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-rw-r--r--uploader/static/css/custom-bootstrap.css23
-rw-r--r--uploader/static/css/styles.css161
-rw-r--r--uploader/static/css/two-column-with-separator.css27
-rw-r--r--uploader/static/images/CITGLogo.pngbin0 -> 11962 bytes
-rw-r--r--uploader/static/js/misc.js6
-rw-r--r--uploader/static/js/select_platform.js70
-rw-r--r--uploader/static/js/upload_progress.js97
-rw-r--r--uploader/static/js/upload_samples.js132
-rw-r--r--uploader/static/js/utils.js10
9 files changed, 526 insertions, 0 deletions
diff --git a/uploader/static/css/custom-bootstrap.css b/uploader/static/css/custom-bootstrap.css
new file mode 100644
index 0000000..67f1199
--- /dev/null
+++ b/uploader/static/css/custom-bootstrap.css
@@ -0,0 +1,23 @@
+/** 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/uploader/static/css/styles.css b/uploader/static/css/styles.css
new file mode 100644
index 0000000..f482c1b
--- /dev/null
+++ b/uploader/static/css/styles.css
@@ -0,0 +1,161 @@
+body {
+ margin: 0.7em;
+ box-sizing: border-box;
+ display: grid;
+ grid-template-columns: 1fr 6fr;
+ grid-template-rows: 5em 100%;
+ grid-gap: 20px;
+
+ font-family: Georgia, Garamond, serif;
+ font-style: normal;
+}
+
+#header {
+ grid-column: 1/3;
+ width: 100%;
+ /* background: cyan; */
+ padding-top: 0.5em;
+ border-radius: 0.5em;
+
+ background-color: #336699;
+ border-color: #080808;
+ color: #FFFFFF;
+ background-image: none;
+}
+
+#header .header {
+ font-size: 2em;
+ display: inline-block;
+ text-align: start;
+}
+
+#header .header-nav {
+ display: inline-block;
+ color: #FFFFFF;
+}
+
+#header .header-nav li {
+ border-width: 1px;
+ border-color: #FFFFFF;
+ vertical-align: middle;
+ margin: 0.2em;
+ border-style: solid;
+ border-width: 2px;
+ border-radius: 0.5em;
+ text-align: center;
+}
+
+#header .header-nav a {
+ color: #FFFFFF;
+ text-decoration: none;
+}
+
+#nav-sidebar {
+ grid-column: 1/2;
+ /* background: #e5e5ff; */
+ padding-top: 0.5em;
+ border-radius: 0.5em;
+ font-size: 1.2em;
+}
+
+#main {
+ grid-column: 2/3;
+ width: 100%;
+ /* background: gray; */
+ border-radius: 0.5em;
+}
+
+.pagetitle {
+ padding-top: 0.5em;
+ /* background: pink; */
+ border-radius: 0.5em;
+ /* background-color: #6699CC; */
+ /* background-color: #77AADD; */
+ background-color: #88BBEE;
+}
+
+.pagetitle h1 {
+ text-align: start;
+ text-transform: capitalize;
+ padding-left: 0.25em;
+}
+
+.pagetitle .breadcrumb {
+ background: none;
+}
+
+.pagetitle .breadcrumb .active a {
+ color: #333333;
+}
+
+.pagetitle .breadcrumb a {
+ color: #666666;
+}
+
+.main-content {
+ font-size: 1.275em;
+}
+
+.breadcrumb {
+ text-transform: capitalize;
+}
+
+dd {
+ margin-left: 3em;
+ font-size: 0.88em;
+ padding-bottom: 1em;
+}
+
+input[type="submit"], .btn {
+ text-transform: capitalize;
+}
+
+.card {
+ margin-top: 0.3em;
+ border-width: 1px;
+ border-style: solid;
+ border-radius: 0.3em;
+ border-color: #AAAAAA;
+ padding: 0.5em;
+}
+
+.activemenu {
+ border-style: solid;
+ border-radius: 0.5em;
+ border-color: #AAAAAA;
+ background-color: #EFEFEF;
+}
+
+.danger {
+ color: #A94442;
+ border-color: #DCA7A7;
+ background-color: #F2DEDE;
+}
+
+.heading {
+ border-bottom: solid #EEBB88;
+}
+
+.subheading {
+ padding: 1em 0 0.1em 0.5em;
+ border-bottom: solid #88BBEE;
+}
+
+form {
+ margin-top: 0.3em;
+ background: #E5E5FF;
+ padding: 0.5em;
+ border-radius:0.5em;
+}
+
+form .form-control {
+ background-color: #EAEAFF;
+}
+
+.sidebar-content .card .card-title {
+ font-size: 1.5em;
+}
+
+.sidebar-content .card-text table tbody td:nth-child(1) {
+ font-weight: bolder;
+}
diff --git a/uploader/static/css/two-column-with-separator.css b/uploader/static/css/two-column-with-separator.css
new file mode 100644
index 0000000..b6efd46
--- /dev/null
+++ b/uploader/static/css/two-column-with-separator.css
@@ -0,0 +1,27 @@
+.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/uploader/static/images/CITGLogo.png b/uploader/static/images/CITGLogo.png
new file mode 100644
index 0000000..ae99fed
--- /dev/null
+++ b/uploader/static/images/CITGLogo.png
Binary files differ
diff --git a/uploader/static/js/misc.js b/uploader/static/js/misc.js
new file mode 100644
index 0000000..cf7b39e
--- /dev/null
+++ b/uploader/static/js/misc.js
@@ -0,0 +1,6 @@
+"Miscellaneous functions and event-handlers"
+
+$(".not-implemented").click((event) => {
+ event.preventDefault();
+ alert("This feature is not implemented yet. Please bear with us.");
+});
diff --git a/uploader/static/js/select_platform.js b/uploader/static/js/select_platform.js
new file mode 100644
index 0000000..4fdd865
--- /dev/null
+++ b/uploader/static/js/select_platform.js
@@ -0,0 +1,70 @@
+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/uploader/static/js/upload_progress.js b/uploader/static/js/upload_progress.js
new file mode 100644
index 0000000..9638b36
--- /dev/null
+++ b/uploader/static/js/upload_progress.js
@@ -0,0 +1,97 @@
+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/uploader/static/js/upload_samples.js b/uploader/static/js/upload_samples.js
new file mode 100644
index 0000000..aed536f
--- /dev/null
+++ b/uploader/static/js/upload_samples.js
@@ -0,0 +1,132 @@
+/*
+ * 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/uploader/static/js/utils.js b/uploader/static/js/utils.js
new file mode 100644
index 0000000..045dd47
--- /dev/null
+++ b/uploader/static/js/utils.js
@@ -0,0 +1,10 @@
+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);
+}
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-20 04:24:19 +0000