def default_repl_keys():
"""Return a dict of default keys for replacement in a
:class:`ParameterStudy`. Each key will in practice be processed by
:class:`FileTemplate`, such that e.g. the key 'foo' becomes the placeholder
'XXXFOO'.
Each of these placeholders can be used in any parameter study in any file
template, indenpendent from `params_lst` to :class:`ParameterStudy`.
Notes
-----
If this function is called, dummy files are written to a temp dir, the
datsbase is read, and the file are deleted.
"""
# HACK!!! Due to the way ParameterStudy.write_input() is coded, we really
# need to set up a dummy ParameterStudy and read out the database to get
# the replacement keys :-)
import tempfile
calc_root = tempfile.mkdtemp()
jobfn_templ = pj(calc_root, 'foo.job')
common.file_write(jobfn_templ, 'dummy job template, go away!')
m = Machine(hostname='foo',
template=FileTemplate(basename='foo.job', templ_dir=calc_root))
print("writing test files to: %s, will be deleted" % calc_root)
params_lst = [[SQLEntry(key='dummy', sqlval=1)]]
study = ParameterStudy(machines=m,
params_lst=params_lst,
calc_root=calc_root)
study.write_input()
db = SQLiteDB(study.dbfn, table='calc')
db_keys = [str(x[0]) for x in db.get_header()]
for kk in ['dummy', 'hostname']:
db_keys.pop(db_keys.index(kk))
db.finish()
ret = {
'ParameterStudy': db_keys,
'Machine': list(m.get_sql_record().keys())
}
shutil.rmtree(calc_root)
return ret
def default_repl_keys():
"""Return a dict of default keys for replacement in a
:class:`ParameterStudy`. Each key will in practice be processed by
:class:`FileTemplate`, such that e.g. the key 'foo' becomes the placeholder
'XXXFOO'.
Each of these placeholders can be used in any parameter study in any file
template, indenpendent from `params_lst` to :class:`ParameterStudy`.
Notes
-----
If this function is called, dummy files are written to a temp dir, the
datsbase is read, and the file are deleted.
"""
# HACK!!! Due to the way ParameterStudy.write_input() is coded, we really
# need to set up a dummy ParameterStudy and read out the database to get
# the replacement keys :-)
import tempfile
calc_root = tempfile.mkdtemp()
jobfn_templ = pj(calc_root, 'foo.job')
common.file_write(jobfn_templ, 'dummy job template, go away!')
m = Machine(hostname='foo',
template=FileTemplate(basename='foo.job',
templ_dir=calc_root))
print ("writing test files to: %s, will be deleted" %calc_root)
params_lst = [[SQLEntry(key='dummy', sqlval=1)]]
study = ParameterStudy(machines=m, params_lst=params_lst,
calc_root=calc_root)
study.write_input()
db = SQLiteDB(study.dbfn, table='calc')
db_keys = [str(x[0]) for x in db.get_header()]
for kk in ['dummy', 'hostname']:
db_keys.pop(db_keys.index(kk))
db.finish()
ret = {'ParameterStudy' : db_keys,
'Machine' : m.get_sql_record().keys()}
shutil.rmtree(calc_root)
return ret
def test_sql():
