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https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local
synced 2024-10-31 19:23:42 +01:00
New design for basis set
This commit is contained in:
Thomas Applencourt
parent
d9fdab2469
commit
7c6812f258
92
EMSL_api.py
92
EMSL_api.py
@ -4,18 +4,18 @@
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"""EMSL Api.
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Usage:
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EMSL_api.py list_basis [--atom=atom_name...]
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[--db_path=db_path]
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EMSL_api.py list_atoms --basis=basis_name
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[--db_path=db_path]
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EMSL_api.py get_basis_data --basis=basis_name
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[--atom=atom_name...]
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[--db_path=db_path]
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EMSL_api.py list_basis [--atom=<atom_name>...]
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[--db_path=<db_path>]
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EMSL_api.py list_atoms --basis=<basis_name>
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[--db_path=<db_path>]
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EMSL_api.py get_basis_data --basis=<basis_name>
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[--atom=<atom_name>...]
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[--db_path=<db_path>]
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[--with_l]
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[(--save [--path=path])]
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[(--save [--path=<path>])]
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EMSL_api.py list_formats
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EMSL_api.py create_db --db_path=db_path
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--format=format
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EMSL_api.py create_db --db_path=<db_path>
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--format=<format>
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[--no-contraction]
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EMSL_api.py (-h | --help)
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EMSL_api.py --version
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@ -59,13 +59,13 @@ if __name__ == '__main__':
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except:
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sys.exit(1)
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# _ _ _ ______ _
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#| | (_) | | | ___ \ (_)
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#| | _ ___| |_ | |_/ / __ _ ___ _ ___
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#| | | / __| __| | ___ \/ _` / __| / __|
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#| |___| \__ \ |_ | |_/ / (_| \__ \ \__ \
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#\_____/_|___/\__| \____/ \__,_|___/_|___/
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#
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# _ _ _ ______ _
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# | | (_) | | | ___ \ (_)
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# | | _ ___| |_ | |_/ / __ _ ___ _ ___
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# | | | / __| __| | ___ \/ _` / __| / __|
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# | |___| \__ \ |_ | |_/ / (_| \__ \ \__ \
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# \_____/_|___/\__| \____/ \__,_|___/_|___/
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if arguments["list_basis"]:
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e = EMSL_local(db_path=db_path)
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@ -75,12 +75,12 @@ if __name__ == '__main__':
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for name, des in l:
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print name, "|", des
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# _ _ _ _____ _ _
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#| | (_) | | | ___| | | |
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#| | _ ___| |_ | |__ | | ___ _ __ ___ ___ _ __ | |_ ___
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#| | | / __| __| | __|| |/ _ \ '_ ` _ \ / _ \ '_ \| __/ __|
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#| |___| \__ \ |_ | |___| | __/ | | | | | __/ | | | |_\__ \
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#\_____/_|___/\__| \____/|_|\___|_| |_| |_|\___|_| |_|\__|___/
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# _ _ _ _____ _ _
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# | | (_) | | | ___| | | |
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# | | _ ___| |_ | |__ | | ___ _ __ ___ ___ _ __ | |_ ___
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# | | | / __| __| | __|| |/ _ \ '_ ` _ \ / _ \ '_ \| __/ __|
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# | |___| \__ \ |_ | |___| | __/ | | | | | __/ | | | |_\__ \
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# \_____/_|___/\__| \____/|_|\___|_| |_| |_|\___|_| |_|\__|___/
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if arguments["list_atoms"]:
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e = EMSL_local(db_path=db_path)
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@ -88,12 +88,12 @@ if __name__ == '__main__':
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l = e.get_list_element_available(basis_name)
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print ", ".join(l)
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#______ _ _ _
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#| ___ \ (_) | | | |
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#| |_/ / __ _ ___ _ ___ __| | __ _| |_ __ _
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#| ___ \/ _` / __| / __| / _` |/ _` | __/ _` |
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#| |_/ / (_| \__ \ \__ \ | (_| | (_| | || (_| |
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#\____/ \__,_|___/_|___/ \__,_|\__,_|\__\__,_|
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# ______ _ _ _
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# | ___ \ (_) | | | |
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# | |_/ / __ _ ___ _ ___ __| | __ _| |_ __ _
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# | ___ \/ _` / __| / __| / _` |/ _` | __/ _` |
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# | |_/ / (_| \__ \ \__ \ | (_| | (_| | || (_| |
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# \____/ \__,_|___/_|___/ \__,_|\__,_|\__\__,_|
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if arguments["get_basis_data"]:
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e = EMSL_local(db_path=db_path)
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basis_name = arguments["--basis"]
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@ -116,23 +116,23 @@ if __name__ == '__main__':
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else:
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print str_
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# _ _ _ __ _
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#| | (_) | | / _| | |
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#| | _ ___| |_ | |_ ___ _ __ _ __ ___ __ _| |_ ___
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#| | | / __| __| | _/ _ \| '__| '_ ` _ \ / _` | __/ __|
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#| |___| \__ \ |_ | || (_) | | | | | | | | (_| | |_\__ \
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#\_____/_|___/\__| |_| \___/|_| |_| |_| |_|\__,_|\__|___/
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# _ _ _ __ _
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# | | (_) | | / _| | |
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# | | _ ___| |_ | |_ ___ _ __ _ __ ___ __ _| |_ ___
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# | | | / __| __| | _/ _ \| '__| '_ ` _ \ / _` | __/ __|
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# | |___| \__ \ |_ | || (_) | | | | | | | | (_| | |_\__ \
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# \_____/_|___/\__| |_| \___/|_| |_| |_| |_|\__,_|\__|___/
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if arguments["list_formats"]:
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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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#/ __ \ | | | | |
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#| / \/_ __ ___ __ _| |_ ___ __| | |__
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#| | | '__/ _ \/ _` | __/ _ \ / _` | '_ \
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#| \__/\ | | __/ (_| | || __/ | (_| | |_) |
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# \____/_| \___|\__,_|\__\___| \__,_|_.__/
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# _____ _ _ _
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# / __ \ | | | | |
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# | / \/_ __ ___ __ _| |_ ___ __| | |__
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# | | | '__/ _ \/ _` | __/ _ \ / _` | '_ \
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# | \__/\ | | __/ (_| | || __/ | (_| | |_) |
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# \____/_| \___|\__,_|\__\___| \__,_|_.__/
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if arguments["create_db"]:
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db_path = arguments["--db_path"]
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format = arguments["--format"]
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@ -149,11 +149,11 @@ 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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# _
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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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if db_path_changed:
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if not(arguments['create_db']) and db_path_changed:
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os.system("rm -f /dev/shm/%d.db" % (os.getpid()))
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BIN
db/Gamess-us.db
BIN
db/Gamess-us.db
Binary file not shown.
@ -6,7 +6,7 @@ import sys
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import os
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import time
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debug = False
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debug = True
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def checkSQLite3(db_path):
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@ -189,7 +189,7 @@ class EMSL_dump:
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elts = re.sub('[["\ \]]', '', tup[3]).split(',')
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des = tup[-1]
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des = re.sub('\s+', ' ', tup[-1])
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if "-ecp" in xml_path.lower():
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continue
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@ -229,18 +229,20 @@ class EMSL_dump:
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elt_long_exp = data_elt.split()[0].lower()
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if "$" in data_elt:
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print "Eror",
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if debug:
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print "Eror",
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raise Exception("WARNING not bad split")
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if elt_long_th == elt_long_exp:
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d.append((name, des, elt, data_elt.strip()))
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d.append([elt, data_elt.strip()])
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else:
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print "th", elt_long_th
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print "exp", elt_long_exp
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print "abv", elt
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if debug:
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print "th", elt_long_th
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print "exp", elt_long_exp
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print "abv", elt
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raise Exception("WARNING not good ELEMENT")
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return d
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return [name, des, d]
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def create_sql(self, list_basis_array):
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"""Create the sql from the list of basis available data"""
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@ -248,9 +250,32 @@ class EMSL_dump:
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conn = sqlite3.connect(self.db_path)
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c = conn.cursor()
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# Create table
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c.execute('''CREATE TABLE all_value
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(name text, description text, elt text, data text)''')
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c.execute('''CREATE TABLE basis_tab(
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basis_id INTEGER PRIMARY KEY AUTOINCREMENT,
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name text,
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description text,
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UNIQUE(name)
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);''')
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c.execute('''CREATE TABLE data_tab(
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basis_id INTEGER,
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elt TEXT,
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data TEXT,
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FOREIGN KEY(basis_id)
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REFERENCES basis_tab(basis_id)
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);''')
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c.execute(''' CREATE VIEW output_tab AS
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SELECT basis_id,
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name,
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description,
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elt,
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data
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FROM basis_tab
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NATURAL JOIN data_tab
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''')
