mirror of
https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local
synced 2024-10-02 06:20:49 +02:00
Check db in many way
This commit is contained in:
Thomas Applencourt
parent
be9c65f77d
commit
dc52d30fac
39
EMSL_api.py
39
EMSL_api.py
@ -36,35 +36,27 @@ import os
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from src.docopt import docopt
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from src.EMSL_utility import EMSL_dump
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from src.EMSL_utility import format_dict
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from src.EMSL_utility import EMSL_local
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from src.EMSL_utility import EMSL_local, checkSQLite3
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if __name__ == '__main__':
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arguments = docopt(__doc__, version='EMSL Api ' + version)
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# ___
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# | ._ o _|_
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# _|_ | | | |_
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#
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if arguments["--db_path"]:
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db_path = arguments["--db_path"]
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else:
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import os
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db_path = os.path.dirname(__file__) + "/db/Gamess-us.db"
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# Check if db file is readable
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if not os.access(db_path,os.R_OK):
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print >>sys.stderr, "Db file %s is not readable"%(db_path)
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sys.exit(1)
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# Check if the file system allows I/O on sqlite3 (lustre)
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# If not, copy on /dev/shm and remove after opening
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# Check the db
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try:
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EMSL_local(db_path=db_path).get_list_basis_available([])
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db_path, db_path_changed = checkSQLite3(db_path)
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except:
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new_db_path = "/dev/shm/%d.db"%(os.getpid())
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os.system("cp %s %s"%(db_path,new_db_path))
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db_path = new_db_path
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# try again to check
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EMSL_local(db_path=db_path).get_list_basis_available([])
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sys.exit(1)
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# _ _ _ ______ _
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#| | (_) | | | ___ \ (_)
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@ -106,7 +98,7 @@ if __name__ == '__main__':
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basis_name = arguments["--basis"]
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elts = arguments["--atom"]
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l = e.get_basis(basis_name, elts,arguments["--with_l"])
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l = e.get_basis(basis_name, elts, arguments["--with_l"])
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str_ = "\n\n".join(l) + "\n"
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if arguments["--save"]:
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@ -130,7 +122,8 @@ if __name__ == '__main__':
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#| |___| \__ \ |_ | || (_) | | | | | | | | (_| | |_\__ \
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#\_____/_|___/\__| |_| \___/|_| |_| |_| |_|\__,_|\__|___/
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if arguments["list_formats"]:
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for i in format_dict:
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e = EMSL_dump()
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for i in e.get_list_format():
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print i
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# _____ _ _ _
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@ -153,7 +146,11 @@ if __name__ == '__main__':
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contraction=contraction)
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e.new_db()
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# _
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# / | _ _. ._ o ._ _
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# \_ | (/_ (_| | | | | | (_|
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# _|
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# Clean up on exit
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os.system("rm -f /dev/shm/%d.db"%(os.getpid()))
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if db_path_changed:
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os.system("rm -f /dev/shm/%d.db" % (os.getpid()))
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@ -8,15 +8,56 @@ import time
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debug = True
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elt_path = os.path.dirname(sys.argv[0]) + "/src/elts_abrev.dat"
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with open(elt_path, "r") as f:
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data = f.readlines()
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def checkSQLite3(db_path):
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dict_ele = dict()
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for i in data:
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l = i.split("-")
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dict_ele[l[1].strip().lower()] = l[2].strip().lower()
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from os.path import isfile, getsize
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# Check if db file is readable
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if not os.access(db_path, os.R_OK):
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print >>sys.stderr, "Db file %s is not readable" % (db_path)
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raise IOError
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if not isfile(db_path):
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print >>sys.stderr, "Db file %s is not... a file!" % (db_path)
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raise IOError
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if getsize(db_path) < 100: # SQLite database file header is 100 bytes
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print >>sys.stderr, "Db file %s is not a SQLite file!" % (db_path)
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raise IOError
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with open(db_path, 'rb') as fd:
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header = fd.read(100)
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if header[:16] != 'SQLite format 3\x00':
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print >>sys.stderr, "Db file %s is not in SQLiteFormat3!" % (db_path)
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raise IOError
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# Check if the file system allows I/O on sqlite3 (lustre)
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# If not, copy on /dev/shm and remove after opening
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try:
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EMSL_local(db_path=db_path).get_list_basis_available()
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except sqlite3.OperationalError:
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print >>sys.stdrerr, "I/O Error for you file system"
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print >>sys.stderr, "Try some fixe"
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new_db_path = "/dev/shm/%d.db" % (os.getpid())
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os.system("cp %s %s" % (db_path, new_db_path))
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db_path = new_db_path
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else:
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changed = False
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return db_path, changed
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#Try again to check
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try:
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EMSL_local(db_path=db_path).get_list_basis_available()
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except:
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print >>sys.stderr, "Sorry..."
