Refactor peptide handling and add digestion configuration support

www/cgi-bin/pampa/pampa-craft.py

@@ -21,7 +21,7 @@ def extract_request(form):
 
     #Options et methodes:
     taxonomy = ["fillin", "homology"]
-    pconfig = ["fillin", "allpeptides", "selection", "deamidation"]
+    pconfig = ["fillin", "allpeptides"]
     spectre = ["allpeptides", "selection"]
 
     error_found = False
@@ -53,6 +53,12 @@ def extract_request(form):
         elif method == "fillin":
             extract_files_from_list([common.FILLIN_PEPTIDE], resdir)
             req["peptides_path"] = resdir + '/' + "fillin_peptides.tsv"
+        elif method == "selection":
+            extract_files_from_list([common.SELECTION_PEPTIDE], resdir)
+            req["peptides_path"] = resdir + '/' + "selection_peptides.tsv"
+        elif method == "deamidation":
+            extract_files_from_list([common.DEAMIDATION_PEPTIDE], resdir)
+            req["peptides_path"] = resdir + '/' + "deamidation_peptides.tsv"
     elif 'peptides_file' in form and form['peptides_file'].filename != "":
         f = form['peptides_file'].filename
         fn = os.path.basename(f)
@@ -126,7 +132,10 @@ def extract_request(form):
         extract_error_margin(form, log, req, error_messages)
 
     if method in spectre:
-        if 'spectra_files' in form:
+        if 'craft-example' in form and method == "selection":
+            extract_files_from_list([common.SELECTION_SPECTRA], abs_spectra_dir)
+            req['spectra_dir'] = abs_spectra_dir
+        elif 'spectra_files' in form:
             # spectres utilisateurs
             fileitems = form['spectra_files']
             if not isinstance(fileitems, list):
@@ -153,13 +162,18 @@ def extract_request(form):
         extract_taxonomy_selection(form, log, req, error_messages, resdir)
 
     if method in pconfig:
-        if form["digestion"].value != "" and form["digestion"].value != "Trypsin":
+        if form["digestion"].value != "" and form["digestion"].value != "trypsin":
             digestion = form["digestion"].value
         else:
             digestion = None
 
         if digestion:
-            req["config"] = digestion
+            with open(f'{common.CONFIG_FILE}', 'r') as f:
+                data = json.load(f)
+                data['enzyme'] = digestion
+                json.dump(data, open(f'{resdir}/config.json', 'w'))
+                log.write(f"Digestion set to {digestion}\n")
+                req['config_file'] = resdir + '/config.json'
 
     log.write("Recap downloads :\n")
     for fn in req['files_uploaded']:
@@ -199,6 +213,9 @@ def launch_software(run_id, req):
     if 'taxo_file' in req:
         taxo_file_arg = req["taxo_file"]
         command += " -t " + taxo_file_arg
+    if 'config_file' in req:
+        config_file_arg = req["config_file"]
+        command += " -c " + config_file_arg
     command += " --web"
     open("acommand.txt", "w").write(f"{command}")  # log