Add "retrieve results" tab

Add a tab to search results of passed analysis by their run ID.
Scripts are made from scratch, maybe functions already existing can do
this job instead.

.gitlab-ci.yml

+stages:
+  - build
+
+build-job:
+  stage: build
+  script:
+    - echo "passed"
+  tags: 
+    - bws
+
 # stages:
 #   - build
 #   - test

www/cgi-bin/pampa/common.py

@@ -13,17 +13,17 @@ DATA_PAMPA_DIR = os.path.join(HTML_PATH, "data_pampa/")
 
 
 # TODO /!\ Remplacer les tables de peptides des Birds Fishes et Reptiles par les vraies tables
-# La table des mammifères sert à combler le manque de données en attendant.
 PEPTIDES_MAMMALS_FILE = DATA_PAMPA_DIR + "table_mammals_with_deamidation.tsv"
-PEPTIDES_BIRDS_FILE = DATA_PAMPA_DIR + "table_mammals_with_deamidation.tsv"
-PEPTIDES_FISHES_FILE = DATA_PAMPA_DIR + "table_mammals_with_deamidation.tsv"
-PEPTIDES_REPTILES_FILE = DATA_PAMPA_DIR + "table_mammals_with_deamidation.tsv"
+PEPTIDES_BIRDS_FILE = DATA_PAMPA_DIR + ".tsv"
+PEPTIDES_FISHES_FILE = DATA_PAMPA_DIR + ".tsv"
+PEPTIDES_REPTILES_FILE = DATA_PAMPA_DIR + ".tsv"
 
 TAXONOMY_ALL_FILE = DATA_PAMPA_DIR + "taxonomy_all.tsv"
 TAXONOMY_REDUCED_FILE = DATA_PAMPA_DIR + "taxonomy_reduced.tsv"
 
 SPECTRA_EXAMPLE_1 = DATA_PAMPA_DIR + "example_1.zip"
 
+
 #Renvoie le pwd pour le dossier tmp/
 def tmp_dir(run_id):    
     tmpdir = os.path.join(TEMP_DIR, run_id)

www/cgi-bin/pampa/render_details.py

@@ -174,6 +174,7 @@ def write_details_page(spectrum_name, run_id, job_name=None):
     
     # Insert HTML header and page head
     html += (open(f"{common.HTML_PATH}/header.php", "r").read())
+    html += '<script> console.log(performance.navigation.type) </script>'
     html += '<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">'
     html += open(f"{common.HTML_PATH}/menu_central.txt", 'r').read()
     html += '</div></div><div id="main"><div id="center">'
@@ -352,6 +353,8 @@ def write_details_page(spectrum_name, run_id, job_name=None):
     html += ('<br>')
     html += ('<br>')
     html += ('</div>')
+    html += '<script> console.log("details loaded")</script>'
+    html += '<script> if (performance.navigation.type == 2 || performance.navigation.type == 0) {location.reload(true);}</script>'
     
     # Insert page footer
     html += '</div></div></body>'

www/cgi-bin/pampa/render_result.py

@@ -147,6 +147,12 @@ def write_main_page(run_id, taxo_used, job_name=None):
     html += (results_output(run_id, job_name=job_name))
     html += ('<br>')
 
+    # Come back later
+    html += '<h3>You want to come back later ?</h3>'
+    html += '<p>Your result stay available for at least one month.</p>'
+    html += f'<p>To access it, you can either save the url or <a id="copy" data-copy="{run_id}">copy</a> the ID {run_id}.</p>'
+    html += ('<br>')
+
     # Insert page footer
     html += '</div></div></body>'
 

www/cgi-bin/pampa/retrieve_results.py

+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+# Modules import
+import cgitb; cgitb.enable()
+import os
+import cgi
+import common
+import sys
+import json
+
+from html_utils import *
+from render_sub_assignment import *
+
+# Functions definition
+def extract_request(form):
+    error = 0
+    error_messages = []
+    url_result = ""
+
+    if "run_id" in form:
+        run_id = form["run_id"].value
+    else:
+        error = 1
+        error_messages.append("The script need the parameter 'run_id'.")
+        run_id = ""
+
+    if error == 0:
+        if os.path.exists(f'{common.RESULT_DIR}{run_id}/results.php'):
+            url_result = f'result/{run_id}/results.php'
+        else:
+            url_result = 'fail_retrieve.php'
+
+    return error, error_messages, url_result, run_id
+    
+
+
+
+# Main
+def main():
+    
+    form = cgi.FieldStorage()
+
+    error, error_messages, url_result, run_id = extract_request(form)
+
+    sys.stdout.write("Content-Type: application/json")
+    sys.stdout.write("\n")
+    sys.stdout.write("\n")
+    result={}
+    if error == 0:
+        result['success'] = True
+        result['url_result'] = url_result 
+        result['comment'] = f'{common.RESULT_DIR}{run_id}/result.php'
+    else:
+        result['success'] = False
+        result['error_messages'] = error_messages
+    sys.stdout.write(json.dumps(result, indent=1))
+    sys.stdout.write("\n")
+
+main()

