LCPQ/EMSL_Basis_Set_Exchange_Local
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New design for basis set

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This commit is contained in:
Thomas Applencourt 2015-01-20 14:20:06 +01:00
parent d9fdab2469
commit 7c6812f258
3 changed files with 107 additions and 69 deletions
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92
EMSL_api.py
View File

@ -4,18 +4,18 @@
"""EMSL Api. """EMSL Api.
Usage: Usage:
EMSL_api.py list_basis [--atom=atom_name...] EMSL_api.py list_basis [--atom=<atom_name>...]
[--db_path=db_path] [--db_path=<db_path>]
EMSL_api.py list_atoms --basis=basis_name EMSL_api.py list_atoms --basis=<basis_name>
[--db_path=db_path] [--db_path=<db_path>]
EMSL_api.py get_basis_data --basis=basis_name EMSL_api.py get_basis_data --basis=<basis_name>
[--atom=atom_name...] [--atom=<atom_name>...]
[--db_path=db_path] [--db_path=<db_path>]
[--with_l] [--with_l]
[(--save [--path=path])] [(--save [--path=<path>])]
EMSL_api.py list_formats EMSL_api.py list_formats
EMSL_api.py create_db --db_path=db_path EMSL_api.py create_db --db_path=<db_path>
--format=format --format=<format>
[--no-contraction] [--no-contraction]
EMSL_api.py (-h | --help) EMSL_api.py (-h | --help)
EMSL_api.py --version EMSL_api.py --version
@ -59,13 +59,13 @@ if __name__ == '__main__':
except: except:
sys.exit(1) sys.exit(1)
# _ _ _ ______ _ # _ _ _ ______ _
#| | (_) | | | ___ \ (_) # | | (_) | | | ___ \ (_)
#| | _ ___| |_ | |_/ / __ _ ___ _ ___ # | | _ ___| |_ | |_/ / __ _ ___ _ ___
#| | | / __| __| | ___ \/ _` / __| / __| # | | | / __| __| | ___ \/ _` / __| / __|
#| |___| \__ \ |_ | |_/ / (_| \__ \ \__ \ # | |___| \__ \ |_ | |_/ / (_| \__ \ \__ \
#\_____/_|___/\__| \____/ \__,_|___/_|___/ # \_____/_|___/\__| \____/ \__,_|___/_|___/
#
if arguments["list_basis"]: if arguments["list_basis"]:
e = EMSL_local(db_path=db_path) e = EMSL_local(db_path=db_path)
@ -75,12 +75,12 @@ if __name__ == '__main__':
for name, des in l: for name, des in l:
print name, "|", des print name, "|", des
# _ _ _ _____ _ _ # _ _ _ _____ _ _
#| | (_) | | | ___| | | | # | | (_) | | | ___| | | |
#| | _ ___| |_ | |__ | | ___ _ __ ___ ___ _ __ | |_ ___ # | | _ ___| |_ | |__ | | ___ _ __ ___ ___ _ __ | |_ ___
#| | | / __| __| | __|| |/ _ \ '_ ` _ \ / _ \ '_ \| __/ __| # | | | / __| __| | __|| |/ _ \ '_ ` _ \ / _ \ '_ \| __/ __|
#| |___| \__ \ |_ | |___| | __/ | | | | | __/ | | | |_\__ \ # | |___| \__ \ |_ | |___| | __/ | | | | | __/ | | | |_\__ \
#\_____/_|___/\__| \____/|_|\___|_| |_| |_|\___|_| |_|\__|___/ # \_____/_|___/\__| \____/|_|\___|_| |_| |_|\___|_| |_|\__|___/
if arguments["list_atoms"]: if arguments["list_atoms"]:
e = EMSL_local(db_path=db_path) e = EMSL_local(db_path=db_path)
@ -88,12 +88,12 @@ if __name__ == '__main__':
l = e.get_list_element_available(basis_name) l = e.get_list_element_available(basis_name)
print ", ".join(l) print ", ".join(l)
#______ _ _ _ # ______ _ _ _
#| ___ \ (_) | | | | # | ___ \ (_) | | | |
#| |_/ / __ _ ___ _ ___ __| | __ _| |_ __ _ # | |_/ / __ _ ___ _ ___ __| | __ _| |_ __ _
#| ___ \/ _` / __| / __| / _` |/ _` | __/ _` | # | ___ \/ _` / __| / __| / _` |/ _` | __/ _` |
#| |_/ / (_| \__ \ \__ \ | (_| | (_| | || (_| | # | |_/ / (_| \__ \ \__ \ | (_| | (_| | || (_| |
#\____/ \__,_|___/_|___/ \__,_|\__,_|\__\__,_| # \____/ \__,_|___/_|___/ \__,_|\__,_|\__\__,_|
if arguments["get_basis_data"]: if arguments["get_basis_data"]:
e = EMSL_local(db_path=db_path) e = EMSL_local(db_path=db_path)
basis_name = arguments["--basis"] basis_name = arguments["--basis"]
@ -116,23 +116,23 @@ if __name__ == '__main__':
else: else:
print str_ print str_
# _ _ _ __ _ # _ _ _ __ _
#| | (_) | | / _| | | # | | (_) | | / _| | |
#| | _ ___| |_ | |_ ___ _ __ _ __ ___ __ _| |_ ___ # | | _ ___| |_ | |_ ___ _ __ _ __ ___ __ _| |_ ___
