big progress

main_taxonomy_filtering.py

@@ -29,7 +29,7 @@ def main():
     primary_taxonomy=ta.parse_taxonomy_simple_file(args.taxonomy)
 
     if not (args.peptide_table or args.fasta or args.directory or args.limit):
-        print("Missing input")
+        # print("Missing input")
         sys.exit()
     
     # parsing models for peptide tables, sequences or limits
@@ -47,8 +47,9 @@ def main():
 
     secondary_taxonomy, lost_taxid=primary_taxonomy.intersection(set_of_taxid)
     if len(lost_taxid)>0:
-        print("The following taxids were not found in "+args.taxonomy)
-        print(lost_taxid)
+        pass
+        # print("The following taxids were not found in "+args.taxonomy)
+        # print(lost_taxid)
     ta.table_print(secondary_taxonomy)
         
     ta.create_taxonomy_file(secondary_taxonomy, args.output)

postgresql/fill_taxo.py

@@ -9,7 +9,10 @@ from config import load_config
 import csv
 import re
 
-def create_table(table):
+
+
+
+def create_table(table, verbose=False):
     config = load_config()
     sql = open(sys.path[0]+"/pampa.sql", "r").read().replace("\n", "").replace("taxonomy", table)
     try:
@@ -18,16 +21,17 @@ def create_table(table):
                 cur.execute(sql, (table))
                 conn.commit()
     except (Exception, psycopg2.DatabaseError) as error:
+        if verbose:
             print(error) 
 
-def load_file(path, run_id=None):
+def load_file(path, run_id=None, verbose=False):
     # idx=0
     
     if run_id :
         runid_pattern = re.compile("^[A-Z][a-z]{2}_[0-9]{2}_[0-9]{4}_[0-9]{2}_[0-9]{2}_[0-9]{2}_[0-9]{1,5}$|^all$|^reduced$")  # Jul_05_2024_12_35_25_5220 or "reduced" or "all"
         assert runid_pattern.match(run_id)
         table = "taxonomy_" + run_id 
-        create_table(table)
+        create_table(table, verbose=verbose)
     else :
         table = "taxonomy"
     with open(path, 'r') as taxo_file:
@@ -42,12 +46,12 @@ def load_file(path, run_id=None):
             # parentId = line[3]
             # rank = line[4]
             # print(line)
-            insert_data(table, line)
+            insert_data(table, line, verbose=verbose)
         
-        #add_root()
-        #re_arrange()
+        #add_root(verbose=verbose)
+        #re_arrange(verbose=verbose)
 
-def insert_data(table, raw):
+def insert_data(table, raw, verbose=False):
     config = load_config()
     taxoId = raw[0]
     commonName = raw[1]
@@ -66,9 +70,10 @@ def insert_data(table, raw):
                 cur.execute(sql, (taxoId, commonName, scientificName, parentId, rank))
                 conn.commit()
     except (Exception, psycopg2.DatabaseError) as error:
+        if verbose:
             print(error)    
 
-def add_root():
+def add_root(verbose=False):
     config = load_config()
     insert = "INSERT INTO taxonomy(taxonid, commonname) VALUES(%s,%s)"  # update with table name as parameter
     update = "UPDATE taxonomy set parent=-1 WHERE rank='subphylum'"
@@ -79,9 +84,10 @@ def add_root():
                 cur.execute(update)
                 conn.commit()
     except (Exception, psycopg2.DatabaseError) as error:
+        if verbose:
             print(error)    
 
