Integrate reduced taxonomy

Add a reduced taxonomy.

All default analysis are based on the reduced taxonomy and the advanced
analysis with provided taxonomy are based on the entire taxonomy.

A script producing the reduced taxonomy (and the datalist associated for
the formular) has te be integrated later.

www/cgi-bin/pampa/common.py

@@ -20,10 +20,7 @@ PEPTIDES_FISHES_FILE = DATA_PAMPA_DIR + "table_mammals_with_deamidation.tsv"
 PEPTIDES_REPTILES_FILE = DATA_PAMPA_DIR + "table_mammals_with_deamidation.tsv"
 
 TAXONOMY_ALL_FILE = DATA_PAMPA_DIR + "taxonomy_all.tsv"
-TAXONOMY_MAMMALS_FILE = DATA_PAMPA_DIR + "taxonomy_mammals.tsv"
-TAXONOMY_BIRDS_FILE = DATA_PAMPA_DIR + ""
-TAXONOMY_FISHES_FILE = DATA_PAMPA_DIR + ""
-TAXONOMY_REPTILES_FILE = DATA_PAMPA_DIR + ""
+TAXONOMY_REDUCED_FILE = DATA_PAMPA_DIR + "taxonomy_reduced.tsv"
 
 SPECTRA_EXAMPLE_1 = DATA_PAMPA_DIR + "example_1.zip"
 

www/cgi-bin/pampa/pampa.py

@@ -104,7 +104,6 @@ def extract_request(form):
     log.write(f"Result directory : {resdir}\n")
 
     peptides_path_dict = {"mammals": common.PEPTIDES_MAMMALS_FILE, "birds": common.PEPTIDES_BIRDS_FILE, "fishes": common.PEPTIDES_FISHES_FILE, "reptiles": common.PEPTIDES_REPTILES_FILE}
-    taxo_path_dict = {"mammals": common.TAXONOMY_MAMMALS_FILE, "birds": common.TAXONOMY_BIRDS_FILE, "fishes": common.TAXONOMY_FISHES_FILE, "reptiles": common.TAXONOMY_REPTILES_FILE, 'all': common.TAXONOMY_ALL_FILE}
     
     req['files_uploaded'] = []  # for the render_result
     
@@ -227,10 +226,7 @@ def extract_request(form):
                 
 
             # Taxonomy selection
-            if "limit_OX" in req or len(tax_groups) > 1:
-                f = taxo_path_dict['all']
-            else:
-                f = taxo_path_dict['all']
+            f = common.TAXONOMY_REDUCED_FILE
             fn = os.path.basename(f)
             extract_files_from_list([f], resdir)
             req["taxo_file"] = resdir + '/' + fn  # for the command
@@ -285,7 +281,7 @@ def extract_request(form):
             if "taxonomy_selection" in form:
                 taxonomy_selection = form["taxonomy_selection"].value
                 if taxonomy_selection == "default":
-                    f = taxo_path_dict['all']
+                    f = common.TAXONOMY_ALL_FILE
                     fn = os.path.basename(f)
                     extract_files_from_list([f], resdir)
                     req["taxo_file"] = resdir + '/' + fn  # for the command

www/html/pampa/form.php

@@ -173,19 +173,7 @@
         </tr>
         <tr>
           <datalist id="taxonomic_node_list">
-            <?php
-              $banned_ranks = array("cohort", "subcohort", "species", "subspecies", "Rank");
-              foreach(file('./data_pampa/taxonomy_all.tsv') as $line) {
-                $line_split = explode("\t", trim($line));
-                if (!in_array($line_split[4], $banned_ranks)) {
-                  if ($line_split[1] == '') {
-                    echo '<option value="' . $line_split[2] . ' - [' . $line_split[0] . '; ' . $line_split[4] . ']"></option>';
-                  } else {
-                    echo '<option value="' . $line_split[2] . ' (' . $line_split[1] . ') - [' . $line_split[0] . '; ' . $line_split[4] . ']"></option>';
-                  }
-                }
-              }  
-            ?>
+            <?php include("datalist_taxo.txt");?>
           </datalist>
           <td>
             <input list="taxonomic_node_list" name="taxonomic_node_1" data-i=1 placeholder="Ex: Mammalia (mammals) - [40674; class]" autocomplete="off"/>