LCPQ/EMSL_Basis_Set_Exchange_Local
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Add dump, remove db

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This commit is contained in:
TApplencourt 2016-01-15 10:09:24 +01:00
parent e8609fbd6a
commit f121c51b14
6 changed files with 717370 additions and 21 deletions
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42
EMSL_api.py
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@ -6,19 +6,19 @@
Usage:
EMSL_api.py list_basis [--basis=<basis_name>...]
[--atom=<atom_name>...]
[--db_path=<db_path>]
[--db_path=<db_path> |--db_dump_path=<db_dump_path>]
[--average_mo_number]
EMSL_api.py list_atoms --basis=<basis_name>
[--db_path=<db_path>]
[--db_path=<db_path> |--db_dump_path=<db_dump_path>]
EMSL_api.py get_basis_data --basis=<basis_name>
[--atom=<atom_name>...]
[--db_path=<db_path>]
[--db_path=<db_path> |--db_dump_path=<db_dump_path>]
[(--save [--path=<path>])]
[--check=<program_name>]
[--treat_l]
EMSL_api.py list_formats
EMSL_api.py create_db --format=<format>
[--db_path=<db_path>]
[--db_path=<db_path> |--db_dump_path=<db_dump_path>]
[--no-contraction]
EMSL_api.py (-h | --help)
EMSL_api.py --version
@ -49,7 +49,6 @@ from src.EMSL_local import EMSL_local
if __name__ == '__main__':
arguments = docopt(__doc__, version='EMSL Api ' + version)
# ___
# | ._ o _|_
# _|_ | | | |_
@ -57,17 +56,24 @@ if __name__ == '__main__':
if arguments["--db_path"]:
db_path = arguments["--db_path"]
db_dump_path = None
elif arguments["--db_dump_path"]:
db_path = None
db_dump_path = arguments["--db_dump_path"]
else:
db_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"db/GAMESS-US.db")
db_dump_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"db/GAMESS-US.dump")
db_path = None
# db_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
# "db/GAMESS-US.db")
# Check the db
try:
if not(arguments['create_db']):
from src.EMSL_local import checkSQLite3
db_path, db_path_changed = checkSQLite3(db_path)
except:
raise
# try:
# if not(arguments['create_db']):
# from src.EMSL_local import checkSQLite3
# db_path, db_path_changed = checkSQLite3(db_path)
# except:
# raise
# _ _ _ ______ _
# | | (_) | | | ___ \ (_)
@ -77,7 +83,7 @@ if __name__ == '__main__':
# \_____/_|___/\__| \____/ \__,_|___/_|___/
if arguments["list_basis"]:
e = EMSL_local(db_path=db_path)
e = EMSL_local(db_path=db_path, db_dump_path=db_dump_path)
l = e.list_basis_available(arguments["--atom"],
arguments["--basis"],
@ -99,7 +105,7 @@ if __name__ == '__main__':
# | |___| \__ \ |_ | |___| | __/ | | | | | __/ | | | |_\__ \
# \_____/_|___/\__| \____/|_|\___|_| |_| |_|\___|_| |_|\__|___/
elif arguments["list_atoms"]:
e = EMSL_local(db_path=db_path)
e = EMSL_local(db_path=db_path, db_dump_path=db_dump_path)
basis_name = arguments["--basis"]
l = e.get_list_element_available(basis_name)
@ -112,7 +118,7 @@ if __name__ == '__main__':
# | |_/ / (_| \__ \ \__ \ | (_| | (_| | || (_| |
# \____/ \__,_|___/_|___/ \__,_|\__,_|\__\__,_|
elif arguments["get_basis_data"]:
e = EMSL_local(db_path=db_path)
e = EMSL_local(db_path=db_path, db_dump_path=db_dump_path)
basis_name = arguments["--basis"][0]
elts = arguments["--atom"]
@ -170,5 +176,5 @@ if __name__ == '__main__':
# _|
# Clean up on exit
if not(arguments['create_db']) and db_path_changed:
os.system("rm -f /dev/shm/%d.db" % (os.getpid()))
# if not(arguments['create_db']) and db_path_changed:
# os.system("rm -f /dev/shm/%d.db" % (os.getpid()))

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db/GAMESS-US.dump Normal file
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13
src/EMSL_local.py
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@ -5,6 +5,7 @@ import re
import sys
import os
from misc.sqlit import connect4git
def checkSQLite3(db_path):
"""Check if the db_path is a good one"""
@ -100,10 +101,16 @@ class EMSL_local(object):
All the method for using the EMSL db localy
"""
def __init__(self, db_path=None):
self.db_path = db_path
def __init__(self, db_path=None, db_dump_path=None):
# print db_path
# print db_dump_path
if db_path:
self.conn = sqlite3.connect(db_path)
if db_dump_path:
self.conn = connect4git(db_dump_path)
self.conn = sqlite3.connect(self.db_path)
self.c = self.conn.cursor()
self.c.execute("SELECT * from format_tab")

