Add digestion enzyme selection and improve peak config handling

www/cgi-bin/pampa/pampa.py

@@ -236,17 +236,30 @@ def extract_request(form):
                 fOut.write(f"PTM={req['limit_PTM']} ")
             fOut.write("\n")
 
+    minimum = None
+    digestion = None
+
+    if "minimum_peaks" in form:
         if form["minimum_peaks"].value != "" and form["minimum_peaks"].value != "5":
             minimum = form["minimum_peaks"].value
-    else:
-        minimum = None
 
-    if minimum:
+    if "digestion" in form:
+        if form["digestion"].value != "" and form["digestion"].value != "trypsin":
+            digestion = form["digestion"].value
+
+
+    if not minimum and not digestion:
+        pass
+    else:
         with open(f'{common.CONFIG_FILE}', 'r') as f:
             data = json.load(f)
+            if minimum:
                 data['min_number_of_peaks'] = minimum
+                log.write(f"Minimum number of peaks set to {minimum}\n")
+            if digestion:
+                data['digestion'] = digestion
+                log.write(f"Digestion set to {digestion}\n")
             json.dump(data, open(f'{resdir}/config.json', 'w'))
-            log.write(f"Digestion set to {minimum}\n")
             req['config_file'] = resdir + '/config.json'
     
     log.write("Recap downloads :\n")

www/html/pampa/form.php

@@ -56,16 +56,6 @@
       </table>
       <br>
 
-      <b>Minimum peaks configuration</b>
-      <table class="vide pampa_choice">
-        <tr>
-          <td>
-            <input type="number" name="minimum_peaks" step="1" min="1" max="100" value="5" required>
-          </td>
-        </tr>
-      </table>
-      <br>
-
       <b>Mass error tolerance</b>
       <table class="vide pampa_choice">
         <tr>
@@ -299,6 +289,47 @@
       </div>
     </div>
 
+        <div class="formulaire">
+      <h2>Configuration <span style="font-weight: normal">(optional) :</span></h2>
+        <table class="vide">
+           <tr>
+            <td class="label">
+              <B>Choose</B> your digestion enzyme.
+            </td>
+          </tr>
+          <tr>
+           <td>
+             <select name="digestion">
+                <option value="arg-c">arg-c</option>
+                <option value="asp-n">asp-n</option>
+                <option value="chymotrypsin high specificity">chymotrypsin high specificity</option>
+                <option value="chymotrypsin low specificity">chymotrypsin low specificity</option>
+                <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+                <option value="pepsin ph1.3">pepsin ph1.3</option>
+                <option value="pepsin ph2.0">pepsin ph2.0</option>
+                <option value="proline endopeptidase">proline endopeptidase</option>
+                <option value="trypsin" selected>trypsin (Default)</option>
+                <option value="trypsin_exception">trypsin_exception</option>
+             </select>
+           </td>
+         </tr>
+        </table>
+        <br>
+        <table>
+          <tr>
+            <td class="label">
+              <b>Minimum peaks configuration</b>
+            </td>
+          </tr>
+          <tr>
+           <td>
+            <input type="number" name="minimum_peaks" step="1" min="1" max="100" value="5" required>
+          </td>
+        </tr>
+      </table>
+      <br>
+    </div>
+
     <div class="center">
       <input type="button" id="example_1" name="example_1" value="Example">
       <input type="submit" id="reset" name="reset" value="Reset" />