From 84ddbb62e180e1e04ef36d8d43bd0698f46b96b7 Mon Sep 17 00:00:00 2001
From: local_comparaison <mathieu.umec@inrae.fr>
Date: Thu, 7 Mar 2024 14:15:09 +0100
Subject: [PATCH] cleaning branches
---
Mapping_using_the_API.py | 54 +++++++---------------------------------
main.py | 23 ++++++-----------
2 files changed, 17 insertions(+), 60 deletions(-)
diff --git a/Mapping_using_the_API.py b/Mapping_using_the_API.py
index 5e5322d..ce1a9cd 100644
--- a/Mapping_using_the_API.py
+++ b/Mapping_using_the_API.py
@@ -12,7 +12,7 @@ from scipy.stats import hypergeom
from utils import excel_file_writer, pre_cut, recup_all_inf_excel, cor_index
FOLDER = "C:\\Users\\mumec\\Desktop\\Mini_codes\\mapping_using_the_api\\"
import certifi
-
+import urlopen
def send_request_to_mapping_api(url, data_json, head, met='POST'):
@@ -27,50 +27,17 @@ def send_request_to_mapping_api(url, data_json, head, met='POST'):
Returns:
Type of return: 1 excel file whith 5 columns
-
- req = request.Request(url, data=data_json, headers=head, method=met)
- with request.urlopen(req) as response:
- result = response.read()
- out_data = result.decode('utf-8')
- return out_data
"""
- print()
- context = ssl.create_default_context(cafile=certifi.where())
- r = requests.post(url, data_json, headers=head, verify=certifi.where())
- print(type(r))
- return r
-
-
-"""
-def send_request_to_mapping_api(url, data_json, head, met='POST'):
-
-
- This function gives the result of mapping of a metabolites list from RAMP.
- Here's an example of 4 metabolites giving 505 lines.
- ["KEGG:C01157","hmdb:HMDB0000064","hmdb:HMDB0000148","chebi:16015"]
-
- Arg:
- url = the url to use
- data_json = the data to post
- head = headers to use
- met = 'POST'
-
- Returns:
- Type of return: 1 excel file with 5 columns
-
- try:
- req = request.Request(url, data=data_json, headers=head, method=met, verify=certifi.where())
+ try :
+ req = request.Request(url, data=data_json, headers=head, method=met)
with request.urlopen(req) as response:
result = response.read()
out_data = result.decode('utf-8')
- return out_data
- except error.HTTPError as e:
- print(f"Error: The server couldn't fulfill the request. {e}")
- return []
- except Exception as e:
- print(f"An unexpected error occurred: {e}")
- return []
-"""
+ except error.URLError as e:
+ r = requests.post(url, data=data_json, headers=head, verify=False)
+ return r.text
+ return out_data
+
def mapping_ramp_api(metabolites_list, outfile, inf="flow"):
"""
@@ -767,8 +734,7 @@ def opti_multimapping(file, outfolder, mapping="flow"):
cpdbf = outfolder+recap[i_map_opt][0]+"_mapping_opti.xlsx"
datas_cpdb = m_ora_cpdb(cpdb_o_opti, acctype, infos="flow",
ofile=cpdbf, cor_inf=[name_opti, cpdb_o_opti])
-
- #Probléme RAMP voir aprés
+ print("CEST AU TOUR DE RAMP")
for line in inf[1:]:
to_test.append(line[1])
l_opt_ramp = []
@@ -814,8 +780,6 @@ def opti_multimapping(file, outfolder, mapping="flow"):
print("lines Ramp", n_map)
l_opt_ramp_tri[0] = "RAMP"
recap.append(l_opt_ramp_tri)
-
- datas_ramp = ["NA" for i in range(len(file)+1) ] # provisoire aussi !!!!
recap.append(modulation)
df_recap = pd.DataFrame(data=recap).transpose()
n_out_f = outfolder+"recap_multimapping.xlsx"
diff --git a/main.py b/main.py
index 92b4a29..b38b180 100644
--- a/main.py
+++ b/main.py
@@ -9,8 +9,7 @@ import pandas as pd
import py4cytoscape as p4c
sys.path.append('C:\\Users\\mumec\\Desktop\\Dossier_gitlab_local\\traitement_des_données')
sys.path.append('C:\\Users\\mumec\\Desktop\\Dossier_gitlab_local\\chebi-ids.git')
-sys.path.append("C:\\Users\\mumec\\Desktop\\Mini_codes\\pdf_PyPDF2")
-from test_pdf import out_pdf_mapping
+from pdf_generation_toolbox import out_pdf_mapping
from Recovery_of_associated_Chebi_IDs import chebi_horizontal
from utils import excel_file_writer, pre_cut, recup_all_inf_excel
from complete_processing_of_mapping_results import c_p_o_m_r
@@ -125,13 +124,12 @@ def workflow(infile, out_folder):
result_cpdb, result_ramp, recap = opti_multimapping(datas_f_map, out_folder,
mapping="flow")
# ajouter la mention ID exact !
- #l_visu = c_p_o_m_r(result_ramp, out_folder, "RAMP", f_view_sav=out_folder,
- # modul="flow", f_modul=recap)
+ l_visu = c_p_o_m_r(result_ramp, out_folder, "RAMP", f_view_sav=out_folder,
+ modul="flow", f_modul=recap)
l_visu_c = c_p_o_m_r(result_cpdb, out_folder, "CPDB", f_view_sav=out_folder,
modul="flow", f_modul=recap)
- #l_visu += l_visu_c[1:]
- #l_visu.append(l_visu_c[0])
- l_visu = l_visu_c # provisooire aussi !
+ l_visu += l_visu_c[1:]
+ l_visu.append(l_visu_c[0])
result_ramp_pdf = []
result_cpdb_pdf = []
recap_pdf = []
@@ -144,9 +142,9 @@ def workflow(infile, out_folder):
new_line.append(str(i_line[i_col]))
liste_reverse[i_liste].append(new_line)
file_path = "Modele_de_pdf_feneratio_en_anglais_rev_19-02-2024.docx"
- #out_pdf_mapping(file_path, data_input, chebi_hori, recap_pdf,
- # result_ramp_pdf[:8], result_cpdb_pdf[:4],
- # out_folder, l_visu)
+ out_pdf_mapping(file_path, data_input, chebi_hori, recap_pdf,
+ result_ramp_pdf[:8], result_cpdb_pdf[:4],
+ out_folder, l_visu)
l_bdd = ["Wikipathways", "KEGG", "EHMN",
"HumanCyc", "INOH", "Reactome"] # "SMPDB" plantage
t2 = time()
@@ -155,23 +153,18 @@ def workflow(infile, out_folder):
for bddnow in l_bdd:
t_i_name = [recap[0] + recap[0], recap[1] + recap[2]] #not opti
print(t_i_name)
- #out_links = out_folder + "CPDB_links_network" + bddnow + "datas_base.xlsx"
out_links = out_folder + "Network CPDB with only "+ bddnow + " pathways.xlsx"
edge_data, nodes_data = paths_link_cpdb(result_cpdb, out_links, recap,
bdd=bddnow, flow=True,
tab_id_name=t_i_name)
- """
if bddnow == "Reactome":
print(network_visu(edge_data[0:3], nodes_data,
bdd=bddnow, sav_fol=out_folder))
else:
print(network_visu(edge_data[0:3], nodes_data, bdd=bddnow))
- """
t3 = time()
- """
print("le temps nécessaires pour effectuer les visualisation a était de ",
t3-t1, "secondes.")
- """
print("le temps total pour faire tourner le programme est a était ",
t3-t1, "secondes.")
--
GitLab