-def re_arrange():
+def re_arrange(verbose=False):
     config = load_config()
     insert = "INSERT INTO taxonomy(taxonid, scientificname, parent) VALUES(%s,%s,%s)"  # update with table name as parameter
     update = "UPDATE taxonomy set parent=0 WHERE scientificname like '%unclassified %'"
@@ -92,11 +98,14 @@ def re_arrange():
                 cur.execute(update)
                 conn.commit()
     except (Exception, psycopg2.DatabaseError) as error:
+        if verbose:
             print(error)   
 
 
 if __name__ == '__main__':
     if len(sys.argv) == 2:
         load_file(sys.argv[1])  # taxonomy_path
-    else:
+    elif len(sys.argv) == 3:
         load_file(sys.argv[1], run_id=sys.argv[2])  # taxonomy_path, run_id
+    elif len(sys.argv) == 4:
+        load_file(sys.argv[1], run_id=sys.argv[2], verbose=True)  # 3e params to pass verbose to True
\ No newline at end of file

postgresql/json_taxo.py

@@ -10,8 +10,11 @@ import json
 import re
 
 
-def execute(taxo_path, run_id=None):
-    print("Generating taxonomy JSON file...")
+
+
+def execute(taxo_path, run_id=None, verbose=False):
+    # print("Generating taxonomy JSON file...")
+
     config = load_config()
     if run_id :
         runid_pattern = re.compile("^[A-Z][a-z]{2}_[0-9]{2}_[0-9]{4}_[0-9]{2}_[0-9]{2}_[0-9]{2}_[0-9]{1,5}$|^all$|^reduced$")  # Jul_05_2024_12_35_25_5220 or "reduced" or "all"
@@ -23,16 +26,17 @@ def execute(taxo_path, run_id=None):
     try:
         with psycopg2.connect(**config) as conn:
             with conn.cursor() as cur:
-                create_json(cur, table, taxo_path)
+                create_json(cur, table, taxo_path, verbose=verbose)
                 # cur.execute(sql, (table))
                 # rows = cur.fetchall()
                 # for row in rows:
                 #    print("taxonId =", row[0])
     except (Exception, psycopg2.DatabaseError) as error:
+        if verbose:
             print(error)
-    print("Done.")
+    # print("Done.")
 
-def create_json(cur, table, taxo_path):
+def create_json(cur, table, taxo_path, verbose=False):
     json_array = [ ]
     json_root = { "id" : 0, "text" : "Taxonomy", "children" : []}
     children = [] # 1 seul element a racine de l'arbre!
@@ -40,7 +44,7 @@ def create_json(cur, table, taxo_path):
     json_root["state"] = state
 
     # on construit children en ajoutant l'element racine -> taxonId = -1 (root)
-    add_childs(cur, table, json_root, 89593)
+    add_childs(cur, table, json_root, 89593, verbose=verbose)
 
     json_array.append(json_root)
     #print(json_array)
@@ -50,7 +54,7 @@ def create_json(cur, table, taxo_path):
     #f = open("taxonomy_mammals.json")
     #data = json.load(f)
 
-def add_childs(cur, table, json, id):
+def add_childs(cur, table, json, id, verbose=False):
     sql = "SELECT * from "+table+" WHERE parent = " + str(id)
     # print("Building childs for taxon", id)
     # print(sql)
@@ -73,11 +77,14 @@ def add_childs(cur, table, json, id):
         json["children"] = childrens
 
     except (Exception, psycopg2.DatabaseError) as error:
+        if verbose:
             print(error)
     # return json
 
 if __name__ == '__main__':
     if len(sys.argv) == 2:
         execute(sys.argv[1])  # dir path for the taxo json created
-    else:
+    elif len(sys.argv) == 3:
         execute(sys.argv[1], sys.argv[2])  # path, run_id
+    elif len(sys.argv) == 4:
+        execute(sys.argv[1], sys.argv[2], verbose=True)  # 3e params to pass verbose to True