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conn.commit()
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import Queue
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import threading
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@ -264,7 +289,7 @@ class EMSL_dump:
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def worker():
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"""get a Job from the q_in, do stuff, when finish put it in the q_out"""
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while True:
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[name, path_xml, des, elts] = q_in.get()
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name, path_xml, des, elts = q_in.get()
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url = "https://bse.pnl.gov:443/bse/portal/user/anon/js_peid/11535052407933/action/portlets.BasisSetAction/template/courier_content/panel/Main/"
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url += "/eventSubmit_doDownload/true"
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@ -286,16 +311,16 @@ class EMSL_dump:
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attemps += 1
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try:
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q_out.put(([name, path_xml, des, elts], basis_data))
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q_out.put(basis_data)
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q_in.task_done()
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except:
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if debug:
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print "Fail on q_out.put", name, path_xml, des
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print "Fail on q_out.put", basis_data
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raise
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def enqueue():
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for [name, path_xml, des, elts] in list_basis_array:
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q_in.put(([name, path_xml, des, elts]))
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q_in.put([name, path_xml, des, elts])
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return 0
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@ -311,17 +336,30 @@ class EMSL_dump:
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nb_basis = len(list_basis_array)
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for i in range(nb_basis):
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[name, path_xml, des, elts], basis_data = q_out.get()
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name, des, d = q_out.get()
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q_out.task_done()
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try:
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c.execute(
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"INSERT INTO basis_tab(name,description) VALUES (?,?)", [
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name, des])
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conn.commit()
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except sqlite3.IntegrityError:
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print '{:>3}'.format(i + 1), "/", nb_basis, name, "fail"
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id_ = c.lastrowid
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try:
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c.executemany(
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"INSERT INTO all_value VALUES (?,?,?,?)", basis_data)
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"INSERT INTO data_tab VALUES (?,?,?)", [
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[id_] + k for k in d])
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conn.commit()
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print '{:>3}'.format(i + 1), "/", nb_basis, name
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except:
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print '{:>3}'.format(i + 1), "/", nb_basis, name, "fail"
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raise
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conn.close()
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q_in.join()
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@ -348,12 +386,12 @@ class EMSL_local:
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if not elts:
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c.execute("SELECT DISTINCT name,description from all_value")
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c.execute("SELECT DISTINCT name,description from basis_tab")
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data = c.fetchall()
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else:
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cmd = [
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"SELECT name,description FROM all_value WHERE elt=?"] * len(elts)
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"SELECT name,description FROM output_tab WHERE elt=?"] * len(elts)
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cmd = " INTERSECT ".join(cmd) + ";"
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c.execute(cmd, elts)
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@ -371,7 +409,7 @@ class EMSL_local:
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c = conn.cursor()
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c.execute(
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"SELECT DISTINCT elt from all_value WHERE name=:name_us COLLATE NOCASE", {
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"SELECT DISTINCT elt from output_tab WHERE name=:name_us COLLATE NOCASE", {
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"name_us": basis_name})
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data = c.fetchall()
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@ -383,6 +421,8 @@ class EMSL_local:
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def get_basis(self, basis_name, elts=None, with_l=False):
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import re
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def get_list_type(l_line):
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l = []
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for i, line in enumerate(l_line):
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@ -398,8 +438,6 @@ class EMSL_local:
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l[-1].append(i + 1)
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return l
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import re
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# __ _
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# /__ _ _|_ _|_ ._ _ ._ _ _ _. |
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# \_| (/_ |_ | | (_) | | | _> (_| |
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@ -412,7 +450,7 @@ class EMSL_local:
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else:
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cmd_ele = ""
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c.execute('''SELECT DISTINCT data from all_value
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c.execute('''SELECT DISTINCT data from output_tab
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WHERE name="{basis_name}" COLLATE NOCASE
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{cmd_ele}'''.format(basis_name=basis_name,
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cmd_ele=cmd_ele))
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