fixing bugs, changing gene list previews. refactoring

IGS · Nov 30, 2023 · 0cf9ca4 · 0cf9ca4
1 parent 417ef27
commit 0cf9ca4
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Showing 13 changed files with 404 additions and 392 deletions.
diff --git a/www/cgi/get_unweighted_gene_cart_preview.cgi b/www/cgi/get_unweighted_gene_cart_preview.cgi
@@ -0,0 +1,59 @@
+#!/opt/bin/python3
+
+"""
+
+"""
+
+import cgi
+import json
+import os
+import string
+import sys
+
+lib_path = os.path.abspath(os.path.join('..', '..', 'lib'))
+sys.path.append(lib_path)
+import geardb
+
+def main():
+    print('Content-Type: application/json\n\n')
+
+    form = cgi.FieldStorage()
+    share_id = form.getvalue('share_id')
+    valid_chars = "%s%s" % (string.ascii_letters, string.digits)
+    share_id = ''.join(c for c in share_id if c in valid_chars)
+
+    result = { 'success': 0 }
+
+    # Get genes from the gene cart
+    if not share_id:
+        result['message'] = 'No share ID provided'
+        result["success"] = 0
+        print(json.dumps(result))
+        return
+
+    gene_cart = geardb.get_gene_cart_by_share_id(share_id)
+    if not gene_cart:
+        result['message'] = 'Invalid share ID'
+        result["success"] = 0
+        print(json.dumps(result))
+        return
+
+    genes = gene_cart.genes
+    organism_id = gene_cart.organism_id
+
+    # Get the Gene objects for this gene cart
+    gene_collection = geardb.GeneCollection()
+    gene_collection.get_by_gene_symbol(gene_symbol=' '.join(genes), organism_id=organism_id, exact=True)
+
+
+    gene_dict = {} # Key is ensembl ID, value is dict of gene symbol and product.
+    # Create an dict of gene symbol to gene object
+    for gene in gene_collection.genes:
+        gene_dict[gene.ensembl_id] = { 'gene_symbol': gene.gene_symbol, 'product': gene.product }
+
+    result["gene_info"] = gene_dict
+    result['success'] = 1
+    print(json.dumps(result))
+
+if __name__ == '__main__':
+    main()
diff --git a/www/cgi/get_weighted_gene_cart_preview.cgi b/www/cgi/get_weighted_gene_cart_preview.cgi
@@ -6,13 +6,13 @@
 
 import cgi
 import json
+import os
 import string
 import sys
 
 import pandas as pd
 import scanpy as sc
 
-import os, sys
 
 gene_cart_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', 'carts')
 ROWS_TO_SHOW = 5
@@ -35,21 +35,21 @@ def main():
     except OSError as e:
         message = "Unable to open file for genecart {}".format(share_id)
         success = -1
-        result = { 'preview_json':[], 'success': success, 'message': message }
+        result = { 'preview_json':[], 'num_genes':-1, 'weights':[], 'success': success, 'message': message }
         print(json.dump(result))
         sys.exit()
 
     adata.var_names_make_unique()
 
-    df1 = pd.DataFrame(adata.X, adata.obs.index, adata.var.index).transpose()
+    # df1 = pd.DataFrame(adata.X, adata.obs.index, adata.var.index).transpose()
     # Merge df1 into adata.var, using the index of df1 as the index of adata.var
     # Reset index so that all column levels are the same.  Numerical index is later dropped for displaying.
-    df = pd.concat([adata.var, df1], axis=1).reset_index()[:ROWS_TO_SHOW]
+    #df = pd.concat([adata.var, df1], axis=1).reset_index()[:ROWS_TO_SHOW]
 
     result["num_genes"] = len(adata.var)
     result["weights"] = adata.obs.index.tolist()
 
-    result['preview_json'] = df.to_html(classes=['weighted-list'], index=False)
+    #result['preview_json'] = df.to_html(classes=['weighted-list'], index=False)
     result['success'] = 1
     print(json.dumps(result))
 

diff --git a/www/css/common.v2.css b/www/css/common.v2.css
@@ -87,15 +87,15 @@ p.menu-label {
     background-color: lightgrey;
 }
 
-.select.is-success select, .input.is-success{
+.select.is-success select, .input.is-success, .textarea.is-success{
     border-color: #539400;  /* overwrite default success for .select */
 }
 
 .select.is-success:not(:hover)::after {
     border-color: #539400; /* overwrite default success for .select */
 }
 
-.select.is-danger select, .input.is-danger{
+.select.is-danger select, .input.is-danger, .textarea.is-danger{
     border-color: #942400; /* overwrite default success for .select */
 }
 
@@ -106,3 +106,11 @@ p.menu-label {
 .js-tree {
     max-height: 200px;  /* a) addresses long lists and b) addresses https://github.com/mar10/wunderbaum/issues/57 */
 }
+
+/* Toast-style notifications for actual alerts */
+.notification.js-toast {
+    position: fixed;
+    top: 30px;
+    right: 10px;
+    z-index:999;
+}
diff --git a/www/css/compare_datasets.v2.css b/www/css/compare_datasets.v2.css
@@ -56,14 +56,6 @@ input[type=number] {
     height:92vh;
 }
 
-/* Toast-style notifications for actual alerts */
-.notification.js-toast {
-    position: fixed;
-    top: 30px;
-    right: 10px;
-    z-index:999;
-}
-
 /* override loader from the themed CSS */
 .button.is-loading::after, .loader, .select.is-loading::after, .control.is-loading::after {
     border-color: black;

diff --git a/www/css/curator_common.css b/www/css/curator_common.css
@@ -29,14 +29,6 @@
     background-color: lightgrey;
 }
 
-/* Toast-style notifications for actual alerts */
-.notification.js-toast {
-    position: fixed;
-    top: 30px;
-    right: 10px;
-    z-index:999;
-}
-
 #post_plot_adjustments select {
     width: 100px;
     white-space: nowrap;

diff --git a/www/css/gene_collection_manager.css b/www/css/gene_collection_manager.css
@@ -7,7 +7,6 @@
 }
 
 hr.gc-list-element-divider {
-    width: 90%;
     background-color: #000000;
     margin-left: auto;
     margin-right: auto;
@@ -20,14 +19,6 @@ hr.gc-list-element-divider {
     border-radius: 4px;
 }
 
-/* Toast-style notifications for actual alerts */
-.notification.js-toast {
-    position: fixed;
-    top: 30px;
-    right: 10px;
-    z-index:999;
-}
-
 /* CSS for Floating UI components */
 
 #delete_gc_popover {

diff --git a/www/css/user_profile.v2.css b/www/css/user_profile.v2.css
@@ -23,11 +23,3 @@ img#submit_wait_indicator {
     width: 30px;
     margin-right: 10px;
 }
-
-/* Toast-style notifications for actual alerts */
-.notification.js-toast {
-    position: fixed;
-    top: 30px;
-    right: 10px;
-    z-index:999;
-}
diff --git a/www/gene_collection_manager.html b/www/gene_collection_manager.html
@@ -159,7 +159,7 @@
                                     </header>
                                     <div class="card-content is-flex-grow-1">
                                         <div class="content has-text-dark">
-                                            Upload a gene list with associated weights, for example from a principal component analysis
+                                            Upload a gene list with associated weights. For example, from a dataset's principal component analysis
                                         </div>
                                     </div>
                                     <footer class="card-footer">
@@ -178,7 +178,7 @@
                                     <div class="card-content is-flex-grow-1">
                                         <div class="content has-text-dark">
                                             <p class="is-subtitle has-text-weight-semibold">COMING SOON</p>
-                                            Upload a file containing a list of genes and associated labels, for example marker genes for cell types
+                                            Upload a file containing a list of genes and associated labels. For example, marker genes for cell types
                                         </div>
                                     </div>
                                     <footer class="card-footer">
@@ -279,7 +279,7 @@
                                         </div>
                                         <div class="field-body">
                                             <div class="buttons has-addons" role="group" aria-label="Gene cart list view preference">
-                                                <button type="button" id="btn_list_view_compact" class="button is-small is-dark active" aria-label="Compact view" data-toggle="popover" data-toggle="tooltip" data-placement="top" title="Compact view">
+                                                <button type="button" id="btn_list_view_compact" class="button is-small is-gear-bg-secondary" aria-label="Compact view" data-toggle="popover" data-toggle="tooltip" data-placement="top" title="Compact view">
                                                     <span class="icon is-small">
                                                         <i class="mdi mdi-format-list-bulleted"></i>
                                                     </span>

diff --git a/www/js/common.v2.js b/www/js/common.v2.js
@@ -357,6 +357,56 @@ const convertToFormData = (object) => {
     return formData;
 }
 
+/**
+ * Creates a toast notification with the given message and level class.
+ * @param {string} msg - The message to display in the toast notification.
+ * @param {string} [levelClass="is-danger"] - The level class for the toast notification. Defaults to "is-danger".
+ */
+const createToast = (msg, levelClass="is-danger") => {
+    const template = `
+    <div class="notification js-toast ${levelClass} animate__animated animate__fadeInUp animate__faster">
+        <button class="delete"></button>
+        ${msg}
+    </div>
+    `
+    const html = generateElements(template);
+
+    const numToasts = document.querySelectorAll(".js-toast.notification").length;
+
+    if (document.querySelector(".js-toast.notification")) {
+        // If .js-toast notifications are present, append under final notification
+        // This is to prevent overlapping toast notifications
+        document.querySelector(".js-toast.notification:last-of-type").insertAdjacentElement("afterend", html);
+        // Position new toast under previous toast with CSS
+        html.style.setProperty("top", `${(numToasts * 70) + 30}px`);
+    } else {
+        // Otherwise prepend to top of main content
+        document.getElementById("main_c").prepend(html);
+    }
+
+    // This should get the newly added notification since it is now the first
+    html.querySelector(".js-toast.notification .delete").addEventListener("click", (event) => {
+        const notification = event.target.closest(".js-toast.notification");
+        notification.remove(notification);
+    });
+
+    // For a success message, remove it after 3 seconds
+    if (levelClass === "is-success") {
+        const notification = document.querySelector(".js-toast.notification:last-of-type");
+        notification.classList.remove("animate__fadeInUp");
+        notification.classList.remove("animate__faster");
+        notification.classList.add("animate__fadeOutDown");
+        notification.classList.add("animate__slower");
+    }
+
+    // remove the toast
+    html.addEventListener("animationend", (event) => {
+        if (event.animationName === "fadeOutDown") {
+            event.target.remove();
+        }
+    });
+}
+
 /**
  * Collapses a JS step element.
  *