# Check for sqlite3 command line tool. In Python 3.3, we can use
# shutil.which().
have_sqlite3 = False
for pp in sys.path:
exe = pj(pp, 'sqlite3')
if os.path.isfile(exe):
print("found:", exe)
have_sqlite3 = True
break
# --- SQLiteDB ----------------------------------------------------
dbfn = pj(testdir, 'test.db')
if os.path.exists(dbfn):
os.remove(dbfn)
header = [('idx', 'INTEGER'), ('foo', 'REAL'), ('bar', 'TEXT')]
db = SQLiteDB(dbfn, table='calc')
db.execute("CREATE TABLE calc (%s)" %','.join("%s %s" %(x[0], x[1]) \
for x in header))
vals = [[0, 1.1, 'a'], [1, 2.2, 'b'], [2, 3.3, 'c']]
for lst in vals:
db.execute("INSERT INTO calc (idx, foo, bar) VALUES (?,?,?)",
tuple(lst))
db.commit()
# get_max_rowid
assert db.get_max_rowid() == 3
# has_table
assert db.has_table('calc')
assert not db.has_table('foo')
# has_column
assert db.has_column('idx')
assert not db.has_column('grrr')
# get_single
assert float(db.get_single("select foo from calc where idx==0")) == 1.1
assert header == db.get_header()
if have_sqlite3:
# call sqlite3, the cmd line interface
assert common.backtick("sqlite3 %s 'select * from calc'" %dbfn) \
== '0|1.1|a\n1|2.2|b\n2|3.3|c\n'
# ret =
# [(0, 1.1000000000000001, u'a'),
# (1, 2.2000000000000002, u'b'),
# (2, 3.2999999999999998, u'c')]
ret = db.execute("select * from calc").fetchall()
for idx, lst in enumerate(vals):
assert list(ret[idx]) == lst
# generator object, yields
# tup = (0, 1.1000000000000001, u'a')
# tup = (1, 2.2000000000000002, u'b')
# tup = (2, 3.2999999999999998, u'c')
itr = db.execute("select * from calc")
for idx, tup in enumerate(itr):
assert list(tup) == vals[idx]
# [(0, 1.1000000000000001, u'a')]
assert db.execute("select * from calc where idx==0").fetchall() == \
[tuple(vals[0])]
# (0, 1.1000000000000001, u'a')
assert db.execute("select * from calc where idx==0").fetchone() == \
tuple(vals[0])
assert db.execute("select bar from calc where idx==0").fetchone()[0] == \
'a'
# get_list1d(), get_array1d(), get_array()
assert db.get_list1d("select idx from calc") == [0, 1, 2]
np.testing.assert_array_equal(db.get_array1d("select idx from calc"),
np.array([0, 1, 2]))
np.testing.assert_array_equal(db.get_array("select idx from calc"),
np.array([0, 1, 2])[:, None])
np.testing.assert_array_equal(
db.get_array("select idx,foo from calc"),
np.array(vals, dtype='S3')[:, :2].astype(float))
# add_column(), fill with values
db.add_column('baz', 'TEXT')
add_header = [('baz', 'TEXT')]
header += add_header
assert db.get_header() == header
db.execute("UPDATE %s SET baz='xx' where idx==0" % db.table)
db.execute("UPDATE %s SET baz='yy' where idx==1" % db.table)
db.execute("UPDATE %s SET baz=? where idx==2" % db.table, ('zz', ))
db.commit()
if have_sqlite3:
print(common.backtick("sqlite3 %s 'select * from calc'" % dbfn))
print(db.execute("select baz from calc").fetchall())
assert db.execute("select baz from calc").fetchall() == \
[('xx',), ('yy',), ('zz',)]
# add even more cols with add_columns()
add_header = [('bob', 'TEXT'), ('alice', 'BLOB')]
header += add_header
db.add_columns(add_header)
assert db.get_header() == header
# create_table()
dbfn2 = pj(testdir, 'test2.db')
header2 = [('a', 'REAL'), ('b', 'TEXT')]
db2 = SQLiteDB(dbfn2, table='foo')
db2.create_table(header2)
assert db2.get_header() == header2
# get_dict()
dct = db.get_dict("select foo,bar from calc")
cols = [x[0] for x in db.get_header()]
for key in ['foo', 'bar']:
assert key in cols
foo = db.get_list1d("select foo from calc")
bar = db.get_list1d("select bar from calc")
assert foo == dct['foo']
assert bar == dct['bar']
def test_sql():