www/html/pampa/fail_retrieve.php

+<?php include('header.php') ?>
+
+
+  <body>
+   
+   
+    <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"><?php include("menu_central.txt")?></div>
+   </div>
+   <div id="main">
+    <div id="center">
+
+    <h2>Query failed</h2>
+    <p>Unfortunately, your request was not successful. No results were found for this ID.</p>
+    <p>The ID may have been incorrectly copied, or the results may have been deleted from our system.</p>
+    <br>
+    <a href="/pampa/result.php" class="aLoad" >Back to search</a>
+    
+
+      </div><!-- center -->
+    </div><!-- main-->
+
+<!-- appel du fichier lib.inc contenant des fonctions php -->
+<?php require("../lib.inc")?>
+
+<!-- appel de la fonction footer qui permet d'afficher au bas de la page (nom du logiciel, un lien vers le mail, la date de modif -->
+<!-- Modifier le nom Example_web_server par le nom de votre logiciel -->
+<?php footer("Pampa","Pampa", "areski.flissi@univ-lille.fr","2024"); ?>
+</div>                                                                                
+
+</body>                                        
+</html>        

www/html/pampa/header.php

@@ -14,7 +14,7 @@
     <!--modifier le nom du dossier ci dessous -->
     <script type="text/javascript" src="/pampa/js/script.js"></script>   
     <script type="text/javascript" src="/pampa/js/pampa.js"></script>  
-    <script type="text/javascript" src="https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js"></script>
+    <script type="text/javascript" src="https://cdn.bokeh.org/bokeh/release/bokeh-3.1.1.min.js"></script>
     <script type="text/javascript">Bokeh.set_log_level("info");</script>
    <title>Bonsai  :: Bioinformatics Software Server</title>
     <script type="text/javascript">

www/html/pampa/js/pampa.js

@@ -47,6 +47,36 @@ $(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"));
+    $.ajax({
+        url: "/cgi-bin/pampa/retrieve_results.py",
+        type: "POST",
+        data: formData, 
+        dataType: "json",
+        contentType: false,
+        cache: false,
+        processData:false,
+        success: function(response){
+            setTimeout(function() {
+                url_result = response.url_result;
+                $('#main').load(url_result+" #center");
+            }, 200);
+        },
+        error: function(request, status, error){
+            $("#main").html(request.responseText);
+        }
+    });
+});
+
 $(document).on("click", "#add_organism", function() {
     var $rows = $("#table_organism");
     var i = $("#table_organism tr:last-child input").data("i") + 1;
@@ -84,3 +114,9 @@ $(document).on("click", "#back_to_normal", function() {
 function open_taxo_tree(name) {
 	window.open(name, 'Taxonomy', 'menubar=no, scrollbars=no, location=no, titlebar=no, status=no, width=800, height=800');
 }
+
+$(document).on("click", "a#copy", function () {
+    var copyText = $(this).data("copy");
+    navigator.clipboard.writeText(copyText);
+    alert("Copied the ID: " + copyText);
+});
\ No newline at end of file

www/html/pampa/menu_central.txt

@@ -4,6 +4,9 @@
      </li>
     <li class="onglet">
 		<a href="/pampa/form.php" class="mc aLoad" >Pampa web</a>
+    </li>
+    <li class="onglet">
+    	<a href="/pampa/result.php" class="mc aLoad" >Results</a>
     </li>
 	<li class="onglet onglet_right">
     	<a href="/pampa/help.php" class="mc aLoad" >Help</a>

www/html/pampa/result.php

+<?php include('header.php') ?>
+
+
+  <body>
+   
+   
+    <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"><?php include("menu_central.txt")?></div>
+   </div>
+   <div id="main">
+    <div id="center">
+      <br>
+
+     <!--Partie à modifier-->
+    <!--h2>Understand the results</h2>
+    <p>
+        The results are composed of 3 files.
+    </p>
+    <p>
+        More details in the <a>help</a> section.
+    </p-->
+
+    <h2>Retrieve analysis results</h2>
+    <p>Results are saved for a minimum of one month.</p>
+    <p>They can be accessed directly via their link if it have been saved. Otherwise, you can enter your run ID in the field below.</p>
+    <form id="retrieve" method="post" enctype="multipart/form-data">
+        <table class="vide pampa-choice">
+          <tr>
+            <td>
+              <input type="text" name="run_id" maxlength="26" style="width: 300px;"/>
+            </td>
+            <td>
+              <input type="button" id="search" name="button" value="Search"/>
+            </td>
+          </tr>
+        </table>
+    </form>
+    
+
+      </div><!-- center -->
+    </div><!-- main-->
+
+<!-- appel du fichier lib.inc contenant des fonctions php -->
+<?php require("../lib.inc")?>
+
+<!-- appel de la fonction footer qui permet d'afficher au bas de la page (nom du logiciel, un lien vers le mail, la date de modif -->
+<!-- Modifier le nom Example_web_server par le nom de votre logiciel -->
+<?php footer("Pampa","Pampa", "areski.flissi@univ-lille.fr","2024"); ?>
+</div>                                                                                
+
+</body>                                        
+</html>