_BF").hide();
-                // Erfolgsaktion (optional)
-                // Aktualisiere den Text mit dem ausgewählten Genus-Wert
-                $("#selectedGenusText").text("Most similar [" + selectedGenus + "] species");
-                console.log("form-select change");
-            },
-            error: function (error) {
-                $("#load_BF").hide();
-                // Fehleraktion (optional)
-                console.error("Fehler beim Senden der Daten an das Backend:", error);
-            }
-        });
-    });
-});
-
-
-$(document).ready(function () {
-    $("#train_new_genus").on("click", async function() {
-        // Verstecke den Start-Text und zeige den Loader an
-        $("#start_text").hide();
-        $("#genus_loader").show();
-        $("#loading_text").show();
-
-        var js_data = $("#genus_text").val();
-
-        $.ajax({
-            url: '/train_new_genus',
-            type: 'post',
-            contentType: 'application/json',
-            data: JSON.stringify({ data: js_data }),
-        }).done(function() {
-            // Verstecke den Loader und zeige den Start-Text an
-            $("#genus_loader").hide();
-            $("#loading_text").hide();
-            $("#genus_text").val("");
-            $("#start_text").show();
-            alert("Genus successfully trained!");
-            // Reload the page to update the genus options
-            location.reload();
-        }).fail(function() {
-            // Verstecke den Loader und zeige den Start-Text an
-            console.error("Fehler beim Trainieren des Genus.");
-            $("#genus_loader").hide();
-            $("#loading_text").hide();
-            $("#genus_text").val("");
-            $("#start_text").show();
-            alert("Some Error occurred, please try again later.");
-        });
-    });
-});
-
-
-$(document).ready(function () {
-    // Lade vorhandene Optionen aus der Datei beim Start
-    loadSavedOptions();
-
-    function loadSavedOptions() {
-        // Lade Optionen aus der Datei
-        $.ajax({
-            url: '/load_saved_options',
-            type: 'get',
-            dataType: 'json',
-            success: function(data) {
-                // Füge die geladenen Optionen zum Select Picker hinzu
-                data.options.forEach(function(option) {
-                    var newOption = new Option(option, option, true, true);
-                    $("#genusSelect").append(newOption);
-                });
-                // Überprüfe, ob die Option mit ID "Preselect" nicht ausgewählt ist
-                var preselect = $("#Preselect");
-                if (preselect.length > 0 && !preselect.prop("selected")) {
-                    // Setze "Preselect" als ausgewählt
-                    preselect.prop("selected", true);
-                    // Aktualisiere den Text mit dem ausgewählten Genus-Wert
-                    $("#selectedGenusText").text("Most similar [Select Genus] species");
-                    console.log("load_saved_options");
-                }
-            },
-            error: function() {
-                console.error("Error while loading saved options.");
-            }
-        });
-    }
-});
-
-
-
-
-