#| | | / __| __| | _/ _ \| '__| '_ ` _ \ / _` | __/ __| # | | | / __| __| | _/ _ \| '__| '_ ` _ \ / _` | __/ __|
#| |___| \__ \ |_ | || (_) | | | | | | | | (_| | |_\__ \ # | |___| \__ \ |_ | || (_) | | | | | | | | (_| | |_\__ \
#\_____/_|___/\__| |_| \___/|_| |_| |_| |_|\__,_|\__|___/ # \_____/_|___/\__| |_| \___/|_| |_| |_| |_|\__,_|\__|___/
if arguments["list_formats"]: if arguments["list_formats"]:
e = EMSL_dump() e = EMSL_dump()
for i in e.get_list_format(): for i in e.get_list_format():
print i print i
# _____ _ _ _ # _____ _ _ _
#/ __ \ | | | | | # / __ \ | | | | |
#| / \/_ __ ___ __ _| |_ ___ __| | |__ # | / \/_ __ ___ __ _| |_ ___ __| | |__
#| | | '__/ _ \/ _` | __/ _ \ / _` | '_ \ # | | | '__/ _ \/ _` | __/ _ \ / _` | '_ \
#| \__/\ | | __/ (_| | || __/ | (_| | |_) | # | \__/\ | | __/ (_| | || __/ | (_| | |_) |
# \____/_| \___|\__,_|\__\___| \__,_|_.__/ # \____/_| \___|\__,_|\__\___| \__,_|_.__/
if arguments["create_db"]: if arguments["create_db"]:
db_path = arguments["--db_path"] db_path = arguments["--db_path"]
format = arguments["--format"] format = arguments["--format"]
@ -149,11 +149,11 @@ if __name__ == '__main__':
contraction=contraction) contraction=contraction)
e.new_db() e.new_db()
# _ # _
# / | _ _. ._ o ._ _ # / | _ _. ._ o ._ _
# \_ | (/_ (_| | | | | | (_| # \_ | (/_ (_| | | | | | (_|
# _| # _|
# Clean up on exit # Clean up on exit
if db_path_changed: if not(arguments['create_db']) and db_path_changed:
os.system("rm -f /dev/shm/%d.db" % (os.getpid())) os.system("rm -f /dev/shm/%d.db" % (os.getpid()))

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db/Gamess-us.db
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84
src/EMSL_utility.py
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@ -6,7 +6,7 @@ import sys
import os import os
import time import time
debug = False debug = True
def checkSQLite3(db_path): def checkSQLite3(db_path):
@ -189,7 +189,7 @@ class EMSL_dump:
elts = re.sub('[["\ \]]', '', tup[3]).split(',') elts = re.sub('[["\ \]]', '', tup[3]).split(',')
des = tup[-1] des = re.sub('\s+', ' ', tup[-1])
if "-ecp" in xml_path.lower(): if "-ecp" in xml_path.lower():
continue continue
@ -229,18 +229,20 @@ class EMSL_dump:
elt_long_exp = data_elt.split()[0].lower() elt_long_exp = data_elt.split()[0].lower()
if "$" in data_elt: if "$" in data_elt:
print "Eror", if debug:
print "Eror",
raise Exception("WARNING not bad split") raise Exception("WARNING not bad split")
if elt_long_th == elt_long_exp: if elt_long_th == elt_long_exp:
d.append((name, des, elt, data_elt.strip())) d.append([elt, data_elt.strip()])
else: else:
print "th", elt_long_th if debug:
print "exp", elt_long_exp print "th", elt_long_th
print "abv", elt print "exp", elt_long_exp
print "abv", elt
raise Exception("WARNING not good ELEMENT") raise Exception("WARNING not good ELEMENT")
return d return [name, des, d]
def create_sql(self, list_basis_array): def create_sql(self, list_basis_array):
"""Create the sql from the list of basis available data""" """Create the sql from the list of basis available data"""
@ -248,9 +250,32 @@ class EMSL_dump:
conn = sqlite3.connect(self.db_path) conn = sqlite3.connect(self.db_path)
c = conn.cursor() c = conn.cursor()
# Create table c.execute('''CREATE TABLE basis_tab(
c.execute('''CREATE TABLE all_value basis_id INTEGER PRIMARY KEY AUTOINCREMENT,
(name text, description text, elt text, data text)''') name text,
description text,
UNIQUE(name)
);''')
c.execute('''CREATE TABLE data_tab(
basis_id INTEGER,
elt TEXT,
data TEXT,
FOREIGN KEY(basis_id)
REFERENCES basis_tab(basis_id)
);''')
c.execute(''' CREATE VIEW output_tab AS
SELECT basis_id,
name,
description,
elt,
data
FROM basis_tab
NATURAL JOIN data_tab
''')
conn.commit()
import Queue import Queue
import threading import threading
@ -264,7 +289,7 @@ class EMSL_dump:
def worker(): def worker():