# Check for sqlite3 command line tool. In Python 3.3, we can use
# shutil.which().
have_sqlite3 = False
for pp in sys.path:
exe = pj(pp, 'sqlite3')
if os.path.isfile(exe):
print "found:", exe
have_sqlite3 = True
break
# --- SQLiteDB ----------------------------------------------------
dbfn = pj(testdir, 'test.db')
if os.path.exists(dbfn):
os.remove(dbfn)
header = [('idx', 'INTEGER'), ('foo', 'REAL'), ('bar', 'TEXT')]
db = SQLiteDB(dbfn, table='calc')
db.execute("CREATE TABLE calc (%s)" %','.join("%s %s" %(x[0], x[1]) \
for x in header))
vals = [[0, 1.1, 'a'],
[1, 2.2, 'b'],
[2, 3.3, 'c']]
for lst in vals:
db.execute("INSERT INTO calc (idx, foo, bar) VALUES (?,?,?)", tuple(lst))
db.commit()
# get_max_rowid
assert db.get_max_rowid() == 3
# has_table
assert db.has_table('calc')
assert not db.has_table('foo')
# has_column
assert db.has_column('idx')
assert not db.has_column('grrr')
# get_single
assert float(db.get_single("select foo from calc where idx==0")) == 1.1
assert header == db.get_header()
if have_sqlite3:
# call sqlite3, the cmd line interface
assert common.backtick("sqlite3 %s 'select * from calc'" %dbfn) \
== '0|1.1|a\n1|2.2|b\n2|3.3|c\n'
# ret =
# [(0, 1.1000000000000001, u'a'),
# (1, 2.2000000000000002, u'b'),
# (2, 3.2999999999999998, u'c')]
ret = db.execute("select * from calc").fetchall()
for idx, lst in enumerate(vals):
assert list(ret[idx]) == lst
# generator object, yields
# tup = (0, 1.1000000000000001, u'a')
# tup = (1, 2.2000000000000002, u'b')
# tup = (2, 3.2999999999999998, u'c')
itr = db.execute("select * from calc")
for idx, tup in enumerate(itr):
assert list(tup) == vals[idx]
# [(0, 1.1000000000000001, u'a')]
assert db.execute("select * from calc where idx==0").fetchall() == \
[tuple(vals[0])]
# (0, 1.1000000000000001, u'a')
assert db.execute("select * from calc where idx==0").fetchone() == \
tuple(vals[0])
assert db.execute("select bar from calc where idx==0").fetchone()[0] == \
'a'
# get_list1d(), get_array1d(), get_array()
assert db.get_list1d("select idx from calc") == [0,1,2]
np.testing.assert_array_equal(db.get_array1d("select idx from calc"),
np.array([0,1,2]))
np.testing.assert_array_equal(db.get_array("select idx from calc"),
np.array([0,1,2])[:,None])
np.testing.assert_array_equal(db.get_array("select idx,foo from calc"),
np.array(vals, dtype='S3')[:,:2].astype(float))
# add_column(), fill with values
db.add_column('baz', 'TEXT')
add_header = [('baz', 'TEXT')]
header += add_header
assert db.get_header() == header
db.execute("UPDATE %s SET baz='xx' where idx==0" %db.table)
db.execute("UPDATE %s SET baz='yy' where idx==1" %db.table)
db.execute("UPDATE %s SET baz=? where idx==2" %db.table, ('zz',))
db.commit()
if have_sqlite3:
print common.backtick("sqlite3 %s 'select * from calc'" %dbfn)
print db.execute("select baz from calc").fetchall()
assert db.execute("select baz from calc").fetchall() == \
[(u'xx',), (u'yy',), (u'zz',)]
# add even more cols with add_columns()
add_header = [('bob', 'TEXT'), ('alice', 'BLOB')]
header += add_header
db.add_columns(add_header)
assert db.get_header() == header
# create_table()
dbfn2 = pj(testdir, 'test2.db')
header2 = [('a', 'REAL'), ('b', 'TEXT')]
db2 = SQLiteDB(dbfn2, table='foo')
db2.create_table(header2)
assert db2.get_header() == header2
# get_dict()
dct = db.get_dict("select foo,bar from calc")
cols = [x[0] for x in db.get_header()]
for key in ['foo', 'bar']:
assert key in cols
foo = db.get_list1d("select foo from calc")
bar = db.get_list1d("select bar from calc")
assert foo == dct['foo']
assert bar == dct['bar']