www/cgi-bin/pampa/main_taxonomy_filtering.py

-#!/usr/bin/env python3
-
-import argparse
-import sys
-import os
-
-# local import
-from src import peptide_table as pt
-from src import sequences as seq
-from src import taxonomy as ta 
-from src import markers
-from src import limit
-from src import fasta_parsing as fa
-#from src import message
-
-
-def main():
-    parser = argparse.ArgumentParser()
-    parser.add_argument("-p", dest="peptide_table",nargs='+', help="Peptide table (TSV file).", type=str)
-    parser.add_argument("-o", dest="output", help="Output path (should include the output file name)", type=str)
-    parser.add_argument("-f", dest="fasta", help="FASTA file that contains new sequences.", type=str)
-    parser.add_argument("-d", dest="directory", help="Directory that contains FASTA files.", type=str)
-    parser.add_argument("-l", dest="limit",  help="Limit file that contains a list of clades (OX=)", type=str)
-    parser.add_argument("-t", dest="taxonomy", help="Taxonomy (TSV file)", type=str, required=True)
-    args = parser.parse_args()
-
-
-    # parsing taxonomy    
-    primary_taxonomy=ta.parse_taxonomy_simple_file(args.taxonomy)
-
-    if not (args.peptide_table or args.fasta or args.directory or args.limit):
-        print("Missing input")
-        sys.exit()
-    
-    # parsing models for peptide tables, sequences or limits
-    set_of_taxid=set()
-    if args.peptide_table :
-        set_of_markers = pt.parse_peptide_tables(args.peptide_table,None, primary_taxonomy)
-        set_of_taxid.update({m.taxid for m in set_of_markers})
-    if args.fasta or  args.directory:
-        set_of_sequences = fa.build_set_of_sequences(args.fasta, args.directory, None, primary_taxonomy)
-        set_of_taxid.update({s.taxid for s in set_of_sequences})
-    if args.limit:
-        list_of_constraints=limit.parse_limits(args.limit)
-        set_of_taxid.update({t for dict in list_of_constraints for t in dict["OX"]}) 
-
-
-    secondary_taxonomy, lost_taxid=primary_taxonomy.intersection(set_of_taxid)
-    if len(lost_taxid)>0:
-        print("The following taxids were not found in "+args.taxonomy)
-        print(lost_taxid)
-    ta.table_print(secondary_taxonomy)
-        
-    ta.create_taxonomy_file(secondary_taxonomy, args.output)
-
-
-    
-if __name__ == "__main__":
-    main()
-
-
-    
-    
-            

www/cgi-bin/pampa/pampa.py

@@ -201,7 +201,7 @@ def extract_request(form):
             i += 1
 
         if len(req['limit_OX']) > 0:
-            tax_groups = ["mammals", "birds", "fishes", "reptiles"]
+            tax_groups = ["mammals"]  # "birds", "fishes", "reptiles" seront dans cette liste aussi quand ils seront ajoutés aux données par défaut
                 
         elif "taxonomic_group_selection" in form:
             items = form["taxonomic_group_selection"]
@@ -419,8 +419,10 @@ def launch_software(run_id, req):
             render_result_dict["data_tables"] = req['peptides_files']
         else :  # 'sequences'
             render_result_dict["data_dir"] = req['sequences_dir']
-        if "limit_file" in req:
-            render_result_dict["limit_file"] = req['limit_file']  # TODO
+        if "limit_OX" in req and len(req["limit_OX"]) > 0 and "limit_file" in req:
+            render_result_dict["limit"] = True
+        else:
+            render_result_dict["limit"] = True
         json.dump(render_result_dict, open(json_file, "w"))
         os.system(f"python render_result.py {json_file}")
 

www/cgi-bin/pampa/render_details.py

@@ -161,8 +161,14 @@ def insert_spectrum(resdir, spectrum_name):
 
 
 
