Rename module: qc_app --> uploader

8 files changed, 0 insertions, 366 deletions

diff --git a/qc_app/static/css/custom-bootstrap.css b/qc_app/static/css/custom-bootstrap.css
deleted file mode 100644
index 67f1199..0000000
--- a/qc_app/static/css/custom-bootstrap.css
+++ /dev/null
@@ -1,23 +0,0 @@
-/** Customize some bootstrap selectors **/
-.btn {
-    text-transform: capitalize;
-}
-
-.navbar-inverse {
-    background-color: #336699;
-    border-color: #080808;
-    color: #FFFFFF;
-    background-image: none;
-}
-
-.navbar-inverse .navbar-nav>li>a {
-    color: #FFFFFF;
-}
-
-.navbar-nav > li > a {
-    padding: 5px;
-}
-
-.navbar {
-    min-height: 30px;
-}
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
deleted file mode 100644
index a88c229..0000000
--- a/qc_app/static/css/styles.css
+++ /dev/null
@@ -1,7 +0,0 @@
-.heading {
-    text-transform: capitalize;
-}
-
-label {
-    text-transform: capitalize;
-}
diff --git a/qc_app/static/css/two-column-with-separator.css b/qc_app/static/css/two-column-with-separator.css
deleted file mode 100644
index b6efd46..0000000
--- a/qc_app/static/css/two-column-with-separator.css
+++ /dev/null
@@ -1,27 +0,0 @@
-.two-column-with-separator {
-    display: grid;
-    grid-template-columns: 9fr 1fr 9fr;
-}
-
-.two-col-sep-col1 {
-    grid-column: 1 / 2;
-}
-
-.two-col-sep-separator {
-    grid-column: 2 / 3;
-    text-align: center;
-    color: #FE3535;
-    font-weight: bolder;
-}
-
-.two-col-sep-col2 {
-    grid-column: 3 / 4;
-}
-
-.two-col-sep-col1, .two-col-sep-col2 {
-    border-style: solid;
-    border-color: #FE3535;
-    border-width: 1px;
-    border-radius: 2em;
-    padding: 2em 3em 2em 3em;
-}
diff --git a/qc_app/static/images/CITGLogo.png b/qc_app/static/images/CITGLogo.png
deleted file mode 100644
index ae99fed..0000000
--- a/qc_app/static/images/CITGLogo.png
+++ /dev/null
diff --git a/qc_app/static/js/select_platform.js b/qc_app/static/js/select_platform.js
deleted file mode 100644
index 4fdd865..0000000
--- a/qc_app/static/js/select_platform.js
+++ /dev/null
@@ -1,70 +0,0 @@
-function radio_column(chip) {
-    col = document.createElement("td");
-    radio = document.createElement("input");
-    radio.setAttribute("type", "radio");
-    radio.setAttribute("name", "genechipid");
-    radio.setAttribute("value", chip["GeneChipId"]);
-    radio.setAttribute("required", "required");
-    col.appendChild(radio);
-    return col;
-}
-
-function setup_genechips(genechip_data) {
-    columns = ["GeneChipId", "GeneChipName"]
-    submit_button = document.querySelector(
-	"#select-platform-form button[type='submit']");
-    elt = document.getElementById(
-	"genechips-table").getElementsByTagName("tbody")[0];
-    remove_children(elt);
-    if((genechip_data === undefined) || genechip_data.length === 0) {
-	row = document.createElement("tr");
-	col = document.createElement("td");
-	col.setAttribute("colspan", "3");
-	text = document.createTextNode("No chips found for selected species");
-	col.appendChild(text);
-	row.appendChild(col);
-	elt.appendChild(row);
-	submit_button.setAttribute("disabled", true);
-	return false;
-    }
-
-    submit_button.removeAttribute("disabled")
-    genechip_data.forEach(chip => {
-	row = document.createElement("tr");
-	row.appendChild(radio_column(chip));
-	columns.forEach(column => {
-	    col = document.createElement("td");
-	    content = document.createTextNode(chip[column]);
-	    col.appendChild(content);
-	    row.appendChild(col);
-	});
-	elt.appendChild(row);
-    });
-}
-
-function genechips() {
-    return JSON.parse(
-	document.getElementById("select-platform-form").getAttribute(
-	    "data-genechips"));
