fix bug and of pathwyas name of CPDB

src/processing_mapping_results/mapping_using_api.py

@@ -195,7 +195,7 @@ def mapping_ramp_api_enrichment(metabolites_list, outfile, inf="all"):
     return (len(list_result[0]), list_result)
 
 
-def mapping_ramp_offline(meta_l_r_off, outfile, conect_id, inf="flow", all_name=False):
+def mapping_ramp_offline(meta_l_r_off, outfile, conect_id, inf="flow", all_name=False): # Version non modifier
     """
     This function gives the result of mapping of a metabolites list from RAMP.
     for the moment this function is not correct but it's work...
@@ -210,8 +210,8 @@ def mapping_ramp_offline(meta_l_r_off, outfile, conect_id, inf="flow", all_name=
 
     Returns:
         1 excel file whith 5 columns
-    """
 
+    """
     if len(meta_l_r_off) == 0:
         badend = " Your metabolite list is empty. Here's an example"
         badend += "['KEGG:C01157','hmdb:HMDB0032566','chebi:16015']"
@@ -324,6 +324,7 @@ def mapping_ramp_offline(meta_l_r_off, outfile, conect_id, inf="flow", all_name=
     return (len(full_results), df_result.transpose().values.tolist())
 
 
+
 def multimapping_ramp(file, num_col, outfiles, infpath="Yes"):
     """
     Processe multimapping from multi list
@@ -623,6 +624,7 @@ def m_ora_cpdb(accnumbers, acctype, cpdbidsbg=None,
         print("Mapping empty")
         return []
     print("CPDB mapping ok")
+    # Shapping API data for upcoming treatment
     details = str(xml_dict_orar["ns1:details"])
     pval = str(xml_dict_orar["ns1:pValue"])[2:-2]
     qval = str(xml_dict_orar["ns1:qValue"])[2:-2]
@@ -680,6 +682,7 @@ def m_ora_cpdb(accnumbers, acctype, cpdbidsbg=None,
             output_1[4][pos] = output_1[4][pos][9:]
     name_splited = name.split("', '")
     source = ["source"]
+    """
     for nam_i, nam in enumerate(name_splited):
         p_ind = nam.index("(")
         sub_nam = nam[p_ind+1:-1]
@@ -688,7 +691,14 @@ def m_ora_cpdb(accnumbers, acctype, cpdbidsbg=None,
             sub_nam = nam[p_ind+2:-1]
         sub_nam = sub_nam.strip("(")
         source.append(sub_nam)
-        name_splited[nam_i] = nam[:p_ind-1]
+        name_splited[nam_i] = nam[:p_ind].strip()
+    """
+    for nam_i, nam in enumerate(name_splited):
+        p_ind = 0
+        for npar in range(nam.count("(")):
+            p_ind += nam[p_ind:].index("(") + 1
+        source.append(nam[p_ind:-1])
+        name_splited[nam_i] = nam[:p_ind-1].strip()
     name_splited.insert(0, "Pathways")
     psplited = pval.split("', '")
     psplited.insert(0, "p-value")
@@ -1188,4 +1198,42 @@ if __name__ == "__main__":
     ID = ["127.0.0.1", "root", "A6y39m26&1608", "ramp_version_2024_04_11"]
     mapping_ramp_offline(metabo_l, FI_OUT, ID, inf="flow", all_name=True)
     """
-    print(try_parameters_cpdb(["16015", "15903"], "chebi", pthreshold=0.05))
+    #print(try_parameters_cpdb(["16015", "15903"], "chebi", pthreshold=0.05))
+    Fold = "C:\\Users\\mumec\\Desktop\\Mini_codes\\ajout_informations_workflow\\"
+    m_ora_cpdb(["16015", "15903", "18019", "16523"], 'chebi', infos="flow",
+               ofile=Fold + "test_out_cpdb.xlsx")
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