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os.system("rm -f /dev/shm/%d.db" % (os.getpid()))
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raise
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else:
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print >>sys.stderr, "Working !"
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changed = True
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return db_path, changed
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def install_with_pip(name):
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@ -54,11 +95,27 @@ def cond_sql_or(table_name, l_value):
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class EMSL_dump:
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format_dict = {"g94": "Gaussian94",
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"gamess-us": "GAMESS-US",
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"gamess-uk": "GAMESS-UK",
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"turbomole": "Turbomole",
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"tx93": "TX93",
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"molpro": "Molpro",
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"molproint": "MolproInt",
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"hondo": "Hondo",
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"supermolecule": "SuperMolecule",
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"molcas": "Molcas",
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"hyperchem": "HyperChem",
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"dalton": "Dalton",
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"demon-ks": "deMon-KS",
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"demon2k": "deMon2k",
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"aces2": "AcesII"
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}
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def __init__(self, db_path=None, format="GAMESS-US", contraction="True"):
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self.db_path = db_path
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self.format = format
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self.contraction = str(contraction)
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try:
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import requests
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except:
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@ -67,10 +124,27 @@ class EMSL_dump:
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finally:
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self.requests = requests
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def get_list_format(self):
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"""List all the format available in EMSL"""
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return self.format_dict
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def set_db_path(self, path):
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"""Define the database path"""
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self.db_path = path
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def get_dict_ele(self):
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"""A dict of element"""
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elt_path = os.path.dirname(sys.argv[0]) + "/src/elts_abrev.dat"
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with open(elt_path, "r") as f:
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data = f.readlines()
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dict_ele = dict()
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for i in data:
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l = i.split("-")
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dict_ele[l[1].strip().lower()] = l[2].strip().lower()
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return dict_ele
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def dwl_basis_list_raw(self):
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print "Download all the name available in EMSL. It can take some time.",
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sys.stdout.flush()
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@ -162,6 +236,8 @@ class EMSL_dump:
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data = data[b + 5:e - 1].split('\n\n')
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dict_ele = self.get_dict_ele()
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for (elt, data_elt) in zip(elts, data):
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elt_long_th = dict_ele[elt.lower()]
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@ -400,26 +476,6 @@ class EMSL_local:
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return l_data
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format_dict = \
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{
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"g94": "Gaussian94",
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"gamess-us": "GAMESS-US",
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"gamess-uk": "GAMESS-UK",
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"turbomole": "Turbomole",
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"tx93": "TX93",
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"molpro": "Molpro",
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"molproint": "MolproInt",
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"hondo": "Hondo",
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"supermolecule": "SuperMolecule",
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"molcas": "Molcas",
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"hyperchem": "HyperChem",
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"dalton": "Dalton",
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"demon-ks": "deMon-KS",
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"demon2k": "deMon2k",
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"aces2": "AcesII",
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}
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if __name__ == "__main__":
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e = EMSL_local(db_path="EMSL.db")
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