New db

EMSL_api.py

@@ -13,9 +13,9 @@ Usage:
                                 [--db_path=db_path]
                                 [--with_l]
                                 [(--save [--path=path])]
-  EMSL_api.py get_list_formats
+  EMSL_api.py list_formats
   EMSL_api.py create_db      --db_path=db_path
-                             --format
+                             --format=format
                              [--no-contraction]
   EMSL_api.py (-h | --help)
   EMSL_api.py --version
@@ -50,7 +50,7 @@ if __name__ == '__main__':
         db_path = arguments["--db_path"]
     else:
         import os
-        db_path = os.path.dirname(sys.argv[0]) + "/db/Gausian_uk.db"
+        db_path = os.path.dirname(sys.argv[0]) + "/db/Gamess-us.db"
 
     # _     _     _    ______           _
     #| |   (_)   | |   | ___ \         (_)
@@ -115,7 +115,7 @@ if __name__ == '__main__':
     #| |   | / __| __| |  _/ _ \| '__| '_ ` _ \ / _` | __/ __|
     #| |___| \__ \ |_  | || (_) | |  | | | | | | (_| | |_\__ \
     #\_____/_|___/\__| |_| \___/|_|  |_| |_| |_|\__,_|\__|___/
-    if arguments["get_list_formats"]:
+    if arguments["list_formats"]:
         for i in format_dict:
             print i
 
@@ -129,7 +129,7 @@ if __name__ == '__main__':
         db_path = arguments["--db_path"]
         format = arguments["--format"]
         if format not in format_dict:
-            print "Format %s doesn't exist. Run get_list_formats to get the list of formats." % (format)
+            print "Format %s doesn't exist. Run list_formats to get the list of formats." % (format)
             sys.exit(1)
         contraction = not arguments["--no-contraction"]
 

src/EMSL_utility.py

@@ -6,7 +6,17 @@ import sys
 import os
 import time
 
-debug = False
+debug = True
+
+elt_path = os.path.dirname(sys.argv[0]) + "/src/elts_abrev.dat"
+
+with open(elt_path, "r") as f:
+    data = f.readlines()
+
+dict_ele = dict()
+for i in data:
+    l = i.split("-")
+    dict_ele[l[1].strip().lower()] = l[2].strip().lower()
 
 
 def cond_sql_or(table_name, l_value):
@@ -118,10 +128,21 @@ class EMSL_dump:
                 print data
             raise Exception("WARNING not DATA")
         else:
+            data = data.replace("PHOSPHOROUS", "PHOSPHORUS")
             data = data[b + 5:e].split('\n\n')
+
             for (elt, data_elt) in zip(elts, data):
 
-                d.append((name, des, elt, data_elt))
+                elt_long_th = dict_ele[elt.lower()]
+                elt_long_exp = data_elt.split()[0].lower()
+
+                if elt_long_th == elt_long_exp:
+                    d.append((name, des, elt, data_elt.strip()))
+                else:
+                    print "th", elt_long_th
+                    print "exp", elt_long_exp
+                    print "abv", elt
+                    raise Exception("WARNING not good ELEMENT")
 
         return d
 
@@ -139,7 +160,7 @@ class EMSL_dump:
         import threading
 
         num_worker_threads = 7
-        num_try_of_dwl = 2
+        attemps_max = 20
 
         q_in = Queue.Queue(num_worker_threads)
         q_out = Queue.Queue(num_worker_threads)
@@ -150,7 +171,8 @@ class EMSL_dump:
                 [name, url, des, elts] = q_in.get()
                 url = self.create_url(url, name, elts)
 
-                for i in range(num_try_of_dwl):
+                attemps = 0
+                while attemps < attemps_max:
                     text = self.requests.get(url).text
                     try:
                         basis_data = self.basis_data_row_to_array(
@@ -158,10 +180,14 @@ class EMSL_dump:
                         break
                     except:
                         time.sleep(0.1)
-                        pass
+                        attemps += 1
 
+                try:
                     q_out.put(([name, url, des, elts], basis_data))
                     q_in.task_done()
+                except:
+                    print name,url,des
+                    raise
 
         def enqueue():
             for [name, url, des, elts] in list_basis_array: