Small modifications and bug fixes

Add a footer to python-generated pages. The footer is described in
footer.php.

Add "push_in_history" in ajax request when retrieving result with ID.

Tabs names are now in lowercase.

www/cgi-bin/pampa/render_details.py

@@ -58,7 +58,7 @@ def peak_parser_mzml(peak_file_name):
     intensity_array = f[0]["intensity array"] #pour avoir l'intensité des pics
  
     for mass, intensity in zip(mass_array.tolist(), intensity_array.tolist()):
-        couple = (float(mass), intfloat((intensity)))
+        couple = (float(mass), float(intensity))
         if couple not in peak_list:
             peak_list.append(couple)
           
@@ -357,7 +357,9 @@ def write_details_page(spectrum_name, run_id, job_name=None):
     html += '<script> if (performance.navigation.type == 2 || performance.navigation.type == 0) {location.reload(true);}</script>'
     
     # Insert page footer
-    html += '</div></div></body>'
+    html += '</div></div>'
+    html += open(f"{common.HTML_PATH}/footer.php", "r").read()
+    html +='</body></html>'
     
     # Write details page
     open(f'{common.RESULT_DIR}{run_id}/details_{os.path.splitext(spectrum_name)[0].replace(" ", "_")}.html', "w").write(html)

www/cgi-bin/pampa/render_error.py

@@ -10,7 +10,12 @@ import common
 def write_main_page(result_path, run_id, error_list):
     """Write a HTML page. This result page display errors made by the user when filling the formular."""
     main_page = open(result_path + run_id + "/results.php", "w")
-    main_page.write('<div id="center">')
+    
+    # Insert page header
+    main_page.write(open(f"{common.HTML_PATH}/header.php", "r").read())
+    main_page.write('<div class="frametitle"><h1 id="title">Pampa</h1></div><div id="center_sup"><div class="theme-border" style="display:none"></div><div id="link_home" style="display:inline-block"><a href="/" class="text_onglet"><img src="/Style/icon/home_w.png" alt="home_general"/></a></div><div class="tabs" id="menu_central" style="display:inline-block">')
+    main_page.write(open(f"{common.HTML_PATH}/menu_central.txt", 'r').read())
+    main_page.write('</div></div><div id="main"><div id="center">')
 
     # Show the error messages
     main_page.write("<div class='formulaire'>")
@@ -22,7 +27,11 @@ def write_main_page(result_path, run_id, error_list):
     # Back to the formular
     main_page.write('<a href="/pampa/form.php" class="aLoad" >Back to PAMPA classify</a>')
 
-    main_page.write("</div>")
+    # Insert page footer
+    html += '</div></div>'
+    html += open(f"{common.HTML_PATH}/footer.php", "r").read()
+    html +='</body></html>'
+
     main_page.close()
 
 

www/cgi-bin/pampa/render_error_pampa.py

@@ -9,7 +9,12 @@ import common
 def write_main_page(run_id):
     """Write a HTML page. This result page display errors made by the user when filling the formular."""
     main_page = open(common.RESULT_DIR + run_id + "/results.php", "w")
-    main_page.write('<div id="center">')
+    
+    # Insert page header
+    main_page.write(open(f"{common.HTML_PATH}/header.php", "r").read())
+    main_page.write('<div class="frametitle"><h1 id="title">Pampa</h1></div><div id="center_sup"><div class="theme-border" style="display:none"></div><div id="link_home" style="display:inline-block"><a href="/" class="text_onglet"><img src="/Style/icon/home_w.png" alt="home_general"/></a></div><div class="tabs" id="menu_central" style="display:inline-block">')
+    main_page.write(open(f"{common.HTML_PATH}/menu_central.txt", 'r').read())
+    main_page.write('</div></div><div id="main"><div id="center">')
 
     # Show the error messages
     main_page.write("<div class='formulaire'>")
@@ -21,7 +26,11 @@ def write_main_page(run_id):
     # Back to the formular
     main_page.write('<a href="/pampa/form.php" class="aLoad" >Back to PAMPA classify</a>')
 
-    main_page.write("</div>")
+    # Insert page footer
+    html += '</div></div>'  # center - main
+    html += open(f"{common.HTML_PATH}/footer.php", "r").read()
+    html +='</body></html>'
+
     main_page.close()
 
 

www/cgi-bin/pampa/render_result.py

@@ -154,7 +154,9 @@ def write_main_page(run_id, taxo_used, job_name=None):
     html += ('<br>')
 