-def write_details_page(spectrum_name, run_id, tree_created, job_name=None):
+def write_details_page(spectrum_name, run_id, taxo_info, job_name=None):
     resdir = f"{common.RESULT_DIR}{run_id}/"
+    if taxo_info == "custom":
+        url_json = f"/pampa/result/{run_id}/taxonomy_{run_id}.json"
+    elif taxo_info == "default":
+        url_json = "/pampa/data_pampa/taxonomy_reduced.json"
+    else:
+        pass # taxo_info=="no" pas d'affichage de l'arbre
 
     content = json.load(open(resdir+"out_"+run_id+".json", "r"))
     content_reduced = [dct for dct in content if dct['spectrum_name'] == spectrum_name]
@@ -206,7 +212,7 @@ def write_details_page(spectrum_name, run_id, tree_created, job_name=None):
         html += ('<br>')
 
         # Taxonomy
-        if tree_created :
+        if taxo_info != "no" :
             assignment_png = assignment["lca_name"].replace(' ', '_') + ".png"
             assignment_tree = assignment["lca_name"].replace(' ', '_') + ".php"
             html += '<p><iframe src="' + assignment_tree + '" height="800px" width="90%"></iframe></p>'
@@ -256,6 +262,7 @@ def write_details_page(spectrum_name, run_id, tree_created, job_name=None):
         content_reduced.sort(key=lambda x: x["pvalue"])
         peak_info_dict = {}
 
+        if taxo_info != "no" :
             assignment_png = spectrum_name + ".png"
             assignment_tree = spectrum_name + ".php"
             html += '<p><iframe src="' + assignment_tree + '" height="850px" width="90%"></iframe></p>'
@@ -276,8 +283,8 @@ def write_details_page(spectrum_name, run_id, tree_created, job_name=None):
                     peak_info_dict[key].append(i)
 
             # build semi-global taxonomic tree for multi-assignation
-            if tree_created:
-                gen_sub_tree(common.RESULT_DIR, run_id, spectrum_name, assignment, color)
+            if taxo_info != "no":
+                gen_sub_tree(common.RESULT_DIR, run_id, spectrum_name, assignment, color, url_json)
 
 
             # General info
@@ -396,21 +403,14 @@ def extract_request(form):
         error = 1
         error_messages.append("The script need the parameter 'job_name'.")
 
-    if "tree" in form:
-        tree_created = form["tree"].value
-        if tree_created == "True":
-            job_name = True
-        elif tree_created == "False":
-            job_name = False
-        else:
-            error = 1
-            error_messages.append("The script need the parameter 'tree'.")
+    if "taxo" in form:
+        taxo_info = form["taxo"].value
     else:
         error = 1
-        error_messages.append("The script need the parameter 'tree'.")
+        error_messages.append("The script need the parameter 'taxo'.")
 
     if error == 0:
-        write_details_page(spectrum_name, run_id, job_name, tree_created)
+        write_details_page(spectrum_name, run_id, taxo_info, job_name)
 
     return error, error_messages, run_id, spectrum_name
     

www/cgi-bin/pampa/render_error.py

@@ -28,9 +28,9 @@ def write_main_page(result_path, run_id, error_list):
     main_page.write('<a href="/pampa/form.php" class="aLoad" >Back to PAMPA classify</a>')
 
     # Insert page footer
-    html += '</div></div>'
-    html += open(f"{common.HTML_PATH}/footer.php", "r").read()
-    html +='</body></html>'
+    main_page.write('</div></div>')
+    main_page.write(open(f"{common.HTML_PATH}/footer.php", "r").read())
+    main_page.write('</body></html>')
 
     main_page.close()
 

www/cgi-bin/pampa/render_error_pampa.py

@@ -27,9 +27,9 @@ def write_main_page(run_id):
     main_page.write('<a href="/pampa/form.php" class="aLoad" >Back to PAMPA classify</a>')
 
     # Insert page footer
-    html += '</div></div>'  # center - main
-    html += open(f"{common.HTML_PATH}/footer.php", "r").read()
-    html +='</body></html>'
+    main_page.write('</div></div>')  # center - main
+    main_page.write(open(f"{common.HTML_PATH}/footer.php", "r").read())
+    main_page.write('</body></html>')
 
     main_page.close()
 

www/cgi-bin/pampa/render_result.py

@@ -7,12 +7,20 @@ import zipfile
 import operator
 from render_sub_assignment import *
 