-}
-
-function update_genechips(event) {
-    genec = genechips();
-
-    species_elt = document.getElementById("species");
-
-    if(event.target == species_elt) {
-	setup_genechips(genec[species_elt.value.toLowerCase()]);
-    }
-}
-
-function select_row_radio(row) {
-    radio = row.getElementsByTagName(
-	"td")[0].getElementsByTagName(
-	    "input")[0];
-    if(radio === undefined) {
-	return false;
-    }
-    radio.setAttribute("checked", "checked");
-    return true;
-}
diff --git a/qc_app/static/js/upload_progress.js b/qc_app/static/js/upload_progress.js
deleted file mode 100644
index 9638b36..0000000
--- a/qc_app/static/js/upload_progress.js
+++ /dev/null
@@ -1,97 +0,0 @@
-function make_processing_indicator(elt) {
-    var count = 0;
-    return function() {
-	var message = "Finalising upload and saving file: "
-	if(count > 5) {
-	    count = 1;
-	}
-	for(i = 0; i < count; i++) {
-	    message = message + ".";
-	}
-	elt.innerHTML = message
-	count = count + 1
-    };
-}
-
-function make_progress_updater(file, indicator_elt) {
-    var progress_bar = indicator_elt.querySelector("#progress-bar");
-    var progress_text = indicator_elt.querySelector("#progress-text");
-    var extra_text = indicator_elt.querySelector("#progress-extra-text");
-    return function(event) {
-	if(event.loaded <= file.size) {
-	    var percent = Math.round((event.loaded / file.size) * 100);
-	    progress_bar.value = percent
-	    progress_text.innerHTML = "Uploading: " + percent + "%";
-	    extra_text.setAttribute("class", "hidden")
-	}
-
-	if(event.loaded == event.total) {
-	    progress_bar.value = 100;
-	    progress_text.innerHTML = "Uploaded: 100%";
-	    extra_text.setAttribute("class", null);
-	    intv = setInterval(make_processing_indicator(extra_text), 400);
-	    setTimeout(function() {clearTimeout(intv);}, 20000);
-	}
-    };
-}
-
-function setup_cancel_upload(request, indicator_elt) {
-    document.getElementById("btn-cancel-upload").addEventListener(
-	"click", function(event) {
-	    event.preventDefault();
-	    request.abort();
-	});
-}
-
-function setup_request(file, progress_indicator_elt) {
-    var request = new XMLHttpRequest();
-    var updater = make_progress_updater(file, progress_indicator_elt);
-    request.upload.addEventListener("progress", updater);
-    request.onload = function(event) {
-	document.location.assign(request.responseURL);
-    };
-    setup_cancel_upload(request, progress_indicator_elt)
-    return request;
-}
-
-function selected_filetype(radios) {
-    for(idx = 0; idx < radios.length; idx++) {
-	if(radios[idx].checked) {
-	    return radios[idx].value;
-	}
-    }
-}
-
-function make_data_uploader(setup_formdata) {
-    return function(event) {
-	event.preventDefault();
-
-	var pindicator = document.getElementById("upload-progress-indicator");
-
-	var form = event.target;
-	var the_file = form.querySelector("input[type='file']").files[0];
-	if(the_file === undefined) {
-	    form.querySelector("input[type='file']").parentElement.setAttribute(
-		"class", "invalid-input");
-	    error_elt = form.querySelector("#no-file-error");
-	    if(error_elt !== undefined) {
-		error_elt.setAttribute("style", "display: block;");
-	    }
-	    return false;
-	}
-	var formdata = setup_formdata(form);
-
-	document.getElementById("progress-filename").innerHTML = the_file.name;
-	var request = setup_request(the_file, pindicator);
-	request.open(form.getAttribute("method"), form.getAttribute("action"));
-	request.send(formdata);
-	return false;
-    }
-}
-
-
-function setup_upload_handlers(formid, datauploader) {
-    console.info("Setting up the upload handlers.")
