From 6932f0dfea99d7586789ad8d925863bb0c6b517a Mon Sep 17 00:00:00 2001
From: local_comparaison <mathieu.umec@inrae.fr>
Date: Fri, 24 Nov 2023 16:40:05 +0100
Subject: [PATCH] changing shape
---
Mapping_using_the_API.py | 102 ++++++++++++++++++++++-----------------
1 file changed, 57 insertions(+), 45 deletions(-)
diff --git a/Mapping_using_the_API.py b/Mapping_using_the_API.py
index f75ec70..27a5bcc 100644
--- a/Mapping_using_the_API.py
+++ b/Mapping_using_the_API.py
@@ -3,15 +3,11 @@ import json
from urllib import request, parse
-def send_request_to_Mapping_API(URL, metabolites_list, head,method='POST'):
+def send_request_to_Mapping_API(URL, data_json, head,method='POST'):
"""
This function gives us the response of the api for the metabolites list
"""
- if len(metabolites_list)==0 :
- return("Stop")
- data_for_request={"analytes": metabolites_list}
- json_data = json.dumps(data_for_request).encode('utf-8')
- req = request.Request(URL, data=json_data, headers=head, method='POST')
+ req = request.Request(URL, data=data_json, headers=head, method='POST')
with request.urlopen(req) as response:
result = response.read()
out_data=result.decode('utf-8')
@@ -39,49 +35,65 @@ The out-file is compose of five columns pathwayName, pathwaySource, pathwayId, i
A line is associated with a metabolite and a metabolic pathway
"""
- API_Datas=send_request_to_Mapping_API('https://rampdb.nih.gov/api/pathways-from-analytes',metabolites_list,{'Accept': '*/*','Content-Type': 'application/json'})
- if API_Datas=="Stop":
- print (" Your metabolite list is empty. Please restart mapping with a non-empty metabolite list. Here's an example ['KEGG:C01157','hmdb:HMDB0000064','hmdb:HMDB0000148','chebi:16015']")
+ if len(metabolites_list)==0 :
+ return (" Your metabolite list is empty. Please restart mapping with a non-empty metabolite list. Here's an example ['KEGG:C01157','hmdb:HMDB0000064','hmdb:HMDB0000148','chebi:16015']")
else:
- len_out_api=len(API_Datas)
- print(API_Datas[-3]+" metabolites were found")
- index_begin_interest=API_Datas.find("[")
- index_end_interest=API_Datas.find("]")
- datas_to_treat=API_Datas[index_begin_interest:index_end_interest+1]
- name_to_search=["pathwayName","pathwaySource","pathwayId","inputId"]
- index = datas_to_treat.find("{")
- index_begin_lines=[index]
- while index != -1:
- index+=1
- index = datas_to_treat.find("{",index)
- index_begin_lines.append(index)
- index_begin_lines[-1]=len(datas_to_treat)
- pathwayName=[]
- inputId=[]
+ data_for_request={"analytes": metabolites_list}
+ json_data = json.dumps(data_for_request).encode('utf-8')
+ API_Datas=send_request_to_Mapping_API('https://rampdb.nih.gov/api/pathways-from-analytes',json_data,{'Accept': '*/*','Content-Type': 'application/json'})
+ len_out_api=len(API_Datas)
+ print(API_Datas[-3]+" metabolites were found")
+ index_begin_interest=API_Datas.find("[")
+ index_end_interest=API_Datas.find("]")
+ datas_to_treat=API_Datas[index_begin_interest:index_end_interest+1]
+ name_to_search=["pathwayName","pathwaySource","pathwayId","inputId"]
+ index = datas_to_treat.find("{")
+ index_begin_lines=[index]
+ while index != -1:
+ index+=1
+ index = datas_to_treat.find("{",index)
+ index_begin_lines.append(index)
+ index_begin_lines[-1]=len(datas_to_treat)