     # Insert page footer
-    html += '</div></div></body>'
+    html += '</div></div>'
+    html += open(f"{common.HTML_PATH}/footer.php", "r").read()
+    html +='</body></html>'
 
     open(common.RESULT_DIR + run_id + "/results.php", "w").write(html)
 

www/html/pampa/footer.php

+<div id='footer'>
+    <table id="footerTable">
+        <tr>
+            <td id='footer_left'></td>
+            <td id='footer_right'>
+                2024 - <a href="http://cristal.univ-lille.fr/bonsai" target="_blank">Bonsai bioinformatics</a>
+                <br>
+            </td>
+        </tr>
+    </table>
+</div> <!-- footer -->
\ No newline at end of file

www/html/pampa/index.php

@@ -26,16 +26,19 @@
 
     <h2>How to use PAMPA ?</h2>
     <p>PAMPA is available in two versions.</p>
-    <p><B>Download :</B> the source code is available at <a href="https://github.com/touzet/pampa" target="_blank">https://github.com/touzet/pampa</a></p>
-    <p><B>Web interface :</B> most facilities</p>
+    <p><B>Download :</B> the source code for local installation is available at <a href="https://github.com/touzet/pampa" target="_blank">https://github.com/touzet/pampa</a>. This version includes the complete range of features offered by the software.</p>
+    <p><B>Web interface :</B> user-friendly web application for fast and easy species identification from mass spectra. It is accessible <a href="/pampa/form.php" class="mc aLoad">here</a>.</p>
 
     <h2>Authors</h2>
     <p>
-    The program has been developed by Hélène Touzet in close collaboration with Fabrice Bray (Lille ZooMS platform).  
-    The web interface has been designed by Yohan Hernandez-Courbevoie, Areski Flissi and Hélène Touzet.
+    The program has been developed by <a href="https://helene-touzet.cnrs.fr/" target="_blank">Hélène Touzet</a> (CRIStAL) in close collaboration with Fabrice Bray (Lille ZooMS platform).  
+    The web interface has been designed by Yohan Hernandez-Courbevoie (CRIStAL), Areski Flissi (CRIStAL) and Hélène Touzet.
     </p>
     
-    <!--h2>Feedbacks</h2-->
+    <h2>Feedbacks</h2>
+    <p>
+      Please send comments and questions to <a href="mailto:pampa@univ-lille.fr?Subject=[Feedbacks]">PAMPA</a>.
+    </p>
 
       </div><!-- center -->
     </div><!-- main-->

www/html/pampa/js/pampa.js

@@ -47,13 +47,6 @@ $(document).on("click", ".link_img", function() {
     });
 });
 
-document.addEventListener('DOMContentLoaded', function() {
-    if (window.location.pathname.includes("details_")) {
-        if (performance.navigation.type == 2 || performance.navigation.type == 0) {
-            location.reload(true);
-        }
-    }
-});
 
 $(document).on("click", "#search", function(){
     var formData = new FormData(document.querySelector("#retrieve"));
@@ -69,6 +62,7 @@ $(document).on("click", "#search", function(){
             setTimeout(function() {
                 url_result = response.url_result;
                 $('#main').load(url_result+" #center");
+                push_in_history(url_result);
             }, 200);
         },
         error: function(request, status, error){
@@ -80,7 +74,7 @@ $(document).on("click", "#search", function(){
 $(document).on("click", "#add_organism", function() {
     var $rows = $("#table_organism");
     var i = $("#table_organism tr:last-child input").data("i") + 1;
-    $rows.append(`<tr><td><input list="taxonomic_node_list" name="taxonomic_node_${i}" data-i=${i} placeholder="Ex: Mammalia (mammals) - [40674; class]" autocomplete="off"/></td></tr>`);
+    $rows.append(`<tr><td><input list="taxonomic_node_list" name="taxonomic_node_${i}" data-i=${i} placeholder="Ex: Mammalia - [40674; class]" autocomplete="off"/></td></tr>`);
 });
 
 $(document).on("click", "#example_1", function() {

www/html/pampa/menu_central.txt

 <ul id="menu">
   <li class="onglet onglet_left">
-        <a href="/pampa/" class="mc aLoad">Pampa</a>
+    <a href="/pampa/" class="mc aLoad">pampa</a>
   </li>
   <li class="onglet">
-		<a href="/pampa/form.php" class="mc aLoad" >Pampa web</a>
+    <a href="/pampa/form.php" class="mc aLoad" >web server</a>
   </li>
   <li class="onglet">
-    	<a href="/pampa/result.php" class="mc aLoad" >Results</a>
+    <a href="/pampa/help.php" class="mc aLoad" >help</a>
   </li>
   <li class="onglet onglet_right">
-    	<a href="/pampa/help.php" class="mc aLoad" >Help</a>
+    <a href="/pampa/result.php" class="mc aLoad" >retrieve result with an ID</a>
   </li>
 </ul>