-    upload_form = document.getElementById(formid);
-    upload_form.addEventListener("submit", datauploader);
-}
diff --git a/qc_app/static/js/upload_samples.js b/qc_app/static/js/upload_samples.js
deleted file mode 100644
index aed536f..0000000
--- a/qc_app/static/js/upload_samples.js
+++ /dev/null
@@ -1,132 +0,0 @@
-/*
- * Read the file content and set the `data-preview-content` attribute on the
- * file element
- */
-function read_first_n_lines(event,
-			    fileelement,
-			    numlines,
-			    firstlineheading = true) {
-    var thefile = fileelement.files[0];
-    var reader = new FileReader();
-    reader.addEventListener("load", (event) => {
-	var filecontent = event.target.result.split(
-	    "\n").slice(
-		0, (numlines + (firstlineheading ? 1 : 0))).map(
-		    (line) => {return line.trim("\r");});
-	fileelement.setAttribute(
-	    "data-preview-content", JSON.stringify(filecontent));
-	display_preview(event);
-    })
-    reader.readAsText(thefile);
-}
-
-function remove_rows(preview_table) {
-    var table_body = preview_table.getElementsByTagName("tbody")[0];
-    while(table_body.children.length > 0) {
-	table_body.removeChild(table_body.children.item(0));
-    }
-}
-
-/*
- * Display error row
- */
-function display_error_row(preview_table, error_message) {
-    remove_rows(preview_table);
-    row = document.createElement("tr");
-    cell = document.createElement("td");
-    cell.setAttribute("colspan", 4);
-    cell.innerHTML = error_message;
-    row.appendChild(cell);
-    preview_table.getElementsByTagName("tbody")[0].appendChild(row);
-}
-
-function strip(str, chars) {
-    var end = str.length;
-    var start = 0
-    for(var j = str.length; j > 0; j--) {
-	if(!chars.includes(str[j - 1])) {
-	    break;
-	}
-	end = end - 1;
-    }
-    for(var i = 0; i < end; i++) {
-	if(!chars.includes(str[i])) {
-	    break;
-	}
-	start = start + 1;
-    }
-    return str.slice(start, end);
-}
-
-function process_preview_data(preview_data, separator, delimiter) {
-    return preview_data.map((line) => {
-	return line.split(separator).map((field) => {
-	    return strip(field, delimiter);
-	});
-    });
-}
-
-function render_preview(preview_table, preview_data) {
-    remove_rows(preview_table);
-    var table_body = preview_table.getElementsByTagName("tbody")[0];
-    preview_data.forEach((line) => {
-	var row = document.createElement("tr");
-	line.forEach((field) => {
-	    var cell = document.createElement("td");
-	    cell.innerHTML = field;
-	    row.appendChild(cell);
-	});
-	table_body.appendChild(row);
-    });
-}
-
-/*
- * Display a preview of the data, relying on the user's selection.
- */
-function display_preview(event) {
-    var data_preview_table = document.getElementById("tbl:samples-preview");
-    remove_rows(data_preview_table);
-
-    var separator = document.getElementById("select:separator").value;
-    if(separator === "other") {
-	separator = document.getElementById("txt:separator").value;
-    }
-    if(separator == "") {
-	display_error_row(data_preview_table, "Please provide a separator.");
-	return false;
-    }
-
-    var delimiter = document.getElementById("txt:delimiter").value;
-
-    var firstlineheading = document.getElementById("chk:heading").checked;
-
-    var fileelement = document.getElementById("file:samples");
-    var preview_data = JSON.parse(
-	fileelement.getAttribute("data-preview-content") || "[]");
-    if(preview_data.length == 0) {
-	display_error_row(
-	    data_preview_table,
-	    "No file data to preview. Check that file is provided.");
-    }
-
-    render_preview(data_preview_table, process_preview_data(
-	preview_data.slice(0 + (firstlineheading ? 1 : 0)),
-	separator,
-	delimiter));
-}
-
-document.getElementById("chk:heading").addEventListener(
-    "change", display_preview);
-document.getElementById("select:separator").addEventListener(
-    "change", display_preview);
-document.getElementById("txt:separator").addEventListener(
-    "keyup", display_preview);
-document.getElementById("txt:delimiter").addEventListener(
-    "keyup", display_preview);
-document.getElementById("file:samples").addEventListener(
-    "change", (event) => {
-	read_first_n_lines(event,
-			   document.getElementById("file:samples"),
-			   30,
-			   document.getElementById("chk:heading").checked);
-    });
diff --git a/qc_app/static/js/utils.js b/qc_app/static/js/utils.js
deleted file mode 100644
index 045dd47..0000000
--- a/qc_app/static/js/utils.js
+++ /dev/null
@@ -1,10 +0,0 @@
-function remove_children(element) {
-    Array.from(element.children).forEach(child => {
-	element.removeChild(child);
-    });
-}
-
-function trigger_change_event(element) {
-    evt = new Event("change");
-    element.dispatchEvent(evt);
-}