182
src/misc/sqlit.py Normal file
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@ -0,0 +1,182 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
try:
import sqlite3
except:
print "Sorry, you need sqlite3"
sys.exit(1)
#
# _____ _ _ _
# / ___| | |(_)| |
# \ `--. __ _ | | _ | |_
# `--. \ / _` || || || __|
# /\__/ /| (_| || || || |_
# \____/ \__, ||_||_| \__|
# | |
# |_|
# You cannot Diff / Merge sqlite binary file. But you can dump it into
# a plain text file with contain the list of command needed to recreate
# the db_file.
# (`sqlite3 db_file .dump > dump_file` For a example of dump file, see below
# in the main section)
#
# This dump_file can be added to your git.
#
# This module ensure the coherencies between the db_file and the dump_file
class ConnectionForGit(sqlite3.Connection):
"""
A sqlite3 connection for Git. It will always dumps the db when needed.
(`sqlite3 db_file .dump > dump_file`)
so now you can add dump_path to your git and work with the db like always.
The main idea is:
- When you create a sqlite3 connection: create or update the .db file
- When you commit: update the .dump file
/!\ If you create a table, you -maybe- need to make a dummy commit
for update the dump
"""
def __init__(self, db_path, dump_path, *args, **kwargs):
super(ConnectionForGit, self).__init__(db_path, *args, **kwargs)
self.db_path = db_path
self.dump_path = dump_path
def commit(self):
'''
0/ Update the DB if needed
(aka if the dump is more recent than the db)
1/ Commit in the DB
2/ Dump the DB
(`sqlite3 db_file .dump > dump_file`)
'''
try:
ConnectionForGit.dump_to_sqlite(self.dump_path, self.db_path)
sqlite3.Connection.commit(self)
except sqlite3.Error:
raise
else:
ConnectionForGit.sqlite_to_dump(self.db_path, self.dump_path)
@staticmethod
def isSQLite3(filename):
"""
Verify is filename is a SQLite3 format db
"""
from os.path import isfile, getsize
if not isfile(filename):
return False
# SQLite database file header is 100 bytes
if getsize(filename) < 100:
return False
with open(filename, 'rb') as fd:
header = fd.read(100)
if header[:16] == 'SQLite format 3\x00':
return True
else:
return False
@staticmethod
def dump_to_sqlite(dump_path, db_path):
"""
Take a dump and populate the db if the dump is the most recent
0/ If no .dump file touch it
1/ If no .db file populate it
2/ Check the date a modify accordingly
"""
if not os.path.isfile(dump_path):
os.system('touch {0}'.format(dump_path))
if not os.path.isfile(db_path):
os.system("sqlite3 {0} < {1}".format(db_path, dump_path))
else:
dump_time = os.path.getmtime(dump_path)
db_time = os.path.getmtime(db_path)
if dump_time > db_time:
os.system("rm {0}".format(db_path))
os.system("sqlite3 {0} < {1}".format(db_path, dump_path))
@staticmethod
def sqlite_to_dump(db_path, dump_path):
"""
Take a db and dump it if the db is the most recent
"""
if not ConnectionForGit.isSQLite3(db_path):
raise sqlite3.Error
dump_time = os.path.getmtime(dump_path)
db_time = os.path.getmtime(db_path)
if db_time > dump_time:
os.system("sqlite3 {0} .dump > {1}".format(db_path, dump_path))
os.system("touch {0}".format(db_path))
def connect4git(dump_path, db_path=None, *args, **kwargs):
'''
dump_path : Is the sqlite dump file you will monitor with git.
db_path : Is the <<dummy>> sqlite3 file.
0/ Update and create the db if needed
(aka if the dump is more recent than the db)
1/ Return a connection the db (a ConnectionForGit instance)
'''
if not db_path:
db_path = "{0}.db".format(os.path.splitext(dump_path)[0])
try:
ConnectionForGit.dump_to_sqlite(dump_path, db_path)
except:
raise
else:
return ConnectionForGit(db_path, dump_path, *args, **kwargs)
# ___ ___ _
# | \/ | (_)
# | . . | __ _ _ _ __
# | |\/| |/ _` | | '_ \
# | | | | (_| | | | | |
# \_| |_/\__,_|_|_| |_|
#
if __name__ == "__main__":
# From the famous http://zetcode.com/db/sqlitepythontutorial/
# It will create a test.dump and a test.db
# You can git add the test.dump and do your work like always in the db.
con = connect4git('test.dump')
with con:
cur = con.cursor()
cur.execute("CREATE TABLE Cars(Id INT, Name TEXT, Price INT)")
cur.execute("INSERT INTO Cars VALUES(1,'Audi',52642)")
cur.execute("INSERT INTO Cars VALUES(2,'Mercedes',57127)")
cur.execute("INSERT INTO Cars VALUES(3,'Skoda',9000)")
cur.execute("INSERT INTO Cars VALUES(4,'Volvo',29000)")
cur.execute("INSERT INTO Cars VALUES(5,'Bentley',350000)")
cur.execute("INSERT INTO Cars VALUES(6,'Citroen',21000)")
cur.execute("INSERT INTO Cars VALUES(7,'Hummer',41400)")
cur.execute("INSERT INTO Cars VALUES(8,'Volkswagen',21600)")
# Test.db :
#
# PRAGMA foreign_keys=OFF;
# BEGIN TRANSACTION;
# CREATE TABLE Cars(Id INT, Name TEXT, Price INT);
# INSERT INTO "Cars" VALUES(1,'Audi',52642);
# INSERT INTO "Cars" VALUES(2,'Mercedes',57127);
# INSERT INTO "Cars" VALUES(3,'Skoda',9000);
# INSERT INTO "Cars" VALUES(4,'Volvo',29000);
# INSERT INTO "Cars" VALUES(5,'Bentley',350000);
# INSERT INTO "Cars" VALUES(6,'Citroen',21000);
# INSERT INTO "Cars" VALUES(7,'Hummer',41400);
# INSERT INTO "Cars" VALUES(8,'Volkswagen',21600);
# COMMIT;