+"""
+NOTES
+
+- en ajoutant de nouvelles tables de peptides par défaut autres que mammals dans nos données, il faut adapter dans la partie de génération de l'arbre taxonomique section 'reduction by taxonomic groups' la vérification que toutes les tables (groupes taxonomiques) ont été inclues.
+
+"""
+
+
 
 def href_dl(link, name):
     result = f'<a href="{link}" download="{name}" target="_blank">{name}</a>'
     return result
 
-def command_builder_taxoreducer(taxonomy, output, peptides_tables=None, sequence_dir=None):
+def command_builder_taxoreducer(taxonomy, output, peptides_tables=None, sequence_dir=None, limit_file=None):
     if os.path.splitext(output) == "":
         output += ".tsv"
     command = f"/usr/bin/python {common.PAMPA_DIR}main_taxonomy_filtering.py -t {taxonomy} -o {output}"
@@ -20,6 +28,8 @@ def command_builder_taxoreducer(taxonomy, output, peptides_tables=None, sequence
         command += f" -p {' '.join(peptides_tables)}"
     if sequence_dir:
         command += f" -d {sequence_dir}"
+    if limit_file:
+        command += f" -l {limit_file}"
     return command
 
 def zip_results(file_names, run_id, job_name=None):
@@ -61,7 +71,7 @@ def results_output(run_id, job_name=None):
 
     return  html
 
-def assignments_output(run_id, taxo_used, tree_created, job_name=""):
+def assignments_output(run_id, taxo_used, taxo_info, job_name=""):
     """Produce a HTML table showing the assignments without detail."""
 
     html = ''
@@ -105,14 +115,14 @@ def assignments_output(run_id, taxo_used, tree_created, job_name=""):
         else:
             row[0] = "-"
             row[-1] = "-"
-        td_row = "".join(f'<td class="link_img" data-spectrumname="{spectrum_name}" data-jobname="{job_name}" data-tree="{tree_created}">{e}</td>' for e in row)
+        td_row = "".join(f'<td class="link_img" data-spectrumname="{spectrum_name}" data-jobname="{job_name}" data-taxo="{taxo_info}">{e}</td>' for e in row)
         html += f'<tr class="{row_class[i%2]}">{td_row}</tr>'
 
     html += '</table>'
         
     return html
 
-def write_main_page(run_id, taxo_used, tree_created, job_name=None):
+def write_main_page(run_id, taxo_used, taxo_info, job_name=None):
     """Write a HTML page. The result page shown first when the PAMPA analysis is done."""
     html = ""
 
@@ -144,7 +154,7 @@ def write_main_page(run_id, taxo_used, tree_created, job_name=None):
 
     # Show the assignments in a table
     html += ('<br>')
-    html += (assignments_output(run_id, taxo_used, tree_created, job_name=job_name))
+    html += (assignments_output(run_id, taxo_used, taxo_info, job_name=job_name))
     html += ('<br>')
 
     # Display assignment thumbnails
@@ -171,11 +181,15 @@ def write_main_page(run_id, taxo_used, tree_created, job_name=None):
     open(common.RESULT_DIR + run_id + "/results.php", "w").write(html)
 
 
-def gen_trees(run_id, url_json):
+def gen_trees(run_id, taxo_custom=False):
     json_content = json.load(open(common.RESULT_DIR + run_id + "/out_" + run_id +".json"))
+    if taxo_custom:
+        url_json = f"/pampa/result/{run_id}/taxonomy_{run_id}.json"
+    else:
+        url_json = "/pampa/data_pampa/taxonomy_reduced.json"
     for assignment in json_content:
         assign = assignment["lca_name"]
-        gen_sub_tree(common.RESULT_DIR, run_id, assign.replace(" ", "_"), assignment, "#0000FF", url_json)
+        gen_sub_tree(common.RESULT_DIR, run_id, assign.replace(" ", "_"), assignment, "#0000FF", url_json=url_json)
 
 
 # Main program
@@ -191,10 +205,10 @@ def main():
         job_name = None
     taxo_source = params["taxo_source"]
     taxo_file = params["taxo_file"]
-    if "limit_taxid" in params:
-        limit_taxid = params['limit_taxid']
+    if "limit" in params:
+        limit = params['limit']
     else:
-        limit_taxid = None
+        limit = False
     if "data_tables" in params:
         data_tables = params['data_tables']
         data_dir = None
@@ -218,53 +232,73 @@ def main():
     # Sous-arbres taxonomiques
     log_tree = open("log.txt", "a")
     tree_created = taxo_used
-    """if taxo_used:
+    info = ""
+    if taxo_used:
         log_tree.write("PAMPA is using a taxonomy. Preparing the tree(s)...\n")
         try:
             if taxo_source == "default_reduced":
                 log_tree.write("using the taxonomy reduced\n")
-                if f"{common.RESULT_DIR}{run_id}/{os.path.basename(common.PEPTIDES_MAMMALS_FILE)}" in data_tables: # if taxo selection by group (can't be tested now because we only have the mammals table)
+
+                if f"{common.RESULT_DIR}{run_id}/{os.path.basename(common.PEPTIDES_MAMMALS_FILE)}" not in data_tables: # if taxo selection by group 
+                    # reduction by taxonomic groups
                     log_tree.write("reduction by taxonomic groups\n")
                     taxo_reduced_file = f"{common.RESULT_DIR}{run_id}/taxonomy_{run_id}.tsv"
-                    os.system(command_builder_taxoreducer(taxo_file, taxo_reduced_file, peptides_tables=data_tables))
-                    log_tree.write(f"reduce passed\n")
-                    os.system(f"/usr/bin/python {common.POSTGRESQL_DIR}fill_taxo.py {taxo_reduced_file} {run_id}")
-                    log_tree.write(f"bdd passed\n")
-                    os.system(f"/usr/bin/python {common.POSTGRESQL_DIR}json_taxo.py {common.RESULT_DIR+run_id} {run_id}")
-                    log_tree.write(f"json passed\n")
-                    url_json = f"{common.RESULT_DIR}{run_id}/taxonomy_{run_id}.json"
-                elif False: # TODO if limits taxo
+                    command_reduce = command_builder_taxoreducer(taxo_file, taxo_reduced_file, peptides_tables=data_tables)
+                    log_tree.write(f"reduce taxo: {command_reduce}\n")
+                    os.system(command_reduce)  # reduces the taxonomy from the taxonomy_reduced.tsv
+                    command_bdd = f"/usr/bin/python {common.POSTGRESQL_DIR}fill_taxo.py {taxo_reduced_file} {run_id}"
+                    log_tree.write(f"bdd: {command_bdd}\n")
+                    os.system(command_bdd)  # creates a BDD from the taxonomy reduced previously
+                    command_json = f"/usr/bin/python {common.POSTGRESQL_DIR}json_taxo.py {common.RESULT_DIR+run_id} {run_id}"
+                    log_tree.write(f"json creation: {command_json}\n")
+                    os.system(command_json)  # creates a json from the BDD
+                    taxo_custom = True
+
+                elif limit: # if limits taxo from the limit_file - reduction by limit file
                     log_tree.write("reduction by limit file\n")
-                    pass  # TODO r(limits,taxo_reduced) / b / d
-                else : # le fichier taxo_reduced est utilisable tel quel
+                    limit_file = f"{common.RESULT_DIR}{run_id}/limitfile.txt"
+                    taxo_reduced_file = f"{common.RESULT_DIR}{run_id}/taxonomy_{run_id}.tsv"
+                    command_reduce = command_builder_taxoreducer(taxo_file, taxo_reduced_file, limit_file=limit_file)
+                    log_tree.write(f"reduce taxo: {command_reduce}\n")
+                    os.system(command_reduce)  # reduces the taxonomy from the taxonomy_reduced.tsv
+                    command_bdd = f"/usr/bin/python {common.POSTGRESQL_DIR}fill_taxo.py {taxo_reduced_file} {run_id}"
+                    log_tree.write(f"bdd: {command_bdd}\n")
+                    os.system(command_bdd)  # creates a BDD from the taxonomy reduced previously
+                    command_json = f"/usr/bin/python {common.POSTGRESQL_DIR}json_taxo.py {common.RESULT_DIR+run_id} {run_id}"
+                    log_tree.write(f"json creation: {command_json}\n")
+                    os.system(command_json)  # creates a json from the BDD
+                    taxo_custom = True
+
+                else : # le fichier taxo_reduced est utilisable tel quel - no reduction
                     log_tree.write("no reduction\n")
-                    url_json = common.DATA_PAMPA_DIR+"taxonomy_reduced.json"
+                    taxo_custom = False
             else:
                 pass
                 # TODO récupère le type de donnnées (table ou séquences)
                 # TODO Récupère les noms de fichiers
                 # TODO fait la r(data; taxo_all) / b / d
-            log_tree.write(f"gentree start\n")
-            url_json = common.DATA_PAMPA_DIR+"taxonomy_reduced.json"
-            gen_trees(run_id, url_json)
-            log_tree.write(f"gentree passed\n")
+
+            # TODO Attention gentrees va échouer pour toutes conditions impliquant une réduction taxonomique sur fichier limite (la réduction supprime les feuilles)
+            gen_trees(run_id, taxo_custom=taxo_custom)
+            
 