"""get a Job from the q_in, do stuff, when finish put it in the q_out""" """get a Job from the q_in, do stuff, when finish put it in the q_out"""
while True: while True:
[name, path_xml, des, elts] = q_in.get() name, path_xml, des, elts = q_in.get()
url = "https://bse.pnl.gov:443/bse/portal/user/anon/js_peid/11535052407933/action/portlets.BasisSetAction/template/courier_content/panel/Main/" url = "https://bse.pnl.gov:443/bse/portal/user/anon/js_peid/11535052407933/action/portlets.BasisSetAction/template/courier_content/panel/Main/"
url += "/eventSubmit_doDownload/true" url += "/eventSubmit_doDownload/true"
@ -286,16 +311,16 @@ class EMSL_dump:
attemps += 1 attemps += 1
try: try:
q_out.put(([name, path_xml, des, elts], basis_data)) q_out.put(basis_data)
q_in.task_done() q_in.task_done()
except: except:
if debug: if debug:
print "Fail on q_out.put", name, path_xml, des print "Fail on q_out.put", basis_data
raise raise
def enqueue(): def enqueue():
for [name, path_xml, des, elts] in list_basis_array: for [name, path_xml, des, elts] in list_basis_array:
q_in.put(([name, path_xml, des, elts])) q_in.put([name, path_xml, des, elts])
return 0 return 0
@ -311,17 +336,30 @@ class EMSL_dump:
nb_basis = len(list_basis_array) nb_basis = len(list_basis_array)
for i in range(nb_basis): for i in range(nb_basis):
[name, path_xml, des, elts], basis_data = q_out.get() name, des, d = q_out.get()
q_out.task_done()
try:
c.execute(
"INSERT INTO basis_tab(name,description) VALUES (?,?)", [
name, des])
conn.commit()
except sqlite3.IntegrityError:
print '{:>3}'.format(i + 1), "/", nb_basis, name, "fail"
id_ = c.lastrowid
try: try:
c.executemany( c.executemany(
"INSERT INTO all_value VALUES (?,?,?,?)", basis_data) "INSERT INTO data_tab VALUES (?,?,?)", [
[id_] + k for k in d])
conn.commit() conn.commit()
print '{:>3}'.format(i + 1), "/", nb_basis, name print '{:>3}'.format(i + 1), "/", nb_basis, name
except: except:
print '{:>3}'.format(i + 1), "/", nb_basis, name, "fail" print '{:>3}'.format(i + 1), "/", nb_basis, name, "fail"
raise raise
conn.close() conn.close()
q_in.join() q_in.join()
@ -348,12 +386,12 @@ class EMSL_local:
if not elts: if not elts:
c.execute("SELECT DISTINCT name,description from all_value") c.execute("SELECT DISTINCT name,description from basis_tab")
data = c.fetchall() data = c.fetchall()
else: else:
cmd = [ cmd = [
"SELECT name,description FROM all_value WHERE elt=?"] * len(elts) "SELECT name,description FROM output_tab WHERE elt=?"] * len(elts)
cmd = " INTERSECT ".join(cmd) + ";" cmd = " INTERSECT ".join(cmd) + ";"
c.execute(cmd, elts) c.execute(cmd, elts)
@ -371,7 +409,7 @@ class EMSL_local:
c = conn.cursor() c = conn.cursor()
c.execute( c.execute(
"SELECT DISTINCT elt from all_value WHERE name=:name_us COLLATE NOCASE", { "SELECT DISTINCT elt from output_tab WHERE name=:name_us COLLATE NOCASE", {
"name_us": basis_name}) "name_us": basis_name})
data = c.fetchall() data = c.fetchall()
@ -383,6 +421,8 @@ class EMSL_local:
def get_basis(self, basis_name, elts=None, with_l=False): def get_basis(self, basis_name, elts=None, with_l=False):
import re
def get_list_type(l_line): def get_list_type(l_line):
l = [] l = []
for i, line in enumerate(l_line): for i, line in enumerate(l_line):
@ -398,8 +438,6 @@ class EMSL_local:
l[-1].append(i + 1) l[-1].append(i + 1)
return l return l
import re
# __ _ # __ _
# /__ _ _|_ _|_ ._ _ ._ _ _ _. | # /__ _ _|_ _|_ ._ _ ._ _ _ _. |
# \_| (/_ |_ | | (_) | | | _> (_| | # \_| (/_ |_ | | (_) | | | _> (_| |
@ -412,7 +450,7 @@ class EMSL_local:
else: else:
cmd_ele = "" cmd_ele = ""
c.execute('''SELECT DISTINCT data from all_value c.execute('''SELECT DISTINCT data from output_tab
WHERE name="{basis_name}" COLLATE NOCASE WHERE name="{basis_name}" COLLATE NOCASE
{cmd_ele}'''.format(basis_name=basis_name, {cmd_ele}'''.format(basis_name=basis_name,
cmd_ele=cmd_ele)) cmd_ele=cmd_ele))