diff --git a/www/js/compare_datasets.v2.js b/www/js/compare_datasets.v2.js
@@ -300,45 +300,6 @@ const createGeneSelectInstance = (idSelector, geneSelect=null) => {
     });
 }
 
-/* Creates a Toast-style message in the upper-corner of the screen. */
-const createToast = (msg, levelClass="is-danger") => {
-    const template = `
-    <div class="notification js-toast ${levelClass} animate__animated animate__fadeInUp animate__faster">
-        <button class="delete"></button>
-        ${msg}
-    </div>
-    `
-    const html = generateElements(template);
-
-    const numToasts = document.querySelectorAll(".js-toast.notification").length;
-
-    if (document.querySelector(".js-toast.notification")) {
-        // If .js-toast notifications are present, append under final notification
-        // This is to prevent overlapping toast notifications
-        document.querySelector(".js-toast.notification:last-of-type").insertAdjacentElement("afterend", html);
-        // Position new toast under previous toast with CSS
-        html.style.setProperty("top", `${(numToasts * 70) + 30}px`);
-    } else {
-        // Otherwise prepend to top of main content
-        document.getElementById("main_c").prepend(html);
-    }
-
-    // This should get the newly added notification since it is now the first
-    document.querySelector(".js-toast.notification .delete").addEventListener("click", (event) => {
-        const notification = event.target.closest(".js-toast.notification");
-        notification.remove(notification);
-    });
-
-    // For a success message, remove it after 3 seconds
-    if (levelClass === "is-success") {
-        const notification = document.querySelector(".js-toast.notification:last-of-type");
-        notification.classList.remove("animate__fadeInUp");
-        notification.classList.remove("animate__faster");
-        notification.classList.add("animate__fadeOutDown");
-        notification.classList.add("animate__slower");
-    }
-}
-
 const downloadSelectedGenes = (event) => {
     event.preventDefault();
 

diff --git a/www/js/curator_common.js b/www/js/curator_common.js
@@ -883,50 +883,6 @@ const createPlot = async (event) => {
 
 }
 
-/**
- * Creates a toast notification with the given message and level class.
- * @param {string} msg - The message to display in the toast notification.
- * @param {string} [levelClass="is-danger"] - The level class for the toast notification. Defaults to "is-danger".
- */
-const createToast = (msg, levelClass="is-danger") => {
-    const template = `
-    <div class="notification js-toast ${levelClass} animate__animated animate__fadeInUp animate__faster">
-        <button class="delete"></button>
-        ${msg}
-    </div>
-    `
-    const html = generateElements(template);
-
-    const numToasts = document.querySelectorAll(".js-toast.notification").length;
-
-    if (document.querySelector(".js-toast.notification")) {
-        // If .js-toast notifications are present, append under final notification
-        // This is to prevent overlapping toast notifications
-        document.querySelector(".js-toast.notification:last-of-type").insertAdjacentElement("afterend", html);
-        // Position new toast under previous toast with CSS
-        html.style.setProperty("top", `${(numToasts * 70) + 30}px`);
-    } else {
-        // Otherwise prepend to top of main content
-        document.getElementById("main_c").prepend(html);
-    }
-
-    // This should get the newly added notification since it is now the first
-    html.querySelector(".js-toast.notification .delete").addEventListener("click", (event) => {
-        console.log(event.target);
-        const notification = event.target.closest(".js-toast.notification");
-        notification.remove(notification);
-    });
-
-    // For a success message, remove it after 3 seconds
-    if (levelClass === "is-success") {
-        const notification = document.querySelector(".js-toast.notification:last-of-type");
-        notification.classList.remove("animate__fadeInUp");
-        notification.classList.remove("animate__faster");
-        notification.classList.add("animate__fadeOutDown");
-        notification.classList.add("animate__slower");
-    }
-}
-
 /**
  * Disables or enables a checkbox and its associated label.
  * If the parent element is a .checkbox class, it will also be disabled or enabled.