         except:
             tree_created = False
             log_tree.write(f"Tree generation failed.\n")
     else:
         tree_created = False
-        log_tree.write(f"\nNo tree was generated because PAMPA did not use any taxonomy for its analysis.\n")"""
+        log_tree.write(f"\nNo tree was generated because PAMPA did not use any taxonomy for its analysis.\n")
     log_tree.close()
 
-    
-    url_json = common.DATA_PAMPA_DIR+"taxonomy_reduced.json"
-    gen_trees(run_id, url_json)
-
     #gen_thumbs(common.RESULT_DIR, run_id)
-
-
-    write_main_page(run_id, taxo_used, tree_created, job_name=job_name)
+    if tree_created:
+        if taxo_custom:
+            taxo_info = "custom"
+        else:
+            taxo_info = "default"
+    else:
+        taxo_info = info
+    write_main_page(run_id, taxo_used, taxo_info, job_name=job_name)
 
 
 main()

www/cgi-bin/pampa/render_sub_assignment.py

@@ -25,7 +25,8 @@ def gen_sub_tree(chemin_result, run_id, assign_name, assignment, color, url_json
     assignment_file.write("<script src='/pampa/js/jstree/jstree.min.js'></script>")
     assignment_file.write("<link style='text/css' rel='stylesheet' href='/Style/css/bioinfo.css'>")
 
-#    url_json = "/pampa/result/" + run_id + "/" + assign_name + ".json"
+    # url_json = "/pampa/result/" + run_id + "/" + taxo_corename + ".json"
+    # url_json = "/pampa/data_pampa/taxonomy_reduced.json"
 
     jstree_function = """
                 <script type="text/javascript">         

www/html/pampa/js/pampa.js

@@ -26,7 +26,7 @@ $(document).on("click", ".link_img", function() {
     formData.append("run_id", curitem[5]);
     formData.append("spectrum_name", $(this).data("spectrumname"));
     formData.append("job_name", $(this).data("jobname"));
-    formData.append("tree", $(this).data("tree"));
+    formData.append("taxo", $(this).data("taxo"));
 
     $.ajax({
         url: "/cgi-bin/pampa/render_details.py",