--- a/data_manager/resource_building.py	Tue Jun 09 15:12:03 2020 +0000
+++ b/data_manager/resource_building.py	Tue Jun 09 16:14:33 2020 +0000
@@ -280,7 +280,7 @@
     ftp.quit()
     return (path)
 
-def download_from_nextprot_ftp(file,target_directory):
+def download_from_nextprot_ftp(file,target_directory) :
     ftp_dir = "pub/current_release/ac_lists/"
     path = os.path.join(target_directory, file)
     ftp = ftplib.FTP("ftp.nextprot.org")
@@ -288,19 +288,19 @@
     ftp.cwd(ftp_dir)
     ftp.retrbinary("RETR " + file, open(path, 'wb').write)
     ftp.quit()
-    return path
+    return (path)
 
-def id_list_from_nextprot_ftp(file) :
+def id_list_from_nextprot_ftp(file,target_directory) :
+    ftp_dir = "pub/current_release/ac_lists/"
+    path = os.path.join(target_directory, file)
     ftp = ftplib.FTP("ftp.nextprot.org")
     ftp.login("anonymous", "anonymous") 
-    r = StringIO()
-    ftp.retrlines("RETR " + file, lambda line: r.write(line + '\n'))
+    ftp.cwd(ftp_dir)
+    ftp.retrbinary("RETR " + file, open(path, 'wb').write)
     ftp.quit()
-    r.seek(0)
-    ids = r.readlines()
-    ids = [id.strip('\n') for id in ids]
-
-    return (ids)
+    with open(path,'r') as nextprot_ids :
+        nextprot_ids = nextprot_ids.read().splitlines()
+    return (nextprot_ids)
 
 #return '' if there's no value in a dictionary, avoid error
 def access_dictionary (dico,key1,key2) :
@@ -544,86 +544,77 @@
 #######################################################################################################
 # 5. nextprot (add protein features)
 #######################################################################################################
+
 def Build_nextprot_ref_file(data_manager_dict,target_directory):
-
-    from requests_futures.sessions import FuturesSession
-    from concurrent.futures import ProcessPoolExecutor
-
-    #Get nextprot ids list
-    ids = id_list_from_nextprot_ftp("pub/current_release/ac_lists/nextprot_ac_list_all.txt")
+    nextprot_ids_file = "nextprot_ac_list_all.txt"
+    ids = id_list_from_nextprot_ftp(nextprot_ids_file,target_directory)
     
     output_file = 'nextprot_ref_'+ time.strftime("%d-%m-%Y") + ".tsv"
     path = os.path.join(target_directory,output_file)
     name = "neXtProt release "+time.strftime("%d-%m-%Y")
     release_id = "nextprot_ref_"+time.strftime("%d-%m-%Y")
-
-    #open output file to write
+    
     output = open(path, 'w')
     writer = csv.writer(output,delimiter="\t")
-    writer.writerow(["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence"])
-
-    subset=100
-    ids_subsets = [ids[x:x+subset] for x in range(0, len(ids), subset)]
-
-    for ids_subset in ids_subsets:
-
-        #Open concurent sessions
-        with FuturesSession(executor=ProcessPoolExecutor(max_workers=8)) as session:
-            futures = [session.get("https://api.nextprot.org/entry/"+id+".json") for id in ids_subset]
-
-        for id,future in zip(ids_subset,futures) :
+        
+    nextprot_file=[["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence"]]
+    writer.writerows(nextprot_file)
+    
+    for id in ids :
+        query="https://api.nextprot.org/entry/"+id+".json"
+        try:
+            resp = requests.get(url=query)
+        except :
+            print ("wainting 1 hour before trying again")
+            time.sleep(3600)
+            resp = requests.get(url=query)
+        data = resp.json()
 
-            #Get json dictionary 
-            try:
-                res = future.result()
-            except:
-                print ("sleep 1 hour")
-                time.sleep(3600)
-                res = future.result()
-            data = res.json()
-
-            #get info from json dictionary
-            mass_mol = data["entry"]["isoforms"][0]["massAsString"]
-            seq_length = data['entry']["isoforms"][0]["sequenceLength"]
-            iso_elec_point = data['entry']["isoforms"][0]["isoelectricPointAsString"]
-            chr_loc = data['entry']["chromosomalLocations"][0]["chromosome"]        
-            protein_existence = "PE"+str(data['entry']["overview"]['proteinExistence']['level'])
+        #get info from json dictionary
+        mass_mol = data["entry"]["isoforms"][0]["massAsString"]
+        seq_length = data['entry']["isoforms"][0]["sequenceLength"]
+        iso_elec_point = data['entry']["isoforms"][0]["isoelectricPointAsString"]
+        chr_loc = data['entry']["chromosomalLocations"][0]["chromosome"]        
+        protein_existence = "PE"+str(data['entry']["overview"]['proteinExistence']['level'])
 
-            #put all subcell loc in a set
-            if "subcellular-location" in data['entry']["annotationsByCategory"].keys() :
-                subcell_locs = data['entry']["annotationsByCategory"]["subcellular-location"]
-                all_subcell_locs = set()
-                for loc in subcell_locs :
-                    all_subcell_locs.add(loc['cvTermName'])
-                all_subcell_locs.discard("")
-                all_subcell_locs = ";".join(all_subcell_locs)
-            else :
-                all_subcell_locs = "NA"
-            
-            #put all subcell loc in a set
-            if ('disease') in data['entry']['annotationsByCategory'].keys() :
-                diseases = data['entry']['annotationsByCategory']['disease']
-                all_diseases = set()
-                for disease in diseases :
-                    if (disease['cvTermName'] is not None and disease['cvTermName'] != ""):
-                        all_diseases.add(disease['cvTermName'])
-                if len(all_diseases) > 0 : all_diseases = ";".join(all_diseases)
-                else : all_diseases="NA"
-            else :
-                all_diseases="NA"
+        #put all subcell loc in a set
+        if "subcellular-location" in data['entry']["annotationsByCategory"].keys() :
+            subcell_locs = data['entry']["annotationsByCategory"]["subcellular-location"]
+            all_subcell_locs = set()
+            for loc in subcell_locs :
+                all_subcell_locs.add(loc['cvTermName'])
+            all_subcell_locs.discard("")
+            all_subcell_locs = ";".join(all_subcell_locs)
+        else :
+            all_subcell_locs = "NA"
+        
+        #put all subcell loc in a set
+        if ('disease') in data['entry']['annotationsByCategory'].keys() :
+            diseases = data['entry']['annotationsByCategory']['disease']
+            all_diseases = set()
+            for disease in diseases :
+                if (disease['cvTermName'] is not None and disease['cvTermName'] != ""):
+                    all_diseases.add(disease['cvTermName'])
+            if len(all_diseases) > 0 : all_diseases = ";".join(all_diseases)
+            else : all_diseases="NA"
+        else :
+            all_diseases="NA"
 
-            #get all tm domain 
-            nb_domains = 0
-            if  "transmembrane-region" in data['entry']['annotationsByCategory'].keys():
-                tm_domains = data['entry']['annotationsByCategory']["transmembrane-region"]
-                all_tm_domains = set()
-                for tm in tm_domains :
-                    all_tm_domains.add(tm['cvTermName'])
-                    nb_domains+=1
+        #get all tm domain 
+        nb_domains = 0
+        if  "transmembrane-region" in data['entry']['annotationsByCategory'].keys():
+            tm_domains = data['entry']['annotationsByCategory']["transmembrane-region"]
+            all_tm_domains = set()
+            for tm in tm_domains :
+                all_tm_domains.add(tm['cvTermName'])
+                nb_domains+=1
+                #print "nb domains ++"
+                #print (nb_domains)
+        nextprot_file[:] = [] 
+        nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence])
+        writer.writerows(nextprot_file)
 
-            writer.writerow([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence])
-
-    id = str(10000000000 - int(time.strftime("%Y%m%d")))
+        id = str(10000000000 - int(time.strftime("%Y%m%d")))
 
     data_table_entry = dict(id=id, release=release_id, name = name, value = path)
     _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_nextprot_ref")