+ pathwayName=[]
+ inputId=[]
+ if infos=="all" :
+ pathwaySource=[]
+ pathwayId=[]
+ commonName=[]
+ for index_pos in range (len(index_begin_lines)-1):
+ one_line=datas_to_treat[index_begin_lines[index_pos]:index_begin_lines[index_pos+1]]
+ pathwayName.append(one_line[16:one_line.find("pathwaySource")-3])
+ inputId.append(one_line[one_line.find("inputId")+10:one_line.find("commonName")-3])
if infos=="all" :
- pathwaySource=[]
- pathwayId=[]
- commonName=[]
- for index_pos in range (len(index_begin_lines)-1):
- one_line=datas_to_treat[index_begin_lines[index_pos]:index_begin_lines[index_pos+1]]
- pathwayName.append(one_line[16:one_line.find("pathwaySource")-3])
- inputId.append(one_line[one_line.find("inputId")+10:one_line.find("commonName")-3])
- if infos=="all" :
- pathwaySource.append(one_line[one_line.find("pathwaySource")+16:one_line.find("pathwayId")-3])
- pathwayId.append(one_line[one_line.find("pathwayId")+12:one_line.find("inputId")-3])
- commonName.append(one_line[one_line.find("commonName")+13:len(one_line)-3])
+ pathwaySource.append(one_line[one_line.find("pathwaySource")+16:one_line.find("pathwayId")-3])
+ pathwayId.append(one_line[one_line.find("pathwayId")+12:one_line.find("inputId")-3])
+ commonName.append(one_line[one_line.find("commonName")+13:len(one_line)-3])
+
+ pathwayName.insert(0,"pathwayName")
+ pathwaySource.insert(0,"pathwaySource")
+ pathwayId.insert(0,"pathwayId")
+ inputId.insert(0,"inputId")
+ commonName.insert(0,"commonName")
+ list_result=[pathwayName, pathwaySource, pathwayId, inputId, commonName]
+ df_result=pd.DataFrame(data=list_result).transpose()
+ excel_file_writer(df_result,outfile, sheetname="Resultats du mapping")
- pathwayName.insert(0,"pathwayName")
- pathwaySource.insert(0,"pathwaySource")
- pathwayId.insert(0,"pathwayId")
- inputId.insert(0,"inputId")
- commonName.insert(0,"commonName")
- list_result=[pathwayName, pathwaySource, pathwayId, inputId, commonName]
- df_result=pd.DataFrame(data=list_result).transpose()
- excel_file_writer(df_result,outfile, sheetname="Resultats du mapping")
+def mapping_from_MA_API(metabolites_list, outfile):
+ if len(metabolites_list)==0 :
+ return (" Your metabolite list is empty. Please restart mapping with a non-empty metabolite list. Here's an example ['1,3-Diaminopropane','2-Ketobutyric acid','2-Hydroxybutyric acid']")
+ else:
+ headers = {'Content-Type':"application/json",'cache-control':"no-cache"}
+ metabo_data=''
+ for name in metabolites_list :
+ metabo_data=metabo_data+name+';'
+ payload = {"queryList": metabo_data,"inputType": "name"}
+ json_data = json.dumps(payload).encode('utf-8')
+ API_Datas=send_request_to_Mapping_API("https://www.xialab.ca/api/mapcompounds",json_data,headers)
+ print(API_Datas)
if __name__ == "__main__":
- met_L=["KEGG:C01157","hmdb:HMDB0000064","hmdb:HMDB0000148","chebi:16015"]
+ met_L=['1,3-Diaminopropane','2-Ketobutyric acid','2-Hydroxybutyric acid']
inf="all" # all,only midfile
outf="C:\\Users\\mumec\\Desktop\\fichier_mis_en_forme_programme_total\\API_RAMP_test.xlsx"
- mapping_from_RAMP_API(met_L,outf)
\ No newline at end of file
+ #mapping_from_RAMP_API(met_L,outf)
+ mapping_from_MA_API(met_L,outf)
\ No newline at end of file
--
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